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Hypophosphatasia (HPP) is a rare, inherited metabolic disease characterized by low tissue‐nonspecific alkaline phosphatase activity due to ALPL gene variants. We describe ALPL variants from the observational, prospective, multinational Global HPP Registry. Inclusion in the analysis required a diagnosis of HPP, low serum ALP activity, and ≥1 ALPL variant. Of 1176 patients enrolled as of September 2022, 814 met inclusion criteria in Europe (48.9%), North America (36.7%), Japan (10.2%), Australia (2.6%), and elsewhere (1.6%). Most patients (74.7%) had 1 ALPL variant; 25.3% had ≥2 variants. Nearly all patients (95.6%) had known disease‐causing variants; 4.4% had variants of uncertain significance. Disease‐causing variants were predominantly missense (770/1556 alleles). The most common variants were c.571G>A (102/1628 alleles), c.1250A>G (66/1628 alleles), and c.1559del (61/1628 alleles). Variant profiles were generally consistent, except in Japan, where a higher proportion of patients (68.7%) had ≥2 ALPL variants, likely because more had disease onset before age 6 months (53.0% vs. 10.1%–23.1% elsewhere). Frameshift mutations (61/164 alleles) and inframe deletions (7/164 alleles) were more common in Japan. Twenty‐three novel variants were discovered, each in a single geographic region, predominantly Europe. Analyses confirmed previously known ALPL variants, identified novel variants, and characterized geographic variation in frequency and type of ALPL variants in a large population. [ABSTRACT FROM AUTHOR]

Long non‐coding RNAs (lncRNAs) and dendritic cells (DC) play crucial roles in the development of acute coronary syndrome (ACS); however, the mechanisms remain unclear. To investigate this, we analysed the differentially expressed lncRNAs in monocyte‐derived DCs (moDCs) from patients with ACS. Peripheral blood mononuclear cells were transformed into moDCs. Cellular morphology and expression levels of moDC‐specific markers (CD80, CD86, CD11c, CD14 and HLA‐DR) were analysed using electron microscopy (EM) and flow cytometry (FCM), respectively. Differentially expressed lncRNAs and their functions were predicted using gene sequencing, gene ontology and the Kyoto Encyclopedia of Genes and Genomes. The expression levels of markers, signalling pathway molecules (p‐PI3K and p‐AKT), inflammatory cytokines (IL‐6 and IL‐12p70) and target gene (C‐C motif chemokine ligand (CCL) 15 and CCL14) were analysed by overexpression or silencing of candidate lncRNAs. EM revealed the cells to be suspended in dendritic pseudopodia. CD11c and HLA‐DR were upregulated, while CD80 and CD86 were downregulated. Comparison between the UA versus ST group showed the highest number of differentially expressed lncRNAs (n = 113), followed by UA versus NST (n = 115), CON versus NST (n = 49) and CON versus ST (n = 35); however, the number was low for CON versus UA and ST versus NST groups. moDC‐specific marker expression, signalling pathway molecules, inflammatory cytokines and CCL14 were upregulated following lentiviral overexpression of smart silencer‐CCL15‐CCL14; however, expression levels decreased following transfection with siRNA. The morphology, function and lncRNA expression of moDCs differ depending on the type of ACS. The differentially expressed lncRNAs, particularly CCL15‐CCL14, regulate the function of moDCs. Thus, our study provides new insights regarding the role of lncRNAs in ACS and indicates the potential use of CCL15‐CCL14 as a novel diagnostic marker and therapeutic target. [ABSTRACT FROM AUTHOR]

With rapid development and mature of single‐cell measurements, single‐cell biology and pathology become an emerging discipline to understand the disease. However, it is important to address concerns raised by clinicians as to how to apply single‐cell measurements for clinical practice, translate the signals of single‐cell systems biology into determination of clinical phenotype, and predict patient response to therapies. The present Perspective proposes a new system coined as the clinical artificial intelligent single‐cell (caiSC) with the dynamic generator of clinical single‐cell informatics, artificial intelligent analyzers, molecular multimodal reference boxes, clinical inputs and outs, and AI‐based computerization. This system provides reliable and rapid information for impacting clinical diagnoses, monitoring, and prediction of the disease at the single‐cell level. The caiSC represents an important step and milestone to translate the single‐cell measurement into clinical application, assist clinicians' decision‐making, and improve the quality of medical services. There is increasing evidence to support the possibility of the caiSC proposal, since the corresponding biotechnologies associated with caiSCs are rapidly developed. Therefore, we call the special attention and efforts from various scientists and clinicians on the caiSCs and believe that the appearance of the caiSCs can shed light on the future of clinical molecular medicine. [ABSTRACT FROM AUTHOR]

