A Protocol for Measurement of Noncoding RNA in Human Serum

MicroRNAs (miRNAs) are small noncoding RNAs that act as regulators of gene expression by targeting mature messenger RNAs. Following the initial report of the presence of miRNAs in serum and plasma a number of studies have successfully demonstrated the use of these miRNAs as biomarkers of disease. Currently, there are many methods of isolating total RNA from liquid samples. Here, we describe a simple, cost effective method for extraction of RNA from human serum as well as subsequent real time PCR analysis of miRNA levels

Epigenetic and Transcriptome Profiling Identifies a Population of Visceral Adipose-Derived Progenitor Cells with the Potential to Differentiate into an Endocrine Pancreatic Lineage

Type 1 diabetes (T1D) is characterized by the loss of insulin-producing β-cells in the pancreas. T1D can be treated using cadaveric islet transplantation, but this therapy is severely limited by a lack of pancreas donors. To develop an alternative cell source for transplantation therapy, we carried out the epigenetic characterization in nine different adult mouse tissues and identified visceral adipose-derived progenitors as a candidate cell population. Chromatin conformation, assessed using chromatin immunoprecipitation (ChIP) sequencing and validated by ChIP-polymerase chain reaction (PCR) at key endocrine pancreatic gene promoters, revealed similarities between visceral fat and endocrine pancreas. Multiple techniques involving quantitative PCR, in-situ PCR, confocal microscopy, and flow cytometry confirmed the presence of measurable (2-1000-fold over detectable limits) pancreatic gene transcripts and mesenchymal progenitor cell markers (CD73, CD90 and CD105; >98%) in visceral adipose tissue-derived mesenchymal cells (AMCs). The differentiation potential of AMCs was explored in transgenic reporter mice expressing green fluorescent protein (GFP) under the regulation of the Pdx1 (pancreatic and duodenal homeobox-1) gene promoter. GFP expression was measured as an index of Pdx1 promoter activity to optimize culture conditions for endocrine pancreatic differentiation. Differentiated AMCs demonstrated their capacity to induce pancreatic endocrine genes as evidenced by increased GFP expression and validated using TaqMan real-time PCR (at least 2-200-fold relative to undifferentiated AMCs). Human AMCs differentiated using optimized protocols continued to produce insulin following transplantation in NOD/SCID mice. Our studies provide a systematic analysis of potential islet progenitor populations using genome-wide profiling studies and characterize visceral adipose-derived cells for replacement therapy in diabetes

Using a 2-Stage Strategy with Respondent-Driven Sampling to Recruit a Hard-to-Reach Population for a Placebo Microbicide Gel Clinical Trial in Nellore, Andhra Pradesh (India)

Traditional recruitment methods for microbicide efficacy trials are labor intensive and may fail to reach high-risk hard-to-reach populations. We report duration of recruitment and lessons learned from a two-stage process to recruit female sex workers (FSWs) into a placebo microbicide trial, and examined characteristics associated with successful recruitment of peers who screened for and enrolled in the trial. FSWs were first recruited via respondent-driven sampling (RDS) to complete a survey and subsequently invited to screen for enrollment into a placebo microbicide trial taking place at a local clinic. It took 6 months to enroll 267 participants into the trial. Successful recruiters of peers who enrolled were more likely to have enrolled themselves (AOR 2.0, CI 1.3–2.9) and less likely to visit Nellore city (AOR 0.5, CI 0.3–0.9). Recruitment of FSWs via a two-stage recruitment strategy with RDS can be a good option for future clinical trials

'Not all that burns is wood': a social perspective on fuel exploitation and use during the Indus urban period (2600-1900 BC)

Ancient civilisations depended heavily on natural fuel resources for a wide array of activities, and this had an impact on such resources that can be traced in the archaeological record. At its urban apex, the populations of the Indus Civilisation (2600–1900 BC) produced a wide range of objects and crafts, several of which involved highly specialised pyrotechnology. In the wake of increasing aridity and a period of weakened monsoon rainfall that affected South Asia from 2100 BC, these activities potentially put pressure on the natural resource base that may have had to be counterbalanced by differentiation in fuel use. The combined analysis of archaeobotanical and geoarchaeological remains from four Indus urban phase archaeological sites, has enable an assessment of the mechanisms through which people exploited wood, and diversified their fuel resources to adapt to the arid to semi-arid environments in which they lived. The combined use of local wood species with alternative fuels, such as dung and crop-processing leftovers, are evidence for resilient socio-ecological practices during the 700 years of Indus urbanism and perhaps beyond.The research was funded by AHRC Doctoral grant (2007/131224), St John’s College [no grant number], Cambridge European Trust (300469695) and The University of Cambridge (Isbel-Fletcher Garden Fund [no grant number], Smuts Memorial Fund [S2007/E2007], and Anthony Wilkin Fund [no grant number])