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Rohaim MA, El Naggar RF, Abdelsabour MA, Mohamed MHA, El-Sabagh IM, Munir M. Evolutionary Analysis of Infectious Bronchitis Virus Reveals Marked Genetic Diversity and Recombination Events. Genes (Basel) 2020; 11:E605. [PMID: 32486006 DOI: 10.3390/genes11060605] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 01/18/2023] Open
Abstract
In the last 5 years, frequent outbreaks of infectious bronchitis virus (IBV) are observed in both broiler and layer chicken flocks in the Kingdom of Saudi Arabia (KSA) in spite of extensive usage of vaccines. The IBV is a widespread avian coronavirus affecting both vaccinated and unvaccinated chicken flocks and is attributed to significant economic losses, around the globe. In the present study, 58 (n = 58) samples were collected from four different commercial poultry flocks from 8 KSA districts during 2019. A total of nine positive isolates (9/58; 15.5%), based on real-time reverse transcriptase PCR targeting nucleocapsid (N) gene, were used for further genetic characterization and evolutionary analysis. Genetic characterization of the partial spike (S1) gene revealed the clustering of the reported isolates into three different genotypes, whereas four additional isolates were grouped within 4/91 genotype, two isolates within IS/885 genotype, one isolate was closely related to IS/1494/06, and two isolates were grouped within classic serotype (vaccine-like strains). Phylodynamic revealed clustering of four isolated viruses within GI-13 lineage, three isolates within GI-23 lineage, and two isolates within GI-1 lineage. Results indicate that there are high evolutionary distances between the newly identified IBV strains in this study and the commercially used vaccines (GI-1), suggesting that IBV strains circulating in the KSA are under constant evolutionary pressures. Selective pressure biostatistics analyses consistently demonstrate the presence of a higher positive score which highlights the role of natural selection, a mechanism of virus evolution on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. Recombination analysis revealed emergence of two isolates through recombination events resulting in new recombinant viruses. Taken together, these finding demonstrate the genetic and evolutionary insights into the currently circulating IBV genotypes in KSA, which could help to better understand the origin, spread, and evolution of infectious bronchitis viruses, and to ascertain the importance of disease monitoring as well as re-evaluation for the currently used vaccines and vaccination programs.
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Ward-Smith H, Arbuckle K, Naude A, Wüster W. Fangs for the Memories? A Survey of Pain in Snakebite Patients Does Not Support a Strong Role for Defense in the Evolution of Snake Venom Composition. Toxins (Basel) 2020; 12:E201. [PMID: 32235759 DOI: 10.3390/toxins12030201] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 12/17/2022] Open
Abstract
Animals use venoms for multiple purposes, most prominently for prey acquisition and self-defense. In snakes, venom composition often evolves as a result of selection for optimization for local diet. However, whether selection for a defensive function has also played a role in driving the evolution of venom composition has remained largely unstudied. Here, we use an online survey of snakebite victims to test a key prediction of a defensive function, that envenoming should result in the rapid onset of severe pain. From the analysis of 584 snakebite reports, involving 192 species of venomous snake, we find that the vast majority of bites do not result in severe early pain. Phylogenetic comparative analysis shows that where early pain after a bite evolves, it is often lost rapidly. Our results, therefore, do not support the hypothesis that natural selection for antipredator defense played an important role in the origin of venom or front-fanged delivery systems in general, although there may be intriguing exceptions to this rule.
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Vidovic N, Vidovic S. Antimicrobial Resistance and Food Animals: Influence of Livestock Environment on the Emergence and Dissemination of Antimicrobial Resistance. Antibiotics (Basel) 2020; 9:antibiotics9020052. [PMID: 32023977 PMCID: PMC7168261 DOI: 10.3390/antibiotics9020052] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 01/26/2020] [Accepted: 01/27/2020] [Indexed: 02/07/2023] Open
Abstract
The emergence and dissemination of antimicrobial resistance among human, animal and zoonotic pathogens pose an enormous threat to human health worldwide. The use of antibiotics in human and veterinary medicine, and especially the use of large quantities of antibiotics in livestock for the purpose of growth promotion of food animals is believed to be contributing to the modern trend of the emergence and spread of bacteria with antibiotic resistant traits. To better control the emergence and spread of antimicrobial resistance several countries from Western Europe implemented a ban for antibiotic use in livestock, specifically the use of antibiotics for growth promotion of food animals. This review article summarizes the recent knowledge of molecular acquisition of antimicrobial resistance and the effects of implementation of antibiotic growth promoter bans on the spread of antimicrobial resistant bacteria in animals and humans. In this article, we also discuss the main zoonotic transmission routes of antimicrobial resistance and novel approaches designed to prevent or slow down the emergence and spread of antimicrobial resistance worldwide. Finally, we provide future perspectives associated with the control and management of the emergence and spread of antimicrobial resistant bacteria.
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Affiliation(s)
- Nikola Vidovic
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK S7K 4H3, Canada;
| | - Sinisa Vidovic
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA
- Correspondence:
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Domínguez-Andrés J, Netea MG. Impact of Historic Migrations and Evolutionary Processes on Human Immunity. Trends Immunol 2019; 40:1105-19. [PMID: 31786023 DOI: 10.1016/j.it.2019.10.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 10/04/2019] [Accepted: 10/09/2019] [Indexed: 12/30/2022]
Abstract
The evolution of mankind has constantly been influenced by the pathogens encountered. The various populations of modern humans that ventured out of Africa adapted to different environments and faced a large variety of infectious agents, resulting in local adaptations of the immune system for these populations. The functional variation of immune genes as a result of evolution is relevant in the responses against infection, as well as in the emergence of autoimmune and inflammatory diseases observed in modern populations. Understanding how host-pathogen interactions have influenced the human immune system from an evolutionary perspective might contribute to unveiling the causes behind different immune-mediated disorders and promote the development of new strategies to detect and control such diseases.
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Petersen G, Darby H, Lam VKY, Pedersen HÆ, Merckx VSFT, Zervas A, Seberg O, Graham SW. Mycoheterotrophic Epirixanthes (Polygalaceae) has a typical angiosperm mitogenome but unorthodox plastid genomes. Ann Bot 2019; 124:791-807. [PMID: 31346602 PMCID: PMC6868387 DOI: 10.1093/aob/mcz114] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/24/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS Fully mycoheterotrophic plants derive carbon and other nutrients from root-associated fungi and have lost the ability to photosynthesize. While mycoheterotroph plastomes are often degraded compared with green plants, the effect of this unusual symbiosis on mitochondrial genome evolution is unknown. By providing the first complete organelle genome data from Polygalaceae, one of only three eudicot families that developed mycoheterotrophy, we explore how both organellar genomes evolved after loss of photosynthesis. METHODS We sequenced and assembled four complete plastid genomes and a mitochondrial genome from species of Polygalaceae, focusing on non-photosynthetic Epirixanthes. We compared these genomes with those of other mycoheterotroph and parasitic plant lineages, and assessed whether organelle genes in Epirixanthes experienced relaxed or intensified selection compared with autotrophic relatives. KEY RESULTS Plastomes of two species of Epirixanthes have become substantially degraded compared with that of autotrophic Polygala. Although the lack of photosynthesis is presumably homologous in the genus, the surveyed Epirixanthes species have marked differences in terms of plastome size, structural rearrangements, gene content and substitution rates. Remarkably, both apparently replaced a canonical plastid inverted repeat with large directly repeated sequences. The mitogenome of E. elongata incorporated a considerable number of fossilized plastid genes, by intracellular transfer from an ancestor with a less degraded plastome. Both plastid and mitochondrial genes in E. elongata have increased substitution rates, but the plastid genes of E. pallida do not. Despite this, both species have similar selection patterns operating on plastid housekeeping genes. CONCLUSIONS Plastome evolution largely fits with patterns of gene degradation seen in other heterotrophic plants, but includes highly unusual directly duplicated regions. The causes of rate elevation in the sequenced Epirixanthes mitogenome and of rate differences in plastomes of related mycoheterotrophic species are not currently understood.
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Affiliation(s)
- G Petersen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- For correspondence. E-mail:
| | - H Darby
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - V K Y Lam
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - H Æ Pedersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - A Zervas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Department of Environmental Science, Aarhus University, Denmark
| | - O Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - S W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
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Cao J, Cheng X. Transcriptome-Based Identification and Molecular Evolution of the Cytochrome P450 Genes and Expression Profiling under Dimethoate Treatment in Amur Stickleback ( Pungitius sinensis). Animals (Basel) 2019; 9:E873. [PMID: 31661806 DOI: 10.3390/ani9110873] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/11/2019] [Accepted: 10/18/2019] [Indexed: 01/08/2023] Open
Abstract
Cytochrome P450s (CYPs) are a family of membrane-bound mono-oxygenase proteins, which are involved in cell metabolism and detoxification of various xenobiotic substances. In this study, we identified 58 putative CYP genes in Amur stickleback (Pungitius sinensis) based on the transcriptome sequencing. Conserved motif distribution suggested their functional relevance within each group. Some present recombination events have accelerated the evolution of this gene family. Moreover, a few positive selection sites were identified, which may have accelerated the functional divergence of this family of proteins. Expression patterns of these CYP genes were investigated and indicated that most were affected by dimethoate treatment, suggesting that CYPs were involved in the detoxication of dimethoate. This study will provide a foundation for the further functional investigation of CYP genes in fishes.
