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Genes Genomics 2021 Apr 10. Epub 2021 Apr 10.

Department of Biological Sciences, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.

Background: In Arabidopsis thaliana (Arabidopsis), clade IIb lateral organ boundary domain (LBD) 37, 38, and 39 proteins negatively regulate anthocyanin biosynthesis and affect nitrogen responses.

Objective: To investigate the possible role of LBD genes in anthocyanin accumulations among green and purple cabbages (Brassica oleracea var. capitata), we determined sequence variations and expression levels of cabbage homologs of Arabidopsis LBD37, 38, and 39. Read More

Insects 2021 Feb 18;12(2). Epub 2021 Feb 18.

Semiochemicals Laboratory, Embrapa Genetic Resources and Biotechnology, Brasília 70770-917, Brazil.

Stink bugs are major pests in diverse crops around the world. Pest management strategies based on insect behavioral manipulation could help to develop biorational management strategies of stink bugs. Insect mating disruption using vibratory signals is an approach with high potential for pest management. Read More

Nat Commun 2021 02 8;12(1):874. Epub 2021 Feb 8.

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Base-pairing interactions mediate many intermolecular target recognition events. Even a single base-pair mismatch can cause a substantial difference in activity but how such changes influence the target search kinetics in vivo is unknown. Here, we use high-throughput sequencing and quantitative super-resolution imaging to probe the mutants of bacterial small RNA, SgrS, and their regulation of ptsG mRNA target. Read More

Cell Syst 2021 Mar 19;12(3):263-271.e4. Epub 2021 Jan 19.

Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Electronic address:

Neuronal loss can considerably diminish neural circuit function, impairing normal behavior by disrupting information flow in the circuit. Here, we use genetically engineered electrical synapses to reroute the flow of information in a C. elegans damaged chemosensory circuit in order to restore organism behavior. Read More

Mol Genet Genomic Med 2021 Jan 20:e1604. Epub 2021 Jan 20.

Department of Medical Genetics, National Health Commission Key Laboratory of Birth Defects Research, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China.

Background: Split hand/foot malformation (SHFM) is a congenital limb developmental disorder, which impairs the fine activities of hand/foot in the affected individuals seriously. SHFM is commonly inherited as an autosomal dominant disease with incomplete penetrance. Chromosomal aberrations such as copy number variations and translocations have been linked to SHFM. Read More

mSphere 2021 01 6;6(1). Epub 2021 Jan 6.

Department of BioSciences, Rice University, Houston, Texas, USA

Traditionally, treatments for bacterial infection have focused on killing the microbe or preventing its growth. As antimicrobial resistance becomes more ubiquitous, the feasibility of this approach is beginning to wane and attention has begun to shift toward disrupting the host-pathogen interaction by improving the host defense. Using a high-throughput, fragment-based screen to identify compounds that alleviate -mediated killing of , we identified over 20 compounds that stimulated host defense gene expression. Read More

BMC Bioinformatics 2021 Jan 6;22(1). Epub 2021 Jan 6.

Structural Bioinformatics Lab, Department of Experimental and Health Science, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain.

Background: Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein-protein interaction (PPI) structures. In previous works we decomposed the statistical potentials in different terms, named Split-Statistical Potentials, accounting for the type of amino acid pairs, their hydrophobicity, solvent accessibility and type of secondary structure. These potentials have been successfully used to identify near-native structures in protein structure prediction, rank protein docking poses, and predict PPI binding affinities. Read More

J Mol Diagn 2021 Mar 29;23(3):358-371. Epub 2020 Dec 29.

Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Centre for Cancer Research, Victorian Comprehensive Cancer Centre, The University of Melbourne, Parkville, Victoria, Australia; Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia. Electronic address:

Patients in whom mismatch repair (MMR)-deficient cancer develops in the absence of pathogenic variants of germline MMR genes or somatic hypermethylation of the MLH1 gene promoter are classified as having suspected Lynch syndrome (SLS). Germline whole-genome sequencing (WGS) and targeted and genome-wide tumor sequencing were applied to identify the underlying cause of tumor MMR deficiency in SLS. Germline WGS was performed on samples from 14 cancer-affected patients with SLS, including two sets of first-degree relatives. Read More

Am J Med Genet A 2021 02 13;185(2):544-548. Epub 2020 Nov 13.

