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Walter NG. Are non-protein coding RNAs junk or treasure?: An attempt to explain and reconcile opposing viewpoints of whether the human genome is mostly transcribed into non-functional or functional RNAs. Bioessays 2024; 46:e2300201. [PMID: 38351661 DOI: 10.1002/bies.202300201] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 03/28/2024]
Abstract
The human genome project's lasting legacies are the emerging insights into human physiology and disease, and the ascendance of biology as the dominant science of the 21st century. Sequencing revealed that >90% of the human genome is not coding for proteins, as originally thought, but rather is overwhelmingly transcribed into non-protein coding, or non-coding, RNAs (ncRNAs). This discovery initially led to the hypothesis that most genomic DNA is "junk", a term still championed by some geneticists and evolutionary biologists. In contrast, molecular biologists and biochemists studying the vast number of transcripts produced from most of this genome "junk" often surmise that these ncRNAs have biological significance. What gives? This essay contrasts the two opposing, extant viewpoints, aiming to explain their bases, which arise from distinct reference frames of the underlying scientific disciplines. Finally, it aims to reconcile these divergent mindsets in hopes of stimulating synergy between scientific fields.
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Affiliation(s)
- Nils G Walter
- Center for RNA Biomedicine, Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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2
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Constable PA, Loh L, Grigg JR. Suspected case of benign familial fleck retina with functional loss. Clin Case Rep 2023; 11:e8362. [PMID: 38130850 PMCID: PMC10733792 DOI: 10.1002/ccr3.8362] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/07/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Key Clinical Message Inherited retinal dystrophies typically affect vision in early childhood; however, this case highlights a late onset retinal dystrophy presenting in midlife and the need for extended visual electrophysiology testing to determine the etiology. Abstract A 53-year-old female was referred for visual electrophysiology following a routine optometric eye examination in which yellow flecks were noted in both fundi and the patient had reported a recent near accident whilst driving at night. There was no reported family history of eye disease. Retinal examination identified bilateral yellow punctate and irregularly shaped lesions throughout the posterior poles sparing the macula region. Fundus autofluorescence showed coinciding hyperfluorescence with the lesions and bilateral hypofluorescent crescents superior to the macular with corresponding retinal thinning. Visual fields and color vision were normal. ISCEV standard 20 min and extended 60-min dark adapted electroretinograms were recorded. Recovery to normal b-wave amplitudes was noted in the DA0.01 flash but reduced a-wave amplitudes were noted in the DA3 and DA10 flash following both dark adapted periods. Cone function was reduced but within normal limits. Genetic screening revealed a previously unreported variant of unknown significance in the gene PLA2G5:c.40 + 5del (rs1364254561) which is a member of the phospholipase A2 family and is associated with familial benign flecked retina.
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Affiliation(s)
- Paul A. Constable
- Flinders University, College of Nursing and Health SciencesCaring Futures InstituteAdelaideSouth AustraliaAustralia
| | - Lynne Loh
- Flinders University, College of Nursing and Health SciencesCaring Futures InstituteAdelaideSouth AustraliaAustralia
| | - John R. Grigg
- Save Sight Institute, Faculty of Medicine and HealthUniversity of SydneySydneyNew South WalesAustralia
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Noda Y, Kido J, Misumi Y, Sugawara K, Ohori S, Fujita A, Matsumoto N, Ueda M, Nakamura K. Heterozygous c.175C>T variant in PURA gene causes severe developmental delay. Clin Case Rep 2023; 11:e7779. [PMID: 37692153 PMCID: PMC10483498 DOI: 10.1002/ccr3.7779] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 09/12/2023] Open
Abstract
Key Clinical Message This case report presents a child with PURA-related neurodevelopmental disorder, caused by the heterozygous pathogenic variant c.175C>T (p.Gln59*). The clinical symptoms included microcephaly, brachygnathia, central and peripheral hypotonia, and developmental delay (non-verbal), among others. On comparison with published literature, even patients with the same mutation present different clinical symptoms. Abstract This case report presents a child with PURA-related neurodevelopmental disorder, caused by the heterozygous pathogenic variant c.175C>T (p.Gln59*), whose symptoms included microcephaly, brachygnathia, the development of a high anterior hairline, hip dysplasia, strabismus, severe hypotonia, developmental delay (non-meaningful verbal), feeding difficulties, and respiratory difficulties. His development ceased with age, such that his development at 10 years corresponded to an infant of 6 months. Moreover, even patients with the same variant can have different clinical symptoms, such as the presence or absence of epilepsy or congenital malformations. Therefore, we should follow his long-term clinical course and provide medical support as necessary.
