Autophagy at the crossroads of catabolism and anabolism.

Autophagy is a conserved catabolic process that degrades cytoplasmic constituents and organelles in the lysosome. Starvation-induced protein degradation is a salient feature of autophagy but recent progress has illuminated how autophagy, during both starvation and nutrient-replete conditions, can mobilize diverse cellular energy and nutrient stores such as lipids, carbohydrates and iron. Processes such as lipophagy, glycophagy and ferritinophagy enable cells to salvage key metabolites to sustain and facilitate core anabolic functions. Here, we discuss the established and emerging roles of autophagy in fuelling biosynthetic capacity and in promoting metabolic and nutrient homeostasis.

In Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium.

The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, ß-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.

Comparative genomics and integrated system biology approach unveiled undirected phylogeny patterns, mutational hotspots, functional patterns, and molecule repurposing for monkeypox virus.

Monkeypox is a viral zoonosis with symptoms that are reminiscent of those experienced in previous smallpox cases. The GSAID database (Global Initiative on Sharing Avian Influenza Data) was used to assess 630 genomes of MPXV. The phylogenetic study revealed six primary clades, as well as a smaller percentage in radiating clades. Individual clades that make up various nationalities may have formed as a result of a particular SNP hotspot type that mutated in a specific population. The most significant mutation based on a mutational hotspot analysis was found at G3729A and G5143A. The gene ORF138, which encodes the Ankyrin repeat (ANK) protein, was found to have the most mutations. This protein mediates molecular recognition via protein-protein interactions. It was shown that 243 host proteins interacted with 10 monkeypox proteins identified as the hub proteins E3, SPI2, C5, K7, E8, G6, N2, B14, CRMB, and A41 through 262 direct connections. The interaction with chemokine system-related proteins provides further evidence that the monkeypox virus suppresses human proteins to facilitate its survival against innate immunity. Several FDA-approved molecules were evaluated as possible inhibitors of F13, a significant envelope protein on the membrane of extracellular versions of the virus. A total of 2500 putative ligands were individually docked with the F13 protein. The interaction between the F13 protein and these molecules may help prevent the monkeypox virus from spreading. After being confirmed by experiments, these putative inhibitors could have an impact on the activity of these proteins and be used in monkeypox treatments.

Atg32-dependent mitophagy sustains spermidine and nitric oxide required for heat-stress tolerance in Saccharomycescerevisiae.

In Saccharomyces cerevisiae, the selective autophagic degradation of mitochondria, termed mitophagy, is critically regulated by the adapter protein Atg32. Despite our knowledge about the molecular mechanisms by which Atg32 controls mitophagy, its physiological roles in yeast survival and fitness remains less clear. Here, we demonstrate a requirement for Atg32 in promoting spermidine production during respiratory growth and heat-induced mitochondrial stress. During respiratory growth, mitophagy-deficient yeast exhibit profound heat-stress induced defects in growth and viability due to impaired biosynthesis of spermidine and its biosynthetic precursor S-adenosyl methionine. Moreover, spermidine production is crucial for the induction of cytoprotective nitric oxide (NO) during heat stress. Hence, the re-addition of spermidine to Atg32 mutant yeast is sufficient to both enhance NO production and restore respiratory growth during heat stress. Our findings uncover a previously unrecognized physiological role for yeast mitophagy in spermidine metabolism and illuminate new interconnections between mitophagy, polyamine biosynthesis and NO signaling.

Phylogenomics-based reclassifications in the genus Psychrobacter including emended descriptions of Psychrobacter pacificensis, Psychrobacter proteolyticus and Psychrobacter submarinus.