Division of Newborn Medicine, Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, Saint Louis Children's Hospital, Saint Louis, Missouri, USA.

Chromodomain helicase DNA-binding protein 7 (CHD7) pathogenic variants are identified in more than 90% of infants and children with CHARGE (Coloboma of the iris, retina, and/or optic disk; congenital Heart defects, choanal Atresia, Retardation of growth and development, Genital hypoplasia, and characteristic outer and inner Ear anomalies and deafness) syndrome. Approximately, 10% of cases have no known genetic cause identified. We report a male child with clinical features of CHARGE syndrome and nondiagnostic genetic testing that included chromosomal microarray, CHD7 sequencing and deletion/duplication analysis, SEMA3E sequencing, and trio exome and whole-genome sequencing (WGS). Read More

J Exp Clin Cancer Res 2020 Oct 21;39(1):222. Epub 2020 Oct 21.

Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.

Background: Radioresistance is the major obstacle in radiation therapy (RT) for hepatocellular carcinoma (HCC). Dysregulation of DNA damage response (DDR), which includes DNA repair and cell cycle checkpoints activation, leads to radioresistance and limits radiotherapy efficacy in HCC patients. However, the underlying mechanism have not been clearly understood. Read More

Commun Biol 2020 Sep 30;3(1):540. Epub 2020 Sep 30.

Department of Entomology, University of Maryland, Collage Park, MD, USA.

Regulatory genes are often multifunctional and constrained, which results in evolutionary conservation. It is difficult to understand how a regulatory gene could be lost from one species' genome when it is essential for viability in closely related species. The gene paired is a classic Drosophila pair-rule gene, required for formation of alternate body segments in diverse insect species. Read More

Malar J 2020 Sep 21;19(1):342. Epub 2020 Sep 21.

Department of Parasitology, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo 8, Sri Lanka.

Background: Sri Lanka was certified as a malaria-free nation in 2016; however, imported malaria cases continue to be reported. Evidence-based information on the genetic structure/diversity of the parasite populations is useful to understand the population history, assess the trends in transmission patterns, as well as to predict threatening phenotypes that may be introduced and spread in parasite populations disrupting elimination programmes. This study used a previously developed Plasmodium vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics of P. Read More

Data Brief 2020 Oct 25;32:106218. Epub 2020 Aug 25.

RCMI Center for Environmental Health, Jackson State University, Jackson, MS 39217, USA.

The datasets of this article present the experimental parameters resulting from the synthesis and characterization of graphene oxide (GO) using scanning and transmission electron microscopy (SEM, TEM) and spectrophotometric (FTIR, AFM, EDX) methods, and the assessment of its toxicological and endocrine-disrupting effects on the Japanese medaka fish by acute toxicity testing, and histopathological evaluations. These datasets support the article "Reproductive and Developmental Effects of Graphene Oxide on Japanese Medaka ()". GO synthesis was performed following the modified Hummer's method. Read More

Stress 2020 Aug 31:1-12. Epub 2020 Aug 31.

Department of Psychology, Northern Illinois University, DeKalb, IL, USA.

Social support from a spouse, long-term partner, or someone who provides emotional or instrumental support may protect against consequences of aging, including mediating behavioral stress reactivity and altering neurobiological process that underlie short-term stress responses. Therefore, long-term social bonding may have behavioral and neurobiological benefits. The socially monogamous prairie vole provides a valuable experimental model for investigating the benefits of long-term social bonds on short-term stress reactivity in aging animals, given their unique social structure of forming enduring opposite-sex bonds, living in family groups, and bi-parental rearing strategies. Read More

bioRxiv 2020 Aug 14. Epub 2020 Aug 14.

Background: SARS-coronavirus 2 (SARS-CoV-2) is currently causing a worldwide pandemic. Potential drugs identified for the treatment of SARS-CoV-2 infection include chloroquine (CQ), its derivative hydroxychloroquine (HCQ), and the anesthetic propofol. Their mechanism of action in SARS-CoV-2 infection is poorly understood. Read More

Cancer Res 2020 10 10;80(19):4114-4128. Epub 2020 Jul 10.

Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, China.

