Alternative splicing events as peripheral biomarkers for motor learning deficit caused by adverse prenatal environments.

Severity of neurobehavioral deficits in children born from adverse pregnancies, such as maternal alcohol consumption and diabetes, does not always correlate with the adversity's duration and intensity. Therefore, biological signatures for accurate prediction of the severity of neurobehavioral deficits, and robust tools for reliable identification of such biomarkers, have an urgent clinical need. Here, we demonstrate that significant changes in the alternative splicing (AS) pattern of offspring lymphocyte RNA can function as accurate peripheral biomarkers for motor learning deficits in mouse models of prenatal alcohol exposure (PAE) and offspring of mother with diabetes (OMD). An aptly trained deep-learning model identified 29 AS events common to PAE and OMD as superior predictors of motor learning deficits than AS events specific to PAE or OMD. Shapley-value analysis, a game-theory algorithm, deciphered the trained deep-learning model's learnt associations between its input, AS events, and output, motor learning performance. Shapley values of the deep-learning model's input identified the relative contribution of the 29 common AS events to the motor learning deficit. Gene ontology and predictive structure-function analyses, using Alphafold2 algorithm, supported existing evidence on the critical roles of these molecules in early brain development and function. The direction of most AS events was opposite in PAE and OMD, potentially from differential expression of RNA binding proteins in PAE and OMD. Altogether, this study posits that AS of lymphocyte RNA is a rich resource, and deep-learning is an effective tool, for discovery of peripheral biomarkers of neurobehavioral deficits in children of diverse adverse pregnancies.

Adipocyte-Derived Small Extracellular Vesicles from Patients with Alzheimer Disease Carry miRNAs Predicted to Target the CREB Signaling Pathway in Neurons.

Alzheimer disease (AD) is characterized by amyloid-ß (Aß) plaques, neurofibrillary tangles, synaptic dysfunction, and progressive dementia. Midlife obesity increases the risk of developing AD. Adipocyte-derived small extracellular vesicles (ad-sEVs) have been implicated as a mechanism in several obesity-related diseases. We hypothesized that ad-sEVs from patients with AD would contain miRNAs predicted to downregulate pathways involved in synaptic plasticity and memory formation. We isolated ad-sEVs from the serum and cerebrospinal fluid (CSF) of patients with AD and controls and compared miRNA expression profiles. We performed weighted gene co-expression network analysis (WGCNA) on differentially expressed miRNAs to identify highly interconnected clusters correlating with clinical traits. The WGCNA identified a module of differentially expressed miRNAs, in both the serum and CSF, that was inversely correlated with the Mini-Mental State Examination scores. Within this module, miRNAs that downregulate CREB signaling in neurons were highly represented. These results demonstrate that miRNAs carried by ad-sEVs in patients with AD may downregulate CREB signaling and provide a potential mechanistic link between midlife obesity and increased risk of AD.

Mesenchymal Stromal Cell Delivery Via Cardiopulmonary Bypass Provides Neuroprotection in a Juvenile Porcine Model.

Oxidative/inflammatory stresses due to cardiopulmonary bypass (CPB) cause prolonged microglia activation and cortical dysmaturation, thereby contributing to neurodevelopmental impairments in children with congenital heart disease (CHD). This study found that delivery of mesenchymal stromal cells (MSCs) via CPB minimizes microglial activation and neuronal apoptosis, with subsequent improvement of cortical dysmaturation and behavioral alteration after neonatal cardiac surgery. Furthermore, transcriptomic analyses suggest that exosome-derived miRNAs may be the key drivers of suppressed apoptosis and STAT3-mediated microglial activation. Our findings demonstrate that MSC treatment during cardiac surgery has significant translational potential for improving cortical dysmaturation and neurological impairment in children with CHD.

Paraduodenal Hernia With Massive Intestinal Gangrene and Its Surgical Management: A Case Report.

Paraduonenal hernia constitutes more than 50% of internal hernia cases. It can result in perilous sequelae like gut ischemia and perforation. We report a case of a patient who presented with acute intestinal obstruction and peritonitis and was diagnosed as a case of complicated paraduodenal as an incidental finding on laparotomy.  A 26-year-old male patient presented with three days history of continuous severe incapacitating diffuse abdominal pain. The pain was associated with multiple episodes of bilious vomiting and absolute constipation. Patient had signs and symptoms of shock. Abdomen examination showed generalized peritonitis. Patient had deranged laboratory investigations. Abdominal X-ray showed acute intestinal obstruction. Patient was resuscitated and taken up for emergency laparotomy. Intraoperatively there was a long segment of gangrenous small bowel entrapped in the paraduodenal sac. Gangrenous gut was released from the sac and excised with proximal and distal ends fashioned as stoma through separate sites. Patient was managed with intravenous fluids with total parental nutrition. Patient gradually started on oral diet and jejunostomy output was refed through the distal stoma. Patient was discharged on postoperative day 14. Patient had uneventful early stoma closure at postoperative day 45 and now is on regular follow-up in the outdoor department. Paraduodenal hernias are one of the rare causes of intestinal obstruction that is difficult to diagnose. Radiologic investigation like abdominal computed tomography (CT) scan can aid in diagnosis of paraduodenal hernia. Surgeons should have clear knowledge about abnormal anatomy of internal hernias and complications they can face during surgery.

