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Pistachio bushy top syndrome (PBTS) is a serious problem for pistachio growers in the western United States, but the cause of this disorder remains controversial. Recently, it was proposed that the Rhodococcus species R. fascians and R. corynebacterioides caused PBTS outbreaks in 2011 and 2015. To investigate the association of Rhodococcus spp. with PBTS in California's pistachio-growing region, Rhodococcus-like isolates were collected from diverse hosts and environments, including pistachio nurseries and orchards. Whole genome sequence analysis of 231 isolates revealed their evolutionary relationships and identified six Rhodococcus species. Combined with data on geography and host of origin, the data reveal that Rhodococcus generally, and R. fascians specifically, is ubiquitous in nature, frequently occurring in both symptomatic and asymptomatic pistachio trees and on other woody and native species. Core gene and single nucleotide polymorphism-based phylogenies and pangenome analyses differentiate R. fascians into distinct genotypes. Although we found examples of common genotypes shared between nurseries and orchards, the observed patterns are most consistent with an environmental source of strains and do not support a scenario in which individual nurseries are point sources of Rhodococcus. Moreover, none of the collected strains harbored known virulence genes, calling into question the role of these common environmental bacteria in causing PBTS. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Ninety days study was conducted in hapas installed in earthen ponds. Fish of an average initial weight (220g) were evenly distributed in triplicate groups within fifteen hapas. Five experimental diets labeled as T1 (25% CP and NRC recommended amino acid level) as control diet, T2 (with 2% low protein and 5% amino acid supplementation), T3 (with 2% low protein and 10% amino acid supplementation), T4 (with 4% low protein and 10% amino acid supplementation) and T5 (with 4% low protein and 20% amino acid supplementation) were prepared. Fish were fed with @3% of their body weight twice a day at 10.00 & 16:00 hour. Significantly higher percent weight gain (420.18 ± 66.84a) and specific growth rate (13499.33±1273.54a) along with improved feed conversion ratio (1.29 ± 0.09b) and hundred percent survivals were recorded during the trial. Furthermore proximate analysis of meat showed significant improvement in the crude protein level (81.77 ± 0.19a) served with diet containing 20% limiting amino acids mixture. Therefore, limiting amino acids can be a source of cost effective feed and use safely in L. rohita diet. Resumo O estudo de 90 dias foi realizado em hapas instalados em tanques de terra. Peixes com peso inicial médio (220 g) foram distribuídos uniformemente em grupos triplicados em 15 hapas. Cinco dietas experimentais rotuladas como T1 (25% de CP e NRC recomendado nível de aminoácidos) como dieta controle, T2 (com 2% de proteína baixa e 5% de suplementação de aminoácidos), T3 (com 2% de proteína baixa e 10% de suplementação de aminoácidos), T4 (com 4% de baixa proteína e 10% de suplementação de aminoácidos) e T5 (com 4% de baixa proteína e 20% de suplementação de aminoácidos) foram preparadas. Os peixes foram alimentados com 3% do seu peso corporal duas vezes por dia às 10h00 e 16h00. Ganho de peso significativamente maior (420,18 ± 66,84a) e taxa de crescimento específico (13499,33 ± 1273,54a) juntamente com taxa de conversão alimentar melhorada (1, 29 ± 0,09b) e sobrevivência de cem por cento foram registrados durante o ensaio. Além disso, a análise aproximada da carne mostrou melhora significativa no nível de proteína bruta (81,77 ± 0,19a) servida com dieta contendo 20% de mistura de aminoácidos limitantes. Portanto, a limitação de aminoácidos pode ser uma fonte de alimentação econômica e usada com segurança na dieta de L. rohita.

The present study was designed to evaluate the effect of different concentrations of Silica gel on the growth and yield of Camelina sativa. A pot experiment was laid out in Completely Randomized Design (CRD) with three replications at Nanotechnology Laboratory, Department of Agronomy, PMAS Arid Agriculture University Rawalpindi. The experiment consisted of 4 levels (0.15 mg/g, 0.30 mg/g, 0.45 mg/g and 0.60 mg/g) of each mentioned nutrient along with control. The data were recorded and analyzed according to recommended procedure for following parameters viz., germination %, root and shoot length (cm), root and shoot biomass (g), relative water content of leaf and leaf membrane stability index. It was observed that 0.60 mg/g silica gel application increased the seed germination (80%), root length (6.67) cm, shoot length (35.33) cm, root biomass (1.7) g, shoot biomass (5.57) g, relative water content of leaf (0.69) and leaf membrane stability index (0.07). The study concluded that significant effect of silica gel application is crucial and important to improve vegetative attributes of false flax.

Background Current year 2021, brought a hope for the world due to availability of various vaccines to prevent COVID 19. Researchers around the Globe, kept working around the clock to dig up various correlations of this infection. So, that morbidity and mortality rates can be reduced. In all this sprint, cases of black fungus came into light in India. The Indian researchers identified strong association of black fungus co infection in COVID patients resulting in high mortality rates. Objectives Therefore, this current systematic review was planned to identify the predisposing factors, clinical presentations and management options for black fungus in COVID 19 patients. Methodology: This ‘systematic review’ was carried out following preferred reporting items for systematic review and meta-analysis (PRISMA) guidelines & various search engines. Total 20(N) articles were selected and included for study. After following PRISMA guidelines and based upon inclusion and exclusion criteria of study, total 05 (N) manuscripts, were included. Results Out of 05(N) selected articles, 80 %( 04) strongly supported strong association of black fungus with COVID 19 patients. The highlighted predisposing factors includes, immunosuppression, anti virals, prolong hospital stay, use of tocilizumab and steroids as management of COVID patients. Timely diagnosis and provision of anti-fungal can be helpful to reduce mortality form this co infection. Conclusion It is concluded that immunosuppression, anti virals, prolong hospital stay, use of tocilizumab and steroids as management of COVID predisposes to black fungus. Timely diagnosis and use of systematic anti fungals can reduce mortality rate form this co infection.

