Characterization of the Extracellular Proteome of a Natural Microbial Community with an Integrated Mass Spectrometric / Bioinformatic Approach

Proteomics comprises the identification and characterization of the complete suite of expressed proteins in a given cell, organism or community. The coupling of high performance liquid chromatography (LC) with high throughput mass spectrometry (MS) has provided the foundation for current proteomic progression. The transition from proteomic analysis of a single cultivated microbe to that of natural microbial assemblages has required significant advancement in technology and has provided greater biological understanding of microbial community diversity and function. To enhance the capabilities of a mass spectrometric based proteomic analysis, an integrated approach combining bioinformatics with analytical preparations and experimental data collection was developed and applied. This has resulted in a deep characterization of the extracellular fraction of a community of microbes thriving in an acid mine drainage system. Among the notable features of this relatively low complexity community, they exist in a solution that is highly acidic (pH \u3c 1) and hot (temperature \u3e 40°C), with molar concentrations of metals. The extracellular fraction is of particular interest due to the potential to identify and characterize novel proteins that are critical for survival and interactions with the harsh environment. The following analyses have resulted in the specific identification and characterization of novel extracellular proteins. In order to more accurately identify which proteins are present in the extracellular space, a combined computational prediction and experimental identification of the extracellular fraction was performed. Among the hundreds of proteins identified, a highly abundant novel cytochrome was targeted and ultimately characterized through high performance MS. In order to achieve deep proteomic coverage of the extracellular fraction, a metal affinity based protein enrichment utilizing seven different metals was developed and employed resulting in novel protein identifications. A combined top down and bottom up analysis resulted in the characterization of the intact molecular forms of extracellular proteins, including the identification of post-translational modifications. Finally, in order to determine the effectiveness of current MS methodologies, a software package was designed to characterize the \u3e 100,000 mass spectra collected during an MS experiment, revealing that specific optimizations in the LC, MS and protein sequence database have a significant impact on proteomic depth

A familial form of convulsive disorder with or without mental retardation limited to females: extension of a pedigree limits possible genetic mechanisms

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66148/1/j.1399-0004.1990.tb03594.x.pd

Norepinephrine-induced acute renal failure: A reversible ischemic model of acute renal failure

Several studies have shown that acute renal failure (ARF) can be produced in the dog by infusing norepinephrine (NE) into a renal artery [1, 2]. In these studies the injury appeared to be confined to the infused kidney, with no changes occurring in systemic hemodynamics or in the function of the contralateral kidney. The hemodynamic changes noted in the infused kidney were comparable to those seen in human ARF. A major criticism of these studies, however, is that the renal failure was not shown to be reversible, as it typically is in man. In the present study, we have reexamined the NE-induced model of ARF in the dog with the particular purpose of finding a set condition which would cause ARF and yet allow recovery of renal function within a period of time comparable to that usually seen in the human disease

Evaluation of Changes in Nutritional Quality of Corn Residue Over Time

Irrigated corn residue was sampled across time in order to determine changes in quality and proportion of corn residue as the plant dried and was exposed to effects of weathering. Corn plants from two hybrids were planted on two different planting dates and harvested at periodic intervals from August 2012 to December 2012. Proportions of stem, blade/sheath, husk/shank, and cob made up smaller components of total plant DM as it matured, with the largest relative reduction occurring in the blade/sheath or stem. Hybrid impacted TDN values primarily because the 119 day hybrid was less mature at the early sampling dates

Habitat Selection by Small Mammals on the Shoreline of a Flood Control Lake in South-Central Iowa

An unusually high water level on a flood control lake shore in Iowa altered the species composition, relative density and spatial relationships of most small mammals. Peromyscus maniculatus disappeared from the study site during flooding but was the earliest invader after water had receded. A few Reithrodontomys megalotis also returned. Sorex cincereus and Blarina brevicauda did not immediately reinhabit recently flooded areas. Miccrotus ochrogaster disappeared from the site. Peromyscus leucopus and M. pennsylvanicus persisted on the unaffected portion during flooding. Both P. maniculatus and P. leucopus reestablished spatial relationships similar to those prior to flooding as vegetation returned

Mapping of the alpha-actinin binding site within the beta 1 integrin cytoplasmic domain.

