DNA-based identification of Lentinula edodes strains with species-specific primers

Lentinula edodes is among the five globally cultivated edible mushrooms, which are wood decaying spore bearing Basidiomycetes possessing separate hyphae. Specific identification of this fungus from others in the division Basidiomycota using specific primers enables a fast and accurate detection through polymerase chain reaction (PCR). As a prelude to additional nutritional and sequence characterization research, we have developed a species specific PCR assay for this fungus after screening four primer-pairs and two universal primer pairs. The primer-pair LE1F/R was specific in amplifications of ATCC-defined L. edodes strains and did not amplify DNA from six medicinally and nutritionally important fungal reference strains, Oyster (Pleurotus ostreatus), Maitake (Grifola frondosa), Enoki (Flammulina velutipes), Baby bella (Agaricus bisporus), Porcini (Boletus edulis), and Chanterelle (Cantharellus cibarius). However, amplifications using the universal primers were positive for all six strains. This assay will therefore serve to validate morphology-based identifications of L. edodes strains.Keywords: Lentinula edodes, LE1F/R, species-specific primer

Bioinformatics Tools and Genomic Resources Available in Understanding the Structure and Function of Gossypium

Cotton is economically and evolutionarily important crop for its fiber. In order to improve fiber quality and yield, and to exploit the natural genetic potential inherent in genotypes, understanding genome structure and function of cultivated cotton is important. In order to achieve this, a functional understanding of bioinformatics resources such as databases, software solutions, and analysis tools is required. But currently, there are very few unified reports on bioinformatics tools and even fewer repositories to access cotton genomic information. Also, resourceful developers and bioinformatics scientists actively addressing complex genomic challenges in cotton genomes are much in need. The primary goal of this chapter is to provide a review of such tools and resources for analyzing the structure and function of the cotton genome with preferential emphasis on this complex and economically important plant species. This discourse begins with a description of concurrent advances in high‐throughput genome sequencing and bioinformatics analyses and focuses on four major sections covering bioinformatics tools and resources for analysis of: (1) genomes; (2) transcriptomes; (3) small RNAs; and (4) epigenomes. In each section, recent advances in cotton have been discussed. Cotton genome sequencing and annotation efforts are outlined within these sections. This review discusses the availability of genome information of both diploid and tetraploid species that have impelled cotton genome research into the post‐genomics era, opening new avenues for exploring regulatory mechanisms associated with fine‐tuning of gene expression of fiber‐related genes. Finally, the potential impacts of these rapid advances, especially the challenges in handling and analyzing the large datasets are discussed

Influence of growth temperature on structural and optical properties of laser MBE grown epitaxial thin GaN films on a-plane sapphire

Epitaxial thin GaN films (similar to 60 nm) have been grown on a-plane sapphire substrates at different growth temperatures (500-700 degrees C) using laser molecular beam epitaxy (LMBE). The effect of growth temperatures on the structural and optical properties of GaN layers grown on low temperature (LT) GaN buffer on prenitridated a-sapphire have been studied systematically. The in situ reflection high energy electron diffraction pattern revealed the three-dimensional epitaxial growth of GaN films on a-sapphire under the adopted growth conditions. The full width at half maximum (FWHM) value of x-ray rocking curves (XRCs) along GaN (0002) and (10-12) planes decreases with increasing growth temperature. The FWHM values of (0002) and (10-12) XRC for the 700 degrees C grown GaN film are 1.09 degrees and 1.08 degrees, respectively. Atomic force microscopy characterization showed that the grain size of GaN increases from 30-60 to 70-125 nm with the increase in growth temperature as GaN coalescence time is shorter at high temperature. The refractive index value for the dense GaN film grown at 600 degrees C is obtained to be similar to 2.19 at the wavelength of 632 nm as deduced by spectroscopic ellipsometry. Photoluminescence spectroscopy confirmed that the epitaxial GaN layers grown on a-sapphire at 600-700 degrees C possess near band edge emission at similar to 3.39 eV, close to bulk GaN. The GaN growth at 700 degrees C without a buffer still produced films with better crystalline and optical properties, but their surface morphology and coverage were inferior to those of the films grown with LT buffer. The results show that the growth temperature strongly influences the structural and optical quality of LMBE grown epitaxial GaN thin films on a-plane sapphire, and a growth temperature of >600 degrees C is necessary to achieve good quality GaN films. Published by the AVS

