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Genetic testing, including whole genome, whole exome, and other next‐generation sequencing technologies, has evolved vastly in the past decade. With this, the number of identified genes and genetic variants is constantly increasing. Although a variety of databases and online tools exist that summarize, categorize, and classify genes, a clear guideline of which information is needed when reporting a gene and what to do when identifying a new gene is lacking. This includes the correct nomenclature, descriptive information about genetic loci and genetic variation, aliases, and correlated phenotypes. This tutorial is meant to serve as an introduction to reporting genes in a paper and provides an overview of available databases and tools to obtain all necessary information on the genes of interest. [ABSTRACT FROM AUTHOR]

In a nuclear or radiological incident, first responders must quickly and accurately measure radiation exposure among civilians as medical countermeasures are radiation dose-dependent and time-sensitive. Although several approaches have been explored to measure absorbed radiation dose, there is an important need to develop point-of-care (POC) bioassay devices that can be used immediately to triage thousands of individuals potentially exposed to radiation. Here we present a proof-of-concept study showing the use of a paper-based vertical flow immunoassay (VFI) to detect radiation dosimetry genes. Using labeled primers during amplification and a multiplex membrane, our results showed that the nucleic acid VFI can simultaneously detect two biodosimetry genes, CDKN1A and DDB2, as well as one housekeeping gene MRPS5. The assay demonstrated good linearity and precision with an inter- and intra-assay coefficient of variance <20% and <10%, respectively. Moreover, the assay showed its ability to discriminate non-irradiated controls (0 Gy) from irradiated samples (1 + 2 Gy) with an overall sensitivity of 62.5% and specificity of 100% (AUC = 0.8672, 95% CI: 0.723–1.000; p = 0.004). Interestingly, the gene combination also showed a dose-dependent response for 0, 1, and 2 Gy, similar to data obtained by real-time PCR benchmark. These preliminary results suggest that a VFI platform can be used to detect simultaneously multiple genes that can be then quantified, thus offering a new approach for a POC biodosimetry assay that could be rapidly deployed on-site to test a large population and help triage and medical management after radiological event. [ABSTRACT FROM AUTHOR]

Objectives: This study aimed to elucidate the connection between osteoclastic forkhead transcription factor O1 (FoxO1) and periodontitis and explore the underlying mechanism by which FoxO1 knockdown regulates osteoclast formation. Materials and Methods: A conventional ligature‐induced periodontitis model was constructed to reveal the alterations in the proportion of osteoclastic FoxO1 in periodontitis via immunofluorescence staining. Additionally, RNA sequencing (RNA‐seq) was performed to explore the underlying mechanisms of FoxO1 knockdown‐mediated osteoclastogenesis, followed by western blotting, quantitative polymerase chain reaction, and enzyme‐linked immunosorbent assay. Results: FoxO1+ osteoclasts were enriched in the alveolar bone in experimental periodontitis. Moreover, FoxO1 knockdown led to impaired osteoclastogenesis with low expression of osteoclast differentiation‐related genes, accompanied by an insufficient osteoclast maturation phenotype. Mechanistically, RNA‐seq revealed that the nuclear factor kappa B (NF‐κB) and nucleotide‐binding oligomerization domain‐like receptor family pyrin domain containing 3 (NLRP3) inflammasome signaling pathways were inhibited in FoxO1‐knockdown osteoclasts. Consistent with this, MCC950, an effective inhibitor of the NLRP3 inflammasome, substantially attenuated osteoclast formation. Conclusions: FoxO1 knockdown contributed to the inhibition of osteoclastogenesis by effectively suppressing NF‐κB signaling and NLRP3 inflammasome activation. This prospective study reveals the role of FoxO1 in mediating osteoclastogenesis and provides a viable therapeutic target for periodontitis treatment. [ABSTRACT FROM AUTHOR]

R.A. Fisher's 1922 paper On the dominance ratio has a strong claim to be the foundation paper for modern population genetics. It greatly influenced subsequent work by Haldane and Wright, and contributed 3 major innovations to the study of evolution at the genetic level. First, the introduction of a general model of selection at a single locus, which showed how variability could be maintained by heterozygote advantage. Second, the use of the branching process approach to show that a beneficial mutation has a substantial chance of loss from the population, even when the population size is extremely large. Third, the invention of the concept of a probability distribution of allele frequency, caused by random sampling of allele frequencies due to finite population size, and the first use of a diffusion equation to investigate the properties of such a distribution. Although Fisher was motivated by an inference that later turned out to lack strong empirical support (a substantial contribution of dominance to quantitative trait variability), and his use of a diffusion equation was marred by a technical mistake, the paper introduced concepts and methods that pervade much subsequent work in population genetics. [ABSTRACT FROM AUTHOR]

Aims: This study was designed to analyse the prevalence of class 1 and class 2 integron integrase genes among antibiotic‐resistant coliform bacteria isolated from paper currency circulating in Pakistan. Methods and Results: A total of 500 individual currency notes were collected from different food vending sites at Lahore, Pakistan. Bacterial population were identified by biochemical and PCR techniques. Antimicrobial susceptibility testing was performed by disc diffusion assay. The highest bacterial population on currency was found from street vendors and butcher shops. Escherichia coli was found to be the most prevalent coliform bacteria followed by Klebsiella sp. and Enterobacter sp. PCR amplification of antimicrobial resistance gene showed the presence of ampC, blaTEM, blaNDM‐1, qnrA, tet(A) and tet(B) genes among coliform isolates. A total of 47 integron integrase bearing strains of coliform bacteria were analysed. Sequence analysis showed the presence of dfrA1‐aadA1, dfrA1, dfrA5, dfrA7, aadA1, aadA4 cassette arrays in class 1 integron and dfrA1‐sat2‐aadA1 in class 2 integrase genes. Conclusion: Circulating currency was heavily contaminated with antimicrobial‐resistant coliform bacteria bearing class 1 and class 2 integron integrase genes. Significance and Impact of the Study: This study describes a potential threat of severe bacterial infections due to improper hand hygiene and community sanitation when dealing with the currency notes. [ABSTRACT FROM AUTHOR]

Nowadays, great efforts are made in developing new technology for rapid detection of specific DNA sequences, for environmental monitoring, forensic analysis and rapid biomedical diagnosis applications. Microfluidic paper-based analytical devices are suitable platforms for the development of point of care devices, due to their simple fabrication protocols, ease of use and low cost. Herein, a methodology for in situ detection of single strand DNA by using a colorimetric assay based on the formation of a DNAzyme within a paper substrate was developed. A DNAzyme that could only be formed in the presence of a specific sequence of the Y human amelogenin gene was designed. The performance of the DNAzyme was followed colorimetrically first in solution and then in paper substrates. The reaction was found to be specific to the Y fragment selected as analyte. The DNAzyme reaction on paper enabled the unequivocal colorimetric identification of the Y single strand DNA fragment both qualitatively, with the naked eye (143 ng), and quantitatively by image analysis (45.7 ng). As a proof of concept, a microfluidic paper-based device, pre-loaded with all DNAzyme reagents, was characterized and implemented for the simultaneous detection of X and Y single strand DNA fragments. Image 1 • Optimized methodology for in situ DNA detection in a paper device format. • Detection based on a DNAzyme using Y human amelogenin fragment. • Presents a non-enzymatic, colorimetric and rapid way to detect DNA sequences. • Detection: quantitatively by calculating the grey intensity values. • Detection: qualitatively by the presence of a green color "coffee ring". [ABSTRACT FROM AUTHOR]