This study aimed to assess the impact of individual as well as combined application of Lysinibacillus macroides and Bacillus safensis in phytoremediation potential of Brassica napus grown in soil contaminated by industrial effluents. In response to five metals; copper, chromium, nickel, lead, and cadmium, results revealed that germination percentage, fresh and dry weights, and photosynthetic pigments of B. napus decreased under contaminated soil. On the other hand, electrolyte leakage due to cellular injury, metabolites (proline and glycine betaine), antioxidant enzymes (superoxide dismutase, catalase, peroxidase, ascorbate peroxidase), accumulation of hydrogen peroxide and metals in plant's roots, shoots and leaves increased. Inoculation significantly reduced these effects as proved by the enhancement of germination percentage, fresh and dry biomass, and photosynthetic pigments. Simultaneously, the antioxidant enzymes, metabolites contents (proline and glycine betaine) and metal concentrations in plant's roots, shoots and leaves decreased. Combined application of both Bacilli strains was found more effective as compared to individual inoculation. It was concluded that metal resistant Bacillus species in combination had growth effects on B. napus and enhanced its phytoremediation efficiency in contaminated soil.Novelty statementBrassica napus; a hyper-accumulator of metals, loses phytoremediation potential with the passage of growth. Two Bacillus species (Lysinibacillus macroides and Bacillus safensis) having known bioremediation abilities were employed individually as well as in combination under metals contaminated soil to increase phytoremediation efficiency of B. napus. The metals containing soil used is a unique aspect in this study because selected soil, contaminated by industrial effluents, has not been evaluated or reported earlier. Combined application of Bacilli improved phytoremediation potential of B. napus more as compared to application of individual Bacillus strain which is yet another unique aspect of this investigation.

OBJECTIVE This study was undertaken to identify susceptibility loci for cluster headache and obtain insights into relevant disease pathways. METHODS We carried out a genome-wide association study, where 852 UK and 591 Swedish cluster headache cases were compared with 5,614 and 1,134 controls, respectively. Following quality control and imputation, single variant association testing was conducted using a logistic mixed model for each cohort. The 2 cohorts were subsequently combined in a merged analysis. Downstream analyses, such as gene-set enrichment, functional variant annotation, prediction and pathway analyses, were performed. RESULTS Initial independent analysis identified 2 replicable cluster headache susceptibility loci on chromosome 2. A merged analysis identified an additional locus on chromosome 1 and confirmed a locus significant in the UK analysis on chromosome 6, which overlaps with a previously known migraine locus. The lead single nucleotide polymorphisms were rs113658130 (p = 1.92 × 10-17 , odds ratio [OR] = 1.51, 95% confidence interval [CI] = 1.37-1.66) and rs4519530 (p = 6.98 × 10-17 , OR = 1.47, 95% CI = 1.34-1.61) on chromosome 2, rs12121134 on chromosome 1 (p = 1.66 × 10-8 , OR = 1.36, 95% CI = 1.22-1.52), and rs11153082 (p = 1.85 × 10-8 , OR = 1.30, 95% CI = 1.19-1.42) on chromosome 6. Downstream analyses implicated immunological processes in the pathogenesis of cluster headache. INTERPRETATION We identified and replicated several genome-wide significant associations supporting a genetic predisposition in cluster headache in a genome-wide association study involving 1,443 cases. Replication in larger independent cohorts combined with comprehensive phenotyping, in relation to, for example, treatment response and cluster headache subtypes, could provide unprecedented insights into genotype-phenotype correlations and the pathophysiological pathways underlying cluster headache. ANN NEUROL 2021;90:193-202.

Under the climate change scenario, high-temperature stress declines crop yields. The present study was designed with the objectives to identify the stable heat-tolerant genotypes for grain yield under normal and heat stress conditions at three locations. The 80 mung bean genotypes and 3 check varieties were sown in three agro-ecological zones of Pakistan, namely, Chakwal, Piplan, and Bhakkar. The experiments were planted in two sowing dates, i.e., the normal sowing and late sowing by using an augmented randomized block design with 6 blocks at each location. The plot size for each genotype was 2.4 m2 at all the locations. All cultural and agronomic practices were carried out as per recommendations. Ten randomly selected plants were used to record the yield-related traits. An infrared gas analyzer (IRGA) was used to measure physiological traits like photosynthesis rate and stomatal conductance. To study the nature of relationship among traits, Pearson correlation analysis was done using SPSS software (v. 16.0). The GGE biplots were constructed to graphically represent the genotype and GE interaction of multi-environment data using the software plant breeding tools. Three views of the GGE biplot were generated to display the comparative performance, rank, and stability of each genotype in the tested environments. Correlation and principal component analysis (PCA) revealed a positive interaction of grain yield with pods plant−1, seed pod−1, 100 grain weight, and harvest index, while days to flowering and maturity had a negative association under normal and heat-stressed conditions. The GGE biplot analysis efficiently explained 85.1% of the total variation and demonstrated that among 8 vertex genotypes of polygon biplot, the G14 and G38 were heat tolerant as these genotypes outclassed others in all the heat-stressed environments. In contrast, the genotypes G51 and G74 produced maximum yield under normal conditions (E3 and E5). Among all the genotypes, genetic diversity was observed for grain yield and other morpho-physiological traits. Significant G × E interaction was observed. The genotypes G14, G38, and G51 were identified as stable and heat tolerant in most of the environments. These findings will be helpful for development of heat-tolerant mung bean breeding material in the future.

Mangrove species are growing in exposed areas which have heavy metal contamination. The safeguard the mangrove ecosystem, it is important to understand their antioxidant responses to heavy metal toxicity. The goal of this study was to determine the effect of multi-heavy metals i.e. (Pb, Cd, Cr and Hg) on two mangrove plants Avicennia marina and Rhizophora mucronata of Indus delta via investigating their antioxidative defence mechanism of leaves and roots. In this regard mangrove seedlings of both species were treated with five different concentrations of four heavy metals and different time durations (15, 30, 45 and 60 days) for ascorbate peroxidase, catalase and superoxide dismutase in leaves and root tissues. The findings indicate that the heavy metals have significantly altered the antioxidant enzyme activities with respect of metals concentration and duration of exposure. With extended exposure higher antioxidant activities was observed in metal treated roots and leaves at higher concentrations. A pronounced stimulation (P

PERCEPTRON is a next-generation freely available web-based proteoform identification and characterization platform for top-down proteomics (TDP). PERCEPTRON search pipeline brings together algorithms for (i) intact protein mass tuning, (ii) de novo sequence tags-based filtering, (iii) characterization of terminal as well as post-translational modifications, (iv) identification of truncated proteoforms, (v) in silico spectral comparison, and (vi) weight-based candidate protein scoring. High-throughput performance is achieved through the execution of optimized code via multiple threads in parallel, on graphics processing units (GPUs) using NVidia Compute Unified Device Architecture (CUDA) framework. An intuitive graphical web interface allows for setting up of search parameters as well as for visualization of results. The accuracy and performance of the tool have been validated on several TDP datasets and against available TDP software. Specifically, results obtained from searching two published TDP datasets demonstrate that PERCEPTRON outperforms all other tools by up to 135% in terms of reported proteins and 10-fold in terms of runtime. In conclusion, the proposed tool significantly enhances the state-of-the-art in TDP search software and is publicly available at https://perceptron.lums.edu.pk. Users can also create in-house deployments of the tool by building code available on the GitHub repository (http://github.com/BIRL/Perceptron)., Graphical Abstract Graphical AbstractPERCEPTRON proteoform identification pipeline for top-down proteomics data. PERCEPTRON processes mass-spectrometry data from top-down experiments in specified formats. The platform pipelines four salient algorithms towards proteoform identification and characterization.