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Abstract
The mutator phenotype hypothesis was postulated almost 40 years ago to reconcile the observation that while cancer cells display widespread mutational burden, acquisition of mutations in non-transformed cells is a rare event. Moreover, it also suggested that cancer evolution could be fostered by increased genome instability. Given the evolutionary conservation throughout the tree of life and the genetic tractability of model organisms, yeast and bacterial species pioneered studies to dissect the functions of genes required for genome maintenance (caretaker genes) or for cell growth control (gatekeeper genes). In this review, we first provide an overview of what we learned from model organisms about the roles of these genes and the genome instability that arises as a consequence of their dysregulation. We then discuss our current understanding of how mutator phenotypes shape the evolution of bacteria and yeast species. We end by bringing clinical evidence that lessons learned from single-cell organisms can be applied to tumor evolution.
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Affiliation(s)
- Federica Natali
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Giulia Rancati
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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Abstract
Antibiotic resistance has been increasingly reported for a wide variety of bacteria of clinical significance. This widespread problem constitutes one of the greatest challenges of the twenty-first century. Faced with this issue, clinicians and researchers have been persuaded to design novel strategies in order to try to control pathogenic bacteria. Therefore, the discovery and elucidation of the mechanisms underlying bacterial pathogenesis and intercellular communication have opened new perspectives for the development of alternative approaches. Antipathogenic and/or antivirulence therapies based on the interruption of quorum sensing pathways are one of several such promising strategies aimed at disarming rather than at eradicating bacterial pathogens during the course of colonization and infection. This review describes mechanisms of bacterial communication involved in biofilm formation. An overview of the potential of marine bacteria and their bioactive components as QS inhibitors is further provided.
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59
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Cao J, Shi F. Comparative Analysis of the aquaporin Gene Family in 12 Fish Species. Animals (Basel) 2019; 9:E233. [PMID: 31086002 DOI: 10.3390/ani9050233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 01/15/2023] Open
Abstract
Simple Summary Aquaporins (Aqps) are a group of membrane proteins. In this study, 166 Aqp genes were identified in 12 fish species. Gene organization, motif distribution, recombination, and selection pressure were performed to investigate their evolutionary characteristics. In addition, expression profiles of Aqps were also examined under pathogens infection and organophosphorus pesticide stress. This study will provide a useful reference for further functional study. Abstract Aquaporins (Aqps) are a class of water channel proteins that play key roles in many physiological functions and cellular processes. Here, we analyzed 166 putative Aqp genes in 12 fish species and divided them into four groups. Gene organization and motif distribution analyses suggested potentially conserved functions in each group. Several recombination events were identified in some members, which accelerate their divergence in evolution. Furthermore, a few positive selection sites were identified, and mutations at these sites could alter the stability of Aqp proteins. In addition, expression profiles of some Aqp genes under pathogen infection and organophosphorus pesticide stress were also investigated. The result implied that several Aqp genes may affect different immune responses and osmoregulation. This study provides a comparative analysis of the fish Aqp gene family to facilitate further functional analyses.
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Cao J, Tan X. Comprehensive Analysis of the Chitinase Family Genes in Tomato ( Solanum lycopersicum). Plants (Basel) 2019; 8:plants8030052. [PMID: 30823433 PMCID: PMC6473868 DOI: 10.3390/plants8030052] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 12/19/2022]
Abstract
Chitinase catalyzes the hydrolysis of chitin β-1,4 linkages. However, plants cannot produce chitin, suggesting that plant chitinases do not have the same function as animals. This study investigated the chitinase gene family in tomato and divided into eight groups via phylogenetic analyses with Arabidopsis and rice members. Conserved gene structures and motif arrangements indicated their functional relevance with each group. These genes were nonrandomly distributed across the tomato chromosomes, and tandem duplication contributed to the expansion of this gene family. Synteny analysis also established orthology relationships and functional linkages between Arabidopsis and tomato chitinase genes. Several positive selection sites were identified, which may contribute to the functional divergence of the protein family in evolution. In addition, differential expression profiles of the tomato chitinase genes were also investigated at some developmental stages, or under different biotic and abiotic stresses. Finally, functional network analysis found 124 physical or functional interactions, implying the diversity of physiological functions of the family proteins. These results provide a foundation for the exploration of the chitinase genes in plants and will offer some insights for further functional studies.
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Affiliation(s)
- Jun Cao
- Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, China.
| | - Xiaona Tan
- Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, China.
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Silva F, Huang Y, Yang V, Mu X, Shi Q, Antunes A. Transcriptomic Characterization of the South American Freshwater Stingray Potamotrygon motoro Venom Apparatus. Toxins (Basel) 2018; 10:E544. [PMID: 30567320 PMCID: PMC6315956 DOI: 10.3390/toxins10120544] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 01/16/2023] Open
Abstract
Venomous animals are found through a wide taxonomic range including cartilaginous fish such as the freshwater stingray Potamotrygon motoro occurring in South America, which can injure people and cause venom-related symptoms. Ensuring the efficacy of drug development to treat stingray injuries can be assisted by the knowledge of the venom composition. Here we performed a detailed transcriptomic characterization of the venom gland of the South American freshwater stingray Potamotrygon motoro. The transcripts retrieved showed 418 hits to venom components (comparably to 426 and 396 hits in other two Potamotrygon species), with high expression levels of hyaluronidase, cystatin and calglandulin along with hits uniquely found in P. motoro such as DELTA-alicitoxin-Pse1b, Augerpeptide hhe53 and PI-actitoxin-Aeq3a. We also identified undescribed molecules with extremely high expression values with sequence similarity to the SE-cephalotoxin and Rapunzel genes. Comparative analyses showed that despite being closely related, there may be significant variation among the venoms of freshwater stingrays, highlighting the importance of considering elicit care in handling different envenomation cases. Since hyaluronidase represents a major component of fish venom, we have performed phylogenetic and selective pressure analyses of this gene/protein across all fish with the available information. Results indicated an independent recruitment of the hyaluronidase into the stingray venom relative to that of venomous bony fish. The hyaluronidase residues were found to be mostly under negative selection, but 18 sites showed evidence of diversifying positive selection (P < 0.05). Our data provides new insight into stingray venom variation, composition, and selective pressure in hyaluronidase.
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Affiliation(s)
- Filipe Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Vítor Yang
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
| | - Xidong Mu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Recreational Fisheries, Ministry of Agriculture, Guangdong Engineering Technology Research Center for Advanced Recreational Fisheries, Guangzhou 510380, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Av. General Norton de Matos, s/n, 4450-208 Porto, Portugal.
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal.
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Jossé L, Singh T, von der Haar T. Experimental determination of codon usage-dependent selective pressure on high copy-number genes in Saccharomyces cerevisiae. Yeast 2018; 36:43-51. [PMID: 30548237 DOI: 10.1002/yea.3373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/15/2018] [Accepted: 12/05/2018] [Indexed: 11/08/2022] Open
Abstract
One of the central hypotheses in the theory of codon usage evolution is that in highly expressed genes, particular codon usage patterns arise because they facilitate efficient gene expression and are thus selected for in evolution. Here, we use plasmid copy number assays and growth rate measurements to explore details of the relationship between codon usage, gene expression level, and selective pressure in Saccharomyces cerevisiae. We find that when high expression levels are required, optimal codon usage is beneficial and provides a fitness advantage, consistent with evolutionary theory. However, when high expression levels are not required, optimal codon usage is surprisingly and strongly selected against. We show that this selection acts at the level of protein synthesis, and we exclude a number of molecular mechanisms as the source for this negative selective pressure including nutrient and ribosome limitations and proteotoxicity effects. These findings deepen our understanding of the evolution of codon usage bias, as well as the design of recombinant protein expression systems.
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Affiliation(s)
- Lyne Jossé
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, U.K
| | - Tarun Singh
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, U.K
| | - Tobias von der Haar
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, U.K
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Chu YMR, Sha JCM, Kawazoe T, Dong X. Sleeping site and tree selection by Sichuan snub-nosed monkeys (Rhinopithecus roxellana) in Baihe Nature Reserve, Sichuan, China. Am J Primatol 2018; 80:e22936. [PMID: 30537389 DOI: 10.1002/ajp.22936] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/05/2018] [Accepted: 10/06/2018] [Indexed: 01/09/2023]
Abstract
For non-human primates to optimize their survival chances, sleeping site selection is crucial as they spend much of their time sleeping. We studied sleeping site and tree selection by a group of wild Sichuan snub-nosed monkeys (Rhinopithecus roxellana) in the temperate forests of Baihe Nature Reserve, Sichuan, China, to assess if certain site and tree characteristics were selected. We identified a total of 39 sleeping sites and 111 sleeping trees over a period of 1 year. We compared nine sleeping site and six sleeping tree variables related to the environment, habitat, and vegetation structure. We found that certain characteristics of sleeping sites and sleeping trees predicted their selection by R. roxellana. On a larger spatial scale, sleeping sites were selected based mainly on four factors: canopy height, slope direction, slope gradient, and vegetation type. They also selected sites with trees that were taller and larger, had larger crown diameters and higher bole branches. On a smaller spatial scale, they selected larger trees with larger crown diameters. The selection of these characteristics could be explained in terms of predator avoidance and thermoregulation efficiency, although it was difficult to delineate which was more important. This could be due to some characteristics of R. roxellana, that is, large groups living in temperate climates, which required a balanced strategy for sleeping site and tree selection in order to optimize their survival chances.