Panel‐based methods are commonly employed for the analysis of novel gene fusions in precision diagnostics and new drug development in cancer. However, these methods are constrained by limitations in ligation yield and the enrichment of novel gene fusions with low variant allele frequencies. In this study, we conducted a pioneering investigation into the stability of double‐stranded adapter DNA, resulting in improved ligation yield and enhanced conversion efficiency. Additionally, we implemented blocker displacement amplification, achieving a remarkable 7‐fold enrichment of novel gene fusions. Leveraging the pre‐enrichment achieved with this approach, we successfully applied it to Nanopore sequencing, enabling ultra‐fast analysis of novel gene fusions within one hour with high sensitivity. This method offers a robust and remarkably sensitive mean of analyzing novel gene fusions, promising the discovery of pivotal biomarkers that can significantly improve cancer diagnostics and the development of new therapeutic strategies. [ABSTRACT FROM AUTHOR]

As a cornerstone of the central dogma of molecular biology, RNA plays vital roles in living organisms. Over the past few decades, many RNA labeling technologies have been developed to elucidate the biological function of RNA. These technologies have significantly advanced our understanding of RNA secondary structure, localization, and turnover. Additionally, taking advantage of these innovative RNA labeling approaches, plenty of tool kits have been devised for the regulation of RNA-related biological process, such as gene expression and gene editing. In this review, we primarily focus on an array of intracellular RNA labeling methods, encompassing chemical probes-based labeling, metabolic labeling, and proximity-dependent labeling. We also provide a brief overview of their applications in the research of RNA biology. Finally, the perspectives of RNA labeling are also discussed. [ABSTRACT FROM AUTHOR]

Background and Objectives: The presence of blood subtypes may lead to difficulties in blood group identification; however, third‐generation sequencing (TGS) can help in accurately identifying difficult blood groups, and study the serological characteristics and molecular mechanism of Ael subtypes. Materials and Methods: ABO blood group was identified by the standard serological technique, weak blood group antigen was identified by adsorption‐elution experiments, ABH substance in the saliva was determined and glycosyltransferase activity of A and B was detected. The ABO gene full‐length sequence and promoter region were amplified by specific primers using single‐molecule real‐time sequencing, with the amplified products being sequenced directly and analysed in real time. Results: The patient was serologically identified as Ael subtype, and TGS analysis revealed new intron mutations in Ael patients (c.467C>T; c.29‐10T>A). Conclusion: The discovery of the new allele and the identification of ABO subtypes can be combined with serological characterization and molecular biological methods. [ABSTRACT FROM AUTHOR]

