Genetic Methods Research Articles

Genomic selection optimization in blueberry: Data-driven methods for marker and training population design.

Genomic prediction is a modern approach that uses genome-wide markers to predict the genetic merit of unphenotyped individuals. With the potential to reduce the breeding cycles and increase the selection accuracy, this tool has been designed to rank genotypes and maximize genetic gains. Despite this importance, its practical implementation in breeding programs requires critical allocation of resources for its application in a predictive framework. In this study, we integrated genetic and data-driven methods to allocate resources for phenotyping and genotyping tailored to genomic prediction. To this end, we used a historical blueberry (Vaccinium corymbosun L.) breeding dataset containing more than 3000 individuals, genotyped using probe-based target sequencing and phenotyped for three fruit quality traits over several years. Our contribution in this study is threefold: (i) for the genotyping resource allocation, the use of genetic data-driven methods to select an optimal set of markers slightly improved prediction results for all the traits; (ii) for the long-term implication, we carried out a simulation study and emphasized that data-driven method results in a slight improvement in genetic gain over 30 cycles than random marker sampling; and (iii) for the phenotyping resource allocation, we compared different optimization algorithms to select training population, showing that it can be leveraged to increase predictive performances. Altogether, we provided a data-oriented decision-making approach for breeders by demonstrating that critical breeding decisions associated with resource allocation for genomic prediction can be tackled through a combination of statistics and genetic methods.

Plant Adaptation and Tolerance to Heat Stress: Advance Approaches and Future Aspects.

Heat stress impacts plant growth at all phases of development, although the particular threshold for heat tolerance varies significantly across different developmental stages. During seed germination, elevated temperatures can either impede or completely halt the process, contingent upon the plant type and the severity of the stress. During advanced stages, high temperatures can have a negative impact on photosynthesis, respiration, water balance, and membrane integrity. Additionally, they can also influence the levels of hormones and primary and secondary metabolites. In addition, during the growth and development of plants, there is an increased expression of various heat shock proteins, as well as other proteins related to stress, and the generation of reactive oxygen species (ROS). These are significant plant responses to heat stress. Plants employ several strategies to deal with heat stress, such as maintaining the stability of their cell membranes, removing harmful reactive oxygen species (ROS), producing antioxidants, accumulating and adjusting compatible solutes, activating mitogen-activated protein kinase (MAPK) and calcium-dependent protein kinase (CDPK) cascades, and, crucially, signaling through chaperones and activating transcription. These molecular-level systems boost the ability of plants to flourish in heat stress. Potential genetic methods to enhance plant heat stress resistance encompass old and modern molecular breeding techniques and transgenic approaches, all of which rely on a comprehensive comprehension of these systems. Although several plants exhibit enhanced heat tolerance through traditional breeding methods, the effectiveness of genetic transformation techniques has been somewhat restricted. The latter results from the current constraints in our understanding and access to genes that have known impacts on plant heat stress tolerance. However, these challenges may be overcome in the future. Besides genetic methods, crops' heat tolerance can be improved through the pre-treatment of plants with various environmental challenges or the external application of osmoprotectants such as glycine betaine and proline. Thermotolerance is achieved through an active process in which plants allocate significant energy to maintain their structure and function to avoid damage induced by heat stress. The practice of nanoparticles has been shown to upgrade both the standard and the quantity of produce when crops are under heat stress. This review provides information on the effects of heat stress on plants and explores the importance of nanoparticles, transgenics, and genomic techniques in reducing the negative consequences of heat stress. Furthermore, it explores how plants might adapt to heat stress by modifying their biochemical, physiological, and molecular reactions.

Development and Application of Genetic Ancestry Reconstruction Methods to Study Diversity of Patient-Derived Models in the NCI PDXNet Consortium.

Understanding whether and how tumor genetic factors drive differences in outcomes among U.S. minority groups is critical to addressing cancer health disparities. Our findings suggest that many additional models will be necessary to understand the genome-driven sources of these disparities.

A Review of Genetic Diversity Based on the Y Chromosome in the Romanian Population.

