Specific Rab GTPase-activating proteins define the Shiga toxin and epidermal growth factor uptake pathways

Rab family guanosine triphosphatases (GTPases) together with their regulators define specific pathways of membrane traffic within eukaryotic cells. In this study, we have investigated which Rab GTPase-activating proteins (GAPs) can interfere with the trafficking of Shiga toxin from the cell surface to the Golgi apparatus and studied transport of the epidermal growth factor (EGF) from the cell surface to endosomes. This screen identifies 6 (EVI5, RN-tre/USP6NL, TBC1D10A–C, and TBC1D17) of 39 predicted human Rab GAPs as specific regulators of Shiga toxin but not EGF uptake. We show that Rab43 is the target of RN-tre and is required for Shiga toxin uptake. In contrast, RabGAP-5, a Rab5 GAP, was unique among the GAPs tested and reduced the uptake of EGF but not Shiga toxin. These results suggest that Shiga toxin trafficking to the Golgi is a multistep process controlled by several Rab GAPs and their target Rabs and that this process is discrete from ligand-induced EGF receptor trafficking

Diffusion Tensor Imaging for Assessment of Response to Neoadjuvant Chemotherapy in Patients With Breast Cancer.

In this study, the prognostic significance of tumor metrics derived from diffusion tensor imaging (DTI) was evaluated in patients with locally advanced breast cancer undergoing neoadjuvant therapy. DTI and contrast-enhanced magnetic resonance imaging were acquired at 1.5 T in 34 patients before treatment and after 3 cycles of taxane-based therapy (early treatment). Tumor fractional anisotropy (FA), principal eigenvalues (λ1, λ2, and λ3), and apparent diffusion coefficient (ADC) were estimated for tumor regions of interest drawn on DTI data. The association between DTI metrics and final tumor volume change was evaluated with Spearman rank correlation. DTI metrics were investigated as predictors of pathological complete response (pCR) by calculating the area under the receiver operating characteristic curve (AUC). Early changes in tumor FA and ADC significantly correlated with final tumor volume change post therapy (ρ = -0.38, P = .03 and ρ = -0.71, P < .001, respectively). Pretreatment tumor ADC was significantly lower in the pCR than in the non-pCR group (P = .04). At early treatment, patients with pCR had significantly higher percent changes of tumor λ1, λ2, λ3, and ADC than those without pCR. The AUCs for early percent changes in tumor FA and ADC were 0.60 and 0.83, respectively. The early percent changes in tumor eigenvalues and ADC were the strongest DTI-derived predictors of pCR. Although early percent change in tumor FA had a weak association with pCR, the significant correlation with final tumor volume change suggests that this metric changes with therapy and may merit further evaluation

Priming Effects on Seed Germination of Tadong Upland Rice Collected in Sabah, Malaysia

Rice (Oryza sativa L.) is a food crop cultivated worldwide and serves as a staple food for more than half of the world’s population. However, the rice production in Malaysia is still unable to reach full sufficiency level and incapable to ensure the national food security as the production levels are still low especially the rice farms in hilly areas. The current self-sufficiency level of rice in Malaysia is 72% and still lacking of 8% from the target of 80% by 2023. Seed priming is one of the techniques to enhance seed performance with respect to uniformity and rate of germination which results better yields in crops. The objective of this research was to determine the priming effects of polyethylene glycol (PEG) 6000 on seed germination of Tadong upland rice. Seed germination of Tadong upland rice was determined under different concentrations of PEG 6000. The experiment was laid out in a completely randomized design with three replications. The priming treatments were five concentrations of 0, -2, -4, -6, and -8 bars using PEG 6000. The data was analyzed using One-way ANOVA and LSD was applied to compare means. The grain size of Tadong upland rice is very long (length of 9.90 mm) and the shape is medium (length/breadth ratio of 2.77). The colour of rice grain with husk is brownish yellow while without husk is reddish black in colour. All the germination traits including germination percentage, germination index, germination rate, mean germination time, germination speed and germination energy showed significant effects among priming concentrations. The highest germination percentage (95.67%), germination index (51.26), germination rate (0.223), germination energy (93.00%) and shortest mean germination time (4.48 days) was found from priming with distilled water (0 bar) but germination speed (100.00%) was found highest when it was treated with -2 bar osmotic potential of PEG 6000. It can be concluded that the higher the PEG concentration (-8 bar), the lower the germination index (35.99), germination rate (0.206), germination speed (94.27%) and germination energy (87.67%) and the longer the mean germination time (4.83 days)

Functional dissection of Rab GTPases involved in primary cilium formation

Primary cilia are sensory structures involved in morphogen signalling during development, liquid flow in the kidney, mechanosensation, sight, and smell (Badano, J.L., N. Mitsuma, P.L. Beales, and N. Katsanis. 2006. Annu. Rev. Genomics Hum. Genet. 7:125–148; Singla, V., and J.F. Reiter. 2006. Science. 313:629–633.). Mutations that affect primary cilia are responsible for several diseases, including neural tube defects, polycystic kidney disease, retinal degeneration, and cancers (Badano et al., 2006; Singla and Reiter, 2006). Primary cilia formation and function requires tight integration of the microtubule cytoskeleton with membrane trafficking (Singla and Reiter, 2006), and this is poorly understood. We show that the Rab GTPase membrane trafficking regulators Rab8a, -17, and -23, and their cognate GTPase-activating proteins (GAPs), XM_037557, TBC1D7, and EVI5like, are involved in primary cilia formation. However, other human Rabs and GAPs are not. Additionally, Rab8a specifically interacts with cenexin/ODF2, a basal body and microtubule binding protein required for cilium biogenesis (Ishikawa, H., A. Kubo, S. Tsukita, and S. Tsukita. 2005. Nat. Cell Biol. 7:517–524), and is the sole Rab enriched at primary cilia. These findings provide a basis for understanding how specific membrane trafficking pathways cooperate with the microtubule cytoskeleton to give rise to the primary cilia

