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The "guiding" principles of noncoding RNA function.

Wiley Interdiscip Rev RNA 2021 Dec 2:e1704. Epub 2021 Dec 2.

Center for Cardiovascular Genetics, Institute of Molecular Medicine, Houston, Texas, USA.

The human genome is pervasively transcribed and yet only a small fraction of these RNAs (less than 2%) are known to code for proteins. The vast majority of the RNAs are classified as noncoding RNAs (ncRNAs) and are further subgrouped as small (shorter than 200 bases) and long noncoding RNAs. The ncRNAs have been identified in all three domains of life and regulate diverse cellular processes through transcriptional and posttranscriptional gene regulation. Read More

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December 2021

Genome sequencing of the vermicompost strain Stenotrophomonas maltophilia UENF-4GII and population structure analysis of the S. maltophilia Sm3 genogroup.

Microbiol Res 2021 Nov 18;255:126923. Epub 2021 Nov 18.

Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Brazil. Electronic address:

The Stenotrophomonas maltophilia complex (Smc) is a cosmopolitan bacterial group that has been proposed an emergent multidrug-resistant pathogen. Taxonomic studies support the genomic heterogeneity of Smc, which comprises genogroups exhibiting a range of phenotypically distinct strains from different sources. Here, we report the genome sequencing and in-depth analysis of S. Read More

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November 2021

Generation of a DKK2 homozygous knockout human embryonic stem cell line using the CRISPR/Cas9 system.

Stem Cell Res 2021 Nov 24;57:102611. Epub 2021 Nov 24.

State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China; Department of Ophthalmology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China. Electronic address:

Dickkopf-2 (DKK2) is an antagonist of canonical Wnt signaling, which is involved invarious biological processes of development, such as epidermal appendage formation andeye development. To identify underlying effects of DKK2 during embryonic development, we generated a DKK2 homozygous knockout human embryonic stem cell (hESC) line through the CRISPR/Cas9 genome-editing technology. This cell line, which maintains normal stem cell morphology and stably expresses pluripotent markers, could provide an ideal platform for exploring the role of DKK2 in embryonic development. Read More

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November 2021

The freshwater water flea Daphnia magna NIES strain genome as a resource for CRISPR/Cas9 gene targeting: The glutathione S-transferase omega 2 gene.

Aquat Toxicol 2021 Nov 11;242:106021. Epub 2021 Nov 11.

Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea. Electronic address:

The water flea Daphnia magna is a small freshwater planktonic animal in the Cladocera. In this study, we assembled the genome of the D. magna NIES strain, which is widely used for gene targeting but has no reported genome. Read More

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November 2021

p53: A Double-Edged Sword in Tumor Ferroptosis.

Pharmacol Res 2021 Nov 29:106013. Epub 2021 Nov 29.

School of pharmaceutical science and technology, Tianjin University, Tianjin, P.R. China. Electronic address:

Ferroptosis is a type of lipid peroxidation-induced cell death that can be regulated in various ways, from changing the activity of antioxidant enzymes to the levels of transcription factors. The p53 tumor suppressor gene is the "guardian of the genome" and is involved in controlling cell survival and division under various pressures. In addition to its effects on apoptosis, autophagy, and cell cycle, p53, through the way of transcription dependent or independent two-way, also regulates the biological processes of tumor cell sensitivity to ferroptosis, including the metabolism of amino acids, nicotinamide adenine dinucleotide phosphate, and lipid peroxidation, as well as the biosynthesis of glutathione, phospholipids, NADPH and coenzyme Q10. Read More

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November 2021

The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes.

Sci Total Environ 2021 Nov 29:152003. Epub 2021 Nov 29.

Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.

The rise of multiresistant bacterial pathogens is currently one of the most critical threats to global health, encouraging a better understanding of the evolution and spread of antimicrobial resistance. In this regard, the role of the environment as a source of resistance mechanisms remains poorly understood. Moreover, we still know a minimal part of the microbial diversity and resistome present in remote and extreme environments, hosting microbes that evolved to resist harsh conditions and thus a potentially rich source of novel resistance genes. Read More

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November 2021

Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY.

Int J Biol Macromol 2021 Nov 29. Epub 2021 Nov 29.

Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China; Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Center for Excellence in Molecular Cell Science, Shanghai, China. Electronic address:

phiYY is a foremost member of Cystoviridae isolated from Pseudomonas aeruginosa. Its P4 protein with NTPase activity is a molecular motor for their genome packing during viral particle assembly. Previously studies on the P4 from four Pseudomonas phages phi6, phi8, phi12 and phi13 reveal that despite of belonging to the same protein family, they are unique in sequence, structure and biochemical properties. Read More

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November 2021

The expression of ADAMTS14 is regulated by promoter DNA methylation and is associated with poor prognosis in colorectal cancer.

