1
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Xie A, Ma Z, Wang J, Zhang Y, Chen Y, Yang C, Chen J, Peng J. Upf3a but not Upf1 mediates the genetic compensation response induced by leg1 deleterious mutations in an H3K4me3-independent manner. Cell Discov 2023; 9:63. [PMID: 37369707 DOI: 10.1038/s41421-023-00550-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 03/29/2023] [Indexed: 06/29/2023] Open
Abstract
Genetic compensation responses (GCRs) can be induced by deleterious mutations in living organisms in order to maintain genetic robustness. One type of GCRs, homology-dependent GCR (HDGCR), involves transcriptional activation of one or more homologous genes related to the mutated gene. In zebrafish, ~80% of the genetic mutants produced by gene editing technology failed to show obvious phenotypes. The HDGCR has been proposed to be one of the main reasons for this phenomenon. It is triggered by mutant mRNA bearing a premature termination codon and has been suggested to depend on components of both the nonsense mRNA-mediated degradation (NMD) pathway and the complex of proteins associated with Set1 (COMPASS). However, exactly which specific NMD factor is required for HDGCR remains disputed. Here, zebrafish leg1 deleterious mutants are adopted as a model to distinguish the role of the NMD factors Upf1 and Upf3a in HDGCR. Four single mutant lines and three double mutant lines were produced. The RNA-seq data from 71 samples and the ULI-NChIP-seq data from 8 samples were then analyzed to study the HDGCR in leg1 mutants. Our results provide strong evidence that Upf3a, but not Upf1, is essential for the HDGCR induced by nonsense mutations in leg1 genes where H3K4me3 enrichment appears not to be a prerequisite. We also show that Upf3a is responsible for correcting the expression of hundreds of genes that would otherwise be dysregulated in the leg1 deleterious mutant.
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Affiliation(s)
- Aixuan Xie
- 1MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhipeng Ma
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Jinyang Wang
- 1MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuxi Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yayue Chen
- 1MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chun Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Jinrong Peng
- 1MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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2
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Wang J, Bai Y, Xie A, Huang H, Hu M, Peng J. Difference in an intermolecular disulfide-bond between two highly homologous serum proteins Leg1a and Leg1b implicates their functional differentiation. Biochem Biophys Res Commun 2021; 579:81-88. [PMID: 34592574 DOI: 10.1016/j.bbrc.2021.09.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022]
Abstract
Zebrafish Liver-enriched gene 1a (Leg1a) and Leg1b are liver-produced serum proteins encoded by two adjacently linked homologous genes leg1a and leg1b, respectively. We previously showed that maternal-zygotic (MZ) leg1a null mutant developed a small liver at 3.5 days post-fertilization (dpf) during winter-time or under UV-treatment and displayed an abnormal stature at its adulthood. It is puzzling why Leg1b, which shares 89.3% identity with Leg1a and co-expressed with Leg1a, cannot fully compensate for the loss-of-function of Leg1a in the leg1azju1 MZ mutant. Here we report that Leg1a and Leg1b share eight cysteine residues but differ in amino acid residue 358, which is a serine in Leg1a but cysteine (C358) in Leg1b. We find that Leg1b forms an intermolecular disulfide bond through C358. Mutating C358 to Methionine (M358) does not affect Leg1b secretion whereas mutating other conserved cysteine residues do. We propose that the intermolecular disulfide bond in Leg1b might establish a rigid structure that makes it functionally different from Leg1a under certain oxidative conditions.
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Affiliation(s)
- Jinyang Wang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yun Bai
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Aixuan Xie
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Heping Huang
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Minjie Hu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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3
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Stannard HJ, Miller RD, Old JM. Marsupial and monotreme milk-a review of its nutrient and immune properties. PeerJ 2020; 8:e9335. [PMID: 32612884 PMCID: PMC7319036 DOI: 10.7717/peerj.9335] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/20/2020] [Indexed: 01/17/2023] Open
Abstract
All mammals are characterized by the ability of females to produce milk. Marsupial (metatherian) and monotreme (prototherian) young are born in a highly altricial state and rely on their mother’s milk for the first part of their life. Here we review the role and importance of milk in marsupial and monotreme development. Milk is the primary source of sustenance for young marsupials and monotremes and its composition varies at different stages of development. We applied nutritional geometry techniques to a limited number of species with values available to analyze changes in macronutrient composition of milk at different stages. Macronutrient energy composition of marsupial milk varies between species and changes concentration during the course of lactation. As well as nourishment, marsupial and monotreme milk supplies growth and immune factors. Neonates are unable to mount a specific immune response shortly after birth and therefore rely on immunoglobulins, immunological cells and other immunologically important molecules transferred through milk. Milk is also essential to the development of the maternal-young bond and is achieved through feedback systems and odor preferences in eutherian mammals. However, we have much to learn about the role of milk in marsupial and monotreme mother-young bonding. Further research is warranted in gaining a better understanding of the role of milk as a source of nutrition, developmental factors and immunity, in a broader range of marsupial species, and monotremes.