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Affiliation(s)
| | - John Chih Mun Sha
- School of Sociology and Anthropology, Sun Yat-Sen University, GuangZhou, China
| | - Tatsuro Kawazoe
- School of Sociology and Anthropology, Sun Yat-Sen University, GuangZhou, China
| | - Xin Dong
- College of Environmental Science and Engineering, China West Normal University, Nanchong, Sichuan, China
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Zhu L, Deng C, Zhao X, Ding J, Huang H, Zhu S, Wang Z, Qin S, Ding Y, Lu G, Yang Z. Endangered Père David's deer genome provides insights into population recovering. Evol Appl 2018; 11:2040-2053. [PMID: 30459847 PMCID: PMC6231465 DOI: 10.1111/eva.12705] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/14/2018] [Accepted: 08/26/2018] [Indexed: 12/30/2022] Open
Abstract
The Milu (Père David's deer, Elaphurus davidianus) were once widely distributed in the swamps (coastal areas to inland areas) of East Asia. The dramatic recovery of the Milu population is now deemed a classic example of how highly endangered animal species can be rescued. However, the molecular mechanisms that underpinned this population recovery remain largely unknown. Here, different approaches (genome sequencing, resequencing, and salinity analysis) were utilized to elucidate the aforementioned molecular mechanisms. The comparative genomic analyses revealed that the largest recovered Milu population carries extensive genetic diversity despite an extreme population bottleneck. And the protracted inbreeding history might have facilitated the purging of deleterious recessive alleles. Seventeen genes that are putatively related to reproduction, embryonic (fatal) development, and immune response were under high selective pressure. Besides, SCNN1A, a gene involved in controlling reabsorption of sodium in the body, was positively selected. An additional 29 genes were also observed to be positively selected, which are involved in blood pressure regulation, cardiovascular development, cholesterol regulation, glycemic control, and thyroid hormone synthesis. It is possible that these genetic adaptations were required to buffer the negative effects commonly associated with a high-salt diet. The associated genetic adaptions are likely to have enabled increased breeding success and fetal survival. The future success of Milu population management might depend on the successful reintroduction of the animal to historically important distribution regions.
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Affiliation(s)
- Lifeng Zhu
- College of life SciencesNanjing Normal UniversityNanjingChina
- University of Nebraska at OmahaOmaha
| | - Cao Deng
- DNA Stories Bioinformatics CenterChengduChina
| | - Xiang Zhao
- PubBio‐Tech Services CorporationWuhanChina
| | | | - Huasheng Huang
- Shanghai Majorbio Bio‐pharm Biotechnology Co. Ltd.ShanghaiChina
| | - Shilin Zhu
- PubBio‐Tech Services CorporationWuhanChina
| | | | | | - Yuhua Ding
- Jiangsu Dafeng Milu National Nature ReserveDafengChina
| | | | - Zhisong Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education)China West Normal UniversityNanchongChina
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Zhang R, Zhang L, Wang W, Zhang Z, Du H, Qu Z, Li XQ, Xiang H. Differences in Codon Usage Bias between Photosynthesis-Related Genes and Genetic System-Related Genes of Chloroplast Genomes in Cultivated and Wild Solanum Species. Int J Mol Sci 2018; 19:E3142. [PMID: 30322061 PMCID: PMC6213243 DOI: 10.3390/ijms19103142] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/30/2018] [Accepted: 10/04/2018] [Indexed: 12/20/2022] Open
Abstract
Solanum is one of the largest genera, including two important crops-potato (Solanum tuberosum) and tomato (Solanum lycopersicum). In this study we compared the chloroplast codon usage bias (CUB) among 12 Solanum species, between photosynthesis-related genes (Photo-genes) and genetic system-related genes (Genet-genes), and between cultivated species and wild relatives. The Photo-genes encode proteins for photosystems, the photosynthetic electron transport chain, and RuBisCO, while the Genet-genes encode proteins for ribosomal subunits, RNA polymerases, and maturases. The following findings about the Solanum chloroplast genome CUB were obtained: (1) the nucleotide composition, gene expression, and selective pressure are identified as the main factors affecting chloroplast CUB; (2) all these 12 chloroplast genomes prefer A/U over G/C and pyrimidines over purines at the third-base of codons; (3) Photo-genes have higher codon adaptation indexes than Genet-genes, indicative of a higher gene expression level and a stronger adaptation of Photo-genes; (4) gene function is the primary factor affecting CUB of Photo-genes but not Genet-genes; (5) Photo-genes prefer pyrimidine over purine, whereas Genet-genes favor purine over pyrimidine, at the third position of codons; (6) Photo-genes are mainly affected by the selective pressure, whereas Genet-genes are under the underlying mutational bias; (7) S. tuberosum is more similar with Solanum commersonii than with Solanum bulbocastanum; (8) S. lycopersicum is greatly different from the analyzed seven wild relatives; (9) the CUB in codons for valine, aspartic acid, and threonine are the same between the two crop species, S. tuberosum and S. lycopersicum. These findings suggest that the chloroplast CUB contributed to the differential requirement of gene expression activity and function between Photo-genes and Genet-genes and to the performance of cultivated potato and tomato.
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Affiliation(s)
- Ruizhi Zhang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China.
| | - Li Zhang
- Department of Math and Information, China West Normal University, Nanchong, Sichuan 637000, China.
| | - Wei Wang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Zhu Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Huihui Du
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Zheng Qu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, NB E3B 4Z7, Canada.
| | - Heng Xiang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China.
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Sawatsky B, Cattaneo R, von Messling V. Canine Distemper Virus Spread and Transmission to Naive Ferrets: Selective Pressure on Signaling Lymphocyte Activation Molecule-Dependent Entry. J Virol 2018; 92:e00669-18. [PMID: 29793948 DOI: 10.1128/JVI.00669-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022] Open
Abstract
Upon infection, morbilliviruses such as measles virus, rinderpest virus, and canine distemper virus (CDV) initially target immune cells via the signaling lymphocyte activation molecule (SLAM) before spreading to respiratory epithelia through the adherens junction protein nectin-4. However, the roles of these receptors in transmission from infected to naive hosts have not yet been formally tested. To experimentally addressing this question, we established a model of CDV contact transmission between ferrets. We show here that transmission of wild-type CDV sometimes precedes the onset of clinical disease. In contrast, transmission was not observed in most animals infected with SLAM- or nectin-4-blind CDVs, even though all animals infected with the nectin-4-blind virus developed sustained viremia. There was an unexpected case of transmission of a nectin-4-blind virus, possibly due to biting. Another unprecedented event was transient viremia in an infection with a SLAM-blind virus. We identified three compensatory mutations within or near the SLAM-binding surface of the attachment protein. A recombinant CDV expressing the mutated attachment protein regained the ability to infect ferret lymphocytes in vitro, but its replication was not as efficient as that of wild-type CDV. Ferrets infected with this virus developed transient viremia and fever, but there was no transmission to naive contacts. Our study supports the importance of epithelial cell infection and of sequential CDV H protein interactions first with SLAM and then nectin-4 receptors for transmission to naive hosts. It also highlights the in vivo selection pressure on the H protein interactions with SLAM.IMPORTANCE Morbilliviruses such as measles virus, rinderpest virus, and canine distemper virus (CDV) are highly contagious. Despite extensive knowledge of how morbilliviruses interact with their receptors, little is known about how those interactions influence viral transmission to naive hosts. In a ferret model of CDV contact transmission, we showed that sequential use of the signaling lymphocytic activation molecule (SLAM) and nectin-4 receptors is essential for transmission. In one animal infected with a SLAM-blind CDV, we documented mild viremia due to the acquisition of three compensatory mutations within or near the SLAM-binding surface. The interaction, however, was not sufficient to cause disease or sustain transmission to naive contacts. This work confirms the sequential roles of SLAM and nectin-4 in morbillivirus transmission and highlights the selective pressure directed toward productive interactions with SLAM.
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Escargueil AE, Prado S, Dezaire A, Clairambault J, Larsen AK, Soares DG. Genotype- or Phenotype-Targeting Anticancer Therapies? Lessons from Tumor Evolutionary Biology. Curr Pharm Des 2018; 22:6625-6644. [PMID: 27587198 DOI: 10.2174/1381612822666160831114002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/25/2016] [Indexed: 11/22/2022]
Abstract
Despite the efficacy of most cancer therapies, drug resistance remains a major problem in the clinic. The eradication of the entire tumor and the cure of the patient by chemotherapy alone are rare, in particular for advanced disease. From an evolutionary perspective, the selective pressure exerted by chemotherapy leads to the emergence of resistant clones where resistance can be associated with many different functional mechanisms at the single cell level or can involve changes in the tumor micro-environment. In the last decade, tumor genomics has contributed to the improvement of our understanding of tumorigenesis and has led to the identification of numerous cellular targets for the development of novel therapies. However, since tumors are by nature extremely heterogeneous, the drug efficacy and economical sustainability of this approach is now debatable. Importantly, tumor cell heterogeneity depends not only on genetic modifications but also on non-genetic processes involving either stochastic events or epigenetic modifications making genetic biomarkers of uncertain utility. In this review, we wish to highlight how evolutionary biology can impact our understanding of carcinogenesis and resistance to therapies. We will discuss new approaches based on applied ecology and evolution dynamics that can be used to convert the cancer into a chronic disease where the drugs would control tumor growth. Finally, we will discuss the way metabolic dysfunction or phenotypic changes can help developing new delivery systems or phenotypetargeted drugs and how exploring new sources of active compounds can conduct to the development of drugs with original mechanisms of action.
