Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique.

Summary: Sketching technologies have recently emerged as a promising solution for real-time, large-scale phylogenetic analysis. However, existing sketching-based phylogenetic tools exhibit drawbacks, including platform restrictions, deficiencies in tree visualization, and inherent distance estimation bias. These limitations collectively impede the overall convenience and efficiency of the analysis.

RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures.

Summary: We propose RabbitKSSD, a high-speed genome distance estimation tool. Specifically, we leverage load-balanced task partitioning, fast I/O, efficient intermediate result accesses, and high-performance data structures to improve overall efficiency. Our performance evaluation demonstrates that RabbitKSSD achieves speedups ranging from 5.

A fast and globally optimal solution for RNA-seq quantification.

Alignment-based RNA-seq quantification methods typically involve a time-consuming alignment process prior to estimating transcript abundances. In contrast, alignment-free RNA-seq quantification methods bypass this step, resulting in significant speed improvements. Existing alignment-free methods rely on the Expectation-Maximization (EM) algorithm for estimating transcript abundances.

Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis.

Here, we develop k -mer substring space decomposition (Kssd), a sketching technique which is significantly faster and more accurate than current sketching methods. We show that it is the only method that can be used for large-scale dataset comparisons at population resolution on simulated and real data. Using Kssd, we prioritize references for all 1,019,179 bacteria whole genome sequencing (WGS) runs from NCBI Sequence Read Archive and find misidentification or contamination in 6164 of these.

Characterization of a Novel Variant With Reduced β-Lactam Resistance From an IncA/C Group Plasmid in a Clinical Isolate.

Similar to other CTX-M family enzymes, KLUC is a recently identified and emerging determinant of cefotaxime resistance that has been recovered from at least three species, including , and . Whether this extended-spectrum β-lactamase (ESBL) has been disseminated among commonly isolated is worthy of further investigation. In this study, we screened 739 nosocomial isolates (240 and 499 strains) and found that one and four isolates harbored the gene.

Characterisation of a class 1 integron associated with the formation of quadruple bla cassettes from an IncP-1β group plasmid in Pseudomonas aeruginosa.

Integrons are genetic platforms responsible for the dissemination of antimicrobial resistance genes among Gram-negative bacteria, primarily due to their association with transposable elements and conjugative plasmids. In this study, a cassette array containing four identical bla genes embedded in a class 1 integron located on an IncP-1β group plasmid from a clinical Pseudomonas aeruginosa strain was identified. Comparative genome analysis and conjugation assay showed that the plasmid pICP-4GES lacked the trbN, trbO and trbP genes but was conjugable.

Genetic-Variation-Driven Gene-Expression Changes Highlight Genes with Important Functions for Kidney Disease.

Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of the US population. Genome-wide association studies (GWASs) have identified sequence variants, localized to non-coding genomic regions, associated with kidney function. Despite these robust observations, the mechanism by which variants lead to CKD remains a critical unanswered question.

Structure-Function Analysis of the Transmembrane Protein AmpG from Pseudomonas aeruginosa.

AmpG is a transmembrane protein with permease activity that transports meuropeptide from the periplasm to the cytoplasm, which is essential for the induction of the ampC encoding β-lactamase. To obtain new insights into the relationship between AmpG structure and function, comparative genomics analysis, secondary and tertiary structure modeling, site-directed mutational analyses and genetic complementation experiments were performed in this study. AmpGs from different genera of bacteria (Escherichia coli, Vibrio cholerae and Acinetobacter baumannii) could complement AmpG function in Pseudomonas aeruginosa.

Identification and molecular characterization of Escherichia coli bla genes in a Chinese teaching hospital.

Escherichia coli (E. coli) commonly reside in human intestine and most E. coli strains are harmless, but some serotypes cause serious food poisoning.

Effects of phycoerythrin from Gracilaria lemaneiformis in proliferation and apoptosis of SW480 cells.

We studied phycoerythrin (PE) in human SW480 tumor cells and the underlying molecular mechanisms of action. PE inhibited cell proliferation as evidenced by CCK-8 assay. The IC50 values of phycoerythrin were 48.

