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Genome-wide DNA arrays profiling unravels the genetic structure of Iranian sheep and pattern of admixture with worldwide coarse-wool sheep breeds.

Genomics 2021 Jul 19. Epub 2021 Jul 19.

Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133 Kerman, Iran. Electronic address:

Archaeological and genetic evidence show that sheep were originally domesticated in area around the North of Zagros mountains, North-west of Iran. The Persian plateau exhibits a variety of native sheep breeds with a common characteristic of coarse-wool production. Therefore, knowledge about the genetic structure and diversity of Iranian sheep and genetic connections with other sheep breeds is of great interest. Read More

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sp. nov., isolated from marine sediment.

Int J Syst Evol Microbiol 2021 Jul;71(7)

Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06974, Republic of Korea.

A Gram-stain-negative, aerobic, non-motile, rod-shaped bacterial strain (CAU 1508) was isolated from marine sediment collected in the Republic of Korea. Growth was observed at 10-45 °C (optimum, 30 °C), pH 4.0-11. Read More

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sp. nov. and sp. nov., isolated from desert biocrust.

Int J Syst Evol Microbiol 2021 Jul;71(7)

Institute for Integrative Systems Biology I2SysBio (Universitat de València-CSIC), Calle del Catedràtic Agustin Escardino Benlloch 9, 46980 Paterna, Spain.

Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6 and T18, were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6 and T18 showed similarities with CGMCC 1. Read More

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Characterization of the complete chloroplast genome of (Rutaceae) from Yunnan Province, China.

Authors:
Ning Zhou Ai-Gen Fu

Mitochondrial DNA B Resour 2021 9;6(8):2288-2290. Epub 2021 Jul 9.

Chinese Education Ministry's Key Laboratory of Western Resources and Modern Biotechnology, Key Laboratory of Biotechnology Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, China.

L. (Rutaceae) has important horticultural and medicinal values. Here, we reported the complete chloroplast (cp) genome of using the next-generation sequencing method. Read More

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The complete chloroplast genome of , an orchid with important ornamental value and medicinal value.

Mitochondrial DNA B Resour 2021 9;6(8):2263-2265. Epub 2021 Jul 9.

School of Life Sciences, Yunnan Normal University, Kunming, China.

is an epiphytic orchid with significant ornamental value and medicinal value. Here, we report the first complete chloroplast genome of . The circular genome was 158,394 bp in length and consisted of a pair of inverted repeats (IR 26,646 bp), which were separated by a large single copy region (LSC 86,603 bp) and a small single copy region (SSC 18,499 bp). Read More

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Estimating Hepatotoxic Doses Using High-Content Imaging in Primary Hepatocytes.

Toxicol Sci 2021 Jul 21. Epub 2021 Jul 21.

Center for Computational Toxicology and Exposure, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA.

Using in vitro data to estimate point of departure (POD) values is an essential component of new approach methodologies (NAM)-based chemical risk assessments. In this case study, we evaluated a NAM for hepatotoxicity based on rat primary hepatocytes, high-content imaging (HCI), and toxicokinetic modeling. First, we treated rat primary hepatocytes with 10 concentrations (0. Read More

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Characterization of the blood and neutrophil-specific microbiomes and exploration of potential bacterial biomarkers for sepsis in surgical patients.

Immun Inflamm Dis 2021 Jul 20. Epub 2021 Jul 20.

Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China.

Introduction: Recent studies have demonstrated the presence of a circulating microbiome in the blood of healthy subjects and chronic inflammatory patients. However, our knowledge regarding the blood microbiome and its potential roles in surgical patients remains very limited. The objective of this study was to determine the blood microbial landscape in surgical patients and to explore its potential associations with postoperative sepsis. Read More

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Description of sp. nov., harboring antibiotic- and toxic compound-resistace genes, isolated from poultry manure.

Int J Syst Evol Microbiol 2021 Jul;71(7)

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696 were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °С, pH 9 and with 1 % NaCl. Read More

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Gene variation and population structure of in the China coast revealed by mitochondrial control region sequences.

Mitochondrial DNA B Resour 2021 6;6(8):2240-2245. Epub 2021 Jul 6.

Key Laboratory of East China Sea Fishery resource Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.

is a commercially important fishery species in the Indo-West Pacific region. In the present study, the genetic variation of among 10 sampling localities along the China coast and one from the Indonesia region was evaluated using mitochondrial DNA control region sequences. As a result, a total of 30 variable sites were detected in the 458 bp segment of the control region among 330 individuals from 11 localities, and 41 haplotypes were defined. Read More

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The complete chloroplast genome of .

Mitochondrial DNA B Resour 2021 6;6(8):2221-2223. Epub 2021 Jul 6.

Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding; National Engineering Research Center for Floriculture, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Landscape Architecture, Beijing Forestry University, Beijing, China.

(Decne.) Rgl. 1879 (family Asteraceae) is a perennial herb with high economic and medicinal values. Read More

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Mutational profile of hereditary breast and ovarian cancer - Establishing genetic testing guidelines in a developing country.

Curr Probl Cancer 2021 Jul 10:100767. Epub 2021 Jul 10.

Department for genetic counseling for hereditary cancers, Institute for Oncology and radiology of Serbia, Belgrade.

Purpose: Because many countries lack the capacity to follow the international guidelines for genetic testing, we suggest the specific approach for establishing local genetic testing guidelines that could be applied in developing countries. We focus on hereditary breast (BC) and ovarian cancer (OC) in Serbia.

Methods: From the cohort of 550 persons who were referred for genetic counseling at the Institute for Oncology and Radiology of Serbia, 392 were selected. Read More

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Methyl donor micronutrients, CD40-ligand methylation and disease activity in systemic lupus erythematosus: A cross-sectional association study.

Lupus 2021 Jul 20:9612033211034559. Epub 2021 Jul 20.

Medical Faculty, Dept. & Hiller Research Unit for Rheumatology, Heinrich-Heine-University, Düsseldorf, Germany.

Objective: Hypomethylation of CD40-ligand (CD40L) in T-cells is associated with increased disease activity in systemic lupus erythematosus (SLE). We therefore investigated possible associations of dietary methyl donors and products with CD40L methylation status in SLE.

Methods: Food frequency questionnaires were employed to calculate methyl donor micronutrients in 61 female SLE patients (age 45. Read More

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sp. nov. and sp. nov., isolated from salt lake and saline soil.

Int J Syst Evol Microbiol 2021 Jul;71(7)

School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China.

Two halophilic archaeal strains, Gai3-2 and NJ-3-1, were isolated from salt lake and saline soil samples, respectively, collected in PR China. The 16S rRNA gene sequences of the two strains were 97.5% similar to each other. Read More

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Developing a Real-time PCR Assay for Direct Identification and Quantification of Soybean Cyst Nematode, Heterodera glycines, in Soil and Its Discrimination from Sugar Beet Cyst Nematode, Heterodera schachtii.

Plant Dis 2021 Jul 20. Epub 2021 Jul 20.

North Dakota State University, Department of Plant Pathology, Walster Hall 322, Dept 7660 PO Box 6050, Fargo, North Dakota, United States, 58108-6050;

The soybean cyst nematode (SCN) Heterodera glycines continues to be a major threat to soybean production worldwide. Morphological discrimination between SCN and other nematodes of the H. schachtii sensu stricto group is not only difficult and time-consuming, but also requires high expertise in nematode taxonomy. Read More

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Litoribacter populi sp. nov., isolated from the soil of a Populus euphratica forest.

Arch Microbiol 2021 Jul 19. Epub 2021 Jul 19.

Institute of Applied Microbiology, Xinjiang Academy of Agricultural Sciences, Xinjiang Laboratory of Special Environmental Microbiology, Urumqi, 830091, Xinjiang, China.

A Gram-stain-negative, rod-shaped, and orange-pigmented bacterium, designated XAAS-A1, was isolated from the soil of a Populus euphratica forest. The main respiratory quinone of XAAS-A1 is MK-7, and the principal cellular fatty acids are iso-C, C ω6c, Iso-C 3OH, and summed feature 3 (Cω6c and/or Cω7c). The major polar lipids are phosphatidylethanolamine, phosphatidylcholine, and two unidentified lipids. Read More

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Photonics of meso-substituted carbocyanine dyes in solutions and in complexes with DNA.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Jul 12;263:120171. Epub 2021 Jul 12.

N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia. Electronic address:

Spectral-fluorescent and photochemical properties (photoisomerization and generation of the triplet state) of meso-substituted cationic carbocyanine dyes, 3,3'-di-(β-hydroxyethyl)-5,5'-dimethoxy-9-ethylthiacarbocyanine iodide (K1) and 3,3'-di-(β-hydroxyethyl)-9-methylthiacarbocyanine iodide (K2), have been studied in solutions and in the presence of DNA. In solutions, on passing from acetonitrile to dioxane, a growth of fluorescence of the dyes is observed due to a shift of the equilibrium of cis/trans isomers toward the fluorescent trans-isomer. Upon flash photolysis of dye solutions in dioxane, the formation and subsequent decay of the cis-photoisomers of the dyes are observed. Read More

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HFS-SLPEE: A Novel Hierarchical Feature Selection and Second Learning Probability Error Ensemble Model for Precision Cancer Diagnosis.

