Genomic Characterization of IS6110 Insertions in Mycobacterium orygis.

Mycobacterium orygis, a subspecies of the Mycobacterium tuberculosis complex (MTBC), has emerged as a significant concern in the context of One Health, with implications for zoonosis or zooanthroponosis or both. MTBC strains are characterized by the unique insertion element IS6110, which is widely used as a diagnostic marker. IS6110 transposition drives genetic modifications in MTBC, imparting genome plasticity and profound biological consequences. While IS6110 insertions are customarily found in the MTBC genomes, the evolutionary trajectory of strains seems to correlate with the number of IS6110 copies, indicating enhanced adaptability with increasing copy numbers. Here, we present a comprehensive analysis of IS6110 insertions in the M. orygis genome, utilizing ISMapper, and elucidate their genetic consequences in promoting successful host adaptation. Our study encompasses a panel of 67 paired-end reads, comprising 11 isolates from our laboratory and 56 sequences downloaded from public databases. Among these sequences, 91% exhibited high-copy, 4.5% low-copy, and 4.5% lacked IS6110 insertions. We identified 255 insertion loci, including 141 intragenic and 114 intergenic insertions. Most of these loci were either unique or shared among a limited number of isolates, potentially influencing strain behavior. Furthermore, we conducted gene ontology and pathway analysis, using eggNOG-mapper 5.0, on the protein sequences disrupted by IS6110 insertions, revealing 63 genes involved in diverse functions of Gene Ontology and 45 genes participating in various KEGG pathways. Our findings offer novel insights into IS6110 insertions, their preferential insertion regions, and their impact on metabolic processes and pathways, providing valuable knowledge on the genetic changes underpinning IS6110 transposition in M. orygis.

Pyrite Dissolution in the Cretaceous Yogou Formation of the Niger (Chad) Basin: Implications for Basin Evolution under a Rift Tectonic Setting.

This is the first study of pyrite minerals in the entire West and Central African Rift System (WCARS). Several polished organic-rich core samples from the Cretaceous Yogou Formation of the Niger (Chad) Basin located in the WCARS were investigated for their pyrite content using FE-SEM and SEM-EDS imaging techniques. An attempt was made to classify the types and provenance of the pyrites and to highlight the control of rift fractures on the oxidation and dissolution of pyrites in the region. Three major types of pyrites are present in the studied formation, including euhedral pyrite (EPy) crystals, pyrite framboids (FPy), and sunflower pyrites (SPy). A statistical analysis of 307 FPy shows that the framboids are diagenetically formed with an average diameter of 6.61 µm. SPy is present in a relatively low amount compared to framboids. The pyrites underwent a variety of diagenetic modifications, from mechanical compaction to oxidation, dissolution, and recrystallization. Unoxidized pyrites primarily contain Fe, S, and C, but oxidized pyrites also contain O, Al, and Si. There is a strong correlation between the fractures and the spatial distribution of the physicochemical alteration of the pyrite in the study. Dissolution in relatively deep-buried samples occurs mainly along fracture planes. The fractures provide a pathway for oxidants and other metal elements to reach the pyrites. The pattern of pyrite dissolution reflects the timing of fracture formation and fracture activities as a purveyor or drainage for fluids in the organic-rich samples investigated. The pyrites are associated intimately with organic matter (OM); thus, the relationship between the fracture and the pyrites' transformation is significant in the assessment of organic matter preservation at deep-burial depth.

Trivalent and pentavalent atoms doped boron nitride nanosheets as Favipiravir drug carriers for the treatment of COVID-19 using computational approaches.

In our DFT investigations, pristine BNNS as well as trivalent and pentavalent atoms doped BNNS have been taken into consideration for Favipiravir (FPV) drug carriers for the treatment of COVID-19. Among the nanosheets, In doped BNNS (BN(In)NS) interacts with FPV by favorable adsorption energies about -2.44 and -2.38 eV in gas and water media respectively. The charge transfer analysis also predicted that a significant amount of charge about 0.202e and 0.27e are transferred to BN(In)NS in gas and water media respectively. HOMO and LUMO energies are greatly affected by the adsorption of FPV on BN(In)NS and energy gap drastically reduced by about 38.80 % and 64.07 % in gas and water media respectively. Similar results are found from the global indices and work function analysis. Therefore, it is clearly seen that dopant In atom greatly modified the BNNS and enhanced the adsorption behavior along with sensitivity, reactivity, polarity towards the FPV.

Tuberculosis caused by Mycobacterium orygis in wild ungulates in Chennai, South India.

