Review
Plant Sciences
Elena Zemlyanskaya, Vladislav A. Dolgikh, Victor G. Levitsky, Victoria Mironova
Summary: Innovative omics technologies, advanced bioinformatics, and machine learning methods are rapidly becoming integral tools for plant functional genomics, with recent comprehensive studies and accumulating omics data bringing plant biologists into the big leagues.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Review
Biochemical Research Methods
Mattia Furlan, Stefano de Pretis, Mattia Pelizzola
Summary: Despite RNA abundance being commonly assumed as a proxy for transcriptional activity, it is now possible to calculate how synthesis, processing, and degradation rates collectively determine the abundance of each gene's RNA. Different transcriptional outputs can correspond to different combinations of kinetic rates, indicating the existence of markedly different modes of gene expression regulation and their profound effects on gene self-expression regulation.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biology
Daniel Crespo-Piazuelo, Herve Acloque, Olga Gonzalez-Rodriguez, Mayrone Mongellaz, Marie-Jose Mercat, Marco C. A. M. Bink, Abe E. Huisman, Yuliaxis Ramayo-Caldas, Juan Pablo Sanchez, Maria Ballester
Summary: Genome-wide association studies on pigs have identified millions of significant associations between genetic polymorphisms and the expression of genes in the duodenum, liver, and muscle. These findings shed light on the regulatory variations that shape end-trait phenotypes and provide valuable insights into molecular mechanisms.
Article
Biochemistry & Molecular Biology
Toray S. Akcan, Sergey Vilov, Matthias Heinig
Summary: DNA and RNA-binding trans-acting factors play a crucial role in regulating promoter-proximal RNA polymerase II (Pol II) pausing, which is a rate-limiting step in gene expression. In this study, we developed a machine learning model that accurately predicts the extent of Pol II pausing based on genomic and transcriptomic data, and identified previously unknown regulators of pausing.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Neurosciences
Shuang-Feng Xu, Zhong-Qiu Pang, Yong-Gang Fan, Yan-Hui Zhang, Yu-Han Meng, Chen-Yang Bai, Meng-Yu Jia, Yan-Hong Chen, Zhan-You Wang, Chuang Guo
Summary: There is growing evidence that circulating lactoferrin (Lf) is involved in peripheral cholesterol metabolism disorders. The distribution of Lf changes in astrocytes of aging brains and those with neurodegenerative diseases, but its role is not yet understood.
Review
Cell Biology
Di Wang, Rong Ye, Zhaokui Cai, Yuanchao Xue
Summary: Pervasive transcription of the human genome generates a large amount of noncoding RNAs that play crucial roles in various biological processes. These RNAs interact with different RNA substrates through RNA-RNA interactions (RRIs), which are facilitated by RNA-binding proteins. High-throughput methods have been developed to study RRIs and these efforts have expanded our understanding of gene regulation.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
Article
Endocrinology & Metabolism
Fei Luo, Chao Xing, Sumeet K. Asrani, Shili Li, Guosheng Liang, Helen H. Hobbs, Jonathan C. Cohen
Summary: This study identified a missense variant in the insulin receptor associated with fatty liver disease in a four generation family, but experiments in mice failed to show a causal relationship between this variant and the disease or any impact on hepatic triglyceride metabolism.
MOLECULAR METABOLISM
(2021)
Article
Multidisciplinary Sciences
Rui Zhou, Guodong Wang, Qi Li, Fanxi Meng, Can Liu, Rui Gan, Dapeng Ju, Meimei Liao, Junjie Xu, Di Sang, Xue Gao, Shuang Zhou, Kejia Wu, Quanzhi Sun, Ying Guo, Chongyang Wu, Zhiyu Chen, Lin Chen, Bihan Shi, Haiyan Wang, Xia Wang, Huaiye Li, Tao Cai, Bin Li, Fengchao Wang, Hiromasa Funato, Masashi Yanagisawa, Eric Erquan Zhang, Qinghua Liu
Summary: This study characterizes a major signaling pathway for the transcriptional regulation of sleep in mice, involving the LKB1-SIK3 pathway and phosphorylation of HDAC4/HDAC5. The findings provide insights into the molecular mechanisms that regulate sleep quantity and offer new potential targets for the treatment of sleep disorders.
