DNA barcode based delineation of freshwater fishes from northern Western Ghats of India,one of the world’s biodiversity hotspots

DNA barcodes analyzed by using relevant techniques provide an imperative approach towards validation of prevailing taxa and putative species. Here, molecular methods were used for assessment of 246 barcodes belonging to 81 fish species from northern Western Ghats of India, using, Barcode gap analysis, barcode index number, automatic barcode gap discovery, Poisson tree processes and general mixed Yule-coalescent, these methods had their potential to discriminate 97.53%, 93.90% 95.06%, 93.82% and 92.59% of species respectively. But, some of them tended to estimate the inconsistent number of species leading to discrepancies between the morphological concept and inference from molecular phylogenetic reconstructions. So, we took a standard approach to recognize those methods that produced consistent results, three of five such methods were identified that revealed three hidden cryptic species complexes in Monopterus indicus, Parambassis ranga and Systomus sarana. Further, to validate these three genetically diverged species, we used diagnostic character based approach along with nine unidentified species through BLOG and WEKAs SMO classifier. Those methods were unable to identify these species, which might be due to the limited number of specimens used for the analysis. This is the first effort to generate the DNA barcode reference library of freshwater fishes from northern Western Ghats of India, one of the world’s biodiversity hotspots. These barcodes when analyzed through the defined workflow, will provide valuable measures to prove the efficiency of molecular species delimitation methods in taxonomic discrimination which aid conservation of biodiversity.     

How Effective Are DNA Barcodes in the Identification of African Rainforest Trees?

Background

DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species.

Methodology/Principal Findings

We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95–100% success), but less for species identification (71–88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84–90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA.

Conclusions/Significance

Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.     

One bat’s waste is another man’s treasure: a DNA metabarcoding approach for the assessment of biodiversity and ecosystem services in Ireland using bat faeces

Biodiversity and Conservation - Arthropod populations are constantly changing due to changes in climate and the globalisation of trade and travel. Effective and diverse monitoring techniques are...     

India’s Biological Diversity Act 2002: An act for the new millenium

Journal of Biosciences -     

New approaches for the treatment of Alzheimer’s disease

Alzheimer’s disease (AD) is the most prevalent chronic neurodegenerative disease. Current approved therapies are symptomatic treatments having some effect on cognitive function. Therapies that target β-amyloid (Aβ) have been the focus of efforts to develop a disease modification treatment for AD but these approaches have failed to show any clinical benefit so far. Beyond the ‘Aβ hypothesis’, there are a number of newer approaches to treat AD with neuroinflammation emerging as a very active area of research based on risk gene analysis. This short review will summarize approved drug therapies, recent clinical trials and new approaches for the treatment of AD.     

Design,synthesis, and multitargeted profiling of N-benzylpyrrolidine derivatives for the treatment of Alzheimer’s disease

Multitarget molecular hybrids of N-benzyl pyrrolidine derivatives were designed, synthesized, and biologically evaluated for the treatment of Alzheimer’s disease (AD). Among the synthesized compounds, 4k and 4o showed balanced enzyme inhibitions against cholinesterases (AChE and BChE) and BACE-1. Both leads showed considerable PAS-AChE binding capability, excellent brain permeation, potential disassembly of Aβ aggregates, and neuroprotective activity against Aβ-induced stress. Compounds 4k and 4o also ameliorated cognitive dysfunction against the scopolamine-induced amnesia model in the Y-maze test. The ex vivo study signified attenuated brain AChE activity and antioxidant potential of compounds 4k and 4o. Furthermore, compound 4o also showed improvement in Aβ-induced cognitive dysfunction by the Morris water maze test with excellent oral absorption characteristics ascertained by the pharmacokinetic study. In silico molecular docking and dynamics simulation studies of leads suggested their consensual binding affinity toward PAS-AChE in addition to aspartate dyad of BACE-1.     

Analysing India’s current national forest inventory for biodiversity information

This study attempts to review the various biodiversity related parameters envisaged in the current national forest inventory (NFI) of India in comparison to those used worldwide as indicators of forest biodiversity. The study reveals that a good amount of biodiversity related parameters are available, covering the structural attribute of biodiversity, tree species composition, and other important functional attributes like deadwood and litter. In spite of this timber-based approach, a number of variables are available to talk on biodiversity aspects of Indian forests. However, the comparison with the parameters found in literature shows that the scope of further improvement does exist in current NFI’s ability to contribute towards a documentation and management of biodiversity. Our gap analysis indicates that enhancing the capacity of the current NFI to generate overall biodiversity information urgently required for safeguarding and conserving the natural wealth of India is strongly needed.     

Areas of high diversity for the world’s inland-breeding waterbirds

Waterbirds are a globally-distributed, species-rich group of birds that are critically dependent upon wetland habitats. They can be used as ecosystem sentinels for wetlands, which as well as providing ecosystem services and functions essential to humans, are important habitats for a wide range of plant and animal taxa. Here we carry out the first global analysis of inland-breeding waterbird distributions using data from 471 waterbird species in 28 families to identify global areas of high waterbird diversity. First we identify the primary area of high diversity for all inland-breeding waterbird species to be in Eastern Africa. For globally threatened inland-breeding waterbirds, the area of highest diversity is in Eastern China. Second, we show that the current network of protected areas provides poor coverage for threatened waterbirds in Eastern and Central Asia, and Northern India. In contrast, there is a higher protected area coverage in most of Europe and Brazil. Targeting the specific areas that have the highest numbers of species and the poorest coverage of protected areas is vital for both waterbird and wetland conservation.     