HSP70 and HSP90 in neurodegenerative diseases.

Molecular chaperones have a role to stabilize proteins or assist them in reaching their native fold. Heat shock proteins (HSPs) are a family of molecular chaperons that protect proteins from cellular stress during the assembly of protein complexes and also prevent the proteins from aggregation and disassembly. The immediate increase of HSPs is crucial for cellular adaptation to environmental changes and protection of other proteins from denaturation, thereby maintaining the cellular homeostasis and increasing the longevity of an organism. HSP70 and HSP90 are the most studied HSPs in this very large HSP family. Notably, HSP90 also stabilizes the disease-related proteins in neurodegenerative disorders. Therefore, small molecules that inhibit the HSP90 but also increase the HSP70 has been tested as potential drugs for neurodegenerative disorders.

ABCD: Alzheimer's disease Biomarkers Comprehensive Database.

Alzheimer's disease (AD) is an age-related, non-reversible, and progressive brain disorder. Memory loss, confusion, and personality changes are major symptoms noticed. AD ultimately leads to a severe loss of mental function. Due to lack of effective biomarkers, no effective medication was available for the complete treatment of AD. There is a need to provide all AD-related essential information to the scientific community. Our resource Alzheimer's disease Biomarkers Comprehensive Database (ABCD) is being planned to accomplish this objective. ABCD is a huge collection of AD-related data of molecular markers. The web interface contains information concerning the proteins, genes, transcription factors, SNPs, miRNAs, mitochondrial genes, and expressed genes implicated in AD pathogenesis. In addition to the molecular-level data, the database has information for animal models, medicinal candidates and pathways involved in the AD and some image data for AD patients. ABCD is coupled with some major external resources where the user can retrieve additional general information about the disease. The database was designed in such a manner that user can extract meaningful information about gene, protein, pathway, and regulatory elements based search options. This database is unique in the sense that it is completely dedicated to specific neurological disorder i.e. AD. Further advance options like AD-affected brain image data of patients and structural compound level information add values to our database. Features of this database enable users to extract, analyze and display information related to a disease in many different ways. The database is available for academic purpose and accessible at http://www.bioinfoindia.org/abcd.

In silico screening of deleterious single nucleotide polymorphisms (SNPs) and molecular dynamics simulation of disease associated mutations in gene responsible for oculocutaneous albinism type 6 (OCA 6) disorder.

Solute carrier family 24 member 5 (SLC24A5) is a gene that is associated with oculocutaneous albinism type 6 (OCA6) disorder and is involved in skin and hair pigmentation. It is involved in the maturation of melanosomes and melanin synthesis. SLC24A5 gene is located in the chromosomal position of 15q21.1. The present study involves the use of computational techniques in order to obtain a detailed picture of the most probable mutations that are associated with SLC24A5. From the observed result it was found that the mutation S145F is most deleterious and disease associated is predicted using several bioinformatics tools. The 3-D structures of native and mutant (S145F) were modeled in order to understand protein functionality using ab initio Robetta server. The modeled structure validation was done with ERRAT, Verify-3D, Procheck and RAMPAGE Ramachandran plot analysis. The most validated structure undergoes molecular dynamics simulations (MDS) study to understand the structural and functional behaviour of the native and mutant proteins. The MDS result showed the more flexibility in the native SLC24A5 structure. Due to mutation in the SLC24A5 protein structure it became more rigid and might disturb the conformational changes and glycosylation function of protein structure and might play role in inducing the OCA6. This study provides a significant insight into the underlying molecular mechanism involved in albinism associated with OCA6. It further helps scientists to develop a drug therapy against OCA 6 disease. Communicated by Ramaswamy H. Sarma.

An integrative approach to develop computational pipeline for drug-target interaction network analysis.

