Adapting beyond borders: Insights from the 19th Student Council Symposium (SCS2023), the first hybrid ISCB Student Council global event.

Summary: The 19th ISCB Student Council Symposium (SCS2023) organized by ISCB-SC adopted a hybrid format for the first time, allowing participants to engage in-person in Lyon, France, and virtually via an interactive online platform. The symposium prioritized inclusivity, featuring on-site sessions, poster presentations, and social activities for in-person attendees, while virtual participants accessed live sessions, interactive Q&A, and a virtual exhibit hall. Attendee statistics revealed a global reach, with Europe as the major contributor. SCS2023's success in bridging in-person and virtual experiences sets a precedent for future events in Computational Biology and Bioinformatics. Availability and Implementation: The details of the symposium, speaker information, schedules, and accepted abstracts, are available in the program booklet (https://doi.org/10.5281/zenodo.8173977). For organizers interested in adopting a similar hybrid model, it would be beneficial to have access to details regarding the online platform used, the types of sessions offered, and the challenges faced. Future iterations of SCS can address these aspects to further enhance accessibility and inclusivity.

Metabolic priming by multiple enzyme systems supports glycolysis, HIF1α stabilisation, and human cancer cell survival in early hypoxia.

Adaptation to chronic hypoxia occurs through changes in protein expression, which are controlled by hypoxia-inducible factor 1α (HIF1α) and are necessary for cancer cell survival. However, the mechanisms that enable cancer cells to adapt in early hypoxia, before the HIF1α-mediated transcription programme is fully established, remain poorly understood. Here we show in human breast cancer cells, that within 3 h of hypoxia exposure, glycolytic flux increases in a HIF1α-independent manner but is limited by NAD+ availability. Glycolytic ATP maintenance and cell survival in early hypoxia rely on reserve lactate dehydrogenase A capacity as well as the activity of glutamate-oxoglutarate transaminase 1 (GOT1), an enzyme that fuels malate dehydrogenase 1 (MDH1)-derived NAD+. In addition, GOT1 maintains low α-ketoglutarate levels, thereby limiting prolyl hydroxylase activity to promote HIF1α stabilisation in early hypoxia and enable robust HIF1α target gene expression in later hypoxia. Our findings reveal that, in normoxia, multiple enzyme systems maintain cells in a primed state ready to support increased glycolysis and HIF1α stabilisation upon oxygen limitation, until other adaptive processes that require more time are fully established.

AFRbase: a database of protein mutations responsible for antifungal resistance.

MOTIVATION: Fungal pathogens are known to cause life threatening invasive infections with rising global mortality rates. Besides, the indiscriminate use of antifungals in both clinics and agriculture has promoted antifungal drug resistance in the last decade. Fungi can show drug resistance by a variety of mechanisms. But primary driver in all these hitherto documented mechanisms is stable and heritable point mutations in the key proteins. Therefore, cataloguing mutations that can confer resistance is the first step toward understanding the mechanisms leading to the emergence of antifungal resistance. RESULTS: In the present, work we have described a database of all the mutations responsible for antifungal resistance. Named as antifungal resistance database (AFRbase), it is better than the existing databases of antifungal resistance namely, FunResDB and MARDy which have a limited scope and inadequate information. Data of AFRbase was collected using both text mining and manual curation. AFRbase provides a separate window for visualization of mutations in the 2D and 3D formats making it easy for researchers to analyze the mutation data and ensures interoperability with other standard molecular biology databases like NCBI and UniProtKB. We hope AFRbase can be useful to both clinicians and basic biomedical scientists as we envision it as an important resource for genotypic susceptibility testing of fungi and to study/predict the course of evolution of antifungal resistance. The current version of AFRbase contains manually curated 3691 unique mutations present in 29 proteins of 32 fungal species along with the information of drugs against which resistance is caused. AVAILABILITY AND IMPLEMENTATION: AFRbase is an open access database available at http://proteininformatics.org/mkumar/afrbase/.

ProSeqAProDB: Prosequence Assisted Protein Database.