Transcriptome analysis of phycocyanin inhibitory effects on SKOV-3 cell proliferation.

Phycocyanin (PC) from Spirulina platensis has inhibitory effects on tumor cell growth. In this research, the transcriptome study was designed to investigate the underlying molecular mechanisms of PC inhibition on human ovarian cancer cell SKOV-3 proliferation. The PC IC50 was 216.

Spirulina phycocyanin induces differential protein expression and apoptosis in SKOV-3 cells.

The present study was designed to determine the effects of phycocyanin (PC) on Human ovarian cancer SKOV-3 cells and the underlying molecular mechanisms of action. The inhibitory effects of PC on the cell proliferation were detected by MTT assay. The IC50 values of PC were 182.

Comparative genomics analysis of pKF3-94 in Klebsiella pneumoniae reveals plasmid compatibility and horizontal gene transfer.

In order to get insights into plasmid evolution and the dissemination of multidrug resistance, we performed extensive comparative genomics analyses of the Klebsiella pneumoniae plasmid pKF3-94 and some of its related plasmids. pKF3-94 is one of three plasmids isolated from the K. pneumoniae strain KF3.

Molecular Epidemiology and Characterization of Genotypes of Acinetobacter baumannii Isolates from Regions of South China.

The aim of this study was to analyze the molecular epidemiologic characteristics of Acinetobacter baumannii. A total of 398 isolates were collected in 7 regions of South China from January to June of 2012. Drug sensitivity was tested toward 15 commonly used antibiotics; thus, 146 multi-drug-resistant strains (resistant to more than 7 drugs) were identified, representing 36.

Molecular variation and horizontal gene transfer of the homocysteine methyltransferase gene mmuM and its distribution in clinical pathogens.

The homocysteine methyltransferase encoded by mmuM is widely distributed among microbial organisms. It is the key enzyme that catalyzes the last step in methionine biosynthesis and plays an important role in the metabolism process. It also enables the microbial organisms to tolerate high concentrations of selenium in the environment.

Co-phylog: an assembly-free phylogenomic approach for closely related organisms.

With the advent of high-throughput sequencing technologies, the rapid generation and accumulation of large amounts of sequencing data pose an insurmountable demand for efficient algorithms for constructing whole-genome phylogenies. The existing phylogenomic methods all use assembled sequences, which are often not available owing to the difficulty of assembling short-reads; this obstructs phylogenetic investigations on species without a reference genome. In this report, we present co-phylog, an assembly-free phylogenomic approach that creates a 'micro-alignment' at each 'object' in the sequence using the 'context' of the object and calculates pairwise distances before reconstructing the phylogenetic tree based on those distances.

Sequencing and genetic variation of multidrug resistance plasmids in Klebsiella pneumoniae.

Background: The development of multidrug resistance is a major problem in the treatment of pathogenic microorganisms by distinct antimicrobial agents. Characterizing the genetic variation among plasmids from different bacterial species or strains is a key step towards understanding the mechanism of virulence and their evolution.

Results: We applied a deep sequencing approach to 206 clinical strains of Klebsiella pneumoniae collected from 2002 to 2008 to understand the genetic variation of multidrug resistance plasmids, and to reveal the dynamic change of drug resistance over time.

Sequence analysis of pKF3-70 in Klebsiella pneumoniae: probable origin from R100-like plasmid of Escherichia coli.

Background: Klebsiella pneumoniae is a clinically significant species of bacterium which causes a variety of diseases. Clinical treatment of this bacterial infection is greatly hindered by the emergence of multidrug-resistant strains. The resistance is largely due to the acquisition of plasmids carrying drug-resistant as well as pathogenic genes, and its conjugal transfer facilitates the spread of resistant phenotypes.

FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families.

Background: The availability of 12 fully sequenced Drosophila species genomes provides an excellent opportunity to explore the evolutionary mechanism, structure and function of gene families in Drosophila. Currently, several important resources, such as FlyBase, FlyMine and DroSpeGe, have been devoted to integrating genetic, genomic, and functional data of Drosophila into a well-organized form. However, all of these resources are gene-centric and lack the information of the gene families in Drosophila.