Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean.

Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477).

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA.

Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the evidence available from transcriptomes and proteomes vary across genomes, between genes, and even along a single gene.

GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.

Large-scale genomic initiatives, such as the Earth BioGenome Project, require efficient methods for eukaryotic genome annotation. Here we present an automatic gene finder, GeneMark-ETP, integrating genomic-, transcriptomic-, and protein-derived evidence that has been developed with a focus on large plant and animal genomes. GeneMark-ETP first identifies genomic loci where extrinsic data are sufficient for making gene predictions with "high confidence.

Species-Specific Responses of Insectivorous Bats to Weather Conditions in Central Chile.

Insectivorous bats play a crucial role in agroecosystems by providing invaluable pest control services. With the escalating impacts of climate change, a comprehensive understanding of the environmental factors influencing bat activity becomes imperative for their conservation in agricultural landscapes. This study investigates the influence of weather conditions, specifically air temperature and relative humidity, on the timing activity and the relative abundance of five insectivorous bat species in central Chile.

The first two chromosome-scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus.

The native, perennial shrub American hazelnut (Corylus americana) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high-value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high-quality reference genomes, a resource that is currently lacking.

Galba: genome annotation with miniprot and AUGUSTUS.

Background: The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes.

Results: Various gene annotation tools have been developed but each has its limitations.

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA.

Gene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the evidence available from transcriptomes and proteomes vary across genomes, between genes and even along a single gene.

β-Cyclodextrin Nanosponges Inclusion Compounds Associated with Silver Nanoparticles to Increase the Antimicrobial Activity of Quercetin.

This work aimed to synthesize and characterize a nanocarrier that consisted of a ternary system, namely β-cyclodextrin-based nanosponge (NS) inclusion compounds (ICs) associated with silver nanoparticles (AgNPs) to increase the antimicrobial activity of quercetin (QRC). The nanosystem was developed to overcome the therapeutical limitations of QRC. The host-guest interaction between NSs and QRC was confirmed by field emission scanning electron microscopy (FE-SEM), X-ray powder diffraction (XRPD), thermogravimetric analysis (TGA), and proton nuclear magnetic resonance (H-NMR).

GALBA: Genome Annotation with Miniprot and AUGUSTUS.

The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. Various gene annotation tools have been developed but each has its limitations.

A new gene finding tool GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.

Large-scale genomic initiatives, such as the Earth BioGenome Project, require efficient methods for eukaryotic genome annotation. Here we present an automatic gene finder, GeneMark-ETP, integrating genomic-, transcriptomic- and protein-derived evidence that has been developed with a focus on large plant and animal genomes. GeneMark-ETP first identifies genomic loci where extrinsic data is sufficient for making gene predictions with 'high confidence'.

A Modeled High-Density Fed-Batch Culture Improves Biomass Growth and β-Glucans Accumulation in .

Algae and microalgae are used as a source of different biomolecules, such as lipids and carbohydrates. Among carbohydrates, polysaccharides, such as β-glucans, are important for their application as antioxidants, antisepsis, and immunomodulators. In the present work, the β-glucans production potential of was assessed using two different culture conditions: a high-density batch and a modeled high-density fed-batch.

A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. "Hillquist").

Blackberries (Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus, including black raspberry (R.

New Insights on the Role of Connexins and Gap Junctions Channels in Adipose Tissue and Obesity.

Due to the inability to curb the excessive increase in the prevalence of obesity and overweight, it is necessary to comprehend in more detail the factors involved in the pathophysiology and to appreciate more clearly the biochemical and molecular mechanisms of obesity. Thus, understanding the biological regulation of adipose tissue is of fundamental relevance. Connexin, a protein that forms intercellular membrane channels of gap junctions and unopposed hemichannels, plays a key role in adipogenesis and in the maintenance of adipose tissue homeostasis.

TSEBRA: transcript selector for BRAKER.

Background: BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains statistical models of protein-coding genes based on provided evidence and, then predicts protein-coding genes in genomic sequences using both the extrinsic evidence and statistical models. For training and prediction, BRAKER1 and BRAKER2 incorporate complementary extrinsic evidence: BRAKER1 uses only RNA-seq data while BRAKER2 uses only a database of cross-species proteins.

