bluuebunny/crossref_metadata_2025 huggingface dataset:
New insights into inhibition of human immunodeficiency virus type 1 replication through mutant tRNALys3
Authors: Wu Chengxiang , Nerurkar Vivek R , Lu Yuanan
Published: October 2013

Background

Host cellular tRNALys3 is exclusively utilized by human immunodeficiency virus type 1 (HIV-1) as a primer for the replication step of reverse transcription (RTion). Consequently, the priming step of HIV-1 RT constitutes a potential target for anti-HIV-1 intervention. Previous studies indicated that a mutant tRNALys3 with 7-nucleotide substitutions in the 3′ terminus resulted in aberrant HIV-1 RTion from the trans-activation response region (TAR) and inhibition of HIV-1 replication. However, the mutant tRNALys3 also directed HIV-1 RTion from the normal primer-binding site (PBS) with potentially weakened anti-HIV-1 activity. To achieve improved targeting of HIV-1 RTion at sites not including the PBS, a series of mutant tRNALys3 with extended lengths of mutations containing up to 18 bases complementary to their targeting sites were constructed and characterized.

Results

A positive correlation between the length of mutation in the 3′ PBS-binding region of tRNALys3 and the specificity of HIV-1 RTion initiation from the targeting site was demonstrated, as indicated by the potency of HIV-1 inhibition and results of priming assays. Moreover, two mutant tRNALys3s that targeted the IN-encoding region and Env gene, respectively, both showed a high anti-HIV-1 activity, suggesting that not only the TAR, but also distant sites downstream of the PBS could be effectively targeted by mutant tRNALys3. To increase the expression of mutant tRNALys3, multiple-copy expression cassettes were introduced into target cells with increased anti-HIV-1 potency.

Conclusions

These results highlight the importance of the length of complementarity between the 3′ terminus of the mutant tRNALys3 and its target site, and the feasibility of targeting multiple sites within the HIV-1 genome through mutant tRNALys3. Intervention of the HIV-1 genome conversion through mutant tRNALys3 may constitute an effective approach for development of novel therapeutics against HIV-1 replication and HIV-1-associated diseases.
Genetic diversity of the highly variable V1 region interferes with Human Immunodeficiency Virus type 1 envelope functionality
Authors: Hamoudi Meriem , Simon-Loriere Etienne , Gasser Romain , Negroni Matteo
Published: October 2013

Background

The HIV envelope (Env) promotes viral entry in the host cell. During this process, Env undergoes several conformational changes to ensure its function. At the same time, the gp120 component of Env is the protein of the virus presenting the largest genetic diversity. Understanding how the virus maintains the balance between the competing requirements for maintenance of functionality and antigenic variation of this protein is central for the comprehension of its strategies of evolution and can highlight vulnerable aspects of its replication cycle. We focused on the variable domains V1 and V2 of the HIV-1 gp120 that are involved in conformational changes and are critical for viral escape from antibody neutralization.

Results

Despite the extensive sequence diversity found in the epidemic for these regions and their location on the external face of the protein, we observed that replacing V1V2 of one primary isolate with that of another severely interferes with Env functionality in more than half of the cases studied. Similar results were obtained for intra- and intersubtype chimeras. These observations are indicative of an interference of genetic diversity in these regions with Env functionality. Therefore, despite the extensive sequence diversity that characterizes these regions in the epidemic, our results show that functional constraints seem to limit their genetic variation. Defects in the V1V2 chimeras were not relieved by the insertion of the V3 region from the same isolate, suggesting that the decrease in functionality is not due to perturbation of potential coevolution networks between V1V2 and V3. Within the V1V2 domain, the sequence of the hypervariable loop of the V1 domain seems to be crucial for the functionality of the protein.

Conclusions

Besides the well-documented role of V1V2 in the interplay with the immune response, this work shows that V1 is also involved in the selection of functional envelopes. By documenting a compromise between the opposing forces of sequence diversification and retention of functionality, these observations improve our understanding of the evolutionary trajectories of the HIV-1 envelope gene.
T cell response specificity and magnitude against SIVmac239 are not concordant in major histocompatibility complex-matched animals
Authors: Cain Brian T , Pham Ngoc H , Budde Melisa L , Greene Justin M , Weinfurter Jason T , Scarlotta Matthew , Harris Max , Chin Emily , O’Connor Shelby L , Friedrich Thomas C , O’Connor David H
Published: October 2013

Background

CD8+ T cell responses, restricted by major histocompatibility complex (MHC) class I molecules, are critical to controlling human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) replication. Previous studies have used MHC-matched siblings and monozygotic twins to evaluate genetic and stochastic influences on HIV-specific T cell responses and viral evolution. Here we used a genetically restricted population of Mauritian cynomolgus macaques (MCM) to characterize T cell responses within nine pairs of MHC-matched animals.

Findings

In MHC-matched animals, there was considerable heterogeneity in the specificity and magnitude of T cell responses detected via individual peptide gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assays. These findings were further supported by full proteome pooled peptide matrix ELISPOT data collected from this cohort at 52 weeks post-infection. Interestingly, peptide regions that elicited dominant T cell responses were more commonly shared between MHC-matched MCM than peptide regions that elicited non-dominant T cell responses.

