Single-frequency, pulsed Yb3+-doped multicomponent phosphate power fiber amplifier

High-power, single-frequency, pulsed fiber amplifiers are required in light detection and ranging, coherent laser detection, and remote sensing applications to reach long range within a short acquisition time. However, the power-scaling of these amplifiers is limited by nonlinearities generated in the optical fibers, in particular by stimulated Brillouin scattering (SBS). In this regard, the use of multicomponent phosphate glasses maximizes the energy extraction and minimizes nonlinearities. Here, we present the development of a single-stage, hybrid, pulsed fiber amplifier using a custom-made multicomponent Yb-doped phosphate fiber. The performance of the phosphate fiber was compared to a commercial Yb-doped silica fiber. While the latter showed SBS limitation at nearly 6.5 kW for 40 cm length, the maximum achieved output peak power for the multicomponent Yb-doped phosphate fiber was 11.7 kW for 9 ns pulses using only 20 cm with no sign of SBS

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts.

It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches2-5. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases6-8. This includes muscle biopsies from patients with undiagnosed rare muscle disorders6,9, and cultured fibroblasts from patients with mitochondrial disorders7. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution

The impact of sex on gene expression across human tissues

Many complex human phenotypes exhibit sex-differentiated characteristics. However, the molecular mechanisms underlying these differences remain largely unknown. We generated a catalog of sex differences in gene expression and in the genetic regulation of gene expression across 44 human tissue sources surveyed by the Genotype-Tissue Expression project (GTEx, v8 release). We demonstrate that sex influences gene expression levels and cellular composition of tissue samples across the human body. A total of 37% of all genes exhibit sex-biased expression in at least one tissue. We identify cis expression quantitative trait loci (eQTLs) with sex-differentiated effects and characterize their cellular origin. By integrating sex-biased eQTLs with genome-wide association study data, we identify 58 gene-trait associations that are driven by genetic regulation of gene expression in a single sex. These findings provide an extensive characterization of sex differences in the human transcriptome and its genetic regulation

The impact of sex on gene expression across human tissues

Many complex human phenotypes exhibit sex-differentiated characteristics, however the underlying molecular mechanisms of these differences remain largely unknown. Here, we present an extensive catalog of both sex differences in gene expression and its genetic regulation across 44 human tissue sources surveyed by GTEx (v8 release). We demonstrate that sex strongly influences gene expression levels and cellular composition of tissue samples across the human body. The effect of sex on gene expression is widespread, with a total of 37% of all genes exhibiting sex-biased expression in at least one tissue. This suggests that many if not most biological processes, and thus complex traits and diseases, are impacted by sex effects on the transciptome. We expand the identification of cis-eQTLs with sex-differentiated effects and characterize their cellular origin. By integrating sex-biased eQTLs with genome-wide association study data, we identify 58 gene-trait associations that are driven by genetic regulation in a single sex, including novel associations not detected with sex-agnostic approaches. Altogether we provide the most comprehensive characterization of sex differences in the human transcriptome and its regulation to date.Peer ReviewedPreprin

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas

Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology

Asthma, hay fever (or allergic rhinitis) and eczema (or atopic dermatitis) often coexist in the same individuals, partly because of a shared genetic origin. To identify shared risk variants, we performed a genome-wide association study (GWAS; n = 360,838) of a broad allergic disease phenotype that considers the presence of any one of these three diseases. We identified 136 independent risk variants (P < 3 × 10-8), including 73 not previously reported, which implicate 132 nearby genes in allergic disease pathophysiology. Disease-specific effects were detected for only six variants, confirming that most represent shared risk factors. Tissue-specific heritability and biological process enrichment analyses suggest that shared risk variants influence lymphocyte-mediated immunity. Six target genes provide an opportunity for drug repositioning, while for 36 genes CpG methylation was found to influence transcription independently of genetic effects. Asthma, hay fever and eczema partly coexist because they share many genetic risk variants that dysregulate the expression of immune-related genes