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Affiliation(s)
- Yusuke Noda
- Department of PediatricsKumamoto University HospitalKumamotoJapan
- Department of Pediatrics Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Jun Kido
- Department of PediatricsKumamoto University HospitalKumamotoJapan
- Department of Pediatrics Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Yohei Misumi
- Department of NeurologyKumamoto University HospitalKumamotoJapan
| | - Keishin Sugawara
- Department of Pediatrics Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Sachiko Ohori
- Department of Human GeneticsYokohama City University Graduate School of MedicineYokohamaJapan
| | - Atsushi Fujita
- Department of Human GeneticsYokohama City University Graduate School of MedicineYokohamaJapan
| | - Naomichi Matsumoto
- Department of Human GeneticsYokohama City University Graduate School of MedicineYokohamaJapan
| | - Mitsuharu Ueda
- Department of NeurologyKumamoto University HospitalKumamotoJapan
| | - Kimitoshi Nakamura
- Department of PediatricsKumamoto University HospitalKumamotoJapan
- Department of Pediatrics Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
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VerStrate CA, Mahon SM. Direct-to-Consumer Genomic Testing Through an Ethics Lens: Oncology Nursing Considerations. Clin J Oncol Nurs 2023; 27:380-388. [PMID: 37677769 DOI: 10.1188/23.cjon.380-388] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
BACKGROUND The use of direct-to-consumer genomic testing (DTCGT) is increasing, but this testing may not be comprehensive and may lack clinical validity and utility. The ethical constructs of beneficence, nonmaleficence, justice, and autonomy provide a framework for coordinating the care of patients and their families. OBJECTIVES This article provides an overview of the DTCGT process and reviews the ethical implications that affect clinical care. METHODS A review of the literature was conducted using the following key words: genetics/genomics and direct-to-consumer testing. Common themes were identified, including test types, regulatory standards, marketing practices, ethics, privacy, and nursing implications. FINDINGS An increased awareness of the clinical and ethical consequences of DTCGT is needed among healthcare providers and the general population. Oncology nurses can assist patients in navigating the field of genomics through consistent and comprehensive risk assessment, patient education about the risks and benefits of DTCGT, and referral to genomics professionals when appropriate.
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Thomas RG. Recurrent pneumonia in a child with Jacobsen syndrome and common variable immune deficiency. Clin Case Rep 2023; 11:e7472. [PMID: 37323257 PMCID: PMC10268222 DOI: 10.1002/ccr3.7472] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/21/2022] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
Recurrent severe respiratory infections in Jacobsen syndrome (JS) are unusual and should prompt evaluation of the immune system. A variety of immune defects have been reported in JS and intravenous immune globulin (IVIG) treatment reduces severe infections.
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Affiliation(s)
- Ryan G. Thomas
- Department of Pediatrics and Human DevelopmentMichigan State UniversityEast LansingMichiganUSA
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Aziz T, Naveed M, Jabeen K, Shabbir MA, Sarwar A, Zhennai Y, Alharbi M, Alshammari A, Alasmari AF. Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir. Front Microbiol 2023; 14:1157615. [PMID: 37152722 PMCID: PMC10158936 DOI: 10.3389/fmicb.2023.1157615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/22/2023] [Indexed: 05/09/2023] Open
Abstract
The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the genetic diversity among strains and to explore the genetic characteristics of the YW11 strain. The genome of L. plantarum YW11 was found to be composed of a circular single chromosome of 4,597,470 bp with a G + C content of 43.2%. A total of 4,278 open reading frames (ORFs) were identified in the genome and the coding density was found to be 87.8%. A comparative genomic analysis was conducted using two other L. plantarum strains, L. plantarum C11 and L. plantarum LMG21703. Genomic comparison revealed that L. plantarum YW11 shared 72.7 and 75.2% of gene content with L. plantarum C11 and L. plantarum LMG21703, respectively. Most of the genes shared between the three L. plantarum strains were involved in carbohydrate metabolism, energy production and conversion, amino acid metabolism, and transcription. In this analysis, 10 previously sequenced entire genomes of the species were compared using an in-silico technique to discover genomic divergence in genes linked with carbohydrate intake and their potential adaptations to distinct human intestinal environments. The subspecies pan-genome was open, which correlated with its extraordinary capacity to colonize several environments. Phylogenetic analysis revealed that the novel genomes were homogenously grouped among subspecies of l Lactiplantibacillus. L. plantarum was resistant to cefoxitin, erythromycin, and metronidazole, inhibited pathogens including Listeria monocytogenes, Clostridium difficile, Vibrio cholera, and others, and had excellent aerotolerance, which is useful for industrial operations. The comparative genomic analysis of L. plantarum YW11 isolated from Tibetan kefir can provide insights into the genetic characteristics of the strain, which can be used to further understand its role in the production of kefir.
