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... Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the Hi ...
chromosomes, etc ; algorithms; heat; heat exchangers; topology; Show all 5 Subjects
Abstract:
... The challenge of heat exchanger network retrofit is often addressed using deterministic algorithms. However, the complexity of the retrofit problems, combined with multi-period operation, makes it very difficult to find any feasible solution. In contrast, stochastic algorithms are more likely to find feasible solutions in complex solution spaces. This work presents a customized evolutionary based ...
chromosomes, etc ; DNA; Trachinotus ovatus; genes; single nucleotide polymorphism; Show all 5 Subjects
Abstract:
... It is difficult to distinguish the sexes of Trachinotus ovatus based on appearance, and little data about sex-determining genes are available for this species. Here, we generated 200 F2 individuals using the parents R404 and R403. DNA samples were collected from 50 individuals of each sex and aggregated into sex-specific DNA pools. Specific-locus amplified fragment sequencing was integrated with b ...
chromosomes, etc ; drought tolerance; genes; genomics; seedlings; winter wheat; Show all 6 Subjects
Abstract:
... To date, very little research on drought tolerance has been conducted at the seedling stage in winter wheat. In this study, two types of traits, namely tolerance and recovery traits, associated with drought tolerance were scored in biparental mapping population (BPP) and association mapping population (A-set). The results of this study revealed no or weak significant correlation between the two ty ...
chromosomes, etc ; Aspergillus; fungi; genome; koji; mitochondrial DNA; nucleotide sequences; Show all 7 Subjects
Abstract:
... Aspergillus luchuensis mut. kawachii is used primarily in the production of shochu, a traditional Japanese distilled alcoholic beverage. Here, we report the chromosome-level genome sequence of A. luchuensis mut. kawachii IFO 4308 (NBRC 4308) and a comparison of the sequence with that of A. luchuensis RIB2601. The genome of strain IFO 4308 was assembled into nine contigs consisting of eight chromos ...
chromosomes, etc ; applied research; data collection; ecology; fish; genome; genomics; Show all 7 Subjects
Abstract:
... The living fishes span a unique and interesting set of animals because of their vast diversity, morphology, ecology, genetics and genomics, and higher importance to biology, economy and culture. During the past decade, the remarkable increase in fish genome sequencing has revolutionized comparative and evolutionary genomics, with the outcome of stimulating insights into vertebrate genome biology. ...
chromosomes, etc ; DNA; Xanthomonas oryzae pv. oryzae; blight; rice; virulence; Show all 6 Subjects
Abstract:
... Xanthomonas oryzae pv. oryzae is the causal agent of bacterial blight, one of the most devastating diseases of rice. Here, a hypervirulent strain, C9-3, defeating Xa1, Xa10, xa13, and Xa23 resistance genes, was used to extract genomic DNA for single molecule real-time (SMRT) sequencing. After assembly, the genome consists of a single-circular chromosome with the size of 4,924,298 bp with G+C conte ...
chromosomes, etc ; DNA; allopolyploidy; cytotypes; data collection; hybridization; phylogeny; tetraploidy; Show all 8 Subjects
Abstract:
... Polyploidy and hybridization are important processes in seed-free plant evolution. However, a major gap lies in our understanding of how these processes affect the evolutionary history of high-ploidy systems. The heterosporous lycophyte genus Isoëtes is a lineage with many putative hybrids and high-level polyploid taxa (ranging from tetraploid to dodecaploid). Here, we use a complex of western Nor ...
chromosomes, etc ; antineoplastic agents; apoptosis; carcinogenesis; drug resistance; genes; neoplasms; Show all 7 Subjects
Abstract:
... miR-30b, which is encoded by the gene located on chromosome 8q24.22, plays an important role in a variety of diseases. In most types of tumors, miR-30b significantly inhibits the proliferation, migration, and invasion of cancer cells through the regulation of target genes. Moreover, miR-30b can inhibit the PI3K/AKT signaling pathway through the regulation of EGFR, AKT, Derlin-1, GNA13, SIX1, and o ...
chromosomes, etc ; biosynthesis; food chemistry; plantaricins; plasmids; transcription (genetics); transcriptome; Show all 7 Subjects
Abstract:
... Whole-genome and transcriptome sequences of Lactiplantibacillus plantarum 163 are provided. There was one circular chromosome and four circular plasmids, with sizes of 3,131,367; 56,674; 49,140; 43,628; and 36,387 bp, respectively, in L. plantarum 163. The regulator Lp_2642 was selected from the genome data, the overexpression of which increased the transcriptional levels of related genes in plant ...
chromosomes, etc ; Populus trichocarpa; Salix; evolution; gene conversion; genomics; plant biology; Show all 7 Subjects
Abstract:
... BACKGROUND: Gene conversion has an important effect on duplicate genes produced by polyploidization. Poplar (Populus trichocarpa) and willow (Salix brachista) are leading models and excellent green plants in the Salicaceae. Although much attention has been paid to the evolution of duplicated genes in poplar and willow, the role of conversion between duplicates generated from polyploidization remai ...
chromosomes, etc ; DNA; exons; genome-wide association study; introns; phenotype; sheep; Show all 7 Subjects
Abstract:
... A genome-wide association study (GWAS) was carried out in Karachaevsky sheep using Illumina Ovine Infinium HD BeadChip 600K DNA biochips to identify single nucleotide polymorphisms (SNPs) associated with the breed. On the basis of the analysis, more than 100 SNPs were identified that have highly significant differences in the frequency of occurrence in animals of the Karachaevsky breed; for subseq ...