The taxonomic status of 43 Psychrobacter species was examined based upon the genome sequences of their type strains. Three groups of type strains were found to be conspecific, Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) and Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450-1455, 2015. 10.1099/ijs.0.000118) and Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835-846, 2000. 10.1099/00207713-50-2-835); and Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44-53, 2001. 10.1078/0723-2020-00006), Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956). For all three groups, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values are > 97.69% and > 80.2%, respectively. This conclusion is supported by similarities in morphology, growth properties, and fatty acid compositions. Based on this evidence, we propose the reclassification of Psychrobacter salsus Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) as a later heterotypic synonym of Psychrobacter submarinus Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291); Psychrobacter oceani Matsuyama et al. (Int J Syst Evol Microbiol 65:1450-1455, 2015. 10.1099/ijs.0.000118) as a later heterotypic synonym of Psychrobacter pacificensis Maruyama et al. (Int J Syst Evol Microbiol 50:835-846, 2000. 10.1099/00207713-50-2-835), and Psychrobacter marincola Romanenko et al. (Int J Syst Evol Microbiol 52:1291-1297, 2002. 10.1099/00207713-52-4-1291) and Psychrobacter adeliensis Shivaji et al. (Syst Appl Microbiol 27:628-635, 2004. 10.1078/0723202042369956) as later heterotypic synonyms of Psychrobacter proteolyticus Denner et al. (Syst Appl Microbiol 24:44-53, 2001. 10.1078/0723-2020-00006).

Microbial Journey: Mount Everest to Mars.

A rigorous exploration of microbial diversity has revealed its presence on Earth, deep oceans, and vast space. The presence of microbial life in diverse environmental conditions, ranging from moderate to extreme temperature, pH, salinity, oxygen, radiations, and altitudes, has provided the necessary impetus to search for them by extending the limits of their habitats. Microbiology started as a distinct science in the mid-nineteenth century and has provided inputs for the betterment of mankind during the last 150 years. As beneficial microbes are assets and pathogens are detrimental, studying both have its own merits. Scientists are nowadays working on illustrating the microbial dynamics in Earth's subsurface, deep sea, and polar regions. In addition to studying the role of microbes in the environment, the microbe-host interactions in humans, animals and plants are also unearthing newer insights that can help us to improve the health of the host by modulating the microbiota. Microbes have the potential to remediate persistent organic pollutants. Antimicrobial resistance which is a serious concern can also be tackled only after monitoring the spread of resistant microbes using disciplines of genomics and metagenomics The cognizance of microbiology has reached the top of the world. Space Missions are now looking for signs of life on the planets (specifically Mars), the Moon and beyond them. Among the most potent pieces of evidence to support the existence of life is to look for microbial, plant, and animal fossils. There is also an urgent need to deliberate and communicate these findings to layman and policymakers that would help them to take an adequate decision for better health and the environment around us. Here, we present a glimpse of recent advancements by scientists from around the world, exploring and exploiting microbial diversity.

Yeast strain Debaryomyces hansenii for amelioration of arsenic stress in rice.

Arsenic (As) is a serious threat for environment and human health. Rice, the main staple crop is more prone to As uptake. Bioremediation strategies with heavy metal tolerant rhizobacteria are well known. The main objective of the study was to characterize arsenic-resistant yeast strains, capable of mitigating arsenic stress in rice. Three yeast strains identified as Debaryomyces hansenii (NBRI-Sh2.11), Candida tropicalis (NBRI-B3.4) and Candida dubliniensis (NBRI-3.5) were found to have As reductase activity. D. hansenii with higher As tolerance has As expulsion ability as compared to other two strains. Inoculation of D. hansenii showed improved detoxification through scavenging of reactive oxygen species (ROS) by the modulation of SOD and APX activity under As stress condition in rice. Modulation of defense responsive gene (NADPH, GST, GR) along with arsR and metal cation transporter are the probable mechanism of As detoxification as evident with improved membrane (electrolyte leakage) stability. Reduced grain As (~40% reduction) due to interaction with D. hansenii (NBRI-Sh2.11) further validated it's As mitigation property in rice. To the best of our knowledge D. hansenii has been reported for the first time for arsenic stress mitigation in rice with improved growth and nutrient status of the plant.

Determination of Immediate-loaded Single Implants' Stability with Periotest.

