DNA structural features and variability of complete MHC locus sequences.

The major histocompatibility (MHC) locus, also known as the Human Leukocyte Antigen (HLA) genes, is located on the short arm of chromosome 6, and contains three regions (Class I, Class II and Class III). This 5 Mbp locus is one of the most variable regions of the human genome, yet it also encodes a set of highly conserved and important proteins related to immunological response. Genetic variations in this region are responsible for more diseases than in the entire rest of the human genome.

Big data in genomic research for big questions with examples from covid-19 and other zoonoses.

Omics research inevitably involves the collection and analysis of big data, which can only be handled by automated approaches. Here we point out that the analysis of big data in the field of genomics dictates certain requirements, such as specialized software, quality control of input data, and simplification for visualization of the results. The latter results in a loss of information, as is exemplified for phylogenetic trees.

Comparison of Monkeypox virus genomes from the 2017 Nigeria outbreak and the 2022 outbreak.

Aims: The current Monkeypox virus (MPX) outbreak is not only the largest known outbreak to date caused by a strain belonging to the West-African clade, but also results in remarkably different clinical and epidemiological features compared to previous outbreaks of this virus. Here, we consider the possibility that mutations in the viral genome may be responsible for its changed characteristics.

Methods And Results: Six genome sequences of isolates from the current outbreak were compared to five genomes of isolates from the 2017 outbreak in Nigeria and to two historic genomes, all belonging to the West-African clade.

The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2.

The genomic diversity of SARS-CoV-2 is the result of a relatively low level of spontaneous mutations introduced during viral replication. With millions of SARS-CoV-2 genome sequences now available, we can begin to assess the overall genetic repertoire of this virus. We find that during 2020, there was a global wave of one variant that went largely unnoticed, possibly because its members were divided over several sublineages (B.

Interactions between the Gut Microbiome, Lung Conditions, and Coronary Heart Disease and How Probiotics Affect These.

The importance of a healthy microbiome cannot be overemphasized. Disturbances in its composition can lead to a variety of symptoms that can extend to other organs. Likewise, acute or chronic conditions in other organs can affect the composition and physiology of the gut microbiome.

Decoding the epitranscriptional landscape from native RNA sequences.

Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct sequencing of native RNA using Oxford Nanopore Technologies (ONT) can allow for directly detecting the RNA base modifications, although these modifications might appear as sequencing errors.

No Genotoxicity Is Detectable for Strain Nissle 1917 by Standard In Vitro and In Vivo Tests.

Probiotic strain Nissle 1917 (EcN) has a long history of safe use. However, the recently discovered presence of a locus in its genome presumably producing colibactin has questioned its safety, as colibactin has been implicated in genotoxicity. Here, we assess the genotoxic potential of EcN.

Comment on "Enumeration of in Probiotic Products. 2019, , 437".

Recently, Zimmer and Dorea published a communication on the enumeration of in probiotic products containing this species [...

Comparative genomics of hepatitis A virus, hepatitis C virus, and hepatitis E virus provides insights into the evolutionary history of Hepatovirus species.

The intraspecies genomic diversity of the single-strand RNA (+) virus species hepatitis A virus (Hepatovirus), hepatitis C virus (Hepacivirus), and hepatitis E virus (Orthohepevirus) was compared. These viral species all can cause liver inflammation (hepatitis), but share no gene similarity. The codon usage of human hepatitis A virus (HAV) is suboptimal for replication in its host, a characteristic it shares with taxonomically related rodent, simian, and bat hepatitis A virus species.

Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks.

To achieve maximum transmission chain tracking in the current Ebola outbreak, whole genome sequencing (WGS) has been proposed to provide optimal information. However, WGS remains a costly and time-intensive procedure that is poorly suited for the large numbers of samples being generated, especially under severe time and work-environment constraints as in the present DRC outbreak. To better prepare for future outbreaks, where an apparent single outbreak may actually represent overlapping outbreaks caused by independent variants, and where rapid identification of emerging new transmission chains will be essential, a more practical method would be to amplify and sequence genomic areas that reveal the highest information to differentiate EBOV variants.

Mechanisms linking preterm birth to onset of cardiovascular disease later in adulthood.

Cardiovascular disease (CVD) rates in adulthood are high in premature infants; unfortunately, the underlying mechanisms are not well defined. In this review, we discuss potential pathways that could lead to CVD in premature babies. Studies show intense oxidant stress and inflammation at tissue levels in these neonates.