We report the isolation of Mycobacterium orygis, a member of Mycobacterium tuberculosis complex (MTBC), from two black bucks (Antelope cervicapra) and one spotted deer (Axis axis) from the Guindy National Park forest range in Chennai, India. Lung tissue and lymph node samples collected during post-mortem examination were processed using NaOH method and cultured in solid and liquid media. DNA extracted from the cultured isolates was used to amplify the mpt64 gene by specific primers and the band visualized at 240 bps confirmed the isolates as a member of MTBC. Further examination of these isolates by spoligotyping and whole-genome sequencing confirmed the isolates as M. orygis and the phylogenetic tree revealed their well-clustered position with other M. orygis isolates around the globe. The deletion of RD7-RD10, RDOryx_1, RDOryx_4, RD12Oryx, RD301 and RD315 further substantiated these isolates as M. orygis. The exact source of infection in animals was untraceable and the pairwise comparison of the genomes based on single-nucleotide polymorphisms difference did not detect any events of transmission within the affected animals. Nevertheless, it would be wise to take into account the environment where there exists a high chance of transmission due to the increased human-animal interaction. Since it is well known that the pathogen is capable of causing infection in both human and animal hosts, systematic surveillance and screening of spotted deer, black buck as well as humans in the vicinity is essential for successful implementation of the One Health approach.

A review on bovine tuberculosis in India.

Bovine tuberculosis (bTB) is a chronic illness in animals, especially in cattle, leading to loss in the productivity and signifies a crucial public health risk. Regardless of the zoonotic threat and significant economic costs associated with the disease, precise estimates of bTB prevalence are deficient in many countries, including India, where national control programs are yet to be instigated. The true burden of the disease remains unknown due to lack of routine surveillance data from most of the developing countries. India is progressing well towards attaining the End TB goal, yet bTB continues to remain largely hidden. Moreover, the paucity of literature on bTB in India might lead to undue complacency and hence has to be scrupulously guarded and prevented from gaining any misconceptions in the minds of the common people. Preventing and controlling bTB at the animal interface is pivotal to evade transmission to human, increase food safety and guard the livelihood of the people. To attain this goal, implementation of strategies based on international norms and a multi-sectoral approach will empower enhanced surveillance and diagnosis of disease in animals and subsequently reduce the risk for humans. As an initiative, we step forward to address this review which briefly summarizes the available data in the literature from early 20th century to date to assess the status of bTB in India. We have discussed in detail, the epidemiology, transmission and diagnosis pertaining to bTB. The review also focuses on the interconnection between the health of people and animal, discuss the preventions and control strategies and recommend the use of vaccination in cattle to reduce the spread of infection among other animals and humans. Implementing One Health approach in India, which recognizes the interdependence of the health of people and animals will help the nation in the fight against TB.

Whole-Genome Sequencing of a Mycobacterium orygis Strain Isolated from Cattle in Chennai, India.

Here, we report the isolation of Mycobacterium orygis from dairy cattle in Chennai, India. Spoligotyping assigned the isolate to spoligotype 587 (ST587), which belongs to M. orygis This species was confirmed as M. orygis using whole-genome sequencing.

Multiple Myeloma Light Chain Amyloidosis Presenting as Hepatic Failure.

Amyloidosis is characterized by abnormal deposition of aggregations of amyloid fibril proteins. Systemic amyloidosis usually involves multiple organs, with kidneys being the most common organ involved, followed by the heart. In general, the presentation of hepatic amyloidosis varies with minimal or no symptoms commonly seen. Hepatic amyloidosis is rarely associated with multiple myeloma. We report here a case of portal hypertension, ascites, and severe intrahepatic cholestasis as the initial presentation of hepatic amyloidosis and multiple myeloma, which followed a rapidly progressive clinical course.

Biofilms Comprise a Component of the Annual Cycle of Vibrio cholerae in the Bay of Bengal Estuary.

