SWALO: scaffolding with assembly likelihood optimization

Scaffolding, i.e. ordering and orienting contigs is an important step in genome assembly. We present a method for scaffolding using second generation sequencing reads based on likelihoods of genome assemblies. A generative model for sequencing is used to obtain maximum likelihood estimates of gaps between contigs and to estimate whether linking contigs into scaffolds would lead to an increase in the likelihood of the assembly. We then link contigs if they can be unambiguously joined or if the corresponding increase in likelihood is substantially greater than that of other possible joins of those contigs. The method is implemented in a tool called Swalo with approximations to make it efficient and applicable to large datasets. Analysis on real and simulated datasets reveals that it consistently makes more or similar number of correct joins as other scaffolders while linking very few contigs incorrectly, thus outperforming other scaffolders and demonstrating that substantial improvement in genome assembly may be achieved through the use of statistical models. Swalo is freely available for download at https://atifrahman.github.io/SWALO/.     

Experimental and theoretical analyses of nano-silver for antibacterial activity based on differential crystal growth temperatures

The modulation of antimicrobial properties of nanomaterials can be achieved through various physical and chemical processes, which ultimately affect subsequent properties. In this study, the antibacterial potential of nano-silver was investigated at 0.5, 1.0, 2.0, and 3.0 g/L, and its differential temperature synthesis was achieved at 20, 50, and 70 °C using the solvent evaporation method. Nano-silver particles exhibited FCC (octahedral) crystalline structure with crystallite sizes ranging between 28 and 39 nm calculated using XRD analysis. Moreover, irregular and non-uniform surface morphology was evident from SEM micrographs. The UV–Vis absorbance spectrum of nano-silver exhibited wave maxima at 433 nm, while the FTIR analysis depicted different modes of vibration indicating the CH, OH, C≡C, C-Cl, and CH₂ functional groups attached to the surface. Lastly, nano-silver caused prominent inhibition (12.5 mm) in the Escherichia coli growth, particularly at 70 °C synthesis temperature and 3.0 g/L dose. It is concluded that both the nano-silver crystal growth temperature and dose contributed substantially to bacterial growth inhibition linked with subsequent size, shape-dependent properties.     

Deciphering distinct biological control and growth promoting potential of multi-stress tolerant Bacillus subtilis PM32 for potato stem canker

Plant growth-promoting rhizobacteria (PGPR) represent a set of microorganisms that play significant role in improving plant growth and controlling the phytopathogens. Unpredictable performance after the application of PGPR has been observed when these were shifted from in-vitro to in-vivo conditions due to the prevalence of various abiotic stress conditions. During growing period, the potato crop is subjected to a combination of biotic and abiotic stresses. Rhizoctonia solani, a soil-borne plant pathogen, causes reduced vigor and yield of potato crop worldwide. In the current study, multi-stress-tolerant rhizobacterial strain, Bacillus subtilis PM32, was isolated from field-grown potato with various plant growth promoting (PGP) traits including zinc and potassium solubilization, biological nitrogen fixation, ammonia and siderophore, as well as extracellular enzyme productions (cellulase, catalase, amylase, protease, pectinase, and chitinase). The strain PM32 exhibited a distinct potential to support plant growth by demonstrating production of indole-3-acetic acid (102.6 μM/mL), ACC-deaminase activity (1.63 μM of α-ketobutyrate/h/mg protein), and exopolysaccharides (2.27 mg/mL). By retarding mycelial growth of R. solani the strain PM32 drastically reduced pathogenicity of R. solani. The strain PM32 also suppressed the pathogenic activity significantly by impeding mycelial expansion of R. solani with inhibition co-efficient of 49.87. The B. subtilis PM32 also depicted significant tolerance towards salt, heavy metal (Pb), heat and drought stress. PCR based amplification of ituC and acds genes coding for iturin and ACC-deaminase activity respectively indicated potential of strain PM32 for lipopeptides production and ACC deaminase enzyme activity. Results of both in-vitro and pot experiments under greenhouse conditions depicted the efficiency of B. subtilis PM32 as a promising bio-control agent for R. solani infection together with enhanced growth of potato plants as deciphered from biomass accumulation, chlorophyll a, b, and carotenoid contents. Therefore, it was envisioned that application of indigenous multi-stress tolerant PGPR may serve to induce biotic and abiotic stress tolerance in crops/plants for pathogen control and sustainable global food supply.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01067-2.     

Protective effect of jasmonic acid and potassium against cadmium stress in peas (Pisum sativum L.)

A combination of mineral nutrients and plant growth regulators should be assessed to improve crop performance under various abiotic stresses. There is a need to include plant growth regulators in fertilization regime of various crops along with essential mineral nutrients, especially when they are irrigated with polluted water with higher levels of heavy metals. The performance of pea was evaluated under cadmium (Cd) stress coupled with potassium (K) and jasmonic acid (JA) supplementation. The Cd stress (50 μM) was applied to soil (sandy loam) grown pea plants as basal dose after a month of sowing. The control and stressed plants were then supplemented with K (5 M), JA (0.5 mM) and their collective application along with control as distilled water. Cd stress showed a marked reduction in growth pattern, however, the collective supplementation sufficiently improved the growth pattern of stressed peas plants as evidenced by improvement in shoot length (cm), root length (cm), number of leaves per plant, leaf area (cm²), plant fresh and dry weight (gm). Potassium application under Cd stress significantly enhanced internodal distance (cm) while the number of seeds per pod and relative water contents remained nonsignificant. The applied treatment (JA + K) under Cd stress prominently improved enzymatic activities, which were measured as nitrate reductase activity (NRA), nitrite reductase activity (NiRA), superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT). Cd stress impacted the biochemical profile by enhancing antioxidant capacity (AC), antioxidant activity (AA), total phenols (TP), while reducing total soluble protein (TSP), chlorophyll ‘a’, chlorophyll ‘b’ and carotenoids. The combined application of JA and K under Cd stress enhanced AC, AA, TP, Chl a and b, TSP and carotenoids. The results indicate that foliar application of JA and K efficiently negated the harmful effects of Cd stress on peas.     