Introduction: Down syndrome as a genetic disorder is a popular research topic in molecular studies. One way to study Down syndrome is via bioinformatics. Methods: In this study, a gene expression profile from a microarray study was selected for more investigation. Results: The study of Down syndrome patients shows specific genes with differential expression and network centrality properties. These genes are introduced as RHOA, FGF2, FYN, and CD44, and their level of expression is high in these patients. Conclusion: This study suggests that besides chromosomes 21, there are additional contributing chromosomes to the risk of Down syndrome development. Besides, these genes could be used for clinical studies after more analysis. [ABSTRACT FROM AUTHOR]

Introduction: Parkinson Disease (PD), the second most common chronic neurodegenerative disorder, is characterized by tremor, bradykinesia, rigidity, and postural instability. SHANK3 (SH3 and multiple ankyrin repeat domain 3) belongs to the extremely conserved ProSAP/Shank family of synaptic scaffolding proteins. Meanwhile, rs9616915 is a non-synonymous SNP (T>C) located in the exon 6 of the SHANK3 gene, which induces substitution of isoleucine to threonine and affects the function of the resulted protein. The present study aimed to evaluate whether rs9616915 polymorphism of SHANK3 is involved in the susceptibility to PD. Methods: The study subjects were 100 patients diagnosed with PD and 100 control volunteers. The obtained samples were evaluated by the polymerase chain reaction-restriction fragment length polymorphism method. Results: A significant association was found in genotype distribution between cases and controls. Individuals with TC genotype had increased risk of PD (P=0.035, OR=1.98, 95% CI=1.04 - 3.74). No significant difference was found in allele distribution (P=0.7). Conclusion: The findings suggest that the SHANK3 rs9616915 polymorphism is associated with an increased risk of PD in the population. Further studies are needed to confirm the role of the SHANK3 gene in PD. [ABSTRACT FROM AUTHOR]

The WOX (WUSCHEL-related homeobox) is a plant-specific transcription factor involved in plant development and stress response. However, few studies have been reported on the WOX gene in woody plants. In this study, 10 BpWOX genes were isolated from paper mulberry by RACE-PCR and categorized into three clades through phylogenetic analysis, ancient, intermediate and WUS clade. Among them, five members had the transcriptional activity detected by yeast one-hybrid and seven were uniquely localized to the nucleus through green fluorescent protein (GFP) observation. The expression patterns of BpWOX genes in different tissues and under diverse treatments were quantified by the qRT-PCR method. Results showed that BpWUS was expressed in the apical bud, stem and root, BpWOX5 and BpWOX7 functioned only in the root tip, and three BpWOXs regulated leaf development redundantly. BpWOX9 and BpWOX10 were induced by indole-3-acetic acid (IAA) or jasmonic acid (JA), while BpWOX2 was repressed by five phytohormones. Interestingly, most BpWOX genes were responsive to the abiotic stress stimuli of drought, salt, cold, and cadmium (CdCl2). Together, our study revealed that BpWOXs were functionally divergent during paper mulberry development and environmental adaptation, which might be related to their evolutionary relationships. Our work will benefit the systematic understanding of the precise function of WOX in plant development and environmental stress responses. [ABSTRACT FROM AUTHOR]

Inflammatory bowel disease (IBD) is a complex disease that develops through a sequence of molecular events that are still poorly defined. This process is driven by a multitude of context-dependent genes that play different roles based on their environment. The complexity and multi-faceted nature of these genes make it difficult to study the genetic basis of IBD. The goal of this article is to review the key genes in the pathophysiology of IBD and highlight new technology that can be used in further research. This paper examines Nanostring RNA probe technology, which uses tissue analyzed without the use of enzymes, transcription, or amplification. Nanostring offers several panels of genes to test, including an inflammation panel of 234 genes. This article analyzes this panel and reviews the literature for each gene's effect in IBD for use as a framework to review the pathophysiology of the disease. The panel was narrowed to 26 genes with significant evidence of mechanistic potential in IBD, which were then categorized into specific areas of pathogenesis. These include gut barrier breakdown, inappropriate recognition of commensal bacteria, immune cell activation, proinflammatory cytokine release, and subsequent impairment of the anti-inflammatory response. The eventual goal of this paper is the creation of a customized panel of IBD genes that can be used to better understand the genetic mechanism of IBD and aid in the development of future therapies in IBD. [ABSTRACT FROM AUTHOR]

• The MoS 2 -AuNPs probe showed uniquely inherited structure and excellent electrochemical characteristic. • The carbon paper functionalized with MoS 2 -AuNPs demonstrated the outstanding detection performance of p53 gene. • The biosensor exhibits a relatively lower detection limit of 68 fM for p53 gene detection. • The planned biosensor could discriminate well between the mutated and wild type p53 gene extracted from tumor cells. p53 gene is one of the most important anticancer genes and has been recognized as a typical biomarker for the early diagnosis, classification, and prognosis evaluation of cancers. In this work, a novel biosensing strategy integrating MoS 2 -AuNPs modified carbon paper (CP) conductive substrate and enzyme signal amplification technique was developed for p53 gene detection. We constructed an immobilized DNA S1 probe and a biotinylated DNA S3 probe, which could induce the formation of an S1-p53-S3 DNA sandwich complex in the presence of target sequence p53. After conjugating avidin-HRP via biotin-avidin reaction, 3,3',5,5'-tetramethylbenzidine would be catalyzed for signal amplification in the presence of H 2 O 2 so that the induced electrochemical response would change with proportional to the abundance of p53 gene. The proposed biosensor exhibited two linearities in the range of 1.0 × 10−15 ∼ 1.0 × 10-12 M and 1.0 × 10-12 ∼ 1.0 × 10-6 M, and the limit of detection (LOD) was 68 fM. No significant interferences were observed during detecting real serum samples. Moreover, it is worth pointing out that the biosensor together with its disposable, low-cost, and stable features can discriminate well between the mutated and wild type p53 gene extracted from tumor cells (wtTP53 in MCF-7 and mutated in SK-BR-3), demonstrating a promising applicability for clinical test. [ABSTRACT FROM AUTHOR]

The relationship between the abundance of three functional genes and their corresponding biochemical reaction rates was investigated in several activated sludge and mill effluent microbial communities. Gene probes were prepared for two key denitrification genes (nirS and nirK) and for one nitrogen-fixation gene (nifH) and were validated using a variety of strains of known nir and nif genotype. ATP-based measures of viable cell numbers were used to provide total population sizes. In certain microbial communities (activated sludge enrichment cultures and multiple samples taken from the same mill primary clarifier), a strong correlation was observed between gene abundance and biochemical activity rates. However, when comparing several different nonenriched activated sludge bioreactors and separate primary clarifier microbial communities, the ratio of specific gene abundance to biochemical activity rates varied widely. These results suggest that in cases where a microbial community is not fully induced for a given biochemical activity or when very different communities are compared, quantitative gene probing can give a better measure of a community's potential to carry out the encoded function than can the relevant biochemical assay. However, the gene quantitation method employed here probably underestimated the true number of probed genes present in the microbial communities due to nirS and nifH genes in the communities having reduced DNA sequence similarity with the probes used.Key words: denitrification, nitrogen fixation, quantitative hybridization, activated sludge, primary clarifier.Nous avons examiné les liens existant entre l'abondance de trois gènes fonctionnels et la vitesse des réactions biochimiques correspondantes dans plusieurs communautés microbiennes de boues activées et d'effluents de papetières. Des sondes génétiques furent conçues pour des gènes clés de la dénitrification (nirS et nirK) et pour un gène de la fixation de l'azote (nifH), et furent validées à l'aide d'une panoplie de souches aux génotypes nir et nif connus. Des mesures de nombres de cellules viables se basant sur l'ATP ont été utilisées afin de procurer une estimation des tailles totales des populations. Dans certaines communautés microbiennes (cultures d'enrichissement de boues activées et échantillons multiples recueillis à partir d'un même clarificateur primaire de papetière), une forte corrélation a été observée entre l'abondance des gènes et les taux d'activités métaboliques. Toutefois, le rapport de l'abondance génétique spécifique sur les taux d'activité métabolique ont varié largement lorsque nous avons comparé divers bioréacteurs de boues non enrichies, ainsi que des communautés microbiennes de clarificateurs primaires de papetière distincts. Ces résultats nous indiquent que dans les cas où une activité biochimique n'est pas complètement induite chez une communauté bactérienne ou lorsque des communautés très différentes sont comparées, le sondage génétique quantitatif est d'avantage apte à fournir une mesure du potentiel d'une communauté à accomplir la fonction codée, que l'analyse biochimique pertinente. Cependant, la méthode de quantification des gènes employée ici a probablement sous-estimé le nombre véritable de gènes sondés présents dans la communauté microbienne, puisque les gènes nirS et nifH dans les communautés microbiennes avaient une similitude de séquence inférieure par rapport aux sondes utilisées.Mots clés : dénitrification, fixation de l'azote, hybridation quantitative, boues activées, clarificateur primaire.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

