Article
Biochemistry & Molecular Biology
Kaining Chen, Congying Chen, Huihui Li, Jiaqi Yang, Mengqing Xiang, Hongwei Wang, Zhi Xie
Summary: The study reveals pervasive translational regulation during retinal development with dynamic changes at the translational level in a developmental stage-specific manner. It also identifies genes whose translational efficiencies are frequently controlled by changes in upstream open reading frame, enriching functions highly important to neurons. Additionally, hundreds of previously uncharacterized micropeptides translated from putative long non-coding RNAs and circular RNAs are discovered, showing potentials in regulating retinal development.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Endocrinology & Metabolism
Florian Le Billan, Gloria Umogbai, Carolyn L. Cummins
Summary: Steroid hormones not only regulate gene transcription but also modulate the alternative splicing of pre-mRNA, acting through binding to nuclear receptors. The effect of steroid hormones on alternative splicing is time-, gene-, and tissue-specific. Mechanisms by which steroid hormones regulate alternative splicing include the recruitment of dual-function proteins, transcriptional regulation of splicing factor levels, alternative splicing of splicing factors or transcription factors, and regulation of elongation rate.
Article
Immunology
Aaron J. Wilk, Madeline J. Lee, Bei Wei, Benjamin Parks, Ruoxi Pi, Giovanny J. Martinez-Colon, Thanmayi Ranganath, Nancy Q. Zhao, Shalina Taylor, Winston Becker, David Jimenez-Morales, Andra L. Blomkalns, Ruth O'Hara, Euan A. Ashley, Kari C. Nadeau, Samuel Yang, Susan Holmes, Marlene Rabinovitch, Angela J. Rogers, William J. Greenleaf, Catherine A. Blish
Summary: The study revealed immune system dysfunctions in COVID-19 patients at different disease severity stages, particularly in severe and fatal cases. It also found a lack of pro-inflammatory cytokine production in severe cases, potentially due to chromatin accessibility changes as a mechanism.
JOURNAL OF EXPERIMENTAL MEDICINE
(2021)
Article
Developmental Biology
Jordan E. Hamden, Katherine M. Gray, Melody Salehzadeh, George V. Kachkovski, Brandon J. Forys, Chunqi Ma, Suzanne H. Austin, Kiran K. Soma
Summary: The study revealed region-specific patterns of corticosterone levels across development in mice, with higher levels in certain brain regions at early stages. Interestingly, local brain corticosterone levels were not positively correlated with blood levels, and correlations across brain regions increased with age. The data suggest that individual brain regions fine-tune local levels of corticosterone during early development, and coupling of glucocorticoid levels across regions increases with age.
DEVELOPMENTAL NEUROBIOLOGY
(2021)
Article
Plant Sciences
Yin Xin, Wenqiang Pan, Xi Chen, Yixin Liu, Mingfang Zhang, Xuqing Chen, Fengping Yang, Jingru Li, Jian Wu, Yunpeng Du, Xiuhai Zhang
Summary: The study identified potential genes and pathways involved in tepal trichome development in a natural lily mutant, which sheds light on the biological function of trichome. Transcriptome analysis of the mutant and validation in other lily species revealed insights into the developmental mechanism of trichome.
PLANT CELL REPORTS
(2021)
Article
Multidisciplinary Sciences
Lukas M. von Ziegler, Amalia Floriou-Servou, Rebecca Waag, Rebecca R. Das Gupta, Oliver Sturman, Katharina Gapp, Christina A. Maat, Tobias Kockmann, Han-Yu Lin, Sian N. Duss, Mattia Privitera, Laura Hinte, Ferdinand von Meyenn, Hanns U. Zeilhofer, Pierre-Luc Germain, Johannes Bohacek
Summary: This study investigates the molecular events in the mouse hippocampus induced by acute stress through the use of swim exposure. The results reveal the complexity and specificity of the acute stress response, highlighting changes in protein phosphorylation, gene transcription, and protein translation. These molecular events efficiently resolve within four hours after stress initiation.
NATURE COMMUNICATIONS
(2022)
Article
Endocrinology & Metabolism
Hannah Collden, Maria E. Nilsson, Anna-Karin Norlen, Andreas Landin, Sara H. Windahl, Jianyao Wu, Karin L. Gustafsson, Matti Poutanen, Henrik Ryberg, Liesbeth Vandenput, Claes Ohlsson
Summary: This study established a comprehensive atlas of sex hormone concentrations in tissues and serum of male mice, revealing the distribution characteristics of sex hormones. Brain sex hormone levels are well correlated with serum levels, and white adipose tissue serves as a major reservoir of sex hormones in mice. Progesterone is the most abundant sex hormone in castrated mice.