BACKGROUND: The potato tuber moth (PTM), Phthorimaea operculella (Zeller) (Lepidoptera: Gelechiidae), is a destructive pest of Solanaceae crops worldwide. α‐solanine and α‐chaconine are toxic steroidal glycoalkaloids (SGAs) in Solanaceae crops and are most abundant in potatoes (Solanum tuberosum L.), accounting for more than 95% of the total SGAs. PTM grows on potatoes with a higher concentration of SGAs. Gut bacteria play an important role in the physiology and behavior of insects. To understand the role of gut bacteria of PTM in host adaptability, we isolated and identified major SGA (α‐chaconine and α‐solanine)‐degrading gut bacteria in the gut of PTM by a selective medium and analyzed their degradability and degradation mechanism. RESULTS: The gut Glutamicibacter halophytocola S2 of PTM with high degradation capacity to α‐solanine and α‐chaconine were detected by liquid chromatography mass spectrometry (LC–MS) and identified by morphological and 16S rRNA gene sequence analysis. A gene cluster involving α‐rhamnosidases, β‐glucosidases, and β‐galactosidases was identified by whole‐genome sequencing of G. halophytocola S2. These genes had higher expression on the α‐solanine medium. PTM inoculated with the isolated G. halophytocola S2 obtained higher fitness than antibiotic‐treated PTM. CONCLUSION: The G. halophytocola S2 in the gut of PTM could degrade the major toxic α‐solanine and α‐chaconine in potatoes. This enhances the fitness of PTM feeding on potatoes with high SGA contents. The results provide a theoretical foundation for the integrated pest management of PTM and provide an effective strain for the treatment of α‐solanine and α‐chaconine in potato food. © 2022 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Main observation and conclusion: As an innate characteristic, DNA length has attracted more and more attention. The length of some important biomarkers such as ctDNA (Circulating tumor DNA) and cffDNA (Cell free fetal DNA) is shorter than that of cell‐free DNA. Researchers have utilized the difference in length to increase the abundance of ctDNA or cffDNA in total cell‐free DNA to overcome the difficulties in detection due to their low abundance. They have developed short‐stranded DNA enrichment technology, which complemented the blind spots of the application range of typical enrichment technology based on DNA sequence differences. However, the existing short‐stranded DNA enrichment technology cannot possess high efficiency and simplicity simultaneously. Herein, we developed the SSB‐PCR (Short‐DNA Specific Blocker PCR) technology to enrich the short‐stranded DNA in an efficient and simple way. Through theoretical and experimental verification, it was proved that this method could increase the abundance of short‐stranded DNA by more than 10 times. Based on this, we have found an application scenario for this method in cffDNA enrichment. Further, a procedure was established to perform a reliable diagnosis of the genotype of cffDNA samples. We believe that this method has great potential to achieve accurate, fast, and cost‐effective non‐invasive prenatal testing. [ABSTRACT FROM AUTHOR]

Dysregulation of gut microbiota is implicated in the pathogenesis of various diseases, including metabolic diseases, inflammatory diseases, and cancer. To date, the link between gut microbiota and myeloid leukemia (ML) remains largely unelucidated. Herein, a total of 29 patients with acute myeloid leukemia (AML), 17 patients with chronic myeloid leukemia (CML), and 33 healthy subjects were enrolled, and gut microbiota were profiled via Illumina sequencing of the 16S rRNA. We evaluated the correlation between ML and gut microbiota. The microbial α‐diversity and β‐diversity exhibited significant differences between ML patients and healthy controls (HCs). Compared to healthy subjects, we found that at the phylum level, the relative abundance of Actinobacteria, Acidobacteria, and Chloroflexi was increased, while that of Tenericutes was decreased. Correspondingly, at the genus level in ML, Streptococcus were increased, especially in AML patients, while Megamonas (P = 0.02), Lachnospiraceae NC2004 group, and Prevotella 9 (P = 0.007) were decreased. Moreover, ML‐enriched species, including Sphingomonas, Lysobacyer, Helicobacter, Lactobacillus, Enterococcus, and Clostridium sensu stricto 1, were identified. Our results indicate that the gut microbiota was altered in ML patients compared to that of healthy subjects, which could contribute to the elucidation of microbiota‐related pathogenesis of ML, and the development of novel therapeutic strategies in the treatment of ML. [ABSTRACT FROM AUTHOR]

BACKGROUND: Gracilibacillus alcaliphilus SK51.001, a strain that produces β‐CGTase (β‐cyclodextrin glucanotransferase) (EC 2.4.1.19), was screened and isolated from Sudanese soil. The objective of this study was to sequence and characterize the β‐CGTase gene from G. alcaliphilus SK51.001. RESULTS: According to 16S rRNA analysis of the strain and its morphological shape, it was identified as G. alcaliphilus. The β‐CGTase gene was successfully cloned, sequenced, and expressed in Escherichia coli BL21. This gene showed 706 amino acid residues including 33 amino acids as a signal peptide. The active site residues of G. alcaliphilus SK51.001CGTase were described using enzyme modeling and docking with the products. The estimated molecular mass of G. alcaliphilus SK51.001CGTase was approximately 74 kDa as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE), and the evaluation of the gel filtration showed approximately 85 kDa, which means G. alcaliphilus SK51.001CGTase is a monomer. The optimum temperature and pH of G. alcaliphilus SK51.001CGTase were 60 °C and 7.0 respectively. Gracilibacillus alcaliphilus SK51.001CGTase was comparatively stable at a pH levels between 6.0 and 9.0 and temperatures of 30–50 °C. The activity of G. alcaliphilus SK51.001CGTase was increased by Ni2+, and Co2+ but inhibited by Al3+ and Fe3+. The kinetic parameters of Km and Vmax were 2068.52 μg mL−1 and 0.13 μmol mL−1 min−1, respectively. CONCLUSION: Gracilibacillus alcaliphilus SK51.001CGTase could hydrolyze soluble starch into α‐, β‐, and γ‐cyclodextrin in a ratio of 2: 83: 15% respectively. This high ratio production of β‐CD could allow the enzyme to be used in β‐CD production. © 2020 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

