Spontaneous mutation rate estimates for the principal malaria vectors Anopheles coluzzii and Anopheles stephensi

Using high-depth whole genome sequencing of F0 mating pairs and multiple individual F1 offspring, we estimated the nuclear mutation rate per generation in the malaria vectors Anopheles coluzzii and Anopheles stephensi by detecting de novo genetic mutations. A purpose-built computer program was employed to filter actual mutations from a deep background of superficially similar artifacts resulting from read misalignment. Performance of filtering parameters was determined using software-simulated mutations, and the resulting estimate of false negative rate was used to correct final mutation rate estimates. Spontaneous mutation rates by base substitution were estimated at 1.00 × 10⁻⁹ (95% confidence interval, 2.06 × 10⁻¹⁰—2.91 × 10⁻⁹) and 1.36 × 10⁻⁹ (95% confidence interval, 4.42 × 10⁻¹⁰—3.18 × 10⁻⁹) per site per generation in A. coluzzii and A. stephensi respectively. Although similar studies have been performed on other insect species including dipterans, this is the first study to empirically measure mutation rates in the important genus Anopheles, and thus provides an estimate of µ that will be of utility for comparative evolutionary genomics, as well as for population genetic analysis of malaria vector mosquito species.

A massive rock and ice avalanche caused the 2021 disaster at Chamoli, Indian Himalaya

On 7 February 2021, a catastrophic mass flow descended the Ronti Gad, Rishiganga, and Dhauliganga valleys in Chamoli, Uttarakhand, India, causing widespread devastation and severely damaging two hydropower projects. More than 200 people were killed or are missing. Our analysis of satellite imagery, seismic records, numerical model results, and eyewitness videos reveals that ~27 × 10⁶ cubic meters of rock and glacier ice collapsed from the steep north face of Ronti Peak. The rock and ice avalanche rapidly transformed into an extraordinarily large and mobile debris flow that transported boulders greater than 20 meters in diameter and scoured the valley walls up to 220 meters above the valley floor. The intersection of the hazard cascade with downvalley infrastructure resulted in a disaster, which highlights key questions about adequate monitoring and sustainable development in the Himalaya as well as other remote, high-mountain environments.

Isolation and characterization of hypoxia inducible heme oxygenase 1 (HMOX1) gene in Labeo rohita

The HMOX1 gene plays role in several biological processes and is also responsive to hypoxia stress. Freshwater carp fish, Labeo rohita, is reported as hypoxia sensitive, but the information of annotated hypoxia genes in public domain is very scanty for this species. Here, an attempt was made to isolate and characterize HMOX1 gene in L. rohita using information from zebrafish. HMOX1 gene was obtained by mapping HMOX1 protein of zebrafish over assembled genome of L. rohita. Aligned region was used for designing primers for HMOX1 amplification. Eight overlapping sets of primers were designed for amplifying ~540 bp long successive overlapping fragments. Splicing of overlapping amplicons generated 3715 bp fragment that was confirmed as HMOX1 gene having full coding region with 6 exons between 184 and 2156 bp positions. HMOX1 characterization is an initiative for L. rohita genes annotation to support the characterization of new genes in the important species.

Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements

Cyprinus carpio is world's most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (-4,900 to +100) sequences of 31,466 protein coding genes was downloaded from "Gene" and "RefSeq" databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes.

NeuroMuscleDB: a Database of Genes Associated with Muscle Development, Neuromuscular Diseases, Ageing, and Neurodegeneration