Y chromosome analysis is used in a number of practical applications, including investigations of criminal cases, establishment of paternity, searching for missing persons, studies on human migration, evolutionary research, and historical and genealogical investigations. Questions about the origin of individual ethnic groups are addressed not only through archaeological, linguistic, and ethnographic methods but also through molecular genetics methods. The study of genetic diversity in Romania is particularly interesting from several perspectives because Romania, located in Southeast Europe, is distinguished by the fact that the Carpathians and the Danube served as natural barriers against the migrations of peoples for centuries, thus influencing the genetic mixture of the population. This is relevant for understanding the history and formation of ethnic groups in the region. In addition, many ethnic minorities live in Romania, which adds an additional dimension of genetic and cultural diversity. This article aims to provide an updated picture of the genetic diversity in Romania and to highlight the significant studies carried out among the Romanian population. By analyzing the articles published in the Web of Science, Scopus, or PubMed databases, which explore genetic diversity using the Y chromosome, the aim is to better understand the current genetic panorama in Romania.

Next-generation mapping of the salicylic acid signaling hub and transcriptional cascade

For over 60 years, salicylic acid (SA) has been known as a plant immune signal required for basal and systemic acquired resistance. SA activates these immune responses by reprogramming ∼20% of the transcriptome through NPR1. However, components in the NPR1 signaling hub, which appears as nuclear condensates, and the NPR1 signaling cascade have remained elusive due to difficulties in studying this transcriptional cofactor, whose chromatin association is indirect and likely transient. To overcome this challenge, we applied TurboID to divulge the NPR1 proxiome, which detected almost all known NPR1 interactors as well as new components of transcription-related complexes. Testing of new components showed that chromatin remodeling and histone demethylation contribute to SA-induced resistance. Globally, the NPR1 proxiome has a striking similarity to the proxiome of GBPL3 that is involved in SA synthesis, except for associated transcription factors (TFs), suggesting that common regulatory modules are recruited to reprogram specific transcriptomes by transcriptional cofactors, like NPR1, through binding to unique TFs. Stepwise green fluorescent protein-tagged factor cleavage under target and release using nuclease (greenCUT&RUN) analyses showed that, upon SA induction, NPR1 initiates the transcriptional cascade primarily through association with TGACG-binding TFs to induce expression of secondary TFs, predominantly WRKYs. Further, WRKY54 and WRKY70 were identified to play a major role in inducing immune-output genes without interacting with NPR1 at the chromatin. Moreover, loss of condensate formation function of NPR1 decreases its chromatin association and transcriptional activity, indicating the importance of condensates in organizing the NPR1 signaling hub and initiating the transcriptional cascade. Collectively, this study demonstrates how combinatorial applications of TurboID and stepwise greenCUT&RUN transcend traditional genetic methods to globally map signaling hubs and transcriptional cascades for in-depth explorations.

Causal role of immune cells in uveitis: a Mendelian randomization study.