The application of precision medicine concept in clinical work needs a period of practice and experience accumulation. The present article introduced an example of functioning approach named "multidisciplinary therapy strategy of precision medicine" (MDTS‐PM), clinical practice and process, decision‐making, and therapies. The MDTS‐PM integrates multidisciplinary experts and develops real‐time therapeutic strategy based on clinical phenomes and gene sequencing of tissue DNA and circulating DNA. The strength of MDTS‐PM is the combination of dynamical clinical phenomes, genetic information, diagnosis, and treatment to make the therapy more targeted and specific. MDTS‐PM provides comprehensive, whole‐process, and personalized diagnosis and treatment services for patients with complex cancer or complex drug resistance progression; provides guidance for further adjustment of drug use; and establishes a multidisciplinary cooperative team, improves the quality of clinical diagnosis and treatment, and optimizes the process of medical services. [ABSTRACT FROM AUTHOR]

Summary: The clinical course of follicular lymphoma (FL) is highly variable. Recently the m7‐FL international prognostic index (FLIPI) integrating performance status, FLIPI score and the mutational status of seven genes, was shown to stratify patients into "low‐risk" and "high‐risk" with respect to 5‐year failure‐free survival after first‐line immunochemotherapy. Our aim was to evaluate the model after rituximab without chemotherapy. The Nordic Lymphoma Group performed two randomized clinical trials on indolent lymphoma patients receiving single rituximab and rituximab with interferon‐α2a. In total, 95 FL patients had sufficient fresh‐frozen diagnostic material for sequencing. A targeted panel for the genes EZH2, ARID1A, MEF2B, EP300, FOXO1, CREBBP and CARD11 was utilized for m7‐FLIPI score calculation. With a median follow‐up of 10·6 years, 76% of patients were alive. No difference in time to treatment failure (TTF), defined as the interval between start of trial therapy and initiation of new therapy or death, nor overall survival (OS) was found between the m7‐FLIPI risk groups (log‐rank P = 0·94 and 0·99, respectively). EZH2 mutations were associated with longer TTF (log‐rank P = 0·04) and in EP300 mutations were associated with shorter TTF (log‐rank P = 0·01). We conclude that the prognostic value of the m7‐FLIPI clinicogenetic model seems dependent on therapeutic regimen. [ABSTRACT FROM AUTHOR]

We have developed a method for spatially resolved genetic analysis of formalin‐fixed paraffin‐embedded (FFPE) cell block and tissue sections. This method involves local sampling using hydrodynamic flow confinement of a lysis buffer, followed by electrokinetic purification of nucleic acids from the sampled lysate. We characterized the method by locally sampling an array of points with a circa 200 μm diameter footprint, enabling the detection of single KRAS and BRAF point mutations in small populations of RKO and MCF‐7 FFPE cell blocks. To illustrate the utility of this approach for genetic analysis, we demonstrate spatially resolved genotyping of FFPE sections of human breast invasive ductal carcinoma. [ABSTRACT FROM AUTHOR]

Pancreatic neuroendocrine tumours (PNET) are relatively rare entities, accounting for 1–2 per cent of pancreatic neoplasms. However, rates of diagnosis have recently increased, in part due to incidental discovery on the widespread use of cross‐sectional imaging. While general consensus exists regarding the treatment of large and/or functional PNET, the management of smaller (<2 cm) asymptomatic lesions is less clear. Recent updates in staging guidelines have improved classification of high‐ and low‐risk tumours, and additional genetic analysis (e.g. Death domain‐associated protein 6 Gene, Alpha Thalassemia/Mental Retardation Syndrome X‐Linked Gene) offers the possibility of enhanced risk stratification to further guide surgical management. In patients who do ultimately require pancreatectomy, the role of minimally‐invasive surgery (laparoscopic or robotic) continues to expand. [ABSTRACT FROM AUTHOR]