AIM AND OBJECTIVE: The aim of this study was to determine the stability of immediate-loaded single implants with periotest. MATERIALS AND METHODS: In this in vivo study, dental implants with a length ranging from 10 to 13 mm and diameter of 3.0-4.2 mm were utilized. Stability of dental implant was evaluated using the Periotest® M handheld device before loading, at 1 month, 3 months, 6 months, and 1 year. RESULTS: Implants 11.5 mm in length had the highest mean periotest value (0) after placement, whereas 10 mm-long implant had a value of -0.31 and 13 mm had a value of -0.48. After 1 month, 10 mm had a value of 1.23, 11.5 mm had a value of -0.32, and 13.0 mm had a value of -0.24. After 6 months, 10 mm had a value of 1.78, 11.5 mm had a value of -0.4, and 13.0 mm had a value of -0.41. After 1 year, 10 mm had a value of -0.54, 11.5 mm had a value of -0.51, and 13.0 mm had a value of -0.48. There was an unconstructive relationship between implant length and the average periotest score. There was also an unconstructive association between the implant diameter and the mean periotest value. CONCLUSION: The implant with long and greatest diameter had higher stability. Periotest can be used to determine dental implant stability. CLINICAL SIGNIFICANCE: Periotest is useful in determining dental implant stability. Large-scale studies may be helpful in obtaining useful results.

Assessment of Various Dental Occupational Hazards and Safety Measures among Dentists of Odisha, India.

AIM AND OBJECTIVE: Dental professionals are more prone to get exposed to various occupational health problems. The aim is to assess various dental occupational hazards and safety measures among dentists of Odisha, India. MATERIALS AND METHODS: The present study was conducted among 572 dental professionals of both genders. A self-administered questionnaire which comprises name, age, gender, number of years of experience, type of occupational hazard, awareness of occupational hazards, safety measures practiced, and working hours per week was given to dental professionals and the responses were recorded. RESULTS: 545 (95.2%) dentists were responded out of 572 participants. Age group 20-40 years had 55 males and 24 females, 40-60 years had 154 males and 84 females, and >60 years had 116 males and 60 females. 220 dentists had 10-15 years of experience, 190 had 5-10 years, 60 had <5 years, 40 had 15-20 years, and 35 had >20 years. The difference was significant (p < 0.05). The most common occupational hazard was musculoskeletal disorders seen in 480 (88%), stress in 273 (50%); maximum occupational hazard (52%) was noticed in dentists with <5 years of working experience; proper safety protocols adopted by dentists were the use of sterilized instruments 99%, gloves 98%, face mask 82%, vaccination against hepatitis 54%, head cap 51%, eyewear 12.6%, and proper waste disposal 7%. The difference was significant (p < 0.05). CONCLUSION: The chances of occupational hazards are more common in dentists. The prevalence was higher among dentists with less than 5 years of experience. CLINICAL SIGNIFICANCE: Knowledge and awareness about occupational hazards can help prevent complications due to occupational hazards in dental practice.

Safety tent for enhanced personal protection from aerosol-generating procedures while handling the COVID-19 patient airway.

The world is going through the COVID-19 pandemic, which has high virulence and transmission rate. More significant the viral load during exposure, the greater is the likelihood of contracting a severe disease. Healthcare workers (HCWs) involved in airway care of COVID-19 patients are at high risk of getting exposed to large viral loads during aerosol-generating actions such as coughing or sneezing by the patient or during procedures such as bag-mask ventilation, intubation, extubation, and nebulization. This viral load exposure to airway caregivers decreases considerably with the use of an aerosol box during intubation. The safety tent proposed in this article is useful in limiting the viral load that HCWs are exposed to during airway procedures. Its role can be expanded beyond just intubation to protect against all aerosol-generating actions and procedures involving the patient's airway.

Practical approach for safe anesthesia in a COVID-19 patient scheduled for emergency laparotomy.

COVID-19 patients presenting for emergency laparotomy require evaluation of surgical illness and viral disease. As these patients are likely to have a wide spectrum of deranged physiology and organ dysfunction, optimization should start preoperatively and continue through intraoperative and postoperative recovery periods along with appropriate antimicrobial cover. The goal should be not to delay damage control surgery in favor of evaluation and optimization. When a COVID-19 positive or suspected patient is to be operated for laparotomy, the situation often demands general anesthesia with invasive monitoring and analgesia complemented by regional anesthesia to minimize postoperative opioid requirements to facilitate early recovery. This particular article addresses the issues related to emergency laparotomy management in relation to COVID-19 patient. Healthcare workers should diligently use effective PPE and practice disinfection to prevent spread. Video-communication is an effective means of evaluation. Information expected from investigations should be weighed against risk of exposure to healthcare workers/laypersons. Simulation and memory aids should be used to familiarize team members with roles and techniques of management while in PPE. Step-wise detailed planning for patient transfer, anesthesia induction, maintenance and emergence, aid in enhancing HCW safety without compromising patient care.