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Affiliation(s)
- Tariq Aziz
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
- Department of Agriculture, University of Ioannina, Ioannina, Greece
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Abid Sarwar
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
| | - Yang Zhennai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Engineering and Technology Research Center of Food Additives, Beijing Technology and Business University, Beijing, China
- *Correspondence: Yang Zhennai,
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F. Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Pocius VM, Majewska AA, Freedman MG. The Role of Experiments in Monarch Butterfly Conservation: A Review of Recent Studies and Approaches. Ann Entomol Soc Am 2022; 115:10-24. [PMID: 35069967 PMCID: PMC8764570 DOI: 10.1093/aesa/saab036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Indexed: 06/14/2023]
Abstract
Monarch butterflies (Danaus plexippus) (Lepidoptera Danaidae Danaus plexippus (Linnaeus)) are an iconic species of conservation concern due to declines in the overwintering colonies over the past twenty years. Because of this downward trend in overwintering numbers in both California and Mexico, monarchs are currently considered 'warranted-but-precluded' for listing under the Endangered Species Act. Monarchs have a fascinating life history and have become a model system in chemical ecology, migration biology, and host-parasite interactions, but many aspects of monarch biology important for informing conservation practices remain unresolved. In this review, we focus on recent advances using experimental and genetic approaches that inform monarch conservation. In particular, we emphasize three areas of broad importance, which could have an immediate impact on monarch conservation efforts: 1) breeding habitat and host plant use, 2) natural enemies and exotic caterpillar food plants, and 3) the utility of genetic and genomic approaches for understanding monarch biology and informing ongoing conservation efforts. We also suggest future studies in these areas that could improve our understanding of monarch behavior and conservation.
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Affiliation(s)
- Victoria M Pocius
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | | | - Micah G Freedman
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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Lee KJ, Janda M, Stark MS, Sturm RA, Soyer HP. On Naevi and Melanomas: Two Sides of the Same Coin? Front Med (Lausanne) 2021; 8:635316. [PMID: 33681261 PMCID: PMC7933521 DOI: 10.3389/fmed.2021.635316] [Citation(s) in RCA: 3] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
Benign naevi are closely linked to melanoma, as risk factors, simulators, or sites of melanoma formation. There is a heavy genetic overlap between the two lesions, a shared environmental influence of ultraviolet radiation, and many similar cellular features, yet naevi remain locally situated while melanomas spread from their primary site and may progress systemically to distal organs. Untangling the overlapping contributors and predictors of naevi and melanoma is an ongoing area of research and should eventually lead to more personalized prevention and treatment strategies, through the development of melanoma risk stratification tools and early detection of evolving melanomas. This will be achieved through a range of complementary strategies: risk-adjusted primary prevention counseling; the use of lesion imaging technologies such as sequential 3D total body photography and consumer-performed lesion imaging; artificial intelligence deep phenotyping and clinical assistance; a better understanding of genetic drivers of malignancy, risk variants, clinical genetics, and polygenic effects; and the interplay between genetics, phenotype and the environment.
