Isolation and Taxonomic Characterization of Novel Haloarchaeal Isolates From Indian Solar Saltern: A Brief Review on Distribution of Bacteriorhodopsins and V-Type ATPases in Haloarchaea

Haloarchaea inhabit high salinity environments worldwide. They are a potentially rich source of crucial biomolecules like carotenoids and industrially useful proteins. However, diversity in haloarchaea present in Indian high salinity environments is poorly studied. In the present study, we isolated 12 haloarchaeal strains from hypersaline Kottakuppam, Tamil Nadu solar saltern in India. 16S rRNA based taxonomic characterization of these isolates suggested that nine of them are novel strains that belong to genera Haloarcula, Halomicrobium, and Haloferax. Transmission electron microscopy suggests the polymorphic nature of these haloarchaeal isolates. Most of the haloarchaeal species are known to be high producers of carotenoids. We were able to isolate carotenoids from all these 12 isolates. The UV-Vis spectroscopy-based analysis suggests that bacterioruberin and lycopene are the major carotenoids produced by these isolates. Based on the visual inspection of the purified carotenoids, the isolates were classified into two broad categories i.e., yellow and orange, attributed to the differences in the ratio of bacterioruberin and lycopene as confirmed by the UV-Vis spectral analysis. Using a PCR-based screening assay, we were able to detect the presence of the bacteriorhodopsin gene (bop) in 11 isolates. We performed whole-genome sequencing for three bop positive and one bop negative haloarchaeal isolates. Whole-genome sequencing, followed by pan-genome analysis identified multiple unique genes involved in various biological functions. We also successfully cloned, expressed, and purified functional recombinant bacteriorhodopsin (BR) from one of the isolates using Escherichia coli as an expression host. BR has light-driven proton pumping activity resulting in the proton gradient across the membrane, which is utilized by V-Type ATPases to produce ATP. We analyzed the distribution of bop and other accessory genes involved in functional BR expression and ATP synthesis in all the representative haloarchaeal species. Our bioinformatics-based analysis of all the sequenced members of genus Haloarcula suggests that bop, if present, is usually inserted between the genes coding for B and D subunits of the V-type ATPases operon. This study provides new insights into the genomic variations in haloarchaea and reports expression of new BR variant having good expression in functional form in E. coli

Atrasentan and renal events in patients with type 2 diabetes and chronic kidney disease (SONAR): a double-blind, randomised, placebo-controlled trial

Background: Short-term treatment for people with type 2 diabetes using a low dose of the selective endothelin A receptor antagonist atrasentan reduces albuminuria without causing significant sodium retention. We report the long-term effects of treatment with atrasentan on major renal outcomes. Methods: We did this double-blind, randomised, placebo-controlled trial at 689 sites in 41 countries. We enrolled adults aged 18–85 years with type 2 diabetes, estimated glomerular filtration rate (eGFR)25–75 mL/min per 1·73 m 2 of body surface area, and a urine albumin-to-creatinine ratio (UACR)of 300–5000 mg/g who had received maximum labelled or tolerated renin–angiotensin system inhibition for at least 4 weeks. Participants were given atrasentan 0·75 mg orally daily during an enrichment period before random group assignment. Those with a UACR decrease of at least 30% with no substantial fluid retention during the enrichment period (responders)were included in the double-blind treatment period. Responders were randomly assigned to receive either atrasentan 0·75 mg orally daily or placebo. All patients and investigators were masked to treatment assignment. The primary endpoint was a composite of doubling of serum creatinine (sustained for ≥30 days)or end-stage kidney disease (eGFR <15 mL/min per 1·73 m 2 sustained for ≥90 days, chronic dialysis for ≥90 days, kidney transplantation, or death from kidney failure)in the intention-to-treat population of all responders. Safety was assessed in all patients who received at least one dose of their assigned study treatment. The study is registered with ClinicalTrials.gov, number NCT01858532. Findings: Between May 17, 2013, and July 13, 2017, 11 087 patients were screened; 5117 entered the enrichment period, and 4711 completed the enrichment period. Of these, 2648 patients were responders and were randomly assigned to the atrasentan group (n=1325)or placebo group (n=1323). Median follow-up was 2·2 years (IQR 1·4–2·9). 79 (6·0%)of 1325 patients in the atrasentan group and 105 (7·9%)of 1323 in the placebo group had a primary composite renal endpoint event (hazard ratio [HR]0·65 [95% CI 0·49–0·88]; p=0·0047). Fluid retention and anaemia adverse events, which have been previously attributed to endothelin receptor antagonists, were more frequent in the atrasentan group than in the placebo group. Hospital admission for heart failure occurred in 47 (3·5%)of 1325 patients in the atrasentan group and 34 (2·6%)of 1323 patients in the placebo group (HR 1·33 [95% CI 0·85–2·07]; p=0·208). 58 (4·4%)patients in the atrasentan group and 52 (3·9%)in the placebo group died (HR 1·09 [95% CI 0·75–1·59]; p=0·65). Interpretation: Atrasentan reduced the risk of renal events in patients with diabetes and chronic kidney disease who were selected to optimise efficacy and safety. These data support a potential role for selective endothelin receptor antagonists in protecting renal function in patients with type 2 diabetes at high risk of developing end-stage kidney disease. Funding: AbbVie