In the regulation processes of gene expression, genomic DNA and nuclear proteins, including histone proteins, cooperate with each other, leading to the distinctive functions of eukaryotic cells such as pluripotency and differentiation. Chemical modification of histone proteins and DNA has been revealed as one of the major driving forces in the complicated epigenetic regulation system. However, understanding of the precise molecular mechanisms is still limited. To address this issue, researchers have proposed both biological and chemical strategies for the preparation and detection of modified proteins and nucleic acids. In this review, we focus on chemical methods around the field of epigenetics. Chemical protein synthesis has enabled the preparation of site‐specifically modified histones and their successful application to various in vitro assays, which have emphasized the significance of posttranslational modifications of interest. We also review the modification‐specific chemical reactions against synthetic and genomic DNA, which enabled discrimination of several modified bases at single‐base resolution. Chemical methods around the field of epigenetics are reviewed. Chemical protein synthesis has enabled the preparation of site‐specifically modified histones. Modification‐specific reactions has been developed for the discrimination of modified DNA bases in the genome. These methods have emphasized the significance of histone and DNA modifications of interest. [ABSTRACT FROM AUTHOR]

To understand the functional roles of RNA in the cell, it is essential to elucidate the dynamics of their production, processing and decay. A recent method for assessing mRNA dynamics is metabolic labeling with 4-thiouridine (4sU), followed by thio-selective attachment of affinity tags. Detection of labeled transcripts by affinity purification and hybridization to microarrays or by deep sequencing then reveals RNA expression levels. Here, we present a novel sequencing method (TUC-seq) that eliminates affinity purification and allows for direct assessment of 4sU-labeled RNA. It employs an OsO4-mediated transformation to convert 4sU into cytosine. We exemplify the utility of the new method for verification of endogenous 4sU in tRNAs and for the detection of pulse-labeled mRNA of seven selected genes in mammalian cells to determine the relative abundance of the new transcripts. The results prove TUC-seq as a straight-forward and highly versatile method for studies of cellular RNA dynamics. [ABSTRACT FROM AUTHOR]

Single-cell biology is considered a new approach to identify and validate disease-specific biomarkers. However, the concern raised by clinicians is how to apply single-cell measurements for clinical practice, translate the message of single-cell systems biology into clinical phenotype or explain alterations of single-cell gene sequencing and function in patient response to therapies. This study is to address the importance and necessity of single-cell gene sequencing in the identification and development of disease-specific biomarkers, the definition and significance of single-cell biology and single-cell systems biology in the understanding of single-cell full picture, the development and establishment of whole-cell models in the validation of targeted biological function and the figure and meaning of single-molecule imaging in single cell to trace intra-single-cell molecule expression, signal, interaction and location. We headline the important role of single-cell biology in the discovery and development of disease-specific biomarkers with a special emphasis on understanding single-cell biological functions, e.g. mechanical phenotypes, single-cell biology, heterogeneity and organization of genome function. We have reason to believe that such multi-dimensional, multi-layer, multi-crossing and stereoscopic single-cell biology definitely benefits the discovery and development of disease-specific biomarkers. [ABSTRACT FROM AUTHOR]

Precision medicine has been initiated and gains more and more attention from preclinical and clinical scientists. A number of key elements or critical parts in precision medicine have been described and emphasized to establish a systems understanding of precision medicine. The principle of precision medicine is to treat patients on the basis of genetic alterations after gene mutations are identified, although questions and challenges still remain before clinical application. Therapeutic strategies of precision medicine should be considered according to gene mutation, after biological and functional mechanisms of mutated gene expression or epigenetics, or the correspondent protein, are clearly validated. It is time to explore and develop a strategy to target and correct mutated genes by direct elimination, restoration, correction or repair of mutated sequences/genes. Nevertheless, there are still numerous challenges to integrating widespread genomic testing into individual cancer therapies and into decision making for one or another treatment. There are wide-ranging and complex issues to be solved before precision medicine becomes clinical reality. Thus, the precision medicine can be considered as an extension and part of clinical and translational medicine, a new alternative of clinical therapies and strategies, and have an important impact on disease cures and patient prognoses. [ABSTRACT FROM AUTHOR]