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Affiliation(s)
- Katie J Lee
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Monika Janda
- Centre for Health Services Research, The University of Queensland, Brisbane, QLD, Australia
| | - Mitchell S Stark
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Richard A Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - H Peter Soyer
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia.,Department of Dermatology, Princess Alexandra Hospital, Brisbane, QLD, Australia
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Goncharova EA, Bogaard HJ, de Jesus Perez VA. Editorial: Pulmonary Hypertension in the Modern Era: Science and Clinical Practice. Front Med (Lausanne) 2021; 8:785181. [PMID: 34778329 PMCID: PMC8581044 DOI: 10.3389/fmed.2021.785181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/08/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Elena A Goncharova
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Lung Center, School of Medicine, University of California, Davis, Davis, CA, United States
| | - Harm J Bogaard
- Department of Pulmonary Medicine, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Vinicio A de Jesus Perez
- Division of Pulmonary, Allergy and Critical Care Medicine, Stanford University Medical Center, Stanford, CA, United States
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10
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Gohel N, Senos R, Goldstein SA, Hankenson KD, Hake ME, Alford AI. Evaluation of global gene expression in regenerate tissues during Masquelet treatment. J Orthop Res 2020; 38:2120-2130. [PMID: 32233004 PMCID: PMC7494657 DOI: 10.1002/jor.24676] [Citation(s) in RCA: 4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/19/2020] [Accepted: 03/25/2020] [Indexed: 02/04/2023]
Abstract
The Masquelet induced-membrane (IM) technique is indicated for large segmental bone defects. Attributes of the IM and local milieu that contribute to graft-to-bone union are unknown. Using a rat model, we compared global gene expression profiles in critically sized femoral osteotomies managed using a cement spacer as per Masquelet to those left empty. At the end of the experiment, IM and bone adjacent to the spacer were collected from the Masquelet side. Nonunion tissue in the defect and bone next to the empty defect were collected from the contralateral side. Tissues were subjected to RNA isolation, sequencing, and differential expression analysis. Cell type enrichment analysis suggested the IM and the bone next to the polymethylmethacrylate (PMMA) spacer were comparatively enriched for osteoblastic genes. The nonunion environment was comparatively enriched for innate and adaptive immune cell markers, but only macrophages were evident in the Masquelet context. iPathwayGuide was utilized to identify cell signaling pathways and protein interaction networks enriched in the Masquelet environment. For IM vs nonunion false-discovery rate correction of P values rendered overall pathway differences nonsignificant, and so only protein interaction networks are presented. For the bone comparison, substantial enrichment of pathways and networks known to contribute to osteogenic mechanisms was revealed. Our results suggest that the PMMA spacer affects the cut bone ends that are in contact with it and at the same time induces the foreign body reaction and formation of the IM. B cells in the empty defect suggest a chronic inflammatory response to a large segmental osteotomy.
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Affiliation(s)
- Nishant Gohel
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan
| | - Rafael Senos
- Department of Morphology, Universidade Federal Fluminense, Niteroi, Rio de Janeiro, Brazil
| | - Steven A. Goldstein
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan
| | - Kurt D. Hankenson
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan
| | - Mark E. Hake
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan.,Address correspondence to Mark E. Hake: Department of Orthopaedic Surgery, University of Michigan School of Medicine, 1500 E Medical Center Drive, 2912 Taubman Center SPC 5328; Ann Arbor, MI 48109; fax: +1-734-647-3277; telephone: +734-936-9839;
| | - Andrea I. Alford
- Department of Orthopaedic Surgery, University of Michigan, Ann Arbor, Michigan.,Address correspondence to Andrea I. Alford: Department of Orthopaedic Surgery, University of Michigan School of Medicine, A. Alfred Taubman Biomedical Sciences Research Building, Room 2009, Ann Arbor, MI, 48109; fax: +1-734 -647-0003; telephone: +1-734-615-6104;
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Rai MF, Brophy RH, Rosen V. Molecular biology of meniscus pathology: Lessons learned from translational studies and mouse models. J Orthop Res 2020; 38:1895-1904. [PMID: 32068295 PMCID: PMC7802285 DOI: 10.1002/jor.24630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/11/2020] [Indexed: 02/04/2023]
Abstract
Injury to any individual structure in the knee interrupts the overall function of the joint and initiates a cascade of biological and biomechanical changes whose endpoint is often osteoarthritis (OA). The knee meniscus is an integral component of knee biomechanics and may also contribute to the biological homeostasis of the joint. Meniscus injury altering knee function is associated with a high risk of OA progression, and may also be involved in the initiation of OA. As the relationship between meniscus injury and OA is very complex; despite the availability of transcript level data on human meniscus injury and meniscus mediated OA, mechanistic studies are lacking, and available human data are difficult to validate in the absence of patient-matched noninjured control tissues. As similarities exist between human and mouse knee joint structure and function, investigators have begun to use cutting-edge genetic and genomic tools to examine the usefulness of the mouse as a model to study the intricate relationship between meniscus injury and OA. In this review, we use evidence from human meniscus research to identify critical barriers hampering our understanding of meniscus injury induced OA and discuss strategies to overcome these barriers, including those that can be examined in a mouse model of injury-mediated OA.
