Antagonistic and cooperative AGO2-PUM interactions in regulating mRNAs.

Approximately 1500 RNA-binding proteins (RBPs) profoundly impact mammalian cellular function by controlling distinct sets of transcripts, often using sequence-specific binding to 3' untranslated regions (UTRs) to regulate mRNA stability and translation. Aside from their individual effects, higher-order combinatorial interactions between RBPs on specific mRNAs have been proposed to underpin the regulatory network. To assess the extent of such co-regulatory control, we took a global experimental approach followed by targeted validation to examine interactions between two well-characterized and highly conserved RBPs, Argonaute2 (AGO2) and Pumilio (PUM1 and PUM2). Transcriptome-wide changes in AGO2-mRNA binding upon PUM knockdown were quantified by CLIP-seq, and the presence of PUM binding on the same 3'UTR corresponded with cooperative and antagonistic effects on AGO2 occupancy. In addition, PUM binding sites that overlap with AGO2 showed differential, weakened binding profiles upon abrogation of AGO2 association, indicative of cooperative interactions. In luciferase reporter validation of candidate 3'UTR sites where AGO2 and PUM colocalized, three sites were identified to host antagonistic interactions, where PUM counteracts miRNA-guided repression. Interestingly, the binding sites for the two proteins are too far for potential antagonism due to steric hindrance, suggesting an alternate mechanism. Our data experimentally confirms the combinatorial regulatory model and indicates that the mostly repressive PUM proteins can change their behavior in a context-dependent manner. Overall, the approach underscores the importance of further elucidation of complex interactions between RBPs and their transcriptome-wide extent

Cas Adaptor Proteins Coordinate Sensory Axon Fasciculation.

Development of complex neural circuits like the peripheral somatosensory system requires intricate mechanisms to ensure axons make proper connections. While much is known about ligand-receptor pairs required for dorsal root ganglion (DRG) axon guidance, very little is known about the cytoplasmic effectors that mediate cellular responses triggered by these guidance cues. Here we show that members of the Cas family of cytoplasmic signaling adaptors are highly phosphorylated in central projections of the DRG as they enter the spinal cord. Furthermore, we provide genetic evidence that Cas proteins regulate fasciculation of DRG sensory projections. These data establish an evolutionarily conserved requirement for Cas adaptor proteins during peripheral nervous system axon pathfinding. They also provide insight into the interplay between axonal fasciculation and adhesion to the substrate

Localization of complement factor H gene expression and protein distribution in the mouse outer retina.

To determine the localization of complement factor H (Cfh) mRNA and its protein in the mouse outer retina.Quantitative real-time PCR (qPCR) was used to determine the expression of Cfh and Cfh-related (Cfhr) transcripts in the RPE/choroid. In situ hybridization (ISH) was performed using the novel RNAscope 2.0 FFPE assay to localize the expression of Cfh mRNA in the mouse outer retina. Immunohistochemistry (IHC) was used to localize Cfh protein expression, and western blots were used to characterize CFH antibodies used for IHC.Cfh and Cfhr2 transcripts were detected in the mouse RPE/choroid using qPCR, while Cfhr1, Cfhr3, and Cfhrc (Gm4788) were not detected. ISH showed abundant Cfh mRNA in the RPE of all mouse strains (C57BL/6, BALB/c, 129/Sv) tested, with the exception of the Cfh(-/-) eye. Surprisingly, the Cfh protein was detected by immunohistochemistry in photoreceptors rather than in RPE cells. The specificity of the CFH antibodies was tested by western blotting. Our CFH antibodies recognized purified mouse Cfh protein, serum Cfh protein in wild-type C57BL/6, BALB/c, and 129/Sv, and showed an absence of the Cfh protein in the serum of Cfh(-/-) mice. Greatly reduced Cfh protein immunohistological signals in the Cfh(-/-) eyes also supported the specificity of the Cfh protein distribution results.Only Cfh and Cfhr2 genes are expressed in the mouse outer retina. Only Cfh mRNA was detected in the RPE, but no protein. We hypothesize that the steady-state concentration of Cfh protein is low in the cells due to secretion, and therefore is below the detection level for IHC

Characterization of the fecal microbiome in cats with inflammatory bowel disease or alimentary small cell lymphoma.

