The Paradox of Shorebird Diversity and Abundance in the West Coast and East Coast of India: A Comparative Analysis

Migratory shorebirds that move across continents along their flyways are undergoing a drastic decline globally. A greater proportion of them that regularly winter along the Indian coasts within the Central Asian Flyway (CAF) are also undergoing severe declines. However, the mechanisms underlying the population trends in these areas remain little understood. This study investigated the diversity, abundance, population dynamics and distribution patterns of shorebirds along the Indian coasts based on the available literature. The west coast of India is relatively less studied than the east coast in the CAF. Further, we observed that the diversity, abundance, population dynamics and distribution pattern of the shorebirds follow different trends on the west coast compared to the east coast. These variations are in accordance with the differences in topography and biotic and abiotic factors between the coasts. Anthropogenic activities have far-reaching effects on the survival and persistence of shorebirds along the coasts. The west coast is evidently more productive than the east coast at every trophic level and thus the west coast is expected to account for more abundance and diversity of shorebirds. Paradoxically, we found that the east coast supports a greater abundance and diversity of shorebirds than the west coast. The west coast, therefore, requires further investigations to obtain a better understanding of the causes of apparent differences in abundance and diversity as well as the observed declines in shorebirds, compared to the east coast of India

Role of voluntary teacher forums (VTFs) in continuous teacher professional development in India: experiences from Rajasthan, Karnataka and Puducherry

The quality of education depends largely upon the teacher. Hence building teacher capacity through continuous professional development of teachers is critical to the quality of education. Systems and programs for continuous professional development for school teachers in the formal educational system in India are inadequate and often illconceived. Apart from other lacunae, they often do not recognize the professional identity and agency of the teacher. Voluntary Teacher Forums (VTFs) that are facilitated by Azim Premji Foundation in different locations of India, as part of an integrated and multimodal approach to continuous professional development, try to address this central issue. This study shows that VTFs are evolving as very useful platforms for collaboration and peer learning amongst teachers in various locations. It shows that given an environment that allows for easy access to meaningful opportunities, teachers will commit their time, talents and resources to their own professional development. The study further recognizes however, that the real issue is to understand how such forums can be made to happen in different locations in a context as complex as the Indian public education system. While this study highlights certain crucial dimensions of the VTFs – including what happens within these forums and the efforts that go behind it – these continue to be subjects for our future research works

Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression

Multiple, complex molecular events characterize cancer development and progression(1,2). Deciphering the molecular networks that distinguish organ- confined disease from metastatic disease may lead to the identification of critical biomarkers for cancer invasion and disease aggressiveness. Although gene and protein expression have been extensively profiled in human tumours, little is known about the global metabolomic alterations that characterize neoplastic progression. Using a combination of high- throughput liquid- and- gas- chromatography- based mass spectrometry, we profiled more than 1,126 metabolites across 262 clinical samples related to prostate cancer ( 42 tissues and 110 each of urine and plasma). These unbiased metabolomic profiles were able to distinguish benign prostate, clinically localized prostate cancer and metastatic disease. Sarcosine, an N- methyl derivative of the amino acid glycine, was identified as a differential metabolite that was highly increased during prostate cancer progression to metastasis and can be detected non- invasively in urine. Sarcosine levels were also increased in invasive prostate cancer cell lines relative to benign prostate epithelial cells. Knockdown of glycine- N- methyl transferase, the enzyme that generates sarcosine from glycine, attenuated prostate cancer invasion. Addition of exogenous sarcosine or knockdown of the enzyme that leads to sarcosine degradation, sarcosine dehydrogenase, induced an invasive phenotype in benign prostate epithelial cells. Androgen receptor and the ERG gene fusion product coordinately regulate components of the sarcosine pathway. Here, by profiling the metabolomic alterations of prostate cancer progression, we reveal sarcosine as a potentially important metabolic intermediary of cancer cell invasion and aggressivity.Early Detection Research Network ; National Institutes of Health ; MTTC ; Clinical Translational Science Award ; Fund for Discovery of the University of Michigan Comprehensive Cancer Center ; University of Michigan Cancer Biostatistics Training Grant ; Doris Duke Charitable FoundationWe thank J. Granger for help in manuscript preparation, J. Siddiqui and R. Varambally for help with the clinical database, and A. Vellaichamy and S. Pullela for technical assistance. We thank K. Pienta for access to metastatic prostate cancer samples from the University of Michigan Prostate SPORE rapid autopsy programme. This work is supported in part by the Early Detection Research Network (A.M.C., J.T.W.), National Institutes of Health (A.S., S.P., J.B., T.M.R., D.G., G.S.O. and A.M.C.) and an MTTC grant (G.S.O. and A.S.). A.M.C. is supported by a Clinical Translational Science Award from the Burroughs Welcome Foundation. A. S. is supported by a grant from the Fund for Discovery of the University of Michigan Comprehensive Cancer Center. L. M. P. is supported by the University of Michigan Cancer Biostatistics Training Grant. A. M. C and S. P. are supported by the Doris Duke Charitable Foundation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62661/1/nature07762.pd