Exp Cell Res 2021 Nov 29:112953. Epub 2021 Nov 29.

Department of Pathology and Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China. Electronic address:

Colorectal cancer (CRC) is one of the most common malignant tumors of digestive system, and its main cause of death is tumor metastasis. The occurrence of CRC is a polygenic and multi-step complex process involving genetic and epigenetic alterations. It has been demonstrated that ADAMTS14 (A disintegrin and metalloproteinase with thrombospondin motifs 14) was hypermethylated in esophageal cancer using whole-genome methylation microarray in our previous report. Read More

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November 2021

Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops.

Cell 2021 Nov 25. Epub 2021 Nov 25.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Genetics, Harvard Medical School, Boston, MA 02114, USA. Electronic address:

Chromosome loops shift dynamically during development, homeostasis, and disease. CCCTC-binding factor (CTCF) is known to anchor loops and construct 3D genomes, but how anchor sites are selected is not yet understood. Here, we unveil Jpx RNA as a determinant of anchor selectivity. Read More

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November 2021

Seeking the truth behind the myth: Argonaute tales from "nuclearland".

Mol Cell 2021 Nov 22. Epub 2021 Nov 22.

Universidad de Buenos Aires (UBA), Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina.

Argonaute proteins have been traditionally characterized as a highly evolutionary conserved family engaged in post-transcriptional gene silencing pathways. The Argonaute family is mainly grouped into the AGO and PIWI clades. The canonical role of Argonaute proteins relies on their ability to bind small-RNAs that recognize complementary sequences on target mRNAs to induce either mRNA degradation or translational repression. Read More

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November 2021

The potential for adverse effects in fish exposed to antidepressants in the aquatic environment.

Environ Sci Technol 2021 Dec 2. Epub 2021 Dec 2.

Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, Devon EX4 4QD, U.K.

Antidepressants are one of the most commonly prescribed pharmaceutical classes for the treatment of psychiatric conditions. They act via modulation of brain monoaminergic signaling systems (predominantly serotonergic, adrenergic, dopaminergic) that show a high degree of structural conservation across diverse animal phyla. A reasonable assumption, therefore, is that exposed fish and other aquatic wildlife may be affected by antidepressants released into the natural environment. Read More

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December 2021

Chloroplast genomes of two Pueraria DC. species: Sequencing, comparative analysis and molecular marker development.

FEBS Open Bio 2021 Dec 2. Epub 2021 Dec 2.

Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China.

Puerariae lobatae radix (Ge-Gen in Chinese) and Puerariae thomsonii radix (Fen-Ge) are widely used as medicine and health products, particularly in Chinese medicine. Puerarin and daidzein are the primary bioactive compounds in Puerariae radix. These isoflavones have been used to treat cardiovascular and cerebrovascular diseases, hypertension, diabetes and osteoporosis. Read More

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December 2021

Membrane composition and organization of Bacillus subtilis 168 and its genome-reduced derivative miniBacillus PG10.

Microb Biotechnol 2021 Dec 1. Epub 2021 Dec 1.

Department of Molecular Genetics, University of Groningen, Groningen, The Netherlands.

A form of lateral membrane compartmentalization in bacteria is represented by functional membrane microdomains (FMMs). FMMs are important for various cellular processes and offer application possibilities in microbial biotechnology. We designed a lipidomics method to directly measure relative abundances of lipids in detergent-resistant and detergent-sensitive membrane fractions of the model bacterium Bacillus subtilis 168 and the biotechnologically attractive miniBacillus PG10 strain. Read More

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December 2021

New insights into genetics underlying of plumage color.

Anim Genet 2021 Dec 1. Epub 2021 Dec 1.

Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, 14115-336, Tehran, Iran.

Plumage color can be considered as a social signal in chickens and a breeding identification tool among breeders. The relationship between plumage color and trait groups of immunity, growth and fertility is still a controversial issue. This research aimed to determine the genome-wide additive and epistatic variants affecting plumage color variation in chickens using the chicken Illumina 60k high-density SNP array. Read More

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December 2021

Sphingosine-1-phosphate promotes tumor development and liver fibrosis in mouse model of congestive hepatopathy.

Hepatology 2021 Dec 2. Epub 2021 Dec 2.

The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan.

Background & Aims: Chronic liver congestion reflecting right-sided heart failure (RHF), Budd-Chiari syndrome, or Fontan-associated liver disease (FALD) is involved in liver fibrosis and hepatocellular carcinoma (HCC). However, molecular mechanisms of fibrosis and HCC in chronic liver congestion remain poorly understood.