Conclusions

Our findings suggest that, while some T cell responses mounted during chronic infection by MHC-matched MCM are similar, the majority of responses are highly variable. Shared responses detected in this study between MHC-matched MCM were directed against epitopes that had previously elicited relatively dominant responses in MCM with the same MHC class I haplotype, suggesting that the factors that influence dominance may influence the reproducibility of responses as well. This may be an important consideration for future T cell-based vaccines aiming to consistently and reproducibly elicit protective T cell responses.
Characterization of simian T-cell leukemia virus type 1 in naturally infected Japanese macaques as a model of HTLV-1 infection
Authors: Miura Michi , Yasunaga Jun-ichiro , Tanabe Junko , Sugata Kenji , Zhao Tiejun , Ma Guangyong , Miyazato Paola , Ohshima Koichi , Kaneko Akihisa , Watanabe Akino , Saito Akatsuki , Akari Hirofumi , Matsuoka Masao
Published: October 2013

Background

Human T-cell leukemia virus type 1 (HTLV-1) causes chronic infection leading to development of adult T-cell leukemia (ATL) and inflammatory diseases. Non-human primates infected with simian T-cell leukemia virus type 1 (STLV-1) are considered to constitute a suitable animal model for HTLV-1 research. However, the function of the regulatory and accessory genes of STLV-1 has not been analyzed in detail. In this study, STLV-1 in naturally infected Japanese macaques was analyzed.

Results

We identified spliced transcripts of STLV-1 corresponding to HTLV-1 tax and HTLV-1 bZIP factor (HBZ). STLV-1 Tax activated the NFAT, AP-1 and NF-κB signaling pathways, whereas STLV-1 bZIP factor (SBZ) suppressed them. Conversely, SBZ enhanced TGF-β signaling and induced Foxp3 expression. Furthermore, STLV-1 Tax activated the canonical Wnt pathway while SBZ suppressed it. STLV-1 Tax enhanced the viral promoter activity while SBZ suppressed its activation. Then we addressed the clonal proliferation of STLV-1+ cells by massively sequencing the provirus integration sites. Some clones proliferated distinctively in monkeys with higher STLV-1 proviral loads. Notably, one of the monkeys surveyed in this study developed T-cell lymphoma in the brain; STLV-1 provirus was integrated in the lymphoma cell genome. When anti-CCR4 antibody, mogamulizumab, was administered into STLV-1-infected monkeys, the proviral load decreased dramatically within 2 weeks. We observed that some abundant clones recovered after discontinuation of mogamulizumab administration.

Conclusions

STLV-1 Tax and SBZ have functions similar to those of their counterparts in HTLV-1. This study demonstrates that Japanese macaques naturally infected with STLV-1 resemble HTLV-1 carriers and are a suitable model for the investigation of persistent HTLV-1 infection and asymptomatic HTLV-1 carrier state. Using these animals, we verified that mogamulizumab, which is currently used as a drug for relapsed ATL, is also effective in reducing the proviral load in asymptomatic individuals.
Reactivation of latent HIV-1 in central memory CD4+T cells through TLR-1/2 stimulation
Authors: Novis Camille L , Archin Nancie M , Buzon Maria J , Verdin Eric , Round June L , Lichterfeld Mathias , Margolis David M , Planelles Vicente , Bosque Alberto
Published: October 2013

Background

Toll-like receptors (TLRs) are crucial for recognition of pathogen-associated molecular patterns by cells of the innate immune system. TLRs are present and functional in CD4+T cells. Memory CD4+T cells, predominantly central memory cells (TCM), constitute the main reservoir of latent HIV-1. However, how TLR ligands affect the quiescence of latent HIV within central memory CD4+T cells has not been studied.

Results

We evaluated the ability of a broad panel of TLR agonists to reactivate latent HIV-1. The TLR-1/2 agonist Pam3CSK4 leads to viral reactivation of quiescent HIV in a model of latency based on cultured TCMand in resting CD4+T cells isolated from aviremic patients. In addition, we investigated the signaling pathway associated with Pam3CSK4 involved in HIV-1 reactivation. We show that the transcription factors NFκB, NFAT and AP-1 cooperate to induce viral reactivation downstream of TLR-1/2 stimulation. Furthermore, increasing levels of cyclin T1 is not required for TLR-mediated viral reactivation, but induction of viral expression requires activated pTEFb. Finally, Pam3CSK4 reactivates latent HIV-1 in the absence of T cell activation or proliferation, in contrast to antigen stimulation.

Conclusions

Our findings suggest that the signaling through TLR-1/2 pathway via Pam3CSK4 or other reagents should be explored as an anti-latency strategy either alone or in combination with other anti-latency drugs.
Proteasome inhibitors act as bifunctional antagonists of human immunodeficiency virus type 1 latency and replication
Authors: Miller Leia K , Kobayashi Yoshifumi , Chen Chiann-Chyi , Russnak Timothy A , Ron Yacov , Dougherty Joseph P
Published: October 2013

Background

Existing highly active antiretroviral therapy (HAART) effectively controls viral replication in human immunodeficiency virus type 1 (HIV-1) infected individuals but cannot completely eradicate the infection, at least in part due to the persistence of latently infected cells. One strategy that is being actively pursued to eliminate the latent aspect of HIV-1 infection involves therapies combining latency antagonists with HAART. However, discordant pharmacokinetics between these types of drugs can potentially create sites of active viral replication within certain tissues that might be impervious to HAART.