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Affiliation(s)
- Hayley J Stannard
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Robert D Miller
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - Julie M Old
- School of Science, Western Sydney University, Penrith, NSW, Australia
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4
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Zhang Z, Wang Z, Dang Y, Wang J, Jayaprakash S, Wang H, He J. Transcriptomic Prediction of Pig Liver-Enriched Gene 1 Functions in a Liver Cell Line. Genes (Basel) 2020; 11:genes11040412. [PMID: 32290278 PMCID: PMC7230230 DOI: 10.3390/genes11040412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 03/27/2020] [Accepted: 04/09/2020] [Indexed: 11/16/2022] Open
Abstract
The newly identified liver-enriched gene 1 (LEG1) encodes a protein with a characteristic domain of unknown function 781 (DUF781/LEG1), constituting a protein family with only one member in mammals. A functional study in zebrafish suggested that LEG1 genes are involved in liver development, while the platypus LEG1 homolog, Monotreme Lactation Protein (MLP), which is enriched in the mammary gland and milk, acts as an antibacterial substance. However, no functional studies on eutherian LEG1s have been published to date. Thus, we here report the first functional prediction study at the cellular level. As previously reported, eutherian LEG1s can be classified into three paralogous groups. Pigs have all three LEG1 genes (pLEG1s), while humans and mice have retained only LEG1a. Hence, pLEG1s might represent an ideal model for studying LEG1 gene functions. RNA-seq was performed by the overexpression of pLEG1s and platypus MLP in HepG2 cells. Enrichment analysis showed that pLEG1a and pLEG1b might exhibit little function in liver cells; however, pLEG1c is probably involved in the endoplasmic reticulum (ER) stress response and protein folding. Additionally, gene set enrichment analysis revealed that platypus MLP shows antibacterial activity, confirming the functional study in platypus. Therefore, our study showed from the transcriptomic perspective that mammalian LEG1s have different functions in liver cells due to the subfunctionalization of paralogous genes.
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Affiliation(s)
- Zhe Zhang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (Z.Z.); (Y.D.); (J.W.)
| | - Zizengchen Wang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (Z.W.); (H.W.)
| | - Yanna Dang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (Z.Z.); (Y.D.); (J.W.)
| | - Jinyang Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (Z.Z.); (Y.D.); (J.W.)
| | - Sakthidasan Jayaprakash
- Department of Chemical Engineering, Hindustan Institute of Technology and Science, Chennai 603103, India;
| | - Huanan Wang
- Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (Z.W.); (H.W.)
| | - Jin He
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; (Z.Z.); (Y.D.); (J.W.)
- Correspondence:
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5
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Dang Y, Wang JY, Liu C, Zhang K, Jinrong P, He J. Evolutionary and Molecular Characterization of liver-enriched gene 1. Sci Rep 2020; 10:4262. [PMID: 32144352 PMCID: PMC7060313 DOI: 10.1038/s41598-020-61208-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/24/2020] [Indexed: 11/30/2022] Open
Abstract
Liver-enriched gene 1 (Leg1) is a newly identified gene with little available functional information. To evolutionarily and molecularly characterize Leg1 genes, a phylogenetic study was first conducted, which indicated that Leg1 is a conserved gene that exists from bacteria to mammals. During the evolution of mammals, Leg1s underwent tandem duplications, which gave rise to Leg1a, Leg1b, and Leg1c clades. Analysis of the pig genome showed the presence of all three paralogs of pig Leg1 genes (pLeg1s), whereas only Leg1a could be found in the human (hLeg1a) or mouse (mLeg1a) genomes. Purifying force acts on the evolution of Leg1 genes, likely subjecting them to functional constraint. Molecularly, pLeg1a and its coded protein, pig LEG1a (pLEG1a), displayed high similarities to its human and mouse homologs in terms of gene organization, expression patterns, and structures. Hence, pLeg1a, hLeg1a, and mLeg1a might preserve similar functions. Additionally, expression analysis of the three Leg1as suggested that eutherian Leg1as might have different functions from those of zebrafish and platypus due to subfunctionalization. Therefore, pLeg1a might provide essential information about eutherian Leg1a. Moreover, a preliminary functional study using RNA-seq suggested that pLeg1a is involved in the lipid homeostasis. In conclusion, our study provides some basic information on the aspects of evolution and molecular function, which could be applied for further validation of Leg1 using pig models.