Silver Nanoparticles and Their Antibacterial Applications.

Silver nanoparticles (AgNPs) have been imposed as an excellent antimicrobial agent being able to combat bacteria in vitro and in vivo causing infections. The antibacterial capacity of AgNPs covers Gram-negative and Gram-positive bacteria, including multidrug resistant strains. AgNPs exhibit multiple and simultaneous mechanisms of action and in combination with antibacterial agents as organic compounds or antibiotics it has shown synergistic effect against pathogens bacteria such as and .

BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.

The task of eukaryotic genome annotation remains challenging. Only a few genomes could serve as standards of annotation achieved through a tremendous investment of human curation efforts. Still, the correctness of all alternative isoforms, even in the best-annotated genomes, could be a good subject for further investigation.

Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of .

Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genome of cells. The distribution of rNMPs in DNA has been studied only in limited genomes. Using the ribose-seq protocol and the Ribose-Map bioinformatics toolkit, we reveal the distribution of rNMPs incorporated into the whole genome of a photosynthetic unicellular green alga, .

GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins.

We have made several steps toward creating a fast and accurate algorithm for gene prediction in eukaryotic genomes. First, we introduced an automated method for efficient gene finding, GeneMark-ES, with parameters trained in iterative mode. Next, in GeneMark-ET we proposed a method of integration of unsupervised training with information on intron positions revealed by mapping short RNA reads.

A surface functionalized with per-(6-amino-6-deoxy)-β-cyclodextrin for potential organic pollutant removal from water.

In this work, we present a solid silicon substrate functionalized with modified β-cyclodextrin monolayers as an optimal surface for organic contaminant uptake. The inclusion and capture of three potential pollutants, 4-chlorophenoxyacetic acid, 4-aminobenzoic acid and phenylethylamine, were studied. H-NMR and ROESY studies revealed the complete inclusion and details of the conformational orientation of the three guests in the per-(6-amino-6-deoxy)-β-cyclodextrin matrix, forming three new inclusion complexes that have not yet been reported.

Florfenicol Binding to Molecularly Imprinted Polymer Nanoparticles in Model and Real Samples.

A simple and straightforward technique for coating microplate wells with molecularly imprinted polymer nanoparticles (nanoMIPs) to develop assays similar to the enzyme-linked immunosorbent (ELISA) assay to determine and quantify florfenicol (FF) in real food samples such as liquid milk and salmon muscle is presented here. The nanoMIPs were synthesized by a solid-phase approach with an immobilized FF (template) and characterized using dynamic light scattering, a SPR-2 biosensor system and transmission electron microscopy. Immobilization of nanoMIPs was conducted by preparing a homogenous solution of FF-nanoMIPs in water mixed with polyvinyl alcohol (PVA) 0.

Evaluation of respiratory chain activity in lymphocytes of patients with Alzheimer disease.

Alzheimer disease (AD) is a progressive neurodegenerative disease associated with cognitive impairment in multiple domains, such as memory and executive functions. Studies reveal damage in the electron transport chain of patients with AD, suggesting that this mitochondrial dysfunction plays an important role in the pathophysiology of the disease. Blood samples were taken from patients with AD (n = 20) and older subjects without dementia (n = 40) to evaluate the activity of complexes I, II, II-III, and IV of the mitochondrial respiratory chain in isolated lymphocytes.

In vivo pefloxacin-resistant Campylobacter fetus responsible for gastro-intestinal infection and bacteremia associated with arthritis of the hip.

The authors report a case of Campylobacter fetus subsp. fetus gastro-intestinal infection and bacteremia with poly-arthritis, mainly of the hip, in a French patient simultaneously suffering from cirrhosis of the liver. The outcome was eventually favorable, however only after a trial of ineffective pefloxacin-gentamicin therapy.

Cerebral potentials evoked by electrical stimulation of the anal canal.

We describe the procedure with which cortical potential responses are evoked by a stimulation of the anal canal to assess the integrity of its sensory pathways. These potentials were recorded in 66 patients. In 44 patients, a cortical evoked response was obtained with a succession of positive and negative peaks, W shaped (35 cases) or V shaped (nine cases).