Article
Plant Sciences
Edith Garot, Stephane Dussert, Frederic Domergue, Thierry Joet, Isabelle Fock-Bastide, Marie-Christine Combes, Philippe Lashermes
Summary: This study combines different methods to investigate leaf adaptive traits in Coffea mauritiana and suggests that cuticular wax composition and genes associated with cell wall remodeling may play key roles in the local adaptation processes of this forest tree. The findings provide new insights into the adaptation of non-model species and highlight the importance of cuticle composition for trees to adapt to high evaporative demand in warm climates.
PLANT AND CELL PHYSIOLOGY
(2021)
Article
Cell Biology
Deena Iskander, Guanlin Wang, Elisabeth F. Heuston, Chrysi Christodoulidou, Bethan Psaila, Kanagaraju Ponnusamy, Hongwei Ren, Zeinab Mokhtari, Mark Robinson, Aristeidis Chaidos, Pritesh Trivedi, Nikolaos Trasanidis, Alexia Katsarou, Richard Szydlo, Carmen G. Palii, Mehmood H. Zaidi, Qais Al-Oqaily, Valentina S. Caputo, Anindita Roy, Yvonne Harrington, Leena Karnik, Kikkeri Naresh, Adam J. Mead, Supat Thongjuea, Marjorie Brand, Josu de la Fuente, David M. Bodine, Irene Roberts, Anastasios Karadimitris
Summary: The study investigates how mutations in ribosomal protein genes affect erythroid progenitor development in Diamond-Blackfan anemia, with RPS-DBA showing erythroid differentiation arrest and RPL-DBA exhibiting relatively preserved abnormal erythroid progenitors and precursors. The findings suggest distinct mechanisms of erythroid failure and phenotype-genotype correlations in DBA, which may aid in identifying therapeutic targets.
SCIENCE TRANSLATIONAL MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Mu-En Chen, Mong-Hsun Tsai, Hsiang-Ting Huang, Ching-Chu Tsai, Mei-Ju Chen, Da-Syuan Yang, Teng-Zhi Yang, John Wang, Rong-Nan Huang
Summary: This study focused on the egg transcriptome of Forcipomyia taiwana, a biting midge, revealing that the down-regulation of key genes laccase2 and DCE/yellow in the melanin synthesis pathway may be responsible for the NaCl-induced inhibition of egg melanization.
Article
Biochemistry & Molecular Biology
Taavi Pall, Hannes Luidalepp, Tanel Tenson, Ulo Maivali
Summary: We evaluated the quality of inferential statistics in the field of differential expression profiling using high-throughput sequencing (HT-seq) by analyzing datasets submitted to the NCBI GEO data repository from 2008 to 2020. Our findings indicate widespread bias and unreliability of statistical methods used to analyze HT-seq data. Only a small percentage of experiments resulted in expected p-value distributions, and many experiments showed indications of differential expression despite assumptions that most genes are not differentially expressed. The choice of differential expression analysis program also influenced the observed patterns.
Article
Biochemistry & Molecular Biology
Dongbo Shi, Virginie Jouannet, Javier Agusti, Verena Kaul, Victor Levitsky, Pablo Sanchez, Victoria V. Mironova, Thomas Greb
Summary: The study presents gene expression profiles of distinct tissues in the mature inflorescence stem of Arabidopsis thaliana using advanced techniques like fluorescence-activated nucleus sorting and RNA sequencing. They identified over 15,000 genes with differential expression in different stem tissues, revealing tissue-specific cellular signatures and potential transcriptional regulators. The datasets generated in this study provide insights into the spatial organization of physiological processes in plants at a high resolution.
Article
Endocrinology & Metabolism
S. Khan, D. E. W. Livingstone, A. Zielinska, C. L. Doig, D. F. Cobice, C. L. Esteves, J. T. Y. Man, N. Z. M. Homer, J. R. Seckl, C. L. Mackay, S. P. Webster, G. G. Lavery, K. E. Chapman, B. R. Walker, R. Andrew
Summary: 11 beta-Hydroxysteroid dehydrogenase 1 (11 beta HSD1) is an important drug target for reducing the adverse effects of excessive glucocorticoids. This study investigated the contribution of 11 beta HSD1 in liver and adipose tissue to circulating glucocorticoid levels. The results showed that adipose tissue plays a greater role in the circulating pool of glucocorticoids compared to the liver.