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Affiliation(s)
- Yanna Dang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China
| | - Jin-Yang Wang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China
| | - Chen Liu
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China
| | - Kun Zhang
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China
| | - Peng Jinrong
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China
| | - Jin He
- Department of Animal Science, College of Animal Sciences, Zhejiang University, Hangzhou, PR China.
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6
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Satoh S, Awata S, Tanaka H, Jordan LA, Kakuda U, Hori M, Kohda M. Bi-parental mucus provisioning in the scale-eating cichlid Perissodus microlepis (Cichlidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractAlthough parental care is known to occur in a wide range of teleost fishes, postnatal provisioning of nutrition has been documented rarely. Here, we describe a novel example of bi-parental care in a teleost, i.e. mucus-provisioning behaviour in the scale-eating cichlid Perissodus microlepis endemic to Lake Tanganyika. Field observations revealed that young guarded by their parents frequently glanced towards the body surface of both parents. Furthermore, analyses of stomach contents of the young found the presence of ingested mucus, confirming that the young feed on the mucus secretions of their parents. The frequency of glancing behaviour increased with size of the young up to ~13 mm in standard length, but then declined with further growth. Additionally, the frequency of glancing of young towards their parents was higher when the frequency of foraging on plankton was lower. Underwater cage experiments revealed a higher rate of growth in the young kept in direct contact with their parents than in those not allowed direct contact. We conclude that glancing behaviour in young P. microlepis is a form of direct parental nourishment that confers growth benefits to the young when food abundance is low.
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Affiliation(s)
- Shun Satoh
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Satoshi Awata
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Hirokazu Tanaka
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan
- Institute of Ecology and Evolution, Department of Behavioural Ecology, University of Bern, Hinterkappelen, Switzerland
| | - Lyndon A Jordan
- Department of Collective Behaviour, Max Planck Institute of Animal Behaviour, Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany
| | - Umi Kakuda
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan
| | | | - Masanori Kohda
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan
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7
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Neerukonda M, Pavuluri S, Sharma I, Kumar A, Sailasree P, Lakshmi JB, Sharp JA, Kumar S. Functional evaluation of a monotreme-specific antimicrobial protein, EchAMP, against experimentally induced mastitis in transgenic mice. Transgenic Res 2019; 28:573-587. [PMID: 31599375 DOI: 10.1007/s11248-019-00174-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/06/2019] [Indexed: 10/25/2022]
Abstract
EchAMP, the tenth most abundant transcript expressed in the mammary gland of echidna, has in vitro broad-spectrum antibacterial effects. However, the effects of EchAMP on mastitis, a condition where inflammation is triggered following mammary gland infection, has not been investigated. To investigate the impact of EchAMP against mastitis, EchAMP transgenic mice were generated. In antibacterial assays, the whey fractions of milk from transgenic mice significantly reduced growth of Staphylococcus aureus, Bacillus subtilis, Escherichia coli and Pseudomonas aeruginosa compared with whey fractions from wildtype mice. Furthermore, a mastitis model created by infecting mammary gland with these four bacterial strains displayed a significant reduction in bacterial load in transgenic mice injected with S. aureus and B. subtilis. On further confirmation, histomorphologic analysis showed absence of necrosis and cell infiltration in the mammary glands of transgenic mice. To understand the role of EchAMP against inflammation, we employed an LPS-injected mastitis mouse model. LPS is known to induce phopshorylation of NF-κB and MAPK pathways, which in turn activate downstream proinflammatory signaling mediators, to promote inflammation. In LPS-treated EchAMP transgenic mice, phosphorylation levels of NF-κB, p38 and ERK1/2 were significantly downregulated. Furthermore, in mammary gland of transgenic mice, there was a significant downregulation of mRNA levels of proinflammatory cytokines, namely TNF-α, IL-6 and IL-1β. Taken together, these data suggest that EchAMP has an antiinflammatory response and is effective against S. aureus and B. subtilis. We suggest that EchAMP may be a potential prophylactic protein against mastitis in dairy animals by expressing this gene in their mammary gland.