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Affiliation(s)
- Alexandre E Escargueil
- Sorbonne Universites, UPMC Univ Paris 06, INSERM, Laboratory of Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine (CRSA), UMR_S 938, F-75012 Paris, France
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68
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Fan W, Xu Y, Zhang P, Chen P, Zhu Y, Cheng Z, Zhao X, Liu Y, Liu J. Analysis of molecular evolution of nucleocapsid protein in Newcastle disease virus. Oncotarget 2017; 8:97127-97136. [PMID: 29228598 PMCID: PMC5722550 DOI: 10.18632/oncotarget.21373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/30/2017] [Indexed: 11/25/2022] Open
Abstract
The present study investigated the molecular evolution of nucleocapsid protein (NP) in different Newcastle disease virus (NDV) genotypes. The evolutionary timescale and rate were estimated using the Bayesian Markov chain Monte Carlo (MCMC) method. The p-distance, Bayesian skyline plot (BSP), and positively selected sites were also analyzed. The MCMC tree indicated that NDV diverged about 250 years ago with a rapid evolution rate (1.059 × 10-2 substitutions/site/year) and that different NDV genotypes formed three lineages. The p-distance results reflected the great genetic diversity of NDV. BSP analysis suggested that the effective population size of NDV has been increasing since 2000 and that the basic reproductive number (R0) of NDV ranged from 1.003 to 1.006. The abundance of negatively selected sites in the NP and the mean dN/dS value of 0.07 indicated that the NP of NDV may have undergone purifying selection. However, the predicted positively selected site at position 370 was located in the known effective epitopic region of the NP. In conclusion, although NDV evolved at a high rate and showed great genetic diversity, the structure and function of the NP had been well conserved. However, R0>1 suggests that NDV might have been causing an epidemic since the time of radiation.
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Affiliation(s)
- Wentao Fan
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an 271018, China
| | - Yuliang Xu
- Research Center for Animal Disease Control Engineering Shandong Province, Shandong Agricultural University, Tai'an 271018, PR China
| | - Pu Zhang
- Central Hospital of Tai'an City, Tai'an 271018, China
| | - Peng Chen
- Research Center for Animal Disease Control Engineering Shandong Province, Shandong Agricultural University, Tai'an 271018, PR China
| | - Yiran Zhu
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China
| | - Ziqiang Cheng
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China
| | - Xiaona Zhao
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China
| | - Yongxia Liu
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China
| | - Jianzhu Liu
- College of Animal Medicine and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, PR China.,Research Center for Animal Disease Control Engineering Shandong Province, Shandong Agricultural University, Tai'an 271018, PR China.,Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Tai'an 271018, China
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69
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Stangherlin LM, de Paula FN, Icimoto MY, Ruiz LGP, Nogueira ML, Braz ASK, Juliano L, da Silva MCC. Positively Selected Sites at HCMV gB Furin Processing Region and Their Effects in Cleavage Efficiency. Front Microbiol 2017; 8:934. [PMID: 28588572 PMCID: PMC5441137 DOI: 10.3389/fmicb.2017.00934] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/08/2017] [Indexed: 12/16/2022] Open
Abstract
Human cytomegalovirus is a ubiquitous infectious agent that affects mainly immunosuppressed, fetuses, and newborns. The virus has several polymorphic regions, in particular in the envelope glycoproteins. The UL55 gene encodes the glycoprotein B that has a variable region, containing a furin cleavage site and according to the variability different genotypes are characterized. Here we investigated variability and existence of selective pressure on the UL55 variable region containing the furin cleavage site in 213 clinical sequences from patients worldwide. We showed the occurrence of positive selective pressure on gB codons 461 and 462, near the furin cleavage site. Cleavage analysis of synthesized peptides demonstrated that most mutations confer better cleavage by furin, suggesting that evolution is acting in order to increase the efficiency cleavage and supporting the hypothesis that gB processing is important in the host. We also demonstrated that peptides containing sequences, that characterize genotypes gB2 and 3, are differentially cleaved by furin. Our data demonstrate for the first time that variability in the cleavage site is related to degree of gB processing by furin.
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Affiliation(s)
- Lucas M Stangherlin
- Center for Natural Sciences and Humanities, Federal University of ABCSanto André, Brazil
| | - Felipe N de Paula
- Center for Natural Sciences and Humanities, Federal University of ABCSanto André, Brazil.,Pasteur InstituteSão Paulo, Brazil
| | - Marcelo Y Icimoto
- Department of Biophysics, Paulista Medical School, Federal University of São PauloSão Paulo, Brazil
| | - Leonardo G P Ruiz
- Medical School of São José do Rio PretoSão José do Rio Preto, Brazil
| | | | - Antônio S K Braz
- Center for Natural Sciences and Humanities, Federal University of ABCSanto André, Brazil
| | - Luiz Juliano
- Department of Biophysics, Paulista Medical School, Federal University of São PauloSão Paulo, Brazil
| | - Maria C C da Silva
- Center for Natural Sciences and Humanities, Federal University of ABCSanto André, Brazil
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Fleming DS, Weigend S, Simianer H, Weigend A, Rothschild M, Schmidt C, Ashwell C, Persia M, Reecy J, Lamont SJ. Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure. G3 (Bethesda) 2017; 7:1525-37. [PMID: 28341699 DOI: 10.1534/g3.117.041228] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed FST, integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population’s indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions.
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71
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Schmitt C, Garant D, Doyon K, Bousquet N, Gaudreau L, Bélisle M, Pelletier F. Patterns of Diversity and Spatial Variability of β-Defensin Innate Immune Genes in a Declining Wild Population of Tree Swallows. J Hered 2017; 108:262-269. [PMID: 28186244 DOI: 10.1093/jhered/esx005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 01/25/2017] [Indexed: 12/26/2022] Open
Abstract
Assessing the genetic variation and distribution of immune genes across heterogeneous environmental conditions in wild species is essential to further our understanding of the role of pathogen pressure and potential resistance or prevalence in hosts. Researchers have recently investigated β-defensin genes in the wild, because their variability suggests that they may play an important role in innate host defense. This study investigated the variation occurring at 6 innate immune genes of the β-defensin family in a declining population of tree swallows (Tachycineta bicolor) in southern Québec, Canada (N = 160). We found that all 6 genes showed synonymous and nonsynonymous single nucleotide polymorphisms (SNPs) within the exon coding for the mature peptide. These results indicated that this group of genes was diverse in tree swallows. Our results suggested a potential interaction of this group of genes with fluctuating pathogen diversity, however, we found no sign of positive or negative selection. We assessed whether or not the distribution of genetic diversity of β-defensin genes in our study population differed between 2 regions that strongly differ in their level of agricultural intensification. Adults are highly philopatric to their breeding sites and their immunological responses differ between these 2 regions. However, we found little evidence that the level and distribution of genetic variability differed between these heterogeneous environmental conditions. Further studies should aim to assess the link between genetic diversity of β-defensin genes and fitness-related traits in wild populations.
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Affiliation(s)
- Clarence Schmitt
- From the Département de biologie, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, CanadaJ1K 2R1
| | - Dany Garant
- From the Département de biologie, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, CanadaJ1K 2R1
| | - Kathy Doyon
- From the Département de biologie, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, CanadaJ1K 2R1
| | - Nicolas Bousquet
- From the Département de biologie, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, CanadaJ1K 2R1
| | - Luc Gaudreau
- From the Département de biologie, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, CanadaJ1K 2R1
| | - Marc Bélisle
- From the Département de biologie, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, CanadaJ1K 2R1
| | - Fanie Pelletier
- From the Département de biologie, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, Québec, CanadaJ1K 2R1
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72
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Wang P, Song H, Li C, Li P, Li A, Guan H, Hou L, Wang X. Genome-Wide Dissection of the Heat Shock Transcription Factor Family Genes in Arachis. Front Plant Sci 2017; 8:106. [PMID: 28220134 PMCID: PMC5292572 DOI: 10.3389/fpls.2017.00106] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 01/18/2017] [Indexed: 05/21/2023]
Abstract
Heat shock transcription factors (Hsfs) are important transcription factors (TFs) in protecting plants from damages caused by various stresses. The released whole genome sequences of wild peanuts make it possible for genome-wide analysis of Hsfs in peanut. In this study, a total of 16 and 17 Hsf genes were identified from Arachis duranensis and A. ipaensis, respectively. We identified 16 orthologous Hsf gene pairs in both peanut species; however HsfXs was only identified from A. ipaensis. Orthologous pairs between two wild peanut species were highly syntenic. Based on phylogenetic relationship, peanut Hsfs were divided into groups A, B, and C. Selection pressure analysis showed that group B Hsf genes mainly underwent positive selection and group A Hsfs were affected by purifying selection. Small scale segmental and tandem duplication may play important roles in the evolution of these genes. Cis-elements, such as ABRE, DRE, and HSE, were found in the promoters of most Arachis Hsf genes. Five AdHsfs and two AiHsfs contained fungal elicitor responsive elements suggesting their involvement in response to fungi infection. These genes were differentially expressed in cultivated peanut under abiotic stress and Aspergillus flavus infection. AhHsf2 and AhHsf14 were significantly up-regulated after inoculation with A. flavus suggesting their possible role in fungal resistance.