The actin cross-linking protein alpha-actinin binds to the cytoplasmic domain of the beta 1 subunit of integrin, suggesting that alpha-actinin may form a direct link between the actin cytoskeleton and the transmembrane fibronectin receptor. In this study, we have used short synthetic peptides to localize the binding site for alpha-actinin within the cytoplasmic domain of beta 1 integrin. Four 13-residue peptides were tested in both an affinity chromatographic assay and a solid-phase binding assay. The results indicated that two regions of sequence contribute to the binding of alpha-actinin: one near where the beta 1 cytoplasmic tail emerges from the membrane and a second segment located near the C terminus of the cytoplasmic tail. This binding pattern was investigated in more detail using an adaptation of the mimotope assay, in which each of the 32 overlapping sequential decapeptide segments from the beta 1 cytoplasmic domain was assembled on the head of a different plastic pin. The peptide-pin constructs were used to detect the binding of 125I-alpha-actinin. As predicted from our initial results, alpha-actinin was found to bind to two distinct clusters of peptide segments. This represents a novel use of the mimotope pin assay to map interactive sites on structural proteins

AMI observations of Lynds Dark Nebulae: further evidence for anomalous cm-wave emission

Observations at 14.2 to 17.9 GHz made with the AMI Small Array towards fourteen Lynds Dark Nebulae with a resolution of 2' are reported. These sources are selected from the SCUBA observations of Visser et al. (2001) as small angular diameter clouds well matched to the synthesized beam of the AMI Small Array. Comparison of the AMI observations with radio observations at lower frequencies with matched uv-plane coverage is made, in order to search for any anomalous excess emission which can be attributed to spinning dust. Possible emission from spinning dust is identified as a source within a 2' radius of the Scuba position of the Lynds dark nebula, exhibiting an excess with respect to lower frequency radio emission. We find five sources which show a possible spinning dust component in their spectra. These sources have rising spectral indices in the frequency range 14.2--17.9 GHz. Of these five one has already been reported, L1111, we report one new definite detection, L675, and three new probable detections (L944, L1103 and L1246). The relative certainty of these detections is assessed on the basis of three criteria: the extent of the emission, the coincidence of the emission with the Scuba position and the likelihood of alternative explanations for the excess. Extended microwave emission makes the likelihood of the anomalous emission arising as a consequence of a radio counterpart to a protostar or a proto-planetary disk unlikely. We use a 2' radius in order to be consistent with the IRAS identifications of dark nebulae (Parker 1988), and our third criterion is used in the case of L1103 where a high flux density at 850 microns relative to the FIR data suggests a more complicated emission spectrum.Comment: submitted MNRA

T Cell Responses to Human Endogenous Retroviruses in HIV-1 Infection

Human endogenous retroviruses (HERVs) are remnants of ancient infectious agents that have integrated into the human genome. Under normal circumstances, HERVs are functionally defective or controlled by host factors. In HIV-1-infected individuals, intracellular defense mechanisms are compromised. We hypothesized that HIV-1 infection would remove or alter controls on HERV activity. Expression of HERV could potentially stimulate a T cell response to HERV antigens, and in regions of HIV-1/HERV similarity, these T cells could be cross-reactive. We determined that the levels of HERV production in HIV-1-positive individuals exceed those of HIV-1-negative controls. To investigate the impact of HERV activity on specific immunity, we examined T cell responses to HERV peptides in 29 HIV-1-positive and 13 HIV-1-negative study participants. We report T cell responses to peptides derived from regions of HERV detected by ELISPOT analysis in the HIV-1-positive study participants. We show an inverse correlation between anti-HERV T cell responses and HIV-1 plasma viral load. In HIV-1-positive individuals, we demonstrate that HERV-specific T cells are capable of killing cells presenting their cognate peptide. These data indicate that HIV-1 infection leads to HERV expression and stimulation of a HERV-specific CD8+ T cell response. HERV-specific CD8+ T cells have characteristics consistent with an important role in the response to HIV-1 infection: a phenotype similar to that of T cells responding to an effectively controlled virus (cytomegalovirus), an inverse correlation with HIV-1 plasma viral load, and the ability to lyse cells presenting their target peptide. These characteristics suggest that elicitation of anti-HERV-specific immune responses is a novel approach to immunotherapeutic vaccination. As endogenous retroviral sequences are fixed in the human genome, they provide a stable target, and HERV-specific T cells could recognize a cell infected by any HIV-1 viral variant. HERV-specific immunity is an important new avenue for investigation in HIV-1 pathogenesis and vaccine design