The platelet-derived growth factor ( PDGF) family of genes and their receptors are involved in angiogenesis and steroid hormone production. A putative member of the family, platelet-derived growth factor receptor-like ( PDGFRL), has been implicated in steroid-based feedback mechanisms within the chicken reproductive system. Three potential variants of PDGFRL were identified in the chicken, supported by in silico prediction and EST sequencing. The three potential transcripts have been further verified and the 5′ terminal regions sequenced in this research. The sum of expression of all three transcripts in broiler breeders (the parents of broiler chickens) has been shown to be consistent with total expression of the gene. However, cumulative expression of the three transcripts in a range of tissues in egg layers was significantly short of total expression, indicating the existence of potential additional variants. Two additional variants were subsequently identified in egg layer cerebellum tissue and the 5′ terminal regions sequenced. Sequence analysis of the three initial variants suggests that only one variant, which was the most abundant in broiler breeders and the majority of egg layer tissues, had a functional signal peptide. Although 5′ RACE identified two additional transcripts in egg layers, the most likely protein translations indicated that these variants possessed no functional signal peptide, suggesting that, if they have a function, it is not a traditional one. [ABSTRACT FROM AUTHOR]

Key Clinical Message Gene panel sequencing in a CMML patient without any detectable genetic abnormality by conventional genetic studies identified four concurrent somatic mutations in three genes. Gene panel mutation analysis is a rapidly emerging clinical tool to demonstrate the clonality in hematologic malignancies, and to identify the potential targets for therapy. [ABSTRACT FROM AUTHOR]

The study of nanochannel-confined DNA is important from biotechnological and biophysical points of view. We produce nanochannels in elastomer with soft lithography and proton beam writing. Issues concerning DNA confined in such quasi one-dimensional channels are discussed. We describe DNA stretching via the control of channel diameter and buffer conditions and how the extension can be interpreted with theory and computer simulation. We then discuss the conformation of nano-confined DNA crowded by neutral polymers and like-charged proteins. As an example of a protein that has an affinity to DNA, the effect of heat-stable nucleoid-structuring protein, H-NS, on the folding and compaction of DNA is reviewed. Compaction of DNA by eukaryotic protamine and unpacking of pre-compacted DNA through an increase in salt concentration are discussed. We review results obtained with a novel, cross-channel device that allows the monitoring of the dynamic, conformational response of DNA after exposure to a ligand or protein and/or a change in buffer conditions in situ. As a biotechnological application, linearization of DNA by bottlebrush coating with a polypeptide copolymer is discussed. It is demonstrated that large-scale genomic organization can be sequenced using single DNA molecules on an array of elastomeric nanochannels. Overall, our results show that the effects of ligands and proteins on the conformation, folding, and condensation of DNA are not only related to classical controlling factors, such as osmotic pressure, charge, and binding, but that the interplay with confinement in a nanospace is of paramount importance. [ABSTRACT FROM AUTHOR]

A thorough understanding of the genetic basis of male infertility has eluded researchers in spite of significant efforts to identify novel genetic causes of the disease, particularly over the past decade. Approximately half of male factor infertility cases have no known cause; however, it is likely that the majority of idiopathic male factor infertility cases have some unidentified genetic basis. Well-established genetic causes of male infertility are limited to Y chromosome microdeletions and Klinefelter's syndrome, together accounting for 10-20% of cases of severe spermatogenic failure. In addition to these, several genetic polymorphisms have been demonstrated to be significantly associated with male infertility. The discovery of new genetic associations with male infertility has been hampered by two primary factors. First, most studies are underpowered because of insufficient sample size and ethnic and phenotypic heterogeneity. Second, most studies evaluate a single gene, an approach that is very inefficient in the context of male infertility, considering that many hundreds of genes are involved in the process of testicular development and spermatogenesis. Significant recent advances in microarray and next-generation sequencing technologies have enabled the application of whole-genome approaches to the study of male infertility. We recently performed a pilot genome-wide association study ( GWAS) for severe spermatogenic failure, and several additional male infertility GWAS have since been published. More recently, genomic microarray tools have been applied to the association of copy number variants with male infertility. These studies are beginning to shed additional light on the genetic architecture of male infertility, and whole-genome studies have proven effective in identifying novel genetic causes of the disease. This review will discuss some of the recent findings of these whole-genome studies as well as future directions for this research that will likely be the most productive moving forward. [ABSTRACT FROM AUTHOR]

