Nodding syndrome: A key role for sources of nutrition?

Nodding Syndrome (NS) has occurred among severely food-stressed communities in northern Uganda and several other East African populations that, with their forced physical displacement, have resorted to nutritional support from available wild plants and fungi, some of which have neurotoxic potential. Among the latter is an agaric mushroom with an unknown content of hydrazine-generating agaritine, namely Agaricus bingensis, the unusually wide consumption of which may relate to the low serum levels of vitamin B6 in Ugandan NS subjects relative to controls. Hydrazine-related compounds induce patterns of DNA damage that promote neuropathological changes (tauopathy) reminiscent of those associated with established NS. While the cause of this childhood brain disease is unknown, we encourage increased attention to the role of malnutrition and B6 hypovitaminosis in the etiology of this devastating brain disease.

Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples.

Genomics has benefited from an explosion in affordable high-throughput technology for whole-genome sequencing. The regulatory and functional aspects in non-coding regions may be an important contributor to oncogenesis. Whole-genome tumor-normal paired alignments were used to examine the non-coding regions in five cancer types and two races. Both a sliding window and a binning strategy were introduced to uncover areas of higher than expected variation for additional study. We show that the majority of cancer associated mutations in 154 whole-genome sequences covering breast invasive carcinoma, colon adenocarcinoma, kidney renal papillary cell carcinoma, lung adenocarcinoma and uterine corpus endometrial carcinoma cancers and two races are found outside of the coding region (4 432 885 in non-gene regions versus 1 412 731 in gene regions). A pan-cancer analysis found significantly mutated windows (292 to 3881 in count) demonstrating that there are significant numbers of large mutated regions in the non-coding genome. The 59 significantly mutated windows were found in all studied races and cancers. These offer 16 regions ripe for additional study within 12 different chromosomes-2, 4, 5, 7, 10, 11, 16, 18, 20, 21 and X. Many of these regions were found in centromeric locations. The X chromosome had the largest set of universal windows that cluster almost exclusively in Xq11.1-an area linked to chromosomal instability and oncogenesis. Large consecutive clusters (super windows) were found (19 to 114 in count) providing further evidence that large mutated regions in the genome are influencing cancer development. We show remarkable similarity in highly mutated non-coding regions across both cancer and race.

COVID-19 Biomarkers in research: Extension of the OncoMX cancer biomarker data model to capture biomarker data from other diseases.

Scientists, medical researchers, and health care workers have mobilized worldwide in response to the outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; SCoV2). Preliminary data have captured a wide range of host responses, symptoms, and lingering problems post-recovery within the human population. These variable clinical manifestations suggest differences in influential factors, such as innate and adaptive host immunity, existing or underlying health conditions, co-morbidities, genetics, and other factors. As COVID-19-related data continue to accumulate from disparate groups, the heterogeneous nature of these datasets poses challenges for efficient extrapolation of meaningful observations, hindering translation of information into clinical applications. Attempts to utilize, analyze, or combine biomarker datasets from multiple sources have shown to be inefficient and complicated, without a unifying resource. As such, there is an urgent need within the research community for the rapid development of an integrated and harmonized COVID-19 Biomarker Knowledgebase. By leveraging data collection and integration methods, backed by a robust data model developed to capture cancer biomarker data we have rapidly crowdsourced the collection and harmonization of COVID-19 biomarkers. Our resource currently has 138 unique biomarkers. We found multiple instances of the same biomarker substance being suggested as multiple biomarker types during our extensive cross-validation and manual curation. As a result, our Knowledgebase currently has 265 biomarker type combinations. Every biomarker entry is made comprehensive by bringing in together ancillary data from multiple sources such as biomarker accessions (canonical UniProtKB accession, PubChem Compound ID, Cell Ontology ID, Protein Ontology ID, NCI Thesaurus Code, and Disease Ontology ID), BEST biomarker category, and specimen type (Uberon Anatomy Ontology) unified with ontology standards. Our preliminary observations show distinct trends in the collated biomarkers. Most biomarkers are related to the immune system (SAA,TNF-∝, and IP-10) or coagulopathies (D-dimer, antithrombin, and VWF) and a few have already been established as cancer biomarkers (ACE2, IL-6, IL-4 and IL-2). These trends align with proposed hypotheses of clinical manifestations compounding the complexity of COVID-19 pathobiology. We explore these trends as we put forth a COVID-19 biomarker resource that will help researchers and diagnosticians alike. All biomarker data are freely available from https://data.oncomx.org/covid19 .