Results

A preliminary reverse genetic screen indicated that the proteasome might be involved in the maintenance of the latent state. This prompted testing to determine the effects of proteasome inhibitors (PIs) on latently infected cells. Experiments demonstrated that PIs effectively activated latent HIV-1 in several model systems, including primary T cell models, thereby defining PIs as a new class of HIV-1 latency antagonists. Expanding upon experiments from previous reports, it was also confirmed that PIs inhibit viral replication. Moreover, it was possible to show that PIs act as bifunctional antagonists of HIV-1. The data indicate that PIs activate latent provirus and subsequently decrease viral titers and promote the production of defective virions from activated cells.

Conclusions

These results represent a proof-of-concept that bifunctional antagonists of HIV-1 can be developed and have the capacity to ensure precise tissue overlap of anti-latency and anti-replication functions, which is of significant importance in the consideration of future drug therapies aimed at viral clearance.
Sub-threshold spinal cord stimulation facilitates spontaneous motor activity in spinal rats
Authors: Gad Parag , Choe Jaehoon , Shah Prithvi , Garcia-Alias Guillermo , Rath Mrinal , Gerasimenko Yury , Zhong Hui , Roy Roland R , Edgerton Victor Reggie
Published: October 2013

Background

Epidural stimulation of the spinal cord can be used to enable stepping on a treadmill (electrical enabling motor control, eEmc) after a complete mid-thoracic spinal cord transection in adult rats. Herein we have studied the effects of eEmc using a sub-threshold intensity of stimulation combined with spontaneous load-bearing proprioception to facilitate hindlimb stepping and standing during daily cage activity in paralyzed rats.

Methods

We hypothesized that eEmc combined with spontaneous cage activity would greatly increase the frequency and level of activation of the locomotor circuits in paralyzed rats. Spontaneous cage activity was recorded using a specially designed swivel connector to record EMG signals and an IR based camcorder to record video.

Results and conclusion

The spinal rats initially were very lethargic in their cages showing little movement. Without eEmc, the rats remained rather inactive with the torso rarely being elevated from the cage floor. When the rats used their forelimbs to move, the hindlimbs were extended and dragged behind with little or no flexion. In contrast, with eEmc the rats were highly active and the hindlimbs showed robust alternating flexion and extension resulting in step-like movements during forelimb-facilitated locomotion and often would stand using the sides of the cages as support. The mean and summed integrated EMG levels in both a hindlimb flexor and extensor muscle were higher with than without eEmc. These data suggest that eEmc, in combination with the associated proprioceptive input, can modulate the spinal networks to significantly amplify the amount and robustness of spontaneous motor activity in paralyzed rats.
Recovery of archaeological wall paintings using novel multispectral imaging approaches
Authors: Legnaioli Stefano , Lorenzetti Giulia , Cavalcanti Gildo H , Grifoni Emanuela , Marras Luciano , Tonazzini Anna , Salerno Emanuele , Pallecchi Pasquino , Giachi Gianna , Palleschi Vincenzo
Published: October 2013

New approaches in the application of multispectral imaging to the recovery of archeological wall paintings are presented, based on statistical techniques and on a novel method of image treatment (Chromatic Derivative Imaging – ChromaDI) which offers a way of embedding information coming from four spectral bands into a standard RGB image. The methods are applied to some wall paintings from the Tomb of the Monkey, an Etruscan tomb in the necropolis of Poggio Renzo, near the city of Chiusi (Siena), Italy, dated around 480-470 BC. It is shown that the techniques described are able to highlight and enhance a number of details that cannot be perceived in either any of the original channel images or any single processed output channel.
Prior criminal charges and outcomes among individuals initiating office-based buprenorphine treatment
Authors: Harris Elizabeth E , Jacapraro Janet S , Rastegar Darius A
Published: October 2013

Background

There is little data on the impact of prior criminal activity on the treatment of opioid dependence with office-based buprenorphine. The goal of this study was to investigate the association between prior criminal charges and treatment outcomes in a cohort of patients initiating buprenorphine treatment in a primary care practice.

Methods

This was a retrospective study of 252 consecutive patients with opioid dependence who were given at least one prescription for buprenorphine in a primary care practice. A public database was used to collect data on criminal charges prior to enrollment. For every month after initiation of treatment, patients who remained in treatment were classified as “opioid-positive” or “opioid-negative” based on urine drug test results, patient report and clinician assessment. The primary outcomes of interest were treatment retention at one year and achieving ≥ 6 “opioid negative” months.