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Affiliation(s)
- Manjusha Neerukonda
- Centre for Cellular and Molecular Biology, Hyderabad, India.,University Medical Centre, Johannes Gutenberg University, Mainz, Germany
| | | | - Isha Sharma
- Centre for Cellular and Molecular Biology, Hyderabad, India.,Northwestern University, Chicago, IL, USA
| | - Alok Kumar
- Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | | | - Julie A Sharp
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Australia
| | - Satish Kumar
- Centre for Cellular and Molecular Biology, Hyderabad, India. .,Department of Biotechnology, School of Life Sciences, Central University of Haryana, Jant-Pali, Mahendergarh, Haryana, 123031, India.
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8
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Abstract
Abstract
Tachyglossus aculeatus (Shaw, 1792) is a monotreme commonly called the short-beaked echidna. Although considered Australia’s most common native mammal because of its continent-wide distribution, its population numbers everywhere are low. It is easily distinguished from all other native Australian mammals because of its spine-covered body, hairless beak, and unique “rolling” gait. The five subspecies, one of which is found in Papua New Guinea, show variations in fur density, spine diameter, length, and number of grooming claws. The Kangaroo Island short-beaked echidna Tachyglossus aculeatus multiaculeatus is listed as “Endangered” but all other Tachyglossus are listed as “Least Concern” in the 2016 International Union for Conservation of Nature and Natural Resources Red List.
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Affiliation(s)
- Peggy D Rismiller
- Pelican Lagoon Research & Wildlife Centre, Penneshaw, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Frank Grutzner
- The Environment Institute, The University of Adelaide, Adelaide, South Australia, Australia
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9
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Manguy J, Shields DC. Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190939. [PMID: 31824707 PMCID: PMC6837221 DOI: 10.1098/rsos.190939] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
Milk alpha-, beta- and kappa-casein proteins assemble into casein micelles in breast epithelial cells. The glycomacropeptide (GMP) tails of kappa-casein that extend from the surface of the micelle are key to assembly and aggregation. Aggregation is triggered by stomach pepsin cleavage of GMP from para-kappa-casein (PKC). While one casein micelle model emphasizes the importance of hydrophobic interactions, another focuses on polar residues. We performed an evolutionary analysis of kappa-casein primary sequence and predicted features that potentially impact on protein interactions. We noted more rapid change in the earlier period (166 to 60 Ma). Pepsin and plasmin cleavage sites were avoided in the GMP, which may partly explain its amino acid composition. Short tandem repeats have led to modest expansions of PKC, and to large GMP expansions, suggesting the GMP is less length constrained. Amino acid compositional constraints were assessed across species. Polarity and hydrophobicity properties were insufficient to explain differences between PKC and GMP. Among polar residues, threonine dominates the GMP, compared to serine, probably reflecting its preference for O-glycosylation over phosphorylation. Glutamine, enriched in the bovine PQ-rich region, is not positionally conserved in other species. Among hydrophobic residues, isoleucine is clearly preferred over leucine in the GMP, and patches of hydrophobicity are not markedly positionally conserved. PKC tyrosine and charged residues showed stronger conservation of position, suggesting a role for pi-interactions, seen in other structurally dynamic protein membraneless assemblies. Independent acquisitions of cysteines are consistent with a trend of increasing stabilization of multimers by covalent disulphide bonds, over evolutionary time. In conclusion, kappa-casein compositional and positional constraints appear to be influenced by modification preferences, protease evasion and protein-protein interactions.
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Affiliation(s)
- Jean Manguy
- UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Food for Health Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Denis C. Shields
- UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland
- Food for Health Ireland, University College Dublin, Belfield, Dublin 4, Ireland
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10
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Kumar A, Parveen S, Sharma I, Pathak H, Deshmukh MV, Sharp JA, Kumar S. Structural and mechanistic insights into EchAMP: A antimicrobial protein from the Echidna milk. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1260-1274. [PMID: 30951703 DOI: 10.1016/j.bbamem.2019.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Antibiotic resistance is a problem that necessitates the identification of new antimicrobial molecules. Milk is known to have molecules with antimicrobial properties (AMPs). Echidna Antimicrobial Protein (EchAMP) is one such lactation specific AMP exclusively found in the milk of Echidna, an egg-laying mammal geographically restricted to Australia and New Guinea. Previous studies established that EchAMP exhibits substantial bacteriostatic activity against multiple bacterial genera. However, the subsequent structural and functional studies were hindered due to the unavailability of pure protein. RESULTS In this study, we expressed EchAMP protein using a heterologous expression system and successfully purified it to >95% homogeneity. The purified recombinant protein exhibits bacteriolytic activity against both Gram-positive and Gram-negative bacteria as confirmed by live-dead staining and scanning electron microscopy. Structurally, this AMP belongs to the family of intrinsically disordered proteins (IDPs) as deciphered by the circular-dichroism, tryptophan fluorescence, and NMR spectroscopy. Nonetheless, EchAMP has the propensity to acquire structure with amphipathic molecules, or membrane mimics like SDS, lipopolysaccharides, and liposomes as again observed through multiple spectroscopic techniques. CONCLUSIONS Recombinant EchAMP exhibits broad-spectrum bacteriolytic activity by compromising the bacterial cell membrane integrity. Hence, we propose that this intrinsically disordered antimicrobial protein interact with the bacterial cell membrane and undergoes conformational changes to form channels in the membrane resulting in cell lysis. GENERAL SIGNIFICANCE EchAMP, the evolutionarily conserved, lactation specific AMP from an oviparous mammal may find application as a broad-spectrum antimicrobial against pathogens that affect mammary gland or otherwise cause routine infections in humans and livestock.
