Sub-unit Specific Regulation of Type-A GABAergic Receptors during Post-Natal Development of the Auditory Cortex

The GABA-A receptor has been strongly implicated in the organization and function of cortical sensory circuits in the adult mammal. In the present work, changes in the expression patterns of select GABA-A subunits were examined as a function of development. The RNA expression profiles for three subunit types were studied, α1, β2/3 and δ at four developmental time points, (p0, p15, p30 and p90). The o1, β2/3 subunits were present at birth and following a modest increase early in life; mRNA expression for these subunits were found at stable levels throughout life. The expression pattern for the δ subunit showed the most dramatic changes in the number of positive cells as a function of age. In early life, p0 through p15 expression of mRNA for the δ subunit was quite low but increased in later life, p30 and p90. Together these data suggest that much of the potential for inhibitory connectivity is laid down in the pre and early post-natal periods.

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Phylogenetic Comparison and Splicing Analysis of the U1 snRNP-specific Protein U1C in Eukaryotes

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.696319 ◽

2021 ◽

Vol 8 ◽

Author(s):

Kai-Lu Zhang ◽

Jian-Li Zhou ◽

Jing-Fang Yang ◽

Yu-Zhen Zhao ◽

Debatosh Das ◽

...

Keyword(s):

Gene Family ◽

Cancer Progression ◽

Expression Profiles ◽

Expression Patterns ◽

Specific Protein ◽

Comprehensive Overview ◽

Small Nuclear Ribonucleoprotein ◽

U1 Snrnp ◽

Multiple Copies ◽

And Function

As a pivotal regulator of 5’ splice site recognition, U1 small nuclear ribonucleoprotein (U1 snRNP)-specific protein C (U1C) regulates pre-mRNA splicing by interacting with other components of the U1 snRNP complex. Previous studies have shown that U1 snRNP and its components are linked to a variety of diseases, including cancer. However, the phylogenetic relationships and expression profiles of U1C have not been studied systematically. To this end, we identified a total of 110 animal U1C genes and compared them to homologues from yeast and plants. Bioinformatics analysis shows that the structure and function of U1C proteins is relatively conserved and is found in multiple copies in a few members of the U1C gene family. Furthermore, the expression patterns reveal that U1Cs have potential roles in cancer progression and human development. In summary, our study presents a comprehensive overview of the animal U1C gene family, which can provide fundamental data and potential cues for further research in deciphering the molecular function of this splicing regulator.

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Comparative transcriptomics identifies differences in the regulation of the floral transition between Arabidopsis and Brassica rapa cultivars

10.1101/2020.08.26.266494 ◽

2020 ◽

Author(s):

Alexander Calderwood ◽

Jo Hepworth ◽

Shannon Woodhouse ◽

Lorelei Bilham ◽

D. Marc Jones ◽

...

Keyword(s):

Gene Expression ◽

Brassica Rapa ◽

Regulatory Networks ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Detailed Comparison ◽

Developmental Time ◽

Floral Transition ◽

Gene Regulatory

AbstractThe timing of the floral transition affects reproduction and yield, however its regulation in crops remains poorly understood. Here, we use RNA-Seq to determine and compare gene expression dynamics through the floral transition in the model species Arabidopsis thaliana and the closely related crop Brassica rapa. A direct comparison of gene expression over time between species shows little similarity, which could lead to the inference that different gene regulatory networks are at play. However, these differences can be largely resolved by synchronisation, through curve registration, of gene expression profiles. We find that different registration functions are required for different genes, indicating that there is no common ‘developmental time’ to which Arabidopsis and B. rapa can be mapped through gene expression. Instead, the expression patterns of different genes progress at different rates. We find that co-regulated genes show similar changes in synchronisation between species, suggesting that similar gene regulatory sub-network structures may be active with different wiring between them. A detailed comparison of the regulation of the floral transition between Arabidopsis and B. rapa, and between two B. rapa accessions reveals different modes of regulation of the key floral integrator SOC1, and that the floral transition in the B. rapa accessions is triggered by different pathways, even when grown under the same environmental conditions. Our study adds to the mechanistic understanding of the regulatory network of flowering time in rapid cycling B. rapa under long days and highlights the importance of registration methods for the comparison of developmental gene expression data.

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A high-resolution mRNA expression time course of embryonic development in zebrafish

eLife ◽

10.7554/elife.30860 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 82

Author(s):

Richard J White ◽

John E Collins ◽

Ian M Sealy ◽

Neha Wali ◽

Christopher M Dooley ◽

...

Keyword(s):

Mrna Expression ◽

Time Course ◽

Expression Profiles ◽

Developmental Time ◽

Rna Seq ◽

Time Points ◽

New Genes ◽

Expression Atlas ◽

Genome Activation ◽

Expression Time

We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.