Differing myocardial response to a single session of hemodialysis in end-stage renal disease with and without type 2 diabetes mellitus and coronary artery disease

BACKGROUND: Though hemodialysis (HD) acutely improves cardiac function, the impact of background diseases like coronary artery disease (CAD) and Type 2 diabetes (DM) in the setting of end-stage renal disease (ESRD) is not known. Tissue velocity echocardiography (TVE) offers a fast choice to follow changes in myocardial function after HD in ESRD with concomitant DM and /or CAD. METHODS: 46 subjects (17 with ESRD, Group 1; 15 with DM, Group 2; 14 with DM+CAD, Group 3) underwent standard and TVE prior to and shortly after HD. Besides standard Doppler variables, regional myocardial systolic and diastolic velocities, as well as systolic strain rate were post processed. RESULTS: Compared with pre-HD, post-HD body weight (kg) significantly decreased in all the three groups (51 ± 9 vs. 48 ± 8, 62 ± 10 vs.59 ± 10, and 61 ± 9 vs. 58 ± 9 respectively; all p < 0.01). Left ventricular end diastolic dimensions (mm) also decreased post- HD (46 ± 5 vs. 42 ± 7, 53 ± 7 vs. 50 ± 7, 51 ± 7 vs. 47 ± 8 respectively; all p < 0.01). Regional longitudinal peak systolic velocity in septum (cm/s) significantly increased post-HD in Group 1(5.7 ± 1.6 vs. 7.2 ± 2.3; p < 0.001) while remained unchanged in the other two groups. Similar trends were noted in other left ventricular walls. When the myocardial velocities (cm/s) were computed globally, the improvement was seen only in Group 1 (6.3 ± 1.5 vs. 7.9 ± 2.0; p < 0.001). Global early regional diastolic velocity (cm/s) improved in Group 1, remained unchanged in Group 2, while significantly decreased in Group 3(-5.9 ± 1.3 vs. -4.1 ± 1.8; p < 0.01). Global systolic strain rate (1/sec) increased in the first 2 Groups but remained unchanged (-0.87 ± 0.4 vs. -0.94 ± 0.3; p = ns) in Group 3. CONCLUSION: A single HD session improves LV function only in ESRD without coexistent DM and/or CAD. The present data suggest that not only dialysis-dependent changes in loading conditions but also co-existent background diseases determine the myocardial response to HD

BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in upland cotton.

