A novel microbe-drug association prediction model based on graph attention networks and bilayer random forest.

Background: In recent years, the extensive use of drugs and antibiotics has led to increasing microbial resistance. Therefore, it becomes crucial to explore deep connections between drugs and microbes. However, traditional biological experiments are very expensive and time-consuming.

Upper respiratory tract mycobiome alterations in different kinds of pulmonary disease.

Introduction: The human respiratory tract is considered to be a polymicrobial niche, and an imbalance in the microorganism composition is normally associated with several respiratory diseases. In addition to the well-studied bacteriome, the existence of fungal species in the respiratory tract has drawn increasing attention and has been suggested to have a significant clinical impact. However, the understanding of the respiratory fungal microbiota (mycobiome) in pulmonary diseases is still insufficient.

Proteome-Wide Identification and Functional Analysis of Lysine Crotonylation in Conidial and Mycelial Stages.

Lysine crotonylation is a newly discovered post-translational modification (PTM) with key roles in various important regulatory pathways. Despite its functional significance, there is limited knowledge about crotonylation in fungi. is the most common fungal pathogen in human infection and is considered a model organism of dermatophytes and human pathogenic filamentous fungi.

Proteome-Wide Identification of Lysine Propionylation in the Conidial and Mycelial Stages of .

Posttranslational modifications (PTMs) exist in a wide variety of organisms and play key roles in regulating various essential biological processes. Lysine propionylation is a newly discovered PTM that has rarely been identified in fungi. () is one of the most common fungal pathogens in the world and has been studied as an important model organism of anthropic pathogenic filamentous fungi.

Integrated microRNA and mRNA analysis in the pathogenic filamentous fungus Trichophyton rubrum.

Background: Trichophyton rubrum (T. rubrum) is an important model organism of dermatophytes, which are the most common fungal pathogens worldwide. Despite the severity and prevalence of the infection caused by these pathogens, current therapies are not sufficient.

The First Whole-Cell Proteome- and Lysine-Acetylome-Based Comparison between Trichophyton rubrum Conidial and Mycelial Stages.

Trichophyton rubrum is the most common fungal pathogen in the world, which has been studied as an important dermatophyte model organism. Despite the prevalence of T. rubrum, the available antifungal therapies are not sufficiently efficient.

The first succinylome profile of Trichophyton rubrum reveals lysine succinylation on proteins involved in various key cellular processes.

Background: Dermatophytes, the most common cause of fungal infections, affect millions of individuals worldwide. They pose a major threat to public health because of the severity and longevity of infections caused by dermatophytes and their refractivity to therapy. Trichophyton rubrum (T.

Proteogenomic Analysis of Trichophyton rubrum Aided by RNA Sequencing.

Infections caused by dermatophytes, Trichophyton rubrum in particular, are among the most common diseases in humans. In this study, we present a proteogenomic analysis of T. rubrum based on whole-genome proteomics and RNA-Seq studies.

Analysis of gene expression changes in Trichophyton rubrum after skin interaction.

Trichophyton rubrum, an anthropophilic and cosmopolitan fungus, is the most common agent of superficial mycoses. In this study, T. rubrum infection was modelled by adding human skin sections to a limited medium containing glucose and cDNA microarrays were used to monitor T.

Identification and characterisation of non-coding small RNAs in the pathogenic filamentous fungus Trichophyton rubrum.

Background: Accumulating evidence demonstrates that non-coding RNAs (ncRNAs) are indispensable components of many organisms and play important roles in cellular events, regulation, and development.

Results: Here, we analysed the small non-coding RNA (ncRNA) transcriptome of Trichophyton rubrum by constructing and sequencing a cDNA library from conidia and mycelia. We identified 352 ncRNAs and their corresponding genomic loci.

Analysis of the secretome and identification of novel constituents from culture filtrate of bacillus Calmette-Guerin using high-resolution mass spectrometry.

Tuberculosis (TB) is an infectious bacterial disease that causes morbidity and mortality, especially in developing countries. Although its efficacy against TB has displayed a high degree of variability (0%-80%) in different trials, Mycobacterium bovis bacillus Calmette-Guérin (BCG) has been recognized as an important weapon for preventing TB worldwide for over 80 years. Because secreted proteins often play vital roles in the interaction between bacteria and host cells, the secretome of mycobacteria is considered to be an attractive reservoir of potential candidate antigens for the development of novel vaccines and diagnostic reagents.

Global gene expression profiles for the growth phases of Trichophyton rubrum.

Trichophyton rubrum (T. rubrum) is a common superficial fungus. Molecular and genetic studies of T.

Complete genome sequence of the extremophilic Bacillus cereus strain Q1 with industrial applications.