With the rapid development of biotechnology, gene sequencing methods are gradually improved. The structure of gene sequences is also more complex. However, the traditional sequence alignment method is difficult to deal with the complex gene sequence alignment work. In order to improve the efficiency of gene sequence analysis, D2 series method of k-mer statistics is selected to build the model of gene sequence alignment analysis. According to the structure of the foreground sequence, the sequence to be aligned can be cut by different lengths and divided into multiple subsequences. Finally, according to the selected subsequences, the maximum dissimilarity in the alignment results is determined as the statistical result. At the same time, the research also designed an application system for the sequence alignment analysis of the model. The experimental results showed that the statistical power of the sequence alignment analysis model was directly proportional to the sequence coverage and cutting length, and inversely proportional to the K value and module length. At the same time, the model was applied to the system designed in this paper. The maximum storage capacity of the system was 71 GB, the maximum disk capacity was 135 GB, and the running time was less than 2.0s. Therefore, the k-mer statistic sequence alignment model and system proposed in this study have considerable application value in gene alignment analysis. [ABSTRACT FROM AUTHOR]

Gene duplication has a central role in evolution; still, little is known on the fates of the duplicated copies, their relative frequency, and on how environmental conditions affect them. Moreover, the lack of rigorous definitions concerning the fate of duplicated genes hinders the development of a global vision of this process. In this paper, we present a new framework aiming at characterizing and formally differentiating the fate of duplicated genes. Our framework has been tested via simulations, where the evolution of populations has been simulated using aevol, an in silico experimental evolution platform. Our results show several patterns that confirm some of the conclusions from previous studies, while also exhibiting new tendencies; this may open up new avenues to better understand the role of duplications as a driver of evolution. [ABSTRACT FROM AUTHOR]

This paper addresses a growing need in clinical diagnostics for parallel, multiplex analysis of biomarkers from small biological samples. It describes a new procedure for assembling arrays of ssDNA and proteins on paper. This method starts with the synthesis of DNA oligonucleotides covalently linked to paper and proceeds to assemble microzones of DNAconjugated paper into arrays capable of simultaneously capturing DNA, DNA-conjugated protein antigens, and DNA-conjugated antibodies. The synthesis of ssDNA oligonucleotides on paper is convenient and effective with 32% of the oligonucleotides cleaved and eluted from the paper substrate being full-length by HPLC for a 32-mer. These ssDNA arrays can be used to detect fluorophore-linked DNA oligonucleotides in solution, and as the basis for DNA-directed assembly of arrays of DNA-conjugated capture antibodies on paper, detect protein antigens by sandwich ELISAs. Paper-anchored ssDNA arrays with different sequences can be used to assemble paper-based devices capable of detecting DNA and antibodies in the same device and enable simple microfluidic paper-based devices. [ABSTRACT FROM AUTHOR]

Background & objectives: Dried blood spotted on to filter paper has been found suitable for a large number of studies. In tropical countries with varying temperature conditions the use of dried blood needs to be validated. We carried out this study to assess the use of blood spotted filter paper as a transport system to study genotyping ofApo E gene. Methods: Fifty five patients visiting Cardiothoracic Neuroscience Centre (CNC) OPD at the All India Institute of Medical Sciences (AIIMS), New Delhi, and referred for lipid investigations to Cardiac Biochemistry Laboratory were selected at random. Blood was spotted on to Whatman 3 MM filter paper, dried and stored at room temperature. Genomic DNA was extracted and genotyping was carried out at the end of 0, 3 and 12 months. The study was further validated using samples collected on to filter paper from four centres and stored for eight years at room temperature. The temperature and humidity conditions of the centre varied widely. Results: Fifty five samples collected on to filter paper showed exact match of the genotyping when compared to fresh blood. In dried blood samples collected and stored for 1 yr at room temperature DNA extraction and apo E genotyping was done successfully. Interpretation & conclusions: The present results showed the feasibility of using dried blood samples on filter paper for apo E genotyping in tropical temperature. The findings need to be validated on a large sample before being recommended for use. [ABSTRACT FROM AUTHOR]

Background: Schizophrenia is a complex neuropsychiatric disorder of unclear etiology. The strongest known genetic risk factor is the 22q11.2 microdeletion. Research has yet to confirm which genes within the deletion region are implicated in schizophrenia. The minimal 1.5 megabase deletion contains MIR185, which encodes microRNA 185. Methods: We determined miR-185 expression in embryonic and adult mouse brains. Common and rare variants at this locus were then investigated using a human genetics approach. First, we performed gene-based analyses for MIR185 common variants and target genes using Psychiatric Genomics Consortium genome-wide association data. Second, MIR185 was resequenced in German patients (n = 1000) and controls (n = 500). We followed up promising variants by genotyping an additional European sample (patients, n = 3598; controls, n = 4082). Results: In situ hybridization in mice revealed miR-185 expression in brain regions implicated in schizophrenia. Gene-based tests revealed association between common variants in 3 MIR185 target genes (ATAT1, SH3PXD2A, NTRK3) and schizophrenia. Further analyses in mice revealed overlapping expression patterns for these target genes and miR185. Resequencing identified 2 rare patient-specific novel variants flanking MIR185. However, follow-up genotyping provided no further evidence of their involvement in schizophrenia. Limitations: Power to detect rare variant associations was limited. Conclusion: Human genetic analyses generated no evidence of the involvement of MIR185 in schizophrenia. However, the expression patterns of miR-185 and its target genes in mice, and the genetic association results for the 3 target genes, suggest that further research into the involvement of miR-185 and its downstream pathways in schizophrenia is warranted. [ABSTRACT FROM AUTHOR]

Background: With the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error level and structure, the analysis of such data demands some database of reference sequences. However, many taxa from complex and diverse environments, have poor representation in publicly available databases. In this paper, we propose the METASEED pipeline for the reconstruction of full-length 16S sequences from such environments, in order to improve the reference for the subsequent use of on-site sequencing. Results: We show that combining high-precision short-read sequencing of both 16S and full metagenome from the same samples allow us to reconstruct high-quality 16S sequences from the more abundant taxa. A significant novelty is the carefully designed collection of metagenome reads that matches the 16S amplicons, based on a combination of uniqueness and abundance. Compared to alternative approaches this produces superior results. Conclusion: Our pipeline will facilitate numerous studies associated with various unknown microorganisms, thus allowing the comprehension of the diverse environments. The pipeline is a potential tool in generating a full length 16S rRNA gene database for any environment. [ABSTRACT FROM AUTHOR]

