Evaluating the role of land cover and climate uncertainties in computing gross primary production in Hawaiian Island ecosystems

Gross primary production (GPP) is the Earth’s largest carbon flux into the terrestrial biosphere and plays a critical role in regulating atmospheric chemistry and global climate. The Moderate Resolution Imaging Spectrometer (MODIS)-MOD17 data product is a widely used remote sensing-based model that provides global estimates of spatiotemporal trends in GPP. When the MOD17 algorithm is applied to regional scale heterogeneous landscapes, input data from coarse resolution land cover and climate products may increase uncertainty in GPP estimates, especially in high productivity tropical ecosystems. We examined the influence of using locally specific land cover and high-resolution local climate input data on MOD17 estimates of GPP for the State of Hawaii, a heterogeneous and discontinuous tropical landscape. Replacing the global land cover data input product (MOD12Q1) with Hawaii-specific land cover data reduced statewide GPP estimates by ~8%, primarily because the Hawaii-specific land cover map had less vegetated land area compared to the global land cover product. Replacing coarse resolution GMAO climate data with Hawaii-specific high-resolution climate data also reduced statewide GPP estimates by ~8% because of the higher spatial variability of photosynthetically active radiation (PAR) in the Hawaii-specific climate data. The combined use of both Hawaii-specific land cover and high-resolution Hawaii climate data inputs reduced statewide GPP by ~16%, suggesting equal and independent influence on MOD17 GPP estimates. Our sensitivity analyses within a heterogeneous tropical landscape suggest that refined global land cover and climate data sets may contribute to an enhanced MOD17 product at a variety of spatial scales

Ancient DNA Resolves Identity and Phylogeny of New Zealand's Extinct and Living Quail (Coturnix sp.)

BACKGROUND: The New Zealand quail, Coturnix novaezealandiae, was widespread throughout New Zealand until its rapid extinction in the 1870's. To date, confusion continues to exist concerning the identity of C. novaezealandiae and its phylogenetic relationship to Coturnix species in neighbouring Australia, two of which, C. ypsilophora and C. pectoralis, were introduced into New Zealand as game birds. The Australian brown quail, C. ypsilophora, was the only species thought to establish with current populations distributed mainly in the northern part of the North Island of New Zealand. Owing to the similarities between C. ypsilophora, C. pectoralis, and C. novaezealandiae, uncertainty has arisen over whether the New Zealand quail is indeed extinct, with suggestions that remnant populations of C. novaezealandiae may have survived on offshore islands. METHODOLOGY/PRINCIPAL FINDINGS: Using fresh and historical samples of Coturnix sp. from New Zealand and Australia, DNA analysis of selected mitochondrial regions was carried out to determine phylogenetic relationships and species status. Results show that Coturnix sp. specimens from the New Zealand mainland and offshore island Tiritiri Matangi are not the New Zealand quail but are genetically identical to C. ypsilophora from Australia and can be classified as the same species. Furthermore, cytochrome b and COI barcoding analysis of the New Zealand quail and Australia's C. pectoralis, often confused in museum collections, show that they are indeed separate species that diverged approximately 5 million years ago (mya). Gross morphological analysis of these birds suggests a parallel loss of sustained flight with very little change in other phenotypic characters such as plumage or skeletal structure. CONCLUSION/SIGNIFICANCE: Ancient DNA has proved invaluable for the detailed analysis and identification of extinct and morphologically cryptic taxa such as that of quail and can provide insights into the timing of evolutionary changes that influence morphology

Chronic insulin treatment of diabetes does not fully normalize alterations in the retinal transcriptome

