Effects of antibiotic growth promoter and its natural alternative on poultry cecum ecosystem: an integrated analysis of gut microbiota and host expression.

Background: In-feed antibiotic growth promoters (AGPs) have been a cornerstone in the livestock industry due to their role in enhancing growth and feed efficiency. However, concerns over antibiotic resistance have driven a shift away from AGPs toward natural alternatives. Despite the widespread use, the exact mechanisms of AGPs and alternatives are not fully understood.

Developing Eco-Friendly 3D-Printing Composite Filament: Utilizing Palm Midrib to Reinforce High-Density Polyethylene Matrix in Design Applications.

Designers actively pursue the use of novel materials and concepts in furniture and interior design. By providing insights into their processing behavior and suitability for 3D-printing processes, this research helps to highlight the potential of using waste materials to create more environmentally friendly and sustainable 3D-printing filaments that can be used in furniture and interior design. Furthermore, the study evaluates the effect of incorporating palm midrib nanoparticles (DPFNPs) to reinforce a high-density polyethylene (HDPE) matrix with different loadings such as 10, 20, 30, 40, and 50 wt.

Unveiling microbial biomarkers of ruminant methane emission through machine learning.

Background: Enteric methane from cow burps, which results from microbial fermentation of high-fiber feed in the rumen, is a significant contributor to greenhouse gas emissions. A promising strategy to address this problem is microbiome-based precision feed, which involves identifying key microorganisms for methane production. While machine learning algorithms have shown success in associating human gut microbiome with various human diseases, there have been limited efforts to employ these algorithms to establish microbial biomarkers for methane emissions in ruminants.

Development of a workflow for the selection, identification and optimization of lactic acid bacteria with high γ-aminobutyric acid production.

Lactic acid bacteria produce γ-aminobutyric acid (GABA) as an acid stress response. GABA is a neurotransmitter that may improve sleep and resilience to mental stress. This study focused on the selection, identification and optimization of a bacterial strain with high GABA production, for development as a probiotic supplement.

Insights into the implication of obesity in hypogonadism among adolescent boys.

Objectives: This research aimed at uncovering the mechanisms behind obesity-related hypogonadism in adolescent boys and to investigate the association between anthropometric characteristics and testicular functions of these boys.

Methods: This study included 60 adolescent boys (12-18 years) with exogenous obesity (BMI≥95th percentile) and 30 age matched lean controls (BMI=15th-85th percentile). Full clinical examination, anthropometric measurements and pubertal assessment were performed.

Mitochondrial DNA maintenance defects: potential therapeutic strategies.

Mitochondrial DNA (mtDNA) replication depends on the mitochondrial import of hundreds of nuclear encoded proteins that control the mitochondrial genome maintenance and integrity. Defects in these processes result in an expanding group of disorders called mtDNA maintenance defects that are characterized by mtDNA depletion and/or multiple mtDNA deletions with variable phenotypic manifestations. As it applies for mitochondrial disorders in general, current treatment options for mtDNA maintenance defects are limited.

Genetic Elements Orchestrating Glycogen Metabolism in the Vagina.

Glycogen in the female lower reproductive tract is a major carbon source for colonization and acidification by common vaginal species, such as . Previously, we identified the amylopullulanase encoding gene of to correlate with the ability to autonomously utilize glycogen for growth. Here, we further characterize genetic variation and differential regulation of affecting the presence of its gene product on the outer surface layer.

Addressing Discrepancies between Experimental and Computational Procedures.

Imaging subject-specific heart valve, a crucial step to its design, has experimental variables that if unaccounted for, may lead to erroneous computational analysis and geometric errors of the resulting model. Preparation methods are developed to mitigate some sources of the geometric error. However, the resulting 3D geometry often does not retain the original dimensions before excision.

Brain Network Analysis of EEG Recordings Can Be Used to Assess Cognitive Function in Teenagers With 15q13.3 Microdeletion Syndrome.

15q13.3 microdeletion syndrome causes a spectrum of cognitive disorders, including intellectual disability and autism. We assessed the ability of the EEG analysis algorithm Brain Network Analysis (BNA) to measure cognitive function in 15q13.

Clinical trials in mitochondrial disorders, an update.

Mitochondrial disorders comprise a molecular and clinically diverse group of diseases that are associated with mitochondrial dysfunction leading to multi-organ disease. With recent advances in molecular technologies, the understanding of the pathomechanisms of a growing list of mitochondrial disorders has been greatly expanded. However, the therapeutic approaches for mitochondrial disorders have lagged behind with treatment options limited mainly to symptom specific therapies and supportive measures.

On the Role of Bioinformatics and Data Science in Industrial Microbiome Applications.

Advances in sequencing and computational biology have drastically increased our capability to explore the taxonomic and functional compositions of microbial communities that play crucial roles in industrial processes. Correspondingly, commercial interest has risen for applications where microbial communities make important contributions. These include food production, probiotics, cosmetics, and enzyme discovery.

Novel sequencing technologies to support industrial biotechnology.

