What are microsatellites and how to choose the best tool: a user-friendly review of SSR and 74 SSR mining tools.

Microsatellites, also known as SSR or STR, are essential molecular markers in genomic research, playing crucial roles in genetic mapping, population genetics, and evolutionary studies. Their applications range from plant breeding to forensics, highlighting their diverse utility across disciplines. Despite their widespread use, traditional methods for SSR analysis are often laborious and time-consuming, requiring significant resources and expertise.

Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2.

Background: Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be beneficial when administered as probiotics. In mycology, the internal transcribed spacer (ITS) region was adopted as the universal marker for classifying fungi.

Arapaima gigas stocks have declined drastically in the lower Tocantins River in the Amazon Microregion.

Arapaima gigas, an emblematic species of the Amazon region and a longstanding primary fishing resource, currently holds a "Data Deficient" status on the International Union for Conservation of Nature Red List, and is listed as an endangered species in Brazil. The Tocantins River is the most extensively modified large tributary of the Amazon Basin, and thus can affect the dynamics of ichthyofaunal populations. Over a period of 1 year, representatives of the fishing communities and fishermen from 25 fishing communities from four municipalities in the lower Tocantins River region were interviewed, and the obtained information was evaluated based on the literature to survey the population abundance status of A.

SATIN: a micro and mini satellite mining tool of total genome and coding regions with analysis of perfect repeats polymorphism in coding regions.

Background: Tandem repeats are specific sequences in genomic DNA repeated in tandem that are present in all organisms. Among the subcategories of TRs we have Satellite repeats, that is divided into macrosatellites, minisatellites, and microsatellites, being the last two of specific interest because they can identify polymorphisms between organisms due to their instability. Currently, most mining tools focus on Simple Sequence Repeats (SSR) mining, and only a few can identify SSRs in the coding regions.

Tools and methodology to phage discovery in freshwater environments.

Freshwater availability is essential, and its maintenance has become an enormous challenge. Due to population growth and climate changes, freshwater sources are becoming scarce, imposing the need for strategies for its reuse. Currently, the constant discharge of waste into water bodies from human activities leads to the dissemination of pathogenic bacteria, negatively impacting water quality from the source to the infrastructure required for treatment, such as the accumulation of biofilms.

Whole-genome sequencing analysis of multidrug-resistant Serratia marcescens isolates in an intensive care unit in Brazil.

Introduction: Serratia marcescens is an opportunistic pathogen found ubiquitously in the environment and associated with a wide range of nosocomial infections. This multidrug-resistant bacterium has been a cause of concern for hospitals and healthcare facilities due to its ability to spread rapidly and cause outbreaks. Next generation sequencing genotyping of bacterial isolates has proven to be a valuable tool for tracking the spread and transmission of nosocomial infections.

EasySSR: a user-friendly web application with full command-line features for large-scale batch microsatellite mining and samples comparison.

Microsatellites, also known as SSRs or STRs, are polymorphic DNA regions with tandem repetitions of a nucleotide motif of size 1-6 base pairs with a broad range of applications in many fields, such as comparative genomics, molecular biology, and forensics. However, the majority of researchers do not have computational training and struggle while running command-line tools or very limited web tools for their SSR research, spending a considerable amount of time learning how to execute the software and conducting the post-processing data tabulation in other tools or manually-time that could be used directly in data analysis. We present EasySSR, a user-friendly web tool with command-line full functionality, designed for practical use in batch identifying and comparing SSRs in sequences, draft, or complete genomes, not requiring previous bioinformatic skills to run.

Environmental Biofilms from an Urban Community in Salvador, Brazil, Shelter Previously Uncharacterized Saprophytic Leptospira.

Biofilms are complex microecosystems with valuable ecological roles that can shelter a variety of microorganisms. Spirochetes from the genus Leptospira have been observed to form biofilms in vitro, in rural environments, and in the kidneys of reservoir rats. The genus Leptospira is composed of pathogenic and non-pathogenic species, and the description of new species is ongoing due to the advent of whole genome sequencing.

Immunoexpression of stem cell markers SOX-2, NANOG AND OCT4 in ameloblastoma.

Background: Ameloblastoma (AME) is characterized by a locally invasive growth pattern. In an attempt to justify the aggressiveness of neoplasms, the investigation of the role of stem cells has gained prominence. The SOX-2, NANOG and OCT4 proteins are important stem cell biomarkers.

The pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum.

Corynebacterium striatum, a common constituent of the human skin microbiome, is now considered an emerging multidrug-resistant pathogen of immunocompromised and chronically ill patients. However, little is known about the molecular mechanisms in the transition from colonization to the multidrug-resistant (MDR) invasive phenotype in clinical isolates. This study performed a comprehensive pan-genomic analysis of C.