This paper engages with the entwined questions of science and ideology through a symptomatic reading of Kazuo Ishiguro’s Never Let Me Go (2005), studying how power, racism, and capital intervene into the genetic enterprise of tampering with the limitations of the human and produce a supplicant race of clones for organ harvest and extraction. I commence by drawing on Donna Haraway’s concept of gene fetishism and Evelyn Fox Keller’s notion of gene talk to trace how an elision of the ideological frameworks of race and capital subtending genomics in Ishiguro’s dystopian world instrumentalizes the creation of the clones as racialized products. I bring into dialogue the clones’ obsessive quest for familial origins with Deborah Bolnick’s exploration of the reification of race as biology through ancestry tests to analyze how technology can be used to create and legitimize racism. Deploying Kaushik Sundar Rajan’s theorization of biocapital and James Doucet-Battle’s analysis of the intersections of race, capitalism, and time, I study how the clones are discursively defined as fungible commodities in service to a futurity from which they are precluded. I conclude by positing the call for “slow science” as a potential strategy against the accelerationism and market-ready speculations that dictate biotechnical enterprises today. [ABSTRACT FROM AUTHOR]

Cottonseed oil, soft in taste and golden in color, plays a crucial role in various foods. In addition, cottonseed oil has attracted much attention due to its unique fatty acid properties, anti-inflammatory and heart protective properties. Therefore, it is of great significance to understand the genetic mechanism that regulates the biosynthesis of cottonseed storage oil, carry out key gene mining, and select high-quality cotton varieties with high oil content. With the rapid development of high-throughput sequencing technology and bioinformatics analysis tools, whole genome sequencing has become simpler and more efficient, genome-wide association analysis (GWAS) has become a key tool for studying complex traits. This paper introduces the principle and research advantages of GWAS, discusses the progress of its application in the research of different oil crops and cotton characters. Some suggestions for future genetic studies of cottonseed oil related traits were put forward. The existing problems were discussed and prospected in order to provide a theoretical basis for future studies on the genetic basis of cottonseed oil traits and marker-assisted breeding by GWAS. [ABSTRACT FROM AUTHOR]

The nonconventional yeast Kluyveromyces marxianus has potential for industrial production, but the lack of advanced synthetic biology tools for precise engineering hinders its rapid development. Here, we introduce a CRISPR-Cas9-mediated multilocus integration method for assembling multiple exogenous genes. Using SlugCas9-HF, a high-fidelity Cas9 nuclease, we enhance gene editing precision. Specific genomic loci predisposed to efficient integration and expression of heterologous genes are identified and combined with a set of paired CRISPR-Cas9 expression plasmids and donor plasmids to establish a CRISPR-based biosynthesis toolkit. This toolkit enables genome integration of large gene modules over 12 kb and achieves simultaneous quadruple-locus integration in a single step with 20% efficiency. As a proof-of-concept, we apply the toolkit to screen for gene combinations that promote heme production, revealing the importance of HEM4Km and HEM12Sc. This CRISPR-based toolkit simplifies the reconstruction of complex pathways in K. marxianus, broadening its application in synthetic biology. Fungi has been widely used as protein and drug production factories, in which efficient heterologous gene expression is fundamental. This paper provides a genome editing tool kit for heterologous gene expression in Kluyveromyces marxianus. [ABSTRACT FROM AUTHOR]

Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole‐genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid‐rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long‐read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids. [ABSTRACT FROM AUTHOR]

Epigenetics in the form of DNA methylation and other processes is an established property of genotypes and a focus of empirical research. Yet, there remain fundamental gaps in the evolutionary theory of epigenetics. To support a comprehensive understanding of epigenetics, this paper investigates theoretically the combined effects of deleterious mutation and epimutation with and without inbreeding. Both spontaneous epimutation and paramutation are considered to cover a broader range of epigenetic phenomena. We find that inbreeding generally reduces the amount of segregating deleterious genetic and epigenetic variation at equilibrium, although interestingly inbreeding can also increase the amount of deleterious genetic or epigenetic variation. Furthermore, we also demonstrate that epimutation indirectly can cause increased or decreased deleterious genetic variation at equilibrium relative to classic expectations, which is particularly evident when paramutation is occurring. With the addition of deleterious epimutation, there may be significantly increased purging of deleterious variation in more inbred populations and a significantly increased amount of segregating deleterious variation in more outbred populations, with notable exceptions. [ABSTRACT FROM AUTHOR]

Front cover: In establishing the left‐right axis of the body in Drosophila, a torsion‐like deformation of the cell occurs (cell chirality). Two myosin Is, Myo1D and Myo1C, are thought to be involved in this process, producing right‐handed and left‐handed cell chirality, respectively. A paper published in the May issue of this journal (Utsunomiya et al. (2024) Genes Cells 29: 380‐396, DOI: 10.1111/gtc.13110) reported that when these myosin Is were expressed in macrophages to observe their interactions with the membrane at the single‐molecule level, Myo1D exhibited mobility consistent with free diffusion, whereas Myo1C showed notably lower mobility. This picture, depicting two vortices in a strait, aptly illustrates their differences. Compared to the fast currents that produce the right‐handed vortex in the back, the currents of the left‐handed vortex in the foreground are docile. Designed by TRAIS Co., Ltd. (Kobe, Japan). [ABSTRACT FROM AUTHOR]

Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield, disease resistance, and stress tolerance. As the number of sequenced genomes grows and the accuracy and contiguity of genome assemblies improve, structural annotation of plant genomes continues to be a significant challenge due to their large size, polyploidy, and rich repeat content. In this paper, we present an overview of the current landscape in crop genomics research, highlighting the diversity of genomic characteristics across various crop species. We also assessed the accuracy of popular gene prediction tools in identifying genes within crop genomes and examined the factors that impact their performance. Our findings highlight the strengths and limitations of BRAKER2 and Helixer as leading structural genome annotation tools and underscore the impact of genome complexity, fragmentation, and repeat content on their performance. Furthermore, we evaluated the suitability of the predicted proteins as a reliable search space in proteomics studies using mass spectrometry data. Our results provide valuable insights for future efforts to refine and advance the field of structural genome annotation. [ABSTRACT FROM AUTHOR]

Background: Currently, no evidence exists on the expression of apoptosis (CASP3), autophagy (BECN1), and mitophagy (BNIP3) genes in the CA3 area after ischemia with long-term survival. Objective: The goal of the paper was to study changes in above genes expression in CA3 area after ischemia in the period of 6–24 months. Methods: In this study, using quantitative RT-PCR, we present the expression of genes associated with neuronal death in a rat ischemic model of Alzheimer's disease. Results: First time, we demonstrated overexpression of the CASP3 gene in CA3 area after ischemia with survival ranging from 0.5 to 2 years. Overexpression of the CASP3 gene was accompanied by a decrease in the activity level of the BECN1 and BNIP3 genes over a period of 0.5 year. Then, during 1-2 years, BNIP3 gene expression increased significantly and coincided with an increase in CASP3 gene expression. However, BECN1 gene expression was variable, increased significantly at 1 and 2 years and was below control values 1.5 years post-ischemia. Conclusions: Our observations suggest that ischemia with long-term survival induces neuronal death in CA3 through activation of caspase 3 in cooperation with the pro-apoptotic gene BNIP3. This study also suggests that the BNIP3 gene regulates caspase-independent pyramidal neuronal death post-ischemia. Thus, caspase-dependent and -independent death of neuronal cells occur post-ischemia in the CA3 area. Our data suggest new role of the BNIP3 gene in the regulation of post-ischemic neuronal death in CA3. This suggests the involvement of the BNIP3 together with the CASP3 in the CA3 in neuronal death post-ischemia. [ABSTRACT FROM AUTHOR]

