Archaea: An under-estimated kingdom in livestock animals

Archaea are considered an essential group of gut microorganisms in both humans and animals. However, they have been neglected in previous studies, especially those involving non-ruminants. In this study, we re-analyzed published metagenomic and metatranscriptomic data sequenced from matched samples to explore the composition and the expression activity of gut archaea in ruminants (cattle and sheep) and monogastric animals (pig and chicken). Our results showed that the alpha and beta diversity of each host species, especially cattle and chickens, calculated from metagenomic and metatranscriptomic data were significantly different, suggesting that metatranscriptomic data better represent the functional status of archaea. We detected that the relative abundance of 17 (cattle), 7 (sheep), 20 (pig), and 2 (chicken) archaeal species were identified in the top 100 archaeal taxa when analyzing the metagenomic datasets, and these species were classified as the “active archaeal species” for each host species by comparison with corresponding metatranscriptomic data. For example, The expressive abundance in metatranscriptomic dataset of Methanosphaera cuniculi and Methanosphaera stadtmanae were 30- and 27-fold higher than that in metagenomic abundance, indicating their potentially important function in the pig gut. Here we aim to show the potential importance of archaea in the livestock digestive tract and encourage future research in this area, especially on the gut archaea of monogastric animals

The role of gut archaea in the pig gut microbiome: a mini-review

The gastrointestinal microbiota of swine harbors an essential but often overlooked component: the gut archaea. These enigmatic microorganisms play pivotal roles in swine growth, health, and yield quality. Recent insights indicate that the diversity of gut archaea is influenced by various factors including breed, age, and diet. Such factors orchestrate the metabolic interactions within the porcine gastrointestinal environment. Through symbiotic relationships with bacteria, these archaea modulate the host’s energy metabolism and digestive processes. Contemporary research elucidates a strong association between the abundance of these archaea and economically significant traits in swine. This review elucidates the multifaceted roles of gut archaea in swine and underscores the imperative for strategic interventions to modulate their population and functionality. By exploring the probiotic potential of gut archaea, we envisage novel avenues to enhance swine growth, health, and product excellence. By spotlighting this crucial, yet under-investigated, facet of the swine gut microbiome, we aim to galvanize further scientific exploration into harnessing their myriad benefits

Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction

In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding RNA genes, such as miRNA and lncRNA. Two main aspects of ab initio gene prediction include the computed values for describing sequence features and used algorithm for training the discriminant function, and by which different combinations are employed into various bioinformatic tools. Herein, we briefly review these well-characterized sequence features in eukaryote genomes and applications to ab initio gene prediction. The main purpose of this article is to provide an overview to beginners who aim to develop the related bioinformatic tools

PopSc in Python and R

PopSc is a bioinformatic toolkit for calculating 45 basic statistics in molecular population genetics, which could be categorized into three classes, including (i) genetic diversity of DNA sequences, (ii) statistical tests for neutral evolution, and (iii) measures of genetic differentiation among populations. The project web of PopSc is at <a href="http://chenshiyi.com/popsc.html">http://chenshiyi.com/popsc.html</a>

A novel polymorphism in the 3′ untranslated region of rabbit TAS1R1 is associated with growth performance and carcass traits but not meat quality

The aim of this study was to investigate the relationship between polymorphisms of the 3′ untranslated region of TAS1R1 and growth traits, carcass traits, and meat quality traits in rabbit. We detected one single nucleotide polymorphism located at 9120 bp (g.9120A>C) in the 3′ untranslated region of TAS1R1 gene by using polymerase chain reaction sequencing. The novel mutation g.9120A>C was subsequently genotyped by MassArray system (Sequenom iPLEX assay) in 249 samples of three breeds (Hyla, 91 animals; Champagne, 84 animals; Tianfu Black, 74 animals). Association analysis suggested that the individuals with AC genotype showed greater body weight at 70 d of age (P < 0.01), body weight at 84 d of age (P < 0.05), and average daily weight gain from 28 to 84 d of age (P < 0.05) than AA. In addition, the individuals with AC genotype had a lower eviscerated slaughter percentage (P < 0.05) and semieviscerated slaughter percentage (P < 0.05). However, association of the genotypes with other production traits was not observed. The results indicate TAS1R1 is one of the candidate genes affecting growth performance and dressing percentage in rabbits, and this may be of potential use in marker-assisted selection for meat quality traits in rabbits.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Micro-/nano-topography of selective laser melting titanium enhances adhesion and proliferation and regulates adhesion-related gene expressions of human gingival fibroblasts and human gingival epithelial cells

