Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Abstract Background Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome. Results Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable – estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation. Conclusions Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation

Melt blending and characterization of carbon nanoparticles-filled thermoplastic polyurethane elastomers

In this work, thermoplastic polyurethane (TPU) elastomers reinforced with carbon nanosized particles were produced by a special melt blending technique. A TPU was melt blended with high-structured carbon black and carbon nanofibres (1 wt%). A miniature asymmetric batch mixer, which applies high shear levels to the melt, ensured good particles dispersion. The TPU material systems were then thoroughly characterized using thermogravimetric analysis, differential scanning calorimetry, tensile mechanical testing, electrical resistance measurements and flammability tests. The different nanofillers exhibited different influences on the TPU properties, these materials featuring interesting and improved multifunctional behaviours, with high propensity for large deformation sensors applications.This work was supported by FCT – Portuguese Foundation for Science and Technology through projects NANOSens – PTDC/CTM/73465/2006

Hybrid assembly with long and short reads improves discovery of gene family expansions

BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation. RESULTS: Compared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies. CONCLUSION: Our results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations

Proton coupled electron transfer reaction of phenols with excited state ruthenium(II) - polypyridyl complexes

The reaction of phenols with the excited state, *[Ru(bpy)3]2+ (E0 = 0.76V) and *[Ru(H2dcbpy)3]2+, (dcbpy = 4,4'-dicarboxy-2,2'-bipyridine) (E0 = 1.55 V vs. SCE) complexes in CH3CN has been studied by luminescence quenching technique and the quenching is dynamic. The formation of phenoxyl radical as a transient is confirmed by its characteristic absorption at 400 nm. The kq value is highly sensitive to the change of pH of the medium and ΔG0 of the reaction. Based on the treatment of kq data in terms of energetics of the reaction and pH of the medium, proton coupled electron transfer (PCET) mechanism has been proposed for the reaction

Impact Of C-Reactive Protein/Albumin Ratio on Intra- Hospital Mortality Among Patients with Spontaneous Intracerebral Hemorrhage

Background: Spontaneous intracerebral hemorrhage (ICH) is a severe neurological emergency associated with high morbidity and mortality. Intra-hospital mortality rates remain substantial, and accurate prediction of outcomes is critical for effective management. The C-reactive protein (CRP)/Albumin ratio has been suggested as a prognostic marker in various diseases, but its role in predicting intra-hospital mortality in ICH patients remains underexplored. Objective: This study aimed to investigate the impact of the CRP/Albumin ratio upon admission on intra-hospital mortality in patients with spontaneous ICH. Methods: A prospective observational study was conducted over one year at Government Theni Medical College and Hospital. A total of 120 patients diagnosed with spontaneous ICH were included, with 80 survivors and 40 non-survivors. Baseline clinical data, including CRP and albumin levels, comorbidities, and treatment regimens, were collected. Statistical analyses were performed to assess the association between the CRP/Albumin ratio and in-hospital mortality. Results: The CRP/Albumin ratio was significantly higher in non-survivors compared to survivors (P < 0.001). Elevated CRP levels (P < 0.001) and lower albumin levels (P < 0.001) were also significantly associated with increased mortality. Other factors such as systolic blood pressure (P < 0.001) and premedication (P = 0.005) were also found to influence survival outcomes, while comorbidities like diabetes and smoking status did not show significant effects on mortality. Conclusion: The CRP/Albumin ratio is a reliable and significant predictor of intra-hospital mortality in patients with spontaneous intracerebral hemorrhage. Monitoring this ratio could aid clinicians in early risk stratification and improve the management of ICH patients. Future studies with larger sample sizes are warranted to further validate these findings and explore additional biomarkers for outcome prediction

A robust nitrobenzene electrochemical sensor based on chitin hydrogel entrapped graphite composite

© 2017 An amperometric nitrobenzene (NB) sensor has been developed based on a glassy carbon electrode (GCE) modified with the composite of chitin hydrogel stabilized graphite (GR-CHI) composite. The physicochemical characterization confirmed the formation of GR-CHI composite and was formed by the strong interaction between GR and CHI. Furthermore, GR-CHI composite modified GCE was used to study the electrochemical reduction behavior of NB by cyclic voltammetry (CV) and compared with GR and CHI modified GCEs. The CV results confirmed that GR-CHI composite modified electrode has high catalytic ability and lower reduction potential toward NB than other modified electrodes due to the combined unique properties of exfoliated GR and CHI. The GR-CHI composite modified electrode can be able to detect the NB in the linear response range from 0.1 to 594.6 µM with the lower detection limit of 37 nM by amperometric i–t method. The selectivity of the sensor is evaluated in the presence of nitroaromatic, biologically active and dihydroxybenzene compounds. The sensor shows appropriate practicality and good repeatability toward detection of NB in lab water samples

An endophyte Paenibacillus dendritiformis strain APL3 promotes Amaranthus polygonoides L. sprout growth and their extract inhibits food-borne pathogens

