Multiomics analyses reveal early metabolic imbalance and mitochondrial stress in neonatal photoreceptors leading to cell death in Pde6brd1/rd1 mouse model of retinal degeneration

Retinal diseases exhibit extensive genetic heterogeneity and complex etiology with varying onset and severity. Mutations in over 200 genes can lead to photoreceptor dysfunction and/or cell death in retinal neurodegeneration. To deduce molecular pathways that initiate and/or drive cell death, we adopted a temporal multiomics approach and examined molecular and cellular events in newborn and developing photoreceptors before the onset of degeneration in a widely-used Pde6brd1/rd1 (rd1) mouse, a model of autosomal recessive retinitis pigmentosa caused by PDE6B mutations. Transcriptome profiling of neonatal and developing rods from the rd1 retina revealed early downregulation of genes associated with anabolic pathways and energy metabolism. Quantitative proteomics of rd1 retina showed early changes in calcium signaling and oxidative phosphorylation, with specific partial bypass of complex I electron transfer, which precede the onset of cell death. Concurrently, we detected alterations in central carbon metabolism, including dysregulation of components associated with glycolysis, pentose phosphate and purine biosynthesis. Ex vivo assays of oxygen consumption and transmission electron microscopy validated early and progressive mitochondrial stress and abnormalities in mitochondrial structure and function of rd1 rods. These data uncover mitochondrial overactivation and related metabolic alterations as determinants of early pathology and implicate aberrant calcium signaling as an initiator of higher mitochondrial stress. Our studies thus provide a mechanistic framework with mitochondrial damage and metabolic disruptions as early drivers of photoreceptor cell death in retinal degeneration.

Comparative Genomics of Host-Symbiont and Free-Living Oceanobacillus Species

Survival in a given environment requires specific functions, so genomic variation is anticipated within in individual taxonomic groups that exhibit a large diversity in lifestyles. In this study, we sequence and assemble the genome of Oceanobacillus faecalis strain HM6, a resident of the human gut. Using the genus Oceanobacillus and the HM6 draft genome sequence, we explore the functional requirements for survival in a symbiotic arrangement within the human gut, in contrast to free living in the environment. Comparative genomics of seven available Oceanobacillus complete genomes highlight a genomically heterogeneous group. Our analysis did not find strict phylogenetic separation between free-living and host–symbiont Oceanobacillus members. By comparing functional gene content between host-associated and free-living species, we identified candidate genes that are potentially involved in symbiotic lifestyles, including phosphotransferase genes, transporters and two component response regulators. This study summarizes genomic and phylogenetic differences in the Oceanobacillus genus. Additionally, we highlight functions that may be key for survival in the human gut community.

Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes

Sustainable innovations in sequencing technologies have resulted in a torrent of microbial genome sequencing projects. However, the prokaryotic genomes sequenced so far are unequally distributed along their phylogenetic tree; few phyla contain the majority, the rest only a few representatives. Accurate genome annotation lags far behind genome sequencing. While automated computational prediction, aided by comparative genomics, remains a popular choice for genome annotation, substantial fraction of these annotations are erroneous. Proteogenomics utilizes protein level experimental observations to annotate protein coding genes on a genome wide scale. Benefits of proteogenomics include discovery and correction of gene annotations regardless of their phylogenetic conservation. This not only allows detection of common, conserved proteins but also the discovery of protein products of rare genes that may be horizontally transferred or taxonomy specific. Chances of encountering such genes are more in rare phyla that comprise a small number of complete genome sequences. We collated all bacterial and archaeal proteogenomic studies carried out to date and reviewed them in the context of genome sequencing projects. Here, we present a comprehensive list of microbial proteogenomic studies, their taxonomic distribution, and also urge for targeted proteogenomics of underexplored taxa to build an extensive reference of protein coding genes.