Results

Most (80%) of the subjects had at least one prior criminal charge. Those with prior criminal charges were more likely to have Medicare or Medicaid insurance, to be unemployed, to use cocaine and to have injected drugs. In the year after initiation of buprenorphine treatment, these subjects had significantly less opioid-negative months than those without criminal charges (5.1 months vs. 6.4 months; p = 0.030), and were less likely to have ≥ 6 opioid-negative months (43.2% vs. 58.4%; p = 0.048). While there was no difference in treatment retention at one-year for those who had any prior history (55.4% vs. 52.0%; p = 0.854), having recent charges (in the previous two years) was associated with poorer treatment retention and drug outcomes. On the other hand, having only distant charges (more than two years prior to treatment initiation) was not associated with poorer outcomes. Using multivariate analysis, recent criminal charges was the only factor significantly associated with treatment retention at one year and achieving ≥ 6 opioid-negative months.

Conclusions

Subjects with recent criminal charges had poorer treatment retention and opioid-abstinence outcomes after initiating office-based buprenorphine treatment. These individuals may benefit from more intensive treatment than is typically offered in a primary care setting.
Neuroprotective effects of donepezil against cholinergic depletion
Authors: Cutuli Debora , De Bartolo Paola , Caporali Paola , Tartaglione Anna Maria , Oddi Diego , D’Amato Francesca Romana , Nobili Annalisa , D’Amelio Marcello , Petrosini Laura
Published: October 2013

Introduction

Intraparenchymal injections of the immunotoxin 192-IgG-saporin into medial septum and nucleus basalis magnocellularis causes a selective depletion of basal forebrain cholinergic neurons. Thus, it represents a valid model to mimic a key component of the cognitive deficits associated with aging and dementia. Here we administered donepezil, a potent acetylcholinesterase inhibitor developed for treating Alzheimer’s disease, 15 days before 192-IgG-saporin injection, and thus we examined donepezil effects on neurodegeneration and cognitive deficits.

Methods

Caspase-3 activity and cognitive performances of lesioned rats pre-treated with donepezil or saline were analyzed and compared to the outcomes obtained in pre-treated sham-lesioned rats.

Results

Cholinergic depletion increased hippocampal and neocortical caspase-3 activity and impaired working memory, spatial discrimination, social novelty preference, and ultrasonic vocalizations, without affecting anxiety levels and fear conditioning. In lesioned animals, donepezil pre-treatment reduced hippocampal and neocortical caspase-3 activity and improved working memory and spatial discrimination performances and partially rescued ultrasonic vocalizations, without preventing social novelty alterations.

Conclusions

Present data indicate that donepezil pre-treatment exerts beneficial effects on behavioral deficits induced by cholinergic depletion, attenuating the concomitant hippocampal and neocortical neurodegeneration.
Very different performance of the power Doppler modalities of several ultrasound machines ascertained by a microvessel flow phantom
Authors: Ten Cate David F , Luime Jolanda J , van der Ven Myrthe , Hazes Johanna MW , Kooiman Klazina , de Jong Nico , Bosch Johannes G
Published: October 2013

Introduction

In many patients with rheumatoid arthritis (RA) subclinical disease activity can be detected with ultrasound (US), especially using power Doppler US (PDUS). However, PDUS may be highly dependent on the type of machine. This could create problems both in clinical trials and in daily clinical practice. To clarify how the PDUS signal differs between machines we created a microvessel flow phantom.

Methods

The flow phantom contained three microvessels (150, 1000, 2000 microns). A syringe pump was used to generate flows. Five US machines were used. Settings were optimised to assess the lowest detectable flow for each US machine.

Results

The minimal detectable flow velocities showed very large differences between the machines. Only two of the machines may be able to detect the very low flows in the capillaries of inflamed joints. There was no clear relation with price. One of the lower-end machines actually performed best in all three vessel sizes.

Conclusions

We created a flow phantom to test the sensitivity of US machines to very low flows in small vessels. The sensitivity of the power Doppler modalities of 5 different machines was very different. The differences found between the machines are probably caused by fundamental differences in processing of the PD signal or internal settings inaccessible to users. Machines considered for PDUS assessment of RA patients should be tested using a flow phantom similar to ours. Within studies, only a single machine type should be used.
Pre-diagnosis oophorectomy, estrogen therapy and mortality in a cohort of women diagnosed with breast cancer
Authors: Nichols Hazel B , Trentham-Dietz Amy , Newcomb Polly A , Egan Kathleen M , Titus Linda J , Hampton John M , Visvanathan Kala
Published: October 2013

Introduction

Pre-diagnosis oophorectomy and estrogen therapy could impact mortality due to breast cancer and cardiovascular disease (CVD) among breast cancer survivors. Elective bilateral oophorectomy at the time of hysterectomy for benign conditions is not uncommon among US women.

Methods

We examined the association between pre-diagnosis total abdominal hysterectomy with bilateral salpingo-oophorectomy (TAHBSO) and both overall and cause-specific mortality in the Collaborative Breast Cancer Studies cohort. Medical history and prior estrogen use were collected during standardized telephone interviews. Vital status, including date and cause of death, was obtained by linkage with the National Death Index. Multivariate hazard ratios (HR) and 95% confidence intervals (CI) for cause-specific mortality were calculated using Cox proportional hazards regression.

