Developments in Plant Proteins Production for Meat and Fish Analogues.

In recent years, there have been significant developments in plant proteins production for meat and fish analogues. Some of the key developments include the use of new plant protein sources such as soy, legumes, grains, potatoes, and seaweed, as well as insect proteins, leaf proteins, mushrooms, and microbial proteins. Furthermore, to improve the technological and functional properties of plant proteins, they can be subjected to traditional and unconventional treatments such as chemical (glycosylation, deamidation, phosphorylation, and acylation), physical (pulsed electric fields, ultrasound, high hydrostatic pressure, dynamic high-pressure treatment, and cold plasma), and biological (fermentation and enzymatic modification).

Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites.

Adaptive radiation is an important mechanism of organismal diversification and can be triggered by new ecological opportunities. Although poorly studied in this regard, parasites are an ideal group in which to study adaptive radiations because of their close associations with host species. Both experimental and comparative studies suggest that the ectoparasitic wing lice of pigeons and doves have adaptively radiated, leading to differences in body size and overall coloration.

Brain Tissue-Derived Extracellular Vesicle Mediated Therapy in the Neonatal Ischemic Brain.

Hypoxic-Ischemic Encephalopathy (HIE) in the brain is the leading cause of morbidity and mortality in neonates and can lead to irreparable tissue damage and cognition. Thus, investigating key mediators of the HI response to identify points of therapeutic intervention has significant clinical potential. Brain repair after HI requires highly coordinated injury responses mediated by cell-derived extracellular vesicles (EVs).

Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini.

We investigated the prevalence of coronaviruses in 44 bats from four families in northeastern Eswatini using high-throughput sequencing of fecal samples. We found evidence of coronaviruses in 18% of the bats. We recovered full or near-full-length genomes from two bat species: Chaerephon pumilus and Afronycteris nana, as well as additional coronavirus genome fragments from C.

Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers.

Extrachromosomal DNA (ecDNA) amplification promotes intratumoral genetic heterogeneity and accelerated tumor evolution; however, its frequency and clinical impact are unclear. Using computational analysis of whole-genome sequencing data from 3,212 cancer patients, we show that ecDNA amplification frequently occurs in most cancer types but not in blood or normal tissue. Oncogenes were highly enriched on amplified ecDNA, and the most common recurrent oncogene amplifications arose on ecDNA.

Author Correction: Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.

Many cellular models aimed at elucidating cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance. Here we introduce a cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that captures authentic cancer pathobiology. Orthotopic engraftment of the neural progenitor cells derived from hiPSCs that have been genome-edited to contain tumor-associated genetic driver mutations revealed by The Cancer Genome Atlas project for glioblastoma (GBM) results in formation of high-grade gliomas.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments.

Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus.

Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e.

Simultaneous radiation of bird and mammal lice following the K-Pg boundary.

The diversification of parasite groups often occurs at the same time as the diversification of their hosts. However, most studies demonstrating this concordance only examine single host-parasite groups. Multiple diverse lineages of ectoparasitic lice occur across both birds and mammals.

ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer.

The integration of viral sequences into the host genome is an important driver of tumorigenesis in many viral mediated cancers, notably cervical cancer and hepatocellular carcinoma. We present ViFi, a computational method that combines phylogenetic methods with reference-based read mapping to detect viral integrations. In contrast with read-based reference mapping approaches, ViFi is faster, and shows high precision and sensitivity on both simulated and biological data, even when the integrated virus is a novel strain or highly mutated.

Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice.

Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins.

HIPPI: highly accurate protein family classification with ensembles of HMMs.

Background: Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon identification and abundance profiling, among others. Yet family identification of sequences that are distantly related to sequences in public databases or that are fragmentary remains one of the more difficult analytical problems in bioinformatics.

Results: We present a new technique for family identification called HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification).

Phylogenomics from Whole Genome Sequences Using aTRAM.

Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data.

Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola).

Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense.

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity.

The standard pipeline for 16S amplicon analysis starts by clustering sequences within a percent sequence similarity threshold (typically 97%) into 'Operational Taxonomic Units' (OTUs). From each OTU, a single sequence is selected as a representative. This representative sequence is annotated, and that annotation is applied to all remaining sequences within that OTU.

Helmet regulation in Vietnam: impact on health, equity and medical impoverishment.

Background: Vietnam's 2007 comprehensive motorcycle helmet policy increased helmet use from about 30% of riders to about 93%. We aimed to simulate the effect that this legislation might have on: (a) road traffic deaths and non-fatal injuries, (b) individuals' direct acute care injury treatment costs, (c) individuals' income losses from missed work and (d) individuals' protection against medical impoverishment.

Methods And Findings: We used published secondary data from the literature to perform a retrospective extended cost-effectiveness analysis simulation study of the policy.

Ultra-large alignments using phylogeny-aware profiles.

Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments and phylogenetic trees of large datasets. However, accurate large-scale multiple sequence alignment is very difficult, especially when the dataset contains fragmentary sequences. We present UPP, a multiple sequence alignment method that uses a new machine learning technique, the ensemble of hidden Markov models, which we propose here.

TIPP: taxonomic identification and phylogenetic profiling.

Motivation: Abundance profiling (also called 'phylogenetic profiling') is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads.

Results: We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP combines SAT\'e-enabled phylogenetic placement a phylogenetic placement method, with statistical techniques to control the classification precision and recall, and results in improved abundance profiles.

Role of alcohol in hospitalized road trauma in Viet nam.

Objective: To assess the blood alcohol concentration (BAC; dependent variable) of patients with road traffic injuries (RTIs) presenting at 3 provincial and central hospitals in the Socialist Republic of Viet Nam by age, sex, and road user type (independent variables). This survey formed part of the Viet Nam Road Traffic Injury Prevention Project, funded by Bloomberg Philanthropies.

Introduction: RTIs are a leading cause of death and disability in Viet Nam, with 14,690 deaths and 143,940 injuries reported by the Ministry of Health (MOH) in 2010.

Measuring compliance with Viet Nam's mandatory motorcycle helmet legislation.

The objective of this roadside observational study was to monitor helmet wearing among motorcycle riders and passengers in three provinces (Yen Bai, Da Nang and Binh Duong) in the Socialist Republic of Viet Nam, before and after a mandatory helmet law took effect on 15 December 2007. A total of 665,428 motorcycle riders and passengers were observed between November 2007 and February 2011 at 45 randomly selected sites covering the entire road network. Across all locations and time periods, correct helmet wearing averaged 40.