Insights into the radiation and oxidative stress mechanisms in genus Deinococcus.

Deinococcus species, noted for their exceptional resistance to DNA-damaging environmental stresses, have piqued scientists' interest for decades. This study dives into the complex mechanisms underpinning radiation resistance in the Deinococcus genus. We have examined the genomes of 82 Deinococcus species and classified radiation-resistance proteins manually into five unique curated categories: DNA repair, oxidative stress defense, Ddr and Ppr proteins, regulatory proteins, and miscellaneous resistance components. This classification reveals important information about the various molecular mechanisms used by these extremophiles which have been less explored so far. We also investigated the presence or lack of these proteins in the context of phylogenetic relationships, core, and pan-genomes, which offered light on the evolutionary dynamics of radiation resistance. This comprehensive study provides a deeper understanding of the genetic underpinnings of radiation resistance in the Deinococcus genus, with potential implications for understanding similar mechanisms in other organisms using an interactomics approach. Finally, this study reveals the complexities of radiation resistance mechanisms, providing a comprehensive understanding of the genetic components that allow Deinococcus species to flourish under harsh environments. The findings add to our understanding of the larger spectrum of stress adaption techniques in bacteria and may have applications in sectors ranging from biotechnology to environmental research.

Microplastics in the soil-water-food nexus: Inclusive insight into global research findings.

Nuisance imposed by biotic and abiotic stressors on diverse agroecosystems remains an area of focus for the scientific fraternity. However, emerging contaminants such as microplastics (MP) have imposed additional dimension (alone or in combinations with other stressors) in agroecosystems and keep escalating the challenges to achieve sustainability. MP are recognized as persistent anthropogenic contaminants, fetch global attention due to their unique chemical features that keeps themselves unresponsive to the decaying process. This review has been theorized to assess the current research trends (along with possible gap areas), widespread use of MP, enhancement of the harshness of heavy metals (HMs), complex interactions with physico-chemical constituents of arable soil, accumulation in the edible parts of field crops, dairy products, and other sources to penetrate the food web. So far, the available review articles are oriented to a certain aspect of MP and lack a totality when considered from in soil-water-food perspective. In short, a comprehensive perspective of the adverse effects of MP on human health has been assessed. Moreover, an agro-techno-socio-health prospective-oriented critical assessment of policies and remedial measures linked with MP has provided an extra edge over other similar articles in influential future courses of research.

From waste management to circular economy: Leveraging thermophiles for sustainable growth and global resource optimization.

Waste of any origin is one of the most serious global and man-made concerns of our day. It causes climate change, environmental degradation, and human health problems. Proper waste management practices, including waste reduction, safe handling, and appropriate treatment, are essential to mitigate these consequences. It is thus essential to implement effective waste management strategies that reduce waste at the source, promote recycling and reuse, and safely dispose of waste. Transitioning to a circular economy with policies involving governments, industries, and individuals is essential for sustainable growth and waste management. The review focuses on diverse kinds of environmental waste sources around the world, such as residential, industrial, commercial, municipal services, electronic wastes, wastewater sewerage, and agricultural wastes, and their challenges in efficiently valorizing them into useful products. It highlights the need for rational waste management, circularity, and sustainable growth, and the potential of a circular economy to address these challenges. The article has explored the role of thermophilic microbes in the bioremediation of waste. Thermophiles known for their thermostability and thermostable enzymes, have emerged to have diverse applications in biotechnology and various industrial processes. Several approaches have been explored to unlock the potential of thermophiles in achieving the objective of establishing a zero-carbon sustainable bio-economy and minimizing waste generation. Various thermophiles have demonstrated substantial potential in addressing different waste challenges. The review findings affirm that thermophilic microbes have emerged as pivotal and indispensable candidates for harnessing and valorizing a range of environmental wastes into valuable products, thereby fostering the bio-circular economy.

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.

Temperature - A critical abiotic paradigm that governs bacterial heterogeneity in natural ecological system.