Authors:
Yajie Meng Min Jin

Front Cell Dev Biol 2021 30;9:696359. Epub 2021 Jun 30.

College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.

The emergence of high-throughput RNA-seq data has offered unprecedented opportunities for cancer diagnosis. However, capturing biological data with highly nonlinear and complex associations by most existing approaches for cancer diagnosis has been challenging. In this study, we propose a novel hierarchical feature selection and second learning probability error ensemble model (named HFS-SLPEE) for precision cancer diagnosis. Read More

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Bioinformatics Analysis of Expression Profiles and Prognostic Values of the Signal Transducer and Activator of Transcription Family Genes in Glioma.

Front Genet 2021 2;12:625234. Epub 2021 Jul 2.

Department of Neurosurgery, Wuxi People's Hospital of Nanjing Medical University, Wuxi, China.

Signal transducer and activator of transcription () family genes-of which there are seven members: , and -have been associated with the progression of multiple cancers. However, their prognostic values in glioma remain unclear. In this study, we systematically investigated the expression, the prognostic value, and the potential mechanism of the family genes in glioma. Read More

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Analysis of the Taxonomy and Pathogenic Factors of L6 Using Whole-Genome Sequencing and Comparative Genomics.

Front Microbiol 2021 2;12:679102. Epub 2021 Jul 2.

Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, College of Plant Protection, Hainan University, Haikou, China.

Soft rot pectobacteria are devastating plant pathogens with a global distribution and a broad host range. L6, previously isolated from leaves of , is a pectolytic bacterial pathogen that causes typical soft rot on . There is a shortage for genome data of , which seriously hinders research on classification and pathogenesis of . Read More

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Alleviation of C⋅C Mismatches in DNA by the Fpg Protein.

Front Microbiol 2021 30;12:608839. Epub 2021 Jun 30.

Department of Chemistry, Bioscience and Environmental Technology, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway.

DNA polymerase III mis-insertion may, where not corrected by its 3'→ 5' exonuclease or the mismatch repair (MMR) function, result in all possible non-cognate base pairs in DNA generating base substitutions. The most thermodynamically unstable base pair, the cytosine (C)⋅C mismatch, destabilizes adjacent base pairs, is resistant to correction by MMR in , and its repair mechanism remains elusive. We present here evidence that C⋅C mismatch can be processed by base excision repair initiated by the formamidopyrimidine-DNA glycosylase (Fpg) protein. Read More

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Usefulness of a 3D-printing air sampler for capturing live airborne bacteria and exploring the environmental factors that can influence bacterial dynamics.

Res Microbiol 2021 Jul 14:103864. Epub 2021 Jul 14.

Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Kita 12 Nishi 5, Kita-ku, Sapporo, Hokkaido 060-0812, Japan. Electronic address:

We created a handmade 3D-printed air sampler to effectively collect live airborne bacteria, and determined which environmental factors influenced the bacteria. Bacterial colony forming units (CFUs) in the air samples (n=37) were monitored by recording the environmental changes occurring over time, then determining the presence/absence of correlations among such changes. The bacterial CFUs changed sharply and were significantly correlated with the DNA concentrations, indicating that the captured bacteria made up most of the airborne bacteria. Read More

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sp. nov., isolated from mangrove soil and the proposal for the reclassification of as comb. nov.

Int J Syst Evol Microbiol 2021 Jul;71(7)

Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Guangdong Open Laboratory of Applied Microbiology, Guangdong Microbial Culture Collection Center (GDMCC), Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China.

A novel Gram-stain-negative, aerobic and rod-shaped bacterial strain designated as 6D45A was isolated from mangrove soil and characterized using a polyphasic taxonomic approach. Strain 6D45A was found to grow at 10-37 °C (optimum, 28 °C), at pH 6.0-9. Read More

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Paenibacillus albiflavus sp. nov., a bacterium isolated from soil.

Arch Microbiol 2021 Jul 16. Epub 2021 Jul 16.

Department of Bio and Environmental Technology, College of Natural Science, Seoul Women's University, Seoul, 139-774, Korea.

Strain 18JY21-1, a Gram-positive, endospore-forming, motile, and rod-shaped bacterium, was isolated from soil in South Korea and was characterised to determine its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene sequence of strain 18JY21-1 revealed that the strain 18JY21-1 belongs to the genus Paenibacillus in the family Paenibacillaceae in the class Bacilli. The highest degree of sequence similarities of strain 18JY21-1 was found with Paenibacillus doosanensis CAU 1055 (97. Read More

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Perylene-Cy3 FRET System to Analyze Photoactive DNA Structures.