Understanding the general principles governing the functioning of biological networks is a major challenge of the current era. Functionality of biological networks can be observed from drug and target interaction perspective. All possible modes of operations of biological networks are confined by the interaction analysis. Several of the existing approaches in this direction, however, are data-driven and thus lack potential to be generalized and extrapolated to different species. In this paper, we demonstrate a systems pharmacology pipeline and discuss how the network theory, along with gene ontology (GO) analysis, co-expression analysis, module re-construction, pathway mapping and structure level analysis can be used to decipher important properties of biological networks with the aim to propose lead molecule for the therapeutic interventions of various diseases.

Comparative de novo transcriptome analysis of male and female Sea buckthorn.

Sea buckthorn is a dioecious medicinal plant found at high altitude. The plant has both male and female reproductive organs in separate individuals. In this article, whole transcriptome de novo assemblies of male and female flower bud samples were carried out using Illumina NextSeq 500 platform to determine the role of the genes involved in sex determination. Moreover, genes with differential expression in male and female transcriptomes were identified to understand the underlying sex determination mechanism. The current study showed 63,904 and 62,272 coding sequences (CDS) in female and male transcriptome data sets, respectively. 16,831 common CDS were screened out from both transcriptomes, out of which 625 were upregulated and 491 were found to be downregulated. To understand the potential regulatory roles of differentially expressed genes in metabolic networks and biosynthetic pathways: KEGG mapping, gene ontology, and co-expression network analysis were performed. Comparison with Flowering Interactive Database (FLOR-ID) resulted in eight differentially expressed genes viz. CHD3-type chromatin-remodeling factor PICKLE (PKL), phytochrome-associated serine/threonine-protein phosphatase (FYPP), protein TOPLESS (TPL), sensitive to freezing 6 (SFR6), lysine-specific histone demethylase 1 homolog 1 (LDL1), pre-mRNA-processing-splicing factor 8A (PRP8A), sucrose synthase 4 (SUS4), ubiquitin carboxyl-terminal hydrolase 12 (UBP12), known to be broadly involved in flowering, photoperiodism, embryo development, and cold response pathways. Male and female flower bud transcriptome data of Sea buckthorn may provide comprehensive information at genomic level for the identification of genetic regulation involved in sex determination.

Publisher Correction: A novel miRNA analysis framework to analyze differential biological networks.

A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper.

Comparative transcriptomics reveals a reduction in carbon capture and flux between source and sink in cytokinin-treated inflorescences of Jatropha curcas L.

The low seed yield of Jatropha curcas has been a stumbling block in realizing its full potential as an ideal bioenergy crop. Low female to male flower ratio is considered as a major limiting factor responsible for low seed yield in Jatropha. An exogenous cytokinin application was performed on floral meristems to increase the seed yield. This resulted in an increase of total flowers count with a higher female to male flower ratio. However, the seed biomass did not increase in the same proportion. The possible reason for this was hypothesized to be the lack of increased photosynthesis efficiency at source tissues which could fulfil the increased demand of photosynthates and primary metabolites in maturing seeds. After cytokinin application, possible molecular mechanisms underlying carbon capture and flux affected between the source and sink in developing flowers, fruits and seeds were investigated. Comparative transcriptome analysis was performed on inflorescence meristems (treated with cytokinin) and control (untreated inflorescence meristems) at time intervals of 15 and 30 days, respectively. KEGG-based functional annotation identified various metabolic pathways associated with carbon capture and flux. Pathways such as photosynthesis, carbon fixation, carbohydrate metabolism and nitrogen metabolism were upregulated after 15 days of cytokinin treatment; however, those were downregulated after 30 days. Five genes FBP, SBP, GS, GDH and AGPase showed significant increase in transcript abundance after 15 days of treatment but showed a significant decrease after 30 days. These genes, after functional validation, can be suitable targets in designing a suitable genetic intervention strategy to increase overall seed yield in Jatropha.

A novel miRNA analysis framework to analyze differential biological networks.

For understanding complex biological systems, a systems biology approach, involving both the top-down and bottom-up analyses, is often required. Numerous system components and their connections are best characterised as networks, which are primarily represented as graphs, with several nodes connected at multiple edges. Inefficient network visualisation is a common problem related to transcriptomic and genomic datasets. In this article, we demonstrate an miRNA analysis framework with the help of Jatropha curcas healthy and disease transcriptome datasets, functioning as a pipeline derived from the graph theory universe, and discuss how the network theory, along with gene ontology (GO) analysis, can be used to infer biological properties and other important features of a network. Network profiling, combined with GO, correlation, and co-expression analyses, can aid in efficiently understanding the biological significance of pathways, networks, as well as a studied system. The proposed framework may help experimental and computational biologists to analyse their own data and infer meaningful biological information.