Article
Plant Sciences
Yu Du, Mei Xi, Yihua Li, Ruifang Zheng, Xiaotian Ding, Xingxing Li, Xiumin Zhang, Li Wang, Jianguo Xing, Bin Hong
Summary: This study investigates the efficiency and mechanisms of tilianin in controlling lipid profile and preventing atherosclerosis. The results show that tilianin improves lipid profiles, reduces LDL-cholesterol levels and decreases atherosclerotic lesions and hepatosteatosis. Additionally, tilianin regulates transcription and enhances the expression of LDLR to lower blood lipid levels.
Article
Biochemistry & Molecular Biology
Pooja Kumari, Lars Harald Thuestad, Rafal Ciosk
Summary: The LIN-41/TRIM71 protein in Caenorhabditis elegans serves as a versatile regulator of mRNA fate, playing different roles in somatic and germline cells. In somatic cells, LIN-41 recognizes specific mRNA sequences and either triggers decay or represses translation. In the germline, LIN-41's targets and regulatory mechanisms are not well understood, but it has been suggested to indirectly control mRNA by interacting with other RNA-binding proteins. This study demonstrates that LIN-41 can directly regulate germline mRNA via specific sequence elements, identifying potential targets and validating one known target involved in chromatin modification.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Noof Aloufi, Aeshah Alluli, David H. Eidelman, Carolyn J. Baglole
Summary: Chronic obstructive pulmonary disease (COPD) is a respiratory disorder characterized by chronic inflammation and emphysema, primarily caused by cigarette smoke. Various cellular processes are altered by cigarette smoke, including post-transcriptional regulation of mRNAs. RNA-binding proteins, microRNAs, and long non-coding RNAs play key roles in regulating RNA biology and may contribute to the pathogenesis of COPD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Qiuqin Ma, Shihui Long, Zhending Gan, Gianluca Tettamanti, Kang Li, Ling Tian
Summary: Autophagy, a widely conserved process in eukaryotes, is regulated by nutrient deprivation, energy stress, and other unfavorable conditions through multiple pathways. It is primarily governed at the RNA and protein levels in a synergistic manner.
Article
Biochemistry & Molecular Biology
Shafaque Zahra, Ajeet Singh, Nikita Poddar, Shailesh Kumar
Summary: The study identified diverse tncRNAs in plants using small RNA-seq samples from six angiosperms, ranging in size from 14 to 50 nucleotides. Codon-dependent generation of tncRNAs suggests specific tRNA cleavage mechanisms, while nucleotide composition analysis indicates precise endoribonucleolytic cleavage. Pathway enrichment analysis shows tncRNA involvement in metabolic and developmental processes, with tissue-specific clusters highlighting their role in plant development and stress resistance.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Microbiology
Laura Piel, K. Shanmugha Rajan, Giovanni Bussotti, Hugo Varet, Rachel Legendre, Caroline Proux, Thibaut Douche, Quentin Giai-Gianetto, Thibault Chaze, Thomas Cokelaer, Barbora Vojtkova, Nadav Gordon-Bar, Tirza Doniger, Smadar Cohen-Chalamish, Praveenkumar Rengaraj, Celine Besse, Anne Boland, Jovana Sadlova, Jean-Francois Deleuze, Mariette Matondo, Ron Unger, Petr Volf, Shulamit Michaeli, Pascale Pescher, Gerald Spath
Summary: Genome instability plays a crucial role in the adaptation and regulation of the protozoan parasite Leishmania, utilizing post-transcriptional and epitranscriptomic regulation to adapt to its host environment.
Article
Endocrinology & Metabolism
David A. Salisbury, David Casero, Zhengyi Zhang, Dan Wang, Jason Kim, Xiaohui Wu, Laurent Vergnes, Aashiq H. Mirza, Paola Leon-Mimila, Kevin J. Williams, Adriana Huertas-Vazquez, Samie R. Jaffrey, Karen Reue, Jianjun Chen, Tamer Sallam
Summary: Salisbury et al. demonstrate that m(6)A modifications play a sex-dependent and dietary-dependent role in regulating hepatic lipid metabolism, triaging lipogenic transcripts for degradation and preventing hepatic triglyceride accumulation. The loss of m(6)A control in male livers under lipid-rich conditions leads to a more 'feminized' hepatic lipid composition, which can be significantly diminished by liver-specific deletion of the m(6)A complex protein Mettl14 in both male and female mice. Additionally, the m(6)A installing machinery is subject to transcriptional control by the sex-responsive BCL6-STAT5 axis in response to dietary conditions, providing insights into the molecular basis for sex-specific differences in hepatic lipid traits.