Approach & Results: Here, we first demonstrated that chronic liver congestion promoted HCC and metastatic liver tumor growth using murine model of chronic liver congestion by partial inferior vena cava ligation (pIVCL). Read More

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December 2021

Association of Clonal Hematopoiesis with Chronic Obstructive Pulmonary Disease.

Blood 2021 Sep 10. Epub 2021 Sep 10.

University of Virginia, Charlottesville, Virginia, United States.

Chronic obstructive pulmonary disease (COPD) is associated with age and smoking, but other determinants of the disease are incompletely understood. Clonal hematopoiesis of indeterminate potential (CHIP) is a common, age-related state in which somatic mutations in clonal blood populations induce aberrant inflammatory responses. Patients with CHIP have an elevated risk for cardiovascular disease, but the association with COPD remains unclear. Read More

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September 2021

Assessing BRCA1 activity in DNA damage repair using human induced pluripotent stem cells as an approach to assist classification of BRCA1 variants of uncertain significance.

PLoS One 2021 2;16(12):e0260852. Epub 2021 Dec 2.

Department of Medical & Molecular Genetics, King's College London, Faculty of Life Sciences & Medicine, London, United Kingdom.

Establishing a universally applicable protocol to assess the impact of BRCA1 variants of uncertain significance (VUS) expression is a problem which has yet to be resolved despite major progresses have been made. The numerous difficulties which must be overcome include the choices of cellular models and functional assays. We hypothesised that the use of induced pluripotent stem (iPS) cells might facilitate the standardisation of protocols for classification, and could better model the disease process. Read More

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December 2021

Patient health records and whole viral genomes from an early SARS-CoV-2 outbreak in a Quebec hospital reveal features associated with favorable outcomes.

PLoS One 2021 2;16(12):e0260714. Epub 2021 Dec 2.

CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada.

The first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from 31 March to 17 April 2020 in 2 local hospitals to assess viral diversity (unknown at the time in Quebec) and potential associations with clinical outcomes. Read More

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December 2021

Genome wide association study of plant height and tiller number in hulless barley.

PLoS One 2021 2;16(12):e0260723. Epub 2021 Dec 2.

State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.

Hulless barley (Hordeum vulgare L. var. nudum), also called naked barley, is a unique variety of cultivated barley. Read More

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December 2021

Comprehensive analysis of an immune infiltrate-related competitive endogenous RNA network reveals potential prognostic biomarkers for non-small cell lung cancer.

PLoS One 2021 2;16(12):e0260720. Epub 2021 Dec 2.

Department of Oncology, the First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.

Globally, non-small cell lung cancer (NSCLC) is the most common malignancy and its prognosis remains poor because of the lack of reliable early diagnostic biomarkers. The competitive endogenous RNA (ceRNA) network plays an important role in the tumorigenesis and prognosis of NSCLC. Tumor immune microenvironment (TIME) is valuable for predicting the response to immunotherapy and determining the prognosis of NSCLC patients. Read More

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December 2021

High-dose drug heat map analysis for drug safety and efficacy in multi-spheroid brain normal cells and GBM patient-derived cells.

PLoS One 2021 2;16(12):e0251998. Epub 2021 Dec 2.

Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea.

To test the safety and efficacy of drugs via a high does drug heat map, a multi-spheroids array chip was developed by adopting a micropillar and microwell structure. In the chip, patient-derived cells were encapsulated in alginate and grown to maturity for more than 7 days to form cancer multi-spheroids. Multi-spheroids grown in conventional well plates require many cells and are easily damaged as a result of multiple pipetting during maintenance culture or experimental procedures. Read More

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December 2021

The bioinformatics analysis of RIOX2 gene in lung adenocarcinoma and squamous cell carcinoma.

PLoS One 2021 2;16(12):e0259447. Epub 2021 Dec 2.

Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China.

Lung cancer is characterized by high morbidity and mortality rates, and it has become an important public health issue worldwide. The occurrence and development of tumors is a multi-gene and multi-stage complex process. As an oncogene, ribosomal oxygenase 2 (RIOX2) has been associated with a variety of cancers. Read More

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December 2021

Evaluation of the genetic structure of populations from chemically and radioactively polluted areas using microsatellite markers from closely related species.

Int J Radiat Biol 2021 Dec 2:1-20. Epub 2021 Dec 2.

Group of Gene and Genome Mapping, Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Stadt Seeland OT Gatersleben 06466, Germany.