Background: Selective laser melting (SLM) titanium is an ideal option to manufacture customized implants with suitable surface modification to improve its bioactivity. The peri-implant soft tissues form a protective tissue barrier for the underlying osseointegration. Therefore, original microrough SLM surfaces should be treated for favorable attachment of surrounding soft tissues. Material and methods: In this study, anodic oxidation (AO) was applied on the microrough SLM titanium substrate to form TiO2 nanotube arrays. After that, calcium phosphate (CaP) nanoparticles were embedded into the nanotubes or the interval of nanotubes by electrochemical deposition (AOC). These two samples were compared to untreated (SLM) samples and accepted mechanically polished (MP) SLM titanium samples. Scanning electron microscopy, energy dispersive spectrometry, X-ray diffraction, surface roughness, and water contact angle measurements were used for surface characterization. The primary human gingival epithelial cells (HGECs) and human gingival fibroblasts (HGFs) were cultured for cell assays to determine adhesion, proliferation, and adhesion-related gene expressions. Results: For HGECs, AOC samples showed significantly higher adhesion, proliferation, and adhesion-related gene expressions than AO and SLM samples (P&lt;0.05) and similar exceptional ability in above aspects to MP samples. At the same time, AOC samples showed the highest adhesion, proliferation, and adhesion-related gene expressions for HGFs (P&lt;0.05). Conclusion: By comparison between each sample, we could confirm that both anodic oxidation and CaP nanoparticles had improved bioactivity, and their combined utilization may likely be superior to mechanical polishing, which is most commonly used and widely accepted. Our results indicated that creating appropriate micro-/nano-topographies can be an effective method to affect cell behavior and increase the stability of the peri-implant mucosal barrier on SLM titanium surfaces, which contributes to its application in dental and other biomedical implants

Generation Mechanism of Nonlinear Rayleigh Surface Waves for Randomly Distributed Surface Micro-Cracks

This paper investigates the propagation of Rayleigh surface waves in structures with randomly distributed surface micro-cracks using numerical simulations. The results revealed a significant ultrasonic nonlinear effect caused by the surface micro-cracks, which is mainly represented by a second harmonic with even more distinct third/quadruple harmonics. Based on statistical analysis from the numerous results of random micro-crack models, it is clearly found that the acoustic nonlinear parameter increases linearly with micro-crack density, the proportion of surface cracks, the size of micro-crack zone, and the excitation frequency. This study theoretically reveals that nonlinear Rayleigh surface waves are feasible for use in quantitatively identifying the physical characteristics of surface micro-cracks in structures

Formation of anodic TiO₂ nanotube arrays with bimodal pore size distribution

It is revealed that TiO2 nanotube arrays fabricated by anodization of the widely used polycrystalline hexagonal Ti foils have a bimodal pore size distribution rather than the commonly believed monomodal distribution manner. As characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM), it is shown that nanotubes grown on the Ti (0001) plane have thinner barrier thickness, smaller pore size, shorter tube length and better crystallinity than those grown on other planes, due to the enhanced electron transfer reaction and lower oxide formation efficiency on the Ti (0001) plane. When (0001) oriented Ti thin films deposited by RF magnetron sputtering are anodized, the pore sizes of the grown anodic TiO2 nanotubes distribute monomodally and are close to the smaller pore size of the bimodally distributed TiO2 nanotubes grown on polycrystalline Ti foils under the same conditions. Keywords: TiO2 nanotubes, Pore size distribution, Electrochemical anodization, Crystallographic orientatio