Expression profiling of lymph nodes in tuberculosis patients reveal inflammatory milieu at site of infection

Extrapulmonary manifestations constitute 15 to 20% of tuberculosis cases, with lymph node tuberculosis (LNTB) as the most common form of infection. However, diagnosis and treatment advances are hindered by lack of understanding of LNTB biology. To identify host response, Mycobacterium tuberculosis infected lymph nodes from LNTB patients were studied by means of transcriptomics and quantitative proteomics analyses. The selected targets obtained by comparative analyses were validated by quantitative PCR and immunohistochemistry. This approach provided expression data for 8,728 transcripts and 102 proteins, differentially regulated in the infected human lymph node. Enhanced inflammation with upregulation of T-helper1-related genes, combined with marked dysregulation of matrix metalloproteinases, indicates tissue damage due to high immunoactivity at infected niche. This expression signature was accompanied by significant upregulation of an immunoregulatory gene, leukotriene A4 hydrolase, at both transcript and protein levels. Comparative transcriptional analyses revealed LNTB-specific perturbations. In contrast to pulmonary TB-associated increase in lipid metabolism, genes involved in fatty-acid metabolism were found to be downregulated in LNTB suggesting differential lipid metabolic signature. This study investigates the tissue molecular signature of LNTB patients for the first time and presents findings that indicate the possible mechanism of disease pathology through dysregulation of inflammatory and tissue-repair processes.

Extensive copy number variations in admixed Indian population of African ancestry: potential involvement in adaptation

Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.

Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative 'Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed 'interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.

Neo-regeneration of urinary bladder: a desired metaplasia of autologous membrane from rectosigmoid colon containing stem cells of intestinal crypts

The current management of diseases of urinary bladder requiring resection is by augmentation cystoplasty or transplantation of ureters. Transplantation of ureters is associated with morbidity and mortality. Ideal management will be by regenerating urinary bladder in vivo. Neo-regeneration of tissues and organs like abdominal wall, aponeurosis etc., has been attempted and patented. After neo-regeneration of mesoderm tissues and organs, regeneration of urinary bladder (developed from endoderm) was. In vivo surgical techniques were developed in dogs. It is known that the embryonic morphogenesis of urinary bladder is from uro-genital sinus of hind gut. A membrane, containing endoderm stem cells in crypts of recto-sigmoid colon, was surgically isolated and colonized with remnant of urinary bladder wall after extensive resection. Experimental study was performed in dogs, for 60 days to one and a half year. Regeneration of all the layers of tissues of the wall of urinary bladder was observed. The neo-regeneration phenomenon has been recognized as "desired metaplasia". The regenerated neo tissue/organ on histological examination and cystometry studies was found compatible with normal urinary bladder. The hypothesis, neo-regeneration and desired metaplasia, is discussed.

Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India

A polyphasic approach was used to characterize a bacterium, GPTSA 11(T), isolated from a warm spring located in a reserve forest in Assam, India. The cells are Gram-variable, strictly aerobic, sporulating motile rods. The major fatty acids of the strain are C(15 : 0) anteiso (48.42 %), C(16 : 0) iso (11.59 %), C(16 : 1)omega11c (6.16 %), C(15 : 0) iso (6.03 %), C(17 : 0) anteiso (5.68 %) and C(16 : 1)omega7c alcohol (5.01 %). The presence of the fatty acid C(16 : 1)omega7c alcohol distinguishes this strain from other closely related species of the genus Paenibacillus. The strain contains MK-7 as the diagnostic menaquinone. The G+C content of the genomic DNA is 41.2 mol%. Analysis of the 16S rRNA gene sequence (1466 nt) revealed the presence of signature sequences PAEN 515F (5'-GAGTAACTGCTCTCGGAATGACGGTACTTGAGAAGAAAGCCCC-3') and PAEN 862F (5'-TCGATACCCTTGGTGCCGAAGT-3'), which were found in the species of the genus Paenibacillus surveyed by Shida et al. [Shida, O., Takagi, H., Kadowaki, K., Nakamura, L. K. & Komagata, K. (1997). Int J Syst Bacteriol 47, 289-298]. The sequence shows closest similarity (95.85 %) to that of Paenibacillus apiarius, followed by Paenibacillus alvei (94.34 %), Paenibacillus cineris (93.87 %), Paenibacillus favisporus (93.80 %), Paenibacillus chibensis (93.47 %) and Paenibacillus azoreducens (93.40 %). Biochemical, physiological, chemotaxonomic and phylogenetic analyses justify placement of the strain in the genus Paenibacillus but not within any existing species. It should, therefore, be considered as representing a novel species, for which the name Paenibacillus assamensis sp. nov. is proposed. The type strain is GPTSA 11T (=MTCC 6934T=JCM 13186T).