Vibrio cholerae, an estuarine bacterium, is the causative agent of cholera, a severe diarrheal disease that demonstrates seasonal incidence in Bangladesh. In an extensive study of V. cholerae occurrence in a natural aquatic environment, water and plankton samples were collected biweekly between December 2005 and November 2006 from Mathbaria, an estuarine village of Bangladesh near the mangrove forests of the Sundarbans. Toxigenic V. cholerae exhibited two seasonal growth peaks, one in spring (March to May) and another in autumn (September to November), corresponding to the two annual seasonal outbreaks of cholera in this region. The total numbers of bacteria determined by heterotrophic plate count (HPC), representing culturable bacteria, accounted for 1% to 2.7% of the total numbers obtained using acridine orange direct counting (AODC). The highest bacterial culture counts, including toxigenic V. cholerae, were recorded in the spring. The direct fluorescent antibody (DFA) assay was used to detect V. cholerae O1 cells throughout the year, as free-living cells, within clusters, or in association with plankton. V. cholerae O1 varied significantly in morphology, appearing as distinctly rod-shaped cells in the spring months, while small coccoid cells within thick clusters of biofilm were observed during interepidemic periods of the year, notably during the winter months. Toxigenic V. cholerae O1 was culturable in natural water during the spring when the temperature rose sharply. The results of this study confirmed biofilms to be a means of persistence for bacteria and an integral component of the annual life cycle of toxigenic V. cholerae in the estuarine environment of Bangladesh.IMPORTANCEVibrio cholerae, the causative agent of cholera, is autochthonous in the estuarine aquatic environment. This study describes morphological changes in naturally occurring V. cholerae O1 in the estuarine environment of Mathbaria, where the bacterium is culturable when the water temperature rises and is observable predominantly as distinct rods and dividing cells. In the spring and fall, these morphological changes coincide with the two seasonal peaks of endemic cholera in Bangladesh. V. cholerae O1 cells are predominantly coccoid within biofilms but are rod shaped as free-living cells and when attached to plankton or to particulate matter in interepidemic periods of the year. It is concluded that biofilms represent a stage of the annual life cycle of V. cholerae O1, the causative agent of cholera in Bangladesh.

A Serine/threonine kinase PknL, is involved in the adaptive response of Mycobacterium tuberculosis.

Mycobacterium tuberculosis adapts itself to various environmental stress conditions to thrive inside the phagosome for establishing a chronic infection. Serine/threonine protein kinases (STPKs) play a major role in the physiology and pathogenesis of Mycobacterium tuberculosis. Some of these STPKs are involved in regulating the growth of the mycobacterium under nutrient stress and starvation conditions. In this study, we have investigated the role of PknL, a STPK in the adaptive responses of M. tuberculosis by conditional inactivation of the gene using antisense technology. The inhibition of PknL in the knockdown strain was validated by RT-PCR. The in vitro growth kinetics of M. tuberculosis strain following inhibition of PknL was found to be bacteriostatic. The knock down strain of PknL exhibited a better survival in pH 5.5 when compared to its growth in pH 7.0. Similarly, it also exhibited more resistance to both SDS(0.01%) and Lysozyme stress (2.5mg/ml), indicating that loss of PknL enhances the growth of mycobacterium under stress conditions. SEM pictographs also represent an increase in the cell length of the knock down strain compared to Wild type stressing its role in cellular integrity. Lastly, the proteome analysis of differentially expressing PknL strains by 2D gel electrophoresis and mass spectrometry identified 19 differentially expressed proteins. Our findings have shown that PknL plays an important role in sensing the host environment and adapting itself in slowing down the growth of the pathogen and persisting within the host.

Glycogenic Hepatopathy: Thinking Outside the Box.

Glycogenic hepatopathy (GH) remains underrecognized in adults as most clinicians mistake it for the more common hepatic abnormality associated with uncontrolled diabetes mellitus in this age group, non-alcoholic fatty liver disease. This is also complicated by the fact that both entities are indistinguishable on liver ultrasound. We herein describe a similar predicament in which a young adult female presented with bilateral upper quadrant abdominal pain, tender hepatomegaly, lactic acidosis and a >10-fold increase in liver enzymes, which worsened after the administration of high-dose steroids. Despite intravenous normal saline resuscitation, serum transaminitis persisted in a fluctuating manner. Ultimately, a liver biopsy confirmed GH. Biochemically, GH is driven by high amounts of both circulating glucose and insulin or by the administration of high-dose steroids. Improving glycemic control is the mainstay of treatment for GH. However, in our case, improvement in glycated hemoglobin of just 0.6% was enough to achieve symptomatic relief, supporting recent claims of the involvement of other identified factors in disease development.

An M/M/c/K State-Dependent Model for Pedestrian Flow Control and Design of Facilities.

Pedestrian overflow causes queuing delay and in turn, is controlled by the capacity of a facility. Flow control or blocking control takes action to avoid queues from building up to extreme values. Thus, in this paper, the problem of pedestrian flow control in open outdoor walking facilities in equilibrium condition is investigated using M/M/c/K queuing models. State dependent service rate based on speed and density relationship is utilized. The effective rate of the Poisson arrival process to the facility is determined so as there is no overflow of pedestrians. In addition, the use of the state dependent queuing models to the design of the facilities and the effect of pedestrian personal capacity on the design and the traffic congestion are discussed. The study does not validate the sustainability of adaptation of Western design codes for the pedestrian facilities in the countries like Bangladesh.