Results

Seventeen percent (N = 1,778) of breast cancer survivors (mean age at diagnosis = 63.5) reported pre-diagnosis TAHBSO. During follow-up (mean = 9.5 years), 2,856 deaths occurred, including 1,060 breast cancer deaths and 459 CVD deaths. Breast cancer deaths occurred a median of 5.1 years after diagnosis; CVD deaths occurred further from diagnosis (median = 9.7 years). Women who reported pre-diagnosis TAHBSO had a 16% decrease in all-cause mortality (HR = 0.84; 95% CI: 0.76, 0.92) compared to those with an intact uterus and ovaries. This overall decrease reflected a 27% lower breast cancer mortality among women who never used postmenopausal hormones (HR = 0.73; CI: 0.55, 0.96) and 43% lower CVD risk among women who reported using estrogen (HR = 0.57; CI: 0.39, 0.83) after TAHBSO.

Conclusions

Information on prior TAHBSO and estrogen use can inform risk of death from both breast cancer and cardiovascular disease among breast cancer survivors.
AVISPA: a web tool for the prediction and analysis of alternative splicing
Authors: Barash Yoseph , Vaquero-Garcia Jorge , González-Vallinas Juan , Xiong Hui Yuan , Gao Weijun , Lee Leo J , Frey Brendan J
Published: October 2013

Transcriptome complexity and its relation to numerous diseases underpins the need to predict in silico splice variants and the regulatory elements that affect them. Building upon our recently described splicing code, we developed AVISPA, a Galaxy-based web tool for splicing prediction and analysis. Given an exon and its proximal sequence, the tool predicts whether the exon is alternatively spliced, displays tissue-dependent splicing patterns, and whether it has associated regulatory elements. We assess AVISPA's accuracy on an independent dataset of tissue-dependent exons, and illustrate how the tool can be applied to analyze a gene of interest. AVISPA is available at http://avispa.biociphers.org.
Sequence signatures extracted from proximal promoters can be used to predict distal enhancers
Authors: Taher Leila , Smith Robin P , Kim Mee J , Ahituv Nadav , Ovcharenko Ivan
Published: October 2013

Background

Gene expression is controlled by proximal promoters and distal regulatory elements such as enhancers. While the activity of some promoters can be invariant across tissues, enhancers tend to be highly tissue-specific.

Results

We compiled sets of tissue-specific promoters based on gene expression profiles of 79 human tissues and cell types. Putative transcription factor binding sites within each set of sequences were used to train a support vector machine classifier capable of distinguishing tissue-specific promoters from control sequences. We obtained reliable classifiers for 92% of the tissues, with an area under the receiver operating characteristic curve between 60% (for subthalamic nucleus promoters) and 98% (for heart promoters). We next used these classifiers to identify tissue-specific enhancers, scanning distal non-coding sequences in the loci of the 200 most highly and lowly expressed genes. Thirty percent of reliable classifiers produced consistent enhancer predictions, with significantly higher densities in the loci of the most highly expressed compared to lowly expressed genes. Liver enhancer predictions were assessed in vivo using the hydrodynamic tail vein injection assay. Fifty-eight percent of the predictions yielded significant enhancer activity in the mouse liver, whereas a control set of five sequences was completely negative.

Conclusions

We conclude that promoters of tissue-specific genes often contain unambiguous tissue-specific signatures that can be learned and used for the de novo prediction of enhancers.
Temporal dynamics and transcriptional control using single-cell gene expression analysis
Authors: Kouno Tsukasa , de Hoon Michiel , Mar Jessica C , Tomaru Yasuhiro , Kawano Mitsuoki , Carninci Piero , Suzuki Harukazu , Hayashizaki Yoshihide , Shin Jay W
Published: October 2013

Background

Changes in environmental conditions lead to expression variation that manifest at the level of gene regulatory networks. Despite a strong understanding of the role noise plays in synthetic biological systems, it remains unclear how propagation of expression heterogeneity in an endogenous regulatory network is distributed and utilized by cells transitioning through a key developmental event.

Results

Here we investigate the temporal dynamics of a single-cell transcriptional network of 45 transcription factors in THP-1 human myeloid monocytic leukemia cells undergoing differentiation to macrophages. We systematically measure temporal regulation of expression and variation by profiling 120 single cells at eight distinct time points, and infer highly controlled regulatory modules through which signaling operates with stochastic effects. This reveals dynamic and specific rewiring as a cellular strategy for differentiation. The integration of both positive and negative co-expression networks further identifies the proto-oncogene MYB as a network hinge to modulate both the pro- and anti-differentiation pathways.

Conclusions

Compared to averaged cell populations, temporal single-cell expression profiling provides a much more powerful technique to probe for mechanistic insights underlying cellular differentiation. We believe that our approach will form the basis of novel strategies to study the regulation of transcription at a single-cell level.
Transplantation of umbilical cord-derived mesenchymal stem cells into the striata of R6/2 mice: behavioral and neuropathological analysis
Authors: Fink Kyle D , Rossignol Julien , Crane Andrew T , Davis Kendra K , Bombard Matthew C , Bavar Angela M , Clerc Steven , Lowrance Steven A , Song Cheng , Lescaudron Laurent , Dunbar Gary L
Published: October 2013