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Affiliation(s)
- Alok Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Sadiya Parveen
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Isha Sharma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Himani Pathak
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Mandar V Deshmukh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India
| | - Julie A Sharp
- Instit for Frontier Materials, Deakin University, Geelong, VIC 3220, Australia
| | - Satish Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, Telangana, India.
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11
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Bino G, Kingsford RT, Archer M, Connolly JH, Day J, Dias K, Goldney D, Gongora J, Grant T, Griffiths J, Hawke T, Klamt M, Lunney D, Mijangos L, Munks S, Sherwin W, Serena M, Temple-Smith P, Thomas J, Williams G, Whittington C. The platypus: evolutionary history, biology, and an uncertain future. J Mammal 2019; 100:308-327. [PMID: 31043761 PMCID: PMC6479513 DOI: 10.1093/jmammal/gyz058] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/25/2019] [Indexed: 12/21/2022] Open
Abstract
The platypus (Ornithorhynchus anatinus) is one of the world's most evolutionarily distinct mammals, one of five extant species of egg-laying mammals, and the only living species within the family Ornithorhynchidae. Modern platypuses are endemic to eastern mainland Australia, Tasmania, and adjacent King Island, with a small introduced population on Kangaroo Island, South Australia, and are widely distributed in permanent river systems from tropical to alpine environments. Accumulating knowledge and technological advancements have provided insights into many aspects of its evolutionary history and biology but have also raised concern about significant knowledge gaps surrounding distribution, population sizes, and trends. The platypus' distribution coincides with many of Australia's major threatening processes, including highly regulated and disrupted rivers, intensive habitat destruction, and fragmentation, and they were extensively hunted for their fur until the early 20th century. Emerging evidence of local population declines and extinctions identifies that ecological thresholds have been crossed in some populations and, if threats are not addressed, the species will continue to decline. In 2016, the IUCN Red Listing for the platypus was elevated to "Near Threatened," but the platypus remains unlisted on threatened species schedules of any Australian state, apart from South Australia, or nationally. In this synthesis, we review the evolutionary history, genetics, biology, and ecology of this extraordinary mammal and highlight prevailing threats. We also outline future research directions and challenges that need to be met to help conserve the species.
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Affiliation(s)
- Gilad Bino
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard T Kingsford
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Archer
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Joanne H Connolly
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia.,Graham Centre for Agricultural Innovation, Wagga Wagga, New South Wales, Australia
| | - Jenna Day
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Kimberly Dias
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - David Goldney
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Tom Grant
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Tahneal Hawke
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Melissa Klamt
- Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Daniel Lunney
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.,Office of Environment and Heritage, Hurstville, New South Wales, Australia
| | - Luis Mijangos
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sarah Munks
- School of Biological Sciences, University of Tasmania, Tasmania, Australia.,Forest Practices Authority, Hobart, Tasmania, Australia
| | - William Sherwin
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Melody Serena
- Australian Platypus Conservancy, Wiseleigh, Victoria, Australia
| | - Peter Temple-Smith
- Department of Obstetrics and Gynaecology, Southern Clinical School, Monash University, Clayton, Victoria, Australia
| | | | - Geoff Williams
- Australian Platypus Conservancy, Wiseleigh, Victoria, Australia
| | - Camilla Whittington