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Differential gene expression patterns in vein regions susceptible versus resistant to neointimal hyperplasia

Physiological Genomics ◽

10.1152/physiolgenomics.00082.2017 ◽

2018 ◽

Vol 50 (8) ◽

pp. 615-627

Author(s):

Sun Hyung Kwon ◽

Li Li ◽

Christi M. Terry ◽

Yan-Ting Shiu ◽

Philip J. Moos ◽

...

Keyword(s):

Gene Expression ◽

Vein Graft ◽

Expression Profiles ◽

Neointimal Hyperplasia ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Yield Potential ◽

Microarray Gene Expression ◽

Graft Placement ◽

Time Points

Arteriovenous hemodialysis graft (AVG) stenosis results in thrombosis and AVG failure, but prevention of stenosis has been unsuccessful due in large part to our limited understanding of the molecular processes involved in neointimal hyperplasia (NH) formation. AVG stenosis develops chiefly as a consequence of highly localized NH formation in the vein-graft anastomosis region. Surprisingly, the vein region just downstream of the vein-graft anastomosis (herein termed proximal vein region) is relatively resistant to NH. We hypothesized that the gene expression profiles of the NH-prone and NH-resistant regions will be different from each other after graft placement, and analysis of their genomic profiles may yield potential therapeutic targets to prevent AVG stenosis. To test this, we evaluated the vein-graft anastomosis (NH-prone) and proximal vein (NH-resistant) regions in a porcine model of AVG stenosis with a porcine microarray. Gene expression changes in these two distinct vein regions, relative to the gene expression in unoperated control veins, were examined at early (5 days) and later (14 days) time points following graft placement. Global genomic changes were much greater in the NH-prone region than in the NH-resistant region at both time points. In the NH-prone region, genes related to regulation of cell proliferation and osteo-/chondrogenic vascular remodeling were most enriched among the significantly upregulated genes, and genes related to smooth muscle phenotype were significantly downregulated. These results provide insights into the spatial and temporal genomic modulation underlying NH formation in AVG and suggest potential therapeutic strategies to prevent and/or limit AVG stenosis.

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Abstract P744: Gene Transcript Clusters Distinguish Time-Dependent Expression Patterns in Monocytes, Neutrophils and Whole Blood After Ischemic Stroke Injury

Stroke ◽

10.1161/str.52.suppl_1.p744 ◽

2021 ◽

Vol 52 (Suppl_1) ◽

Author(s):

Paulina Carmona-Mora ◽

Glen C Jickling ◽

Xinhua Zhan ◽

Marisa Hakoupian ◽

Heather Hull ◽

...

Keyword(s):

Gene Expression ◽

Ischemic Stroke ◽

Whole Blood ◽

Temporal Dynamics ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Expression Profiles ◽

Time Dependent ◽

Gene Transcript ◽

Time Points

Introduction: After ischemic stroke (IS), peripheral leukocytes infiltrate the damaged region and modulate the response to injury. We previously showed that peripheral blood cells display different gene expression profiles after IS and these transcriptional programs reflect the changes in immune processes in response to IS. Dissecting the temporal dynamics of gene expression after IS improves our understanding of the changes of molecular and cellular pathways involved in acute brain injury. Methods: We analyzed the transcriptomic profiles of 33 IS patients in isolated monocytes, neutrophils and whole blood. RNA-sequencing was performed on all the stroke samples as well as 12 controls with vascular risk factors (diabetes and/or hypertension and/or hypercholesterolemia). To identify differentially expressed genes, subjects were split into time points (TPs) from stroke onset (TP1= 0-24 h; TP2= 24-48 h; and TP3= > 48 h), and controls were assigned TP0. A linear regression model including time and the interaction of diagnosis x TP with cutoff of p<0.02 and fold-change>|1.2| was used. Time dependent changes were analyzed using artificial neural networks to identify clusters of genes that behave in a similar way across TPs. Results: Unique patterns of temporal expression were distinguished for the three sample types. These include genes not expressed in TP0 that peak only within the first 24 h, others that peak or decrease in TP2 and TP3, and more complex patterns. Genes that peak at TP1 in monocytes and neutrophils are related to cell adhesion and leukocyte differentiation/migration, respectively. Early peaks in whole blood occur in genes related to transcriptional regulation. In monocytes, interleukin pathways are enriched across all TPs, whereas there is a trend of suppression after 24 h in neutrophils. The inflammasome pathway is enriched in the earlier TPs in neutrophils, while not enriched in monocytes until over 48 hours. Conclusion: Our analyses on gene expression dynamics and cluster patterns allow identification of key genes and pathways at different time points following ischemic injury that are valuable as IS biomarkers and may be possible treatment targets.