Introduction

Huntington’s disease (HD) is an autosomal dominant disorder caused by an expanded CAG repeat on the short arm of chromosome 4 resulting in cognitive decline, motor dysfunction, and death, typically occurring 15 to 20 years after the onset of motor symptoms. Neuropathologically, HD is characterized by a specific loss of medium spiny neurons in the caudate and the putamen, as well as subsequent neuronal loss in the cerebral cortex. The transgenic R6/2 mouse model of HD carries the N-terminal fragment of the human HD gene (145 to 155 repeats) and rapidly develops some of the behavioral characteristics that are analogous to the human form of the disease. Mesenchymal stem cells (MSCs) have shown the ability to slow the onset of behavioral and neuropathological deficits following intrastriatal transplantation in rodent models of HD. Use of MSCs derived from umbilical cord (UC) offers an attractive strategy for transplantation as these cells are isolated from a noncontroversial and inexhaustible source and can be harvested at a low cost. Because UC MSCs represent an intermediate link between adult and embryonic tissue, they may hold more pluripotent properties than adult stem cells derived from other sources.

Methods

Mesenchymal stem cells, isolated from the UC of day 15 gestation pups, were transplanted intrastriatally into 5-week-old R6/2 mice at either a low-passage (3 to 8) or high-passage (40 to 50). Mice were tested behaviorally for 6 weeks using the rotarod task, the Morris water maze, and the limb-clasping response. Following behavioral testing, tissue sections were analyzed for UC MSC survival, the immune response to the transplanted cells, and neuropathological changes.

Results

Following transplantation of UC MSCs, R6/2 mice did not display a reduction in motor deficits but there appeared to be transient sparing in a spatial memory task when compared to untreated R6/2 mice. However, R6/2 mice receiving either low- or high-passage UC MSCs displayed significantly less neuropathological deficits, relative to untreated R6/2 mice.

Conclusions

The results from this study demonstrate that UC MSCs hold promise for reducing the neuropathological deficits observed in the R6/2 rodent model of HD.
An integrated seismic reservoir characterization workflow to predict hydrocarbon production capacity in unconventional plays
Authors: Leiceaga Gorka Garcia , Norton Mark , Calvez Joël Le
Published: October 2013

Seismic-derived elastic properties may be used to help evaluate hydrocarbon production capacity in unconventional plays such as tight or shale formations. By combining prestack seismic and well log data, inversion-based volumes of elastic properties may be produced. Moreover, a petrophysical evaluation and rock physics analysis may be carried out, thus leading to a spatial distribution of hydrocarbon production capacity. The result obtained is corroborated with the available well information, confirming our ability to accurately predict hydrocarbon production capacity in unconventional plays.
Seismic azimuthal anisotropy analysis after hydraulic fracturing
Authors: Zhang Kui , Guo Yanxia , Zhang Bo , Trumbo Amanda M. , Marfurt Kurt J.
Published: October 2013

Many tight sandstone, limestone, and shale reservoirs require hydraulic fracturing to provide pathways that allow hydrocarbons to reach the well bore. Most of these tight reservoirs are now produced using multiple stages of fracturing through horizontal wells drilled perpendicular to the present-day azimuth of maximum horizontal stress. In a homogeneous media, the induced fractures are thought to propagate perpendicularly to the well, parallel to the azimuth of maximum horizontal stress, thereby efficiently fracturing the rock and draining the reservoir. We evaluated what may be the first anisotropic analysis of a Barnett shale-gas reservoir after extensive hydraulic fracturing and focus on mapping the orientation and intensity of induced fractures and any preexisting factures, with the objective being the identification of reservoir compartmentalization and bypassed pay. The Barnett Shale we studied has near-zero permeability and few if any open natural fractures. We therefore hypothesized that anisotropy is therefore due to the regional northeast–southwest maximum horizontal stress and subsequent hydraulic fracturing. We found the anisotropy to be highly compartmentalized, with the compartment edges being defined by ridges and domes delineated by the most positive principal curvature [Formula: see text]. Microseismic work by others in the same survey indicates that these ridges contain healed natural fractures that form fracture barriers. Mapping such heterogeneous anisotropy field could be critical in planning the location and direction of any future horizontal wells to restimulate the reservoir as production drops.
Characterizing a Mississippian tripolitic chert reservoir using 3D unsupervised and supervised multiattribute seismic facies analysis: An example from Osage County, Oklahoma
Authors: Roy Atish , Dowdell Benjamin L. , Marfurt Kurt J.
Published: October 2013

Seismic interpretation is based on the identification of reflector configuration and continuity, with coherent reflectors having a distinct amplitude, frequency, and phase. Skilled interpreters may classify reflector configurations as parallel, converging, truncated, or hummocky, and use their expertise to identify stratigraphic packages and unconformities. In principal, a given pattern can be explicitly defined as a combination of waveform and reflector configuration properties, although such “clustering” is often done subconsciously. Computer-assisted classification of seismic attribute volumes builds on the same concepts. Seismic attributes not only quantify characteristics of the seismic reflection events, but also measure aspects of reflector configurations. The Mississippi Lime resource play of northern Oklahoma and southern Kansas provides a particularly challenging problem. Instead of defining the facies stratigraphically, we need to define them either diagenetically (tight limestone, stratified limestone and nonporous chert, and highly porous tripolitic chert) or structurally (fractured versus unfractured chert and limestone). Using a 3D seismic survey acquired in Osage County Oklahoma, we use Kohonen self-organizing maps to classify different diagenetically altered facies of the Mississippi Lime play. The 256 prototype vectors (potential clusters) reduce to only three or four distinct “natural” clusters. We use ground truth of seismic facies seen on horizontal image logs to fix three average attribute data vectors near the well locations, resulting in three “known” facies, and do a minimum Euclidean distance supervised classification. The predicted clusters correlate well to the poststack impedance inversion result.
Seismic attribute driven integrated characterization of the Woodford Shale in west-central Oklahoma
Authors: Gupta Nabanita , Sarkar Supratik , Marfurt Kurt J.
Published: October 2013