Phosphate solubilizing bacteria (PSB) is renowned for its excellent potential of converting unavailable forms of phosphorus (P) to a simpler available form in the soil. This P availability not only...

IncC from the low-copy number plasmid RK2, is a member of the ParA family of proteins required for partitioning DNA in many bacteria and plasmids. It is an ATPase that binds DNA and its ParB protein partner, KorB. Together, the proteins move replicated DNA to appropriate cellular positions, so that each daughter cell inherits a copy on cell division. IncC from RK2 is expressed in two forms. IncC2 is homologous to bacterial ParA proteins, while IncC1 has an N-terminal extension of 105 amino acids and is similar in length to ParA homologues in other plasmids. We have been examining the role of this extension, here called IncC NTD. We present its backbone NMR chemical shift assignments and show that it is entirely intrinsically disordered. The assignments were achieved using C-detected, CON-based spectra, complemented by HNN spectra to obtain connectivities from three adjacent amino acids. We also observed evidence of deamidation of the protein at a GNGG sequence, to give isoAsp, giving 2 sets of peaks for residues up to 5 amino acids on either side of the modification. We have assigned resonances from around the position of modification for this form of the protein.

Continuous inhalation of coal dust among coal workers leads to a variety of disorders. The present study aims to evaluate the potential oxidative stress associated with coal dust generated from coal mining activities among exposed workers through the antioxidant enzyme system, including superoxide dismutase (SOD), catalase (CAT), and glutathione (GSH). In this study cohort, intensive coal mine workers were assessed for antioxidant variations. Blood samples were collected from dust-exposed workers (engaged in different activities at coal mines; n = 311) and residents of the same city (nonexposed, control group; n = 50). The workers' exposure to coal dust was categorized based on working area (administrative group, surface workers, underground workers), working hours (up to 8 h and more than 8 h), and time of service. The results showed significantly altered activities of SOD, CAT, and GSH among the whole exposed group and its categories compared to the control group. A significant difference was also observed between high- and low-exposure groups. Statistical analysis revealed a negative correlation between antioxidant activity (catalase and SOD) and coal dust levels. Besides, coal exposure was associated with the time of service, smoking status, and dietary habits. The findings of this study reveal higher oxidative stress among highly exposed coal mine workers (underground workers > surface workers > administrative group > nonexposed group), and longer working hours have more pronounced adverse effects on workers' health.

In the last two decades, poultry and animal industries became increasingly interested in using plant-based feed supplements, herbs and their derivatives to retain or enhance their health and productivity. These health benefits for the host mainly attributed to the secondary plant metabolites, namely polyphenols. Polyphenols are renowned for their antioxidant, immunomodulatory, anti-mutagenic and anti-inflammatory properties. However, despite these advantages of polyphenols, they have been characterized by poor absorption in the gut and low concentration in target cells that compromise their role as effective antioxidants. The low bioavailability of polyphenols necessitates the need for further investigations to harness their full potential in poultry farms. This review is existing evidence about the bioavailability of polyphenols and their antioxidant, immunomodulatory, antimicrobial, detoxification properties and their impacts on poultry performance.

In the Mediterranean climate, plants, e.g., Quercus brantii Lindl, have evolved and adapted to bear up low soil-water and soil-phosphorus conditions. Quercus brantii Lindl. is a dominant tree speci...

The attempts toward addition of biocontrol agents in dairy products have gained popularity. Here, we worked on analysing the antifungal activity of binary and ternary combinations of three Lactic Acid Bacteria (LAB) against five spoilage yeasts in yogurt. The yogurt samples were characterized in terms of pH, acidity, WHC, textural parameters, viscosity, survivability and antifungal activity of LAB and sensorial properties during cold storage. The results showed that the inoculation of LAB in yogurt gave rise in significant reduction of pH throughout cold storage while titrable acidity and WHC decreased (p

© 2020 The Authors. Histopathology published by John Wiley & Sons Ltd Aims: Tumour genotype and phenotype are related and can predict outcome. In this study, we hypothesised that the visual assessment of breast cancer (BC) morphological features can provide valuable insight into underlying molecular profiles. Methods and results: The Cancer Genome Atlas (TCGA) BC cohort was used (n=743) and morphological features, including Nottingham grade and its components and nucleolar prominence, were assessed utilising whole-slide images (WSIs). Two independent scores were assigned, and discordant cases were utilised to represent cases with intermediate morphological features. Differentially expressed genes (DEGs) were identified for each feature, compared among concordant/discordant cases and tested for specific pathways. Concordant grading was observed in 467 of 743 (63%) of cases. Among concordant case groups, eight common DEGs (UGT8, DDC, RGR, RLBP1, SPRR1B, CXorf49B, PSAPL1 and SPRR2G) were associated with overall tumour grade and its components. These genes are related mainly to cellular proliferation, differentiation and metabolism. The number of DEGs in cases with discordant grading was larger than those identified in concordant cases. The largest number of DEGs was observed in discordant grade 1:3 cases (n=1185). DEGs were identified for each discordant component. Some DEGs were uniquely associated with well-defined specific morphological features, whereas expression/co-expression of other genes was identified across multiple features and underlined intermediate morphological features. Conclusion: Morphological features are probably related to distinct underlying molecular profiles that drive both morphology and behaviour. This study provides further evidence to support the use of image-based analysis of WSIs, including artificial intelligence algorithms, to predict tumour molecular profiles and outcome.

In this study, oleanolic acid and its derivatives were studied for their invivo nematicidal activity against root-knot nematode (RKN) Meloidogyne incognita. A series of C-28-oleanolates including five new (5, 7–10) and seven known (1–4, 6, 11, 12) compounds were synthesised and their nematicidal activity was determined and compared with the standard nematicide furadan for the first time. The structures of the compounds were elucidated through 1H NMR, 13C NMR and EIMS. Compounds 4, 5, 7, 8 and 10 showed ∼ 90% inhibition of RKN at 0.125% concentration after 72 h showing their potential use in nematicidal control.