Undifferentiated carcinoma of pancreas: a rare entity with aggressive behavior and possible genetic link.

UNLABELLED: An aggressive undifferentiated carcinoma of pancreas is a rare tumor, especially with a strong personal and family history of malignant melanoma. Limited literature review and few case reports described a genetic association between distinct types of pancreatic cancer and malignant melanoma. CASE REPORT: We present an uncommon case of an aggressive undifferentiated carcinoma of the pancreas in a 50-year-old Caucasian female. Initially, she presented with intermittent epigastric postprandial pain and mild nausea. A computed tomography scan of the abdomen showed a 5 cm heterogenous pancreatic tail mass, which on biopsy was found to be a poorly differentiated non-small cell carcinoma. Past medical history included malignant melanoma, with extensive family history of pancreatic cancer and malignant melanoma. However, not genetically confirmed, a hereditary pancreatic linkage was highly suspected. A week later, repeat computed tomography demonstrated tremendous enlargement of the pancreatic tail mass. Within a few weeks, the patient developed aggressive metastasis in various organ systems, followed by multiple surgeries. An emergent first round of chemotherapy was started, followed by an intensive care unit stay, and she eventually died. CONCLUSION: Our case exposes the aggressive behavior of undifferentiated carcinoma of pancreas, along with possible hereditary link between pancreatic cancer and malignant melanoma.

Fecal carriage of multi-drug resistant and extended spectrum ß-lactamases producing E. coli in household pigeons, Bangladesh.

Antibiotic resistance and ESBL constitute a risk to human and animal health. Birds residing close to humans could mirror the spectrum of human associated antibiotic resistance. Household pigeons were screened in Bangladesh to shed light on human associated, as well as, environmental antibiotic resistance. Escherichia coli from pigeons (n=150) were tested against 11 antibiotics. 89% E. coli isolates were resistant to one or more critically important human antibiotics like ampicillin, cefadroxil, mecillinam, ciprofloxacin, gentamicin and tigecycline. No carbapenamase-producers were detected and the lower ESBL prevalence (5%) in pigeons. ESBL-producing E. coli isolates had blaCTX-M-15 genes. Pigeons shared some bacterial clones and had bird associated sequence types like E. coli ST1408. Fecal carriage of bacteria resistance of critically important human antibiotics, together with examples of shared genotypes among pigeons, indicate the human-birds and bird to bird transmissions are important in the epidemiology of antibiotic resistance.

Unusual case of gastroparesis leading to severe gastromegaly with demyelinating disease as a rare cause.

INTRODUCTION: Gastroparesis is an entity of symptomatic abnormal gastric emptying, with diabetes mellitus, postsurgical and idiopathic etiologies accounting for majority of the cases. CASE REPORT: We report the case of a young African American female, who presented with abdominal discomfort, inability to tolerate a regular diet and intermittent episodes of numbness, tingling and cramps in her extremities. CT scan of the abdomen and pelvis showed a massively distended stomach, compressing the intestines and liver. A gastric emptying study revealing markedly worsened gastroparesis. Severe gastroparesis causing massive gastromegaly secondary to multiple sclerosis was diagnosed. CONCLUSION: This case illustrates severe gastromegaly that is rarely seen to this extent and identifies multiple sclerosis (MS) as a rare cause of gastroparesis. MS should be considered in the differential diagnosis of gastroparesis in appropriate clinical settings.

Verrucous carcinoma of the esophagus: a potential diagnostic dilemma.

Verrucous carcinoma of the esophagus is a rare variant of squamous cell carcinoma associated with human papillomavirus. We report the case of a 58-year-old female who presented with ongoing symptoms of dysphagia. On previous endoscopies she had been noted to have a large polyp-like mass involving the esophagus, with negative biopsies for malignancy. Repeat endoscopy with concurrent endoscopic ultrasound showed a large semi-pedunculated polyp in the distal esophagus and a hypoechoic, irregular mass involving the gastroesophageal junction with esophageal thickening. Deep layer biopsies showed pseudoepitheliomatous hyperplasia with immunohistochemical staining positive for human papillomavirus. The patient was subsequently treated with chemo-radiation followed by esophagectomy.

Polymorphism in the RD1 locus and its effect on downstream genes among South Indian clinical isolates of Mycobacterium tuberculosis.