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease

THE EFFECTS OF ROOT INTERVENTION ON STAND ESTABLISHMENT RATE OF GRAFTED WATERMELON (CITRULLUS AEDULIS L) SEEDLINGS UNDER SALINE CONDITIONS

Abstract A commercial watermelon (Citrullus aedulis L) variety was grafted onto a commercial variety rootstock (Cucurbita maxima x C. moschata ). Two different grafting methods; splice grafting (SG) and root pruned splice grafting (RPSG) were simultaneously applied. End of nursery period, a sufficient number of 14 day old seedlings of each grafting method were transplanted in large pots filled with a mixture of peat compost and vermiculite (3:1). The plants were split in three equal groups and in the following 14 days each group was periodically irrigated with equal amounts of respectively tap water or saline water (50 mM NaCl and 100 mM NaCL). The relative growth rate (RGR) and its components; net assimilation rate (NAR) and leaf area ratio (LAR), root relative growth rate (RRGR), stem elongation rate (SER) and leaf expansion relative rate (LER) were computed for each experimental plot. Additionally to that, equal weights of fresh roots from seedlings of both grafting methods were washed out carefully with tap water and immersed into equal quantities of methanol. Several diluted solutions (10% vol/vol, 15% vol/vol and 20% vol/vol) were prepared from each root extracts, parallel with control solutions (0.01, 0.05 and 0.1 ppm) of artificial cytokinins, and used as rooting medium for 20 day old cuttings of tepary bean (Phaseoulus acutifolius). The average number of root nodes and lateral roots as well as the average length of lateral roots of tepary bean cuttings was used to indicate the difference between RPSG and SG seedlings regarding the nature and quantity of growth hormones extracted from the fresh rootstock roots. A significantly higher relative growth rate was found for root pruned splice grafted seedlings after transplanting, mostly due to higher net assimilation rate, as well as a higher root relative growth rate indicating a faster stand establishment rate for RPSG seedlings. Generally speaking, the relative growth rate of transplanted seedlings was drastically reduced due to the increase of nutrient solution salinity. However, significantly higher values were recorded for root pruned splice grafted seedlings compared to splice grafted ones. The same was true regarding root relative growth rate, stem elongation rate and leaf expansion rate. A higher concentration of cytokinins, was indicated by a higher rooting index of Phaseoulus acutifolius, from the extracts of RPSG seedlings and to that is attributed their significantly higher stand establishment rate

Combined application of arbuscular mycorrhizae fungi and plant growth promoting bacteria improves growth and nutrient uptake efficiency of pea (Pisum sativum L.) plants

The study aimed to investigate the effects of commercially available AMF inoculate (a mixture of Rhizophagus intraradices, Claroideoglomus etunicatum, Funneliformis mossea, Funneliformis geosporum, Rhizophagus clarus) and plant growth promoting bacteria (Rhizobium leguminosarum and Burkholderia sp.), either supplied individually or in combination with each other, on growth, root morphology and nutrient uptake capabilities in field pea (Pisum sativum L.) plants. Inoculated and non-inoculated pea plants were subjected to three levels of salinity (0, 20 and 50 mM) by the addition of sodium chloride into tap water. Morphology of root system was analyzed and dry matter of roots and shoots were individually measured several times during the growing cycle in randomly selected plants. The dry matter of roots and shoots was mixed together and concentration of N, P, K and Na was analytically determined. The raise of salinity in the irrigation water has strongly diminished the growth of pea plants by significantly reducing the weight, length, and surface area of root system, and deteriorating its nutrient capabilities. The inoculation of either AM fungi or PGPB in the growing substrate has contributed to alleviating the salinity stress effects through promoting growth and enhancing nutrient uptake capabilities of the root system. The combined application of AM fungi and PGPB could further enhance the nutrient uptake capabilities of pea plants under adverse salinity conditions