Identification of Medically Actionable Secondary Findings in the 1000 Genomes

The American College of Medical Genetics and Genomics (ACMG) recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD) Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379) and Americas (4/181) ancestry groups, with fewer findings in Asian (2/286) and African (1/246) ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092) of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be selected for return. Our results also confirm that understudied populations will not reap proportionate benefits of genomic medicine, highlighting the need for continued research efforts on genetic diseases in these populations.     

Recovery of thrombopoietin during purification

A thrombocytopoiesis-stimulating factor (TSF or thrombopoietin) was previously purified by a six-step purification procedure. However, the exact quantity of TSF that was recovered, through the various purification procedures, was unknown because of the absence of a method for establishing a unit of measure of TSF. In the present work dose-response relationships on both the crude TSF preparations and on the more highly purified TSF were determined. TSF units were calculated from the dose-response curves. A unit of TSF is defined as the amount of material (mg) that is required to increase the percentages 35S incorporation into platelets of immunothrombocythemic mice by 50% above the baseline. The results of determining the TSF units on the crude TSF preparation indicated that 0.11 unit (U) of TSF/mg protein was present. Results showed that the specific activity of TSF can be increased to about 3.6 U/mg by a single purification procedure using Sephadex G-75 column chromatography. Increased specific activities were obtained by additional purification steps, i.e., DEAE-cellulose column chromatography, SE-HPLC, DEAE-HPLC, and SDS-PAGE. The purified product appears to have a specific activity of about 11,000 U/mg of protein with 0.00003% of the protein and 1.1% of the TSF recovered from the starting material. Establishing a unit of measure for TSF will allow calculations of its degree of purity, provide a method for quantitation of recoveries of activities after various purification procedures, and allow comparisons of results from different experiments and different laboratories.     

Functional and phenotypic changes associated with the in vitro development of human monocytes into activated macrophages

Freshly isolated human peripheral blood monocytes had minimal cytotoxic effect in vitro on the schistosomula of Schistosoma mansoni. However, stimulation of the cells with either interferon gamma (IFN) or specific anti-parasite antiserum caused an increase in cytotoxicity. Additionally, the normal development of monocytes into macrophages over 7 days was associated with a sharp increase in cytotoxicity. The non-cytotoxic monocytes were compared with activated macrophages to assess whether cytotoxicity was associated with changes in immunophenotype. As monocytes developed into macrophages there were marked increases in transferrin receptors (HB21), macrophage cellular integrin (3.9), and Fc receptors (KB61). A further three markers showed increased expression in 7-day-old macrophages stimulated by IFN, namely a high affinity Fc gamma receptor (10.1), MHC Class II (1B5) and tumour necrosis factor (TNF).     

Anthocyanin production in chl-rich and chl-poor seedlings

Screening by chlorophyll (Chl) affects photoconversion rates and photoequilibrium ratios of phytochrome in vivo and may cause distortion of the action spectra of photomorphogenesis (N Kazarinova-Fukshansky, M Seyfried, E Schäfer 1985 Photochem Photobiol 41: 689-702). Inhibitors that reduce the Chl content of seedlings are sometimes used in photomorphogenesis research to decrease the effects of Chl screening on the state of phytochrome in vivo. Streptomycin is one of the inhibitors that can be used for this purpose. The effects of streptomycin on phytochrome-mediated anthocyanin accumulation in young seedlings are significantly different in closely related systems. The use of `Chl-bleachers' in photomorphogenesis studies may produce undesirable side effects. At the level of the expression of a photoregulated response, the effects of differences in the state of phytochrome between water-grown Chl-rich and inhibitor-treated Chl-poor seedlings may be difficult to evaluate because they may be masked by the effects of the inhibitor on the response.     

Comparative effects of trichothecene mycotoxins on bovine platelet function: Acetyl T-2 toxin,a more potent inhibitor than T-2 toxin

The effects of the trichothecene mycotoxins (acetyl T-2 toxin, T-2 toxin, HT-2 toxin, palmityl T-2 toxin, diacetoxyscirpenol (DAS), deoxynivalenol (DON), and T-2 tetraol) on bovine platelet function were examined in homologous plasma stimulated with platelet activating factor (PAF). The mycotoxins inhibited platelet function with the following order of potency: acetyl T-2 toxin > palmityl T-2 toxin = DAS > HT-2 toxin = T-2 toxin. While T-2 tetraol was completely ineffective as an inhibitor, DON exhibited minimal inhibitory activity at concentrations above 10×10^?4M. The stability of the platelet aggregates formed was significantly reduced in all mycotoxin treated platelets compared to that of the untreated PAF controls. It is suggested that the increased sensitivity of PAF stimulated bovine platelets to the more lipophilic mycotoxins may be related to their more efficient partitioning into the platelet membrane compared to the more hydrophilic compounds.     