Chemistry 2021 Jul 16. Epub 2021 Jul 16.

Nagoya University: Nagoya Daigaku, Department of Biomolecular Engineering, JAPAN.

We report a new FRET system for structural analyses of DNA duplexes using perylene and Cy3 as donor and acceptor, respectively, linked at the termini of a DNA duplex via D-threoninol. Experimentally obtained FRET efficiencies were in good agreement with theoretical values calculated based on canonical B-form DNA. Due to the relatively long Förster radius, this system can be used to analyze large DNA structures, and duplexes containing photo-reactive molecules can be analyzed since perylene can be excited with visible light. Read More

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Topoisomerase IIa protein expression analysis in oral squamous cell carcinoma.

J BUON 2021 May-Jun;26(3):769-773

1st ENT Department, Hippocration Hospital, University of Athens, Athens, Greece.

Purpose: Topoisomerases represent a super-family of nucleic enzymes involved in the DNA replication, transcription, recombination, and also chromosome topological formation. Topoisomerase II alpha (Topo IIa-gene location 17q21) is a critical gene associated with response to chemotherapeutic agents such as anthracyclines especially in breast adenocarcinoma. Our aim was to investigate the role of aberrant Topo IIa protein expression in oral squamous cell carcinoma (OSCC). Read More

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Cutaneous human papillomaviruses and the risk of keratinocyte carcinomas.

Cancer Res 2021 Jul 15. Epub 2021 Jul 15.

Infections and Cancer Biology, International Agency for Research on Cancer/World Health Organization.

Cutaneous human papillomavirus (cuHPV) infections may be novel targets for skin cancer prevention and treatment, but critical information regarding the development of virus-positive skin cancers following cuHPV infection has been lacking. In this study, baseline cuHPV infection was measured by serology and viral DNA detection in eyebrow hairs (EBH) and forearm skin swabs (SSW) among 1,008 individuals undergoing routine skin cancer screening exams and followed for incidence of basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (cuSCC). Baseline beta-HPV detection, particularly in SSW, significantly predicted cuSCC (Hazard Ratio [HR]=4. Read More

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Low extracellular pH inhibits nucleotide excision repair.

Mutat Res 2021 Jul 18;867:503374. Epub 2021 Jun 18.

Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Shizuoka 422-8526, Japan. Electronic address:

Nucleotide excision repair (NER) is the main pathway to repair bulky DNA damages including pyrimidine dimers, and the genetic dysregulation of NER associated proteins is well known to cause diseases such as cancer and neurological disorder. Other than the genetic defects, 'external factors' such as oxidative stress and environmental chemicals also affect NER. In this study, we examined the impact of extracellular pH on NER. Read More

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High-molecular weight DNA extraction, clean-up and size selection for long-read sequencing.

PLoS One 2021 15;16(7):e0253830. Epub 2021 Jul 15.

Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia.

Rapid advancements in long-read sequencing technologies have transformed read lengths from bps to Mbps, which has enabled chromosome-scale genome assemblies. However, read lengths are now becoming limited by the extraction of pure high-molecular weight DNA suitable for long-read sequencing, which is particularly challenging in plants and fungi. To overcome this, we present a protocol collection; high-molecular weight DNA extraction, clean-up and size selection for long-read sequencing. Read More

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sp. nov., isolated from a cave, and proposals that is a later synonym of , and are later synonyms of , and and are later synonyms of .

Int J Syst Evol Microbiol 2021 Jul;71(7)

Department of Biological Sciences and Biotechnology, Hannam University, Daejon 34054, Republic of Korea.

Two novel actinobacterial strains, designated C9-5 and C3-43, were isolated from soil samples of a cave in Jeju Island, Republic of Korea, and subjected to taxonomic study by a polyphasic approach. The organisms exhibited a typical rod-coccus developmental cycle during growth and grew at 10-30 °C, pH 5-9 and 0-3 % (w/v) NaCl. In 92 single-copy core gene sequence analysis, strain C9-5 was loosely associated with , albeit sharing low 16S rRNA gene sequence similarity (97. Read More

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Phycicoccus avicenniae sp. nov., a novel endophytic actinomycete isolated from a branch of Avicennia mariana.

Antonie Van Leeuwenhoek 2021 Jul 15. Epub 2021 Jul 15.

Life Sciences Institute, Zunyi Medical University, Zunyi, 563006, People's Republic of China.

A novel endophytic actinomycete, designated strain BSK3Z-2, was isolated from a surface-sterilised branch of Avicennia mariana from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. Cells were observed to be Gram-stain positive, aerobic, asporogenous and rod-shaped. Strain BSK3Z-2 was found to grow optimally at 30 °C, pH 7. Read More

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