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Affiliation(s)
- Pengfei Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Hui Song
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Changsheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Pengcheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Aiqin Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Hongshan Guan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
- *Correspondence: Lei Hou
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, China
- College of Life Sciences, Shandong Normal UniversityJinan, China
- Xingjun Wang
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Roquet C, Coissac É, Cruaud C, Boleda M, Boyer F, Alberti A, Gielly L, Taberlet P, Thuiller W, Van Es J, Lavergne S. Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae). Ann Bot 2016; 118:885-896. [PMID: 27443299 PMCID: PMC5055816 DOI: 10.1093/aob/mcw135] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/09/2016] [Accepted: 05/12/2016] [Indexed: 05/19/2023]
Abstract
Background and Aims Plant plastid genomes are highly conserved in size, gene content and structure; however, parasitic plants are a noticeable exception to this evolutionary stability. Although the evolution of parasites could help to better understand plastome evolution in general, complete plastomes of parasites have been sequenced only for some lineages so far. Here we contribute to filling this gap by providing and analysing the complete plastome sequence of Cytinus hypocistis, the first parasite sequenced for Malvales and a species suspected to have an extremely small genome. Methods We sequenced and assembled de novo the plastid genome of Cytinus hypocistis using a shotgun approach on genomic DNA. Phylogenomic analyses based on coding regions were performed on Malvidae. For each coding region present in Cytinus, we tested for relaxation or intensification of selective pressures in the Cytinus lineage compared with autotrophic Malvales. Key Results Cytinus hypocistis has an extremely divergent genome that is among the smallest sequenced to date (19·4 kb), with only 23 genes and no inverted repeat regions. Phylogenomic analysis confirmed the position of Cytinus within Malvales. All coding regions of Cytinus plastome presented very high substitution rates compared with non-parasitic Malvales. Conclusions Some regions were inferred to be under relaxed negative selection in Cytinus, suggesting that further plastome reduction is occurring due to relaxed purifying selection associated with the loss of photosynthetic activity. On the other hand, increased selection intensity and strong positive selection were detected for rpl22 in the Cytinus lineage, which might indicate an evolutionary role in the host-parasite arms race, a point that needs further research.
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Affiliation(s)
- Cristina Roquet
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
- *For correspondence. E-mail
| | - Éric Coissac
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Corinne Cruaud
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France
| | - Martí Boleda
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Frédéric Boyer
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Adriana Alberti
- CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France
| | - Ludovic Gielly
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Pierre Taberlet
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
| | - Jérémie Van Es
- Conservatoire Botanique National Alpin, Domaine de Charance, FR-05000 Gap, France
| | - Sébastien Lavergne
- Laboratoire d’Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France
- Laboratoire d’Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France
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Cuypers L, Li G, Neumann-Haefelin C, Piampongsant S, Libin P, Van Laethem K, Vandamme AM, Theys K. Mapping the genomic diversity of HCV subtypes 1a and 1b: Implications of structural and immunological constraints for vaccine and drug development. Virus Evol 2016; 2:vew024. [PMID: 27774307 PMCID: PMC5072459 DOI: 10.1093/ve/vew024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Despite significant progress in hepatitis C (HCV) treatment, global viral eradication remains a challenge. An in-depth map of its genome diversity within the context of structural and immunological constraints could contribute to the design of pan-genotypic antivirals and preventive vaccines. For such analyses, extensive information is only available for the highly prevalent HCV genotypes (GT) 1a and 1b. Using 647 GT1a and 408 GT1b full-genome sequences obtained from the Los Alamos database, we found that respectively 3 per cent and 82 per cent of all codon positions are under positive and negative selective pressure, suggesting variation mainly accumulates due to random genetic drift. An association between conservation and both structured RNA and secondary protein structures confirmed the important role of structural elements at nucleotide and at amino acid level. Remarkably, CD8+ T-cell epitopes in HCV GT1a were significantly more conserved, while at the same time containing more sites under positive selection. Similarly, CD4+ T-cell epitopes were significantly more conserved in both HCV subtypes, but under less positive selective pressure in GT1b and more negative selective pressure in GT1a. In contrast, B-cell epitopes in both subtypes were less conserved and under less stringent negative selection. These findings argue against immune selective pressure as the main force of between-host diversifying evolution. Despite its high variability, HCV is under strict evolutionary constraints, most probably to keep its genes and proteins functional during the replication cycle. These are encouraging findings for vaccine and drug design, which could consider these newly established genetic diversity profiles.
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Affiliation(s)
- Lize Cuypers
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Guangdi Li
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 3000 Leuven, Belgium; Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Christoph Neumann-Haefelin
- Department of Medicine II, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
| | - Supinya Piampongsant
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 3000 Leuven, Belgium; Department of Electrical Engineering ESAT, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, University of Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium
| | - Pieter Libin
- Artificial Intelligence Lab, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Kristel Van Laethem
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Anne-Mieke Vandamme
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 3000 Leuven, Belgium; Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Rua da Junqueira 100, Lisbon, 1349-008, Portugal
| | - Kristof Theys
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 3000 Leuven, Belgium
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75
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Deregowska A, Adamczyk J, Kwiatkowska A, Gurgul A, Skoneczny M, Skoneczna A, Szmatola T, Jasielczuk I, Magda M, Rawska E, Pabian S, Panek A, Kaplan J, Lewinska A, Wnuk M. Shifts in rDNA levels act as a genome buffer promoting chromosome homeostasis. Cell Cycle 2016; 14:3475-87. [PMID: 26566866 DOI: 10.1080/15384101.2015.1093705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The nucleolus is considered to be a stress sensor and rDNA-based regulation of cellular senescence and longevity has been proposed. However, the role of rDNA in the maintenance of genome integrity has not been investigated in detail. Using genomically diverse industrial yeasts as a model and array-based comparative genomic hybridization (aCGH), we show that chromosome level may be balanced during passages and as a response to alcohol stress that may be associated with changes in rDNA pools. Generation- and ethanol-mediated changes in genes responsible for protein and DNA/RNA metabolism were revealed using next-generation sequencing. Links between redox homeostasis, DNA stability, and telomere and nucleolus states were also established. These results suggest that yeast genome is dynamic and chromosome homeostasis may be controlled by rDNA.
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Affiliation(s)
- Anna Deregowska
- a Department of Genetics ; University of Rzeszow ; Rzeszow , Poland
| | - Jagoda Adamczyk
- a Department of Genetics ; University of Rzeszow ; Rzeszow , Poland
| | | | - Artur Gurgul
- b Department of Genomics and Molecular Biology of Animals ; Laboratory of Genomics; National Research Institute of Animal Production ; Cracow , Poland
| | - Marek Skoneczny
- c Department of Genetics ; Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland
| | - Adrianna Skoneczna
- d Laboratory of Mutagenesis and DNA Repair; Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland
| | - Tomasz Szmatola
- b Department of Genomics and Molecular Biology of Animals ; Laboratory of Genomics; National Research Institute of Animal Production ; Cracow , Poland
| | - Igor Jasielczuk
- b Department of Genomics and Molecular Biology of Animals ; Laboratory of Genomics; National Research Institute of Animal Production ; Cracow , Poland
| | - Michal Magda
- a Department of Genetics ; University of Rzeszow ; Rzeszow , Poland
| | - Ewa Rawska
- a Department of Genetics ; University of Rzeszow ; Rzeszow , Poland
| | - Sylwia Pabian
- a Department of Genetics ; University of Rzeszow ; Rzeszow , Poland
| | - Anita Panek
- a Department of Genetics ; University of Rzeszow ; Rzeszow , Poland
| | - Jakub Kaplan
- a Department of Genetics ; University of Rzeszow ; Rzeszow , Poland
| | - Anna Lewinska
- e Department of Biochemistry and Cell Biology ; University of Rzeszow; Rzeszow , Poland
| | - Maciej Wnuk
- a Department of Genetics ; University of Rzeszow ; Rzeszow , Poland
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76
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Friedman ND, Temkin E, Carmeli Y. The negative impact of antibiotic resistance. Clin Microbiol Infect 2015; 22:416-22. [PMID: 26706614 DOI: 10.1016/j.cmi.2015.12.002] [Citation(s) in RCA: 378] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 11/25/2015] [Accepted: 12/03/2015] [Indexed: 12/12/2022]
Abstract
Antibacterial therapy is one of the most important medical developments of the twentieth century; however, the spread of resistance in healthcare settings and in the community threatens the enormous gains made by the availability of antibiotic therapy. Infections caused by resistant bacteria lead to up to two-fold higher rates of adverse outcomes compared with similar infections caused by susceptible strains. These adverse outcomes may be clinical or economic and reflect primarily the failure or delay of antibiotic treatment. The magnitude of these adverse outcomes will be more pronounced as disease severity, strain virulence, or host vulnerability increases. The negative impacts of antibacterial resistance can be measured at the patient level by increased morbidity and mortality, at the healthcare level by increased resource utilization, higher costs and reduced hospital activity and at the society level by antibiotic treatment guidelines favouring increasingly broad-spectrum empiric therapy. In this review we will discuss the negative impact of antibiotic resistance on patients, the healthcare system and society.
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Affiliation(s)
- N D Friedman
- Departments of Medicine and Infectious Diseases, Barwon Health, Geelong, Vic., Australia
| | - E Temkin
- Division of Epidemiology, Tel Aviv Sourasky Medical Centre, Tel Aviv, Israel
| | - Y Carmeli
- Division of Epidemiology, Tel Aviv Sourasky Medical Centre, Tel Aviv, Israel.
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77
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Kaltenegger E, Ober D. Paralogue Interference Affects the Dynamics after Gene Duplication. Trends Plant Sci 2015; 20:814-821. [PMID: 26638775 DOI: 10.1016/j.tplants.2015.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/28/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
Proteins tend to form homomeric complexes of identical subunits, which act as functional units. By definition, the subunits are encoded from a single genetic locus. When such a gene is duplicated, the gene products are suggested initially to cross-interact when coexpressed, thus resulting in the phenomenon of paralogue interference. In this opinion article, we explore how paralogue interference can shape the fate of a duplicated gene. One important outcome is a prolonged time window in which both copies remain under selection increasing the chance to accumulate mutations and to develop new properties. Thereby, paralogue interference can mediate the coevolution of duplicates and here we illustrate the potential of this phenomenon in light of recent new studies.
