Status and Role of Antioxidant Enzymes in Sexual and Apomictic Species of \u3cem\u3eBoechera\u3c/em\u3e

Enzymatic and non-enzymatic antioxidation systems provide protection against the toxic effects of activated oxygen species including scavenging H2O2. It is evident that during stress plants produce different ROS which play a negative role in regulating the antioxidant system and a positive role in signaling events that regulate ion channel activity and gene expression Microarray data indicate that ovules and pistils from apomictic Boechera differ in gene expression from those of sexual Boechera. Specifically, these differences involve genes responsible for stress response, RNA processing, ribosome synthesis and function, photosynthesis and cell cycle regulation. Thus, in the present study, activities of three antioxidant enzymes viz. guaiacol peroxidase, catalase and ascorbate peroxidase were measured in the young unopened buds of two sexual (B. stricta and B. yellowstonensis) and two apomictic (B. retrofracta x stricta and B. microphylla). The activity staining of these enzymes were performed to detect isozymes of these enzymes in a species-specific manner

Prospective isolation and global gene expression analysis of definitive and visceral endoderm

AbstractIn spite of the therapeutic importance of endoderm derivatives such as the pancreas, liver, lung, and intestine, there are few molecular markers specific for early endoderm. In order to identify endoderm-specific genes as well as to define transcriptional differences between definitive and visceral endoderm, we performed microarray analysis on E8.25 definitive and visceral endoderm. We have developed an early endoderm gene expression signature, and clarified the transcriptional similarities and differences between definitive and visceral endoderm. Additionally, we have developed methods for flow cytometric isolation of definitive and visceral endoderm. These results shed light on the mechanism of endoderm formation and should facilitate investigation of endoderm formation from embryonic stem cells

Carbonyl sulfide and carbon disulfide: Large-scale distributions over the western Pacific and emissions from Asia during TRACE-P

An extensive set of carbonyl sulfide (OCS) and carbon disulfide (CS2) observations were made as part of the NASA Transport and Chemical Evolution over the Pacific (TRACE-P) project, which took place in the early spring 2001. TRACE-P sampling focused on the western Pacific region but in total included the geographic region 110°E to 290°E longitude, 5°N to 50°N latitude, and 0–12 km altitude. Substantial OCS and CS2 enhancements were observed for a great many air masses of Chinese and Japanese origin during TRACE-P. Over the western Pacific, mean mixing ratios of long-lived OCS and shorter-lived CS2 showed a gradual decrease by about 10% and a factor of 5–10, respectively, from the surface to 8–10 km altitude, presumably because land-based sources dominated their distribution during February through April 2001. The highest mean OCS and CS2levels (580 and 20 pptv, respectively, based on 2.5° × 2.5° latitude bins) were observed below 2 km near the coast of Asia, at latitudes between 25°N and 35°N, where urban Asian outflow was strongest. Ratios of OCS versus CO for continental SE Asia were much lower compared to Chinese and Japanese signatures and were strongly associated with biomass burning/biofuel emissions. We present a new inventory of anthropogenic Asian emissions (including biomass burning) for OCS and CS2 and compare it to emission estimates based on regional relationships of OCS and CS2 to CO and CO2. The OCS and CS2 results for the two methods compare well for continental SE Asia and Japan plus Korea and also for Chinese CS2 emissions. However, it appears that the inventory underestimates Chinese emissions of OCS by about 30–100%. This difference may be related to the fact that we did not include natural sources such as wetland emissions in our inventory, although the contributions from such sources are believed to be at a seasonal low during the study period. Uncertainties in OCS emissions from Chinese coal burning, which are poorly characterized, likely contribute to the discrepancy

Discovery of non-directional and directional pioneer transcription factors by modeling DNase profile magnitude and shape

Here we describe Protein Interaction Quantitation (PIQ), a computational method that models the magnitude and shape of genome-wide DNase profiles to facilitate the identification of transcription factor (TF) binding sites. Through the use of machine learning techniques, PIQ identified binding sites for >700 TFs from one DNase-seq experiment with accuracy comparable to ChIP-seq for motif-associated TFs (median AUC=0.93 across 303 TFs). We applied PIQ to analyze DNase-seq data from mouse embryonic stem cells differentiating into pre-pancreatic and intestinal endoderm. We identified (n=120) and experimentally validated eight ‘pioneer’ TF families that dynamically open chromatin, enabling other TFs to bind to adjacent DNA. Four pioneer TF families only open chromatin in one direction from their motifs. Furthermore, we identified a class of ‘settler’ TFs whose genomic binding is principally governed by proximity to open chromatin. Our results support a model of hierarchical TF binding in which directional and non-directional pioneer activity shapes the chromatin landscape for population by settler TFs

Force-velocity-power and Force-pCa Relationships of Human Soleus Fibers After 17 Days of Bed Rest

Soleus muscle fibers from the rat display a reduction in peak power and Ca2+ sensitivity after hindlimb suspension. To examine human responses to non-weight bearing, we obtained soleus biopsies from eight adult men before and immediately after 17 days of bed rest (BR). Single chemically skinned fibers were mounted between a force transducer and a servo-controlled position motor and activated with maximal (isotonic properties) and/or submaximal (Ca2+ sensitivity) levels of free Ca2+. Gel electrophoresis indicated that all pre- and post-BR fibers expressed type I myosin heavy chain. Post-BR fibers obtained from one subject displayed increases in peak power and Ca2+ sensitivity. In contrast, post-BR fibers obtained from the seven remaining subjects showed an average 11% reduction in peak power (P \u3c 0.05), with each individual displaying a 7–27% reduction in this variable. Post-BR fibers from these subjects were smaller in diameter and produced 21% less force at the shortening velocity associated with peak power. However, the shortening velocity at peak power output was elevated 13% in the post-BR fibers, which partially compensated for their lower force. Post-BR fibers from these same seven subjects also displayed a reduced sensitivity to free Ca2+(P \u3c 0.05). These results indicate that the reduced functional capacity of human lower limb extensor muscles after BR may be in part caused by alterations in the cross-bridge mechanisms of contraction