In continuation of our work on Tagetes spp., the current study deals with the nematicidal activity of flavonoids, which are structurally related to two marker compounds, patuletin and patulitrin isolated from Tagetes patula flowers. The activity was determined against root-knot nematode, Meloidogyne incognita to establish structure activity relationship. In vitro examination of flavonoids belonging to flavone and flavonol classes revealed significant differences in nematicidal ability depending on their structural motif, concentration, and time of exposure. In case of flavonols the most efficient compounds were found to be fisetin, galangin, isorhamnetin, morin, and myricetin which exhibited 100% mortality of 2nd stage juveniles after 24 h of incubation. Whereas, among flavones which showed the same excellent activity parameters, were simple flavone, 6-hydroxy flavone, chrysin, 6-methoxy apigenin, apigenin-7-O-glucoside and 6-methoxy luteolin. These results revealed that flavonoids possess promising nematicidal activity and may have potential use in crop management as active agents.

Evolution of drug-resistant microbial species is one of the major challenges to global health. Development of new antimicrobial treatments such as antimicrobial peptides needs to be accelerated to combat this threat. However, the discovery of novel antimicrobial peptides is hampered by low-throughput biochemical assays. Computational techniques can be used for rapid screening of promising antimicrobial peptide candidates prior to testing in the wet lab. The vast majority of existing antimicrobial peptide predictors are non-targeted in nature, i.e., they can predict whether a given peptide sequence is antimicrobial, but they are unable to predict whether the sequence can target a particular microbial species. In this work, we have used zero and few shot machine learning to develop a targeted antimicrobial peptide activity predictor called AMP0. The proposed predictor takes the sequence of a peptide and any N/C-termini modifications together with the genomic sequence of a microbial species to generate targeted predictions. Cross-validation results show that the proposed scheme is particularly effective for targeted antimicrobial prediction in comparison to existing approaches and can be used for screening potential antimicrobial peptides in a targeted manner with only a small number of training examples for novel species. AMP0 webserver is available at http://ampzero.pythonanywhere.com.

Sesame cultivars perform differently in various environments comprising specific locations and years. Micronutrient fertilizers increase crop yields and can enhance resistance to environmental hazards and contribute to potential yield. For assessing the effect of environment and micronutrients, field experiments were carried out at three different locations (BARI, URF and NARC) of Pothwar region, Pakistan, in two succeeding years (2014, 2015). Four sesame cultivars and three micronutrients (Zn, B and Mn) with a control treatment were used in RCB design with a split-plot procedure and four replications. The results showed significant differences in the main effects of all tested factors (cultivars, micronutrients, locations and years). Maximum mean values of plant height, capsules plant−1, biomass yield and seed yield were recorded for SG-30, while TH-6 was the lowest for these parameters. Maximum mean values of capsule length, capsule weight, seeds capsules−1 and the weight of 1000 seeds were recorded for TH-6 but vice versa for SG-30. Maximum capsule length and seeds capsule−1 were observed at NARC, while other growth and yield attributes were maximum at BARI and URF, including biomass yield and seed yield. The interactive effect of cultivar × location × year was highly significant for all growth and yield traits except capsule length. Sesame cultivars revealed a differential response for all traits at three locations during both years. Application of micronutrients significantly augmented all growth and yield features of sesame. Micronutrient fertilizers (i.e., ZnSO4 at 10 kg ha−1, borax at 10 kg ha−1 and MnSO4 at 5 kg ha−1) would increase yield and yield-attributing traits in low- or medium-precipitation areas where suitable cultivars have been designated.

Case report - Introduction Juvenile-onset systemic lupus erythematosus (jSLE) is a rare systemic autoimmune-disease affecting children, with an incidence between 0.5 and 6 per 100,000. A 20-year-old female with known jSLE was diagnosed six years ago, age 14, following multiple attendances to A&E with non-specific symptoms. She was initially discharged with simple analgesia but later admitted to the paediatric ward with severe central chest pain. Investigations confirmed pleuro-pericardial effusion and positive lupus antibodies. She subsequently had recurrent flares with predominantly renal involvement. She remained symptomatic despite multiple combined immunosuppressive agents including biological therapies. Unfortunately, her kidney-functions deteriorated, requiring close monitoring in the Advanced Kidney-Care Clinic. Case report - Case description A 14-year-old female who was otherwise fit and healthy with no family history of autoimmune conditions presented to the Emergency department with constant throbbing limb-pain and recurrent episodes of chest pains. Immunological investigations revealed positive anti-nuclear antibodies (ANA), anti-double-stranded(ds)-DNA antibodies, C1Q-antibody and lupus inhibitor on two repeat tests. Echocardiogram showed pleuro-pericardial effusion and due to the high risk of cardiac tamponade, she was transferred to a tertiary centre for further management. She had intravenous steroid with good resolution of symptoms, and subsequently received maintenance therapy of azathioprine and hydroxychloroquine. She stayed in remission for approximately one year before her clinical condition worsened. She started to develop active inflammatory arthritis and serositis, with increasing anti-dsDNA titres, reducing complement levels, worsening anaemia and a positive direct antiglobulin test. Oral corticosteroids were recommenced and azathioprine was switched to mycophenolate-mofetil. She subsequently had recurrent flares; predominantly renal involvement and worsening proteinuria. This did not improve with repeat courses of antibiotics given for presumed urinary tract infections (UTIs), prompting renal biopsy which confirmed active renal lupus (combined Class III and V lupus nephritis). Rituximab and tacrolimus were initiated but rituximab was withheld after the first dose due to severe, widespread desquamating rash, mucosal ulceration and fever, biopsy-proven and drug-induced. Short-term remission after 1 dose of rituximab and then renal relapse with repeat renal biopsy showed class 5 lupus nephritis. Intravenous cyclophosphamide with Euro-lupus regimen was given. 5 months after discontinuation of cyclophosphamide her renal disease relapsed again with rising anti-dsDNA, ESR and proteinuria to > 6g/l, despite mycophenolate. Repeat and extended course of cyclophosphamide was restarted. Combination MMF and tacrolimus did not maintain control of disease and renal function continued to decline. Belimumab IV-monthly was added in combination and proteinuria halved, with stabilisation of renal function, although now with eGFR 25ml/min. The most recent biopsy shows chronic damage. SLEDAI-improved from 22 to 10. Case report - Discussion In children, adolescent females are predominantly affected as observed in this case. The peak age of onset is around 12 years, often with more severe disease presentation than lupus in adults; with a higher incidence of major organ involvement and aggressive disease course with a higher chance of developing complications. She developed uncontrolled hypertension and nephrotic syndrome requiring treatment with multiple antihypertensive agents and thrombosis prevention with DOACs. The patient was offered but refused anaemia treatment with erythropoietin. She received infection prevention treatment (PCP prophylaxis) and GnRH agonist injections to preserve ovarian function while on cyclophosphamide. Later, she developed iatrogenic cushingoid syndrome and severe facial acne. Poor compliance, commonly seen in this age group, possibly contributed to the poor outcomes. Other medication-related complications included retinal hydroxychloroquine toxicity that led to dose reduction. Allergy to rituximab (Mabthera) prevented its further use; given the severity of reaction concerns, other biosimilar humanized anti-CD20 antibodies were considered, but difficult to obtain; deteriorating renal function with predominantly damaged kidneys and class V nephritis on biopsy and aiming to control immunology along with other active symptoms (arthritis, serositis–pleurisy, systemic symptoms, anaemia) options were limited. There was increasing evidence to use belimumab plus tacrolimus +/- Mycophenolate-Mofetil to maintain remission. Belimumab was used after a repeat course of cyclophosphamide for this patient, after discussion with tertiary renal centres. During the course of her illness, she had progressively deteriorating renal function, which prompted discussion for renal replacement therapy or renal transplant. Considering that this was affecting her at such a young age, she was advised to keep an up-to-date vaccination status. Her worsening condition as well as its associated complications related to treatment and polypharmacy have significantly affected her mental health and quality of life in many ways, including suffering from depression and fatigue. Frequent hospital visits for investigations and treatment also hampered her education. This emphasizes the importance of social, family, and educational support for patients with this condition. In conclusion, despite a multidisciplinary approach and access to specialist services severe relapsing course of SLE and multiple diseases and treatment-related complications developed with co-morbidity, leading to life-changing organ damage and impact on quality of life. Case report - Key learning points > To conclude, jSLE is a challenging disease that is both difficult to diagnose and to treat. Clinicians should be aware of the greater risk of systemic complications in children with SLE.