The organic-rich, silty Woodford Shale in west-central Oklahoma is a prolific resource play producing gas and liquid hydrocarbons. We calibrated seismic attributes and prestack inversion using well logs and core information within a seismic geomorphologic framework to define the overall basin architecture, major stratigraphic changes, and related variations in lithologies. Core measurements of elastic moduli and total organic content (TOC) indicated that the Woodford Shale can be broken into three elastic petrotypes important to well completion and hydrocarbon enrichment. Upscaling these measurements facilitates regional mapping of petrotypes from prestack seismic inversion of surface data. Seismic attributes highlight rugged topography of the basin floor of the Paleo Woodford Sea, which controls the lateral and vertical distribution of different lithofacies containing variable quantity of TOC as well as quartz, which controls brittleness. Depressions on the basin floor contain TOC-lean cherty lithofacies alternating with TOC-rich lithofacies, resulting in brittle-ductile rock couplets. In contrast, basin floor highs are characterized by overall TOC-rich ductile lithofacies. Seismic attributes illuminate complex post-Woodford tectonic deformation. The Woodford Shale is known to be naturally fractured on outcrop. Image log analysis in other shale plays showed a good correlation between such tectonic features and natural fractures. These features need to be correlated with well trajectories and production data to determine which hypothesized “fracture sets,” if any, improve well performance.
Reducing risk and improving production in unconventional plays
Authors: Rebec Tony , Pareja Marino , Zhao Zhiyong
Published: October 2013

Using seismic data to reduce risk and improve production in unconventional plays requires careful preplanning based on the nature of the play, plus acquiring the right seismic, processing the seismic correctly, extracting the optimum information, and then transforming the information into business values. We discuss these criteria and focus on extracting the optimum information.
Characterization of SNARE Proteins in Human Pituitary Adenomas: Targeted Secretion Inhibitors as a New Strategy for the Treatment of Acromegaly?
Authors: Garcia Edwin A. , Trivellin Giampaolo , Aflorei Elena D. , Powell Michael , Grieve Joana , Alusi Ghassan , Pobereskin Luis , Shariati Babak , Cudlip Simon , Roncaroli Federico , Mendoza Nigel , Grossman Ashley B. , Harper Elaine A. , Korbonits Márta
Published: October 2013

Context:

Targeted secretion inhibitors (TSIs), a new class of recombinant biotherapeutic proteins engineered from botulinum toxin, represent a novel approach for treating diseases with excess secretion. They inhibit hormone secretion from targeted cell types through cleavage of SNARE (soluble N-ethylmaleimide-sensitive factor-activating protein receptor) proteins. qGHRH-LHN/D is a TSI targeting pituitary somatotroph through binding to the GHRH-receptor and cleavage of the vesicle-associated membrane protein (VAMP) family of SNARE proteins.

Objective:

Our objective was to study SNARE protein expression in pituitary adenomas and to inhibit GH secretion from somatotropinomas using qGHRH-LHN/D.

Design:

We analyzed human pituitary adenoma analysis for SNARE expression and response to qGHRH-LHN/D treatment.

Setting:

The study was conducted in University Hospitals.

Patients:

We used pituitary adenoma samples from 25 acromegaly and 47 nonfunctioning pituitary adenoma patients.

Outcome:

Vesicle-SNARE (VAMP1–3), target-SNARE (syntaxin1, SNAP-23, and SNAP-25), and GHRH-receptor detection with RT-qPCR, immunocytochemistry, and immunoblotting. Assessment of TSI catalytic activity on VAMPs and release of GH from adenoma cells.

Results:

SNARE proteins were variably expressed in pituitary samples. In vitro evidence using recombinant GFP-VAMP2&3 or pituitary adenoma lysates suggested sufficient catalytic activity of qGHRH-LHN/D to degrade VAMPs, but was unable to inhibit GH secretion in somatotropinoma cell cultures.