B chromosomes, etc ; chromatin; chromosome number; gametophytes; males; meiosis; stickiness; India; Show all 8 Subjects
Abstract:
... Plants of Tinantia erecta (Jacq.) Fenzl were collected from four localities of Mussoorie, Uttarakhand (India) to investigate their cytological status and course of male meiosis. Three populations revealed the presence of n = 32 and one population showed the presence of n = 34 as the gametophytic chromosome count which is being reported for the first time from India. Presence of B- chromosomes (n = ...
chromosomes, etc ; Escherichia coli; cephalosporins; genes; growth curves; hybridization; plasmids; China; Show all 8 Subjects
Abstract:
... The use of antimicrobials in food animals is the major determinant for the propagation of resistant bacteria in the animal reservoir. The objective of this study was to investigate the presence and distribution of third-generation cephalosporin (3GC) -resistant and plasmid-mediated AmpC (pAmpC)-producing Escherichia coli isolated from food animals in Southern China. In total, 744 3GC-resistant and ...
chromosomes, etc ; Coccinia grandis; chromosome number; males; meiosis; mitosis; pollen viability; India; Show all 8 Subjects
Abstract:
... In our present study, three wild ♂ accessions of Coccinia grandis from Jammu, Samba and Kathua of Jammu province (J&K, India) have been worked out for cytological details. To determine the chromosome behavior, both meiotic and mitotic details were worked out for plants of all three locations. While Samba and Kathua accessions had somatic cells with uniform chromosome count of 2n = 24, few plants o ...
chromosomes, etc ; autophagy; cell division; glucose; hepatocytes; insulin resistance; liver; research; therapeutics; Show all 9 Subjects
Abstract:
... Insulin resistance (IR) attributed by the deficiency of lipophagy, is an abnormal state of downregulation of insulin-mediated glucose uptake and use into the liver. Chromosome 9 open reading frame 72 (C9orf72) variously modulates autophagy. We investigated the role and the downstream pathway of C9orf72 in hepatic IR. We found that C9orf72 knockdown alleviated hepatic IR by lipophagy promotion in T ...
chromosomes, etc ; RNA; Rhodobacteraceae; bacteria; cold; genomics; lifestyle; nucleotide sequences; plasmids; seawater; Show all 10 Subjects
Abstract:
... Parasedimentitalea marina W43ᵀ is a novel psychrotolerant and piezotolerant Rhodobacteraceae bacterium isolated from deep-sea water (4000 m) of the New Britain Trench. Here we present the first complete genome sequence of the bacterial genus Parasedimentitalea, which contains a circular chromosome and four plasmids. The 5,080,916 bp long genome exhibits a G + C content of 55.9 mol% and contains 50 ...
chromosomes, etc ; Escherichia coli; amino acid sequences; chromosome morphology; crystal structure; research; Show all 6 Subjects
Abstract:
... The SMC (structural maintenance of chromosomes) proteins are known to be involved in chromosome pairing or aggregation and play an important role in cell cycle and division. Different from SMC–ScpAB complex maintaining chromosome structure in most bacteria, the MukB–MukE–MukF complex is responsible for chromosome condensation in E. coli and some γ-proteobacter. Though different models were propose ...
chromosomes, etc ; Arachis; fish; genetic improvement; genomics; homozygosity; hybridization; irradiation; karyotyping; peanuts; Show all 10 Subjects
Abstract:
... Oligo probe staining is a low-cost and efficient chromosome identification technique. In this study, oligo genomic in situ hybridization (Oligo-GISH) technology was established in peanut. Peanut A and B subgenome-specific interspersed repeat (IR) oligo probe sets were developed based on clustering and electronic localization of tandem repeat sequences in the reference genome of Tifrunner. The Olig ...
chromosomes, etc ; DNA methylation; Triticum turgidum subsp. durum; alleles; durum wheat; genomics; Show all 6 Subjects
Abstract:
... Semi-dwarf and dwarf genes were widely used in wheat breeding for improving lodging resistant and increasing yield. Rht14 dwarf gene was identified and deployed in durum wheat, where it showed advantage on important agronomic potential. The reciprocal F₂ populations derived of Castelporziano (CP) and Langdon (L) were used for mapping of Rht14, which was located in intervals 4.8 cM and 10.38 cM by ...