Uveitis refers to a group inflammation affecting the uvea, retina, retinal blood vessels as well as vitreous body, which is one of the common causes of blindness. There is growing evidence linking different types of immune cells to uveitis, although it remains uncertain if these associations imply causal relationships. Recent advancements in high-density genetic markers like SNPs or CNVs for genotyping, along with the progress in genome-wide association studies (GWAS) technologies, have improved our understanding of the immunological mechanisms involved in ocular diseases. Therefore, our objective was to investigate the potential causal link between immune cells and uveitis using a Mendelian randomization study. The exposure and outcome GWAS data for this study were sourced from an open-access database (https://gwas.mrcieu.ac.uk/). Two-sample MR analysis was utilized to evaluate the causal relationship between 731 immune cell features and uveitis. Various MR methods were employed to reduce bias and obtain dependable estimates of the causal link between the immune cell variables and the outcomes. Instrumental variable selection criteria were carefully chosen to enhance the accuracy and efficacy of the causal relationship between different immune cell types and the risk of uveitis. Using two-sample MR, IVW modeling showed that GAD had significant effect on immunophenotypes. CD3 levels on CD45RA- CD4+ T cells (OR = 1.087, 95%CI = 1.029 ~ 1.147, p = 0.003) and CD3 levels on CM CD4+ T cells (OR = 1.086, 95%CI = 1.033 ~ 1.141, p = 0.001) were found to be elevated in cases of uveitis. HLA DR levels in CD14- CD16+ monocyte cells (OR = 0.735, 95% CI = 0.635 ~ 0.850, p < 0.001) and HLA DR levels in NK cells (OR = 0.910, 95% CI = 0.851 ~ 0.972, p = 0.005) were observed to be reduced in individuals with uveitis. Furthermore, Two cells were identified to be significantly associated with uveitis risk: HLA DR on in NK cells (OR = 0.938, 95%CI = 0.899 ~ 0.979, p = 0.003), HLA DR on CD14- CD16+ monocytes (OR = 0.924, 95%CI = 0.878 ~ 0.972, p = 0.002). This study highlights the intricate relationship between immune cells and generalized anxiety disorder using genetic methods, offering valuable insights for future clinical investigations.

The Current Research Status and Progress of Bipolar Disorder

Bipolar disorder is a common but serious mental illness with extremely high mortality and a high suicide rate. It has variable symptoms of both depression and mania and can separate into three types of sub-types---bipolar disorder type I, bipolar disorder type II and Rapid cycling bipolar disorder. So far, scientists and medical researchers had got a lot of success in the field of bipolar disorder. Therefore, this paper proposes to conclude the recent research to discuss the status and progress of bipolar disorder, which mainly discusses the history of bipolar disorder, symptoms, treatments, and possible etiology; this paper will discuss them from the view of genetic and environmental. Besides, this paper specifically focuses on the recent innovative discovery of genetic etiology and genetic model treatment methods.

Creating a novel method for chicken primordial germ cell health monitoring using the fluorescent ubiquitination-based cell cycle indicator reporter system

The most current in vitro genetic methods, including gene preservation, gene editing and developmental modelling, require a significant number of healthy cells. In poultry species, primordial germ cells (PGCs) are great candidates for all the above-mentioned purposes, given their easy culturing and well-established freezing method for chicken. However, the constant monitoring of cultures can be financially challenging and consumes large amounts of solutions and accessories. This study aimed to introduce the Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) complex into the chicken PGCs. FUCCI is a powerful transgenic tool based on the periodic protein expression changes during the cell cycle. It includes chromatin licensing and DNA replication factor 1 attached monomeric Kusabira-Orange and Geminin-attached monomeric Azami-Green fluorescent proteins, that cause the cells to express a red signal in the G1 phase and a green signal in S and G2 phases. Modification of the chicken PGCs was done via electroporation and deemed to be successful according to confocal microscopy, DNA sequencing and timelapse video analysis. Stable clone cell lines were established, cryopreserved, and injected into recipient embryos to prove the integrational competency. The cell health monitoring was tested with medium change experiments, that proved the intended reactions of the FUCCI transgene. These results established the future for FUCCI experiments in chicken, including heat treatment and toxin treatment.

A phased small interfering RNA-derived pathway mediates lead stress tolerance in maize.