Background: Although, several studies have assessed the association of the phospholipase A2 receptor (PLA2R) and HLA-DQA1 SNPs with primary membranous nephropathy (PMN), results were inconsistent and between-studies heterogeneity needs to be investigated. Objectives: The aim of this review was to summarize existing data on the contribution of 10 SNPs in the PLA2R and HLA-DQA1 genes to PMN susceptibility and to investigate the between-studies heterogeneity by subgroup analyses and meta-regressions. Design: This study was performed according to the PRISMA guidelines for systematic reviews and meta-analyses. Data sources and methods: An electronic literature search for eligible studies among all papers published prior to January 10, 2024, was conducted through PubMed, EMBASE, Web of science and Scopus databases. Meta-analyses together with subgroup analyses and meta-regressions were performed for the 10 following SNPs: rs4664308, rs3749117, rs3749119, rs35771982, rs3828323, rs16844715, rs1511223, rs6757188, rs2715918, and rs2187668. Results: Combined analyses revealed a significant increase in PMN risk conferred by the following alleles: rs4664308*A, rs3749117*T, rs3749119*C, rs35771982*G, rs3828323*C, rs16844715*C, rs1511223*A, rs2715918*A, and rs2187668*A, all P -values <.001. Moreover, the PLA2R-rs4664308/HLA-DQA1-rs2187668 interaction was significantly associated with an increased PMN risk, P <.001. However, there was a substantial between-studies heterogeneity for some SNPs. Subgroup analyses by ethnicity for the 9 PLA2R SNPs did not show any cross-ethnic disparity. Inversely, the risk conferred by the HLA-DQA1 rs2187668*A allele was significantly higher in Caucasians (OR [95% CI] = 3.929 [3.251–4.748]) than in Asians (OR [95% CI] = 2.537 [1.94–3.318], P =.007. Besides, meta-regressions revealed for the majority of investigated SNPs significant correlations of the effect size with albumin, 24-hours proteinuria, serum creatinine, and eGFR levels. Hence, the influence on PMN risk conferred by the PLA2R and HLA-DQA1 SNPs was rather noted in patients with a severe disease. Conclusion: This meta-analysis showed that 9 out of the 10 investigated SNPs in PLA2R and HLA-DQA1 genes were associated with increased PMN risk. Heterogeneity could be due to disparate patient groups in terms of disease presentation for almost all SNPs, and ethnicity for the HLA-DQA1 rs2187668 SNP. Registration: This review has been registered on PROSPERO: CRD42024506729. Available from: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42024506729 Plain language summary: Genetic factors in primary membranous nephritis Why was the study done? Primary membranous nephritis (PMN) is the most common etiology of adult-onset nephrotic syndrome. Understanding risk factors, particularly genetic ones, would provide a better understanding of its pathophysiological mechanisms in order to prevent and treat patients more effectively. What did the researchers do? The research team summarized published data on genetic factors associated with PMN including phospholipase A2 receptor (PLA2R) and HLA-DQA1 genes. What did the researchers find? The total number of included studies was 27. Nine out of ten genetic factors were found to be associated with PMN risk. Moreover, we noted significant interaction between PLA2R and HLA-DQA1 in potentializing PMN risk. Nevertheless, there was a significant between-studies heterogeneity which was found to be explained in part by disease severity. What do the findings mean? This study has identified some important some genetic factors associated with PMN together with confounding factors that could influence the aforementioned association. [ABSTRACT FROM AUTHOR]

Background and Aims: This study aimed to report nine Charcot–Marie–Tooth disease (CMT) families with six novel IGHMBP2 mutations in our CMT2 cohort and to summarize the genetic and clinical features of all AR‐CMT2S patients reported worldwide. Methods: General information, clinical and neurophysiological data of 275 axonal CMT families were collected. Genetic screening was performed by inherited peripheral neuropathy related genes panel or whole exome sequencing. The published papers reporting AR‐CMT2S from 2014 to 2023 were searched in Pubmed and Wanfang databases. Results: In our CMT2 cohort, we detected 17 AR‐CMT2S families carrying IGHMBP2 mutations and eight were published previously. Among these, c.743 T > A (p.Val248Glu), c.884A > G (p.Asp295Gly), c.1256C > A (p.Ser419*), c.2598_2599delGA (p.Lys868Sfs*16), c.1694_1696delATG (p.Asp565del) and c.2509A > T (p.Arg837*) were firstly reported. These patients prominently presented with early‐onset typical axonal neuropathy and without respiratory dysfunction. So far, 56 AR‐CMT2S patients and 57 different mutations coming from 43 families have been reported in the world. Twenty‐nine of 32 missense mutations were clustered in helicase domain and ATPase region. The age at onset ranged from 0.11to 20 years (Mean ± SD: 3.43 ± 3.88 years) and the majority was infantile‐onset (<2 years). The initial symptoms included weakness of limbs (19, 29.7%), delayed milestones (12, 18.8%), gait disturbance (11, 17.2%), feet deformity (8, 12.5%), feet drop (8, 12.5%), etc. Interpretation: AR‐CMT2S accounted for 6.2% in our CMT2 cohort. We firstly reported six novel IGHMBP2 mutations which expanded the genotypic spectrum of AR‐CMT2S. Furthermore, 17 AR‐CMT2S families could provide more resources for natural history study, drug research and development. [ABSTRACT FROM AUTHOR]

Wheat (Triticum aestivum L.) is a fundamental crop essential for both human and animal consumption. Addressing the challenge of enhancing wheat yield involves sophisticated applications of molecular genetics and genomic techniques. This review synthesizes current research identifying and characterizing pivotal genes that impact traits such as grain size, number, and weight, critical factors influencing overall yield. Key genes including TaSPL17, ABP7, TaGNI, TaCKX6, TaGS5, TaDA1, WAPO1, TaRht1, TaTGW-7A, TaGW2, TaGS5-3A, TaSus2-2A, TaSus2-2B, TaSus1-7A, and TaSus1-7B are examined for their roles in these traits. The review also explores genes responsive to environmental changes, which are increasingly significant under current climate variability. Multi-trait regulatory genes and quantitative trait loci (QTLs) that contribute to these traits are discussed, highlighting their dual influences on grain size and yield. Furthermore, the paper underscores the utility of emerging technologies such as CRISPR/Cas9, Case13, and multi-omics approaches. These innovations are instrumental for future discoveries and are poised to revolutionize wheat breeding by enabling precise genetic enhancements. Facing unprecedented challenges from climate change, the identification and utilization of these candidates is crucial. This review aims to be a comprehensive resource for researchers, providing an integrative understanding of complex traits in wheat and proposing new avenues for research and crop improvement strategies. [ABSTRACT FROM AUTHOR]

For sequencing-based spatial transcriptomics data, the gene-spot count matrix is highly sparse. This feature is similar to scRNA-seq. The goal of this paper is to identify whether there exist genes that are frequently under-detected in Visium compared to bulk RNA-seq, and the underlying potential mechanism of under-detection in Visium. We collected paired Visium and bulk RNA-seq data for 28 human samples and 19 mouse samples, which covered diverse tissue sources. We compared the two data types and observed that there indeed exists a collection of genes frequently under-detected in Visium compared to bulk RNA-seq. We performed a motif search to examine the last 350 bp of the frequently under-detected genes, and we observed that the poly (T) motif was significantly enriched in genes identified from both human and mouse data, which matches with our previous finding about frequently under-detected genes in scRNA-seq. We hypothesized that the poly (T) motif may be able to form a hairpin structure with the poly (A) tails of their mRNA transcripts, making it difficult for their mRNA transcripts to be captured during Visium library preparation. [ABSTRACT FROM AUTHOR]