A baseline data has been presented here to prove that among the abiotic factors, temperature is the most critical factor that regulates and governs the bacterial diversity in a natural ecosystem. Present study in Yumesamdong hot springs riverine vicinity (Sikkim), parades a gamut of bacterial communities in it and hosts them from semi-frigid region (- 4-10 °C) to fervid region (50-60 °C) via an intermediate region (25-37 °C) within the same ecosystem. This is an extremely rare intriguing natural ecosystem that has no anthropogenic disturbances nor any artificial regulation of temperature. We scanned the bacterial flora through both the culture-dependent and culture-independent techniques in this naturally complex thermally graded habitat. High-throughput sequencing gave bacterial and archaeal phyla representatives of over 2000 species showcasing their biodiversity. Proteobacteria, Firmicutes, Bacteroidetes and Chloroflexi were the predominant phyla. A concave down-curve significance was found in temperature-abundance correlation as the number of microbial taxa decreased when the temperature increased from warm (35 °C) to hot (60 °C). Firmicutes showed significant linear increase from cold to hot environment whereas Proteobacteria followed the opposite trend. No significant correlation was observed for physicochemical parameters against the bacterial diversity. However, only temperature has shown significant positive correlation to the predominant phyla at their respective thermal gradients. The antibiotic resistance patterns correlated with temperature gradient where the prevalence of antibiotic resistance was higher in case of mesophiles than that of psychrophiles and there was no resistance in thermophiles. The antibiotic resistant genes obtained were solely from mesophiles as it conferred high resistance at mesophilic conditions enabling them to adapt and metabolically compete for survival. Our study concludes that the temperature is a major factor that plays a significant contribution in shaping the bacterial community structure in any thermal gradient edifice.

First report on metagenomics and their predictive functional analysis of fermented bamboo shoot food of Tripura, North East India.

Moiya pansung, mileye amileye, moiya koshak, and midukeye are naturally fermented bamboo shoot foods of Tripura. The present study aimed to reveal the whole microbial community structure of naturally fermented moiya pangsung, mileye amileye, moiya koshak, and midukeye along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. The metataxonomic profile of moiya pangsung, mileye amileye, moiya koshak, and midukeye samples showed different domains, viz., bacteria (97.70%) followed by the virus (0.76%), unclassified (0.09%), eukaryotes (1.46%) and archaea (0.05%). Overall, 49 phyla, 409 families, 841 genera, and 1,799 species were found in all the fermented bamboo shoot samples collected from different places of Tripura. Firmicutes was the most abundant phylum (89.28%) followed by Proteobacteria (5.13%), Bacteroidetes (4.38%), Actinobacteria (1.02%), and Fusobacteria (0.17%). Lactiplantibacillus plantarum was the most abundant species in moiya pangsung, mileye amileye, moiya koshak, and midukeye followed by Lactococcus lactis, Levilactobacillus brevis, Leuconostoc mesenteroides, Weissella paramesenteroides, Leuconostoc kimchii, Pediococcus pentosaceus, Leuconostoc gasicomitatum, and Lacticaseibacillus casei. A few phyla of fungus were found, viz., Ascomycota, Basidiomycota, and Glomeromycota, where Ascomycota was present in high abundance. Functional analysis of moiya pangsung, mileye amileye, moiya koshak, and midukeye metagenome revealed the genes for the synthesis and metabolism of a wide range of bioactive compounds including, various essential amino acids, and conjugated amino acids. The abundance profile and predictive analysis of fermented bamboo shoots revealed a huge plethora of essential microorganisms and KEGG analysis revealed genes for amino acid metabolism, pectin degradation, lipid metabolism, and many other essential pathways that can be essential for the improvement of nutritional and sensory qualities of the fermented bamboo shoot products.

Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity.

Here we present the construction and characterization of metagenome assembled genomes (MAGs) from two hot springs residing in the vicinity of Indian Himalayan Geothermal Belt (IHGB). A total of 78 and 7 taxonomic bins were obtained for Old Yume Samdong (OYS) and New Yume Samdong (NYS) hot springs respectively. After passing all the criteria only 21 and 4 MAGs were further studied based on the successful prediction of their 16 S rRNA. Various databases were used such as GTDB, Kaiju, EzTaxon, BLAST XY Plot and NCBI BLAST to get the taxonomic classification of various 16 S rRNA predicted MAGs. The bacterial genomes found were from both thermophilic and mesophilic bacteria among which Proteobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the abundant phyla. However, in case of OYS, two genomes belonged to archaeal Methanobacterium and Methanocaldococcus. Functional characterization revealed the richness of CAZymes such as Glycosyl Transferase (GT) (56.7%), Glycoside Hydrolase (GH) (37.4%), Carbohydrate Esterase family (CE) (8.2%), and Polysaccharide Lyase (PL) (1.9%). There were negligible antibiotic resistance genes in the MAGs however, a significant heavy metal tolerance gene was found in the MAGs. Thus, it may be assumed that there is no coexistence of antibiotic and heavy metal resistance genes in these hot spring microbiomes. Since the selected hot springs possess good sulfur content thus, we also checked the presence of genes for sulfur and nitrogen metabolism. It was found that MAGs from both the hot springs possess significant number of genes related to sulfur and nitrogen metabolism.

