scholarly journals Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
John A. Lees ◽  
Minna Vehkala ◽  
Niko Välimäki ◽  
Simon R. Harris ◽  
Claire Chewapreecha ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Enrichment Analysis ◽  
Sequence Element ◽  
Element Enrichment

scholarly journals Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

2016 ◽  
Author(s):  
John A. Lees ◽  
Minna Vehkala ◽  
Niko Välimäki ◽  
Simon R. Harris ◽  
Claire Chewapreecha ◽  
...  
Keyword(s):  
Enrichment Analysis ◽  
Genetic Associations ◽  
Human Pathogens ◽  
Bacterial Genomes ◽  
Sequence Element ◽  
Clonal Population ◽  
Sequence Elements ◽  
String Mining ◽  
Clonal Population Structure ◽  
Element Enrichment

AbstractBacterial genomes vary extensively in terms of both gene content and gene sequence – this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. Here we introduce a computationally scalable and widely applicable statistical method (SEER) for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable-length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogensStreptococcus pneumoniaeandStreptococcus pyogenes, SEER identifies relevant previously characterised resistance determinants for several antibiotics and discovers potential novel factors related to the invasiveness ofS. pyogenes. We thus demonstrate that our method can answer important biologically and medically relevant questions.

scholarly journals Transcriptome analysis reveals the genetic basis underlying the development of skin appendages and immunity in hedgehog(Atelerix albiventris)

2020 ◽  
Author(s):  
Hui-Ming Li ◽  
Bi-Ze Yang ◽  
Xiu-Juan Zhang ◽  
Hai-Ying Jiang ◽  
Lin-Miao Li ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mammal Species ◽  
Appendage Development ◽  
Skin Appendage ◽  
Hair Type ◽  
Spine Development ◽  
Skin Appendages ◽  
Development And Differentiation

Abstract Background: The expression of hair features is an evolutionary adaptation resulting from interactions between many organisms and their environment. Elucidation of the mechanisms that underlie the expression of such traits is a topic in evolutionary biology research; however, the genetic basis of skin appendage development and differentiation remains poorly understood. Therefore, we assessed the de novo transcriptome of the hedgehog ( Atelerix albiventris ) at three developmental stages and compared gene expression profiles between abdomen hair and dorsal spine tissues. Results: We identified 328,576 unigenes in our transcriptome, among which 3,598 were differentially expressed between hair- and spine-type tissues. We identified 3 keratin genes related to hair and spine development through comparative analysis of tissues before and after growth of skin appendages. Dorsal and abdomen skin tissues 5 days after birth were compared and the resulting differentially expressed genes (DEGs) were mainly enriched in keratin filament, intermediate filament, epithelium cell differentiation, and epidermis development based on GO enrichment analysis, and tight junction, p53, and cell cycle signaling pathways based on KEGG enrichment analysis. Expression variations of MBP8, SFN, Wnt10, KRT1 , and KRT2 may be the main factors regulating hair and spine differentiation for the hedgehog. Strikingly, DEGs in hair-type tissues were also significantly enriched in immune-related terms and pathways with hair-type tissues exhibiting more upregulated immune genes than spine-type tissues. Thus, we propose that spine development was an adaptation that provided protection against injuries or stress and reduced hedgehog vulnerability to infection. Conclusion: Our study provided a list of potential genes involved in the regulation of skin appendage development and differentiation in A. albiventris . This is the first transcriptome survey of hair traits for a non-model mammal species, and the candidate genes provided here may provide valuable information for further studies of skin appendages and skin disorder treatments.

scholarly journals Transcriptional Regulations on the Low-Temperature-Induced Floral Transition in anOrchidaceaeSpecies,Dendrobium nobile: An Expressed Sequence Tags Analysis

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Shan Liang ◽  
Qing-Sheng Ye ◽  
Rui-Hong Li ◽  
Jia-Yi Leng ◽  
Mei-Ru Li ◽  
...  
Keyword(s):  
Expressed Sequence Tags ◽  
Genetic Basis ◽  
Protein Biosynthesis ◽  
Enrichment Analysis ◽  
Gene Clusters ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Floral Transition ◽  
Dendrobium Nobile ◽  
Expressed Sequence

Vernalization-induced flowering is a cold-relevant adaptation in many species, but little is known about the genetic basis behind inOrchidaceaespecies. Here, we reported a collection of 15017 expressed sequence tags (ESTs) from the vernalized axillary buds of anOrchidaceaespecies,Dendrobium nobile, which were assembled for 9616 unique gene clusters. Functional enrichment analysis showed that genes in relation to the responses to stresses, especially in the form of low temperatures, and those involving in protein biosynthesis and chromatin assembly were significantly overrepresented during 40 days of vernalization. Additionally, a total of 59 putative flowering-relevant genes were recognized, including those homologous to known key players in vernalization pathways in temperate cereals orArabidopsis, such as cerealVRN1,FT/VRN3, andArabidopsis AGL19. Results from this study suggest that the networks regulating vernalization-induced floral transition are conserved, but just in a part, inD. nobile, temperate cereals, andArabidopsis.

scholarly journals FertilityOnline, a straight pipeline for functional gene annotation and disease mutation discovery, identifies novel infertility causative mutations in SYCE1 and STAG3

2020 ◽  
Author(s):  
Jianing Gao ◽  
Huan Zhang ◽  
Xiaohua Jiang ◽  
Asim Ali ◽  
Daren Zhao ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Animal Species ◽  
Gene Annotation ◽  
Enrichment Analysis ◽  
Web Interface ◽  
Mutation Discovery ◽  
Human Genes ◽  
Intensive Investigation ◽  
User Friendly ◽  
Functional Gene Annotation