Article
Veterinary Sciences
Jessica K. Suagee, Rebecca K. Splan, Kelcey L. Swyers, Raymond J. Geor, Benjamin A. Corl
JOURNAL OF EQUINE VETERINARY SCIENCE
(2015)
Article
Biochemistry & Molecular Biology
Cristina Caldari-Torres, Michael L. McGilliard, Benjamin A. Corl
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY
(2016)
Article
Agriculture, Dairy & Animal Science
Y. Yang, G. Ferreira, C. L. Teets, B. A. Corl, W. E. Thomason, C. A. Griffey
JOURNAL OF DAIRY SCIENCE
(2017)
Article
Agriculture, Dairy & Animal Science
Y. Yang, G. Ferreira, C. L. Teets, B. A. Corl, W. E. Thomason, C. A. Griffey
JOURNAL OF DAIRY SCIENCE
(2018)
Article
Agriculture, Dairy & Animal Science
Y. Yang, G. Ferreira, B. A. Corl, B. T. Campbell
JOURNAL OF DAIRY SCIENCE
(2019)
Article
Biotechnology & Applied Microbiology
Kayla Carey, Junghyun Ryu, Kyungjun Uh, Andrea J. Lengi, Sherrie Clark-Deener, Benjamin A. Corl, Kiho Lee
Article
Nutrition & Dietetics
D. E. Rico, J. E. Parales, B. A. Corl, A. Lengi, P. Y. Chouinard, R. Gervais
BRITISH JOURNAL OF NUTRITION
(2020)
Article
Agriculture, Dairy & Animal Science
G. Ferreira, L. L. Martin, C. L. Teets, B. A. Corl, S. L. Hines, G. E. Shewmaker, M. E. De Haro-Marti, M. Chahine
Summary: The study aimed to investigate the impact of drought stress on NDF and LIG concentrations, as well as IVDMD and IVNDFD of corn for silage. Drought stress increased NDF concentration, decreased IVDMD and IVNDFD, but had minimal effect on LIG concentration.
ANIMAL FEED SCIENCE AND TECHNOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
H. Taga, M. P. Dallaire, R. Gervais, F. J. Richard, L. Ma, B. A. Corl, P. Y. Chouinard
Summary: The study aimed to characterize lipid raft microdomains in mammary gland tissue and investigate the effects of dietary fatty acids on lipid raft markers in mammary cells, as well as their relationships with lactation performance in dairy cows. The results indicated a positive relationship between the abundance of GM-1 and lipid raft markers in DRM fraction with milk yield, protein yield, and lactose yield.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
H. H. Hanling, M. L. McGilliard, B. A. Corl
Summary: Increasing milking frequency can boost milk yield, but different milking intervals did not significantly affect milk component yields. By using uneven milking intervals, labor efficiency can be improved while still optimizing milk production in early-lactation cows.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Liang Chen, Andrea J. Lengi, Benjamin A. Corl
Summary: The conjugated linoleic acid t10,c12 plays a role in regulating SREBP1 activation by delaying Insig1 degradation, leading to reduced transcription of lipogenic genes in bovine mammary epithelial cells.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Andrea J. Lengi, Jacob W. Stewart, Melissa Makris, Michelle L. Rhoads, Benjamin A. Corl
Summary: This study found that heat stress affects the composition and viability of somatic cells in milk, which has implications for milk production and the immunocompetence of dairy cows.
Meeting Abstract
Agriculture, Dairy & Animal Science
J. Suagee-Bedore, S. Hebrock, B. Corl, A. Lengi, O. Sundin, K. Cole, M. Worth
JOURNAL OF ANIMAL SCIENCE
(2018)
Proceedings Paper
Agriculture, Dairy & Animal Science
L. Chen, B. Corl
TRI-STATE DAIRY NUTRITION CONFERENCE, 2016
(2016)
Meeting Abstract
Agriculture, Dairy & Animal Science
H. Hanling, M. McGilliard, B. Corl
JOURNAL OF DAIRY SCIENCE
(2019)