Constrictive pericarditis following necrotising pneumococcal pneumonia in an immunocompetent child.

Purulent pericarditis leading to constrictive pericarditis is a rare but serious complication following invasive pneumococcal infection. Early recognition of this complication is crucial to prevent mortality. Here, we report a previously healthy child who developed constrictive pericarditis due to purulent pericarditis following necrotising pneumococcal pneumonia, which is not common in this current antibiotic and pneumococcal vaccine era. The child was successfully treated with pericardiectomy.

Ratio of height-to-thyromental distance and ratio of height-to-sternomental distance as predictors of laryngoscopic grade in children.

BACKGROUND AND AIMS: Failure to secure the airway is an important cause of morbidity and mortality in children. Children are often uncooperative for routine examination and pose problems for obtaining external measurements. We aimed to evaluate ratio of height-to-thyromental distance (RHTMD) and ratio of height-to-sternomental distance (RHSMD) as predictors of laryngoscopic grade in children aged 1-12 years. MATERIAL AND METHODS: This study was an observational study conducted in children aged between 1 and 12 years scheduled for elective surgery under general anesthesia. Children unable to stand, having limited mouth opening/neck mobility, cleft palate or with midline neck masses were excluded. Weight, height, and thyromental and sternomental distances were measured preoperatively. Following induction of anesthesia and full-muscle relaxation, laryngoscopy was performed and Cormack-Lehane view with Cook's modification was noted. Receiver operating characteristic (ROC) curve analysis using RHTMD and RHSMD was performed for predicting poor laryngoscopic view. RESULTS: A total of 138 children with mean age of 6.6 ± 3.4, RHTMD of 17.7 ± 2.1, and RHSMD of 10.0 ± 1.0 were included. No Grade 3 or 4 laryngoscopic views were obtained. ROC curve analysis was done for predicting 2b view (restricted), incidence of which was 10.1%. RHTMD was a better predictor of 2b laryngoscopic view with an area under curve (AUC) of 0.792 compared to RHSMD (AUC = 0.463). CONCLUSIONS: In children aged 1-12 years, RHTMD is a better predictor of restricted view compared to RHSMD.

Laboratory and field scale bioremediation of hexachlorocyclohexane (HCH) contaminated soils by means of bioaugmentation and biostimulation.

Hexachlorocyclohexane (HCH) contaminated soils were treated for a period of up to 64 days in situ (HCH dumpsite, Lucknow) and ex situ (University of Delhi) in line with three bioremediation approaches. The first approach, biostimulation, involved addition of ammonium phosphate and molasses, while the second approach, bioaugmentation, involved addition of a microbial consortium consisting of a group of HCH-degrading sphingomonads that were isolated from HCH contaminated sites. The third approach involved a combination of biostimulation and bioaugmentation. The efficiency of the consortium was investigated in laboratory scale experiments, in a pot scale study, and in a full-scale field trial. It turned out that the approach of combining biostimulation and bioaugmentation was most effective in achieving reduction in the levels of α- and ß-HCH and that the application of a bacterial consortium as compared to the action of a single HCH-degrading bacterial strain was more successful. Although further degradation of ß- and δ-tetrachlorocyclohexane-1,4-diol, the terminal metabolites of ß- and δ-HCH, respectively, did not occur by the strains comprising the consortium, these metabolites turned out to be less toxic than the parental HCH isomers.

Functional screening of enzymes and bacteria for the dechlorination of hexachlorocyclohexane by a high-throughput colorimetric assay.

Two distinct microbial dehalogenases are involved in the first steps of degradation of hexachlorocyclohexane (HCH) isomers. The enzymes, LinA and LinB, catalyze dehydrochlorination and dechlorination reactions of HCH respectively, each with distinct isomer specificities. The two enzymes hold great promise for use in the bioremediation of HCH residues in contaminated soils, although their kinetics and isomer specificities are currently limiting. Here we report the functional screening of a library of 700 LinA and LinB clones generated from soil DNA for improved dechlorination activity by means of a high throughput colorimetric assay. The assay relies upon visual colour change of phenol red in an aqueous medium, due to the pH drop associated with the dechlorination reactions. The assay is performed in a microplate format using intact cells, making it quick and simple to perform and it has high sensitivity, dynamic range and reproducibility. The method has been validated with quantitative gas chromatographic analysis of promising clones, revealing some novel variants of both enzymes with superior HCH degrading activities. Some sphingomonad isolates with potentially superior activities were also identified.