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Affiliation(s)
- Elisabeth Kaltenegger
- Department of Biochemical Ecology and Molecular Evolution, Botanical Institute, Christian-Albrechts-University, 24098 Kiel, Germany.
| | - Dietrich Ober
- Department of Biochemical Ecology and Molecular Evolution, Botanical Institute, Christian-Albrechts-University, 24098 Kiel, Germany
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78
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Bailey LD, van de Pol M. Tackling extremes: challenges for ecological and evolutionary research on extreme climatic events. J Anim Ecol 2015; 85:85-96. [PMID: 26433114 DOI: 10.1111/1365-2656.12451] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 09/04/2015] [Indexed: 11/30/2022]
Abstract
Extreme climatic events (ECEs) are predicted to become more frequent as the climate changes. A rapidly increasing number of studies - though few on animals - suggest that the biological consequences of ECEs can be severe. However, ecological research on the impacts of ECEs has been limited by a lack of cohesiveness and structure. ECEs are often poorly defined and have often been confusingly equated with climatic variability, making comparison between studies difficult. In addition, a focus on short-term studies has provided us with little information on the long-term implications of ECEs, and the descriptive and anecdotal nature of many studies has meant it is still unclear what the key research questions are. Synthesizing the current state of work is essential to identify ways to make progress. We conduct a synthesis of the literature and discuss conceptual and practical challenges faced by research on ECEs. We consider three steps to advance research. First, we discuss the importance of choosing an ECE definition and identify the pros and cons of 'climatological' and 'biological' definitions of ECEs. Secondly, we advocate research beyond short-term descriptive studies to address questions concerning the long-term implications of ECEs, focussing on selective pressures and phenotypically plastic responses and how they might differ from responses to a changing climatic mean. Finally, we encourage a greater focus on multi-event studies that help us understand the implications of changing patterns of ECEs, through the combined use of modelling, experimental and observational field studies. This study aims to open a discussion on the definitions, questions and methods currently used to study ECEs, which will lead to a more cohesive approach to future ECE research.
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Affiliation(s)
- Liam D Bailey
- Division of Evolution, Ecology & Genetics, Research School of Biology, Australian National University, Canberra, 0200, ACT, Australia
| | - Martijn van de Pol
- Division of Evolution, Ecology & Genetics, Research School of Biology, Australian National University, Canberra, 0200, ACT, Australia.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
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79
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Vasileiadis S, Puglisi E, Trevisan M, Scheckel KG, Langdon KA, McLaughlin MJ, Lombi E, Donner E. Changes in soil bacterial communities and diversity in response to long-term silver exposure. FEMS Microbiol Ecol 2015; 91:fiv114. [PMID: 26391377 DOI: 10.1093/femsec/fiv114] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 11/13/2022] Open
Abstract
Silver-induced selective pressure is becoming increasingly important due to the growing use of silver (Ag) as an antimicrobial agent in biomedical and commercial products. With demonstrated links between environmental resistomes and clinical pathogens, it is important to identify microbial profiles related to silver tolerance/resistance. We investigated the effects of ionic Ag stress on soil bacterial communities and identified resistant/persistent bacterial populations. Silver treatments of 50-400 mg Ag kg(-1) soil were established in five soils. Chemical lability measurements using diffusive gradients in thin-film devices confirmed that significant (albeit decreasing) labile Ag concentrations were present throughout the 9-month incubation period. Synchrotron X-ray absorption near edge structure spectroscopy demonstrated that this decreasing lability was due to changes in the Ag speciation to less soluble forms such as Ag(0) and Ag2S. Real-time PCR and Illumina MiSeq screening of 16S rRNA bacterial genes showed β-diversity changes, increasing α-diversity in response to Ag pressure, and immediate and significant reductions in 16S rRNA gene counts with varying degrees of recovery. These effects were more strongly influenced by exposure time than by Ag dose at these rates. Ag-selected dominant OTUs principally resided in known persister taxa (mainly Gram positive), including metal-tolerant bacteria and slow-growing Mycobacteria.
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Affiliation(s)
- Sotirios Vasileiadis
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, SA 5095, Australia Istituto di Chimica Agraria e Ambientale, Universitá Cattolica del Sacro Cuore, 29122 Piacenza, Italia
| | - Edoardo Puglisi
- Istituto di Microbiologia, Universitá Cattolica del Sacro Cuore, 29122 Piacenza, Italia
| | - Marco Trevisan
- Istituto di Chimica Agraria e Ambientale, Universitá Cattolica del Sacro Cuore, 29122 Piacenza, Italia
| | - Kirk G Scheckel
- National Risk Management Research Laboratory, US EPA, Cincinnati, OH 45224, USA
| | - Kate A Langdon
- CSIRO Minerals Down Under Flagship, Glen Osmond, SA 5064, Australia
| | | | - Enzo Lombi
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Erica Donner
- Centre for Environmental Risk Assessment and Remediation, University of South Australia, Mawson Lakes, SA 5095, Australia
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80
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Xiong W, Sun Y, Ding X, Wang M, Zeng Z. Selective pressure of antibiotics on ARGs and bacterial communities in manure-polluted freshwater-sediment microcosms. Front Microbiol 2015; 6:194. [PMID: 25814986 PMCID: PMC4356103 DOI: 10.3389/fmicb.2015.00194] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 02/23/2015] [Indexed: 01/22/2023] Open
Abstract
The aim of this study was to investigate selective pressure of antibiotics on antibiotic resistance genes (ARGs) and bacterial communities in manure-polluted aquatic environment. Three treatment groups were set up in freshwater-sediment microcosms: tetracyclines group, sulfonamides group and fluoroquinolones group. Sediment and water samples were collected on day 14 after treatment. Antibiotic concentrations, ARGs abundances and bacterial community composition were analyzed. Antibiotic concentrations were determined by ultra-performance liquid chromatography-electrospray tandem mass spectrometry. ARGs abundances were quantified by real time quantitative PCR. Bacterial community composition was analyzed based on amplicon sequencing. Of the three classes of antibiotics analyzed in the treatment groups, accumulation amounts were tetracyclines> fluoroquinolone> sulfonamides in the sediment samples, while they were sulfonamides> fluoroquinolone> tetracyclines in the water samples. In the treatment groups, the relative abundances of some tet resistance genes [tet(W) and tet(X)] and plasmid-mediated quinolone resistance (PMQR) genes [oqx(B) and aac(6′)-Ib] in sediment samples were significantly higher than those in the paired water samples. Tetracyclines significantly selected the bacterial classes including Gammaproteobacteria, Clostridia, and the genera including Salmonella, Escherichia/Shigella, Clostridium, Stenotrophomonas in sediment samples. The significant selection on bacterial communities posed by sulfonamides and fluoroquinolones was also observed. The results indicated that sediment may supply an ideal setting for maintenance and persistence of tet resistance genes [tet(W) and tet(X)] and PMQR genes [oqx(B) and aac(6′)-Ib] under antibiotic pollution. The results also highlighted that antibiotics significantly selected specific bacterial communities including the taxa associated with opportunistic pathogens.
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Affiliation(s)
- Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Xueyao Ding
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Mianzhi Wang
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
| | - Zhenling Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University Guangzhou, China
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81
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Castelli EC, Ramalho J, Porto IOP, Lima THA, Felício LP, Sabbagh A, Donadi EA, Mendes-Junior CT. Insights into HLA-G Genetics Provided by Worldwide Haplotype Diversity. Front Immunol 2014; 5:476. [PMID: 25339953 PMCID: PMC4186343 DOI: 10.3389/fimmu.2014.00476] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/18/2014] [Indexed: 12/12/2022] Open
Abstract
Human leukocyte antigen G (HLA-G) belongs to the family of non-classical HLA class I genes, located within the major histocompatibility complex (MHC). HLA-G has been the target of most recent research regarding the function of class I non-classical genes. The main features that distinguish HLA-G from classical class I genes are (a) limited protein variability, (b) alternative splicing generating several membrane bound and soluble isoforms, (c) short cytoplasmic tail, (d) modulation of immune response (immune tolerance), and (e) restricted expression to certain tissues. In the present work, we describe the HLA-G gene structure and address the HLA-G variability and haplotype diversity among several populations around the world, considering each of its major segments [promoter, coding, and 3′ untranslated region (UTR)]. For this purpose, we developed a pipeline to reevaluate the 1000Genomes data and recover miscalled or missing genotypes and haplotypes. It became clear that the overall structure of the HLA-G molecule has been maintained during the evolutionary process and that most of the variation sites found in the HLA-G coding region are either coding synonymous or intronic mutations. In addition, only a few frequent and divergent extended haplotypes are found when the promoter, coding, and 3′UTRs are evaluated together. The divergence is particularly evident for the regulatory regions. The population comparisons confirmed that most of the HLA-G variability has originated before human dispersion from Africa and that the allele and haplotype frequencies have probably been shaped by strong selective pressures.