Phased small interfering RNAs (phasiRNAs) are a distinct class of endogenous small interfering RNAs, which regulate plant growth, development and environmental stress response. To determine the effect of phasiRNAs on maize (Zea mays L.) tolerance to lead (Pb) stress, the roots of 305 maize lines under Pb treatment were subjected to generation of individual databases of small RNAs. We identified 55 high-confidence phasiRNAs derived from 13 PHAS genes (genes producing phasiRNAs) in this maize panel, of which 41 derived from nine PHAS loci were negatively correlated with Pb content in the roots. The potential targets of the 41 phasiRNAs were enriched in ion transport and import. Only the expression of PHAS_1 (ZmTAS3j, Trans-Acting Short Interference RNA3) was regulated by its cis-expression quantitative trait locus and thus affected the Pb content in the roots. Using the Nicotiana benthamiana (N. benthamiana) transient expression system, 5'-rapid amplification of cDNA ends, and Arabidopsis heterologously expressed, we verified that ZmTAS3j was cleaved by zma-miR390 and thus generated tasiRNA targeting ARF genes (tasiARFs), and that the 5' and 3' zma-miR390 target sites of ZmTAS3j were both necessary for efficient biosynthesis and functional integrity of tasiARFs. We validated the involvement of the zma-miR390-ZmTAS3j-tasiARF-ZmARF3-ZmHMA3 pathway in Pb accumulation in maize seedlings using genetic, molecular, and cytological methods. Moreover, the increased Pb tolerance in ZmTAS3j-overexpressed lines was likely attributed to the zma-miR390-ZmTAS3j-tasiARF-ZmARF3-SAURs pathway, which elevated indole acetic acid levels and thus reactive oxygen species scavenging capacity in maize roots. Our study reveals the importance of the TAS3-derived tasiRNA pathway in plant adaptation to Pb stress.

Diagnosis of Chronic Granulomatous Disease: Strengths and Challenges in the Genomic Era.

Chronic granulomatous disease (CGD) is a group of rare primary inborn errors of immunity characterised by a defect in the phagocyte respiratory burst, which leads to severe and life-threatening infective and inflammatory complications. Despite recent advances in our understanding of the genetic and molecular pathophysiology of X-linked and autosomal recessive CGD, and growth in the availability of functional and genetic testing, there remain significant barriers to early and accurate diagnosis. In the current review, we provide an up-to-date summary of CGD pathophysiology, underpinning current methods of diagnostic testing for CGD and closely related disorders. We present an overview of the benefits of early diagnosis and when to suspect and test for CGD. We discuss current and historical methods for functional testing of NADPH oxidase activity, as well as assays for measuring protein expression of NADPH oxidase subunits. Lastly, we focus on genetic and genomic methods employed to diagnose CGD, including gene-targeted panels, comprehensive genomic testing and ancillary methods. Throughout, we highlight general limitations of testing, and caveats specific to interpretation of results in the context of CGD and related disorders, and provide an outlook for newborn screening and the future.

Investigation of Targeted Genes and Identification of Novel Variants with Next Generation Sequencing Method in Hearing Loss.

Hearing loss is a widespread condition throughout the world. It may affect patients from newborns to the elderly. There are too many reasons for hearing loss, including congenital hearing loss, virus infections, age-related situations, and traumatic situations, which may be related to the immune-mediated system. Fifty percent of hearing loss is related to genetic mutations and defects; genetic causes are highly heterogeneous, so the analysis of new variants are important for diagnosis. We aimed to describe the importance of detected gene variations by using targeted gene panels in the Next-Generation-Sequencing (NGS) platform. Eighty-one hearing loss targeted genes were investigated using Illumina NextSeq550 technology in 100 participants with hearing loss between 2017 and 2022 in our Genetic Diseases Evaluation Center. Targeted genes were performed on 100 patients with hearing loss diagnosis. The total number of detected variants was 77. Forty-seven cases have likely pathogenic/pathogenic variants. Thirty of them have uncertain clinical significance variants, and from the detected variants, 8 are novel. In this research, we highlighted that earlier detection of hearing loss using molecular genetic methods may help us understand the etiology and orient for a better prognosis. Results detected by using the NGS platform can assist and improve the diagnosis. In this study, the diagnostic rate with targeted genes was detected as 35.29%. It has an important role in clinical practice as the recommendation of cochlear implants. Clarifying the genotype and phenotype correlation helps us figure out the etiology of hearing loss and also the worth of genetic counseling in hereditary hearing loss.

An automated sleep staging tool based on simple statistical features of mice electroencephalography (EEG) and electromyography (EMG) data.