In early 1990s, several proteins were shown to depend on additional stretches of polypeptide (termed as prosequence/prodomain) for their folding. These regions of the protein were often termed as IMCs (Intra Molecular Chaperones), since they would be cleaved from the mature folded protein eventually. Such proteins were hypothesized to face a kinetic barrier to their folding, which was probably lowered by the prosequences. In last three decades, numerous examples of such proteins have accumulated in literature. Yet, no study has been reported so far attempting to understand the evolutionary differences and similaritess of such proteins. Till date such proteins are continued to be treated as anomalous variants, rather than as representatives of any alternate protein folding strategy. Do such proteins have any distinctive structural facets OR typical biological roles, necessitating an unconventional strategy of protein folding? Do prosequences carry any unique or conserved features that are essential to their function? ProSeqAProDb: ProSequence Assisted Protein Database, (which can be accessed at https://proseqaprodb.mkulab.in) was built as a comprehensive database, to systematically study such proteins along with their pro-sequences. The database currently contains 2140 prosequence assisted proteins (1848 eukaryotic, 255 bacterial, 24 viral and 13 archaeal proteins), from 690 organisms later categorised into 960 families. We envisage that the availability of this curated dataset will enable the researchers worldwide to further their investigation in the origin, importance and evolution of such proteins, leading to better understanding of the protein folding process as a whole.

Designing dual inhibitors against potential drug targets of Plasmodium falciparum -M17 Leucyl Aminopeptidase and Plasmepsins.

Malaria is one of the major diseases of concern worldwide, especially in the African regions. According to a recent WHO report, 95% of deaths that occur due to malaria are in the African regions. Resistance to present antimalarial drugs is increasing rapidly and becoming a problem of concern. M17 Leucyl Aminopeptidase (PfM17LAP) and vacuolar Plasmepsins (PfPM) are two important enzymes involved in the haemoglobin degradation pathway of Plasmodium falciparum. PfM17LAP regulates the release of amino acids and PfPM mediates the conversion of haemoglobin proteins to oligopeptides. These enzymes thus play an essential role in the survival of malaria parasites inside the human body. In the present study, we used in-silico molecular docking, simulation and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) studies to find potential dual inhibitors of PfPM and PfM17LAP using the ChEMBL antimalarial library. Absorption, distribution, metabolism, excretion and toxicity (ADMET) profiling of the top ten ranked molecules was done using the BIOVIA Discovery Studio. The present investigation revealed that the compound CHEMBL426945 is stable in the binding site of both PfPM and PfM17LAP. In this study, we have reported novel dual-inhibitors that may act better than the present antimalarial drugs.Communicated by Ramaswamy H. Sarma.

Intramedullary Crossed K-wire Fixation for the Hand Fractures is a Useful Treatment Modality: A Prospective Observational Study.

Background: Various modalities of treatment have been used for the management of metacarpal and phalangeal fractures which include K-wire fixation, mini plates, lag screws fixation, intramedullary screw fixation and external fixator application. The aim of this study was to analyse complications and patient-related functional outcomes after antegrade or retrograde crossed intramedullary K-wire fixation of metacarpal and proximal phalangeal fractures. Methods: Thirty-one patients (36-fractures, 16-metacarpals, 20-proximal phalanx) meeting the study criteria were included in this prospective study. Fixation of the fractures was done by use of crossed intramedullary K-wire using the principles of 3-point fixation. Results: The mean preoperative angulation of the fractures noted in this study was 35.8° which was significantly reduced at final follow-up. Union was noted at a mean period of 4.2 ± 6.8 weeks. The mean range of motion at the metacarpophalangeal and proximal interphalangeal joint was 96.4% and 86.3%, respectively as compared to the opposite hand. Stiffness (n = 3, 14.2%) and persistent pain (n = 2, 9.5%) at the joints were the most common complications noted in this study. Conclusion: Crossed percutaneous intramedullary fixation of small bone fractures of the hand is a versatile method with advantages such as cost-effectiveness and lesser operative time when compared to other modalities of fixation. Earlier range of motion (ROM) exercises can be started due to preservation of gliding planes, no surgical wound along with good fracture stability and minimal hardware impingement. How to cite this article: Ahmad S, Gupta T, Ansari S, et al. Intramedullary Crossed K-wire Fixation for the Hand Fractures is a Useful Treatment Modality: A Prospective Observational Study. Strategies Trauma Limb Reconstr 2022;17(2):74-80.