Nodding syndrome phenotypes.

Nodding syndrome (NS) is a progressive encephalopathy of children and adolescents characterized by seizures, including periodic vertical head nodding. Epidemic NS, which has affected parts of East Africa, appears to have clinical overlap with sub-Saharan Nakalanga syndrome (NLS), a brain disorder associated with pituitary dwarfism that appears to have a patchy distribution across sub-Sahara. Clinical stages of NS include inattention and blank stares, vertical head nodding, convulsive seizures, multiple impairments, and severe cognitive and motorsystem disability, including features suggesting parkinsonism. Head nodding episodes occur in clusters with an electrographic correlate of diffuse high-amplitude slow waves followed by an electrodecremental pattern with superimposed diffuse fast activity. Brain imaging reveals differing degrees of cerebral cortical and cerebellar atrophy. Brains of NS-affected children with mild frontotemporal cortical atrophy display neurofibrillary pathology and dystrophic neurites immunopositive for tau, consistent with a progressive neurodegenerative disorder. The etiology of NS and NLS appears to be dominated by environmental factors, including malnutrition, displacement, and nematode infection, but the specific cause is unknown.

Impact of germline and somatic missense variations on drug binding sites.

Advancements in next-generation sequencing (NGS) technologies are generating a vast amount of data. This exacerbates the current challenge of translating NGS data into actionable clinical interpretations. We have comprehensively combined germline and somatic nonsynonymous single-nucleotide variations (nsSNVs) that affect drug binding sites in order to investigate their prevalence. The integrated data thus generated in conjunction with exome or whole-genome sequencing can be used to identify patients who may not respond to a specific drug because of alterations in drug binding efficacy due to nsSNVs in the target protein's gene. To identify the nsSNVs that may affect drug binding, protein-drug complex structures were retrieved from Protein Data Bank (PDB) followed by identification of amino acids in the protein-drug binding sites using an occluded surface method. Then, the germline and somatic mutations were mapped to these amino acids to identify which of these alter protein-drug binding sites. Using this method we identified 12 993 amino acid-drug binding sites across 253 unique proteins bound to 235 unique drugs. The integration of amino acid-drug binding sites data with both germline and somatic nsSNVs data sets revealed 3133 nsSNVs affecting amino acid-drug binding sites. In addition, a comprehensive drug target discovery was conducted based on protein structure similarity and conservation of amino acid-drug binding sites. Using this method, 81 paralogs were identified that could serve as alternative drug targets. In addition, non-human mammalian proteins bound to drugs were used to identify 142 homologs in humans that can potentially bind to drugs. In the current protein-drug pairs that contain somatic mutations within their binding site, we identified 85 proteins with significant differential gene expression changes associated with specific cancer types. Information on protein-drug binding predicted drug target proteins and prevalence of both somatic and germline nsSNVs that disrupt these binding sites can provide valuable knowledge for personalized medicine treatment. A web portal is available where nsSNVs from individual patient can be checked by scanning against DrugVar to determine whether any of the SNVs affect the binding of any drug in the database.

Low detection of Vibrio cholerae carriage in healthcare workers returning to 12 Latin American countries from Haiti.

SUMMARY This investigation was undertaken to characterize the prevalence of intestinal Vibrio cholerae in healthcare workers (HCWs) returning from Haiti due to the ongoing cholera epidemic. Eight hundred and fifty asymptomatic HCWs of the Cuban Medical Brigade, who planned to leave Haiti, were studied by laboratory screening of stool culture for V. cholerae. A very low percentage (0.23%) of toxigenic V. cholerae serogroup O1, serotype Ogawa was found. To the best of our knowledge, this study represents the largest reported screening study for V. cholerae infection in asymptomatic HCWs returning from a cholera-affected country. Cholera transmission to health personnel highlights a possible risk of transmitting cholera during mobilization of the population for emergency response. Aid workers are encouraged to take precautions to reduce their risk for acquiring cholera and special care should be taken by consuming safe water and food and practising regular hand washing.