In the last decade, intensive research has been invested in marker-assisted selection (MAS). In parallel, there have been great advances in high-throughput genomic technology, such as microarrays and next-generation sequencing. These technologies overcome barriers for crops that do not have genomic information available and shorten the time from genomic darkness to discovery of an overwhelming number of markers. Consequently, MAS has become an available approach for any crop. Herein, the bioinformatics tools for high-throughput marker discovery using microarrays and high-throughput sequencing are reviewed and options for using them in MAS are suggested. [ABSTRACT FROM AUTHOR]

A network of biological databases is reviewed, supplying a framework for studies of human genes and the association of their genomic variations with human phenotypes. The network is composed of GeneCards, the human gene compendium, which provides comprehensive information on all known and predicted human genes, along with its suite members GeneDecks and GeneLoc. Two databases are shown that address genes and variations focusing on olfactory reception (HORDE) and transduction (GOSdb). In the realm of disease scrutiny, we portray MalaCards, a novel comprehensive database of human diseases and their annotations. Also shown is GeneKid, a tool aimed at generating novel kidney disease biomarkers using systems biology, as well as Xome, a database for whole-exome next-generation DNA sequences for human diseases in the Israeli population. Finally, we show LifeMap Discovery, a database of embryonic development, stem cell research and regenerative medicine, which links to both GeneCards and MalaCards. [ABSTRACT FROM AUTHOR]

Abstract: Molecular pathology as applied to neoplasia is a rapidly expanding component of the discipline of pathology that uses molecular biology tools in addition to conventional morphologic, immunohistochemical and chemical analyses of abnormalities in tissues and cells to understand the etiology and pathogenesis of tumors, establish their diagnosis, and contribute to prognostication and therapeutic decisions for cancer patient care. Biomarkers are a fundamental component of personalized cancer care, and the discipline of molecular pathology therefore contributes throughout the continuum from biomarker research to use in standard-of-care personalized cancer therapy. This brief review addresses some of the specific roles of molecular pathology in that continuum. [Copyright &y& Elsevier]

Global trade in the North American bullfrog Rana catesbeiana has been implicated in the introduction and spread of the amphibian pathogen Batrachochytrium dendrobatidis. Large-scale production of the North American bullfrog for human consumption has been ongoing since the early part of the 20th century, particularly in Brazil, a pioneer in bullfrog farming following its introduction in the 1930s. In order to determine whether bullfrogs introduced to Brazil and farmed for the food trade serve as reservoirs for amphibian disease, we tested individuals located in the Brazilian states of São Paulo and Pará to determine the prevalence of B. dendrobatidis infections. We were able to confirm B. dendrobatidis on five farms (78.5% infection prevalence overall) by PCR. Isolates were obtained from three of the five farms and genotyped at 17 loci using multilocus sequence typing. Five isolates from the Brazilian farms were genotypically similar to each other as well as to isolates from Central and South America. Isolates from farmed bullfrogs were more similar to isolates from introduced populations in Venezuela than those from the native range of the bullfrog in eastern North America. These results could have important implications for the origin and spread of B. dendrobatidis in Brazil, its neighboring regions and the conservation of native amphibian fauna. They may also suggest a potential for prior recombination within B. dendrobatidis in bullfrogs, which may have implications for the recent emergence of this pathogen. [ABSTRACT FROM AUTHOR]