Lysosomal GPCR-like protein LYCHOS signals cholesterol sufficiency to mTORC1.

Lysosomes coordinate cellular metabolism and growth upon sensing of essential nutrients, including cholesterol. Through bioinformatic analysis of lysosomal proteomes, we identified lysosomal cholesterol signaling (LYCHOS, previously annotated as G protein-coupled receptor 155), a multidomain transmembrane protein that enables cholesterol-dependent activation of the master growth regulator, the protein kinase mechanistic target of rapamycin complex 1 (mTORC1). Cholesterol bound to the amino-terminal permease-like region of LYCHOS, and mutating this site impaired mTORC1 activation. At high cholesterol concentrations, LYCHOS bound to the GATOR1 complex, a guanosine triphosphatase (GTPase)-activating protein for the Rag GTPases, through a conserved cytoplasm-facing loop. By sequestering GATOR1, LYCHOS promotes cholesterol- and Rag-dependent recruitment of mTORC1 to lysosomes. Thus, LYCHOS functions in a lysosomal pathway for cholesterol sensing and couples cholesterol concentrations to mTORC1-dependent anabolic signaling.

Calcific Myonecrosis: Solving the Diagnostic Dilemma.

We report the clinico radiological presentation of an unusual case of an ossified soft tissue mass in the leg in a 74-year-old man. Calcific myonecrosis is a rare soft tissue condition characterized by calcified mass within a compartment. Differential diagnosis of myonecrosis include myositis ossificans and sarcomas with propensity for extra-osseous calcification like extra-skeletal osteosarcoma, Ewing's sarcoma and epithelioid sarcoma. This entity is a late complication to trauma and prolonged high pressure state within the leg compartments. With imaging alone, the differential of soft tissue sarcoma could be ruled out but typical natural history of disease and radiopathological features aided in the diagnosis.

Salvaging the Unsalvageable Giant Cell Tumors of Bone: The 'Longitudinal Sandwich Technique'.

Management of Campanacci Grade III Giant Cell Tumors of bone (GCT) is challenging. Although selected cases of Grade III GCTs can still be managed with intralesional extended curettage, wide excision of the lesion is usually recommended when there is extensive cortical destruction. This study describes the outcome of 'longitudinal sandwich technique' for extended curettage of Grade III GCTs with more than 50% cortical destruction. Here, the deficiency of cortex was made up for by using bone graft/graft substitute, used alongside cement placed in a longitudinal fashion. Twelve patients operated with this technique between Jan 2012 and Jan 2018 were reviewed. Majority of the lesions involved the lower limbs. Bone graft was used in eight whereas commercial bone graft substitute was used in the remaining four, along with bone cement in all. On follow-up ranging from 38 to 84 months (median follow-up 59 months), there were 4 local recurrences (33.33%). All recurrences were managed successfully with repeat surgery without the need for bony resection. Mean MSTS score during the last follow-up was 25.08 ± 2.31 and all patients were disease-free during the last follow-up. 'Longitudinal sandwich technique' helps to expand the indications of extended curettage even for aggressive Grade III GCTs, with satisfactory outcomes.

Organelle transporters and inter-organelle communication as drivers of metabolic regulation and cellular homeostasis.