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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Newman J, Sharp JA, Enjapoori AK, Bentley J, Nicholas KR, Adams TE, Peat TS. Structural characterization of a novel monotreme-specific protein with antimicrobial activity from the milk of the platypus. Acta Crystallogr F Struct Biol Commun 2018; 74:39-45. [PMID: 29372906 PMCID: PMC5947691 DOI: 10.1107/s2053230x17017708] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 11/10/2022] Open
Abstract
Monotreme lactation protein (MLP) is a recently identified protein with antimicrobial activity. It is present in the milk of monotremes and is unique to this lineage. To characterize MLP and to gain insight into the potential role of this protein in the evolution of lactation, the crystal structure of duck-billed platypus (Ornithorhynchus anatinus) MLP was determined at 1.82 Å resolution. This is the first structure to be reported for this novel, mammalian antibacterial protein. MLP was expressed as a FLAG epitope-tagged protein in mammalian cells and crystallized readily, with at least three space groups being observed (P1, C2 and P21). A 1.82 Å resolution native data set was collected from a crystal in space group P1, with unit-cell parameters a = 51.2, b = 59.7, c = 63.1 Å, α = 80.15, β = 82.98, γ = 89.27°. The structure was solved by SAD phasing using a protein crystal derivatized with mercury in space group C2, with unit-cell parameters a = 92.7, b = 73.2, c = 56.5 Å, β = 90.28°. MLP comprises a monomer of 12 helices and two short β-strands, with much of the N-terminus composed of loop regions. The crystal structure of MLP reveals no three-dimensional similarity to any known structures and reveals a heretofore unseen fold, supporting the idea that monotremes may be a rich source for the identification of novel proteins. It is hypothesized that MLP in monotreme milk has evolved to specifically support the unusual lactation strategy of this lineage and may have played a central role in the evolution of these mammals.
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Affiliation(s)
- Janet Newman
- Biomedical Manufacturing, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Julie A. Sharp
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3217, Australia
| | | | - John Bentley
- Biomedical Manufacturing, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Kevin R. Nicholas
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3217, Australia
| | - Timothy E. Adams
- Biomedical Manufacturing, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Thomas S. Peat
- Biomedical Manufacturing, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia
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Sharp JA, Wanyonyi S, Modepalli V, Watt A, Kuruppath S, Hinds LA, Kumar A, Abud HE, Lefevre C, Nicholas KR. The tammar wallaby: A marsupial model to examine the timed delivery and role of bioactives in milk. Gen Comp Endocrinol 2017; 244:164-177. [PMID: 27528357 PMCID: PMC6408724 DOI: 10.1016/j.ygcen.2016.08.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 07/29/2016] [Accepted: 08/11/2016] [Indexed: 12/12/2022]
Abstract
It is now clear that milk has multiple functions; it provides the most appropriate nutrition for growth of the newborn, it delivers a range of bioactives with the potential to stimulate development of the young, it has the capacity to remodel the mammary gland (stimulate growth or signal cell death) and finally milk can provide protection from infection and inflammation when the mammary gland is susceptible to these challenges. There is increasing evidence to support studies using an Australian marsupial, the tammar wallaby (Macropus eugenii), as an interesting and unique model to study milk bioactives. Reproduction in the tammar wallaby is characterized by a short gestation, birth of immature young and a long lactation. All the major milk constituents change substantially and progressively during lactation and these changes have been shown to regulate growth and development of the tammar pouch young and to have roles in mammary gland biology. This review will focus on recent reports examining the control of lactation in the tammar wallaby and the timed delivery of milk bioactivity.
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Affiliation(s)
- Julie A Sharp
- Institute for Frontier Materials, Deakin University, Geelong 3216, Australia; Cancer Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton 3800, Victoria, Australia.