Coexistence of Heavy Metal Tolerance and Antibiotic Resistance in Thermophilic Bacteria Belonging to Genus Geobacillus.

Hot springs are thought to be potential repositories for opportunistic infections, such as antibiotic-resistant strains. However, there is a scarcity of information on the mechanisms of antibiotic resistance gene (ARG) uptake, occurrence, and expression in thermophilic bacteria. Furthermore, because the genesis and proliferation of ARGs in environmental microorganisms are unknown, the research on antibiotic resistance profiles and probable mechanisms in thermophilic bacteria will become increasingly important. The goals of this study are to explore bacterial diversity, antibiotic and heavy metal resistance, and the prevalence and presence of ARG and metal resistance gene (MRG) in Geobacillus species. The 16S rRNA sequencing was used to determine the culturable bacterium diversity of 124 isolates. Standard Kirby Bauer Disc Diffusion and tube dilution procedures were used to determine antibiotic sensitivity and minimum inhibitory concentration (MIC). The tube dilution method was also used to check metal tolerance. To detect ARG and heavy MRG (HMRG), whole genome sequencing studies of the type species of the genus Geobacillus and five randomly selected Geobacillus species were performed. Graph Pad Prism and XLSTAT were used to perform statistical analyses such as ANOVA, EC50 analysis, and principal component analysis (PCA). The phylum Firmicutes and the genus Geobacillus dominated the culture-dependent bacterial diversity. Surprisingly, all thermophilic isolates, i.e., Geobacillus species, were sensitive to at least 10 different antibiotics, as evidenced by the lack of ARGs in whole genome sequencing analysis of numerous Geobacillus species. However, some of these isolates were resistant to at least five different heavy metals, and whole genome sequencing revealed the presence of MRGs in these thermophilic bacteria. The thermophilic genus Geobacillus is generally antibiotic sensitive, according to this study. In contrast, heavy metal is tolerated by them. As a result, it is possible that ARGs and MRGs do not coexist in these bacteria living in hot springs.

RNA thermometers in bacteria: Role in thermoregulation.

An array of external factors, an important one being temperature, decide the fate of survival in a microbe. The ability of microbes to sense external cues and to regulate the expression of genes accordingly is critical for its likely survival. Among a myriad of cellular defence mechanisms, a strategy to recuperate stress involves RNA regulatory elements. RNAs own a repertoire of functions in a cell as messengers, for transfer or as a component of ribosomes. A shift from its indigenous role is as regulators of gene expression, where in the cis-encoded RNA termed as "RNA Thermometers" play a pivotal role in translational level of gene expression. In this paper, we review the occurrence, the different types and molecular mechanism of gene regulation by RNATs, with a special focus limited to the domain Bacteria. We discuss the role of RNATs in mediating expression of temperature-responsive genes like heat shock/cold attributing in heat/cold shock response and a cascade of virulence genes to evade host defence mechanisms.

Hunt for α-amylase from metagenome and strategies to improve its thermostability: a systematic review.

With the advent of green chemistry, the use of enzymes in industrial processes serves as an alternative to the conventional chemical catalysts. A high demand for sustainable processes for catalysis has brought a significant attention to hunt for novel enzymes. Among various hydrolases, the α-amylase has a gamut of biotechnological applications owing to its pivotal role in starch-hydrolysis. Industrial demand requires enzymes with thermostability and to ameliorate this crucial property, various methods such as protein engineering, directed evolution and enzyme immobilisation strategies are devised. Besides the traditional culture-dependent approach, metagenome from uncultured bacteria serves as a bountiful resource for novel genes/biocatalysts. Exploring the extreme-niches metagenome, advancements in protein engineering and biotechnology tools encourage the mining of novel α-amylase and its stable variants to tap its robust biotechnological and industrial potential. This review outlines α-amylase and its genetics, its catalytic domain architecture and mechanism of action, and various molecular methods to ameliorate its production. It aims to impart understanding on mechanisms involved in thermostability of α-amylase, cover strategies to screen novel genes from futile habitats and some molecular methods to ameliorate its properties.