Pharmacognostical and Phytochemical Evaluation of the leaves of Bauhinia purpurea Linn.

Various pharmacognostic parameters including macroscopy, microscopy, chemomicroscopy and behaviour of powdered drug on treatment with different chemical reagents were studied on the leaves of Bauhinia purpurea Linn. (Family Caesalpinaceae). Phytochemical screening of the plant part with various solvents revealed the presence of phenolic compounds, tannins, flavonoids, phytosterols, saponins and glycosides in it.

An emerging cyberinfrastructure for biodefense pathogen and pathogen-host data.

The NIAID-funded Biodefense Proteomics Resource Center (RC) provides storage, dissemination, visualization and analysis capabilities for the experimental data deposited by seven Proteomics Research Centers (PRCs). The data and its publication is to support researchers working to discover candidates for the next generation of vaccines, therapeutics and diagnostics against NIAID's Category A, B and C priority pathogens. The data includes transcriptional profiles, protein profiles, protein structural data and host-pathogen protein interactions, in the context of the pathogen life cycle in vivo and in vitro. The database has stored and supported host or pathogen data derived from Bacillus, Brucella, Cryptosporidium, Salmonella, SARS, Toxoplasma, Vibrio and Yersinia, human tissue libraries, and mouse macrophages. These publicly available data cover diverse data types such as mass spectrometry, yeast two-hybrid (Y2H), gene expression profiles, X-ray and NMR determined protein structures and protein expression clones. The growing database covers over 23 000 unique genes/proteins from different experiments and organisms. All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers. The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/protein(s) via UniProtKB accession numbers or protein function keywords. The system is accessible at http://www.proteomicsresource.org/.

Studies on Pharmacognostical features of Curcuma domestica Val.

The microscopic and macroscopic characters of the rhizome of Curcuma domestica Val. were studied. The behavior of the powdered drug in the presence of various chemicals was also studied. Preliminary phytochemical screening on the various extracts of the rhizome was done in order to ascertain the various chemical constituents present. These studies were carried out to identify this plant for future research work.

Anthelmintic activity of root bark of Carissa carandas.

The anthelmintic activity of the Imethanolic extract of the root bark of Carissa carandas was evaluated on adult Indian earthworm (Pheretima posthuma) using albendazole as a reference standard. The extract caused paralysis followed by the death of worm at the tested dose level. The extract at the highest tested concentration has anthelmintic activity comparable with that of standard drug albendazole.

Antidiarrhoeal evaluation of Aegle Marmelos (Correa) Linn. root extract.

A study was undertaken to evaluate the in vitro and in vivo antidiarrhoeal potential of chloroform extract of the root of Aegle marmelos (Correa) Linn. The in vitro activity was determined by agar dilution and disc diffusion techniques. The extract was studied in vivo in rats. Of the 35 tested pathogenic diarrhoea causing strains, the extract was found to be mostly active against the strains of Vibrio cholerae, followed by Escherichia coli and Shigella spp. The in vitro activity was found to be comparable to that of ciprofloxacin. Further, Aegle marmelos root extract (AMRE) treated animals showed significant inhibitory activity against castor oil-induced diarrhoea. The results so obtained thus established the efficacy of AMRE as an effective antidiarrhoeal agent.

Effect of Mesua ferrea Linn. flower extract on Salmonella.

Based on its traditional uses in folk medicine, the whole flower extract of Mesua ferrea Linn. was tested for its in vitro antimicrobial efficacy against five different strains of Salmonella spp. All the strains were found to be highly sensitive to the extract, MIC of the extract against each organism being 50 microg/ml. The extract was tested in vitro for its mode of antibacterial activity against S. Typhimurium NCTC 74 and it was found to be bactericidal in action. In vivo studies of this extract offered significant protection to Swiss albino mice at doses approximately 2 and 4 mg/mouse when challenged with 50 median lethal dose of S. Typhimurium NCTC 74. Further, the extract caused statistically significant reduction in viable count of the strain in liver, spleen and heart blood of challenged mice.

PHARMACOGNOSTICAL STUDIES ON THE LEAVES OF Cassia tora Linn. (FAM. CAESALPINIACEAE).