Copy number gain in chromosome 8q21 is frequently detected in breast cancer, yet the oncogenic potential underlying this amplicon in breast carcinogenesis remains to be delineated. We report here that ZNF704, a gene mapped to 8q21, is recurrently amplified in various malignancies including breast cancer. ZNF704 acted as a transcriptional repressor and interacted with the transcriptional corepressor SIN3A complex. Read More

Chemosphere 2020 Nov 22;259:127221. Epub 2020 Jun 22.

RCMI Center for Environmental Health, Jackson State University, Jackson, MS, 39217, USA. Electronic address:

Due to its unique properties, graphene oxide (GO) has potential for biomedical and electronic applications, however environmental contamination including aquatic ecosystem is inevitable. Moreover, potential risks of GO in aquatic life are inadequately explored. Present study was designed to evaluate GO as an endocrine disrupting chemical (EDC) using the model Japanese medaka (Oryzias latipes). Read More

Proc Natl Acad Sci U S A 2020 07 29;117(28):16333-16338. Epub 2020 Jun 29.

Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322;

Bacterial transfer RNAs (tRNAs) contain evolutionarily conserved sequences and modifications that ensure uniform binding to the ribosome and optimal translational accuracy despite differences in their aminoacyl attachments and anticodon nucleotide sequences. In the tRNA anticodon stem-loop, the anticodon sequence is correlated with a base pair in the anticodon loop (nucleotides 32 and 38) to tune the binding of each tRNA to the decoding center in the ribosome. Disruption of this correlation renders the ribosome unable to distinguish correct from incorrect tRNAs. Read More

PLoS One 2020 9;15(6):e0234114. Epub 2020 Jun 9.

Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, NV, United States of America.

We previously reported that a single 5 ns high intensity electric pulse (NEP) caused an E-field-dependent decrease in peak inward voltage-gated Na+ current (INa) in isolated bovine adrenal chromaffin cells. This study explored the effects of a pair of 5 ns pulses on INa recorded in the same cell type, and how varying the E-field amplitude and interval between the pulses altered its response. Regardless of the E-field strength (5 to 10 MV/m), twin NEPs having interpulse intervals ≥ than 5 s caused the inhibition of TTX-sensitive INa to approximately double relative to that produced by a single pulse. Read More

Am J Hum Genet 2020 06 28;106(6):846-858. Epub 2020 May 28.

IMIM (Hospital del Mar Research Institute), Barcelona 08003, Spain; Department of Experimental and Health Sciences (CEXS), Universitat Pompeu Fabra, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona 08003, Spain; Women's and Children's Hospital, South Australian Health and Medical Research Institute & University of Adelaide, Adelaide, SA 5005, Australia.

The burden of several common diseases including obesity, diabetes, hypertension, asthma, and depression is increasing in most world populations. However, the mechanisms underlying the numerous epidemiological and genetic correlations among these disorders remain largely unknown. We investigated whether common polymorphic inversions underlie the shared genetic influence of these disorders. Read More

Antioxid Redox Signal 2021 Apr 30;34(12):915-935. Epub 2020 Apr 30.

Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, Nebraska, USA.

T lymphocytes, as part of the adaptive immune system, possess the ability to activate and function in extreme cellular microenvironments, which requires these cells to remain highly malleable. One mechanism in which T lymphocytes achieve this adaptability is by responding to cues from both reactive oxygen and nitrogen species, as well as metabolic flux, which together fine-tune the functional fate of these adaptive immune cells. To date, examinations of the redox and metabolic effects on T lymphocytes have primarily investigated these biological processes as separate entities. Read More

Curr Biol 2020 03 20;30(5):802-814.e8. Epub 2020 Feb 20.

Department of Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Unit 3043, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, 67 North Eagleville Road, Storrs, CT 06269, USA. Electronic address:

Many organisms exhibit visually striking spotted or striped pigmentation patterns. Developmental models predict that such spatial patterns can form when a local autocatalytic feedback loop and a long-range inhibitory feedback loop interact. At its simplest, this self-organizing network only requires one self-activating activator that also activates a repressor, which inhibits the activator and diffuses to neighboring cells. Read More

Mol Genet Genomic Med 2020 04 5;8(4):e1154. Epub 2020 Feb 5.

Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.