Pan-genomic analysis of gives insights into molecular mechanisms underpinning the transition to a pathogenic phenotype.

is a nonlipophilic coryneform which is increasingly being recognized as a relevant human and animal pathogen showing multidrug resistance to commonly used antibiotics. However, little is known about the molecular mechanisms involved in transition from colonization to the MDR invasive phenotype in clinical isolates. In this study, we performed a comprehensive pan-genomic analysis of , including 26 isolates from different countries.

approach to identify microsatellite candidate biomarkers to differentiate the biovar of genomes.

is the causative bacterial agent of the zoonotic disease known as caseous lymphadenitis, and it presents several mechanisms of response to host defenses, including the presence of virulence factors (VFs). The genomes of these bacteria have several polymorphic markers known as microsatellites, or simple sequence repeats (SSRs), that can be used to characterize the genome, to study possible polymorphisms existing among strains, and to verify the effects of such polymorphic markers in coding regions and regions associated with VFs. In this study, several SSRs were identified within coding regions throughout the 54 genomes of this species, revealing possible polymorphisms associated with coding regions that could be used as strain-specific or serotype-specific identifiers of .

Strain AE59-TE2 Is Highly Antagonistic towards Multidrug-Resistant Human Pathogens, What Does Its Genome Tell Us?

Multidrug-resistant bacteria are of critical importance and a problem for human health and food preservation; the discovery of new antimicrobial substances to control their proliferation is part of the solution. This work reports on 57 antagonistic strains, of which 38 strains were antagonistic towards problematic human pathogens. The genome of the most antagonistic strain was sequenced and identified as .

Impacts of soybean agriculture on the resistome of the Amazonian soil.

The soils of the Amazon are complex environments with different organisms cohabiting in continuous adaptation processes; this changes significantly when these environments are modified for the development of agricultural activities that alter the chemical, macro, and microbiological compositions. The metagenomic variations and the levels of the environmental impact of four different soil samples from the Amazon region were evaluated, emphasizing the resistome. Soil samples from the organic phase from the different forest, pasture, and transgenic soybean monocultures of 2-14 years old were collected in triplicate at each site.

Unraveling the Genomic Potential of the Thermophilic Bacterium from an Antarctic Geothermal Environment.

Antarctica is a mosaic of extremes. It harbors active polar volcanoes, such as Deception Island, a marine stratovolcano having notable temperature gradients over very short distances, with the temperature reaching up to 100 °C near the fumaroles and subzero temperatures being noted in the glaciers. From the sediments of Deception Island, we isolated representatives of the genus Anoxybacillus, a widely spread genus that is mainly encountered in thermophilic environments.

Text mining for identification of biological entities related to antibiotic resistant organisms.

Antimicrobial resistance is a significant public health problem worldwide. In recent years, the scientific community has been intensifying efforts to combat this problem; many experiments have been developed, and many articles are published in this area. However, the growing volume of biological literature increases the difficulty of the biocuration process due to the cost and time required.

HIF-1 Is Associated with Resistance to Hypoxia-Induced Apoptosis in Ameloblastoma.

Background: Ameloblastoma (AMB) is a benign odontogenic tumour, with an aggressive local behaviour and a high rate of recurrence. Previous studies have demonstrated that hypoxia-induced factor alpha 1 (HIF-1) and activated caspase-3 contribute to tumour invasiveness and cytogenesis in ameloblastoma. Hypoxia increases HIF-1 levels, which triggers a number of signalling pathways.

The experience of teaching introductory programming skills to bioscientists in Brazil.

Computational biology has gained traction as an independent scientific discipline over the last years in South America. However, there is still a growing need for bioscientists, from different backgrounds, with different levels, to acquire programming skills, which could reduce the time from data to insights and bridge communication between life scientists and computer scientists. Python is a programming language extensively used in bioinformatics and data science, which is particularly suitable for beginners.

COVID-PA Bulletin: reports on artificial intelligence-based forecasting in coping with COVID-19 pandemic in the state of Pará, Brazil.

Objective: To report the university extension research result entitled 'The COVID-PA Bulletin', which presented forecasts on the behavior of the pandemic in the state of Pará, Brazil.

Methods: The artificial intelligence technique also known as 'artificial neural networks' was used to generate 13 bulletins with short-term forecasts based on historical data from the State Department of Public Health information system.

Results: After eight months of predictions, the technique generated reliable results, with an average accuracy of 97% (observed for147 days) for confirmed cases, 96% (observed for 161 days) for deaths and 86% (observed for 72 days) for Intensive Care Unit bed occupancy.