Skeletal muscle is a highly complex, heterogeneous tissue that serves a multitude of biological functions in living organisms. With the advent of methods, such as microarrays, transcriptome analysis, and proteomics, studies have been performed at the genome level to gain insight of changes in the expression profiles of genes during different stages of muscle development and of associated diseases. In the present study, a database was conceived for the straightforward retrieval of information on genes involved in skeletal muscle formation, neuromuscular diseases (NMDs), ageing, and neurodegenerative disorders (NDs). The resulting database named NeuroMuscleDB ( http://yu-mbl-muscledb.com/NeuroMuscleDB ) is the result of a wide literature survey, database searches, and data curation. NeuroMuscleDB contains information of genes in Homo sapiens, Mus musculus, and Bos Taurus, and their promoter sequences and specified roles at different stages of muscle development and in associated myopathies. The database contains information on ~ 1102 genes, 6030 mRNAs, and 5687 proteins, and embedded analytical tools that can be used to perform tasks related to gene sequence usage. The authors believe NeuroMuscleDB provides a platform for obtaining desired information on genes related to myogenesis and their associations with various diseases (NMDs, ageing, and NDs). NeuroMuscleDB is freely available on the web at http://yu-mbl-muscledb.com/NeuroMuscleDB and supports all major browsers.

FisOmics: A portal of fish genomic resources

An online portal, accessible at URL: http://mail.nbfgr.res.in/FisOmics/, was developed that features different genomic databases and tools. The portal, named as FisOmics, acts as a platform for sharing fish genomic sequences and related information in addition to facilitating the access of high-performance computational resources for genome and proteome data analyses. It provides the ability for quarrying, analysing and visualizing genomic sequences and related information. The featured databases in FisOmics are in the World Wide Web domain already. The aim to develop portal was to provide a nodal point to access the featured databases and work conveniently. Presently, FisOmics includes databases on barcode sequences, microsatellite markers, mitogenome sequences, hypoxia-responsive genes and karyology of fishes. Besides, it has a link to other molecular resources and reports on the on-going activities and research achievements.

ADNCD: a compendious database on anti-diabetic natural compounds focusing on mechanism of action

Diabetes is a deteriorating metabolic ailment which negatively affects different organs; however, its prime target is insulin secreting pancreatic β-cells. Although, different medications have been affirmed for diabetes management and numerous drugs are undergoing clinical trials, no significant breakthrough has yet been achieved. Available drugs either show some side effects or provide only short-term alleviation. The rationales behind the failure of current anti-diabetic treatment strategy are association of complex patho-physiologies and participation of various organs. Consequently, there is a critical need to search for multi-effect drugs that might impede various patho-physiological mechanisms related to diabetes. Fortunately, one natural compound could act on several diabetes linked targets. Thus, natural compounds might be regarded as a viable alternative choice to improve the progression as well as side effects of diabetes. Despite the fact that immense literatures are available on natural compounds indicating promising outcomes against diabetes, more systematic studies are still needed to establish them as effective anti-diabetic agents. Till date, we are unable to access all the information regarding modes of action, toxicity risks and physicochemical properties of anti-diabetic natural compounds on one platform. Hence, anti-diabetic natural compounds database (ADNCD) has been created to categorize each anti-diabetic natural compound on the basis of their mode of action and to provide compendious information of their physicochemical properties and toxicity risks. In short, ADNCD has imperative information for the researchers working in the field of diabetes drug development.

Genetic characterization of canine parvovirus from dogs in Pakistan

Canine parvoviruses (CPV) exist as antigenic variants with varying frequencies and genetic variabilities across the globe. Given the endemicity and high prevalence in Pakistan, we characterized the CPVs originating from dogs-population to elucidate viral diversity and evolution. Fecal samples from clinically diseased pups (n = 17) of different breeds and age (2-6 months) were processed for hemagglutination assay (HA), and later for partial amplification of VP2 gene sequence and amino acid analysis. A total of 11 samples (64.71%) were found positive both in hemagglutination and PCR assays. Phylogenetic and evolutionary analysis demonstrated higher genetic heterogeneity in studied strains and constituted seven clusters within the CPV-2a group, however, they shared high level of identity with Chinese strains. Further studies are necessary to elucidate genetic analysis and epidemiology of CPV variants across a wide geographical area of the country.

HRGFish: A database of hypoxia responsive genes in fishes

Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. ‘Fish Karyome’ database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes.