Comparative evaluation of cefpodoxime versus cefixime in children with lower respiratory tract infections

OBJECTIVE

The emergence of penicillin and macrolide resistant strains, responsible for Acute Lower Respiratory Tract Infections in children has offered third generation cephalosporins the platform to perform. The aim of the present study was to evaluate two third generation oral cephalosporins for their empirical use in community acquired lower respiratory tract infections in pediatric patients. An assessment of the clinical cure and bacteriological eradication rates and an overall tolerability was made.

METHODS

It was a prospective, open, comparative, multicentric study. 776 children (Mean age 10 years) with LRTIs were included and randomly allotted to two groups respectively. A total of 396 children were given cefpodoxime susp 5 mg/kg b.i.d. and 380 patients on cefixime 4 mg/kg b.i.d. for 10-14 days.

RESULTS

At the end of therapy, the clinical success with cefpodoxime was 97% as against 86.8% with cefixime. Bacterial eradication was 93.4% with cefpodoxime and 82.9% with cefixime.

CONCLUSION

Cefpodoxime has been found to be a well-tolerated and superior alternative to cefixime synergistically documenting the extended spectrum of activity.

A minisatellite sequence in the upstream region of the DURA3 gene from the halotolerant yeast Debaryomyces hansenii

The URA3 gene of Debaryomyces hansenii, encoding orotidine 5'-phosphate decarboxylase enzyme, was isolated by complementation in the yeast Saccharomyces cerevisiae. The deduced amino acid sequence is highly similar to Ura3 proteins from other yeast and fungal species. Analysis of the region upstream of the coding sequence revealed the presence of AG-rich minisatellite DNA sequences. In addition, upstream of the DURA3 sequence, we have found the 3'-terminal of a gene encoding a GEA2-like protein.

A PBS2 homologue from Debaryomyces hansenii shows a differential effect on calcofluor and polymyxin B sensitivity in Saccharomyces cerevisiae

The PBS2 gene encodes a MAP kinase kinase that plays a pivotal role in osmosensing signal-transduction pathway in the yeast Saccharomyces cerevisiae. Mutation in the PBS2 gene has a pleotropic effect. Besides being osmosensitive, pbs2 mutants show altered sensitivity to polymyxin B and calcofluor. Recent studies revealed that Pbs2p plays a different role in osmoadaptation and calcofluor sensitivity. We have isolated a gene homologous to PBS2 from the highly salt-tolerant yeast Debaryomyces hansenii by phenotypic complementation. DNA sequencing of the clone revealed that the gene encoded a protein of 683 amino acid residues. Like Pbs2p, this protein also has a proline-rich motif. Further characterization revealed that this gene could complement polymyxin B sensitivity but did not affect calcofluor sensitivity. Thus, it appeared that Pbs2p also has an independent role in these two physiological processes. The GenBank Accession No. of this sequence is AF371315.

DNA flow cytometry and bladder irrigation cytology in detection of bladder carcinoma