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Affiliation(s)
- Muhammad Farooq Rai
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO, United States of America,Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Robert H. Brophy
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Vicki Rosen
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, United States of America
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Xu J, Henry A, Sreenivasulu N. Rice yield formation under high day and night temperatures-A prerequisite to ensure future food security. Plant Cell Environ 2020; 43:1595-1608. [PMID: 32112422 DOI: 10.1111/pce.13748] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [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: 12/26/2019] [Accepted: 02/18/2020] [Indexed: 05/13/2023]
Abstract
Increasing temperatures resulting from climate change dramatically impact rice crop production in Asia. Depending on the specific stage of rice development, heat stress reduces tiller/panicle number, decreases grain number per plant and lower grain weight, thus negatively impacting yield formation. Hence improving rice crop tolerance to heat stress in terms of sustaining yield stability under high day temperature (HDT), high night temperature (HNT), or combined high day and night temperature (HDNT) will bolster future food security. In this review article, we highlight the phenological alterations caused by heat and the underlying molecular-physiological and genetic mechanisms operating under different types of heat conditions (HDT, HNT, and HDNT) to understand heat tolerance. Based on our synthesis of HDT, HNT, and HDNT effects on rice yield components, we outline future breeding strategies to contribute to sustained food security under climate change.
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Affiliation(s)
- Jiemeng Xu
- International Rice Research Institute, Los Baños, Philippines
| | - Amelia Henry
- International Rice Research Institute, Los Baños, Philippines
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Laforest M, Martin SL, Bisaillon K, Soufiane B, Meloche S, Page E. A chromosome-scale draft sequence of the Canada fleabane genome. Pest Manag Sci 2020; 76:2158-2169. [PMID: 31951071 DOI: 10.1002/ps.5753] [Citation(s) in RCA: 9] [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: 11/15/2019] [Revised: 12/23/2019] [Accepted: 01/07/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Due to the accessibility of underlying technologies the 'Omics', in particular genomics, are becoming commonplace in several fields of research, including the study of agricultural pests. The weed community is starting to embrace these approaches; genome sequences have been made available in the past years, with several other sequencing projects underway, as promoted by the International Weed Genome Consortium. Chromosome-scale sequences are essential to fully exploit the power of genetics and genomics. RESULTS We report such an assembly for Conyza canadensis, an important agricultural weed. Third-generation sequencing technology was used to create a genome assembly of 426 megabases, of which nine chromosome-scale scaffolds cover more than 98% of the entire assembled sequence. As this weed was the first to be identified with glyphosate resistance, and since we do not have a firm handle on the genetic mechanisms responsible for several herbicide resistances in the species, the genome sequence was annotated with genes known to be associated with herbicide resistance. A high number of ABC-type transporters, cytochrome P450 and glycosyltransferases (159, 352 and 181, respectively) were identified among the list of ab initio predicted genes. CONCLUSION As C. canadensis has a small genome that is syntenic with other Asteraceaes, has a short life cycle and is relatively easy to cross, it has the potential to become a model weed species and, with the chromosome-scale genome sequence, contribute to a paradigm shift in the way non-target site resistance is studied. © 2020 Her Majesty the Queen in Right of CanadaPest Management Science © 2020 Society of Chemical Industry.