Apospory and Diplospory in Diploid Boechera (Brassicaceae) May Facilitate Speciation by Recombination-Driven Apomixis-to-Sex Reversals

Apomixis (asexual seed formation) in angiosperms occurs either sporophytically, through adventitious embryony, or gametophytically, where an unreduced female gametophyte (embryo sac) forms and produces an unreduced egg that develops into an embryo parthenogenetically. Multiple types of gametophytic apomixis occur, and these are differentiated based on where and when the unreduced gametophyte forms, a process referred to as apomeiosis. Apomeiotic gametophytes form directly from ameiotic megasporocytes, as in Antennaria-type diplospory, from unreduced spores derived from 1st division meiotic restitutions, as in Taraxacum-type diplospory, or from cells of the ovule wall, as in Hieracium-type apospory. Multiple types of apomeiosis occasionally occur in the same plant, which suggests that the different types occur in response to temporal and/or spatial shifts in termination of sexual processes and onset timing of apomeiosis processes. To better understand the origins and evolutionary implications of apomixis in Boechera (Brassicaceae), we determined apomeiosis type for 64 accessions representing 44 taxonomic units. Plants expressing apospory and diplospory were equally common, and these generally produced reduced and unreduced pollen, respectively. Apospory and diplospory occurred simultaneously in individual plants of seven taxa. In Boechera, apomixis perpetuates otherwise sterile or semisterile interspecific hybrids (allodiploids) through multiple generations. Accordingly, ample time, in these multigenerational clones, is available for rare meioses to produce haploid, intergenomically recombined male and female gametes. The fusion of such gametes could then produce segmentally autoploidized progeny. If sex re-emerges among such progeny, then new and genomically unique sexual species could evolve. Herein, we present evidence that such apomixis-facilitated speciation is occurring in Boechera, and we hypothesize that it might also be occurring in facultatively apomictic allodiploids of other angiospermous taxa

New insights into the classification and nomenclature of cortical GABAergic interneurons.

A systematic classification and accepted nomenclature of neuron types is much needed but is currently lacking. This article describes a possible taxonomical solution for classifying GABAergic interneurons of the cerebral cortex based on a novel, web-based interactive system that allows experts to classify neurons with pre-determined criteria. Using Bayesian analysis and clustering algorithms on the resulting data, we investigated the suitability of several anatomical terms and neuron names for cortical GABAergic interneurons. Moreover, we show that supervised classification models could automatically categorize interneurons in agreement with experts' assignments. These results demonstrate a practical and objective approach to the naming, characterization and classification of neurons based on community consensus

Research and Analysis of Fisheries in Illinois

Reports on progress and results for the following project objectives: sport fish population and sport fishing metrics; enhanced field sampling of sport fish populations; determination of factors affecting fishing quality; coordination with ongoing fisheries research projects; support for and enhance of web interface; fishes of Champaign County; recovery of urban stream sport fisheries.Illinois Department of Natural Resources, Division of Fisheries, Federal Aid Project F-69-R Segment 28unpublishednot peer reviewedOpe

Development of a decision support tool to facilitate primary care management of patients with abnormal liver function tests without clinically apparent liver disease [HTA03/38/02]. Abnormal Liver Function Investigations Evaluation (ALFIE)

Liver function tests (LFTs) are routinely performed in primary care, and are often the gateway to further invasive and/or expensive investigations. Little is known of the consequences in people with an initial abnormal liver function (ALF) test in primary care and with no obvious liver disease. Further investigations may be dangerous for the patient and expensive for Health Services. The aims of this study are to determine the natural history of abnormalities in LFTs before overt liver disease presents in the population and identify those who require minimal further investigations with the potential for reduction in NHS costs

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal–fetal interface

HLA-G, a nonclassical HLA molecule uniquely expressed in the placenta, is a central component of fetus-induced immune tolerance during pregnancy. The tissue-specific expression of HLA-G, however, remains poorly understood. Here, systematic interrogation of the HLA-G locus using massively parallel reporter assay (MPRA) uncovered a previously unidentified cis-regulatory element 12 kb upstream of HLA-G with enhancer activity, Enhancer L. Strikingly, clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9-mediated deletion of this enhancer resulted in ablation of HLA-G expression in JEG3 cells and in primary human trophoblasts isolated from placenta. RNA-seq analysis demonstrated that Enhancer L specifically controls HLA-G expression. Moreover, DNase-seq and chromatin conformation capture (3C) defined Enhancer L as a cell type-specific enhancer that loops into the HLA-G promoter. Interestingly, MPRA-based saturation mutagenesis of Enhancer L identified motifs for transcription factors of the CEBP and GATA families essential for placentation. These factors associate with Enhancer L and regulate HLA-G expression. Our findings identify long-range chromatin looping mediated by core trophoblast transcription factors as the mechanism controlling tissue-specific HLA-G expression at the maternal–fetal interface. More broadly, these results establish the combination of MPRA and CRISPR/Cas9 deletion as a powerful strategy to investigate human immune gene regulation