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Magnetic Bead Adsorption Extraction of Xyloglucan Endoglucosidase/Hydrolase Gene and Its Expression Analysis in Land Cotton

Journal of Biobased Materials and Bioenergy ◽

10.1166/jbmb.2021.2091 ◽

2021 ◽

Vol 15 (4) ◽

pp. 478-490

Author(s):

Xianliang Li ◽

Hang Liu ◽

Zhichang Zhao

Keyword(s):

Gene Family ◽

Developmental Stages ◽

Expression Profiles ◽

Expression Patterns ◽

Magnetic Bead ◽

Evolutionary Significance ◽

Cotton Fibers ◽

Expression Levels ◽

Duplication Events ◽

And Function

The xyloglucan Endotransglucosylase/hydrolase (XTH) genes are proposed to encode enzymes responsible for cleaving and reattaching xyloglucan polymers. Despite prior identification of the XTH gene family in Arabidopsis and rice, the XTH family in upland cotton, a tetraploid plant whose fiber cell is an excellent model for the study of plant cell elongation, is yet uncharacterized. In this study, iron tetroxide based magnetic nanobead (Fe3O4 NPs) was successfully prepared and applied to extract xyloglucan endoglucosidase/hydrolase genes. Analysis of the genes can provide insight into the evolutionary significance and function of the XTH gene family. A total of 41 XTH genes found by searching the phytozomev 10 database were classified into three groups based on their phylogeny and the motifs of individual genes. The 25 and 5 GhXTH genes occurred as clusters resulting from the segmental and tandem duplication. More frequent duplication events in cotton contributed to the expansion of the family. Global microarray analysis of GhXTH gene expression in cotton fibers showed that 18 GhXTH genes could be divided into two clusters and four subclusters based on their expression patterns. Accumulated expression levels were relatively high at the elongation stages of the cotton fibers, suggesting that cotton fiber elongation requires high amounts of the GhXTH protein. The expression profiles of GhXTH3 and GhXTH4 showed by quantitative realtime PCR were similar to those determined by microarray. Additionally, the expression levels of GhXTH3 and GhXTH4 in Gossypium barbadense were higher than those in Gossypium hirsutum at developmental stages, indicating that expression levels of GhXTH3 and GhXTH4 in fibers varied among cultivars differing in fiber length.

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A Computational Method for Classifying Different Human Tissues with Quantitatively Tissue-Specific Expressed Genes

Genes ◽

10.3390/genes9090449 ◽

2018 ◽

Vol 9 (9) ◽

pp. 449 ◽

Cited By ~ 10

Author(s):

JiaRui Li ◽

Lei Chen ◽

Yu-Hang Zhang ◽

XiangYin Kong ◽

Tao Huang ◽

...

Keyword(s):

Expression Profiles ◽

Expression Patterns ◽

Machine Learning Algorithms ◽

Computational Method ◽

Support Vector ◽

Specific Gene ◽

Human Tissues ◽

Tissue Development ◽

Tissue Specific ◽

And Function

Tissue-specific gene expression has long been recognized as a crucial key for understanding tissue development and function. Efforts have been made in the past decade to identify tissue-specific expression profiles, such as the Human Proteome Atlas and FANTOM5. However, these studies mainly focused on “qualitatively tissue-specific expressed genes” which are highly enriched in one or a group of tissues but paid less attention to “quantitatively tissue-specific expressed genes”, which are expressed in all or most tissues but with differential expression levels. In this study, we applied machine learning algorithms to build a computational method for identifying “quantitatively tissue-specific expressed genes” capable of distinguishing 25 human tissues from their expression patterns. Our results uncovered the expression of 432 genes as optimal features for tissue classification, which were obtained with a Matthews Correlation Coefficient (MCC) of more than 0.99 yielded by a support vector machine (SVM). This constructed model was superior to the SVM model using tissue enriched genes and yielded MCC of 0.985 on an independent test dataset, indicating its good generalization ability. These 432 genes were proven to be widely expressed in multiple tissues and a literature review of the top 23 genes found that most of them support their discriminating powers. As a complement to previous studies, our discovery of these quantitatively tissue-specific genes provides insights into the detailed understanding of tissue development and function.