Modular Design of Picroside-II Biosynthesis Deciphered through NGS Transcriptomes and Metabolic Intermediates Analysis in Naturally Variant Chemotypes of a Medicinal Herb, Picrorhiza kurroa.

Picroside-II (P-II), an iridoid glycoside, is used as an active ingredient of various commercial herbal formulations available for the treatment of liver ailments. Despite this, the knowledge of P-II biosynthesis remains scarce owing to its negligence in Picrorhiza kurroa shoots which sets constant barrier for function validation experiments. In this study, we utilized natural variation for P-II content in stolon tissues of different P. kurroa accessions and deciphered its metabolic route by integrating metabolomics of intermediates with differential NGS transcriptomes. Upon navigating through high vs. low P-II content accessions (1.3-2.6%), we have established that P-II is biosynthesized via degradation of ferulic acid (FA) to produce vanillic acid (VA) which acts as its immediate biosynthetic precursor. Moreover, the FA treatment in vitro at 150 µM concentration provided further confirmation with 2-fold rise in VA content. Interestingly, the cross-talk between different compartments of P. kurroa, i.e., shoots and stolons, resolved spatial complexity of P-II biosynthesis and consequently speculated the burgeoning necessity to bridge gap between VA and P-II production in P. kurroa shoots. This work thus, offers a forward looking strategy to produce both P-I and P-II in shoot cultures, a step toward providing a sustainable production platform for these medicinal compounds via-à-vis relieving pressure from natural habitat of P. kurroa.

A Simple Innovative Alternative for Irrigation-Aspiration in Orthopedic Infections Using a Foley Catheter.

BACKGROUND: The purpose of the study was to investigate the role of the Foley catheter in maximizing surgical debridement in patients with chronic osteomyelitis. PATIENTS AND METHODS: During surgical debridement in patients with chronic osteomyelitis, the medullary cavity is reamed thoroughly. The bulb of the Foley catheter is inflated with saline to facilitate the removal of the outer wall of the bulb using scissors. A guide wire is fed into the larger lumen of the Foley catheter up to its tip. Once the catheter is negotiated into the medullary cavity of the distal fragment, the guide wire is removed. The system is ready for irrigation. Through the smaller lumen of the catheter, which is open distally, copious irrigation is possible, delivering the fluid where it is required. At the same time, suction is connected to the proximal tip of the Foley catheter using a sterile adaptor. Constant suction is applied until the aspirated fluid is clear. The final aspirate is analyzed by semi-quantitative Gram staining and culture and sensitivity tests. RESULTS: In all nine patients, the semi-quantitative Gram stain test was reported as one plus, suggesting that the bacterial population was less than one per oil immersion field. The post-operative culture results in all nine patients were reported as negative. All nine patients experienced primary healing. There was no evidence of recurrence in any patient, even after 12 months of follow-up. CONCLUSION: We describe an effective, inexpensive, and readily available method to aid in the debridement of an infected medullary cavity.

Management of pseudoaneurysm of internal maxillary artery resulting from trauma.

Pseudoaneurysm of internal maxillary artery following trauma is a rare clinical entity. A rapidly growing swelling in the facial region following fracture of the mandibular subcondylar region is an indication of a developing aneurysm. A case of pseudoaneurysm of the internal maxillary artery following condylar fracture of mandible is reported. The case was treated successfully by surgery.

A novel method of using mini external fixator for maintaining web space after the release of contracture and syndactyly.

Syndactyly and postburn contracture of the digits are the common cases seen in a hand clinic. Their management can be roughly divided into 3 stages. In stage 1, syndactyly/postburn contracture of the digits are surgically released; in stage 2, surgical wound care is provided; and in stage 3, the patient undergoes physiotherapy (rehabilitation). The most common method of immobilizing the digit after the release is by plaster of Paris splints. Its demerit includes loss of correction, painful postoperative dressing, and suboptimal graft uptake due to improper immobilization and maceration. We describe a simple and effective method of mitigating the above-mentioned drawbacks using a mini external fixator, after the release of the contracted fingers. The use of this fixator also helps during the surgery (stage 1) as resurfacing of the raw areas becomes quick because 2 surgeons can perform this simultaneously. The web can be further opened up using the fixator to facilitate the suturing of the FTG/flap, after which it can be brought back to its normal position. As the dimension of the raw area created is fully defined it becomes easier to suture the flap/graft with appropriate tension and tie-over dressing. The postoperative dressings become easier and pain free. The maceration of the skin graft and skin margin is reduced as the compressive dressing can be applied to individual fingers rather than a collective dressing. It is advantageous even in stage 3 as it allows the surgeon to customize the splint for each finger.