Industrial biotechnology develops and applies microorganisms for the production of bioproducts and enzymes with applications ranging from food and feed ingredients and processing to bio-based chemicals, biofuels and pharmaceutical products. Next generation DNA sequencing technologies play an increasingly important role in improving and accelerating microbial strain development for existing and novel bio-products via screening, gene and pathway discovery, metabolic engineering and additional optimization and understanding of large-scale manufacturing. In this mini-review, we describe novel DNA sequencing and analysis technologies with a focus on applications to industrial strain development, enzyme discovery and microbial community analysis.

Hormonal, metabolic and skeletal phenotype of Schaaf-Yang syndrome: a comparison to Prader-Willi syndrome.

Background: Nonsense and frameshift mutations in the maternally imprinted, paternally expressed gene located in the Prader-Willi critical region 15q11-15q13, have been reported to cause Schaaf-Yang syndrome (SYS), a genetic disorder that manifests as developmental delay/intellectual disability, hypotonia, feeding difficulties and autism spectrum disorder. Prader-Willi syndrome (PWS) is a genetic disorder characterised by severe infantile hypotonia, hypogonadotrophic hypogonadism, early childhood onset obesity/hyperphagia, developmental delay/intellectual disability and short stature. Scoliosis and growth hormone insufficiency are also prevalent in PWS.

High-Resolution Screening of Viral Communities and Identification of New Pathogens in Fish Using Next-Generation Sequencing.

Discovery of viral genomes in fish has historically been based on viral enrichment, random priming, cloning, and Sanger sequencing. However, the development of next-generation sequencing has enabled the possibility to sequence the entire virome of a tissue sample. This has led to an enormous increase in discovery of new viruses.

The complex behavioral phenotype of 15q13.3 microdeletion syndrome.

Background: Chromosome 15q13.3 represents a hotspot for genomic rearrangements due to repetitive sequences mediating nonallelic homologous recombination. Deletions of 15q13.

Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping.

Candida albicans biofilm formation is an important virulence factor in the pathogenesis of disease, a characteristic which has been shown to be heterogeneous in clinical isolates. Using an unbiased computational approach we investigated the central metabolic pathways driving biofilm heterogeneity. Transcripts from high (HBF) and low (LBF) biofilm forming isolates were analysed by RNA sequencing, with 6312 genes identified to be expressed in these two phenotypes.

Assessment of Cognitive Outcome Measures in Teenagers with 15q13.3 Microdeletion Syndrome.

15q13.3 microdeletion syndrome causes a spectrum of cognitive disorders, including intellectual disability and autism. We aimed to determine if any or all of three cognitive testing systems (the KiTAP, CogState, and Stanford-Binet) are suitable for assessment of cognitive function in affected individuals.

metaModules identifies key functional subnetworks in microbiome-related disease.

Motivation: The human microbiome plays a key role in health and disease. Thanks to comparative metatranscriptomics, the cellular functions that are deregulated by the microbiome in disease can now be computationally explored. Unlike gene-centric approaches, pathway-based methods provide a systemic view of such functions; however, they typically consider each pathway in isolation and in its entirety.

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.

Massively parallel sequencing of microbial genetic markers (MGMs) is used to uncover the species composition in a multitude of ecological niches. These sequencing runs often contain a sample with known composition that can be used to evaluate the sequencing quality or to detect novel sequence variants. With NGS-eval, the reads from such (mock) samples can be used to (i) explore the differences between the reads and their references and to (ii) estimate the sequencing error rate.

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations.

Motivation: 16S rDNA pyrosequencing is a powerful approach that requires extensive usage of computational methods for delineating microbial compositions. Previously, it was shown that outcomes of studies relying on this approach vastly depend on the choice of pre-processing and clustering algorithms used. However, obtaining insights into the effects and accuracy of these algorithms is challenging due to difficulties in generating samples of known composition with high enough diversity.

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins.

Motivation: To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full atomistic molecular simulation methods do have this potential, but are completely unfeasible for large-scale applications in terms of computational cost required.

Presymptomatic differences in Toll-like receptor function in infants who have allergy.

Background: Microbial exposure might play a key role in allergy development, but little is known about the role of Toll-like receptors (TLRs).

Objective: This study explored the association between neonatal TLR microbial recognition/function, allergy risk (maternal allergy), and prospective allergy development.

Methods: Cord blood mononuclear cells (n = 111) were cultured either alone or with optimal concentrations of TLR ligands: lipoteichoic acid (TLR2), polyinosinicpolycytidylic acid (TLR3), LPS with IFN-gamma (TLR4), flagellin (TLR5), imiquimod R837 (TLR7), or CpG (TLR9).

NOS1 polymorphism is associated with atopy but not exhaled nitric oxide levels in healthy children.

Exhaled nitric oxide (FENO) is raised in atopy. The mechanism for this is unclear. The aim of this study was to investigate whether the number of AAT repeats in intron 20 of the NOS1 gene, recently associated with variations in FENO in adults with asthma and cystic fibrosis, was associated with the raised FENO in healthy atopic children.