Electroencephalogram (EEG) and electromyogram (EMG) are fundamental tools in sleep research. However, investigations into the statistical properties of rodent EEG/EMG signals in the sleep-wake cycle have been limited. The lack of standard criteria in defining sleep stages forces researchers to rely on human expertise to inspect EEG/EMG. The recent increasing demand for analysing large-scale and long-term data has been overwhelming the capabilities of human experts. In this study, we explored the statistical features of EEG signals in the sleep-wake cycle. We found that the normalized EEG power density profile changes its lower and higher frequency powers to a comparable degree in the opposite direction, pivoting around 20-30 Hz between the NREM sleep and the active brain state. We also found that REM sleep has a normalized EEG power density profile that overlaps with wakefulness and a characteristic reduction in the EMG signal. Based on these observations, we proposed three simple statistical features that could span a 3D space. Each sleep-wake stage formed a separate cluster close to a normal distribution in the 3D space. Notably, the suggested features are a natural extension of the conventional definition, making it useful for experts to intuitively interpret the EEG/EMG signal alterations caused by genetic mutations or experimental treatments. In addition, we developed an unsupervised automatic staging algorithm based on these features. The developed algorithm is a valuable tool for expediting the quantitative evaluation of EEG/EMG signals so that researchers can utilize the recent high-throughput genetic or pharmacological methods for sleep research.

Personalized approach to immune system rehabilitation in patients with year-round allergic rhinitis suffering from recurrent ARVI and recurrent herpes virus infections

Introduction. The problem of treating patients with respiratory allergopathology associated with recurrent infectious diseases, such as rARVI, frequent exacerbations of rCHVI, is becoming urgent. The presence of persistent inflammation and co-infection significantly complicates the treatment of immunocompromised patients with year-round allergic rhinitis (YAR) and necessitates the development of personalized programs, with the inclusion of immunomodulatory agents for restoring disorders in the immune system (IS) and interferon system (IFN). Materials and methods. The study group (SG) included 65 patients of both sexes aged 23–60 years, suffering from YAR associated with rARVI and rCHVI. The comparison group (CG) consisted of 50 healthy individuals, comparable in sex and age. All patients underwent standard physical, immunological and allergological examinations, including the use of serological (ELISA, ImmunoCUP), molecular genetic (PCR-RV) methods, FC, etc. Voluntary informed consent was obtained from all patients. The StatPlus computer program was used for statistical analysis. Results and discussion. In patients with YAR associated with rARVI and rCHVI, two variants of disorders in IS have been established, which are defined as pathological immunophenotypes (PIF). The PIF1 is characterized by a deficiency in the induced production of IFNα, a decrease in CD3⁻CD16⁺CD56+ EKKs, and a decrease in neutrophil granulocytes (NG). In the PIF2, along with a shortage of IFNα production, a decrease in EKKs is observed in combination with a decrease in CTLs, as well as a decrease in NGs. The clinical criteria for immunocompromising in this cohort of patients were studied. The severity of YAR symptoms was assessed by VAS. In order to correct the identified disorders in the IS and IFN system, complex personified IFN- and immunotherapy programs have been developed for each PIF, including prolonged local and systemic therapy with rIFNα2b in combination with antioxidants, as well as GMDP for patients of SG1, and for patients of SG2 — GMDP and hexapeptide. The high immunological and clinical efficacy of IFN- and immunotherapy was shown, which was expressed in the tendency to restore existing disorders, as well as in achieving control over the symptoms of YAR, with the possibility of reducing the volume of basic antiallergic pharmacotherapy.

Diseases Caused by Faulty Gene Expression. There are Several Hereditary Diseases that may be Entirely Cured if Detected and Treated Early Enough

Many genes and environmental factors often work together to cause a disease. The identification of significant genetic factors is useful for both medical (by aiding drug development and personalised therapy) and scientific (by shedding light on mechanistic and evolutionary aspects of illness) purposes. Linkage analysis (which joins loci that have a propensity to be inherited together) and association studies are two of the many genetic methods that have shown correlations between illnesses and particular sections of the genome (mapping correlation between alleles at different loci). Several hundreds of genes are examined in these types of studies, much too numerous to be tested experimentally as potential disease genes. The use of computer methods to assess the possibility of individual genes within a certain chromosomal area being disease genes is thus quite useful. Many diseases' susceptibilities have been demonstrated to a fair degree. changes in the rate at which genes are expressed in various cell types. In instance, if a gene or gene cluster is more common in sick individuals than in healthy people, it's likely that the gene plays a role in illness. Microarray studies were the major method for detecting the differences in expression levels.