Database URL:http://mail.nbfgr.res.in/Fish_Karyome

FMiR: A Curated Resource of Mitochondrial DNA Information for Fish

Mitochondrial genome sequences have been widely used for evolutionary and phylogenetic studies. Among vertebrates, fish are an important, diverse group, and their mitogenome sequences are growing rapidly in public repositories. To facilitate mitochondrial genome analysis and to explore the valuable genetic information, we developed the Fish Mitogenome Resource (FMiR) database to provide a workbench for mitogenome annotation, species identification and microsatellite marker mining. The microsatellites are also known as simple sequence repeats (SSRs) and used as molecular markers in studies on population genetics, gene duplication and marker assisted selection. Here, easy-to-use tools have been implemented for mining SSRs and for designing primers to identify species/habitat specific markers. In addition, FMiR can analyze complete or partial mitochondrial genome sequence to identify species and to deduce relational distances among sequences across species. The database presently contains curated mitochondrial genomes from 1302 fish species belonging to 297 families and 47 orders reported from saltwater and freshwater ecosystems. In addition, the database covers information on fish species such as conservation status, ecosystem, family, distribution and occurrence downloaded from the FishBase and IUCN Red List databases. Those fish information have been used to browse mitogenome information for the species belonging to a particular category. The database is scalable in terms of content and inclusion of other analytical modules. The FMiR is running under Linux operating platform on high performance server accessible at URL http://mail.nbfgr.res.in/fmir.

In silico analysis of SSRs in mitochondrial genomes of fishes

The availability of fish mitochondrial (mt) genomes provides an opportunity to explore the simple sequence repeats. In the present study, mt genomes of 85 fish species reported from Indian subcontinent were downloaded from NCBI and computationally analysed for finding SSRs types, frequency of occurrence, mutation and evolutionary adaptation across species. A total of 92 microsatellites in different nucleotide combinations were detected in 59 species. 26 interspersed SSRs, mostly poly (AT)n were found in the D-loop regions in the species of Cyprinidae. Fifty-six SSRs of 12 bp fixed length were observed in eight genes only. Further, identical repeat motifs were found on the same location in ATP6 and ND4 genes, which were biased towards particular habitat. The comparison of ATP6 and ND4 gene sets to other homologous sequences showed point mutations. This study explores the SSRs discovery and their utility as marker for species and population identification.

FishMicrosat: a microsatellite database of commercially important fishes and shellfishes of the Indian subcontinent

Background

Microsatellite DNA is one of many powerful genetic markers used for the construction of genetic linkage maps and the study of population genetics. The biological databases in public domain hold vast numbers of microsatellite sequences for many organisms including fishes. The microsatellite data available in these data sources were extracted and managed into a database that facilitates sequences analysis and browsing relevant information. The system also helps to design primer sequences for flanking regions of repeat loci for PCR identification of polymorphism within populations.

Description

FishMicrosat is a database of microsatellite sequences of fishes and shellfishes that includes important aquaculture species such as Lates calcarifer, Ctenopharyngodon idella, Hypophthalmichthys molitrix, Penaeus monodon, Labeo rohita, Oreochromis niloticus, Fenneropenaeus indicus and Macrobrachium rosenbergii. The database contains 4398 microsatellite sequences of 41 species belonging to 15 families from the Indian subcontinent. GenBank of NCBI was used as a prime data source for developing the database. The database presents information about simple and compound microsatellites, their clusters and locus orientation within sequences. The database has been integrated with different tools in a web interface such as primer designing, locus finding, mapping repeats, detecting similarities among sequences across species, and searching using motifs and keywords. In addition, the database has the ability to browse information on the top 10 families and the top 10 species, through record overview.

Conclusions

FishMicrosat database is a useful resource for fish and shellfish microsatellite analyses and locus identification across species, which has important applications in population genetics, evolutionary studies and genetic relatedness among species. The database can be expanded further to include the microsatellite data of fishes and shellfishes from other regions and available information on genome sequencing project of species of aquaculture importance.