Increasing yield is an important goal of barley breeding. In this study, 54 papers published from 2001–2022 on QTL mapping for yield and yield-related traits in barley were collected, which contained 1080 QTLs mapped to the barley high-density consensus map for QTL meta-analysis. These initial QTLs were integrated into 85 meta-QTLs (MQTL) with a mean confidence interval (CI) of 2.76 cM, which was 7.86-fold narrower than the CI of the initial QTL. Among these 85 MQTLs, 68 MQTLs were validated in GWAS studies, and 25 breeder's MQTLs were screened from them. Seventeen barley orthologs of yield-related genes in rice and maize were identified within the hcMQTL region based on comparative genomics strategy and were presumed to be reliable candidates for controlling yield-related traits. The results of this study provide useful information for molecular marker-assisted breeding and candidate gene mining of yield-related traits in barley. [ABSTRACT FROM AUTHOR]

Simple Summary: The role of neurogenic locus notch homolog protein 1 (NOTCH1)- and nuclear factor erythroid 2-related factor 2 (NRF2)-related pathways is highly heterogeneous in small cell lung cancer (SCLC) and, when they are both abnormally activated, they can synergistically cause neoplastic proliferation. In this paper, we investigate the possible role of KEAP1 silencing in NRF2 and NOTCH axis deregulation in SCLC by evaluating its impact on the modulation of cellular defense systems, cell growth, and differentiation. We also investigate the impact of these systems' impairment in response to conventional chemotherapies and NOTCH inhibitors in silenced SCLC cell lines with different Kelch-like ECH-associated protein 1 (KEAP1) alterations. The KEAP1/NRF2 pathway is a master regulator of several redox-sensitive genes implicated in the resistance of tumor cells against therapeutic drugs. The dysfunction of the KEAP1/NRF2 system has been correlated with neoplastic patients' outcomes and responses to conventional therapies. In lung tumors, the growth and the progression of cancer cells may also involve the intersection between the molecular NRF2/KEAP1 axis and other pathways, including NOTCH, with implications for antioxidant protection, survival of cancer cells, and drug resistance to therapies. At present, the data concerning the mechanism of aberrant NRF2/NOTCH crosstalk as well as its genetic and epigenetic basis in SCLC are incomplete. To better clarify this point and elucidate the contribution of NRF2/NOTCH crosstalk deregulation in tumorigenesis of SCLC, we investigated genetic and epigenetic dysfunctions of the KEAP1 gene in a subset of SCLC cell lines. Moreover, we assessed its impact on SCLC cells' response to conventional chemotherapies (etoposide, cisplatin, and their combination) and NOTCH inhibitor treatments using DAPT, a γ-secretase inhibitor (GSI). We demonstrated that the KEAP1/NRF2 axis is epigenetically controlled in SCLC cell lines and that silencing of KEAP1 by siRNA induced the upregulation of NRF2 with a consequent increase in SCLC cells' chemoresistance under cisplatin and etoposide treatment. Moreover, KEAP1 modulation also interfered with NOTCH1, HES1, and DLL3 transcription. Our preliminary data provide new insights about the downstream effects of KEAP1 dysfunction on NRF2 and NOTCH deregulation in this type of tumor and corroborate the hypothesis of a cooperation of these two pathways in the tumorigenesis of SCLC. [ABSTRACT FROM AUTHOR]

The gene products of PRS1-PRS5 in Saccharomyces cerevisiae are responsible for the production of PRPP (5-phospho-D-ribosyl-α-1-pyrophosphate). However, it has been demonstrated that they are also involved in the cell wall integrity (CWI) signalling pathway as shown by protein–protein interactions (PPIs) with, for example Slt2, the MAP kinase of the CWI pathway. The following databases: SGD, BioGRID and Hit Predict, which collate PPIs from various research papers, have been scrutinized for evidence of PPIs between Prs1-Prs5 and components of the CWI pathway. The level of certainty in PPIs was verified by interaction scores available in the Hit Predict database revealing that well-documented interactions correspond with higher interaction scores and can be graded as high confidence interactions based on a score > 0.28, an annotation score ≥ 0.5 and a method-based high confidence score level of ≥ 0.485. Each of the Prs1-Prs5 polypeptides shows some degree of interaction with the CWI pathway. However, Prs5 has a vital role in the expression of FKS2 and Rlm1, previously only documented by reporter assay studies. This report emphasizes the importance of investigating interactions using more than one approach since every method has its limitations and the use of different methods, as described herein, provides complementary experimental and statistical data, thereby corroborating PPIs. Since the experimental data described so far are consistent with a link between PRPP synthetase and the CWI pathway, our aim was to demonstrate that these data are also supported by high-throughput bioinformatic analyses promoting our hypothesis that two of the five PRS-encoding genes contain information required for the maintenance of CWI by combining data from our targeted approach with relevant, unbiased data from high-throughput analyses. [ABSTRACT FROM AUTHOR]

Inference of cell–cell communication (CCC) provides valuable information in understanding the mechanisms of many important life processes. With the rise of spatial transcriptomics in recent years, many methods have emerged to predict CCCs using spatial information of cells. However, most existing methods only describe CCCs based on ligand–receptor interactions, but lack the exploration of their upstream/downstream pathways. In this paper, we proposed a new method to infer CCCs, called Intercellular Gene Association Network (IGAN). Specifically, it is for the first time that we can estimate the gene associations/network between two specific single spatially adjacent cells. By using the IGAN method, we can not only infer CCCs in an accurate manner, but also explore the upstream/downstream pathways of ligands/receptors from the network perspective, which are actually exhibited as a new panoramic cell-interaction-pathway graph, and thus provide extensive information for the regulatory mechanisms behind CCCs. In addition, IGAN can measure the CCC activity at single cell/spot resolution, and help to discover the CCC spatial heterogeneity. Interestingly, we found that CCC patterns from IGAN are highly consistent with the spatial microenvironment patterns for each cell type, which further indicated the accuracy of our method. Analyses on several public datasets validated the advantages of IGAN. [ABSTRACT FROM AUTHOR]

Summary: Greenbeards are selfish genetic elements that make their bearers behave either altruistically towards individuals bearing similar greenbeard copies or harmfully towards individuals bearing different copies. They were first proposed by W. D. Hamilton over 50 yr ago, to illustrate that kin selection may operate at the level of single genes. Examples of greenbeards have now been reported in a wide range of taxa, but they remain undocumented in plants. In this paper, we discuss the theoretical likelihood of greenbeard existence in plants. We then question why the greenbeard concept has never been applied to plants and speculate on how hypothetical greenbeards could affect plant–plant interactions. Finally, we point to different research directions to improve our knowledge of greenbeards in plants. [ABSTRACT FROM AUTHOR]

Functional genes encode various biological functions required for the life activities of organisms. By analyzing the functional genes of edible and medicinal fungi, varieties of edible and medicinal fungi can be improved to enhance their agronomic traits, growth rates, and ability to withstand adversity, thereby increasing yield and quality and promoting industrial development. With the rapid development of functional gene research technology and the publication of many whole-genome sequences of edible and medicinal fungi, genes related to important biological traits have been mined, located, and functionally analyzed. This paper summarizes the advantages and disadvantages of different functional gene research techniques and application examples for edible and medicinal fungi; systematically reviews the research progress of functional genes of edible and medicinal fungi in biological processes such as mating type, mycelium and fruit growth and development, substrate utilization and nutrient transport, environmental response, and the synthesis and regulation of important active substances; and proposes future research directions for functional gene research for edible and medicinal fungi. The overall aim of this study was to provide a valuable reference for further promoting the molecular breeding of edible and medicinal fungi with high yield and quality and to promote the wide application of edible and medicinal fungi products in food, medicine, and industry. [ABSTRACT FROM AUTHOR]