Characterization of Proximal Small Intestinal Microbiota in Patients With Suspected Small Intestinal Bacterial Overgrowth: A Cross-Sectional Study

OBJECTIVES: The composition of the small intestinal microbiota has not yet been characterized thoroughly using culture-independent techniques. We compared small intestinal microbial communities in patients with and without small intestinal bacterial overgrowth (SIBO) using culture-dependent and culture-independent bacterial identification approaches. METHODS: Small bowel aspirate and mucosal samples were collected from patients with suspected SIBO. The aspirates were cultured to diagnose SIBO, defined as ≥10 colony-forming units/mL coliform or ≥10 colony-forming units/mL upper aerodigestive tract bacteria. Bacteria in the aspirates and mucosa were identified using 16S rRNA gene sequencing. We compared small intestinal microbiome composition between groups with and without a culture-based SIBO diagnosis. RESULTS: Analysis of the aspirate and mucosal microbial communities from 36 patients revealed decreased α-diversity but no differences in β-diversity in patients with SIBO compared with those without SIBO. There were no significant differences in the relative abundance of individual taxa from the aspirates or mucosa after adjustment for false discovery rate between patients with and without SIBO. Subgroup analysis revealed significant differences in mucosal β-diversity between the coliform and upper aerodigestive tract subgroups. Relative abundances of a mucosal Clostridium spp. (P = 0.05) and an aspirate Granulicatella spp. (P = 0.02) were higher in coliform SIBO vs non-SIBO subgroups. The microbial composition and relative abundance of multiple taxa significantly differed in the mucosal and aspirate specimens. DISCUSSION: Culture-based results of small bowel aspirates do not correspond to aspirate microbiota composition but may be associated with species richness of the mucosal microbiota

Obesity due to melanocortin 4 receptor (MC4R) deficiency is associated with delayed gastric emptying.

OBJECTIVE: People who are severely obese due to melanocortin-4 receptor (MC4R) deficiency experience hyperphagia and impaired fullness after a meal (satiety). Meal-induced satiety is influenced by hormones, such as peptide-YY (PYY), which are released by enteroendocrine cells upon nutrient delivery to the small intestine. DESIGN: We investigated whether gastric emptying and PYY levels are altered in MC4R deficiency. METHODS: Gastric emptying was measured with a gastric scintigraphy protocol using technetium-99m (99 Tcm )-Tin Colloid for 3.5 h in individuals with loss of function MC4R variants and a control group of similar age and weight. In a separate study, we measured plasma PYY levels before and at multiple time points after three standardised meals given to individuals with MC4R deficiency and controls. Fasting PYY (basal secretion) and postprandial PYY levels were measured and the area under the curve and inter-meal peak were calculated. RESULTS: We found that gastric emptying time was significantly delayed and percentage meal retention increased in individuals with MC4R deficiency compared to obese controls. In addition, fasting and mean PYY secretion throughout the day were decreased in MC4R deficiency, whereas postprandial PYY secretion was unaltered. CONCLUSION: Delayed gastric emptying and reduced basal PYY secretion may contribute to impaired satiety in people with obesity due to MC4R deficiency

The extent and variability of storm-induced temperature changes in lakes measured with long-term and high-frequency data

The intensity and frequency of storms are projected to increase in many regions of the world because of climate change. Storms can alter environmental conditions in many ecosystems. In lakes and reservoirs, storms can reduce epilimnetic temperatures from wind-induced mixing with colder hypolimnetic waters, direct precipitation to the lake's surface, and watershed runoff. We analyzed 18 long-term and high-frequency lake datasets from 11 countries to assess the magnitude of wind- vs. rainstorm-induced changes in epilimnetic temperature. We found small day-to-day epilimnetic temperature decreases in response to strong wind and heavy rain during stratified conditions. Day-to-day epilimnetic temperature decreased, on average, by 0.28 degrees C during the strongest windstorms (storm mean daily wind speed among lakes: 6.7 +/- 2.7 m s(-1), 1 SD) and by 0.15 degrees C after the heaviest rainstorms (storm mean daily rainfall: 21.3 +/- 9.0 mm). The largest decreases in epilimnetic temperature were observed >= 2 d after sustained strong wind or heavy rain (top 5(th) percentile of wind and rain events for each lake) in shallow and medium-depth lakes. The smallest decreases occurred in deep lakes. Epilimnetic temperature change from windstorms, but not rainstorms, was negatively correlated with maximum lake depth. However, even the largest storm-induced mean epilimnetic temperature decreases were typicallyPeer reviewe

A global analysis of Y-chromosomal haplotype diversity for 23 STR loci

In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend toward smaller genetic distances resulting from larger numbers of markers became apparent.Peer reviewe