Lipopolysaccharides in Food, Food Supplements, and Probiotics: Should We be Worried?

The fever-inducing effect of lipopolysaccharides (LPS) is well known, and human blood is extremely responsive to this pyrogen. Recently, the safety of LPS-containing food supplements and probiotic drugs as immune-stimulants has been questioned, although these products are orally taken and do not reach the bloodstream undigested. The concerns are understandable, as endotoxaemia is a pathological condition, but the oral uptake of probiotic products containing LPS or Gram-negative bacteria does not pose a health risk, based on the available scientific evidence, as is reviewed here.

Case of Microcephaly after Congenital Infection with Asian Lineage Zika Virus, Thailand.

We sequenced the virus genomes from 3 pregnant women in Thailand with Zika virus diagnoses. All had infections with the Asian lineage. The woman infected at gestational week 9, and not those infected at weeks 20 and 24, had a fetus with microcephaly.

E. coli and colorectal cancer: a complex relationship that deserves a critical mindset.

To the multiple factors that may eventually result in colorectal cancer (CRC), strains of E. coli have now been added, in particular strains producing colibactin from their polyketide synthesis (pks) locus. The evidence and mechanistic explanations for this unfortunate effect of what is in most cases a harmless commensal are discussed in the first part of this review.

Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes.

Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C.

Suggested mechanisms for Zika virus causing microcephaly: what do the genomes tell us?

Background: Zika virus (ZIKV) is an emerging human pathogen. Since its arrival in the Western hemisphere, from Africa via Asia, it has become a serious threat to pregnant women, causing microcephaly and other neuropathies in developing fetuses. The mechanisms behind these teratogenic effects are unknown, although epidemiological evidence suggests that microcephaly is not associated with the original, African lineage of ZIKV.

A secreted antibacterial neuropeptide shapes the microbiome of Hydra.

Colonization of body epithelial surfaces with a highly specific microbial community is a fundamental feature of all animals, yet the underlying mechanisms by which these communities are selected and maintained are not well understood. Here, we show that sensory and ganglion neurons in the ectodermal epithelium of the model organism hydra (a member of the animal phylum Cnidaria) secrete neuropeptides with antibacterial activity that may shape the microbiome on the body surface. In particular, a specific neuropeptide, which we call NDA-1, contributes to the reduction of Gram-positive bacteria during early development and thus to a spatial distribution of the main colonizer, the Gram-negative Curvibacter sp.

Three Complete Genome Sequences of Genotype G Mumps Virus from the 2016 Outbreak in Arkansas, USA.

We present here the complete genome sequences of three mumps virus (MuV) strains isolated from patients who tested positive for the mumps virus during a mumps outbreak in Springdale, AR (USA), in 2016. The virus genomes, sequenced with Oxford Nanopore technology, belong to genotype G and have an average length of 15,342 nucleotides (nt).

Insights from 100 Years of Research with Probiotic .

A century ago, Alfred Nissle discovered that intentional intake of particular strains of could treat patients suffering from infectious diseases. Since then, one of these strains became the most frequently used probiotic in research and was applied to a variety of human conditions. Here, properties of that Nissle 1917 strain are compared with other commercially available probiotic strains, with emphasis on their human applications.

The Gene Has Recently Spread between Rolling Circle Plasmids of , Indicative of a Novel Gene Transfer Mechanism.

Resistance of species to quaternary ammonium compounds, frequently used as disinfectants and biocides, can be attributed to genes. Most gene products belong to the Small Multidrug Resistant (SMR) protein family, and are often encoded by rolling-circle (RC) replicating plasmids. Four classes of SMR-type gene families have been described in species: , and .

Integrated MRSA-Management (IMM) with prolonged decolonization treatment after hospital discharge is effective: a single centre, non-randomised open-label trial.

Background: Guidelines for the control of hospital-acquired MRSA include decolonization measures to end MRSA carrier status in colonized and infected patients. Successful decolonization typically requires up to 22 days of treatment, which is longer than the average hospital length of stay (LOS). Incomplete decolonization is therefore common, with long-term MRSA carriage as a consequence.

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity.

Ebolavirus comparative genomics.

The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes.

The prediction of virulence based on presence of virulence genes in E. coli may not always be accurate.

Now that microbial whole genome sequencing is in reach of many researchers, it is common to infer virulent properties of a given bacterial isolate based on the presence of virulence genes. However, this may lead to inaccurate presumptions of virulence. Using the findings of a recent publication (Da Silva Santos et al.