Patronus1 is expressed in meiotic prophase i to regulate centromeric cohesion in arabidopsis and shows synthetic lethality with osd1

Background: Retention of sister centromere cohesion during meiosis I and its dissolution at meiosis II is necessary for balanced chromosome segregation and reduction of chromosome number. PATRONUS1 (PANS1) has recently been proposed to regulate centromere cohesion in Arabidopsis after meiosis I, during interkinesis. pans1 mutants lose centromere cohesion prematurely during interkinesis and segregate randomly at meiosis II. PANS1 protein interacts with components of the Anaphase Promoting Complex/Cyclosome (APC/C). Results: We show here that PANS1 protein is found mainly in prophase I of meiosis, with its level declining late in prophase I during diplotene. PANS1 also shows expression in dividing tissues. We demonstrate that, in addition to the previously reported premature loss of centromere cohesion during interkinesis, pans1 mutants show partially penetrant defects in centromere cohesion during meiosis I. We also determine that pans1 shows synthetic lethality at the level of the sporophyte, with Omission of Second Division 1 (osd1), which encodes a known inhibitor of the APC/C that is required for cell cycle progression during mitosis, as well as meiosis I and II. Conclusions: Our results show that PANS1 is expressed mainly in meiosis I where it has an important function and together with previous studies indicate that PANS1 and OSD1 are part of a network linking centromere cohesion and cell cycle progression through control of APC/C activity

COVID-19 is associated with a high prevalence of Liver Damage: A Systematic Review and Meta-Analysis : COVID-19 and liver damage

Introduction: The Coronavirus Disease 2019 (COVID-19) outbreak is a serious threat to humans, and the impact of COVID-19 on the liver remains unexplored. At present, no meta-analysis has summarized available findings of COVID-19 patients with liver injury in depth. Thus, we aimed to scrutinize the association of the liver in COVID-19 patients and approximate the prognosis of COVID-19 patients with liver injury thoroughly.   Method: We searched different databases for qualified studies between December 2019 to May 2021. Finally, meta-analysis was carried out using fixed-effect or random-effect models based on the heterogeneity.   Result: Our Meta-analysis includes 32 studies with a total of 6,933 COVID-19 patients. The pooled prevalence of chronic liver disease (CLD) was 3.5%. Overall, the rates of severity and mortality in COVID-19 patients with underlying CLD were 4.6% and 19.2%, respectively. Additionally, the incidence of acute on chronic failure (ACLF) among COVID-19 patients with CLD was 25.1%. The prevalence of an increase in serum ALT, AST, TBil, and LDH levels was 39.5%, 28.6%, 26.5%, and 55.5%, respectively. Similarly, PT was prolonged in 8.3% of cases, and albumin was decreased in 66.8% of cases. The pooled prevalence of liver injury among COVID-19 patients was 28.2%. Strikingly, the patients with liver injury had significantly more severe disease (42.3%) and a higher incidence of mortality (18.5%) than the patients without liver injury.   Conclusion: In conclusion, more than one in five of the COVID-19 patients is at risk of developing a liver injury. Further, patients with liver injury have significantly more severe disease and a higher incidence of mortality than patients without liver injury. Thus, careful monitoring of liver function is advisable while treating COVID-19 patients

Piriformospora indica: a Friend in Need is a Friend in Deed

Piriformospora indica is an endophytic root-colonizing fungal species classified in the genus Piriformospora of the order Sebacinales. The chlamydospores of P. indica has a typical pear-shape and it was first discovered from the orchid plants in the Thar desert in Rajasthan, India and thus named P. indica P. indica has shown to be very versatile as it is capable of colonizing a variety of different plants, but the research studies has been done so far to understand molecular mechanisms underlying symbiosis has basically on the agronomical important monocotyledonous crop plant barley (Hordeum vulgare) and the dicotyledonous genetic model plant Arabidopsis thalian

Interobserver reproducibility of RENAL nephrometry score in comparison to simplified PADUA Renal nephrometry score