<p>Abstract</p> <p>Background</p> <p>Diabetic retinopathy (DR) is a leading cause of blindness in working age adults. Approximately 95% of patients with Type 1 diabetes develop some degree of retinopathy within 25 years of diagnosis despite normalization of blood glucose by insulin therapy. The goal of this study was to identify molecular changes in the rodent retina induced by diabetes that are not normalized by insulin replacement and restoration of euglycemia.</p> <p>Methods</p> <p>The retina transcriptome (22,523 genes and transcript variants) was examined after three months of streptozotocin-induced diabetes in male Sprague Dawley rats with and without insulin replacement for the later one and a half months of diabetes. Selected gene expression changes were confirmed by qPCR, and also examined in independent control and diabetic rats at a one month time-point.</p> <p>Results</p> <p>Transcriptomic alterations in response to diabetes (1376 probes) were clustered according to insulin responsiveness. More than half (57%) of diabetes-induced mRNA changes (789 probes) observed at three months were fully normalized to control levels with insulin therapy, while 37% of probes (514) were only partially normalized. A small set of genes (5%, 65 probes) was significantly dysregulated in the insulin-treated diabetic rats. qPCR confirmation of findings and examination of a one month time point allowed genes to be further categorized as prevented or rescued with insulin therapy. A subset of genes (Ccr5, Jak3, Litaf) was confirmed at the level of protein expression, with protein levels recapitulating changes in mRNA expression.</p> <p>Conclusions</p> <p>These results provide the first genome-wide examination of the effects of insulin therapy on retinal gene expression changes with diabetes. While insulin clearly normalizes the majority of genes dysregulated in response to diabetes, a number of genes related to inflammatory processes, microvascular integrity, and neuronal function are still altered in expression in euglycemic diabetic rats. Gene expression changes not rescued or prevented by insulin treatment may be critical to the pathogenesis of diabetic retinopathy, as it occurs in diabetic patients receiving insulin replacement, and are prototypical of metabolic memory.</p

Multi-Modal Proteomic Analysis of Retinal Protein Expression Alterations in a Rat Model of Diabetic Retinopathy

As a leading cause of adult blindness, diabetic retinopathy is a prevalent and profound complication of diabetes. We have previously reported duration-dependent changes in retinal vascular permeability, apoptosis, and mRNA expression with diabetes in a rat model system. The aim of this study was to identify retinal proteomic alterations associated with functional dysregulation of the diabetic retina to better understand diabetic retinopathy pathogenesis and that could be used as surrogate endpoints in preclinical drug testing studies.A multi-modal proteomic approach of antibody (Luminex)-, electrophoresis (DIGE)-, and LC-MS (iTRAQ)-based quantitation methods was used to maximize coverage of the retinal proteome. Transcriptomic profiling through microarray analysis was included to identify additional targets and assess potential regulation of protein expression changes at the mRNA level. The proteomic approaches proved complementary, with limited overlap in proteomic coverage. Alterations in pro-inflammatory, signaling and crystallin family proteins were confirmed by orthogonal methods in multiple independent animal cohorts. In an independent experiment, insulin replacement therapy normalized the expression of some proteins (Dbi, Anxa5) while other proteins (Cp, Cryba3, Lgals3, Stat3) were only partially normalized and Fgf2 and Crybb2 expression remained elevated.These results expand the understanding of the changes in retinal protein expression occurring with diabetes and their responsiveness to normalization of blood glucose through insulin therapy. These proteins, especially those not normalized by insulin therapy, may also be useful in preclinical drug development studies

Survey of Pigeon River algal communities: distribution and abundance of species at varying depths.

We studied algal communities and their variation between two different depths of the Pigeon River in July and August, 1992 at the University of Michigan Biological Station, Pellston, Michigan. The purpose of our study was to do a general survey of the algae in the Pigeon River and to determine the variation in community makeup in deep versus shallow areas. We made collections from natural substrates in the river, then used a sequential comparison index and a Palmer index to estimate diversity and abundance of algal genera and species. Our results showed that the deep water algal communities were both more diverse and more dense. We concluded that the greater diversity and abundance of genera in the deeper water was most likely because of slower currents than in the shallows and year-round availability of water.http://deepblue.lib.umich.edu/bitstream/2027.42/54356/1/2792.pdfDescription of 2792.pdf : Access restricted to on-site users at the U-M Biological Station

Pigeon River algal communities.

We studied algal communities and their variation between two different depths of the Pigeon River in July and August, 1992 at the University of Michigan Biological Station, Pellston, Michigan. The purpose of our study was to do a general survey of the algae in the Pigeon River and to determine the variation in community makeup in deep versus shallow areas. We made collections from natural substrates in the river, then used an S.C.I. and a Palmer index to estimate diversity and abundance of algal genera and species. Our results showed that the deep water algal communities were both more diverse and more dense. We concluded that the greater diversity and abundance of genera in the deeper water was most likely because of slower currents than in the shallows and year-round availability of water.http://deepblue.lib.umich.edu/bitstream/2027.42/54349/1/2785.pdfDescription of 2785.pdf : Access restricted to on-site users at the U-M Biological Station