Computational analysis of transcriptome of Indian major carp, Labeo rohita (Hamilton-Buchanan, 1822) for functional annotation

A total of 1671 ESTs of Labeo rohita were retrieved from dbEST database and analysed for functional annotation using various computational approaches. The result indicated 1387 non-redundant (184 contigs and 1203 singletons) putative transcripts with an average length of 542 bp. These 1387 transcript sequences were matched with Refseq_RNA, UniGene and Swiss-Prot on high threshold cut-off for functional annotation along with help of gene ontology and SSRs markers. We developed extensive Perl programming based modules for processing all alignment files, comparing and extracting common hits from all files on a threshold, evaluating statistics for alignment results and assigning gene ontology terms. In this study, 92 putative transcripts predicted as orthologous genes and among those, 44 putative transcripts were annotated with gene ontology terms. The annotated orthologous gene of our result associated with some very important proteins of L. rohita involved in biotic and abiotic stresses and glucose metabolism of spermatogenic cells etc. The unidentified transcripts, if found important in expression profiling can be vital resource after re-sequencing. The predicted genes can further be used for enhancing productivity and controlling disease of L. rohita.

FBIS: A regional DNA barcode archival & analysis system for Indian fishes

DNA barcode is a new tool for taxon recognition and classification of biological organisms based on sequence of a fragment of mitochondrial gene, cytochrome c oxidase I (COI). In view of the growing importance of the fish DNA barcoding for species identification, molecular taxonomy and fish diversity conservation, we developed a Fish Barcode Information System (FBIS) for Indian fishes, which will serve as a regional DNA barcode archival and analysis system. The database presently contains 2334 sequence records of COI gene for 472 aquatic species belonging to 39 orders and 136 families, collected from available published data sources. Additionally, it contains information on phenotype, distribution and IUCN Red List status of fishes. The web version of FBIS was designed using MySQL, Perl and PHP under Linux operating platform to (a) store and manage the acquisition (b) analyze and explore DNA barcode records (c) identify species and estimate genetic divergence. FBIS has also been integrated with appropriate tools for retrieving and viewing information about the database statistics and taxonomy. It is expected that FBIS would be useful as a potent information system in fish molecular taxonomy, phylogeny and genomics.

AVAILABILITY

The database is available for free at http://mail.nbfgr.res.in/fbis/

Decreasing incidence of gastric MALT lymphomas in the era of anti-Helicobacter pylori interventions: results from a population-based study on extranodal marginal zone lymphomas

BACKGROUND

Few studies have been carried out to date that have addressed the epidemiology of extranodal marginal zone lymphomas (EN-MZLs).

PATIENTS AND METHODS

We carried out a population-based study to investigate incidence rates (IRs) and time trends of EN-MZL diagnosed in the province of Modena (Italy) from 1997 to 2007.

RESULTS

One hundred and sixty-five cases were identified from the Modena Cancer Registry that corresponded to an age-standardized IR of 2.3 cases per 100 000. A bimodal distribution of age was shown with the group of young patients mostly represented by males with cutaneous lymphoma. No time trends were observed for the IR; the incidence of gastric mucosa-associated lymphoid tissue (g-MALT) lymphomas (N = 51) markedly declined during the study period, dropping from 1.4 in 1997 to 0.2 in 2002 and then remaining stable until 2007; the calculated annual percent change for g-MALT was -17.0% (95% confidence interval -26.6% to -6.2%). We also observed a significant decrease in the rate of g-MALT associated with Helicobacter pylori (HP) infection from 61% to 17% of patients diagnosed before and after 2002 (P = 0.007; P for trend = 0.016).

CONCLUSION

This population-based study provides new insights into recent changes in the epidemiology of EN-MZL, mainly represented by the sharp reduced incidence of HP-positive g-MALT lymphomas.