The central conclusions of "The Gene: An Appraisal" are that genetic variance does not underpin biological evolution, and, therefore, that genes are not Mendel's units of inheritance. In this response, I will address the criticisms I have received via commentaries on that paper by defending the following statements: 1. Epistasis does not explain the power-law fitness profile of the Long-Term Evolution Experiment (LTEE). The data from the evolution of natural systems displays the power-law form ubiquitously. Epistasis plays no role in evolution. 2. The common characteristics of living things (natural systems) are described by the principle of least action in de Maupertuis's original form, which is synonymous with the 2nd law of thermodynamics and Newton's 2nd law of motion in its complete form, i.e., F = dp/dt. Organisms strive to achieve free energy balance with their environments. 3. Based on an appraisal of the scientific environment between 1880 and 1911, I conclude that Johannsen's genotype conception was perhaps, the only option available to him. 4. The power-law fitness profile of the LTEE falsifies Fisher's Genetical Theory of Natural Selection, Johannsen's genotype conception, and the idea that 'Darwinian evolution' is an exception to the generic thermodynamic process of evolution in natural systems. 5. The use of the technique of genome-wide association to identify the causes and the likelihoods of inherited common diseases and behavioural traits is a 'wild goose chase' because genes are not the units of inheritance. [ABSTRACT FROM AUTHOR]

Reception of chemical information from the environment is crucial for insects' survival and reproduction. The chemosensory reception mainly occurs by the antennae and mouth parts of the insect, when the stimulus contacts the chemoreceptors located within the sensilla. Chemosensory receptor genes have been well-studied in some social hymenopterans such as ants, honeybees, and wasps. However, although stingless bees are the most representative group of eusocial bees, little is known about their odorant, gustatory, and ionotropic receptor genes. Here, we analyze the transcriptome of the proboscis and antennae of the stingless bee Tetragonisca fiebrigi. We identified and annotated 9 gustatory and 15 ionotropic receptors. Regarding the odorant receptors, we identified 204, and we were able to annotate 161 of them. In addition, we compared the chemosensory receptor genes of T. fiebrigi with those annotated for other species of Hymenoptera. We found that T. fiebrigi showed the largest number of odorant receptors compared with other bees. Genetic expansions were identified in the subfamilies 9-exon, which was also expanded in ants and paper wasps; in G02A, including receptors potentially mediating social behavior; and in GUnC, which has been related to pollen and nectar scent detection. Our study provides the first report of chemosensory receptor genes in T. fiebrigi and represents a resource for future molecular and physiological research in this and other stingless bee species. [ABSTRACT FROM AUTHOR]

To illustrate the results achieved by genes in premature ovarian insufficiency (POI) and collaborations in the field, and to explore key themes and future directions. Articles and reviews related to POI genes published between 1990 and 2022 were retrieved from the Web of Science core collection (WoSCC) for the total bibliometric analysis. Tools were analyzed for publication, country, institution, journal, authors, reference, keywords, subject categories, funding agencies, and research hotspots using a bibliometric online analysis platform, Bibliographic Co-occurrence Matrix Builder (BICOMB), CiteSpace V, and VOSviewer. A total of 2,232 papers were included in this study. Articles were published in 52 countries, with the United States publishing the most, followed by China. A total of 308 institutions contributed to relevant publications. Shandong University published the most papers. Qin Y's team published the most relevant papers. Human reproduction and fertility and sterility are the two journals with the most papers. X-chromosome abnormalities, transcription factor mutations, and FMR1 genes are the directions of more POI, and DNA repair is the keyword of the research frontier in recent years. This study summarizes the relevant literature on POI gene research for the first time and analyzes the current hotspots and future trends in this field. The findings can further reveal the etiology, diagnosis, and treatment of POI, which is beneficial for researchers to grasp the genetic dynamics of POI women. [ABSTRACT FROM AUTHOR]

Background: This review is a summarized study on CAD, CVD, atherosclerosis, and its association with the ABCA1 gene. Only 13 clinical as well as epidemiological and peer-reviewed research papers published in the associated field were chosen for the review from out of 55 articles. Main body: The research papers have been collected and studied from PubMed, Research Gate, and Google Scholar search engines. In the study, it has been found that GWAS, cell culture, and data-based studies were done to figure out the relationship of the ABCA1 gene with heart diseases. Blood samples were collected and diagnosed both biochemically and genetically to find out the lipid level and its functioning in the efflux of cholesterol and its effect and association with the ABCA1 gene, and with CAD researchers. Conclusions: Dysregulation of DNA methylation can be re-expressed epigenetically. These studies of the ABCA1 gene and its polymorphic variants would help in future research studies and further can develop new drugs and methods the for treatment of heart disease and CAD. [ABSTRACT FROM AUTHOR]

This invited commentary paper discusses the concept of elevated antibiotic resistance genes as a global change factor. [ABSTRACT FROM AUTHOR]

As a first step for the development of biosensing inks for inexpensive paper-based biodetection, we prepared paper strips printed with carboxylic poly( N-isopropylacrylamide) microgels that were modified either with an antibody or with a DNA aptamer. We found that the antibody and the DNA aptamer retained their recognition capabilities when coupled to microgel. The printed microgel remains stationary during chromatographic elution while the microgel-supported molecular recognition elements are accessible to their intended targets present in the elution solution. Our work indicates that microgels, large enough to isolate the biosensors from the paper surface, are sufficiently hydrophilic to be wetted during chromatographic elution, exposing the gel-supported affinity probes to their targets. [ABSTRACT FROM AUTHOR]

Avery's et al.'s 1944 paper provides the first direct evidence of DNA having gene-like properties and marks the beginning of a new phase in early molecular genetics (with a strong focus on chemistry and DNA). The study of its reception shows that on the whole, Avery's results were immediately appreciated and motivated new research on transformation, the chemical nature of DNA's biological specificity and bacteria genetics. It shows, too, that initial problems of transferring transformation to other systems and prominent criticism of its results nurtured skepticism. Avery's experiment was downplayed and neglected particularly by many of those scientists who worked in the new fields of biochemical and biophysical genetics, genetic phage, and TMV research. This was not due to the fact that the implications of the paper could not be connected to generally accepted knowledge. Contrary to a widespread belief, the assumed uniformity of DNA as opposed to proteins was not used as an argument against the validity of Avery's et al.'s finding. The indifference rather reflected, among other things, the disciplinary gap between the chemically oriented microbiologists and the old and new geneticists who remained committed to genetic and physical methods (in particular x-ray studies) and clung to the assumption that proteins were the sole carriers of biological specificity. The responses to Avery's et al.'s paper show how different research interests in the areas between microbiology, genetics, and biochemistry interacted with the prejudices, dogmas, individual farsightedness or short-sightedness, and scientific authority during a pivotal period of early molecular biology. [ABSTRACT FROM AUTHOR]

The article discusses a study which examined real-time PCR detection of Plasmodium directly from whole blood and filter paper samples. The study evaluated reagents designed to specifically overcome PCR inhibition and quenching of fluorescence for real-time PCR amplification of Plasmodium DNA directly from blood. The study found that the sensitivity and specificity ranged from 93-100% compared with PCR performed on purified Plasmodium DNA.