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Affiliation(s)
- Martin Laforest
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada Saint-Jean-sur-Richelieu, Quebec, Canada
| | - Sara L Martin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Katherine Bisaillon
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada Saint-Jean-sur-Richelieu, Quebec, Canada
| | - Brahim Soufiane
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada Saint-Jean-sur-Richelieu, Quebec, Canada
| | - Sydney Meloche
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON, Canada
| | - Eric Page
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON, Canada
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Abstract
PURPOSE OF REVIEW Although primarily designed for medical documentation and billing purposes, the electronic health record (EHR) has significant potential for translational research. In this article, we provide an overview of the use of the EHR for genomics research with a focus on heritable lipid disorders. RECENT FINDINGS Linking the EHR to genomic data enables repurposing of vast phenotype data for genomic discovery. EHR data can be used to study the genetic basis of common and rare disorders, identify subphenotypes of diseases, assess pathogenicity of novel genomic variants, investigate pleiotropy, and rapidly assemble cohorts for genomic medicine clinical trials. EHR-based discovery can inform clinical practice; examples include use of polygenic risk scores for assessing disease risk and use of phenotype data to interpret rare variants. Despite limitations such as missing data, variable use of standards and poor interoperablility between disparate systems, the EHR is a powerful resource for genomic research. SUMMARY When linked to genomic data, the EHR can be leveraged for genomic discovery, which in turn can inform clinical care, exemplifying the virtuous cycle of a learning healthcare system.
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Affiliation(s)
- Maya S Safarova
- Atherosclerosis and Lipid Genomics Laboratory and Department of Cardiovascular Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Seale K, Burger M, Posthumus M, Häger CK, Stattin E, Nilsson KG, Collins M, September AV. The Apoptosis Pathway and CASP8 Variants Conferring Risk for Acute and Overuse Musculoskeletal Injuries. J Orthop Res 2020; 38:680-688. [PMID: 31692049 DOI: 10.1002/jor.24504] [Citation(s) in RCA: 4] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 10/14/2019] [Indexed: 02/04/2023]
Abstract
Rotator cuff tendinopathy (RCT), anterior cruciate ligament (ACL) ruptures, and carpal tunnel syndrome (CTS), are examples of chronic (RCT and CTS) and acute (ACL ruptures) musculoskeletal soft tissue injuries. These injuries are multifactorial in nature, with several identified intrinsic and extrinsic risk factors. Previous studies have implicated specific sequence variants within genes encoding structural and regulatory components of the extracellular matrix of tendons and/ligaments to predispose individuals to these injuries. An example, includes the association of sequence variants within the apoptotic regulatory gene, caspase-8 (CASP8) with other musculoskeletal injury phenotypes, such as Achilles tendinopathy. The primary aim of this study was, therefore, to investigate previously implicated DNA sequence variants within CASP8: rs3834129 (ins/del) and rs1045485 (G/C), and the rs13113 (T/A) identified using a whole exome sequencing approach, with risk of musculoskeletal injury phenotypes (RCT, ACL ruptures, and CTS) in three independent studies. In addition, the aim was to implicate a CASP8 genomic interval in the modulation of risk of RCT, ACL ruptures, or CTS. It was found that the AA genotype of CASP8 rs13113 (T/A) was independently associated with increased risk for CTS. In addition, it was found that the del-C haplotype (rs3834129-rs1045485) was significantly associated with non-contact ACL ruptures, which is in alignment with previous research findings. Collectively, the results of this study implicate the apoptosis pathway as biologically significant in the underlying pathogenesis of musculoskeletal injury phenotypes. These findings should be repeated in larger sample cohorts and across different populations. © 2019 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 38:680-688, 2020.