JOURNAL OF ENDOCRINOLOGY
(2023)
Article
Genetics & Heredity
Yiqing Yang, Yuanyuan Zhou, Xuan Li, Yinlin He, Yinshan Bai, Bingyun Wang, Shengfeng Chen, Canying Liu
Summary: This study comprehensively explored the effects of PG1 on porcine GCs using transcriptome profiling. The results revealed that PG1 regulates several genes associated with GC function and ovarian follicle development. GO and KEGG pathway analyses identified genes related to the immune system, infectious disease, and signaling pathways. Additionally, PPI analysis uncovered DEGs involved in cytokine-cytokine receptor interaction, neuroactive ligand-receptor interaction, and chemokine signaling pathway. This study expanded our understanding of the role of PG1 in immune defense and mammalian ovarian follicular development.
Article
Plant Sciences
Xinqiao Zhan, Yingpeng Tong
Summary: In this study, comparative transcriptome analyses revealed significant enrichment of terpenoid biosynthesis and cytochrome P450 pathways in Sinocalycanthus chinensis. Phylogenetic analysis showed high sequence similarity of terpene synthases between S. chinensis and Arabidopsis, classified into three subfamilies. Most phytohormone pathway-related genes were upregulated in flowers and downregulated in leaves.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Urology & Nephrology
Ethan D. Grober, Yonah Krakowsky, Mohit Khera, Daniel T. Holmes, Jay C. Lee, John E. Grantmyre, Premal Patel, Richard A. Bebb, Ryan Fitzpatrick, Jeffrey D. Campbell, Serge Carrier, Abraham Morgentaler
CUAJ-CANADIAN UROLOGICAL ASSOCIATION JOURNAL
(2021)
Letter
Medicine, General & Internal
Gregory A. Kline, Christopher J. Symonds, Daniel T. Holmes
CANADIAN MEDICAL ASSOCIATION JOURNAL
(2021)
Article
Endocrinology & Metabolism
Melody Salehzadeh, Jordan E. Hamden, Michael X. Li, Hitasha Bajaj, Ruolan S. Wu, Kiran K. Soma
Summary: This study assessed the effects of lipopolysaccharide (LPS) on lymphoid levels of progesterone and glucocorticoids (GCs), as well as the expression of steroidogenic enzymes and key components of the hypothalamic-pituitary-adrenal (HPA) axis. The results showed that LPS had different effects on steroid levels in lymphoid organs and blood at different developmental stages. LPS predominantly affected steroidogenic enzyme expression in the spleen, and also had an impact on the expression of HPA axis components in lymphoid organs.
Article
Biochemistry & Molecular Biology
Yuying Lin, Iulia Darolti, Benjamin L. S. Furman, Pedro Almeida, Benjamin A. Sandkam, Felix Breden, Alison E. Wright, Judith E. Mank
Summary: Differences in allele frequencies between sexual and autosomal genes can be caused by sexual conflict or sequence similarity. Through studying the guppy genome, it was found that only a few genes show evidence of sexual conflict, suggesting that the Y chromosome may accumulate genes with male-specific functions.
Article
Ecology
Rebecca C. Fuller, Katie E. McGhee, Benjamin Sandkam, Matthew Schrader, Joseph Travis
Summary: Research on color variation in male bluefin killifish showed that color variations are mainly attributed to two axes: a red-yellow axis and a blue axis, controlled by genetics and phenotypic plasticity; plasticity variations among populations suggest adaptiveness in some but not in others; plasticity variations among sires in the swamp population indicate balancing selection may be acting on both the red-yellow polymorphism and plasticity for blue coloration.
Article
Endocrinology & Metabolism
Ryan J. Tomm, Desiree R. Seib, George Kachkovski, Helen R. Schweitzer, Daniel J. Tobiansky, Stan B. Floresco, Kiran K. Soma
Summary: The study found that neurally-produced androgens modulate behavioral flexibility through modification of dopamine signaling, which in turn affects executive functions.