BACKGROUND: Spatial compartmentalization of metabolic pathways within membrane-separated organelles is key to the ability of eukaryotic cells to precisely regulate their biochemical functions. Membrane-bound organelles such as mitochondria, endoplasmic reticulum (ER) and lysosomes enable the concentration of metabolic precursors within optimized chemical environments, greatly accelerating the efficiency of both anabolic and catabolic reactions, enabling division of labor and optimal utilization of resources. However, metabolic compartmentalization also poses a challenge to cells because it creates spatial discontinuities that must be bridged for reaction cascades to be connected and completed. To do so, cells employ different methods to coordinate metabolic fluxes occurring in different organelles, such as membrane-localized transporters to facilitate regulated metabolite exchange between mitochondria and lysosomes, non-vesicular transport pathways via physical contact sites connecting the ER with both mitochondria and lysosomes, as well as localized regulatory signaling processes that coordinately regulate the activity of all these organelles. SCOPE OF REVIEW: This review covers how cells use membrane transporters, membrane contact sites, and localized signaling pathways to mediate inter-organelle communication and coordinate metabolism. We also describe how disruption of inter-organelle communication is an emerging driver in a multitude of diseases, from cancer to neurodegeneration. MAJOR CONCLUSIONS: Effective communication among organelles is essential to cellular health and function. Identifying the major molecular players involved in mediating metabolic coordination between organelles will further our understanding of cellular metabolism in health and lead us to design better therapeutics against dysregulated metabolism in disease.

Infection and utilization rates of bone allografts in a hospital-based musculoskeletal tissue bank in north India.

BACKGROUND: The bone bank unit of interest in this article was established in January 2018, in a tertiary care teaching institute of north India. Aim of this article is to describe the sources of allografts obtained, discard rates of allografts and infection rates in the recipients after use. MATERIAL AND METHODS: All the relevant details of donors and recipients were maintained, and donors were screened for standard inclusion and exclusion criteria before obtaining the grafts. Aerobic culture was performed before storage and just prior to use. Samples with incomplete documentation, incomplete donor screening or positive cultures were discarded. Data on surgical site infection in recipients was collected from hospital records retrospectively. Initially ELISA based serological tests were used for screening. Donor has to undergo these tests again after 6 months to account for the window period of proliferation of viruses. Nucleic acid amplification tests (NAAT) for these viral agents were introduced in the hospital in May 2018. RESULTS: Allografts from a total of 196 donors were obtained in the bone bank over 2 years. Major source of bone was femoral heads harvested during total hip arthroplasty or hemi-arthroplasty. 44(22.4%) grafts had to be discarded. 95 allografts were used in 88 patients during this time. Most common indication for use was surgery for bone tumors (40%), followed by complex primary or revision arthroplasty (30.5%). Three (3.4%) recipients developed deep infection postoperatively. CONCLUSION: Frozen allograft bone from hospital based bone banks is a reliable source of allografts. When meticulous precautions for sterility are followed, risk of infection is low. Monitoring of such bone banks should fall within a framework of the local legislature. Incomplete documentation is the major reason for wastage of the samples obtained. NAAT may be useful in screening of donors, as it reduces the wastage and the holding time of the allografts.

Symptom Interval in Cases of Benign Cystic Lesions of Bone and its correlation with Surgical Intervention.

INTRODUCTION: Benign lesions in bone are less studied in terms of progression and prognosis. There is presently no literature studying symptom interval (SI) in neoplastic bone lesions or determinants of delay in Indian setting. The literature is also sparse on SI in benign lesions of bone, since benign bone lesions have seemingly less menacing symptoms and slow progression as compared to their malignant counterparts. Social and cultural issues peculiar to the region of study have an impact on the symptom interval of benign bony lesions. METHOD: A prospective, observational study was conducted at a tertiary level University teaching hospital from December 2017 to August 2019. The study included 55 patients presenting with benign cystic lesions of bone. Appropriate radiological investigations along with tissue biopsy were done. All the patients were enquired as per a preformed questionnaire to determine the delay and its determinants. RESULT: Out of the 55 patients included in the study, wide variety of cystic lesions was observed with varied presentation and delay. Median SI of 175 days (range 27-3705 days) was observed in the present study. However, it was found that longer SI did not have a statistically significant effect on the type of procedure done (p = 0.206) though diagnostic delay was significantly related to the intervention required (p = 0.004). It was observed that tumor behavior at the time of presentation such as histopathological diagnosis (p = 0.000), presence of cortical breach (p = 0.001), stage of tumor (0.001), and articular involvement (p = 0.000) remained as some of the most important factors in determining the prognosis and outcome in case of benign cystic lesions of bone.