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Affiliation(s)
- Kirsten Seale
- Department of Human Biology, Division of Exercise Science and Sports Medicine, Faculty of Health Sciences, University of Cape Town, Postal: No 1 Boundary Road, ESSM Level 3, SISSA Building Newlands, Cape Town, 7700, South Africa
| | - Marilize Burger
- Department of Human Biology, Division of Exercise Science and Sports Medicine, Faculty of Health Sciences, University of Cape Town, Postal: No 1 Boundary Road, ESSM Level 3, SISSA Building Newlands, Cape Town, 7700, South Africa.,Department of Surgical Sciences, Division of Orthopaedic Surgery, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Michael Posthumus
- Department of Human Biology, Division of Exercise Science and Sports Medicine, Faculty of Health Sciences, University of Cape Town, Postal: No 1 Boundary Road, ESSM Level 3, SISSA Building Newlands, Cape Town, 7700, South Africa
| | - Charlotte K Häger
- Department of Community Medicine and Rehabilitation, Umeå University, Umeå, Sweden
| | - Evalena Stattin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kjell G Nilsson
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Malcolm Collins
- Department of Human Biology, Division of Exercise Science and Sports Medicine, Faculty of Health Sciences, University of Cape Town, Postal: No 1 Boundary Road, ESSM Level 3, SISSA Building Newlands, Cape Town, 7700, South Africa
| | - Alison V September
- Department of Human Biology, Division of Exercise Science and Sports Medicine, Faculty of Health Sciences, University of Cape Town, Postal: No 1 Boundary Road, ESSM Level 3, SISSA Building Newlands, Cape Town, 7700, South Africa.,Division of Exercise Science and Sports Medicine, International Federation of Sports Medicine (FIMS) Collaborative Centre of Sports Medicine, Cape Town, South Africa.,UCT Research Centre for Health through Physical Activity, Lifestyle and Sport (HPALS), Division of Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
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Adadey SM, Awandare G, Amedofu GK, Wonkam A. Public Health Burden of Hearing Impairment and the Promise of Genomics and Environmental Research: A Case Study in Ghana, Africa. OMICS 2018; 21:638-646. [PMID: 29140768 DOI: 10.1089/omi.2017.0145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hearing impairment (HI) is one of the most disabling conditions of major global health burden that contributes adversely to the social and economic development of a country, if not managed properly. A proper assessment of the nationwide burden and etiology of HI is instrumental in the prevention, treatment, and management of the condition. This article sought to perform an expert review of HI in Ghana to determine the present knowledge of its burden and possible causes of the condition. A literature search was conducted in PubMed using the following keywords: "hearing loss" OR "hearing impairment" OR "deafness" AND "Ghana." The literature was scanned until July 20, 2017, with specific inclusion of targeted landmark and background articles on HI. From the search, 18 of out 5869 articles were selected and considered for the review. The results of the search indicated that there were no extensive studies to determine the national burden of HI in Ghana. However, the few studies assessed suggested that the disease is either acquired or inherited. The burden of acquired HI was higher in adults than children, women than men, and people working in a noisy environment. Regarding the genetic cause, specific founder mutations in GJB2 gene (R143W, L79P, V178A, R184Q, A197S, I203K, and L214P) was the only identified genetic cause of HI in Ghana, but the other HI genes were not investigated. There has been some modest effort to study HI in Ghana, but comprehensive studies on the genetic and environmental etiologies (using the "multi-OMICS" approaches), classification, and burden of HI on Ghana are needed.
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Affiliation(s)
- Samuel Mawuli Adadey
- 1 West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana , Accra, Ghana
| | - Gordon Awandare
- 1 West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana , Accra, Ghana
| | | | - Ambroise Wonkam
- 3 Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
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Abstract
The 37th San Antonio Breast Cancer Symposium (SABCS) was held at the Henry B. Gonzalez Conference Centre in San Antonio, Texas, USA between the 9 and 13th of December 2014. It brought together an interaction between basic scientists and clinicians involved in the management of breast cancer. The symposium included six general sessions, poster discussion, and poster sessions. The most important highlights in the fields of advancing endocrine therapy; hormone receptor positive advanced breast cancer and hormonal resistant therapy; targeted therapies; genetics and genomics; supportive (adjunct) care; chemotherapy treatments; breast screening and risk stratification; male breast cancer and future potential directions were included here.
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Affiliation(s)
- M Ahmed
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital Campus, London SE1 9RT, UK
| | - E Esposito
- Research Oncology, Division of Cancer Studies, King's College London, Guy's Hospital Campus, London SE1 9RT, UK ; Department of Clinical Medicine and Surgery, Breast Unit, University of Naples Federico II, Naples 80131, Italy
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