Cytological Evaluation of Pathological Male Breast Lesions.

OBJECTIVE: This study aimed to determine the cytodiagnostic spectrum of various male breast lesions, which were corroborated on histopathology as appropriate, to describe the process of the cytomorphology of some uncommon pathological lesions, and to discuss the reasons of their misdiagnoses. MATERIALS AND METHODS: In this 8-year study, a total of 114 patients underwent fine needle aspiration cytology (FNAC). In a representative case, nipple discharge from an 8-month-old child was examined. Confirmatory histopathology was obtained in 38 cases only. RESULTS: Gynecomastia was the most common (63.5%) male breast pathology. Invasive breast carcinoma of no special type was the most common variant of male breast malignancy. Half of the "gray zone" of cytological lesions was confirmed as cancer, but the rest were diagnosed as fibrocystic disease and intraductal papilloma. All cases with malignant cytology matched their corresponding histopathology. However, a tumor from an intraductal papillary carcinoma was miscued as ductal carcinoma on previous FNAC. CONCLUSION: Cytological evaluation of male breast lesions provides highly sensitive and specific results with excellent histologic reproducibility. Thus, it should be the ideal pretherapeutic diagnostic procedure for male breasts. However, some benign pathological conditions, which are particularly associated with epithelial hyperplasia, perplex the cytomorphologic scenario into the "gray zone."

Cytological Evaluation of Palpebral Lesions: An Insight into its Limitations Aided with Histopathological Corroboration.

CONTEXT: Eyelids by virtue of its unique histomorphology give rise to multitudes of different pathological conditions. Appropriate preoperative cytological diagnoses of these cases are necessary to determine their optimal therapy. AIMS: The aims of this study were to evaluate the utility of various cytological techniques in diagnosing the definite pathology for palpebral lesions and thereby to highlight the drawbacks associated with cytology in this context. MATERIALS AND METHODS: Fine-needle cytology with or without applying the aspiration was the preferable method. Ulcerated lesions were sampled through scrapings. RESULTS: Totally 62 cases were examined. Cytologically, 22 lesions were diagnosed as nonneoplastic, 38 lesions were neoplastic, and nondiagnostic material was obtained twice. Malignant tumors predominated among the neoplastic cases. Basal cell carcinoma (BCC) was the most common malignancy observed. On histopathological corroboration, benign skin adnexal tumor was found to be the most frequently misinterpreted entity. Two (out of four cases) of those tumors were confirmed as melanocytic nevus and BCC. A single case of squamous cell carcinoma was also cytodiagnostically erred into sebaceous carcinoma. CONCLUSIONS: Cytologically palpebral pathologies, including the neoplastic ones, are at times vulnerable to misinterpretation. To avert such dilemma, it is better to readily excise any recurrent lesion, basaloid neoplasm, or any necrohemorrhagic lesion presumptive of overshadowing the neoplastic pathology underneath.

Importance of Ki-67 Labeling in Oral Leukoplakia with Features of Dysplasia and Carcinomatous Transformation: An Observational Study over 4 Years.

Background Early detection of dysplastic changes within oral potentially malignant disorders is the mainstay to prevent oral cancer. Ki-67 is one of the most useful antigens in this purpose. Aims The study aims were to recognize and mutually compare the proliferative status of idiopathic oral leukoplakia (OL) patches, which presented through different forms of dysplasia and carcinoma. Settings and Design In 4 years of observation, cumulatively 140 OL lesions were included for examination. The wholesome Ki-67 labeling scores in each of the subgroups were calculated. Subjects and Methods The World Health Organization recommended histopathological classification was used to categorize the dysplastic and malignant lesions. Paraffin-embedded tissue sections were processed for Ki-67 immunostaining. The labeling indices (LIs) were quantified semiquantitatively at the site of maximal reactive cells on tissue sections. Statistical Analysis The statistical comparison was performed by means of the SPSS software (Version 16.0 SPSS Inc.). A p- value < 0.05 was considered as the benchmark for statistical significance. Results A steady and significant increment in Ki-67 expression was discovered from dysplastic to malignant OL patches compared with normal mucosa. The labeling differences were significant between normal mucosa and mild dysplasia, as well as between mild, moderate, and severe dysplasia. However, the expression did not differ significantly with the severity of oral cancers. Conclusions Ki-67 is a useful molecular marker of carcinogenesis in OL. It also serves worthwhile in separating marginally dysplastic lesions, such as mild dysplasia or verrucous carcinoma from their benign epigones.