The leaves and seeds of Cassia tora (Family Caesalpinaceae) are used in the treatment of leprosy, ring worm, flatulence, colic, dyspepsia, constipation, cough, bronchitis and cardiac disorders in the Ayurvedic systems of medicine. The present study deals with the study of macroscopic characters of the leaves, ash values, extractive values, behavior on treatment with different chemical reagents and fluorescence characters under ultraviolet light. Preliminary phytochemical studies on different extractives of the leaves were also performed. These studies will help in the identification of the plant for further research.

STUDIES ON PHARMCOGNOSTICAL FEATURES OF Zizyphus mauritiana LINN. ROOT (FAMILY : RHAMNACEAE).

Description of the root of the plant, Zizyphus mauritiana Linn. the microscopical characters of the powdered root, its behavior on treatment with different chemical reagents, and the fluorescence character under ultraviolet light after treatment were studied to fix some pharmacognostical parameters. Preliminary phytochemical screening on the various extracts of the root of the plant was also performed. These studies were carried out to identify this plant for further research work.

High efficiency degradation of tetrahydrofuran (THF) using a membrane bioreactor: identification of THF-degrading cultures of Pseudonocardia sp. strain M1 and Rhodococcus ruber isolate M2.

A mixed microbial culture capable of growing aerobically on tetrahydrofuran (THF) as a sole carbon and energy source was used as the inoculum in a 10 l working volume membrane bioreactor. Following start-up, the reactor was operated in batch mode for 24 h and then switched to continuous feed with 100% biomass recycle. On average, greater than 96% of THF fed to the reactor was removed during the 8-month study. THF loading rates ranged from 0.62 to 9.07 g l(-1) day(-1) with a hydraulic retention time of 24 h. THF concentrations as high as 800 mg/l were tolerated by the culture. Biomass production averaged 0.28 kg total suspended solids/kg chemical oxygen demand removed, i.e., comparable to a conventional wastewater treatment process. Periodic batch wasting resulted in a solids retention time of 7-14 days. Reactor biomass typically ranged from 4 to 10 g/l volatile suspended solids and the effluent contained no solids. Pure THF-degrading cultures were isolated from the mixed culture based on morphological characteristics, Gram-staining and THF degradation. Based on 16S rDNA analysis the isolates were identified as Pseudonocardia sp. M1 and Rhodococcus ruber M2.

ANTIMICROBIAL ACTION OF THE LEAF EXTRACT OF Lagerstroemia parviflora Roxb.

The benzene extract of the leaves of Lagerstroemia paviflora Roxb was tested for its Minimum Inhibitory Concentration (MIC) against Gram Positive Staphylococcus aureus, Bacillus subtilis, Bacillus cereus, Klebsiella pneumoniae, Streptococcus pneumoniae, Lactobacillus arabinosus and gram negative strains E.Coli, Shigella dysenteriae, shigella sonnei, shigella boydii, Salmonella typhimurium, Proteus mirabilis and Vibrio cholerae. Further the zones of inhibition Produced by the crude extract against four selected bacterial strains were measured and compared with those produced by the standard antibiotic Ciprofloxacin against the same bacterial strains.

Phytochemical observation on leaf of lagerstromia parviflora (roxb).

Phytochemical studies of leaf of the plant Lagerstroemia Parviflora Roxb (Lythraceae) reveals the presence of phytosterols, tannins, alkaloids, glycosides and absence of saponin, flavanoid and triterpenoids have been reported in this plant for the first time.

Trifluoperazine: a broad spectrum bactericide especially active on staphylococci and vibrios.

Trifluoperazine showed some significant antimicrobial activity when tested against 293 strains from two Gram-positive and eight Gram-negative genera. Minimum inhibitory concentrations of the drug were measured using an agar dilution technique. Forty six of 55 strains of Staphylococcus aureus were inhibited by 10-50 microg/ml of trifluoperazine. This drug also inhibited strains of Shigella spp., Vibrio cholerae and V. parahaemolyticus at a concentration of 10-100 microg/ml. Other bacteria including Pseudomonas spp. were moderately sensitive to trifluoperazine. In the in vivo studies this compound offered significant protection to Swiss albino mice at a concentration of 30 microg/mouse (P<0.001) when challenged with 50 median lethal dose of Salmonella typhimurium NCTC 74.