Allelic Imbalance of Recurrently Mutated Genes in Acute Myeloid Leukaemia

The patho-mechanism of somatic driver mutations in cancer usually involves transcription, but the proportion of mutations and wild-type alleles transcribed from DNA to RNA is largely unknown. We systematically compared the variant allele frequencies of recurrently mutated genes in DNA and RNA sequencing data of 246 acute myeloid leukaemia (AML) patients. We observed that 95% of all detected variants were transcribed while the rest were not detectable in RNA sequencing with a minimum read-depth cut-off (10x). Our analysis focusing on 11 genes harbouring recurring mutations demonstrated allelic imbalance (AI) in most patients. GATA2, RUNX1, TET2, SRSF2, IDH2, PTPN11, WT1, NPM1 and CEBPA showed significant AIs. While the effect size was small in general, GATA2 exhibited the largest allelic imbalance. By pooling heterogeneous data from three independent AML cohorts with paired DNA and RNA sequencing (N = 253), we could validate the preferential transcription of GATA2-mutated alleles. Differential expression analysis of the genes with significant AI showed no significant differential gene and isoform expression for the mutated genes, between mutated and wild-type patients. In conclusion, our analyses identified AI in nine out of eleven recurrently mutated genes. AI might be a common phenomenon in AML which potentially contributes to leukaemogenesis.Peer reviewe

Traditional fishing activities enhance the abundance of selected waterbird species in a wetland in India

Abstract Background Waterbirds are globally declining as a result of habitat loss, alteration or degradation. Fishing activities may affect waterbird distribution, abundance and diversity, and traditional fishing activities often enhance waterbird abundance. We tested this hypothesis by studying the abundance and diversity of selected common waterbird species in the Kadalundi–Vallikkunnu Community Reserve, a globally significant wetland in southwestern India in relation to fishing activities. Methods We monitored waterbird abundance four times a month from 2012 to 2015 using direct observation method during low tide. Traditional bamboo fish traps were deployed during the first and third weeks of each month. ANOVAs (one-way and multi-way) were used to examine how waterbird counts diversity varied in relation to years, seasons and period of fishing traps. Additionally we conducted a linear regression to examine the relationship between fish occurrence and waterbird counts and diversity. Results Waterbird counts varied with years and seasons, with the maximum counts being recorded during the post-monsoon (winter). Individual species varied in their responses to trap deployment. Small waterbird species usually forage in shallow shorelines, increased during trap deployment whereas the larger waterbirds were not affected by trap deployment because they tend to hunt in deeper waters. The total fish captured was an important predictor of both waterbird abundance and diversity. Conclusion In this study we documented a positive association between traditional fish trap deployment and waterbird counts and diversity. Providing high quality habitats for waterbirds as well as effective sustainable livelihoods through traditional fisheries is a critical management issue

The Paradox of Shorebird Diversity and Abundance in the West Coast and East Coast of India: A Comparative Analysis

Migratory shorebirds that move across continents along their flyways are undergoing a drastic decline globally. A greater proportion of them that regularly winter along the Indian coasts within the Central Asian Flyway (CAF) are also undergoing severe declines. However, the mechanisms underlying the population trends in these areas remain little understood. This study investigated the diversity, abundance, population dynamics and distribution patterns of shorebirds along the Indian coasts based on the available literature. The west coast of India is relatively less studied than the east coast in the CAF. Further, we observed that the diversity, abundance, population dynamics and distribution pattern of the shorebirds follow different trends on the west coast compared to the east coast. These variations are in accordance with the differences in topography and biotic and abiotic factors between the coasts. Anthropogenic activities have far-reaching effects on the survival and persistence of shorebirds along the coasts. The west coast is evidently more productive than the east coast at every trophic level and thus the west coast is expected to account for more abundance and diversity of shorebirds. Paradoxically, we found that the east coast supports a greater abundance and diversity of shorebirds than the west coast. The west coast, therefore, requires further investigations to obtain a better understanding of the causes of apparent differences in abundance and diversity as well as the observed declines in shorebirds, compared to the east coast of India

Long-term anthropogenic stressors cause declines in kingfisher assemblages in wetlands in southwestern India