Chemotherapy is a general treatment procedure for cancer. The diversity in cancer incidence and the failure of therapy due to chemoresistance lead to increased cancer-related deaths. Therefore, new drugs with fewer secondary complications targeting diverse pathways are the need of the hour. Geranyl isovalerate (GIV), one of the active ingredients of ethyl acetate fraction of Argyreia nervosa is routinely used as a food flavoring agent. In this study, we found that GIV also exhibits anticancer activity when tested against the HCT116 cell line. It influenced the viability of the cells in a dose- and time-dependent manner. We examined whether GIV could induce oxidative stress and affect the mitochondrial membrane potential, thereby leading to apoptosis induction. Moreover, GIV could suppress the expression of antiapoptotic genes, such as BCl2 and PARP, and induce the expression of proapoptotic genes, such as Caspase 3 and 9. This is the first study demonstrating the anticancer activity of GIV and providing evidence for its mechanism of action. In conclusion, this study proposes GIV as a potential lead or supplementary molecule in treating and preventing colorectal cancer (CRC). Based on our findings, we conclude that GIV may be a viable lead or supplementary molecule for treating and preventing CRC.

The study aimed to investigate the effect of various doses of betaine supplemented dietary on Japanese quail performance, carcass characteristics, and blood chemistry. Therefore, 400 seven days old Japanese quails were classified randomly into four equal groups. Each group was subdivided into five replicates of 20 birds each. Four rations were formulated using four different betaine levels (0, 0.75, 1.5 and 2.25 g/kg, respectively) for five successive weeks. All groups received feed and clean water ad-libitum. The results of this trial indicated that the feed intake was lowered in groups fed with betaine (p ≤ 0.05) when compared with the control one. The highest weight gain (p ≤ 0.05) was noticed in groups fed diets BS4 (betaine supplementation at the rate of 2.25 g/kg). No difference among groups was observed in body length, shank length, shank diameter, and keel bone length or breast width. Also, the carcass weight and breast yield were highest (p ≤ 0.05) in the group reared on the BS4 diet. In addition, intestinal length and weight were significantly higher (p ≤ 0.05) in groups fed betaine with a concentration of 2.25 g/kg. Fat weight was lower in the group fed BS4 than in the untreated group. Significantly higher values of high-density lipoprotein (p ≤ 0.05) were observed in the group fed BS4. All groups fed a ration containing betaine showed lower levels of liver enzymes such as alanine amino transferase, alkaline phosphatase, and aspartate amino transferase (p ≤ 0.05) and lowered low-density lipoprotein level. The quails fed BS4 had the greatest growth hormones and insulin (p ≤ 0.05) and the lowest thyroxin level. We concluded that dietary betaine supplementation positively impacts Japanese quail growth performance, carcass traits, and blood chemistry.

Stripe rust (yellow rust), caused by Puccinia striiformis f. sp. tritici (Pst), is considered as a major threat to the wheat production worldwide, including Pakistan. In the current study, 80 wheat landraces collected from different agroecological zones of Pakistan were screened for their stripe rust resistance. Molecular markers were used to identify/postulate the stripe rust genes in these landraces. The results indicated that 46 (57.5%) landraces had all-stage resistance, and only 4 (5%) landraces showed adult-plant resistance. The possible stripe rust resistance genes in these entries were postulated by the using already reported linked molecular markers of all-stage resistance and adult plant stage resistance genes (Yr4 Yr5, Yr10, Yr15 and Yr24/26 and adult-plant resistance genes Yr18, Yr29 and Yr32). Molecular analysis indicated that resistant genes Yr4, Yr5, Yr10, Yr15, Yr17, Yr18, Yr26/24, Yr29 and Yr32 were found in 16(20%), 12(15%), 4(5%), 15(18.75%), 16(20%), 13(16.25%), 39(48.75%), 20(25%) and 7(7.5%) of landraces, respectively. Majority of the landraces showed the presence of more than one gene. These lines could be used effectively in the wheat breeding programs.

As a well-known edible fungus that generally grows at low temperature, Flammulina velutipes is believed to be able to withstand most undesirable microbes. However, in this study, we discovered and isolated cold-adapted bacteria that developed rapidly and caused soft rot in the stipe of F. velutipes. The pathogen was identified as Mycetocola saprophilus based on morphology, 16S rRNA sequences, and multilocus sequence typing analysis. To further understand the pathogenic mechanisms of soft rot disease in F. velutipes, we sequenced and analyzed the genome of strain JXN-3 using PacBio sequencing. The de-novo assembly of the genome of strain JXN-3 was ∼3.47 Mb, with a GC content of 66.32%. The genome was composed of 3276 genes, of which 3094 were protein coding. Many of the identified protein-coding genes were associated with the synthesis of cell wall-degrading enzymes and antifungal compounds, including chitin deacetylase, chitinase, 1,4-beta-D-glucan glucohydrolase, beta-glucanase, endoglucanase Acf2, exo-beta-1,3-glucanase and bacteriocin. Compared with other members of Mycetocola, we also found a JXN-3-unique gene cluster for synthesizing bacteriocin. These genes may contribute to the pathogenesis of soft rot in F. velutipes stipes. Future studies should further investigate the involvement of these proteins in the incidence and progression of soft rot disease in F. velutipes.