Acknowledgments “Dedicated to Dr. Ramesh Kantety, a mentor, colleague and friend”. We would like to acknowledge the support offered by Padmini Sripathi during data analysis and submissions. Author Contributions Conceived and designed the experiments: RVK JZY. Performed the experiments: RB ZX SM GBW. Analyzed the data: RB. Contributed reagents/materials/analysis tools: RVK RB JZY RJK BAR. Wrote the manuscript: RB. Revised the manuscript: RB RVK JZY RGP BAR GCS. Advised the research: RVK JZY RGP BAR GCS.Author Contributions Conceived and designed the experiments: RVK JZY. Performed the experiments: RB ZX SM GBW. Analyzed the data: RB. Contributed reagents/materials/analysis tools: RVK RB JZY RJK BAR. Wrote the manuscript: RB. Revised the manuscript: RB RVK JZY RGP BAR GCS. Advised the research: RVK JZY RGP BAR GCS.Although new and emerging next-generation sequencing (NGS) technologies have reduced sequencing costs significantly, much work remains to implement them for de novo sequencing of complex and highly repetitive genomes such as the tetraploid genome of Upland cotton (Gossypium hirsutum L.). Herein we report the results from implementing a novel, hybrid Sanger/454-based BAC-pool sequencing strategy using minimum tiling path (MTP) BACs from Ctg-3301 and Ctg-465, two large genomic segments in A12 and D12 homoeologous chromosomes (Ctg). To enable generation of longer contig sequences in assembly, we implemented a hybrid assembly method to process ~35x data from 454 technology and 2.8-3x data from Sanger method. Hybrid assemblies offered higher sequence coverage and better sequence assemblies. Homology studies revealed the presence of retrotransposon regions like Copia and Gypsy elements in these contigs and also helped in identifying new genomic SSRs. Unigenes were anchored to the sequences in Ctg-3301 and Ctg-465 to support the physical map. Gene density, gene structure and protein sequence information derived from protein prediction programs were used to obtain the functional annotation of these genes. Comparative analysis of both contigs with Arabidopsis genome exhibited synteny and microcollinearity with a conserved gene order in both genomes. This study provides insight about use of MTP-based BAC-pool sequencing approach for sequencing complex polyploid genomes with limited constraints in generating better sequence assemblies to build reference scaffold sequences. Combining the utilities of MTP-based BAC-pool sequencing with current longer and short read NGS technologies in multiplexed format would provide a new direction to cost-effectively and precisely sequence complex plant genomes.Yeshttp://www.plosone.org/static/editorial#pee

Mapping local patterns of childhood overweight and wasting in low- and middle-income countries between 2000 and 2017

A double burden of malnutrition occurs when individuals, household members or communities experience both undernutrition and overweight. Here, we show geospatial estimates of overweight and wasting prevalence among children under 5 years of age in 105 low- and middle-income countries (LMICs) from 2000 to 2017 and aggregate these to policy-relevant administrative units. Wasting decreased overall across LMICs between 2000 and 2017, from 8.4% (62.3 (55.1–70.8) million) to 6.4% (58.3 (47.6–70.7) million), but is predicted to remain above the World Health Organization’s Global Nutrition Target of <5% in over half of LMICs by 2025. Prevalence of overweight increased from 5.2% (30 (22.8–38.5) million) in 2000 to 6.0% (55.5 (44.8–67.9) million) children aged under 5 years in 2017. Areas most affected by double burden of malnutrition were located in Indonesia, Thailand, southeastern China, Botswana, Cameroon and central Nigeria. Our estimates provide a new perspective to researchers, policy makers and public health agencies in their efforts to address this global childhood syndemic

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

CdS based chemiresistor with Schottky contact: Toxic gases detection with enhanced sensitivity and selectivity at room temperature

Surmounting the selectivity issue of gas sensors and detecting low ppm concentration of gases is highly significant for widespread deployments of sensors to build networks in applications including vehicular emission, fuel-based household appliances, and industrial emissions. Herein, a strategy is proposed to improve the selectivity and sensitivity of the cadmium sulfide (CdS) based sensor via changes in contact material by utilizing different metals. CdS was deposited via the SILAR method on three different glass substrates which have Au, ITO, and Ag contacts, respectively, through which Schottky barrier height (SBH) was adjusted between CdS and metal contact. CdS was thoroughly verified by structural and morphological characterization techniques. As-fabricated devices were tested, and gas sensing results suggest that Au and ITO contacts have significantly superior selectivity towards NO2 and CO gases over other gases. Further, experimental values reveal that sensors can detect up to 0.3 ppm and 1.25 ppm, respectively. Good selectivity can be attributed to the regulation of the SBH. Additionally, as-fabricated devices displayed good long-term stability and short response and recovery times. The present study may provide a rational design for fabricating a high-performance chemiresistive gas sensor for the detection of sub-ppm levels of hazardous gases present in the environment. © 2022 Elsevier B.V