In this study we assessed the role of DNA flow cytometry (FCM) as an adjunct to bladder irrigation cytology to detect carcinoma of the bladder. We selected only those cases who had urinary symptoms and cystoscopic examination or histology-proven cases of bladder cancer who underwent cystoscopy for a follow-up study. Cystoscopy, cytologic examination, and DNA FCM were performed in every case. There were 9 fresh cases and 21 follow-up cases of proven transitional-cell carcinoma (TCC) of the bladder. Cystoscopy revealed growth in all 9 fresh cases as well as in 11 follow-up cases. Cytology was positive in 16 cases, out of which there were 8 each of fresh and recurrent cases. None of the cases showed positive cytology with negative cystoscopy findings. DNA FCM was positive in 13 cases. Aneuploidy was detected in 5 cases, out of which there were 3 hyperdiploid and 2 hypodiploid cases. Nine cases had high (equal or more than 10%) S and G2-M phase cells, ranging from 10-19.36%. One case showed aneuploidy along with high S-G2M phase. Both cytology and DNA FCM were positive in 9 cases. In 2 cases, DNA FCM showed aneuploidy, but cytology and cystoscopy were negative. The sensitivity and specificity of the bladder wash cytology were 80% and 100%, and those for DNA FCM were 55% and 83.3%, respectively. We conclude that both bladder wash cytology and DNA FCM techniques should be done in all the cases of suspected TCC to detect more number of positive cases.

Quantitation of spermatogenesis by DNA flow cytometry from fine-needle aspiration cytology material

DNA flow cytometry (FCM) was performed from fine-needle aspiration cytology (FNAC) of testis in 15 cases of male infertility to quantitate spermatogenesis. The results were correlated with FNAC findings. DNA FCM showed a ploidy relationship of haploid (1N) > diploid (2N) > tetraploid (4N) in cases of normal spermatogenesis. A ploidy relation of 2N > 1N > 4N was observed in cases of hypospermatogenesis or maturation arrest. In Sertoli cell-only cases, there were only 2N populations of cells. With the help of DNA FCM, a rapid and objective assessment of spermatogenesis is possible from FNAC of the testis.

Isolation and sequence of the HOG1 homologue from Debaryomyces hansenii by complementation of the hog1Delta strain of Saccharomyces cerevisiae

The HOG1 gene encodes a MAP kinase that plays an essential role in maintaining water homeostasis in the yeast Saccharomyces cerevisiae. A gene homologous to S. cerevisiae HOG1 has been isolated from a highly salt-tolerant yeast, Debaryomyces hansenii, by phenotypic complementation. DNA sequencing of the clone revealed the presence of an open reading frame encoding a protein 387 amino acids long. The deduced amino acid sequence showed very high similarity with homologous genes identified from S. cerevisiae, Candida albicans and Zygosaccharomyces rouxii. In addition, it has also TGY motif characteristics of hyperosmolarity-activated MAP kinases. The Genbank Accession No. of this sequence is AF185278.

Ordered cloned DNA map of the genome of Vibrio cholerae 569B and localization of genetic markers

By using a low-resolution macrorestriction map as the foundation (R. Majumder et al., J. Bacteriol. 176:1105-1112, 1996), an ordered cloned DNA map of the 3.2-Mb chromosome of the hypertoxinogenic strain 569B of Vibrio cholerae has been constructed. A cosmid library the size of about 4,000 clones containing more than 120 Mb of V. cholerae genomic DNA (40-genome equivalent) was generated. By combining landmark analysis and chromosome walking, the cosmid clones were assembled into 13 contigs covering about 90% of the V. cholerae genome. A total of 92 cosmid clones were assigned to the genome and to regions defined by NotI, SfiI, and CeuI macrorestriction maps. Twenty-seven cloned genes, 9 rrn operons, and 10 copies of a repetitive DNA sequence (IS1004) have been positioned on the ordered cloned DNA map.

Protein profile of the allergenic pollen of Ipomoea fistulosa L.--a comparative study

The pollen of Ipomoea fistulosa L. is an important aeroallergen of India. The pollen of this plant was collected from full bloomed flowers growing in different places of West Bengal, India. Protein content and profile were studied by SDS-PAGE. Skin-prick tests with pollen antigens of all the samples were also performed. Considerable variation in the protein content and profile was noted with the highest protein content in the collected sample of Calcutta showing highest number of protein bands (10) designated as IF1 to IF10 with their weights ranging between 31 kDa to 89 kDa and 3 bands (IF8, IF9 and IF10) having molecular weights less than 29 kDa. Skin-prick tests also revealed highest degree of sensitivity to the Calcutta sample giving positive response in 52% of the patients. Skin reactivity ranged between 1+ to 3+.