| | - Stephen Wanyonyi
- School of Medicine, Deakin University, Geelong 3216, Australia; Institute for Agriculture and the Environment, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | | | - Ashalyn Watt
- Institute for Frontier Materials, Deakin University, Geelong 3216, Australia
| | | | - Lyn A Hinds
- CSIRO Health and Biosecurity, Canberra, ACT 2601, Australia
| | - Amit Kumar
- School of Medicine, Deakin University, Geelong 3216, Australia; PeterMac Callum Cancer Research Institute, East Melbourne 3002, Victoria, Australia
| | - Helen E Abud
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton 3800, Victoria, Australia
| | - Christophe Lefevre
- School of Medicine, Deakin University, Geelong 3216, Australia; Division of Bioinformatics, Walter and Eliza Hall Medical Research Institute, Melbourne, Victoria 3000, Australia; PeterMac Callum Cancer Research Institute, East Melbourne 3002, Victoria, Australia; Department of Medical Biology (WEHI), The University of Melbourne, Melbourne 3000, Victoria, Australia
| | - Kevin R Nicholas
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton 3800, Victoria, Australia
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Enjapoori AK, Lefèvre CM, Nicholas KR, Sharp JA. Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes. Gen Comp Endocrinol 2017; 242:38-48. [PMID: 26673872 DOI: 10.1016/j.ygcen.2015.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 11/27/2015] [Accepted: 12/04/2015] [Indexed: 12/16/2022]
Abstract
Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied. However, the evolution of this complex regulation that began with monotremes is unknown. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated. Here we characterised the proximal promoter and hormonal regulation of two platypus milk protein genes, Beta-lactoglobulin (BLG), a whey protein and monotreme lactation protein (MLP), a monotreme specific milk protein, using in vitro reporter assays and a bovine mammary epithelial cell line (BME-UV1). Insulin and dexamethasone alone provided partial induction of MLP, while the combination of insulin, dexamethasone and prolactin was required for maximal induction. Partial induction of BLG was achieved by insulin, dexamethasone and prolactin alone, with maximal induction using all three hormones. Platypus MLP and BLG core promoter regions comprised transcription factor binding sites (e.g. STAT5, NF-1 and C/EBPα) that were conserved in marsupial and eutherian lineages that regulate caseins and whey protein gene expression. Our analysis suggests that insulin, dexamethasone and/or prolactin alone can regulate the platypus MLP and BLG gene expression, unlike those of therian lineage. The induction of platypus milk protein genes by lactogenic hormones suggests they originated before the divergence of marsupial and eutherians.
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Affiliation(s)
- Ashwantha Kumar Enjapoori
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, Victoria 3216, Australia.
| | - Christophe M Lefèvre
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, Victoria 3216, Australia.
| | - Kevin R Nicholas
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, Victoria 3216, Australia; Department of Anatomy and Cell Biology, Monash University, Clayton, Victoria 3800, Australia.
| | - Julie A Sharp
- School of Medicine, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, Victoria 3216, Australia; Department of Anatomy and Cell Biology, Monash University, Clayton, Victoria 3800, Australia; Institute for Frontier Materials, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, Victoria 3216, Australia.
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Hu M, Bai Y, Zhang C, Liu F, Cui Z, Chen J, Peng J. Liver-Enriched Gene 1, a Glycosylated Secretory Protein, Binds to FGFR and Mediates an Anti-stress Pathway to Protect Liver Development in Zebrafish. PLoS Genet 2016; 12:e1005881. [PMID: 26901320 PMCID: PMC4764323 DOI: 10.1371/journal.pgen.1005881] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/28/2016] [Indexed: 01/19/2023] Open
Abstract
Unlike mammals and birds, teleost fish undergo external embryogenesis, and therefore their embryos are constantly challenged by stresses from their living environment. These stresses, when becoming too harsh, will cause arrest of cell proliferation, abnormal cell death or senescence. Such organisms have to evolve a sophisticated anti-stress mechanism to protect the process of embryogenesis/organogenesis. However, very few signaling molecule(s) mediating such activity have been identified. liver-enriched gene 1 (leg1) is an uncharacterized gene that encodes a novel secretory protein containing a single domain DUF781 (domain of unknown function 781) that is well conserved in vertebrates. In the zebrafish genome, there are two copies of leg1, namely leg1a and leg1b. leg1a and leg1b are closely linked on chromosome 20 and share high homology, but are differentially expressed. In this report, we generated two leg1a mutant alleles using the TALEN technique, then characterized liver development in the mutants. We show that a leg1a mutant exhibits a stress-dependent small liver phenotype that can be prevented by chemicals blocking the production of reactive oxygen species. Further studies reveal that Leg1a binds to FGFR3 and mediates a novel anti-stress pathway to protect liver development through enhancing Erk activity. More importantly, we show that the binding of Leg1a to FGFR relies on the glycosylation at the 70th asparagine (Asn70 or N70), and mutating the Asn70 to Ala70 compromised Leg1’s function in liver development. Therefore, Leg1 plays a unique role in protecting liver development under different stress conditions by serving as a secreted signaling molecule/modulator. Although being challenged by stresses from their living environment during embryogenesis, teleost fish harbor a robust genetic program dictating liver development as long as any environmental change, including temperature or natural UV irradiation, is not detrimental. It is therefore of interest to explore the mechanism(s) behind this phenomenon. We showed that Liver-enriched gene 1 (Leg1) plays a unique role in protecting liver development under different stress conditions by serving as a secretory signaling molecule/modulator that binds to FGF receptor and activates the Erk signaling pathway. This finding may explain the adaption of teleost fish in coping with environmental changes.