Genome-Wide Association Study as an Efficacious Approach to Discover Candidate Genes Associated with Body Linear Type Traits in Dairy Cattle.

Body shape traits are very important and play a crucial role in the economic development of dairy farming. By improving the accuracy of selection for body size traits, we can enhance economic returns across the dairy industry and on farms, contributing to the future profitability of the dairy sector. Registered body conformation traits are reliable and cost-effective tools for use in national cattle breeding selection programs. These traits are significantly related to the production, longevity, mobility, health, fertility, and environmental adaptation of dairy cows. Therefore, they can be considered indirect indicators of economically important traits in dairy cows. Utilizing efficacious genetic methods, such as genome-wide association studies (GWASs), allows for a deeper understanding of the genetic architecture of complex traits through the identification and application of genetic markers. In the current review, we summarize information on candidate genes and genomic regions associated with body conformation traits in dairy cattle worldwide. The manuscript also reviews the importance of body conformation, the relationship between body conformation traits and other traits, heritability, influencing factors, and the genetics of body conformation traits. The information on candidate genes related to body conformation traits provided in this review may be helpful in selecting potential genetic markers for the genetic improvement of body conformation traits in dairy cattle.

Competition between sympatric hare species in the Alps is boostered by climate change and hybridisation

Climatic variation along the elevation gradient promotes the natural parapatric occurrence of the European hare (Lepus europaeus) and Alpine mountain hare (Lepus timidus varronis) in the Alps. Recent data indicate a displacement of mountain hares caused by competition with the European hare. Competitive exclusion might take place at a fine spatial scale and hybrids may sharpen competition. Genetic non-invasive sampling (gNIS) demonstrates to be effective to retrieve information from wild animals. However, based on the accuracy of the differing genetic analysis methods, the selection of the method might decisively influence results. To examine habitat preferences of Alpine mountain hares, European hares and their hybrids with particular interest in the influence of the accuracy of the genetic analysis method on the results, we performed gNIS in Grisons (Switzerland) for four years and compared habitat associations of the genotyped samples. We recorded 137 individuals (i.e., 35 hybrids, 49 European hares, 53 Alpine mountain hares). Combined nuclear and mitochondrial DNA analysis including individual identification revealed to be the most accurate indirect method for the study of habitat preferences of hares. Alpine mountain hares had a narrow habitat breadth and used little habitat diversity. Hybrids showed great similarities in their habitat preferences to European hares. Hybrids might increase the competition in favour of European hares and the displacement of Alpine mountain hares, since they show similar patterns of habitat use to European hares. Ongoing climate change potentiate the niche overlap between species, increasing the risk of Alpine hare decline due to hybridisation and displacement.

Detection of foodborne methicillin-resistant Staphylococcus aureus via fluorescence-encoded microsphere and Argonaute-mediated decoding

Molecular diagnosis of foodborne methicillin-resistant Staphylococcus aureus (MRSA) is crucial for controlling its dissemination and ensuring food safety. However, existing genetic methods are limited by susceptibility to aerosol contamination and restricted to single-gene detection. Herein, a fluorescent biosensor employing fluorescence-encoded microspheres and Argonaute-mediated decoding is developed, enabling ultrasensitive, accurate, and duplex detection of MRSA genes. This assay utilizes a target-triggered polymerization/nicking reaction to cyclically produce specific guide DNA, guiding Argonaute protein to site-specifically cleave the molecular beacon on the microsphere, thereby decoding a fluorescent signal. Notably, the fluorescence-encoded microsphere, designed via on-tetrahedron rolling circle amplification, achieves high fluorescence loadings in a unit area. This biosensor demonstrates simultaneous detection of two unamplified MRSA genes, mecA and femA, at concentrations as low as 0.63 fM and 0.48 fM, respectively. Moreover, the method exhibited excellent recoveries in milk, egg, and pork samples ranging from 73% to 112%, highlighting its practicability in real scenarios.

