Candidate Genes Detected in Transcriptome Studies Are Strongly Dependent on Genetic Background

Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds

The GCP molecular marker toolkit, an instrument for use in breeding food security crops

Crop genetic resources carry variation useful for overcoming the challenges of modern agriculture. Molecular markers can facilitate the selection of agronomically important traits. The pervasiveness of genomics research has led to an overwhelming number of publications and databases, which are, nevertheless, scattered and hence often difficult for plant breeders to access, particularly those in developing countries. This situation separates them from developed countries, which have better endowed programs for developing varieties. To close this growing knowledge gap, we conducted an intensive literature review and consulted with more than 150 crop experts on the use of molecular markers in the breeding program of 19 food security crops. The result was a list of effectively used and highly reproducible sequence tagged site (STS), simple sequence repeat (SSR), single nucleotide polymorphism (SNP), and sequence characterized amplified region (SCAR) markers. However, only 12 food crops had molecular markers suitable for improvement. That is, marker-assisted selection is not yet used for Musa spp., coconut, lentils, millets, pigeonpea, sweet potato, and yam. For the other 12 crops, 214 molecular markers were found to be effectively used in association with 74 different traits. Results were compiled as the GCP Molecular Marker Toolkit, a free online tool that aims to promote the adoption of molecular approaches in breeding activities

Reference genes for quantitative reverse transcription-polymerase chain reaction expression studies in wild and cultivated peanut

<p>Abstract</p> <p>Background</p> <p>Wild peanut species (<it>Arachis </it>spp.) are a rich source of new alleles for peanut improvement. Plant transcriptome analysis under specific experimental conditions helps the understanding of cellular processes related, for instance, to development, stress response, and crop yield. The validation of these studies has been generally accomplished by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) which requires normalization of mRNA levels among samples. This can be achieved by comparing the expression ratio between a gene of interest and a reference gene which is constitutively expressed. Nowadays there is a lack of appropriate reference genes for both wild and cultivated <it>Arachis</it>. The identification of such genes would allow a consistent analysis of qRT-PCR data and speed up candidate gene validation in peanut.</p> <p>Results</p> <p>A set of ten reference genes were analyzed in four <it>Arachis </it>species (<it>A. magna</it>; <it>A. duranensis</it>; <it>A. stenosperma </it>and <it>A. hypogaea</it>) subjected to biotic (root-knot nematode and leaf spot fungus) and abiotic (drought) stresses, in two distinct plant organs (roots and leaves). By the use of three programs (GeNorm, NormFinder and BestKeeper) and taking into account the entire dataset, five of these ten genes, <it>ACT1 </it>(actin depolymerizing factor-like protein), <it>UBI1 </it>(polyubiquitin), <it>GAPDH </it>(glyceraldehyde-3-phosphate dehydrogenase), <it>60S </it>(60S ribosomal protein L10) and <it>UBI2 </it>(ubiquitin/ribosomal protein S27a) emerged as top reference genes, with their stability varying in eight subsets. The former three genes were the most stable across all species, organs and treatments studied.</p> <p>Conclusions</p> <p>This first in-depth study of reference genes validation in wild <it>Arachis </it>species will allow the use of specific combinations of secure and stable reference genes in qRT-PCR assays. The use of these appropriate references characterized here should improve the accuracy and reliability of gene expression analysis in both wild and cultivated Arachis and contribute for the better understanding of gene expression in, for instance, stress tolerance/resistance mechanisms in plants.</p

The Physiology and Proteomics of Drought Tolerance in Maize: Early Stomatal Closure as a Cause of Lower Tolerance to Short-Term Dehydration?

Understanding the response of a crop to drought is the first step in the breeding of tolerant genotypes. In our study, two maize (Zea mays L.) genotypes with contrasting sensitivity to dehydration were subjected to moderate drought conditions. The subsequent analysis of their physiological parameters revealed a decreased stomatal conductance accompanied by a slighter decrease in the relative water content in the sensitive genotype. In contrast, the tolerant genotype maintained open stomata and active photosynthesis, even under dehydration conditions. Drought-induced changes in the leaf proteome were analyzed by two independent approaches, 2D gel electrophoresis and iTRAQ analysis, which provided compatible but only partially overlapping results. Drought caused the up-regulation of protective and stress-related proteins (mainly chaperones and dehydrins) in both genotypes. The differences in the levels of various detoxification proteins corresponded well with the observed changes in the activities of antioxidant enzymes. The number and levels of up-regulated protective proteins were generally lower in the sensitive genotype, implying a reduced level of proteosynthesis, which was also indicated by specific changes in the components of the translation machinery. Based on these results, we propose that the hypersensitive early stomatal closure in the sensitive genotype leads to the inhibition of photosynthesis and, subsequently, to a less efficient synthesis of the protective/detoxification proteins that are associated with drought tolerance