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Affiliation(s)
- Minjie Hu
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yun Bai
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Chunxia Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zongbin Cui
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, China
- * E-mail: (JC); (JP)
| | - Jinrong Peng
- MOE Key Laboratory for Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, China
- * E-mail: (JC); (JP)
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Abstract
It has been thirty years since the first genetically engineered animal with altered milk composition was reported. During the intervening years, the world population has increased from 5bn to 7bn people. An increasing demand for protein in the human diet has followed this population expansion, putting huge stress on the food supply chain. Many solutions to the grand challenge of food security for all have been proposed and are currently under investigation and study. Amongst these, genetics still has an important role to play, aiming to continually enable the selection of livestock with enhanced traits. Part of the geneticist's tool box is the technology of genetic engineering. In this Invited Review, we indicate that this technology has come a long way, we focus on the genetic engineering of dairy animals and we argue that the new strategies for precision breeding demand proper evaluation as to how they could contribute to the essential increases in agricultural productivity our society must achieve.
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Aboitiz F, Montiel JF. Olfaction, navigation, and the origin of isocortex. Front Neurosci 2015; 9:402. [PMID: 26578863 PMCID: PMC4621927 DOI: 10.3389/fnins.2015.00402] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 10/12/2015] [Indexed: 11/23/2022] Open
Abstract
There are remarkable similarities between the brains of mammals and birds in terms of microcircuit architecture, despite obvious differences in gross morphology and development. While in reptiles and birds the most expanding component (the dorsal ventricular ridge) displays an overall nuclear shape and derives from the lateral and ventral pallium, in mammals a dorsal pallial, six-layered isocortex shows the most remarkable elaboration. Regardless of discussions about possible homologies between mammalian and avian brains, a main question remains in explaining the emergence of the mammalian isocortex, because it represents a unique phenotype across amniotes. In this article, we propose that the origin of the isocortex was driven by behavioral adaptations involving olfactory driven goal-directed and navigating behaviors. These adaptations were linked with increasing sensory development, which provided selective pressure for the expansion of the dorsal pallium. The latter appeared as an interface in olfactory-hippocampal networks, contributing somatosensory information for navigating behavior. Sensory input from other modalities like vision and audition were subsequently recruited into this expanding region, contributing to multimodal associative networks.
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Affiliation(s)
- Francisco Aboitiz
- Departamento de Psiquiatría, Escuela de Medicina, Centro Interdisciplinario de Neurociencia, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Juan F. Montiel
- Facultad de Medicina, Centro de Investigación Biomédica, Universidad Diego PortalesSantiago, Chile
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of OxfordOxford, UK
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Titz B, Sewer A, Schneider T, Elamin A, Martin F, Dijon S, Luettich K, Guedj E, Vuillaume G, Ivanov NV, Peck MJ, Chaudhary NI, Hoeng J, Peitsch MC. Alterations in the sputum proteome and transcriptome in smokers and early-stage COPD subjects. J Proteomics 2015; 128:306-20. [DOI: 10.1016/j.jprot.2015.08.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/15/2015] [Indexed: 12/15/2022]
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Urashima T, Inamori H, Fukuda K, Saito T, Messer M, Oftedal OT. 4-O-Acetyl-sialic acid (Neu4,5Ac2) in acidic milk oligosaccharides of the platypus (Ornithorhynchus anatinus) and its evolutionary significance. Glycobiology 2015; 25:683-97. [DOI: 10.1093/glycob/cwv010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/13/2015] [Indexed: 12/15/2022] Open
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Sharp JA, Modepalli V, Enjapoori AK, Bisana S, Abud HE, Lefevre C, Nicholas KR. Bioactive Functions of Milk Proteins: a Comparative Genomics Approach. J Mammary Gland Biol Neoplasia 2014; 19:289-302. [PMID: 26115887 DOI: 10.1007/s10911-015-9331-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/19/2015] [Indexed: 12/21/2022] Open
Abstract
The composition of milk includes factors required to provide appropriate nutrition for the growth of the neonate. However, it is now clear that milk has many functions and comprises bioactive molecules that play a central role in regulating developmental processes in the young while providing a protective function for both the suckled young and the mammary gland during the lactation cycle. Identifying these bioactives and their physiological function in eutherians can be difficult and requires extensive screening of milk components that may function to improve well-being and options for prevention and treatment of disease. New animal models with unique reproductive strategies are now becoming increasingly relevant to search for these factors.
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Affiliation(s)
- Julie A Sharp
- Institute for Frontier Materials, Deakin University, Geelong, 3216, Australia,
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