Fine needle aspiration cytology of epididymal nodules and its corroboration with ultrasonographic-histological findings.

BACKGROUND: Fine needle aspiration cytology (FNAC) assisted with scrotal ultrasonography is the best preoperative diagnostic modality for palpable epididymal nodules. It also aids in their successive remedial approach as well as serves semi-therapeutically in cystic lesions. The objectives of this study are to recognize the spectrum of pathological conditions giving rise to epididymal nodules, then to compare them with corresponding ultrasound images, and to evaluate the histological features wherever practicable. METHODS: Total 62 patients underwent FNAC as well as sonographic evaluation for their epididymal nodules. Histopathology was performed in only 20 cases. RESULTS: Epididymitis either caused by tuberculosis (30.6%), or in its acute (11.3%) and chronic (8.1%) forms remained the commonest cytological diagnosis. Neoplastic lesions included mostly adenomatoid tumors (8.1%), and another case of seminomatous spread from ipsilateral testicular primary. Nineteen of the excised masses corroborated with their respective cytodiagnoses. The discrepant lesion was actually a papillary cystadenoma, which was cytologically misinterpreted as adenomatoid tumor. CONCLUSIONS: FNAC becomes the first-hand investigative measure for epididymal nodules, by virtue of its early, easy and highly accurate diagnostic implications. It segregates the patients into proper therapeutic protocol and thereby estranges those who really need operative management. When deployed together with ultrasound, the diagnostic accuracy of FNAC improves further.

Two unusual reports of urogenital tuberculosis: One 'putty' kidney and another in association with benign prostatic hyperplasia.

In India urogenital tuberculosis is the second commonest form of extra-pulmonary tuberculosis. Kidney is the highest and prostate is the least affected urogenital organ. But the extreme stage of renal tuberculosis named as 'putty' kidney is a rare manifestation. In general most cases of urogenital tuberculosis are quasi-symptomatic, and therefore an uttermost apprehension is needed from physicians to intercept such cases at the earliest. In this presentation we describe a case of 'putty' kidney, and another incidental association of prostate tuberculosis with benign prostatic hyperplasia.

Pitfalls in the cytological diagnosis of tenosynovial giant cell tumor: An illustration of eight discordant cases.

Tenosynovial giant cell tumor (TSGCT) is a highly recurrent benign tumor of the extremities. Wide local excision is usually sufficient to achieve its recurrence-free outcome. However, that needs a confident pre-operative cytological diagnosis as TSGCT. Aspirates from this tumor express the characteristic polymorphic cytological pattern, enough to impose a definite diagnosis. However rarely so, inadequate sampling from smaller tumors or due to faulty techniques, and selective sampling from topographic clusters of any individual component may lead to wrong interpretation. An unorthodox location near the larger limb joints further complicates the diagnostic misery on occasions. Such tumors are amenable to incomplete removal and risk for future recurrence. In this report, we describe eight cases of TSGCTs that were cytologically diagnosed otherwise. The cytological features of these discrepant tumors and the factors attributable to such dilemma are elaborated. Finally, a possible remedy has been proposed at conclusion in order to avoid future inconveniences.

Follicular Hybrid Cyst with Rare Juxtaposition of Epidermal Cyst and Steatocystoma.

Any cutaneous cyst differentiating toward two or more pilosebaceous components is known as follicular hybrid cyst (FHC). A combination of epidermal and trichilemmal cyst is its most frequent example. Other combinations of pilosebaceous derivatives occur uncommonly as well. The histogenesis of this condition has been controversial. In this latest report, we describe an unusual FHC from the earlobe of a 19-year-old male, which expressed the cohabitation of epidermal cyst and steatocystoma. A sharp transition was noted between the two kinds of epithelial components.