Functional outcome in giant cell tumor of distal radius treated with excision and fibular arthroplasty: a case series.

INTRODUCTION: Giant cell tumor (GCT) of bone is a locally aggressive benign neoplasm that is associated with a wide spectrum of biological activity ranging from latent benign to highly recurrent and has occasional metastatic potential. It affects the meta-epiphyseal region of long bones of young adults with most common site involved is the distal femur, followed by the distal radius. Plain radiographs and contrast-enhanced magnetic resonance imaging are the imaging modalities widely used followed by definite histopathology for diagnosis. Surgical treatment with curettage is considered optimal for local tumor control. Tumor excision with tumor-free margins is associated with lesser recurrence rates; however, for periarticular lesions this is usually accompanied with a suboptimal functional outcome. METHODS: Eleven eligible patients (all females, mean age 39.2 years) with Campanacci grade III GCT of the distal radius who were treated by en bloc resection and reconstruction with non-vascularized proximal fibular autografts at a single centre between July 2016 and December 2017 were included in the study. The patients had a clinical and radiographic review every month for the first 6 months, then biannually for minimum of 2 years. The functional, oncologic and radiological outcomes of the patients were analyzed and recorded. RESULTS: The mean duration of follow-up was 31.9 months. Bony union was achieved in all cases. The mean VAS score at 6 months was 1.1 (range 0-2). The mean Mayo Wrist score was 66.36 (range 55-80) with mean MSTS score was 21.09 (range 18-24). The average range of motion of the wrist was: 37.3° ± 6.9° of flexion, 47.1° ± 7.5° of extension, 57.3° ± 7.8° of supination and 63.6° ± 6.4° of pronation. The average graft length used was 15.6 cm. The complications noted were lung metastases which developed preoperatively, local site recurrence, wrist joint subluxation, foot drop and wound complication. DISCUSSION AND CONCLUSIONS: The primary aim of treating GCT distal radius is oncologically sound resection with good functional outcome and cosmesis being secondary. Reconstruction with a non-vascularized proximal fibular autograft is a reasonable option after en bloc resection of the distal radius for giant cell tumor of bone having comparable results with other treatment modalities.

Last Breath in the Emergency Department.

BACKGROUND: Early and aggressive time to intervention has been shown to increase the odds of survival and decrease mortality in critically ill patients. Since emergency medicine is a nascent specialty in India, a review and assessment of the mortality profile in the Emergency Department (ED) would help improve the quality of care. AIMS: The aim of the study is to determine the mortality profile and causes of preventable deaths at large ED in South India. METHODS: This retrospective chart review was conducted between January and December 2017. Patients admitted with Triage priority 1 and priority 2 of our ED, who died, despite treatment, were recruited in the study. Two ED consultants blinded from each other, independently audited all the charts to determine preventable and nonpreventable causes of death. RESULTS: There were a total of 69,369 patients during the study period who presented to the ED. Despite resuscitation 189 (0.7%) died, the mortality rate was 2.43%. Cardiac-related (32%) and sepsis-related (31%) causes were the most common cause of death, 23.8% were due to preventable causes and 16.9% of which were due to inappropriate management. In patients with sepsis, the odds of death due to preventable causes were significantly high (odds ratio 4.31, 95% confidence intervals: 1.96-9.47; P < 0.001). CONCLUSIONS: Cardiac- and sepsis-related causes of death, together accounted for most of the mortality. In patients with sepsis, the odds of death due to preventable causes were more than four times higher than those without preventable causes.

Author Correction: MCT2 mediates concentration-dependent inhibition of glutamine metabolism by MOG.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Spinal holocord epidural abscess evacuated with double thoracic interval laminectomy: a rare case report with literature review.