Challenges in management of blast injuries in Intensive Care Unit: Case series and review.

Blast injuries are rare, but life-threatening medical emergencies. We report the clinical presentation and management of four bomb blast victims admitted in Intensive Care Unit of Trauma center of our hospital in 2011. Three of them had lung injury; hemothorax (2) and pneumothorax (1). Traumatic brain injury was present in only one. Long bone fractures were present in all the victims. Presence of multiple shrapnels was a universal finding. Two blast victims died (day 7 and day 9); cause of death was multi-organ failure and septic shock. Issues relating to complexity of injuries, complications, management, and outcome are discussed.

Comparative genomics of seven genomes of genus Idiomarina reveals important halo adaptations and genes for stress response.

The genus Idiomarina consists of halophilic and/or haloalkaliphilic organisms. We compared the complete genomes of seven strains of the genus Idiomarina to investigate its adaptation to saline environment. A total of 1,313 core genes related to salinity tolerance, stress response, antibiotic resistance genes, virulence factors, and drug targets were found. Comparative genomics revealed various genes involved in halo adaptations of these organisms, including transporters and influx or efflux systems for elements such as Fe, Cu, Zn, Pb, and Cd. In agreement with their isolation sources (such as hydrothermal vents and marine sediments) and environments abundant in heavy metals, various resistance proteins and transporters associated with metal tolerance were also identified. These included copper resistance proteins, zinc uptake transcriptional repressor Zur, MerC domain-containing protein, Cd(II)/Pb(II)-responsive transcriptional regulator, Co/Zn/Cd efflux system protein, and mercuric transporter. Interestingly, we observed that the carbohydrate metabolism pathways were incomplete in all the strains and transporters used for absorption of small sugars were also not found in them. Also, the presence of higher proportion of genes involved in protein metabolism than carbohydrate metabolism indicates that proteinaceous substrates act as the major food substrates for these bacterial strains than carbohydrates. Genomic islands were detected in some species, highlighting the role of horizontal gene transfer for acquisition in novel genes. Genomic rearrangements in terms of partially palindromic regions were detected in all strains. To our knowledge, this is the first comprehensive comparative genomics study among the genus Idiomarina revealing unique genomic features within bacterial species inhabiting different ecological niches. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03887-3.

Integrated genome-transcriptome analysis unveiled the mechanism of Debaryomyces hansenii-mediated arsenic stress amelioration in rice.

Globally, rice is becoming more vulnerable to arsenic (As) pollution, posing a serious threat to public food safety. Previously Debaryomyces hansenii was found to reduce grain As content of rice. To better understand the underlying mechanism, we performed a genome analysis to identify the key genes in D. hansenii responsible for As tolerance and plant growth promotion. Notably, genes related to As resistance (ARR, Ycf1, and Yap) were observed in the genome of D. hansenii. The presence of auxin pathway and glutathione metabolism-related genes may explain the plant growth-promoting potential and As tolerance mechanism of this novel yeast strain. The genome annotation of D. hansenii indicated that it contains a repertoire of genes encoding antioxidants, well corroborated with the in vitro studies of GST, GR, and glutathione content. In addition, the effect of D. hansenii on gene expression profiling of rice plants under As stress was also examined. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed 307 genes, annotated in D. hansenii-treated rice, related to metabolic pathways (184), photosynthesis (12), glutathione (10), tryptophan (4), and biosynthesis of secondary metabolite (117). Higher expression of regulatory elements like AUX/IAA and WRKY transcription factors (TFs), and defense-responsive genes dismutases, catalases, peroxiredoxin, and glutaredoxins during D. hansenii+As exposure was also observed. Combined analysis revealed that D. hansenii genes are contributing to stress mitigation in rice by supporting plant growth and As-tolerance. The study lays the foundation to develop yeast as a beneficial biofertilizer for As-prone areas.