A total of 73 Erwinia amylovora strains obtained from 13 Maloideae host species and from Rubus spp., and isolated from different geographic areas, were assessed using RFLP and DNA sequencing analysis of the 3′ hrpN gene and/or of a fragment of 1341 bp of the dspA/E region. An Erwinia pyrifoliae strain, used as outgroup, was checked in the same way. For the three strains isolated from Rubus spp. and for one strain from Amelanchier sp., RFLP analysis of the hrpN gene using the RsaI enzyme yielded a PCR product 60 bp smaller than that of all the other strains. Sequence analysis of the gene revealed this was due to the absence of a 60 bp fragment in the noncoding region downstream of the gene. The strain PD 2915, isolated from Amelanchier sp. grown in Canada, showed five same-sense substitutions and one missense substitution at position 868 of the hrpN gene, converting aspartic acid into asparagine. Also, restriction analysis of a fragment of 613 bp of the dspA/E region with CfoI revealed an RFLP pattern suitable for differentiating the E. amylovora strains isolated from Rubus spp. and Amelanchier sp. from all the others. In the dspA/E coding region, the four strains showed 13–14 missense point mutations, in some cases yielding drastic amino acid substitutions. In addition, partial sequencing of the dspA/E region of PD 2915 from Amelanchier sp. indicated a higher similarity to E. amylovora strains isolated from Rubus spp. than towards strains from other Maloideae hosts. The E. pyrifoliae strain showed 23 single nucleotide substitutions along the hrpN gene and 88% of nucleotide identity with E. amylovora strains in the portion of dspA/E region. Artificial inoculations on immature pear fruits and young shoots of Maloideae and Ruboideae showed a restricted pathogenicity for the strains from Rubus and Amelanchier, with the latter inciting blight symptoms only on Amelanchier. [ABSTRACT FROM AUTHOR]

The article discusses the polymorphic microsatellite markers used to distinguish loggerhead shrikes for CA repeats. The authors examine the decline of the loggerhead shrike populations worldwide. It is reported that migration patterns can be mapped by using microsatellite primers. Various alleles that make up the primers are listed, as well as the microsatellites in the separate loggerhead populations sampled. It is concluded that biotin capture enrichment is the most promising method for cloning of microsatellites.

Summary: Background: Early childhood obesity is a public health problem worldwide. It affects different aspects of physical and mental child's health. Identifying the etiologies, especially treatable and preventable causes, can direct health professionals toward proper management. Analysis of serum leptin levels and leptin gene mutations is a rapid and easy step toward the diagnosis of congenital leptin deficiency that is considered an important cause in early childhood obesity. Objectives: The aim of this study was to diagnose monogenic leptin deficiency in Egyptian children presenting with early onset obesity (EOO). Methods: The current cross‐sectional study included 80 children who developed obesity during the first year of life with BMI > 2 SD (for age and sex). The studied population was subjected to history taking, auxological assessment, serum leptin assay, and leptin gene sequencing. Results: Ten cases had leptin deficiency (12.5%), while 18 cases showed elevated leptin levels (22.5%). Leptin gene variants in the coding region were identified in 30% of the leptin‐deficient group: two novel homozygous disease‐causing variants (c.104 T > G and c.34 delC) and another previously reported homozygous pathogenic variant (c.313C > T). Conclusion: Leptin deficiency is considered a significant cause of monogenic obesity in Egyptian children with early‐onset obesity as the diagnosis of these patients would be a perfect target for recombinant leptin therapy. [ABSTRACT FROM AUTHOR]

Background: Fetal femur length (FL) is an important biometric index in prenatal screening. The etiology of short femur is diverse, with some pathogenic causes leading to adverse outcomes. To improve the accuracy and practicability of diagnosis, we investigated the value of genetic analysis in prenatal diagnosis of short femur. Methods: We examined chromosomal microarray analysis (CMA) (64 fetuses) and karyotyping (59 fetuses) data retrospectively for short femur without fetal growth restriction (FGR). Genetic testing was conducted for 15 fetuses. Results: Karyotyping and CMA detected chromosomal aberrations at rates of 13.6% and 27.2%, respectively. Among fetuses with other abnormalities, detection rates were 21.0% higher with CMA than karyotyping. CMA identified chromosomal abnormalities in 36.4% of cases with a FL 2–4 standard deviations (SDs) below the gestational age (GA) mean. Abnormality detection by CMA reached 38.5% in the second trimester. Duplication of 12p, 16p13.1 deletion, and uniparental disomy 16 were identified by CMA in three cases of short femur. Gene sequencing detected clinically notable mutations in 12/15 fetuses, among which 9/12 fetuses had FLs >4 SDs below the GA mean. Conclusions: CMA yielded a higher detection value than karyotyping in fetuses with other abnormalities or a FL 2–4 SDs below the GA mean during the second trimester. Gene sequencing should be performed when FL is >4 SDs below the mean. [ABSTRACT FROM AUTHOR]