Introduction: Holocord spinal cord epidural abscess is an uncommon condition that may result in serious neurological complications. Prompt diagnosis and early treatment is of paramount importance for an optimum clinical outcome. This case report describes a novel technique of interval laminectomy at two sites in the thoracic spine and surgical decompression with the help of infant feeding tubes in a case of holocord spinal epidural abscess (HSEA). Case presentation: An 18-year-old male presented to the emergency department with high-grade fever and low back ache of 2 weeks duration and loss of bowel and bladder control for 4 days. Neurological examination revealed intact motor power and sensation in all four limbs at presentation; however, there was a rapid deterioration to complete quadriplegia within 24 h. A diagnosis of holocord epidural abscess was made. Emergent decompression via interval thoracic laminectomy was done and appropriate antimicrobial therapy was instituted. At 10 months of follow-up, the individual showed complete neurological recovery. Discussion: The technique used in this case is unique with respect to the level of laminectomy and the manoeuvre employed for pus evacuation. Complete neurological and functional recovery was achieved despite complete paralysis pre-operatively. The outcome indicates that there may be good prognosis for individuals with HSEA accompanied with neurological deficit and emergent surgical decompression.

MCT2 mediates concentration-dependent inhibition of glutamine metabolism by MOG.

α-Ketoglutarate (αKG) is a key node in many important metabolic pathways. The αKG analog N-oxalylglycine (NOG) and its cell-permeable prodrug dimethyloxalylglycine (DMOG) are extensively used to inhibit αKG-dependent dioxygenases. However, whether NOG interference with other αKG-dependent processes contributes to its mode of action remains poorly understood. Here we show that, in aqueous solutions, DMOG is rapidly hydrolyzed, yielding methyloxalylglycine (MOG). MOG elicits cytotoxicity in a manner that depends on its transport by monocarboxylate transporter 2 (MCT2) and is associated with decreased glutamine-derived tricarboxylic acid-cycle flux, suppressed mitochondrial respiration and decreased ATP production. MCT2-facilitated entry of MOG into cells leads to sufficiently high concentrations of NOG to inhibit multiple enzymes in glutamine metabolism, including glutamate dehydrogenase. These findings reveal that MCT2 dictates the mode of action of NOG by determining its intracellular concentration and have important implications for the use of (D)MOG in studying αKG-dependent signaling and metabolism.

Correlation analysis of targeted proteins and metabolites to assess and engineer microbial isopentenol production.

The ability to rapidly assess and optimize heterologous pathway function is critical for effective metabolic engineering. Here, we develop a systematic approach to pathway analysis based on correlations between targeted proteins and metabolites and apply it to the microbial production of isopentenol, a promising biofuel. Starting with a seven-gene pathway, we performed a correlation analysis to reduce pathway complexity and identified two pathway proteins as the primary determinants of efficient isopentenol production. Aided by the targeted quantification of relevant pathway intermediates, we constructed and subsequently validated a conceptual model of isopentenol pathway function. Informed by our analysis, we assembled a strain which produced isopentenol at a titer 1.5 g/L, or 46% of theoretical yield. Our engineering approach allowed us to accurately identify bottlenecks and determine appropriate pathway balance. Paired with high-throughput cloning techniques and analytics, this strategy should prove useful for the analysis and optimization of increasingly complex heterologous pathways.

Capillary electrophoretic separation-based approach to determine the labeling kinetics of oligodeoxynucleotides.

With the recent advances in electron microscopy (EM), computation, and nanofabrication, the original idea of reading DNA sequence directly from an image can now be tested. One approach is to develop heavy atom labels that can provide the contrast required for EM imaging. While evaluating tentative labels for the respective nucleobases in synthetic oligodeoxynucleotides (oligos), we developed a streamlined CE protocol to assess the label stability, reactivity, and selectivity. We report our protocol using osmium tetroxide 2,2'-bipyridine (Osbipy) as a thymidine (T) specific label. The observed rates show that the labeling process is kinetically independent of both the oligo length, and the base composition. The conditions, i.e. temperature, optimal Osbipy concentration, and molar ratio of reagents, to promote 100% conversion of the starting oligo to labeled product were established. Hence, the optimized conditions developed with the oligos could be leveraged to allow osmylation of effectively all Ts in ssDNA, while achieving minimal mislabeling. In addition, the approach and methods employed here may be adapted to the evaluation of other prospective contrasting agents/labels to facilitate next-generation DNA sequencing by EM.