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Affiliation(s)
- Erick C Castelli
- Department of Pathology, School of Medicine of Botucatu, Universidade Estadual Paulista , Botucatu , Brazil
| | - Jaqueline Ramalho
- Department of Pathology, School of Medicine of Botucatu, Universidade Estadual Paulista , Botucatu , Brazil
| | - Iane O P Porto
- Department of Pathology, School of Medicine of Botucatu, Universidade Estadual Paulista , Botucatu , Brazil
| | - Thálitta H A Lima
- Department of Pathology, School of Medicine of Botucatu, Universidade Estadual Paulista , Botucatu , Brazil
| | - Leandro P Felício
- Biological Sciences Institute, Federal University of Goias , Goiânia , Brazil
| | - Audrey Sabbagh
- UMR 216, Institut de Recherche pour le Développement, MERIT , Paris , France ; Faculté de Pharmacie, Université Paris Descartes, Sorbonne Paris Cité , Paris , France
| | - Eduardo A Donadi
- Division of Clinical Immunology, Department of Medicine, School of Medicine of Ribeirão Preto, University of São Paulo , Ribeirão Preto , Brazil
| | - Celso T Mendes-Junior
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, University of São Paulo , Ribeirão Preto , Brazil
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82
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Monestier O, Servin B, Auclair S, Bourquard T, Poupon A, Pascal G, Fabre S. Evolutionary origin of bone morphogenetic protein 15 and growth and differentiation factor 9 and differential selective pressure between mono- and polyovulating species. Biol Reprod 2014; 91:83. [PMID: 25100713 DOI: 10.1095/biolreprod.114.119735] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Bone morphogenetic protein 15 (BMP15) and growth and differentiation factor 9 (GDF9) are TGFbeta-like oocyte-derived growth factors involved in ovarian folliculogenesis as critical regulators of many granulosa cell processes and ovulation rate. Ovarian phenotypic effect caused by alterations in BMP15 and GDF9 genes appears to differ between species and may be relevant to their mono- or polyovulating status. Through phylogenetic analysis we recently showed that these two paralogous genes are strongly divergent and in rapid evolution as compared to other members of the TGFbeta superfamily. Here, we evaluate the amino acid substitution rates of a set of proteins implicated in the ovarian function, including BMP15 and GDF9, with special attention to the mono- or polyovulating status of the species. Among a panel of mono- and polyovulating mammals, we demonstrate a better conservation of some areas in BMP15 and GDF9 within mono-ovulating species. Homology modeling of BMP15 and GDF9 homodimer and heterodimer 3-D structures was suggestive that these areas may be involved in dimer formation and stability. A phylogenetic study of BMP15/GDF9-related proteins reveals that these two genes diverged from the same ancestral gene along with BMP3 and GDF10, two other paralogous genes. A substitution rate analysis based on this phylogenetic tree leads to the hypothesis of an acquisition of BMP15/GDF9-specific functions in ovarian folliculogenesis in mammals. We propose that high variations observed in specific areas of BMP15 and GDF9 in polyovulating species change the equilibrium between homodimers and heterodimers, modifying the biological activity and thus allowing polyovulation to occur.
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Affiliation(s)
- Olivier Monestier
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France Université de Toulouse, Institut National Polytechnique de Toulouse, École Nationale Supérieure Agronomique de Toulouse, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France Université de Toulouse, Institut National Polytechnique de Toulouse, École nationale vétérinaire de Toulouse, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France
| | - Bertrand Servin
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France Université de Toulouse, Institut National Polytechnique de Toulouse, École Nationale Supérieure Agronomique de Toulouse, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France Université de Toulouse, Institut National Polytechnique de Toulouse, École nationale vétérinaire de Toulouse, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France
| | - Sylvain Auclair
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 85 Physiologie de la Reproduction et des Comportements, Nouzilly, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7247 Physiologie de la Reproduction et des Comportements, Nouzilly, France Université François Rabelais de Tours, Tours, France Institut Français du Cheval et de l'Equitation, Nouzilly, France
| | - Thomas Bourquard
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 85 Physiologie de la Reproduction et des Comportements, Nouzilly, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7247 Physiologie de la Reproduction et des Comportements, Nouzilly, France Université François Rabelais de Tours, Tours, France Institut Français du Cheval et de l'Equitation, Nouzilly, France
| | - Anne Poupon
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 85 Physiologie de la Reproduction et des Comportements, Nouzilly, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7247 Physiologie de la Reproduction et des Comportements, Nouzilly, France Université François Rabelais de Tours, Tours, France Institut Français du Cheval et de l'Equitation, Nouzilly, France
| | - Géraldine Pascal
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France Université de Toulouse, Institut National Polytechnique de Toulouse, École Nationale Supérieure Agronomique de Toulouse, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France Université de Toulouse, Institut National Polytechnique de Toulouse, École nationale vétérinaire de Toulouse, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France
| | - Stéphane Fabre
- Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France Université de Toulouse, Institut National Polytechnique de Toulouse, École Nationale Supérieure Agronomique de Toulouse, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France Université de Toulouse, Institut National Polytechnique de Toulouse, École nationale vétérinaire de Toulouse, Unité Mixte de Recherche 1388 Génétique, Physiologie et Systèmes d'Elevage, Toulouse, France
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83
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Zhou LW, Wei YL, Dai YC. Phylogenetic analysis of ligninolytic peroxidases: preliminary insights into the alternation of white-rot and brown-rot fungi in their lineage. Mycology 2014; 5:29-42. [PMID: 24772372 PMCID: PMC3979444 DOI: 10.1080/21501203.2014.895784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 02/14/2014] [Indexed: 11/04/2022] Open
Abstract
White-rot and brown-rot fungi employ different mechanisms to degrade lignocellulose. These fungi are not monophyletic and even alternate in their common lineage. To explore the reason for this, seventy-six ligninolytic peroxidases (LPs), including 14 sequences newly identified from available basidiomycetous whole-genome and EST databases in this study, were utilized for phylogenetic and selective pressure analyses. We demonstrate that LPs were subjected to the mixed process of concerted and birth-and-death evolution. After the duplication events of original LPs, various LP types may originate from mutation events of several key residues driven by positive selection, which may change LP types and even rot types in a small fraction of wood-decaying fungi. Our findings provide preliminary insights into the cause for the alternation of the two fungal rot types within the same lineage.
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Affiliation(s)
- Li-Wei Zhou
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, P. R. China
| | - Yu-Lian Wei
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, P. R. China
| | - Yu-Cheng Dai
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, P. R. China
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84
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Schmitt P, Rosa RD, Duperthuy M, de Lorgeril J, Bachère E, Destoumieux-Garzón D. The Antimicrobial Defense of the Pacific Oyster, Crassostrea gigas. How Diversity may Compensate for Scarcity in the Regulation of Resident/Pathogenic Microflora. Front Microbiol 2012; 3:160. [PMID: 22783227 PMCID: PMC3390580 DOI: 10.3389/fmicb.2012.00160] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 04/10/2012] [Indexed: 12/31/2022] Open
Abstract
Healthy oysters are inhabited by abundant microbial communities that vary with environmental conditions and coexist with immunocompetent cells in the circulatory system. In Crassostrea gigas oysters, the antimicrobial response, which is believed to control pathogens and commensals, relies on potent oxygen-dependent reactions and on antimicrobial peptides/proteins (AMPs) produced at low concentrations by epithelial cells and/or circulating hemocytes. In non-diseased oysters, hemocytes express basal levels of defensins (Cg-Defs) and proline-rich peptides (Cg-Prps). When the bacterial load dramatically increases in oyster tissues, both AMP families are driven to sites of infection by major hemocyte movements, together with bactericidal permeability/increasing proteins (Cg-BPIs) and given forms of big defensins (Cg-BigDef), whose expression in hemocytes is induced by infection. Co-localization of AMPs at sites of infection could be determinant in limiting invasion as synergies take place between peptide families, a phenomenon which is potentiated by the considerable diversity of AMP sequences. Besides, diversity occurs at the level of oyster AMP mechanisms of action, which range from membrane lysis for Cg-BPI to inhibition of metabolic pathways for Cg-Defs. The combination of such different mechanisms of action may account for the synergistic activities observed and compensate for the low peptide concentrations in C. gigas cells and tissues. To overcome the oyster antimicrobial response, oyster pathogens have developed subtle mechanisms of resistance and evasion. Thus, some Vibrio strains pathogenic for oysters are equipped with AMP-sensing systems that trigger resistance. More generally, the known oyster pathogenic vibrios have evolved strategies to evade intracellular killing through phagocytosis and the associated oxidative burst.
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Affiliation(s)
- Paulina Schmitt
- Ecology of Coastal Marine Systems, UMR 5119, CNRS, Université Montpellier 2, IRD, Ifremer, and Université Montpellier 1, Place Eugène Bataillon Montpellier, France
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85
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MacLean EL, Matthews LJ, Hare BA, Nunn CL, Anderson RC, Aureli F, Brannon EM, Call J, Drea CM, Emery NJ, Haun DBM, Herrmann E, Jacobs LF, Platt ML, Rosati AG, Sandel AA, Schroepfer KK, Seed AM, Tan J, van Schaik CP, Wobber V. How does cognition evolve? Phylogenetic comparative psychology. Anim Cogn 2012; 15:223-38. [PMID: 21927850 PMCID: PMC3980718 DOI: 10.1007/s10071-011-0448-8] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 07/21/2011] [Accepted: 08/26/2011] [Indexed: 02/02/2023]
Abstract
Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.
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Affiliation(s)
- Evan L MacLean
- Department of Evolutionary Anthropology, Duke University, Box 90383, Durham, NC 27708, USA.