AbstractExploring the genetic basis of human infertility is currently under intensive investigation. However, only a handful of genes are validated in animal models as disease-causing genes in infertile men. Thus, to better understand the genetic basis of spermatogenesis in human and to bridge the knowledge gap between human and other animal species, we have constructed FertilityOnline database, which is a resource that integrates the functional genes reported in literature related to spermatogenesis into an existing spermatogenic database, SpermatogenesisOnline 1.0. Additional features like functional annotation and statistical analysis of genetic variants of human genes, are also incorporated into FertilityOnline. By searching this database, users can focus on the top candidate genes associated with infertility and can perform enrichment analysis to instantly refine the number of candidates in a user-friendly web interface. Clinical validation of this database is established by the identification of novel causative mutations in SYCE1 and STAG3 in azoospermia men. In conclusion, FertilityOnline is not only an integrated resource for analysis of spermatogenic genes, but also a useful tool that facilitates to study underlying genetic basis of male infertility.AvailabilityFertilityOnline can be freely accessed at http://mcg.ustc.edu.cn/bsc/spermgenes2.0/index.html.

Molecular Basis and Clinical Aspects of Hereditary Megakaryocyte and Platelet Membrane Glycoprotein Disorders

1996 ◽  
Vol 16 (02) ◽  
pp. 114-138 ◽  
Author(s):  
R. E. Scharf
Keyword(s):  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Molecular Genetic ◽  
Platelet Membrane ◽  
Clinical Aspects ◽  
Membrane Glycoprotein ◽  
Membrane Glycoproteins ◽  
Membrane Expression ◽  
Receptor Complexes ◽  
Platelet Membrane Glycoprotein

SummarySpecific membrane glycoproteins (GP) expressed by the megakaryocyte-platelet system, including GPIa-lla, GPIb-V-IX, GPIIb-llla, and GPIV are involved in mediat-ing platelet adhesion to the subendothelial matrix. Among these glycoproteins, GPIIb-llla plays a pivotal role since platelet aggregation is exclusively mediated by this receptor and its interaction with soluble macromolecular proteins. Inherited defects of the GPIIb-llla or GPIb-V-IX receptor complexes are associated with bleeding disorders, known as Glanzmann's thrombasthenia, Bernard-Soulier syndrome, or platelet-type von Willebrand's disease, respectively. Using immuno-chemical and molecular biology techniques, rapid advances in our understanding of the molecular genetic basis of these disorders have been made during the last few years. Moreover, analyses of patients with congenital platelet membrane glycoprotein abnormalities have provided valuable insights into molecular mechanisms that are required for structural and functional integrity, normal biosynthesis of the glycoprotein complexes and coordinated membrane expression of their constituents. The present article reviews the current state of knowledge of the major membrane glycoproteins in health and disease. The spectrum of clinical bleeding manifestations and established diagnostic criteria for each of these dis-orders are summarized. In particular, the variety of molecular defects that have been identified so far and their genetic basis will be discussed.

Anti-Myelin Oligodendrocyte Glycoprotein Encephalomyelitis and Extensive Longitudinal Transverse Myelitis Associated with Compound Heterozygous NLRP3 Missense Mutations in a Young Child

2020 ◽  
Author(s):  
Deirdre O'Sullivan ◽  
Michael Moore ◽  
Susan Byrne ◽  
Andreas O. Reiff ◽  
Susanna Felsenstein
Keyword(s):  
Young Child ◽  
Genetic Basis ◽  
Transverse Myelitis ◽  
Acute Disseminated Encephalomyelitis ◽  
Myelin Oligodendrocyte Glycoprotein ◽  
Compound Heterozygous ◽  
Missense Mutations ◽  
Childhood Onset

AbstractAcute disseminated encephalomyelitis in association with extensive longitudinal transverse myelitis is reported in a young child with positive anti-myelin oligodendrocyte glycoprotein (MOG) antibody with heterozygous NLRP3 missense mutations; p.(Arg488Lys) and p.(Ser159Ile). This case may well present an exceptional coincidence, but may describe a yet unrecognized feature of the spectrum of childhood onset cryopyrinopathies that contribute to the understanding of the genetic basis for anti-MOG antibody positive encephalomyelitis. Based on this observation, a larger scale study investigating the role of NLRP3 and other inflammasomes in this entity would provide important pathophysiological insights and potentially novel avenues for treatment.

Reading the Image of Race: Neurocriminology, Medical Imaging Technologies and Literary Intervention

2018 ◽  
Author(s):  
Lindsey Andrews ◽  
Jonathan M. Metzl
Keyword(s):  
Twentieth Century ◽  
Wall Street Journal ◽  
Genetic Basis ◽  
Three Dimensional ◽  
Criminal Behaviour ◽  
Dominant Model ◽  
Wall Street ◽  
Behavioural Genetics ◽  
Black And White ◽  
Brain Scan

On 26 April 2013, the Wall Street Journal published an essay by neurocriminologist Adrian Raine promoting his newest book, The Anatomy of Violence: The Biological Roots of Crime. On the newspaper’s website, an image of a black-and-white brain scan overlaid with handcuffs headed the essay. Clicking ‘play’ turned the image into a video filled with three-dimensional brain illustrations and Raine’s claims that some brains are simply more biologically prone to violence than others. Rejecting what he describes as ‘the dominant model for understanding criminal behaviour in the twentieth century’ – a model based ‘almost exclusively on social and sociological’ explanations – Raine wrote that ‘the genetic basis of criminal behaviour is now well established’ through molecular and behavioural genetics.

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