Bacillus cereus strain Q1 was isolated from a deep-subsurface oil reservoir in the Daqing oil field in northeastern China. This strain is able to produce biosurfactants and to survive in extreme environments. Here we report the finished and annotated genome sequence of this organism.

Genotypic characterization of Neisseria meningitidis serogroup B strains circulating in China.

Objective: In China, comparatively little research has been directed at serogroup B meningococci, which are mainly isolated from healthy individuals. We attempted to study the genotypic characterization of Neisseria meningitidis serogroup B strains.

Methods: We analyzed 150 N.

Comparative analysis of whole genome structure of Streptococcus suis using whole genome PCR scanning.

An outbreak associated with Streptococcus suis infection in humans emerged in Sichuan province, China in 2005. The outbreak is atypical for the apparent large number of human cases, high fatality rate and geographical spread. To determine whether the bacterium has changed, we compared both human and animal isolates from the Sichuan outbreak with those collected previously within China and in other countries using whole genome PCR scanning (WGPScaning) comparative sequencing of several known virulence factor genes and multilocus sequence typing (MLST) analysis.

Characterization of ST-4821 complex, a unique Neisseria meningitidis clone.

Ten outbreaks of a new serogroup C meningococcal disease emerged during 2003-2005 in China. The multilocus sequence typing results indicated that unique sequence type 4821 clone meningococci were responsible for these outbreaks. Herein, we determined the entire genomic DNA sequence of serogroup C isolate 053442, which belongs to ST-4821.

Molecular characterization of serogroup C Neisseria meningitidis isolated in China.

An increase in the number of serogroup C meningococcal disease cases occurred in China from September 2003 to January 2006 as a result of several successive outbreaks. In addition, the proportion of serogroup C Neisseria meningitidis isolates from sporadic cases and carriers has also increased. In this study, 113 serogroup C meningococcal isolates were characterized by multilocus sequence typing (MLST) and PorA typing.

Genotypic analysis of serogroups other than A, B or C of Neisseria meningitidis in China.

To serologically and genetically characterize other serogroups (except A, B, and C) of Neisseria meningitidis isolates in China, we collected 56 strains of other serogroups, identified by serogroup typing and multilocus sequence typing (MLST). All of them are non-invasive isolates. The serogroups of the 56 Chinese isolates were W135 (11 isolates), Y (4), X (15), 29E (15), D (1), H (4), I (3), K (2), and non-groupable (1).

The use of global transcriptional analysis to reveal the biological and cellular events involved in distinct development phases of Trichophyton rubrum conidial germination.

Background: Conidia are considered to be the primary cause of infections by Trichophyton rubrum.

Results: We have developed a cDNA microarray containing 10250 ESTs to monitor the transcriptional strategy of conidial germination. A total of 1561 genes that had their expression levels specially altered in the process were obtained and hierarchically clustered with respect to their expression profiles.

Revisiting the molecular evolutionary history of Shigella spp.

The theory that Shigella is derived from multiple independent origins of Escherichia coli (Pupo et al. 2000) has been challenged by recent findings that the virulence plasmids (VPs) and the chromosomes share a similar evolutionary history (Escobar-Paramo et al. 2003), which suggests that an ancestral VP entered an E.

Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags.

Background: Dermatophytes are the primary causative agent of dermatophytoses, a disease that affects billions of individuals worldwide. Trichophyton rubrum is the most common of the superficial fungi. Although T.

Rapid identification of small interfering RNA that can effectively inhibit the replication of multiple influenza B virus strains.

Influenza B virus is a cause of substantial morbidity and mortality in humans and current vaccination strategies and antiviral drugs only provide limited protection. Here, we report the evaluation of small interfering RNA (siRNA) for repression of viral replication in cultured cells as well as in chicken embryos. Several siRNAs targeting conserved regions of the virus (in chemically synthesized or plasmid-encoded forms) were found to effectively block the replication of the influenza B virus.

Construction, detection and microarray analysis on Shigella dysenteriae a1 IroN, ShuA single, double mutants.

In this study, we constructed single mutants MTS-1, MTS-2 of IroN and ShuA gene and double mutant MTS of them in Shigella dysenteriae A1 strain 51197 by insert and absence. The functional detection of every mutant was performed at the level of culture medium and cell experiment. The gene expression profiles of the mutants and the wild-type strains under iron-enriched and iron-limited conditions were analyzed by the SD51197 whole genomic microarray.

Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a.

Background: Shigella bacteria cause dysentery, which remains a significant threat to public health. Shigella flexneri is the most common species in both developing and developed countries. Five Shigella genomes have been sequenced, revealing dynamic and diverse features.