We report herein the biological activities of several imidazolium aurate(I) salts. The cytotoxicity on three cell-lines (i. e. Hela, H460 and 3T3), enzyme inhibition on a panel of five enzymes (i. e. prolyl endopeptidase, butyrylcholinesterase, tyrosinase, dipeptidyl peptidase and carbonic anhydrase), iron chelation and in vitro Leishmanicidal assay for promastigotes are described. A comparison with other data found in the literature using similar standards to our control experiment is also discussed. Finally, all these data lead us to establish some structure-activity correlations and to determine the potential importance of the gold moiety in these salts.

Chromium (Cr) toxicity is becoming one of a major issue for the cultivation of crops. Toxicity of Cr directly affects synthesis of chlorophyll and restricts Fe intake, which decreases crop growth. It is well documented that the reduction of Cr toxicity through the application of biochar. However, current experiment was carried out to investigate any positive effect of, banana peel waste biochar (BC) and foliar application of Fe (FFe) on growth and chlorophyll content of Spinacia oleracea L. under different levels of Cr toxicity. Seeds of Spinacia oleracea L. were grown under three levels of Cr i.e. control (Cr0), Cr35 (35 mg Cr kg−1 soil) and Cr70 (70 mg Cr kg-1 soil). Analyzed data confirmed that Spinacia oleracea L. seeds grown in 1% BC amended soils and 1000mM FFe, showed significantly better growth, Fe uptake and chlorophyll content as compared to control at Cr35 and Cr70. A significant improvement in shoot length (16.9 and 26.9%), root length (16.3 and 20.9%), plant fresh (15.5 and 28.3%) and dry weight (70.3 and 77.8%) as compared to control under Cr35 and Cr70, respectively, validated the efficacious functioning of 1% BC and FFe to mitigate Cr toxicity in Spinacia oleracea L. It is concluded that both 1% banana peel waste BC and 1000mM FFe have potential but sole application of FFe is more effective to alleviate Cr toxicity in Spinacia oleracea L. Fortification of Fe by foliar application is more effective comparative to banana peel waste biochar for improvement in growth, chlorophyll content and accessory pigments synthesis in spinach under chromium (IV) toxicity.

Internet of Things (IoT) technologies are beginning to transform rural water supply in sub-Saharan Africa. Such information and communications technologies (ICTs) can facilitate change away from cu...

Objective: Preclinical or latent RA is characterized by the presence of autoantibodies in the absence of clinical symptoms. The objective of this study was to identify the prevalence of preclinical RA in patients with Celiac disease in order to determine whether or not such individuals should be screened for RA based on the high-risk. Method: A cross-sectional study was carried out on patients with celiac disease in a tertiary care center in Rawalpindi, Pakistan. After initial assessment, RA-autoantibody levels (Rheumatoid factor and anti-CCP) were checked. Descriptive analysis was performed on the data gathered. Results: Sixteen patients with known celiac disease were identified to have positive rheumatoid factor and/or anti-CCP levels with an overall prevalence rate of 35%. This trend was significant for celiac patients having history of inflammatory arthritis and active celiac disease. No statistical significance was seen in baseline characteristics for categories of patients with positive rheumatoid factor versus with positive anti-CCP antibodies. Conclusion: Patients with CD can be considered as a high-risk group based on the high prevalence rate of rheumatoid factor/anti-CCP positivity observed in this study and should be considered for further RA screening/preventive studies. Abbreviations: RA = Rheumatoid arthritis; CD = Celiac disease; anti-CCP = anti-citrullinated cyclic peptide) antibodies; RF = Rheumatoid factor; GFD = Gluten-free diet

Objective: To determine the level of serotonin in patients of vasovagal syncope and postural tachycardia syndrome after head-up tilt test. Method: The cross-sectional analytical study was conducted at the Islamic International Medical College and the Department of Electrophysiology, Armed Forces Institute of Cardiology, Rawalpindi, from April 2017 to March 2018. Group A comprised cases of vasovagal syncope, group B had patients of postural tachycardia syndrome, and group C had healthy controls. Cases were chosen on the basis of history, episodes of syncope and findings of head-up tilt test. After the test, blood samples were taken for hormonal analysis of serotonin using enzyme-linked immunosorbent assay. Data was analysed using SPSS 21. Results: Of the 80 subjects, 35(43.8%) were in group A, 35(43.8%) in group B and 10(12.4%) in group C. Mean serotonin value in group A was 918.39±380.16nM, in group B it was 1188.70±449.55nM., while in control group C the mean value was 771.40±376.14nM (p

The SARS CoV-2 pandemic has affected millions of people around the globe. Despite many efforts to find some effective medicines against SARS CoV-2, no established therapeutics are available yet. The use of phytochemicals as antiviral agents provides hope against the proliferation of SARS-CoV-2. Several natural compounds were analyzed by virtual screening against six SARS CoV-2 protein targets using molecular docking simulations in the present study. More than a hundred plant-derived secondary metabolites have been docked, including alkaloids, flavonoids, coumarins, and steroids. SARS CoV-2 protein targets include Main protease (MPro), Papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), Spike glycoprotein (S), Helicase (Nsp13), and E-Channel protein. Phytochemicals were evaluated by molecular docking, and MD simulations were performed using the YASARA structure using a modified genetic algorithm and AMBER03 force field. Binding energies and dissociation constants allowed the identification of potentially active compounds. Ligand-protein interactions provide an insight into the mechanism and potential of identified compounds. Glycyrrhizin and its metabolite 18-β-glycyrrhetinic acid have shown a strong binding affinity for MPro, helicase, RdRp, spike, and E-channel proteins, while a flavonoid Baicalin also strongly binds against PLpro and RdRp. The use of identified phytochemicals may help to speed up the drug development and provide natural protection against SARS-CoV-2.

NODULE-INCEPTION-like proteins (NLPs) are plant specific transcription factors that play significant role in orchestrating nitrogen response. NLPs have been widely studied in vascular plants but very less is known about NLPs in non-vascular bryophytes till date. In current study, first, the in silico tools were employed for identification and characterization of NLPs in model bryophyte Physcomitrella patens genome. Furthermore, the expression profiles of PpNLPs were assessed under variable supply of nitrogen. A total of 6 Physcomitrella patens NLP genes (PpNLPs) were identified that shared resemblance in their physical and chemical attributes with Arabidopsis thaliana NLPs (AtNLPs). PpNLP genes possesses similarities in there iso-electric point and hydropathicity values with those of AtNLPs while gene lengths, protein lengths, and molecular weights were found higher in PpNLPs than AtNLPs. It was further observed that all PpNLPs, except PpNLP6, yield acidic hydrophilic proteins localized in nucleus and share a significant degree of homology in their gene structures and protein motifs with AtNLPs. Phylogenetic analysis indicated that PpNLPs possess significant evolutionary linkage with Arabidopsis thaliana, Oryza sativa, and Zea mays. Protein-protein interaction analysis suggested that PpNLPs possess substantial coordination with nitrogen responsive genes like nitrate reductase. Expressions of all PpNLPs were up-regulated in the availability of nitrate (5 and 10 mM) as sole nitrogen source while no significant increment was observed in the absence (0 mM) of nitrogen. The expression levels increased with increasing retention-time treatment of 0, 6, 12, 24, 48, and 72 hours. Results proposed that NLPs are responsive to as well as significantly regulated by nitrogen supply.