Chickpea

The narrow genetic base of cultivated chickpea warrants systematic collection, documentation and evaluation of chickpea germplasm and particularly wild Cicer species for effective and efficient use in chickpea breeding programmes. Limiting factors to crop production, possible solutions and ways to overcome them, importance of wild relatives and barriers to alien gene introgression and strategies to overcome them and traits for base broadening have been discussed. It has been clearly demonstrated that resistance to major biotic and abiotic stresses can be successfully introgressed from the primary gene pool comprising progenitor species. However, many desirable traits including high degree of resistance to multiple stresses that are present in the species belonging to secondary and tertiary gene pools can also be introgressed by using special techniques to overcome pre- and post-fertilization barriers. Besides resistance to various biotic and abiotic stresses, the yield QTLs have also been introgressed from wild Cicer species to cultivated varieties. Status and importance of molecular markers, genome mapping and genomic tools for chickpea improvement are elaborated. Because of major genes for various biotic and abiotic stresses, the transfer of agronomically important traits into elite cultivars has been made easy and practical through marker-assisted selection and marker-assisted backcross. The usefulness of molecular markers such as SSR and SNP for the construction of high-density genetic maps of chickpea and for the identification of genes/QTLs for stress resistance, quality and yield contributing traits has also been discussed

Sichere Injektions- und Infusionstechniken einschließlich Umgang mit Medikamentenfläschchen in einem Zentrum der Tertiärversorgung: eine Initiative zur Qualitätsverbesserung

Introduction: There is a risk of transmission of viruses and microbial pathogens during routine health care procedures due to improper injection, infusion, and medication-vial practices. Unsafe practices lead to outbreaks of infection resulting in unacceptable and devastating events in patients. The present study was undertaken to assess the compliance of nurses with safe injection and infusion practices in our hospital and to identify staff education requirements in relation to the safe-injection and infusion practices policy.Methods: Baseline data were collected and high risk areas were identified on this basis, a quality improvement project was implemented by infection control team. FOCUS PDCA methodology was used to conduct the improvement process. The study was performed from March to September 2021. An audit checklist based on the CDC guidelines was used for monitoring compliance with safe injection and infusion practices. Results: Poor compliance with safe injection and infusion practices in few clinical areas at baseline. During the pre-intervention period, non-compliance was mainly seen with the following elements: aseptic technique (79%), rubber septum disinfected with alcohol (66%), labelling of all IV lines and medications with date and time (83%), compliance with multidose-vial policy (77%), use of multidose vials for single patient (84%), safe disposal of sharps (84%), using trays instead of clothing/pockets to carry medications (81%).There was significant improvement in compliance with the following elements of safe injection and infusion practices in the post-intervention period: aseptic technique (94%), rubber septum disinfected with alcohol (83%), compliance with multidose-vial policy (96%), use of multidose vials for single patient only (98%), safe disposal of sharps (96%).Conclusion: Adherence to safe injection and infusion practices is very important to prevent outbreaks of infection in health care settings.Einführung: Im Fall unsachgemäßer Injektion, Infusion und fehlerhaften Umgangs mit Medikamenten besteht das Risiko der Übertragung von Viren und Mikroorganismen. Fehlerhafte Praktiken können zum Ausbruch von Infektionen mit drastischen Folgen für die Patienten führen. Die vorliegende Studie wurde durchgeführt, um die Einhaltung sicherer Injektions- und Infusionspraktiken in unserem Krankenhaus durch das Pflegepersonal zu bewerten und den Schulungsbedarf des Personals zu ermitteln.Methoden: Die Analyse der Ausgangssituation ergab eine schlechte Einhaltung sicherer Injektions- und Infusionspraktiken in einigen klinischen Bereichen. In den identifizierten Bereichen mit hohem Risiko wurde vom Infektionskontrollteam ein Qualitätsverbesserungsprojekt etabliert. Zur Durchführung wurde die FOCUS PDCA-Methode verwendet. Die Studie erstreckte sich von März bis September 2021. Zur Überwachung der Einhaltung sicherer Injektions- und Infusionspraktiken wurde eine Audit-Checkliste auf der Grundlage der CDC-Richtlinien verwendet.Ergebnisse: Während der Zeit vor der Intervention wurde die Nichteinhaltung hauptsächlich in Bezug auf folgende Elemente festgestellt: Aseptische Technik (79%), mit Alkohol desinfiziertes Gummiseptum (66%), Kennzeichnung aller Infusionsleitungen und Medikamente mit Datum und Uhrzeit (83%), Einhaltung der Richtlinie für Mehrdosisfläschchen (77%), Verwendung von Mehrdosisfläschchen für einen einzelnen Patienten (84%), sichere Entsorgung von scharfen Gegenständen (84%), Tragen von Medikamenten in Kleidung/Taschen anstatt auf dem Tablett (81%).Es gab eine signifikante Verbesserung bei der Einhaltung der folgenden Elemente sicherer Injektions- und Infusionspraktiken nach der Intervention: Aseptische Technik (94%), mit Alkohol desinfiziertes Gummiseptum (83%), Einhaltung der Richtlinie für Mehrdosis-Durchstechflaschen (96%), Verwendung von Mehrdosis-Durchstechflaschen für einen einzelnen Patienten (98%), sichere Entsorgung scharfer Gegenstände (96%).Schlussfolgerung: Die Einhaltung sicherer Injektions- und Infusionspraktiken ist unerlässlich, um Ausbrüche nosokomialer Infektionen zu verhindern

Biomimetic polymer MEMS haircells with high-aspect ratio for high accuracy flow sensing

This paper presents the fabrication and testing of a bio-inspired polymer MEMS flow sensor. The sensor consists of a liquid crystal polymer (LCP) sensing membrane and a polymer haircell that extends into the flow. High-aspect ratio Si60 polymer haircells are fabricated by stereolithography. The device demonstrates high sensitivity in the air and water flow velocity sensing tests that are conducted.4 page(s