Green leafy vegetables are rich sources of antioxidants and minerals, which prevent food-borne pathogen infections during our diet. This study was aimed to isolate and identify the plant growth-promoting endophytic bacterium from several plant species to enhance the growth of Amaranthus polygonoides L. and their antimicrobial potential against food-borne pathogens. Seven endophytic bacterial isolates were tested on two Amaranthus species to identify the suitable beneficial bacterium. The antioxidants capacity and antimicrobial activity of bacterial isolate (APL3) treated plants were analyzed. The bacterial isolate, APL3 showed a significantly higher growth of A. polygonoides L. than other isolates. It was identified as Paenibacillus dendritiformis strain APL3 by 16S rRNA gene sequencing and phylogenetic analysis. The endophyte (APL3) treated A. polygonoides L. sprouts had higher antioxidants potentials and significantly inhibited the growth of Escherichia coli, Salmonella sp., Staphylococcus sp. and Pseudomonas sp. The results of the present study suggest that utilization of P. dendritiformis strain APL3 triggers the growth of A. polygonoides L. and induces metabolic changes in plants to improve their antimicrobial properties to prevent foodborne pathogens

An overview of the utilisation of microalgae biomass derived from nutrient recycling of wet market wastewater and slaughterhouse wastewater

Microalgae have high nutritional values for aquatic organisms compared to fish meal, because microalgae cells are rich in proteins, lipids, and carbohydrates. However, the high cost for the commercial production of microalgae biomass using fresh water or artificial media limits its use as fish feed. Few studies have investigated the potential of wet market wastewater and slaughterhouse wastewater for the production of microalgae biomass. Hence, this study aims to highlight the potential of these types of wastewater as an alternative superior medium for microalgae biomass as they contain high levels of nutrients required for microalgae growth. This paper focuses on the benefits of microalgae biomass produced during the phycore-mediation of wet market wastewater and slaughterhouse wastewater as fish feed. The extraction techniques for lipids and proteins as well as the studies conducted on the use of microalgae biomass as fish feed were reviewed. The results showed that microalgae biomass can be used as fish feed due to feed utilisation efficiency, physiological activity, increased resistance for several diseases, improved stress response, and improved protein retention

Effectiveness of pharmacogenomic tests including CYP2D6 and CYP2C19 genomic variants for guiding the treatment of depressive disorders: Systematic review and meta-analysis of randomized controlled trials

Major depressive disorders are prevalent conditions with limited treatment response and remission. Pharmacogenomics tests including CYP2D6 and CYP2C19 genomic variants provide the most reliable actionable approach to guide choice and dosing of antidepressants in major depression to improve outcome. We carried out a meta-analysis and meta-regression analyses of randomised controlled trials evaluating pharmacogenomic tests with CYP2D6 and CYP2C19 polymorphisms in major depression. A systematic review was conducted according to PRISMA and Cochrane guidelines to search several electronic databases. Logarithmically transformed odds ratios (OR) and confidence intervals (CI) for improvement, response and remission were calculated. A random-effects meta-analysis and meta-regression analyses were subsequently carried out. Twelve randomised controlled trials were included. Pharmacogenomic tests in the treatment of depression were more effective than treatment as usual for improvement (OR:1.63, CI: 1.19-2.24), response (OR: 1.46; CI: 1.16-1.85) and remission (OR: 1.85; CI: 1.23-2.76) with no evidence of publication bias. Remission was less favourable in recent studies. The results are promising but cautious use of pharmacogenomics in major depression is advisable. PROSPERO registration ID: CRD42021261143

The Usefulness of Gridded Climate Data Products in Characterizing Climate Variability and Assessing Crop Production

A sparse rain gauge network in dryland regions has been a major challenge for accessing high quality observed data needed to understand variability and trends in climate. Gridded estimates of weather parameters produced through data assimilation algorithms that integrate satellite and irregularly distributed on-ground observations from multiple observing networks are a potential alternative. Questions remain about the application of such climate data sources for assessing climate variability and crop productivity. This study assessed the usefulness and limitations of gridded data from four different sources i.e. AgMERRA, CHIRPS, NASA Power, and TAMSAT in estimating climate impacts on crop productivity using Agricultural Production Systems Simulator (APSIM). The study used data for 11 locations from Africa and India. The agreement between these data sets and observed data both in the amount and distribution of rainfall was evaluated before and after bias correction statistically. A deviation of more than 100 mm per season was observed in 13%, 20%, 25%, and 40% of the seasons in CHIRPS, AgMERRA, NASA Power, and TAMSAT data sets respectively. The differences were reduced significantly when data sets were bias-corrected. The number of rainy days is better estimated by TAMSAT and CHIRPS with a deviation of 4% and 6% respectively while AgMERRA and NASA Power overestimated by 28% and 67% respectively. The influence of these differences on crop growth and productivity was estimated by simulating maize yields with APSIM. Simulated crop yields with all gridded data sets were poorly correlated with observed data. The normalized root-mean-square error (NRMSE) of maize yield simulated with observed and gridded data was <30% for two locations in the case of AgMERRA and CHIRPS and three locations in the case of NASA Power. The NRMSE was > 30% for all locations with TAMSAT data. When yields were simulated with data after bias correction using the linear scaling technique, results were slightly improved. The results of our study thus indicate that the gridded data sets are usefully applied for characterizing climate variability, i.e. trends and seasonality in rainfall, however their use in driving crop model simulations of smallholder farm level production should be carefully interpreted