RD1, the region of difference between the virulent strains of Mycobacterium tuberculosis and Mycobacterium bovis BCG, is the most explored region in terms of mycobacterial virulence and vaccine design. This study found a polymorphic intergenic region between two genes, Rv3870 and Rv3871, in the RD1 region. Sequence analysis revealed a 53 bp repeat element that created a polymorphism among the clinical isolates, reported previously as the mycobacterial interspersed repetitive unit (MIRU) 39 locus. The discriminatory power of this locus was found to be high for EAI strains, as indicated by a Hunter-Gaston diversity index value of 0.58, and low for Beijing (0.26) and CAS (0.29) strains. The presence and variability of MIRU 39 in the intergenic region led us to investigate the functional role of the repeat element by measuring the transcription levels of the downstream genes Rv3871 and Rv3874 by quantitative RT-PCR among the different clades of clinical strains. Higher transcription levels of Rv3871 were observed in strains with four copies of the repeat element in the upstream region, whereas the transcription level of Rv3874 was higher in strains with six copies of the repeat element. These data suggest that changes in transcription levels resulting from insertion of different copy numbers of the repeat element may affect regulation of gene expression in M. tuberculosis.

Esophageal perforation: a rare complication of transesophageal echocardiography in a patient with asymptomatic esophagitis.

Transesophageal echocardiography (TEE) is a commonly used procedure in patients with suspected endocarditis. A rare but dreadful complication of this procedure is perforation of the esophagus. We report the case of an elderly female with multiple comorbidities, who presented with polyarticular septic arthritis. TEE was performed to rule out endocarditis. Though the standard procedure protocol was followed, she developed esophageal perforation. It was managed with esophageal stenting but she developed multiorgan failure and did not survive. This case highlights the potential of severe morbidity and mortality associated with TEE. Appropriate screening must be done and high-risk individuals must be identified before such procedures are attempted.

A pyridinium cation-π interaction sensor for the fluorescent detection of alkyl halides.

N-alkylation of a novel pyridine sensor results in pyridinium salts whose conformations are stabilised by pyridinium cation-π interactions resulting in a fluorescent response that can be used to sense the presence of alkylating agents in solution at low concentration.

Essential medicines for reproductive health: developing evidence based interagency list.

OBJECTIVES: Although poor reproductive health constitutes a significant proportion of the disease burden in developing countries, essential medicines for reproductive health are often not available to the population. The objective was to analyze the guiding principles for developing national Essential Medicines Lists (EML). The second objective was to compare the reproductive health medicines included on these EMLs to the 2002 WHO/UNFPA list of essential drugs and commodities for reproductive health. Another objective was to compare the medicines included in existing international lists of medicines for reproductive health. METHODS: The authors calculated the average number of medicines per clinical groups included in 112 national EMLs and compared these average numbers with the number of medicines per clinical group included on the WHO/UNFPA List. Additionally, they compared the content of the lists of medicines for reproductive health developed by various international agencies. RESULTS: In 2003, the review of the 112 EMLs highlighted that medicines for reproductive health were not consistently included. The review of the international lists identified inconsistencies in their recommendations. The reviews' outcomes became the catalyst for collaboration among international agencies in the development of the first harmonized Interagency List of Essential Medicines for Reproductive Health. Additionally, WHO, UNFPA and PATH published guidelines to support the inclusion of essential medicines for reproductive health in national medicine policies and EMLs. The Interagency List became a key advocacy tool for countries to review their EMLs.In 2009, a UNFPA/WHO assessment on access to reproductive health medicines in six countries demonstrated that the major challenge was that the Interagency List had not been updated recently and was inconsistently used. CONCLUSION: The addition of cost-effective medicines for reproductive health to EMLs can result in enhanced equity in access to and cost containment of these medicines, and improve quality of care. Action is required to ensure their inclusion in national budget lines, supply chains, policies and programmatic guidance.

Localized advanced hürthle cell carcinoma with symptomatic intrathoracic goiter.

INTRATHORACIC GOITERS ARE DIVIDED INTO TWO CATEGORIES: primary and secondary. Intrathoracic goiters (IG) can cause upper airway obstruction. The presence of obstructive symptoms secondary to increased thyroid growth and tracheal compression is major indication for surgery; however, goiters do not always require immediate surgical attention. In addition, although some diagnostic tests indicate upper airway obstruction, many patients remain asymptomatic. Surgeries to remove IG are performed routinely however, they are not without risk. In some cases, intrathoracic goiters present as thyroid cancers. Very rare cancers such as Hürthle cell carcinoma (HCC) can create a challenge for the surgeon when surgical intervention is vital.