Introduction: Nephron-sparing surgery (NSS) is the standard of care for renal tumors, especially in the early stages. RENAL Nephrometry scores provide a comprehensive presurgical predictive module for the choice of NSS or Radical Nephrectomy. The validity and reliability of Nephrometry scores is being tested continuously with advancement in the surgical techniques. The Simplified PADUA Nephrometry score (SPARE NS) is a newer proposed score which aims to better the reproducibility of the previously established nephrometry scores. Materials and Methods: The retrospective observational study studied the comparative inter-observer reliability of RENAL (RENAL NS) and SPARE nephrometry scoring systems amongst two radiologists while assessing solid renal tumors in contrast-enhanced computed tomography scans of 42 patients. Interobserver reliability for all components of both scores, final scores and risk grading was done by Kendall's Concordance Coefficient (Tau). Results: Both RENAL NS and SPARE NS showed strong to excellent agreement (RENAL NS = 78.57% and SPARE NS = 88.09%) among observers with comparable correlation co-efficient (RENAL NS = 0.944 and SPARE NS = 0.935). Lesion radius and exophytic/endophytic properties were the most reproducible components of RENAL NS with 97.61% and 92.85% agreement, respectively. Location across polar lines was the least reproducible component with 85.71% agreement among observers. Exophytic rate (97.61%) and Rim location were the most reproducible components of SPARE NS. The final lesion risk stratification by both observers for both was concordant in 92.85% of cases. Conclusion: The SPARE system of scoring matches up to the RENAL NS in total score and risk stratification reproducibility. However, the individual components of the SPARE score are more reproducible than those of RENAL NS, bringing about better compliance among radiology consultants. Comparable reproducibility with the RENAL NS, lesser number of variables, and ease of doing make SPARE NS a plausible option for the customary preoperative assessment of renal tumors

The FANCC–FANCE–FANCF complex is evolutionarily conserved and regulates meiotic recombination

At meiosis, programmed meiotic DNA double-strand breaks are repaired via homologous recombination, resulting in crossovers (COs). From a large excess of DNA double-strand breaks that are formed, only a small proportion gets converted into COs because of active mechanisms that restrict CO formation. The Fanconi anemia (FA) complex proteins AtFANCM, MHF1 and MHF2 were previously identified in a genetic screen as anti-CO factors that function during meiosis in Arabidopsis thaliana. Here, pursuing the same screen, we identify FANCC as a new anti-CO gene. FANCC was previously only identified in mammals because of low primary sequence conservation. We show that FANCC, and its physical interaction with FANCE-FANCF, is conserved from vertebrates to plants. Further, we show that FANCC, together with its subcomplex partners FANCE and FANCF, regulates meiotic recombination. Mutations of any of these three genes partially rescues CO-defective mutants, which is particularly marked in female meiosis. Functional loss of FANCC, FANCE, or FANCF results in synthetic meiotic catastrophe with the pro-CO factor MUS81. This work reveals that FANCC is conserved outside mammals and has an anti-CO role during meiosis together with FANCE and FANCF. Plain language summary The Fanconi Anemia (FA) pathway is the subject of intense interest owing to the role of FA as a tumor suppressor. Three FA complex proteins, FANCM, MHF1 and MHF2, were identified as factors that suppress crossover during meiosis in the model plant Arabidopsis thaliana. Here, the authors extended these findings and identified a novel anti-crossover factor and showed that it encodes the plant FANCC homolog, which was previously thought to be vertebrate-specific. They further showed that FANCC regulates meiotic crossover together with two other FA proteins, FANCE and FANCF. This suggests that the FANCC–E–F subcomplex was already regulating DNA repair in the common ancestor of all living eukaryotes

A translation proofreader of archaeal origin imparts multi-aldehyde stress tolerance to land plants

Aldehydes, being an integral part of carbon metabolism, energy generation, and signalling pathways, are ingrained in plant physiology. Land plants have developed intricate metabolic pathways which involve production of reactive aldehydes and its detoxification to survive harsh terrestrial environments. Here, we show that physiologically produced aldehydes, i.e., formaldehyde and methylglyoxal in addition to acetaldehyde, generate adducts with aminoacyl-tRNAs, a substrate for protein synthesis. Plants are unique in possessing two distinct chiral proofreading systems, D-aminoacyl-tRNA deacylase1 (DTD1) and DTD2, of bacterial and archaeal origins, respectively. Extensive biochemical analysis revealed that only archaeal DTD2 can remove the stable D-aminoacyl adducts on tRNA thereby shielding archaea and plants from these system-generated aldehydes. Using Arabidopsis as a model system, we have shown that the loss of DTD2 gene renders plants susceptible to these toxic aldehydes as they generate stable alkyl modification on D-aminoacyl-tRNAs, which are recycled only by DTD2. Bioinformatic analysis identifies the expansion of aldehyde metabolising repertoire in land plant ancestors which strongly correlates with the recruitment of archaeal DTD2. Finally, we demonstrate that the overexpression of DTD2 offers better protection against aldehydes than in wild type Arabidopsis highlighting its role as a multi-aldehyde detoxifier that can be explored as a transgenic crop development strategy