Changes in survival from metastatic breast cancer during the last twenty-years: A population based study in Northern Italy

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Background: A significant improvement in overall survival was observed in the last two decades in patients with breast cancer due to early diagnosis and more effective therapies. However, a significant improvement in metastatic setting has been questioned. Our population based study was aimed to investigate the outcome of metastatic breast cancer from 1988 to 2005. Methods: Women with stage IV de novo or relapsed breast cancer diagnosed between 1988 and 2005 were identified by the Modena Cancer Registry (MCR). For all patients overall survival (OS) was measured from the date of first distant metastases to the date of death from any cause or last follow-up and compared across groups for four periods of similar duration time: 1988–1993 (A), 1994–1997(B), 1998–2001(C), 2002–2005(D). Results: Among 8,654 patients with breast cancer identified by the MCR, 409 had an initial metastatic disease (4.8%) and 693 (8.4%) had a distant recurrence. Median age at onset was 66 versus 59 years in de novo vs relapsed disease (p = 0.001). Significant differences for postmenopausal age (80% vs 71%) and for positive estrogen receptors (72% vs 63%) were registered in de novo and relapsed disease, respectively (p = 0.001). After a 27 months median follow-up for initial metastatic disease, the five-year OS was 12%, 14%, 9%, and 13% in the A, B, C, and D periods, respectively, (p = 0.5). Conversely, in relapsed breast cancer, after a 29 months median follow-up, a significant survival improvement was observed between the first and the other three periods, being the 5 year-survival rate after recurrence 10%, 22%, 30%, and 25%, respectively (p = 0.001). A survival improvement was seen in the last ten years for relapsed breast cancer using aromatase inhibitors (p < 0.0001) while for initial metastatic disease the same treatment provided a better outcome only in the last 4 years (p < 0.0001). Conclusions: Data from our study show that the outcome of initial metastatic breast cancer is still discouraging, despite the availability of several new drugs in recent years. A limited improvement was observed in relapsed breast cancer with the aromatase inhibitors introduction. In any case, the finish line is still far away, and robust investments in basic and translational research are still absolutely necessary.

No significant financial relationships to disclose.

Bilirubin binding to normal and modified human erythrocyte membranes: effect of phospholipases, neuraminidase, trypsin and CaCl2

Binding of bilirubin to human erythrocyte membranes was studied after various enzymatic treatments as well as calcium loading. Whereas phospholipase D treatment of erythrocyte membranes resulted in 23% increase in bilirubin binding, phospholipase C-treated membranes showed remarkable enhancement in bilirubin binding. Polar head groups in general and negatively charged phosphate moieties, in particular, of phospholipids of the membrane appear to inhibit a large amount of bilirubin from binding to the membranes. Neuraminidase treatment of the membranes also led to a slight increase in bilirubin binding as compared to untreated membranes. Membrane proteins and carbohydrates seem to play significant regulatory role in bilirubin binding. However, no direct correlation was found between the increase in bilirubin binding and the amount of carbohydrate released upon tryptic digestion of membranes. Increase in bilirubin binding to trypsin-treated membranes can be ascribed to the increase in free bilirubin concentration in the incubation mixture as a result of tryptic hydrolysis of albumin by the membrane-bound tryptic activity. Calcium-loaded erythrocyte membranes also showed remarkable increase in bilirubin binding as a result of negative charge shielding and calcium-induced hydrophobic aggregation. Taken together, these results suggest the inhibitory role of polar head groups of phospholipids (phosphate in particular), carbohydrate and sialic acid in the binding of bilirubin to erythrocyte membranes.

Biological studies of indigenous medicinal plants--I: physicochemical and antimicrobial screening of non-alkaloidal constituents of some solanaceous seeds

The seeds of Atropa belladonna Datura fastuosa D. stramoniurn and Hyoscyamus niger were investigated for the isolation and anti-microbial activity of non-alkaloidal constituents. The compounds were separated by column chromatography and spectral studies i.e. IR and UV were performed to ascertain their chemical nature. The anti-microbial activity of crude extracts and purified compounds was tested against Gram positive and Gram negative bacteria and a fungus. All the micro-organisms tested were markedly inhibited, however, the crude extracts as well as the purified compounds isolated from the seeds of A. belladonna and D. fastuosa showed little inhibitory activity.