Targeting Estrogen Receptors for the Treatment of Alzheimer’s Disease

The significantly higher incidence of Alzheimer's disease (AD) in women than in men has been attributed to loss of estrogen and a variety of related mechanisms at the molecular, cellular, and hormonal levels, which subsequently elucidate neuroprotective roles of estrogen against AD-related pathology. Recent studies have proposed that beneficial effects of estrogen on AD are directly linked to its ability to reduce amyloid-β peptides and tau aggregates, two hallmark lesions of AD. Despite high expectations, large clinical trials with postmenopausal women indicated that the beneficial effects of estrogen therapies were insignificant and, in fact, elicited adverse effects. Here, we review the current status of AD prevention and treatment using estrogens focusing on recent understandings of their biochemical links to AD pathophysiology. This review also discusses development of selective ligands that specifically target either estrogen receptor α (ERα) or ERβ isoforms, which are potentially promising strategies for safe and efficient treatment of AD.     

The Role of Mitochondrial DNA Individuality in the Pathogenesis of Parkinson’s Disease

Russian Journal of Genetics - The present article reviews the rapidly growing body of research on the role of mitochondrial DNA (mtDNA) in the realization of individual risk of Parkinson’s...     

Entangled Matters—Alzheimer’s,Interiority, and the ‘Unflattening’ of the World

When, in the 1980s, Alzheimer's disease became a disease of major public concern, 'personhood' also became an important, related topic of discussion. Those in caring professions (psychology, social work, etc.) and caregiver groups advocated for the 'person within' who was getting lost in a forgetful body and in a reductionist biomedical system. This essay aims to critically approach the dualism of this kind of argument by focusing on the moral positioning of claims such as personhood or biomedical reductionism.     

Bergmann’s rule for Neomys fodiens in the middle of the distribution range

The body size of Palearctic Sorex shrews decreases at higher latitudes, and as such the Bergmann’s rule does not work. However, no analysis has ever been done for water shrew (Neomys fodiens) in the middle of distribution range. Analysis of available literature data showed that some body and skull measurements of N. fodiens are negatively correlated to latitude. Measurements of 158 water shrews from Estonia and Lithuania were also analyzed with respect to the short scale latitudinal pattern. We found that populations are separated (Wilk’s lambda = 0.363, p<0.0001). Differences are related to PC1 (skull size), explaining 49.80% of the variance and PC2 (body size), explaining 10.06% of the variance. Estonian shrews are smaller in their body and skull (most differences significant) and their skulls are relatively shorter and wider in the area of the brain case. Thus, the negative correlation of body and skull size to latitude in N. fodiens is applicable even over quite short latitudinal distances. Further analysis of diagnostic characters between N. fodiens and N. anomalus is required.     

Population genetic diversity of Prenant’s schizothoracin, Schizothorax prenanti, inferred from the mitochondrial DNA control region

Wild populations of Prenant’s schizothoracin, Schizothorax prenanti, were collected from the Qingyi, Dadu, and Muli rivers in upper reaches of the Yangtze River. Genetic variation and population structure were examined based on analysis of the mitochondrial DNA control region. Nucleotide sequence analysis defined 30 haplotypes in 41 individuals. The nucleotide and haplotype diversities were very high, and genetic distances between the Dadu and Qingyi populations were much smaller than between either of them and the Muli population. The analysis of molecular variance demonstrated that most variation occurred within samples, and the differentiation between Muli and Dadu or Qingyi was significant. Estimates of gene flow indicated reproductive isolation between Muli and the other populations, and this divergence might be related to geographical location. The results are mostly consistent with the findings from AFLP analysis and also suggested considerable genetic diversity of the populations in the Muli, Dadu, and Qingyi rivers.     

Management of Type 2 Diabetes Mellitus in the Very Elderly: One Practice’s Experience

ObjectiveType 2 diabetes mellitus (T2DM) affects 25% of adults over age 65. Nevertheless, few clinical trials include patients over age 75.MethodsThis case series reports retrospective data on a cohort of 85 patients aged 80 and over (mean 88.1, range 80-104) with T2DM, managed by a single endocrinologist. The practice’s computerized data base was searched for all patients 80 years of age and older with a diagnosis of T2DM.ResultsThe major observations were the significant decrease in the use of agents associated with hypoglycemia (sulfonylureas and insulin), and the beneficial and well-tolerated use of glucagon like peptide-1 receptor analogues (GLP-1 RA). The mean A1c in the entire cohort dropped from 7.6% to 6.6% over a mean of 9 months. Nearly one-half of the cohort were treated with GLP1-RA, reflecting studies demonstrating the safety and efficacy of this class of drugs in less elderly patients. At presentation, 75% were on sulfonylurea and/or insulin; this number was reduced to 27%. Furthermore, none of the patients required short-acting (bolus) insulin to achieve the individualized A1c target.ConclusionPatients with T2DM aged 80 and over respond well to GLP1-RA drugs, drastically reducing the need for agents associated with hypoglycemia. The important question, which will require larger and prospective studies, is whether the lowering of A1c, as shown in this paper, and the use of GLP-1 RA specifically, are associated with improved morbidity and mortality in the very elderly.