The Ability of the Indigenous Bacteria Chromobacterium haemolyticum strain W15 to Degrade Chromium (Cr) and Lead (Pb) in Liquid Coal Waste

The use of coal as a raw material for power plants has a good economic impact, but it also has a detrimental environmental impact, particularly due to the presence of Cr and Pb, heavy metals with bioaccumulation and biomagnification qualities. Efforts to control Pb and Cr in liquid coal waste can be achieved by bioremediation. The goal of this study is to screen indigenous bacteria, identify, and test biodegradation on the best bacteria capable of degrading Cr and Pb. Bacterial screening is done experimentally in the lab. Bacterial identification is done using morphological, biochemical, and molecular genetic methods. Using atomic absorption spectroscopy to validate Cr and Pb biodegradation research. Biodegradation experiments revealed that the efficacy of indigenous bacteria reduced Pb by 216% (0.238 ppm to 0.11 ppm) and Cr by 195% (0.34 ppm to 0.174 ppm). The findings of biochemical, morphological, and molecular genetic studies revealed that the top bacterial strains were up to 96% related. using Chromobacterium haemolyticum strain W15. Chromobacterium haemolyticum strain X, an indigenous bacteria capable of degrading Cr and Pb, was successfully isolated from liquid waste.

Hospital environment microbiome

The aim of the review is to give a brief description of the biodiversity and structure of the hospital environment microbiome based on molecular genetic research methods. Until a certain time, studies of the hospital environment microbiota for the purposes of epidemiological surveillance and control of healthcare-associated infections (HAIs) were based on routine microbiological identification of clinically relevant bacterial taxa. Discovery of DNA, the development of sequencing technologies, PCR and cloning techniques enabled the investigation of microbial communities using cultivation-independent, DNA and RNA-based approaches. At the current level of knowledge, the hospital environment can be considered as a superorganism with its own microbiome. Multiomic technologies, including meta-transcriptomic, meta-proteomic and metabolomic approaches, provide detailed information about microbial activity in the environment. Now it has been established that there is a stable core of the hospital microbiome where the vast majority of microorganisms are necessary for the functioning of the hospital ecosystem and are not classified as human pathogens. The hospital microbiome has a homogeneous structure composed by a massive dominance of a few taxa and microbial network with low connectivity forming a clustered topology. A keystone species is a taxon whose importance for maintaining community structure is relatively higher than others and its identification is of paramount importance. Due to the lack of knowledge of the hospital environment microbiome by molecular genetic technologies, there is no single shared point of view on the microbial diversity in different healthcare facilities. But there is no doubt that molecular genetic technologies will shed light on the evolution of hospital strains and determine which indicators are the most informative for monitoring and prognosis of HAIs.

Functional Characterization of the Human BRCA1 ∆11 Splicing Isoforms in Yeast.

BRCA1, a crucial tumor suppressor gene, has several splicing isoforms, including Δ9-11, Δ11, and Δ11q, which lack exon 11, coding for significant portions of the protein. These isoforms are naturally present in both normal and cancerous cells, exhibiting altered activity compared to the full-length BRCA1. Despite this, the impact on cancer risk of the germline intronic variants promoting the exclusive expression of these Δ11 isoforms remains uncertain. Consequently, they are classified as variants of uncertain significance (VUS), posing challenges for traditional genetic classification methods due to their rarity and complexity. Our research utilizes a yeast-based functional assay, previously validated for assessing missense BRCA1 variants, to compare the activity of the Δ11 splicing isoforms with known pathogenic missense variants. This approach allows us to elucidate the functional implications of these isoforms and determine whether their exclusive expression could contribute to increased cancer risk. By doing so, we aim to provide insights into the pathogenic potential of intronic VUS-generating BRCA1 splicing isoforms and improve the classification of BRCA1 variants.