Fragile wetland habitats are susceptible to multiple threats from anthropogenic activities. Direct waste deposition, habitat modification and overexploitation of fish have caused alternations in food webs in wetlands. Kingfishers are ecological indicators with the potential ability to respond to the minute changes in their microenvironment. Their abundance and distribution at wetland habitats are affected by multiple environmental factors. We studied the kingfisher assemblages in India to determine proximate and ultimate causes of their decline. We recorded the abundance of five species of kingfishers across five wetland habitats from 2011 to 2020 in Kerala, southwest coast of India. Kingfishers were counted twice in a month between 6.00 and 12.00 hrs. Air temperature, water temperature, humidity and turbidity were recorded. We measured fish diversity and abundance and organic waste as an additional explanatory variable. One-way ANOVA, Autoregressive Integrated Moving Average model and structural equation modelling were used to determine which explanatory variables affected kingfisher populations. Air temperature, water temperature and turbidity increased significantly during the study and had negative effects on the abundance of kingfishers. Humidity decreased significantly but had no effect on the kingfisher abundance. Fish abundance declined and had a strong positive effect on the abundance of kingfishers. The analysis of incidence of wastes across the study areas revealed that, all the sites were severely polluted. We also observed drastic decline in the abundance of all the species of kingfishers studied across the sites with a rapid decline in Pied Kingfisher and slower decline in White-throated Kingfisher. Black-capped Kingfisher is a local migrant to the study areas and is already red listed and categorized as Vulnerable (VU). This study suggests that kingfisher assemblages are declining along with the health status of the habitat. Urgent action is needed to help in designing and implementing effective management strategies for the sustainability of wetlands in the region.Peer reviewe

Clonal heterogeneity of FLT3-ITD detected by high-throughput amplicon sequencing correlates with adverse prognosis in acute myeloid leukemia

In acute myeloid leukemia (AML), internal tandem duplications (ITDs) of FLT3 are frequent mutations associated with unfavorable prognosis. At diagnosis, the FLT3-ITD status is routinely assessed by fragment analysis, providing information about the length but not the position and sequence of the ITD. To overcome this limitation, we performed cDNA-based high-throughput amplicon sequencing (HTAS) in 250 FLT3-ITD positive AML patients, treated on German AML Cooperative Group (AMLCG) trials. FLT3-ITD status determined by routine diagnostics was confirmed by HTAS in 242 out of 250 patients (97%). The total number of ITDs detected by HTAS was higher than in routine diagnostics (n = 312 vs. n = 274). In particular, HTAS detected a higher number of ITDs per patient compared to fragment analysis, indicating higher sensitivity for subclonal ITDs. Patients with more than one ITD according to HTAS had a significantly shorter overall and relapse free survival. There was a close correlation between FLT3-ITD mRNA levels in fragment analysis and variant allele frequency in HTAS. However, the abundance of long ITDs (≥75nt) was underestimated by HTAS, as the size of the ITD affected the mappability of the corresponding sequence reads. In summary, this study demonstrates that HTAS is a feasible approach for FLT3-ITD detection in AML patients, delivering length, position, sequence and mutational burden of this alteration in a single assay with high sensitivity. Our findings provide insights into the clonal architecture of FLT3-ITD positive AML and have clinical implications

Wild-type EGFR Is Stabilized by Direct Interaction with HSP90 in Cancer Cells and Tumors

The epidermal growth factor receptor (EGFR) has been targeted for inhibition using tyrosine kinase inhibitors and monoclonal antibodies, with improvement in outcome in subsets of patients with head and neck, lung, and colorectal carcinomas. We have previously found that EGFR stability plays a key role in cell survival after chemotherapy and radiotherapy. Heat shock protein 90 (HSP90) is known to stabilize mutant EGFR and ErbB2, but its role in cancers with wild-type (WT) WT-EGFR is unclear. In this report, we demonstrate that fully mature, membrane-bound WT-EGFR interacts with HSP90 independent of ErbB2. Further, the HSP90 inhibitors geldanamycin (GA) and AT13387 cause a decrease in WT-EGFR in cultured head and neck cancer cells. This decrease results from a significantly reduced half-life of WT-EGFR. WT-EGFR was also lost in head and neck xenograft specimens after treatment with AT13387 under conditions that inhibited tumor growth and prolonged survival of the mice. Our findings demonstrate that WT-EGFR is a client protein of HSP90 and that their interaction is critical for maintaining both the stability of the receptor as well as the growth of EGFR-dependent cancers. Furthermore, these findings support the search for specific agents that disrupt HSP90's ability to act as an EGFR chaperone