The ecotoxicological and radiobiological effects can be manifested in a decrease in genetic diversity with an increase in toxic and radiation load, in an increase in the frequencies of rare and/or unique (private) alleles in impact samples, and in a decrease in the differentiation of populations within each pollution area. We have selected a collection of primers for , consisting of 21 microsatellite (SSR) loci from , and . The level of toxic load (chemically polluted area) was 4-19 conventional units, and the absorbed dose rate (the Kyshtym accident area) varied from 0. Read More

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December 2021

Lack of variation in nuclear DNA content in avian muscle.

Genome 2021 Dec 2:1-9. Epub 2021 Dec 2.

Department of Biology, Colgate University, Hamilton, NY 13346, USA.

The avian pectoralis muscle demonstrates plasticity with regard to size, so that temperate birds facing winter conditions or birds enduring a migration bout tend to have significant increases in the size and mass of this tissue due to muscular hypertrophy. Myonuclear domain (MND), the volume of cytoplasm a myonuclei services, in the pectoralis muscle of birds seems to be altered during thermal stress or changing seasons. However, there is no information available regarding muscle DNA content or ploidy level within the avian pectoralis. Read More

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December 2021

Hubble's successor, at last.

Authors:
Ellen Stofan

Science 2021 Dec 2;374(6572):1175. Epub 2021 Dec 2.

Ellen Stofan is the under secretary for Science and Research, Smithsonian Institution, Washington, DC, USA, and is a member of the Space Telescope Institute Council.

Government investment in big, innovative science changes the world-it has allowed us to witness the collision of black holes, create a Global Positioning System that we can carry in our pockets, and unlock the human genome. Government investments in big research and infrastructure yield ever bigger breakthroughs. The James Webb Space Telescope (JWST), scheduled for liftoff on 22 December, represents a major international commitment. Read More

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December 2021

Information Theoretic Approach in Allometric Scaling Relations of DNA and Proteins.

Authors:
Yekbun Adiguzel

Chem Biol Drug Des 2021 Dec 2. Epub 2021 Dec 2.

Department of Biophysics, School of Medicine, Altinbas University, Kartaltepe Mahallesi, Incirli Caddesi No: 11, Bakirkoy Istanbul, Turkey.

Allometric scaling relations can be observed in between molecular parameters. Hence, we looked for presence of such relation among sizes (i.e. Read More

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December 2021

Identification and characterization of homeobox gene clusters in harpacticoid and calanoid copepods.

J Exp Zool B Mol Dev Evol 2021 Dec 2. Epub 2021 Dec 2.

Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon, South Korea.

In this study, we have identified the entire complement of typical homeobox (Hox) genes (Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) in harpacticoid and calanoid copepods and compared them with the cyclopoid copepod Paracyclopina nana. The harpacticoid copepods Tigriopus japonicus and Tigriopus kingsejongensis have seven Hox genes (Lab, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) and the Pb and Ftz genes are also present in the cyclopoid copepod P. nana. Read More

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December 2021

Two steps are better than one - improving gene editing to treat cancer.

Authors:
Francesca Minter

FEBS Open Bio 2021 Dec 2. Epub 2021 Dec 2.

FEBS Open Bio Editorial Office, Cambridge, UK.

Gene editing enables scientists to make precise changes to the genome of an organism using the cell's own ability to repair damaged DNA using a supplied DNA template. In recent years, gene editing has been applied clinically in the treatment of diseases such as cancer. Gene editing has been used in a type of immunotherapy, known as CAR-T, to restore the body's ability to find and kill specific cancer cells. Read More

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December 2021

Metagenomics studies for the diagnosis and treatment of prostate cancer.

Prostate 2021 Dec 2. Epub 2021 Dec 2.

Department of Physical Therapy, School of Rehabilitation Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.

Aim: Mutation occurs in the prostate cell genes, leading to abnormal prostate proliferation and ultimately cancer. Prostate cancer (PC) is one of the most common cancers amongst men, and its prevalence worldwide increases relative to men's age. About 16% of the world's cancers are the result of microbes in the human body. Read More

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December 2021

Understanding the role of SWEET genes in fruit development and abiotic stress in pomegranate (Punica granatum L.).

Mol Biol Rep 2021 Dec 2. Epub 2021 Dec 2.

National Agri-Food Biotechnology Institute (NABI), Sector 80, SAS Nagar, Mohali, Punjab, 140306, India.

Background: The Sugar Will Eventually Be Exported Transporters (SWEET), consisting of the MtN3 and salvia domain, are sugar transporters having an active role in diverse activities in plants such as pollen nutrition, phloem loading, nectar secretion, reproductive tissue development, and plant-pathogen interaction. The SWEET genes have been characterized only in a few fruit crop species.

Methods And Results: In this study, a total of 15 SWEET genes were identified in the pomegranate (Punica granatum) genome. Read More

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December 2021