Mixed Convective Peristaltic Flow of Water Based Nanofluids with Joule Heating and Convective Boundary Conditions

Main objective of present study is to analyze the mixed convective peristaltic transport of water based nanofluids using five different nanoparticles i.e. (Al₂O_3, CuO, Cu, Ag and TiO₂). Two thermal conductivity models namely the Maxwell''s and Hamilton-Crosser''s are used in this study. Hall and Joule heating effects are also given consideration. Convection boundary conditions are employed. Furthermore, viscous dissipation and heat generation/absorption are used to model the energy equation. Problem is simplified by employing lubrication approach. System of equations are solved numerically. Influence of pertinent parameters on the velocity and temperature are discussed. Also the heat transfer rate at the wall is observed for considered five nanofluids using the two phase models via graphs.     

Infection of humanized mice with a novel phlebovirus presented pathogenic features of severe fever with thrombocytopenia syndrome

Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne emerging phlebovirus with high mortality rates of 6.0 to 30%. SFTSV infection is characterized by high fever, thrombocytopenia, leukopenia, hemorrhage and multiple organ failures. Currently, specific therapies and vaccines remain elusive. Suitable small animal models are urgently needed to elucidate the pathogenesis and evaluate the potential drug and vaccine for SFTSV infection. Previous models presented only mild or no pathogenesis of SFTS, limiting their applications in SFTSV infection. Therefore, it is an urgent need to develop a small animal model for the investigation of SFTSV pathogenesis and evaluation of therapeutics. In the current report, we developed a SFTSV infection model based on the HuPBL-NCG mice that recapitulates many pathological characteristics of SFTSV infection in humans. Virus-induced histopathological changes were identified in spleen, lung, kidney, and liver. SFTSV was colocalized with macrophages in the spleen and liver, suggesting that the macrophages in the spleen and liver could be the principle target cells of SFTSV. In addition, histological analysis showed that the vascular endothelium integrity was severely disrupted upon viral infection along with depletion of platelets. In vitro cellular assays further revealed that SFTSV infection increased the vascular permeability of endothelial cells by promoting tyrosine phosphorylation and internalization of the adhesion molecule vascular endothelial (VE)–cadherin, a critical component of endothelial integrity. In addition, we found that both virus infection and pathogen-induced exuberant cytokine release dramatically contributed to the vascular endothelial injury. We elucidated the pathogenic mechanisms of hemorrhage syndrome and developed a humanized mouse model for SFTSV infection, which should be helpful for anti-SFTSV therapy and pathogenesis study.     

Cymbopogon schoenanthus (Ethkher) ameliorates cadmium induced toxicity in swiss albino mice

Cadmium is among the toxic and hazardous metal widely dispersed in the environment in high levels. Current studies have provided new insights into antioxidant properties of bioflavonoid which have emerged as probable therapeutic and nutraceutical agents. The present study is geared to investigate the possible role of Cymbopogon schoenanthus (L.) Spreng. (or Ethkher) on heavy metal cadmium (Cd) induced oxidative stress in mice. Mice were randomly divided into four groups and treated for 15 days as follows: group 1: normal control-treated (saline); group 2: Ethkher leaves extract-treated (100 mg/kg); group 3: cadmium chloride (CdCl₂) treated; group 4: CdCl₂ plus Ethkher leaves extract. The results showed a significant reduction in hemoglobin, RBC and hematocrit in cadmium-treated mice as compared to control. Exposure to Cd caused a significant increase in the number of white blood cells (P < 0.05) indicating the occurrence of systemic inflammation. The results of this study also revealed that the mice intoxicated with Cd showed a significant increase in bilirubin, aspartate aminotransferase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP) and gamma-glutamyl transpeptidase (GGTP) activities. Cd intoxication leads to suppression in humoral immunity. However, pretreatment with Ethkher extract reversed almost all the abnormalities in the blood parameters showing noteworthy protection against cadmium induced toxicity in mice. The outcome of the present study revealed that the Ethkher possessed significant immunomodulatory activity and had a preventive effect on the hematological alterations in Cd intoxicated mice.     

Tracing the Genetic Legacy of the Tibetan Empire in the Balti

The rise and expansion of Tibetan Empire in the 7th to 9th centuries AD affected the course of history across East Eurasia, but the genetic impact of Tibetans on surrounding populations remains undefined. We sequenced 60 genomes for four populations from Pakistan and Tajikistan to explore their demographic history. We showed that the genomes of Balti people from Baltistan comprised 22.6–26% Tibetan ancestry. We inferred a single admixture event and dated it to about 39–21 generations ago, a period that postdated the conquest of Baltistan by the ancient Tibetan Empire. The analyses of mitochondrial DNA, Y, and X chromosome data indicated that both ancient Tibetan males and females were involved in the male-biased dispersal. Given the fact that the Balti people adopted Tibetan language and culture in history, our study suggested the impact of Tibetan Empire on Baltistan involved dominant cultural and minor demic diffusion.