15N resonance assignments of oxidized and reducedChromatium vinosum high-potential iron protein

The¹⁵N resonances in reduced and oxidizedChromatium vinosum high-potential iron protein have been assigned by use of¹H-¹H COSY spectra and¹H-¹⁵N HMQC, HMQC-COSY, and HMQC-NOESY spectra. Unambiguous assignment of 70 of 85 backbone¹⁵N resonances in the reduced protein and 62 of 85 resonances in the oxidized protein are made, as are 12 of 21 side-chain¹⁵N resonances.     

Prediction of near-term climate change impacts on UK wheat quality and the potential for adaptation through plant breeding

Wheat is a major crop worldwide, mainly cultivated for human consumption and animal feed. Grain quality is paramount in determining its value and downstream use. While we know that climate change threatens global crop yields, a better understanding of impacts on wheat end-use quality is also critical. Combining quantitative genetics with climate model outputs, we investigated UK-wide trends in genotypic adaptation for wheat quality traits. In our approach, we augmented genomic prediction models with environmental characterisation of field trials to predict trait values and climate effects in historical field trial data between 2001 and 2020. Addition of environmental covariates, such as temperature and rainfall, successfully enabled prediction of genotype by environment interactions (G × E), and increased prediction accuracy of most traits for new genotypes in new year cross validation. We then extended predictions from these models to much larger numbers of simulated environments using climate scenarios projected under Representative Concentration Pathways 8.5 for 2050–2069. We found geographically varying climate change impacts on wheat quality due to contrasting associations between specific weather covariables and quality traits across the UK. Notably, negative impacts on quality traits were predicted in the East of the UK due to increased summer temperatures while the climate in the North and South-west may become more favourable with increased summer temperatures. Furthermore, by projecting 167,040 simulated future genotype–environment combinations, we found only limited potential for breeding to exploit predictable G × E to mitigate year-to-year environmental variability for most traits except Hagberg falling number. This suggests low adaptability of current UK wheat germplasm across future UK climates. More generally, approaches demonstrated here will be critical to enable adaptation of global crops to near-term climate change.     

An extensive review on antifungal approaches in the treatment of mucormycosis

During the period of COVID-19, the occurrences of mucormycosis in immunocompromised patients have increased significantly. Mucormycosis (black fungus) is a rare and rapidly progressing fungal infection associated with high mortality and morbidity in India as well as globally. The causative agents for this infection are collectively called mucoromycetes which are the members of the order Mucorales. The diagnosis of the infection needs to be performed as soon as the occurrence of clinical symptoms which differs with types of Mucorales infection. Imaging techniques magnetic resonance imaging or computed tomography scan, culture testing, and microscopy are the approaches for the diagnosis. After the diagnosis of the infection is confirmed, rapid action is needed for the treatment in the form of antifungal therapy or surgery depending upon the severity of the infection. Delaying in treatment declines the chances of survival. In antifungal therapy, there are two approaches first-line therapy (monotherapy) and combination therapy. Amphotericin B ( 1 ) and isavuconazole ( 2 ) are the drugs of choice for first-line therapy in the treatment of mucormycosis. Salvage therapy with posaconazole ( 3 ) and deferasirox ( 4 ) is another approach for patients who are not responsible for any other therapy. Adjunctive therapy is also used in the treatment of mucormycosis along with first-line therapy, which involves hyperbaric oxygen and cytokine therapy. There are some drugs like VT-1161 ( 5 ) and APX001A ( 6 ), Colistin, SCH 42427, and PC1244 that are under clinical trials. Despite all these approaches, none can be 100% successful in giving results. Therefore, new medications with favorable or little side effects are required for the treatment of mucormycosis.     

Use of Plant Strategy Ordination,DCA and ANOVA to elucidate relationships among habitats of Salix planifolia and Salix monticola

Abstract. Detrended Correspondence Analysis (DCA) was used on a data set of 112 species from 14 stands dominated by Salix planifolia and/or S. monticola. Environmental variables were determined which might be important to explain differences in stand vegetation composition, and willow stature (height), in willow carrs in the Rocky Mountain National Park. Correlation of environmental variables with DCA stand scores indicate that peat depth and soil redox potential are highly related to the primary DCA axis. Soils in stands of S. planifolia are more reduced in the early summer and have greater peat depths, than soils in stands of S. monticola. The second DCA axis is related to a water chemistry gradient of hydrogen ion, sulphate, and ammonium concentration. Four environmental variables selected by correlation analysis were regressed on stand scores from the first two DCA axes. Regression coefficients of August soil redox potential and soil water pH were significantly non-zero on the primary DCA axis. In addition to overall vegetation relationships elucidated by DCA, the relationships between willow stature and environmental variables were tested by simultaneous ANOVAs. ANOVA results and DCA ordinations indicate that S. planifolia and S. monticola plants achieve the greatest stature in the least reduced soils, and in shallow peat. Competitive, stress tolerant, and ruderal plant strategy theory applied to the vegetation data produced an arrangement of stands highly correlated to the DCA Axis 1 stand arrangement. These correlations indicate that the primary axis of vegetation structure can be extracted either by species composition, or species morphology/physiology relationships. Concurrent use of DCA and plant strategy theory is suggested as a tool for the prediction of community composition.