Thrive With Me: Protocol for a Randomized Controlled Trial to Test a Peer Support Intervention to Improve Antiretroviral Therapy Adherence Among Men Who Have Sex With Men

Background: The suboptimal rate of viral suppression among persons aged 13 years and older and residing in 37 states and the District of Columbia leaves considerable opportunities for onward transmission and contributes to poor health outcomes. Men who have sex with men (MSM) represent one of the most at-risk groups in the United States. There is a clear and continued need for innovative adherence support programs to optimize viral suppression. To address this gap, we designed and are implementing a randomized controlled trial (RCT) to test the efficacy of the Thrive with Me intervention for MSM living with HIV. Critical components of the protocol are presented. Objective: The aim of this study is to describe the protocol for rigorously testing the efficacy of Thrive with Me to improve antiretroviral therapy (ART) adherence among HIV-positive MSM residing in New York City. Methods: A community advisory board and beta testing were used to obtain feedback from HIV-positive MSM on the overall look and feel of Thrive with Me and problems with navigation to finalize intervention components and content. We will enroll 400 HIV-positive MSM residing in the New York City area into a two-arm prospective RCT and follow them for 17 months. Men in the Thrive with Me experimental intervention arm will have access to Thrive with Me for 5 months. Thrive with Me has three primary components: (1) a private social networking feature; (2) tailored HIV and ART adherence information; and (3) medication reminders, self-monitoring, and reflection. Gamification components include badges and leveling up to increase intrinsic motivation to engage with the intervention. Men randomized to the control condition will view a weekly newsletter for 5 months. The newsletter will be delivered via email and contains information on topics related to HIV with the exception of ART adherence. Study assessments will occur at enrollment and 5, 11, and 17 months post enrollment. The primary study outcome is HIV viral load, which is considered an objective indicator of ART adherence. Results: Participant recruitment for the RCT began in October 2016, and the data collection period is anticipated to end in the Fall of 2019. Conclusions: The efficacy trial of Thrive with Me will help to fill gaps in understanding about the utility of multicomponent, technology-based interventions to improve ART adherence among HIV-positive MSM. Of importance is the ability for the results of the Thrive with Me trial to inform best practices for conducting technology-based interventions that incorporate social media features

Implementation of AI/Deep Learning Disruption Predictor into a Plasma Control System

This paper reports on advances to the state-of-the-art deep-learning disruption prediction models based on the Fusion Recurrent Neural Network (FRNN) originally introduced a 2019 Nature publication. In particular, the predictor now features not only the disruption score, as an indicator of the probability of an imminent disruption, but also a sensitivity score in real-time to indicate the underlying reasons for the imminent disruption. This adds valuable physics-interpretability for the deep-learning model and can provide helpful guidance for control actuators now that it is fully implemented into a modern Plasma Control System (PCS). The advance is a significant step forward in moving from modern deep-learning disruption prediction to real-time control and brings novel AI-enabled capabilities relevant for application to the future burning plasma ITER system. Our analyses use large amounts of data from JET and DIII-D vetted in the earlier NATURE publication. In addition to when a shot is predicted to disrupt, this paper addresses reasons why by carrying out sensitivity studies. FRNN is accordingly extended to use many more channels of information, including measured DIII-D signals such as (i) the n1rms signal that is correlated with the n =1 modes with finite frequency, including neoclassical tearing mode and sawtooth dynamics, (ii) the bolometer data indicative of plasma impurity content, and (iii) q-min, the minimum value of the safety factor relevant to the key physics of kink modes. The additional channels and interpretability features expand the ability of the deep learning FRNN software to provide information about disruption subcategories as well as more precise and direct guidance for the actuators in a plasma control system