Analysis of the free amino acid content in pollen of nine Asteraceae species of known allergenic activity

The study reports the free amino acid composition of the pollen of nine members of the family Asteraceae, i.e. Ageratum conyzoides L., Blumea oxyodonta DC., Eupatorium odoratum L., Gnaphalium indicum L., Mikania scandens Willd., Parthenium hysterophorus L., Spilanthes acmella Murr., Vernonia cinerea (L.) Lees. and Xanthium strumarium L. by thin layer chromatography. The amino acid content was found to vary from 0.5-4.0% of the total dry weight. Fourteen amino acids were identified, among which amino-n-butyric acid, aspartic acid and proline were present in almost all pollen samples. The other major amino acids present in free form included arginine, cystine, glutamic acid, glycine, isoleucine, leucine, methionine, ornithine, tryptophan and tyrosine.

Temperature dependence of transcriptional activity of yeast 3-phosphoglycerokinase promoter in Escherichia coli

We have studied the activity of yeast PGK promoter in E. coli at different temperatures using lacZ as the reporter gene. The B-galactosidase activity was found to be less at 42 degrees C than at 30 degrees C. Northern blot analysis showed that the level of lacZ transcript was less in recombinant cells grown at 42 degrees C, whereas plasmid copy number per cell was more as compared to recombinant cells grown at 30 degrees C. Data suggest that the yeast PGK promoter is less active at 42 degrees C and that this activity is regulated at the level of transcription.

Elastic fibres in retinal detachment

Generalised abnormalities have been described previously in familial and bilateral retinal detachment 1.2.3. Some studies have shown the presence of specific histological skin changes in cases of retinal detachment per se as well as in other syndromes having associated retinal detachment, hence pointing towards a generalised abnormality of constitution3.9.12. Drawing an analogy from these observations, the aim of our study was to study the histological changes in the skin of patients with rhegmatogenous retinal detachment and to relate its a etiopathogenesis to a generalized abnormality.

Effect of isosorbide dinitrate on enzymatically estimated infarction size and on clinical condition of the patients of acute myocardial infarction

With the aim of reducing myocardial infarction size, isosorbide dinitrate (ISDN) was tried in 27 patients of acute myocardial infarction (AMI). There was 11% reduction of infarction size, in the ISDN treated group, in comparison to that of non treated group, though the result was not statistically significant. But, many of the in-hospital complications were significantly less in the treated group. After a critical analysis of the result it was concluded that a statistically insignificant result, as regard reduction of infarction size in AMI, cannot always exclude the utility of a drug therapy in AMI.

Corneal thickness and I.O.P. changes in rhegmatogenous retinal detachment

Twenty patients with Rhegmatogenous retinal detachment were subjected to applanation tonometry and Corneal Thickness measurement to ascertain (i) the change in central & peripheral corneal thickness and (ii) effect of Intra Ocular Pressure on these corneal changes. Twenty age and sex matched controls also underwent similar investigation. It was observed that both the mean Intra Ocular Pressure and the corneal thickness (both Peripheral Corneal Thickness and Central Corneal Thickness] of the affected eye showed statistically significant reduction (P 0.001) when compared to Intra Ocular Pressure and Corneal Thickness changes of fellow-eyes and eyes of control subjects. In addition to these even the fellow eyes which had normal Intra Ocular Pressure, showed statistically low Central Corneal Thickness measurement, when compared with controls. In view of the above observation and reduction in Corneal Thickness measurement, the present study indicates generalised corneal changes in Rhegmatogenous retinal detachment unrelated to intraocular pressure.

N-Substituted indanamines as potential hypoglycemic agents

A number of indanamines substituted at the terminal amino nitrogen with various aliphatic, alicyclic, heterocyclic, and aromatic ring systems were synthesized and screened for hypoglycemic activity. None was found to possess significant activity compared to tolbutamide.