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Intestinal microbiota during early life – impact on health and disease

Proceedings of The Nutrition Society ◽

10.1017/s0029665114000627 ◽

2014 ◽

Vol 73 (4) ◽

pp. 457-469 ◽

Cited By ~ 29

Author(s):

Lotta Nylund ◽

Reetta Satokari ◽

Seppo Salminen ◽

Willem M. de Vos

Keyword(s):

Intestinal Microbiota ◽

Early Life ◽

Later Life ◽

Related Factors ◽

Life Impact ◽

Health And Disease ◽

And Function ◽

The Impact

In the first years after birth, the intestinal microbiota develops rapidly both in diversity and complexity while being relatively stable in healthy adults. Different life-style-related factors as well as medical practices have an influence on the early-life intestinal colonisation. We address the impact of some of these factors on the consecutive microbiota development and later health. An overview is presented of the microbial colonisation steps and the role of the host in that process. Moreover, new early biomarkers are discussed with examples that include the association of microbiota and atopic diseases, the correlation of colic and early development and the impact of the use of antibiotics in early life. Our understanding of the development and function of the intestinal microbiota is constantly improving but the long-term influence of early-life microbiota on later life health deserves careful clinical studies.

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The role of early life nutrition in programming of reproductive function

Journal of Developmental Origins of Health and Disease ◽

10.1017/s204017441300038x ◽

2013 ◽

Vol 5 (1) ◽

pp. 2-15 ◽

Cited By ~ 16

Author(s):

S. Chadio ◽

B. Kotsampasi

Keyword(s):

Early Life ◽

Reproductive Function ◽

Later Life ◽

Research Area ◽

Obesity Epidemic ◽

Specific Effects ◽

Stage Of Development ◽

Underlying Mechanisms ◽

Epigenetic Modulation ◽

And Function

Accumulating evidence suggest that the concept of programming can also be applied to reproductive development and function, representing an ever expanding research area. Recently issues such as peri- or even preconceptional nutrition, transgenerational effects and underlying mechanisms have received considerable attention. The present chapter presents the existed evidence and reviews the available data from numerous animal and human studies on the effects of early life nutritional environment on adult reproductive function. Specific outcomes depend on the severity, duration and stage of development when nutritional perturbations are imposed, while sex-specific effects are also manifested. Apart from undernutrition, effects of relative overnutrition as well as the complex interactions between pre- and postnatal nutrition is of high importance, especially in the context of our days obesity epidemic. Mechanisms underlying reproductive programming are yet unclear, but may include a role for epigenetic modifications. Epigenetic modulation of critical genes involved in the control of reproductive function and potential intergenerational effects represent an exciting area of interdisciplinary research toward the development of new nutritional approaches during pre- and postnatal periods to ensure reproductive health in later life.

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A cohort of Indigenous Australian women and their children through pregnancy and beyond: the Gomeroi gaaynggal study

Journal of Developmental Origins of Health and Disease ◽

10.1017/s204017441600009x ◽

2016 ◽

Vol 7 (4) ◽

pp. 357-368 ◽

Cited By ~ 11

Author(s):

A. M. Ashman ◽

C. E. Collins ◽

L. Weatherall ◽

L. J. Brown ◽

M. E. Rollo ◽

...

Keyword(s):

Later Life ◽

Indigenous Australians ◽

Indigenous Research ◽

Indigenous Australian ◽

Smoking During Pregnancy ◽

Time Points ◽

South Wales ◽

Pregnancy And Postpartum ◽

Women And Children ◽

And Function

Indigenous Australians have high rates of chronic diseases, the causes of which are complex and include social and environmental determinants. Early experiences in utero may also predispose to later-life disease development. The Gomeroi gaaynggal study was established to explore intrauterine origins of renal disease, diabetes and growth in order to inform the development of health programmes for Indigenous Australian women and children. Pregnant women are recruited from antenatal clinics in Tamworth, Newcastle and Walgett, New South Wales, Australia, by Indigenous research assistants. Measures are collected at three time points in pregnancy and from women and their children at up to eight time points in the child’s first 5 years. Measures of fetal renal development and function include ultrasound and biochemical biomarkers. Dietary intake, infant feeding and anthropometric measurements are collected. Standardized procedures and validated tools are used where available. Since 2010 the study has recruited over 230 women, and retained 66 postpartum. Recruitment is ongoing, and Gomeroi gaaynggal is currently the largest Indigenous pregnancy-through-early-childhood cohort internationally. Baseline median gestational age was 39.1 weeks (31.5–43.2, n=110), median birth weight was 3180 g (910–5430 g, n=110). Over one third (39.3%) of infants were admitted to special care or neonatal nursery. Nearly half of mothers (47.5%) reported tobacco smoking during pregnancy. Results of the study will contribute to knowledge about origins of chronic disease in Indigenous Australians and nutrition and growth of women and their offspring during pregnancy and postpartum. Study strengths include employment and capacity-building of Indigenous staff and the complementary ArtsHealth programme.

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