Background: Dihydropteridine reductase (DHPR) is one of the key enzymes for maintaining in the organism the supply of tetrahydrobiopterin (BH ), an essential cofactor for aromatic amino acid hydroxylases. Its dysfunction causes the condition of hyperphenylalaninemia together with the lack of neurotransmitters.

Methods: We report a patient with biochemically diagnosed DHPR deficiency, with extensive molecular investigations undertaken to detect variations in quinoid dihydropteridine reductase (QDPR) gene. Read More

J Physiol 2020 03 18;598(6):1169-1186. Epub 2020 Feb 18.

Department of Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, V6T 1Z3 Vancouver, BC, Canada.

Key Points: Mutations in the calmodulin protein (CaM) are associated with arrhythmia syndromes. This study focuses on understanding the structural characteristics of CaM disease mutants and their interactions with the voltage-gated calcium channel Ca 1.2. Read More

BMC Bioinformatics 2019 Dec 12;20(1):666. Epub 2019 Dec 12.

Division of Applied Mathematics, Brown University, Providence, RI, USA.

Background: A pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved that contribute to a directed and efficient folding process, including catalytic proteins and error-detecting chaperones. Among structural RNA molecules we make a distinction between "bound" molecules, which are active as part of ribonucleoprotein (RNP) complexes, and "unbound," with physiological functions performed without necessarily being bound in RNP complexes. Read More

Physiol Plant 2019 Dec 11. Epub 2019 Dec 11.

Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea.

ABCG subfamily proteins are highly enriched in terrestrial plants. Many of these proteins secrete secondary metabolites that repel or inhibit pathogens. To establish why the ABCG subfamily proteins proliferated extensively during evolution, we constructed phylogenetic trees from a broad range of eukaryotic organisms. Read More

Plant Biotechnol J 2020 07 20;18(7):1526-1536. Epub 2019 Dec 20.

Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.

MicroRNAs (miRNAs) are 20-24 nucleotides (nt) small RNAs functioning in eukaryotes. The length and sequence of miRNAs are not only related to the biogenesis of miRNAs but are also important for downstream physiological processes like ta-siRNA production. To investigate these roles, it is informative to create small mutations within mature miRNA sequences. Read More

Neurotoxicol Teratol 2020 May - Jun;79:106840. Epub 2019 Nov 12.

Department of Biological Sciences, NC State University, Raleigh, NC 27695, USA; Center for Human Health and the Environment, NC State University, Raleigh, NC 27695, USA. Electronic address:

The rapidly rising incidence of neurodevelopmental disorders with social deficits is raising concern that developmental exposure to environmental contaminants may be contributory. Firemaster 550 (FM 550) is one of the most prevalent flame-retardant (FR) mixtures used in foam-based furniture and baby products and contains both brominated and organophosphate components. We and others have published evidence of developmental neurotoxicity and sex specific effects of FM 550 on anxiety-like and exploratory behaviors. Read More

J Phys Chem B 2019 12 27;123(49):10505-10513. Epub 2019 Nov 27.

Institut Català d'Investigació Química (ICIQ) , The Barcelona Institute of Science and Technology , Av. Països Catalans, 17 , Tarragona 43007 , Spain.

Molecular dynamics simulations in aqueous solution reveal the existence of two distinct patterns of aggregation in low and high charge density Lindqvist-type polyoxometalates (POMs). Our results indicate the presence of contact and solvent-shared ion pairs and specific and preferential interactions of alkalis with POMs. Highly charged POMs are capable of breaking apart the Li and Cs solvation shell, thus enhancing the formation of long-lived alkali-POM contact ion pairs, where alkalis act as an electrostatic "glue" forming large oligomers. Read More

Biophys J 2020 02 6;118(4):861-872. Epub 2019 Sep 6.

University of Copenhagen, Copenhagen, Denmark. Electronic address:

Despite the sequence homology between acid-sensing ion channels (ASICs) and epithelial sodium channel (ENaCs), these channel families display very different functional characteristics. Whereas ASICs are gated by protons and show a relatively low degree of selectivity for sodium over potassium, ENaCs are constitutively active and display a remarkably high degree of sodium selectivity. To decipher if some of the functional diversity originates from differences within the transmembrane helices (M1 and M2) of both channel families, we turned to a combination of computational and functional interrogations, using statistical coupling analysis and mutational studies on mouse ASIC1a. Read More