Salinity is among the major abiotic stresses negatively affecting the growth and productivity of crop plants. Sodium nitroprusside (SNP) -an external nitric oxide (NO) donor- has been found effective to impart salinity tolerance to plants. Soybean (Glycine max L.) is widely cultivated around the world; however, salinity stress hampers its growth and productivity. Therefore, the current study evaluated the role of SNP in improving morphological, physiological and biochemical attributes of soybean under salinity stress. Data relating to biomass, chlorophyll and malondialdehyde (MDA) contents, activities of various antioxidant enzymes, ion content and ultrastructural analysis were collected. The SNP application ameliorated the negative effects of salinity stress to significant extent by regulating antioxidant mechanism. Root and shoot length, fresh and dry weight, chlorophyll contents, activities of various antioxidant enzymes, i.e., catalase (CAT), superoxide dismutase (SOD), peroxidase (POD) and ascorbate peroxidase (APX) were improved with SNP application under salinity stress compared to control treatment. Similarly, plants treated with SNP observed less damage to cell organelles of roots and leaves under salinity stress. The results revealed pivotal functions of SNP in salinity tolerance of soybean, including cell wall repair, sequestration of sodium ion in the vacuole and maintenance of normal chloroplasts with no swelling of thylakoids. Minor distortions of cell membrane and large number of starch grains indicates an increase in the photosynthetic activity. Therefore, SNP can be used as a regulator to improve the salinity tolerance of soybean in salt affected soils.

Determining the aggressiveness of renal cell carcinoma (RCC) noninvasively is a critical part of the diagnostic workup for treating this disease that kills more than 15,000 people annually in the USA. Recently, we have shown that not only the amount of lactate produced, as a consequence of the Warburg effect, but also its efflux out of the cell, is a critical marker of RCC aggressiveness and differentiating RCCs from benign renal tumors. Enzymatic conversions can now be measured in situ with hyperpolarized (HP) (13)C magnetic resonance (MR) on a sub-minute time scale. Using RCC models, we have shown that this technology can interrogate in real time both lactate production and compartmentalization, which are associated with tumor aggressiveness. The dynamic HP MR data have enabled us to robustly characterize parameters that have been elusive to measure directly in intact living cells and murine tumors thus far. Specifically, we were able to measure the same intracellular lactate longitudinal relaxation time in three RCC cell lines of 16.42 s, and lactate efflux rate ranging from 0.14 to 0.8 s(−1) in the least to the most aggressive RCC cell lines and correlate it to monocarboxylate transporter isoform 4 expression. We also analyzed dynamic HP lactate and pyruvate data from orthotopic murine RCC tumors using a simplified one-compartment model, and showed comparable apparent pyruvate to lactate conversion rate (k(PL)) values with those measured in vitro. This kinetic modeling was then extended to characterize the lactate dynamics in patient-derived living RCC tissue slices; and even without direct measurement of the extracellular lactate signal the efflux parameter was still assessed and was distinct between the benign renal tumors and RCCs. Across all these preclinical models, the rate parameters of k(PL) and lactate efflux correlated to cancer aggressiveness, demonstrating the validity of our modeling approach for noninvasive assessment of RCC aggressiveness.

Alzheimer’s disease (AD) causes dementia and continuous damage to brain cells. Cholinesterase inhibitors can alleviate the condition by increasing communication between the nerve cells and reducing the risk of dementia. In an effort to treat Alzheimer’s disease, we synthesized flurbiprofen-based diamines (1,2 diaminoethane and 1,3 diaminopropane) Zn(II), Cu(II) metal complexes and characterized them by single-crystal X-ray analysis, NMR, (FT)-IR, UV-Vis, magnetic susceptibility, elemental analysis and conductivities measurements. Synthesized diamine metal complexes appeared in ionic forms and have distorted octahedral geometry based on conductivity studies, magnetic susceptibility and electronic studies. Single crystal X-ray diffraction analysis confirmed (2b) Cu(H2O)2(L1)2(L2)2 complex formation. Moreover, we tested all synthesized metal complexes against the cholinesterase enzyme that showed higher inhibition potential. In general, copper metal complexes showed higher inhibitory activities than simple metal complexes with flurbiprofen. These synthesized metal complexes may derive more effective and safe inhibitors for cholinesterases.

SummaryBackgroundDetermining molecular pathways involved in the development of colorectal cancer (CRC) and knowing the status of key mutations are crucial for deciding optimal target therapy. The goal of this study is to explore machine learning to predict the status of the three main CRC molecular pathways – microsatellite instability (MSI), chromosomal instability (CIN), CpG island methylator phenotype (CIMP) – and to detect BRAF and TP53 mutations as well as to predict hypermutated (HM) CRC tumors from whole-slide images (WSIs) of colorectal cancer (CRC) slides stained with Hematoxylin and Eosin (H&E).MethodsWe propose a novel iterative draw-and-rank sampling (IDaRS) algorithm to select representative sub-images or tiles from a WSI given a single WSI-level label, without needing any detailed annotations at the cell or region levels. IDaRS is used to train a deep convolutional network for predicting key molecular parameters in CRC (in particular, prediction of HM tumors and the status of three main CRC molecular pathways – MSI, CIN, CIMP – as well as the detection of two key mutations, BRAF and TP53) from digitized images of routine H&E stained tissue slides of CRC patients (n=497 for TCGA cohort and n=47 cases for the Pathology AI Platform or PAIP cohort). Visual fields most predictive of each pathway and HM tumors identified by IDaRS are analyzed for verification of known histological features for the first time to reveal novel histological features. This is achieved by systematic, data-driven analysis of the cellular composition of strongly predictive tiles.FindingsIDaRS yields high prediction accuracy for prediction of the three main CRC genetic pathways and key mutations by deep learning based analysis of the WSIs of H&E stained slides. It achieves the state-of-the-art AUROC values of 0.90, 0.83, and 0.81 for prediction of the status of MSI, CIN, and HM tumors for the TCGA cohort, which is significantly higher than any other currently published methods on that cohort. We also report prediction of status of CIMP pathway (CIMP-High and CIMP-Low) from H&E slides, with an AUROC of 0.79. We analyzed key discriminative histological features associated with HM tumors and each molecular pathway in a data-driven manner, via an automated quantitative analysis of the cellular composition of tiles strongly predictive of the corresponding molecular status. A key feature of the proposed method is that it enables a systematic and data-driven analysis of the cellular composition of image tiles strongly predictive of the various molecular parameters. We found that relatively high proportion of tumor infiltrating lymphocytes and necrosis are found to be strongly associated with HM and MSI, and moderately associated with CIMP-H and genome-stable (GS) cases, whereas relatively high proportions of neoplastic epithelial type 2 (NEP2), mesenchymal and neoplastic epithelial type 1 (NEP1) cells are found to be associated with CIN cases.InterpretationAutomated prediction of genetic pathways and key mutations from image analysis of simple H&E stained sections with a high accuracy can provide time and cost-effective decision support. This work shows that a deep learning algorithm can mine both visually recognizable as well as sub-visual histological patterns associated with molecular pathways and key mutations in CRC in a data-driven manner.FundingThis study was funded by the UK Medical Research Council (award MR/P015476/1).