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86
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Abstract
Commonly used in biotechnology applications, filamentous M13 phage are non-lytic viruses that infect E. coli and other bacteria, with the potential to promote horizontal gene transfer in natural populations with synthetic biology implications for engineering community systems. Using the E. coli strain TG1, we have investigated how a selective pressure involving elevated levels of toxic chromate, mimicking that found in some superfund sites, alters population dynamics following infection with either wild-type M13 phage or an M13-phage encoding a chromate reductase (Gh-ChrR) capable of the reductive immobilization of chromate (ie, M13-phageGh-ChrR). In the absence of a selective pressure, M13-phage infection results in a reduction in bacterial growth rate; in comparison, in the presence of chromate there are substantial increases in both cellular killing and biomass formation following infection of E. coli strain TG1with M13-phageGh-ChrR that is dependent on chromate-reductase activity. These results are discussed in terms of community structures that facilitate lateral gene transfer of beneficial traits that enhance phage replication, infectivity, and stability against environmental change.
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Affiliation(s)
- Hongjun Jin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Thomas C Squier
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - Philip E Long
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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87
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Huhn S, Ingelfinger D, Bermejo JL, Bevier M, Pardini B, Naccarati A, Steinke V, Rahner N, Holinski-Feder E, Morak M, Schackert HK, Görgens H, Pox CP, Goecke T, Kloor M, Loeffler M, Büttner R, Vodickova L, Novotny J, Demir K, Cruciat CM, Renneberg R, Huber W, Niehrs C, Boutros M, Propping P, Vodička P, Hemminki K, Försti A. Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications. Int J Mol Epidemiol Genet 2011; 2:36-50. [PMID: 21537400 PMCID: PMC3077237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 11/23/2010] [Indexed: 05/30/2023]
Abstract
Colorectal cancer (CRC) is a complex disease related to environmental and genetic risk factors. Several studies have shown that susceptibility to complex diseases can be mediated by ancestral alleles. Using RNAi screening, CTNNBL1 was identified as a putative regulator of the Wnt signaling pathway, which plays a key role in colorectal carcinogenesis. Recently, single nucleotide polymorphisms (SNPs) in CTNNBL1 have been associated with obesity, a known risk factor for CRC. We investigated whether genetic variation in CTNNBL1 affects susceptibility to CRC and tested for signals of recent selection. We applied a tagging SNP approach that cover all known common variation in CTNNBL1 (allele frequency >5%; r(2)>0.8). A case-control study was carried out using two well-characterized study populations: a hospital-based Czech population composed of 751 sporadic cases and 755 controls and a family/early onset-based German population (697 cases and 644 controls). Genotyping was performed using allele specific PCR based TaqMan® assays (Applied Biosystems, Weiterstadt, Germany). In the Czech cohort, containing sporadic cases, the ancestral alleles of three SNPs showed evidence of association with CRC: rs2344481 (OR 1.44, 95%CI 1.06-1.95, dominant model), rs2281148 (OR 0.59, 95%CI 0.36-0.96, dominant model) and rs2235460 (OR 1.38, 95%CI 1.01-1.89, AA vs. GG). The associations were less prominent in the family/early onset-based German cohort. Data derived from several databases and statistical tests consistently pointed to a likely shaping of CTNNBL1 by positive selection. Further studies are needed to identify the actual function of CTNNBL1 and to validate the association results in other populations.
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Affiliation(s)
- Stefanie Huhn
- Department of Molecular Genetic Epidemiology; German Cancer Research Center (DKFZ)Heidelberg; Germany
| | - Dierk Ingelfinger
- Division of Signaling and Functional Genomics; German Cancer Research Center (DKFZ) and University of HeidelbergGermany
| | - Justo Lorenzo Bermejo
- Department of Molecular Genetic Epidemiology; German Cancer Research Center (DKFZ)Heidelberg; Germany
- Institute of Medical Biometry and Informatics; University Hospital HeidelbergGermany
| | - Melanie Bevier
- Department of Molecular Genetic Epidemiology; German Cancer Research Center (DKFZ)Heidelberg; Germany
| | - Barbara Pardini
- Department of Molecular Biology of Cancer at the Institute of Experimental Medicine; Academy of Sciences of the Czech RepublicPrague; Czech Republic
| | - Alessio Naccarati
- Department of Molecular Biology of Cancer at the Institute of Experimental Medicine; Academy of Sciences of the Czech RepublicPrague; Czech Republic
| | - Verena Steinke
- Institute of Human Genetics; Rheinische Friedrich-Wilhelms-UniversitätBonn; Germany
| | - Nils Rahner
- Institute of Human Genetics; Rheinische Friedrich-Wilhelms-UniversitätBonn; Germany
| | - Elke Holinski-Feder
- Department of Internal Medicine, Campus Innenstadt; University Hospital of the Ludwig-Maximilians-University MunichGermany
| | - Monika Morak
- Department of Internal Medicine, Campus Innenstadt; University Hospital of the Ludwig-Maximilians-University MunichGermany
| | - Hans K Schackert
- Department of Surgical Research at the Universitätsklinikum Carl Gustav Carus; Technische Universität DresdenGermany
| | - Heike Görgens
- Department of Surgical Research at the Universitätsklinikum Carl Gustav Carus; Technische Universität DresdenGermany
| | - Christian P Pox
- Medical Department at the Knappschaftskrankenhaus Bochum; Ruhr University BochumGermany
| | - Timm Goecke
- Institute of Human Genetics and Anthropology; Heinrich-Heine-Universität DüsseldorfGermany
| | - Matthias Kloor
- Department of Applied Tumour Biology at the Institute of Pathology; Ruprecht-Karls-Universität HeidelbergGermany
| | - Markus Loeffler
- Faculty of Medicine, Institute of Medical Informatics, Statistics and Epidemiology; University of LeipzigGermany
| | - Reinhard Büttner
- Institute of Pathology; Rheinische Friedrich-Wilhelms-Universität BonnGermany
| | - Ludmila Vodickova
- Department of Molecular Biology of Cancer at the Institute of Experimental Medicine; Academy of Sciences of the Czech RepublicPrague; Czech Republic
- Department of Toxicogenomics; National Institute of Public HealthPrague; Czech Republic
| | - Jan Novotny
- Department of Oncology; General Teaching HospitalPrague; Czech Republic
| | - Kubilay Demir
- Division of Signaling and Functional Genomics; German Cancer Research Center (DKFZ) and University of HeidelbergGermany
| | - Cristina-Maria Cruciat
- Division of Molecular Embryology; German Cancer Research Center (DKFZ)Heidelberg; Germany
| | | | | | - Christof Niehrs
- Division of Molecular Embryology; German Cancer Research Center (DKFZ)Heidelberg; Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics; German Cancer Research Center (DKFZ) and University of HeidelbergGermany
| | - Peter Propping
- Institute of Human Genetics; Rheinische Friedrich-Wilhelms-UniversitätBonn; Germany
| | - Pavel Vodička
- Department of Molecular Biology of Cancer at the Institute of Experimental Medicine; Academy of Sciences of the Czech RepublicPrague; Czech Republic
| | - Kari Hemminki
- Department of Molecular Genetic Epidemiology; German Cancer Research Center (DKFZ)Heidelberg; Germany
- Center of Primary Health Care Research at the Clinical Research Center; Lund UniversityMalmö; Sweden
| | - Asta Försti
- Department of Molecular Genetic Epidemiology; German Cancer Research Center (DKFZ)Heidelberg; Germany
- Center of Primary Health Care Research at the Clinical Research Center; Lund UniversityMalmö; Sweden
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88
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Preuschoft H. Mechanisms for the acquisition of habitual bipedality: are there biomechanical reasons for the acquisition of upright bipedal posture? J Anat 2004; 204:363-84. [PMID: 15198701 PMCID: PMC1571303 DOI: 10.1111/j.0021-8782.2004.00303.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2004] [Indexed: 11/30/2022] Open
Abstract
Morphology and biomechanics are linked by causal morphogenesis ('Wolff's law') and the interplay of mutations and selection (Darwin's 'survival of the fittest'). Thus shape-based selective pressures can be determined. In both cases we need to know which biomechanical factors lead to skeletal adaptation, and which ones exert selective pressures on body shape. Each bone must be able to sustain the greatest regularly occurring loads. Smaller loads are unlikely to lead to adaptation of morphology. The highest loads occur primarily in posture and locomotion, simply because of the effect of body weight (or its multiple). In the skull, however, it is biting and chewing that result in the greatest loads. Body shape adapted for an arboreal lifestyle also smooths the way towards bipedality. Hindlimb dominance, length of the limbs in relation to the axial skeleton, grasping hands and feet, mass distribution (especially of the limb segments), thoracic shape, rib curvatures, and the position of the centre of gravity are the adaptations to arboreality that also pre-adapt for bipedality. Five divergent locomotor/morphological types have evolved from this base: arm-swinging in gibbons, forelimb-dominated slow climbing in orangutans, quadrupedalism/climbing in the African apes, an unknown mix of climbing and bipedal walking in australopithecines, and the remarkably endurant bipedal walking of humans. All other apes are also facultative bipeds, but it is the biomechanical characteristics of bipedalism in orangutans, the most arboreal great ape, which is closest to that in humans. If not evolutionary accident, what selective factor can explain why two forms adopted bipedality? Most authors tend to connect bipedal locomotion with some aspect of progressively increasing distance between trees because of climatic changes. More precise factors, in accordance with biomechanical requirements, include stone-throwing, thermoregulation or wading in shallow water. Once bipedality has been acquired, development of typical human morphology can readily be explained as adaptations for energy saving over long distances. A paper in this volume shows that load-carrying ability was enhanced from australopithecines to Homo ergaster (early African H. erectus), supporting an earlier proposition that load-carrying was an essential factor in human evolution.
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