For clinical diagnosis, a small number of targets (2–10 biomarkers) are often all that is required for disease assessment and accurate early disease diagnosis. In the current paper we have developed novel, carrier-resolved, single-label-based multiplexed assays for the simultaneous detection and quantification of a limited number of DNA targets associated with breast cancer. In contrast to current encoding strategies, every hybridization signal for the corresponding DNA target in our protocol is uniquely immobilized onto one carrier vehicle with a unique and intrinsic physico-chemical signature. Moreover, a simple chemiluminescence setup is employed to read the carrier code instead of expensive and complicated flow-cytometer or imaging-systems commonly used for multiplexed assays. Herein we demonstrate a new protocol using three homogeneous carriers, i.e.thermo-sensitive poly(N-isopropylacrylamide) (PNIP), polystyrene beads, and magnetic beads respectively. This new methodology allowed for the simultaneous determination of three oligonucleotide sequences (60 bases in length) associated with the breast cancer gene (BRCA1) and showed high selectivity and attomolar–femtomolar sensitivity. The mixture of three different capture probe conjugates first hybridizes with three corresponding target sequences, sandwiches with three biotinylated DNAs, and then reacts with peroxidase–streptavidin polymer in a single vessel without any washing, leading to the development of a ‘one-pot reaction system’. Only one washing step in our protocol is required prior to detection leading to our whole procedure being simple and efficient. The results show that the hybridization response to sample mixtures containing increasing levels of each target is proportional to the amount of corresponding DNA targets, indicating minimal cross-interferences. The work presented here validates the design and concept of a system for the detection of a limited number of DNA targets and provides the foundation for the development of highly sensitive techniques with increased multi-analyte capabilities. [ABSTRACT FROM AUTHOR]

Celecoxib, a selective cyclooxygenase 2 inhibitor, is known to have anti-inflammatory activity and to induce apoptosis in various types of cancer cells. Here, we examined the molecular mechanism of celecoxib-induced apoptosis in cervical cancer cell lines (HeLa, CaSki and C33A). Screening of a microarray cDNA-chip containing 225 different genes revealed that growth arrest and DNA damage inducible gene (GADD153), a transcription factor involved in apoptosis, showed the strongest differential expression following celecoxib treatment in all three cervical cancer cell lines. Notably, siRNA-induced silencing of GADD153 suppressed celecoxib-induced apoptosis in all the three cell lines, and exogenous expression of GADD153 triggered apoptosis in cervical cancer cells in the absence of other apoptotic stimuli. A luciferase reporter gene assay and mRNA stability tests revealed that expression of GADD153 was regulated at both the transcriptional and post-transcriptional levels following celecoxib treatment. The region between −649 and −249, containing an intact C/EBP-ATF binding site, was required for the basal activity and celecoxib-induced stimulation of GADD153 promoter activity. Also, mRNA stability test showed that celecoxib prolonged the half-life of GADD153 mRNA. In terms of signaling pathway, addition of the NF-κB inhibitor, N-tosyl-l phenylalanyl-chloromethyl ketone (TPCK), had no effect on GADD153 expression levels. Celecoxib treatment induced Bak expression, whereas cell treated with siGADD153 or TPCK showed lower levels of celecoxib-induced Bak up-regulation. These novel findings collectively suggest that GADD153 may play a key role in celecoxib-induced apoptosis in cervical cancer cells by regulating the expression of proapoptotic proteins such as Bak. [ABSTRACT FROM AUTHOR]

Background: The alkalistable and thermostable xylanases are in high demand for pulp bleaching in paper industry and generating xylooligosaccharides by hydrolyzing xylan component of agro-residues. The compost-soil samples, one of the hot environments, are expected to be a rich source of microbes with thermostable enzymes. Methodology/Principal Findings: Metagenomic DNA from hot environmental samples could be a rich source of novel biocatalysts. While screening metagenomic library constructed from DNA extracted from the compost-soil in the p18GFP vector, a clone (TSDV-MX1) was detected that exhibited clear zone of xylan hydrolysis on RBB xylan plate. The sequencing of 6.321 kb DNA insert and its BLAST analysis detected the presence of xylanase gene that comprised 1077 bp. The deduced protein sequence (358 amino acids) displayed homology with glycosyl hydrolase (GH) family 11 xylanases. The gene was subcloned into pET28a vector and expressed in E. coli BL21 (DE3). The recombinant xylanase (rMxyl) exhibited activity over a broad range of pH and temperature with optima at pH 9.0 and 80uC. The recombinant xylanase is highly thermostable having T1/2 of 2 h at 80°C and 15 min at 90°C. Conclusion/Significance: This is the first report on the retrieval of xylanase gene through metagenomic approach that encodes an enzyme with alkalistability and thermostability. The recombinant xylanase has a potential application in paper and pulp industry in pulp bleaching and generating xylooligosaccharides from the abundantly available agro-residues. [ABSTRACT FROM AUTHOR]

An opaque biochemical definition, an insufficient functional characterization, an interpolated database description, and a beautiful 3D structure with a wrong reaction. All these are elements of an exemplar case of misannotation in biological databases and confusion in the scientific literature concerning genes and enzymes acting on ureidoglycolate, an intermediate of purine catabolism. Here we show biochemical evidence for the relocation of genes assigned to EC 3.5.3.19 (ureidoglycolate hydrolase, releasing ammonia), such as allA of Escherichia coli or DAL3 of Saccharomyces cerevisiae, to EC 4.3.2.3 (ureidoglycolate lyase, releasing urea). The EC 3.5.3.19 should be more appropriately named ureidoglycolate amidohydrolase and include genes equivalent to UAH of Arabidopsis thaliana. The distinction between ammonia- or urea-releasing activities from ureidoglycolate is relevant for the understanding of nitrogen metabolism in various organisms and of virulence factors in certain pathogens rather than a nomenclature problem. We trace the original fault in database annotation and provide a rationale for its incorporation and persistence in the scientific literature. Notwithstanding the technological distance, yet not surprising for the constancy of human nature, error categories and mechanisms established in the study of the work of amanuensis monks still apply to the modern curation of biological databases. [ABSTRACT FROM AUTHOR]

The article discusses the role played by epigenetics in the field of reproductive medicine. The natural times when developmental epigenetic reprogramming takes place in gametes almost matches the time of human assisted reproduction when the gametes and embryos are handled in an in vitro environemnt. Information is also given on genomic imprinting and in vitro culture of embryos.

Sepsis, a disease caused by severe infection, has a high mortality rate. At present, there is a lack of reliable algorithmic models for biomarker mining and diagnostic model construction for sepsis. Programmed cell death (PCD) has been shown to play a vital role in disease occurrence and progression, and different PCD-related genes have the potential to be targeted for the treatment of sepsis. In this paper, we analyzed PCD-related genes in sepsis. Implicated PCD processes include apoptosis, necroptosis, ferroptosis, pyroptosis, netotic cell death, entotic cell death, lysosome-dependent cell death, parthanatos, autophagy-dependent cell death, oxeiptosis, and alkaliptosis. We screened for diagnostic-related genes and constructed models for diagnosing sepsis using multiple machine-learning models. In addition, the immune landscape of sepsis was analyzed based on the diagnosis-related genes that were obtained. In this paper, 10 diagnosis-related genes were screened for using machine learning algorithms, and diagnostic models were constructed. The diagnostic model was validated in the internal and external test sets, and the Area Under Curve (AUC) reached 0.7951 in the internal test set and 0.9627 in the external test set. Furthermore, we verified the diagnostic gene via a qPCR experiment. The diagnostic-related genes and diagnostic genes obtained in this paper can be utilized as a reference for clinical sepsis diagnosis. The results of this study can act as a reference for the clinical diagnosis of sepsis and for target discovery for potential therapeutic drugs. [ABSTRACT FROM AUTHOR]