JOURNAL OF NEUROENDOCRINOLOGY
(2022)
Article
Endocrinology & Metabolism
Jordan E. Hamden, Katherine M. Gray, Melody Salehzadeh, Kiran K. Soma
Summary: The profound programming effects of early life stress on brain and behavior are mediated by adrenal glucocorticoids. This study reveals the rapid and profound changes in stress physiology during neonatal development, suggesting that neurosteroid production may be a mechanism by which early life stress has enduring effects on brain and behavior.
JOURNAL OF ENDOCRINOLOGY
(2022)
Article
Behavioral Sciences
Brittney Russell, Wendy K. Adams, Kelly M. Hrelja, Fiona D. Zeeb, Matthew D. Taves, Sukhbir Kaur, Kiran K. Soma, Catharine A. Winstanley
Summary: Social isolation is a known risk factor for mental illness and impaired immune function. Research shows that neuroinflammatory processes may contribute to mental illness through cytokine-induced neural activity modulation. The study examined the effects of LPS administration and social home cage environment on cognitive performance and corticosterone and cytokine levels in rats. The results suggest that social isolation and LPS administration can both affect cognitive performance and hormone levels in rats.
BEHAVIOURAL BRAIN RESEARCH
(2022)
Article
Marine & Freshwater Biology
Sri Pratima Nandamuri, Jane E. Schulte, Miranda R. Yourick, Benjamin A. Sandkam, Kristen A. Behrens, Melissa M. Schreiner, Maya Dayanim, Garrett Sweatt, Matthew A. Conte, Scott A. Juntti, Karen L. Carleton
Summary: African cichlids are ideal for studying genes responsible for mate choice and species divergence. By studying these fishes, researchers have identified quantitative trait loci and candidate genes that influence cone opsin expression. However, experimental results on the effect of the MITFA gene on opsin expression contradict expectations.
Review
Immunology
Matthew D. Taves, Jonathan D. Ashwell
Summary: Sex steroid hormones have significant effects on the thymus, causing thymic atrophy. Thymic epithelial cells (TEC), which are highly responsive to sex steroids, play a crucial role. Endogenous steroids have remarkable programming effects on the synthesis of T cell receptor (TCR) repertoire through TEC.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medical Laboratory Technology
Gregory A. Kline, Daniel T. Holmes
Summary: Bone turnover markers (BTM) are important for understanding the effect of anti-resorptives on osteoclast activity. Post-hoc trial data suggests that a 40% reduction in BTM may represent an appropriate response to therapy. However, applying this target threshold in individual patients is problematic due to measurement uncertainty and natural variation.
CLINICAL BIOCHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Iulia Darolti, Lydia J. M. Fong, Benjamin A. Sandkam, David C. H. Metzger, Judith E. Mank
Summary: By analyzing sequence divergence and polymorphism data across multiple poeciliid fish species, this study investigates the relationship between X chromosome evolution and hemizygosity, revealing the causes for Fast-X effects. The results show that the rate of X chromosome evolution is higher than autosomes in species with high levels of X hemizygosity in males, indicating Fast-X evolution. However, in species with lower levels of X hemizygosity and homomorphic sex chromosomes, there is no change in the rate of X-linked evolution. The study also tests the time of origin of the sex chromosomes in this clade.
Article
Behavioral Sciences
Desiree R. Seib, Daniel J. Tobiansky, John Meitzen, Stan B. Floresco, Kiran K. Soma
Summary: The review summarizes the evidence that cells in the mesocorticolimbic system produce neurosteroids and express steroid receptors, focusing on neuroandrogens and neuroestrogens and their effects on dopamine signaling and executive functions in the system.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2023)
Article
Multidisciplinary Sciences
Lucia Zubizarreta, Cecilia Jalabert, Ana C. Silva, Kiran K. Soma, Laura Quintana
Summary: Steroids play a crucial role in modulating brain and behavior. The brain itself produces neurosteroids. Non-breeding aggression in weakly electric fish depends on estrogen signaling, which is detectable in the brain.
Article
Medical Laboratory Technology
Daniel T. Holmes, Mahdi Mobini, Christopher R. McCudden
Summary: With the development of mature open-source tools in multiple language paradigms, including R and RMarkdown, a completely reproducible manuscript preparation pipeline has been described. This process allows for submission-ready PDF and JMSACL-compatible LaTeX code to be generated, improving research transparency and reproducibility.
JOURNAL OF MASS SPECTROMETRY AND ADVANCES IN THE CLINICAL LAB
(2021)