CRISPR–Cas is an anti-viral mechanism of prokaryotes that has been widely adopted for genome editing. To make CRISPR–Cas genome editing more controllable and safer to use, anti-CRISPR proteins have been recently exploited to prevent excessive/prolonged Cas nuclease cleavage. Anti-CRISPR (Acr) proteins are encoded by (pro)phages/(pro)viruses, and have the ability to inhibit their host's CRISPR–Cas systems. We have built an online database AcrDB (http://bcb.unl.edu/AcrDB) by scanning ∼19 000 genomes of prokaryotes and viruses with AcrFinder, a recently developed Acr-Aca (Acr-associated regulator) operon prediction program. Proteins in Acr-Aca operons were further processed by two machine learning-based programs (AcRanker and PaCRISPR) to obtain numerical scores/ranks. Compared to other anti-CRISPR databases, AcrDB has the following unique features: (i) It is a genome-scale database with the largest collection of data (39 799 Acr-Aca operons containing Aca or Acr homologs); (ii) It offers a user-friendly web interface with various functions for browsing, graphically viewing, searching, and batch downloading Acr-Aca operons; (iii) It focuses on the genomic context of Acr and Aca candidates instead of individual Acr protein family and (iv) It collects data with three independent programs each having a unique data mining algorithm for cross validation. AcrDB will be a valuable resource to the anti-CRISPR research community.

Background: Only a few studies have presented long-term trends in antimicrobial resistance (AMR) at a nationwide level in Pakistan. This study presents a comprehensive situational analysis of AMR trends among pathogens isolated from blood and cerebrospinal fluid (CSF) cultures, between 2011 and 2015, in Pakistan. Methods: A retrospective analysis of AMR data on pathogens isolated from Blood and CSF over a five year period was carried out. Susceptibility data on these pathogens was obtained from Chughtai Laboratory (CL). Then, proportion of the resistant pathogens were calculated and analyzed. Results: Our results show that highest resistance rates against all tested antimicrobials were observed in Acinetobacter species. We observed a steep rise in carbapenem resistant Acinetobacter species from 50 to 95.5% between 2011 and 2015. Our results also highlight the emergence of third and fourth generation cephalosporins resistance in Salmonella enterica serovar Typhi in Pakistan. While we observed a rise in AMR in other major pathogens, we unexpectedly found decreasing resistance trends in Staphylococcus aureus. Conclusions: Taken together, our results show an overall increase in AMR in pathogens isolated from blood and CSF cultures in Pakistan between 2011 and 2015.

The COVID-19, caused by a novel coronavirus, was declared as a global pandemic by WHO more than five months ago, and we are still experiencing a state of global emergency. More than 74.30 million confirmed cases of the COVID-19 have been reported globally so far, with an average fatality rate of almost 3.0%. Seven different types of coronaviruses had been detected from humans; three of them have resulted in severe outbreaks, i.e., MERS-CoV, SARS-CoV, and SARS-CoV-2. Phylogenetic analysis of the genomes suggests that the possible occurrence of recombination between SARS-like-CoVs from pangolin and bat might have led to the origin of SARS-CoV-2 and the COVID-19 outbreak. Coronaviruses are positive-sense, single-stranded RNA viruses and harbour a genome (30 kb) consisting of two terminal untranslated regions and twelve putative functional open reading frames (ORFs), encoding for non-structural and structural proteins. There are sixteen putative non-structural proteins, including proteases, RNA-dependent RNA polymerase, helicase, other proteins involved in the transcription and replication of SARS-CoV-2, and four structural proteins, including spike protein (S), envelope (E), membrane (M), and nucleocapsid (N). SARS-CoV-2 infection, with a heavy viral load in the body, destroys the human lungs through cytokine storm, especially in elderly persons and people with immunosuppressed disorders. A number of drugs have been repurposed and employed, but still, no specific antiviral medicine has been approved by the FDA to treat this disease. This review provides a current status of the COVID-19, epidemiology, an overview of phylogeny, mode of action, diagnosis, and possible treatment methods and vaccines.

Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P. punjabense SS95T, which contains a circular chromosome of 4.793 Mb with a GC content of 50.7%.

The increasing use of CRISPR-Cas9 in medicine, agriculture and synthetic biology has accelerated the drive to discover new CRISPR-Cas inhibitors as potential mechanisms of control for gene editing applications. Many such anti-CRISPRs have been found in mobile genetic elements that disable the CRISPR-Cas adaptive immune system. However, comparing all currently known anti-CRISPRs does not reveal a shared set of properties that can be used for facile bioinformatic identification of new anti-CRISPR families. Here, we describe AcRanker, a machine learning based method for identifying new potential anti-CRISPRs directly from proteomes using protein sequence information only. Using a training set of known anti-CRISPRs, we built a model based on XGBoost ranking and extensively benchmarked it through non-redundant cross-validation and external validation. We then applied AcRanker to predict candidate anti-CRISPRs from self-targeting bacterial genomes and discovered two previously unknown anti-CRISPRs: AcrllA16 (ML1) and AcrIIA17 (ML8). We show that AcrIIA16 strongly inhibits Streptococcus iniae Cas9 (SinCas9) and weakly inhibits Streptococcus pyogenes Cas9 (SpyCas9). We also show that AcrIIA17 inhibits both SpyCas9 and SauCas9 with low potency. The addition of AcRanker to the anti-CRISPR discovery toolkit allows researchers to directly rank potential anti-CRISPR candidate genes for increased speed in testing and validation of new anti-CRISPRs. A web server implementation for AcRanker is available online at http://acranker.pythonanywhere.com/.