Feline chronic enteropathy (CE) is a common gastrointestinal disorder in cats and mainly comprises inflammatory bowel disease (IBD) and small cell lymphoma (SCL). Both IBD and SCL in cats share features with chronic enteropathies such as IBD and monomorphic epitheliotropic intestinal T-cell lymphoma in humans. The aim of this study was to characterize the fecal microbiome of 38 healthy cats and 27 cats with CE (13 cats with IBD and 14 cats with SCL). Alpha diversity indices were significantly decreased in cats with CE (OTU p = 0.003, Shannon Index p = 0.008, Phylogenetic Diversity p = 0.019). ANOSIM showed a significant difference in bacterial communities, albeit with a small effect size (P = 0.023, R = 0.073). Univariate analysis and LEfSE showed a lower abundance of facultative anaerobic taxa of the phyla Firmicutes (families Ruminococcaceae and Turicibacteraceae), Actinobacteria (genus Bifidobacterium) and Bacteroidetes (i.a. Bacteroides plebeius) in cats with CE. The facultative anaerobic taxa Enterobacteriaceae and Streptococcaceae were increased in cats with CE. No significant difference between the microbiome of cats with IBD and those with SCL was found. Cats with CE showed patterns of dysbiosis similar to those in found people with IBD

Influence of asymptomatic pneumonia on the response to hemorrhage and resuscitation in swine

INTRODUCTION: Investigation of resuscitation fluids in our swine hemorrhage model revealed moderate to severe chronic pneumonia in five swine at necropsy. Our veterinary staff suggested that we perform a retrospective analysis of prospectively collected data from these animals. We compared the data to that of ten healthy swine to determine the physiologic consequences of the added stress on our hemorrhage/resuscitation model. METHODS: Anesthetized, immature female swine (40 ± 5 kg) were instrumented for determining arterial and venous pressures, cardiac output and urine production. A controlled hemorrhage of 20 ml/kg over 4 min 40 sec was followed at 30 min by a second hemorrhage of 8 ml/kg and resuscitation with 1.5 ml/kg/min of LR solutions to achieve and maintain systolic blood pressure at 80 ± 5 mmHg for 3.5 hrs. Chemistries and arterial and venous blood gasses were determined from periodic blood samples along with hemodynamic variables. RESULTS: There were significant decreases in survival, urine output, cardiac output and oxygen delivery at 60 min and O2 consumption at 120 min in the pneumonia group compared to the non-pneumonia group. There were no differences in other metabolic or hemodynamic data between the groups. CONCLUSION: Although pneumonia had little influence on pulmonary gas exchange, it influenced cardiac output, urine output and survival compared to healthy swine, suggesting a decrease in the physiologic reserve. These data may be relevant to patients with subclinical infection who are stressed by hemorrhage and may explain in part why some similarly injured patients require more resuscitation efforts than others

Microarrays in cancer research

Microarray technology has presented the scientific community with a compelling approach that allows for simultaneous evaluation of all cellular processes at once. Cancer, being one of the most challenging diseases due to its polygenic nature, presents itself as a perfect candidate for evaluation by this approach. Several recent articles have provided significant insight into the strengths and limitations of microarrays. Nevertheless, there are strong indications that this approach will provide new molecular markers that could be used in diagnosis and prognosis of cancers (1, 2). To achieve these goals it is essential that there is a seamless integration of clinical and molecular biological data that allows us to elucidate genes and pathways involved in various cancers. To this effect we are currently evaluating gene expression profiles in human brain, ovarian, breast and hematopoetic, lung, colorectal, head and neck and biliary tract cancers. To address the issues we have a joint team of scientists, doctors and computer scientists from two Virginia Universities and a major healthcare provider. The study has been divided into several focus groups that include; Tissue Bank Clinical & Pathology Laboratory Data, Chip Fabrication, QA/QC, Tissue Devitalization, Database Design and Data Analysis, using multiple microarray platforms. Currently over 300 consenting patients have been enrolled in the study with the largest number being that of breast cancer patients. Clinical data on each patient is being compiled into a secure and interactive relational database and integration of these data elements will be accomplished by a common programming interface. This clinical database contains several key parameters on each patient including demographic (risk factors, nutrition, co-morbidity, familial history), histopathology (non genetic predictors), tumor, treatment and follow-up information. Gene expression data derived from the tissue samples will be linked to this database, which allows us to query the data at multiple levels. The challenge of tissue acquisition and processing is of paramount importance to the success of this venture. A tissue devitalization timeline protocol was devised to ensure sample and RNA integrity. Stringent protocols are being employed to ascertain accurate tumor homogeneity, by serial dissection of each tumor sample at 10\u3bcM frozen sections followed by histopathological evaluation. The multiple platforms being utilized in this study include Affimetrix, Oligo-Chips and custom-designed cDNA arrays. Selected RNA samples will be evaluated on each platform between the groups. Analysis steps will involve normalization and standardization of gene expression data followed by hierarchical clustering to determine co-regulation profiles. The aim of this conjoint effort is to elucidate pathways and genes involved in various cancers, resistance mechanisms, molecular markers for diagnosis and prognosis

Variability Across Implanting Centers in Short and Long-Term Mortality and Adverse Events in Patients on HeartMate 3 Support: A Momentum 3 Secondary Analysis

Purpose: We aimed to characterize center-specific variability in HeartMate 3 (HM3) patient survival within the MOMENTUM 3 studies and to examine the correlation between implanting center survival and major adverse events (AEs). Methods: Center HM3 implant volume during the MOMENTUM 3 pivotal (n=515) and continued access protocol (n=1685) trials were tallied. Centers implanting ≤16 HM3 patients (25th percentile) were excluded. De-identified center variability in mortality was assessed at 90 days and 2 years using direct adjusted survival while accounting for key baseline risk factors. The 90-day frequency and 2-year rates of stroke, bleeding, and infection were compared across centers and correlations between survival and event rate variability were assessed. Results: Among 48 centers, 1957 HM3 patients were included in this analysis with site implants ranging between 17 to 103 patients. Patient cohorts differed across the sites by age (average 52-68 years), sex (60-95% male), destination therapy intent (25-100%), and %INTERMACS profile 1-2 (2-81%). At 90 days, center adjusted median mortality was 6.5%, nadiring at ≤3.2% (25th percentile) and peaking at ≥10.5% (75th percentile). Median 2-year center adjusted mortality was 18.6%, nadiring at ≤14.0% and peaking at ≥25.2% (figure A). AEs were also highly variable across centers; centers with low mortality tended to have lower AE rates at 2 years (figure B). Conclusion: Patient characteristics and outcomes were highly variable across MOMENTUM 3 centers despite trial preoperative inclusion/exclusion criteria. Many centers had exemplary risk-adjusted HM3 patient outcomes. Studies are needed to improve our understanding of top performing centers’ best practices as they relate to HM3 care in the pre, interoperative, and chronic support stages in an effort to further improve HM3 LVAD-associated clinical outcomes

In-beam spectroscopy using the (t,p) reaction: recent results near A = 100

Charged particle spectroscopy using the (t,p) reaction has been employed for more than two decades to study the low-energy structure of nuclei. This reaction has contributed significantly to the elucidation of single-particle and collective phenomena for neutron rich nuclei in virtually every mass region. We have begun to use the (t,p) reaction in conjunctionuclei with in-beam ..gamma..-ray and conversion-electron spectroscopy to bring additional understanding to low-energy nuclear structure. In this report we briefly discuss the experimental considerations in using this reaction for in-beam spectroscopy, and present some results for nuclei with mass near 100

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses, and disease, testing enhancer activity in animals remains tedious, with a minority of enhancers having been characterized. Here, we have developed ‘enhancer-FACS-Seq’ (eFS) technology for highly parallel identification of active, tissue-specific enhancers in Drosophila embryos. Analysis of enhancers identified by eFS to be active in mesodermal tissues revealed enriched DNA binding site motifs of known and putative, novel mesodermal transcription factors (TFs). Naïve Bayes classifiers using TF binding site motifs accurately predicted mesodermal enhancer activity. Application of eFS to other cell types and organisms should accelerate the cataloging of enhancers and understanding how transcriptional regulation is encoded within them

Genetic Diversity of a Parasitic Weed, Striga hermonthica, on Sorghum and Pearl Millet in Mali

Eleven populations of witchweed, Striga hermonthica, were collected in four regions of Mali and investigated with 12 microsatellite markers. Extensive genetic diversity was observed, with most plants heterozygous for most markers. Allelic diversity was broadly distributed across populations with little genetic differentiation and large amounts of gene flow. Nearby fields of pearl millet and sorghum were found to have indistinguishable witchweed populations. Some population structure was apparent, but did not correlate with the local environment or host genotype, suggesting that seed transportation or other human-driven variables act to differentiate central Malian S. hermonthica populations from southern Malian populations