Conclusions:

SNARE proteins are present in human pituitary somatotroph adenomas that can be targeted by TSIs to inhibit GH secretion. qGHRH-LHN/D was unable to inhibit GH secretion from human somatotroph adenoma cells. Further studies are required to understand how the SNARE proteins drive GH secretion in human somatotrophs to allow the development of novel TSIs with a potential therapeutic benefit.
The Traditions of Race Men
Authors: Jennings Willie James
Published: October 2013

The idea of tradition has become in many ways a religious vision that reaches beyond its origin in Christian thought to now exist as a way to narrate identity quests, frame one’s spirituality, and especially situate the intellectual life. It has become a theology itself that reflects the spatial dimensions of subjectivity and in particular a powerful example of the spatial register through which white masculine subjectivity might be performed. Yet this new theological deployment of tradition needs to be read inside a wider historical frame of modern racial masculine longing. This essay articulates that frame.
Blackness Past, Blackness Future—and Theology
Authors: Copeland M. Shawn
Published: October 2013

After sketching the development of black theology and its unmasking of white racism at the heart of Christianity in the United States, the article turns to the seminal work of historian of religions Charles H. Long in order to understand more adequately the emergence of black religion. Such understanding prompts the conclusion that the future of black theology may lie in the exploration of the mystical aspects of black religion.
The Metastasis of Economic Hate
Authors: Brown Pamela
Published: October 2013

The neoliberal construct of perpetual indebtedness to nonhuman financial entities has created a populace so focused on debts “owed” to Wall Street that we have almost no memory of any other kinds of debts. If Malcolm X was correct that we “cannot have capitalism without racism,” we have to ask ourselves whether racism has really declined with color blindness or whether color blindness might be neoliberalism’s corollary. The article examines how color-blind ideologies naturalized racial inequality, allowing the process of predatory lending to be understood as class based and made it acceptable to turn a blind eye to the economic attack on African American communities. It was under the invisibility of color blindness that a predatory debt system was advanced that stripped African Americans of all economic gains subsequent to civil rights and that spread throughout the rest of the economy, impacting generations to come.
We Are All Debtors
Authors: Larson Ann
Published: October 2013

For the last three decades, cities and towns across the United States have grappled with a severe reduction in public funding which has weakened municipalities’ ability to provide basic services. As a result, municipal governments are increasingly financed by debt. Public Authorities (PA), such as New York’s Empire State Development Corporation, are authorized to issue debt backed by tax dollars. There are tens of thousands of such entities across the United States, a “shadow government” not accountable to voters. PAs operate based on a corporate model in which overleveraged holdings are hidden in subsidiary corporations. Such entities have proved so profitable to the investor class that a new brand of PAs has been created for the sole purpose of issuing “phantom bonds,” money that never reaches the public but is instead siphoned off by investors and bond insurers. The transformation of PAs from vehicles of reform to tools of exploitation illustrates that the solution to the debt crisis is a new economy in which our debts are to our families and our communities, not Wall Street.
S-adenosylmethionine limitation induces p38 mitogen activated protein kinase and triggers cell cycle arrest in G1
Authors: Lin Da-Wei , Chung Benjamin P. , Kaiser Peter
Published: October 2013

The primary methyl group donor S-adenosylmethionine (SAM) is important for a plethora of cellular pathways including methylation of nucleic acids, proteins, and the 5′ cap structure of mRNAs, as well as biosynthesis of phospholipids and polyamines. In addition, as the co-factor for chromatin methylation, SAM is an important metabolite connected to establishment and maintenance of epigenetic marks. Here we demonstrate that cells halt cell proliferation when SAM levels become low. Cell cycle arrest occurs primarily in the G1 phase of the cell cycle and is accompanied by activation of the mitogen activated protein kinase p38 and subsequent phosphorylation of MAPK-activated protein kinase-2. Surprisingly, Cdk4 activity remains high during cell cycle arrest while Cdk2 activity decreases concomitantly with cyclin E levels. Cell cycle arrest was induced by both pharmacological and genetic manipulation of SAM synthesis through inhibition or downregulation of methionine adenosyltransferase, respectively. Depletion of methionine, the precursor of SAM, from the growth medium induced a similar cell cycle arrest. Surprisingly, neither methionine depletion nor inhibition of methionine adenosyltransferase significantly affected mTORC1 signaling, suggesting that the cellular response to SAM limitation is independent from this major nutrient sensing pathway. These results demonstrate a G1 cell cycle checkpoint that responds to limiting levels of the principal cellular methyl group donor S-adenosylmethionine. This metabolic checkpoint may play important roles in maintenance of epigenetic stability and general cellular integrity.
Evolutionary and ontogenetic changes in RNA editing in human, chimpanzee, and macaque brains
Authors: Li Zhongshan , Bammann Hindrike , Li Mingshuang , Liang Hongyu , Yan Zheng , Phoebe Chen Yi-Ping , Zhao Min , Khaitovich Philipp
Published: October 2013

Adenosine-to-inosine (A-to-I) substitutions are the most common type of RNA editing in mammals. A-to-I RNA editing is particularly widespread in the brain and is known to play important roles in neuronal functions. In this study we investigated RNA-editing changes during human brain development and maturation, as well as evolutionary conservation of RNA-editing patterns across primates. We used high-throughput transcriptome sequencing (RNA-seq) to quantify the RNA-editing levels and assess ontogenetic dynamics of RNA editing at more than 8000 previously annotated exonic A-to-I RNA-editing sites in two brain regions—prefrontal cortex and cerebellum—of humans, chimpanzees, and rhesus macaques. We observed substantial conservation of RNA-editing levels between the brain regions, as well as among the three primate species. Evolutionary changes in RNA editing were nonetheless evident, with 40% of the annotated editing sites studied showing divergent editing levels among the three species and 16.5% of sites displaying statistically significant human-specific editing patterns. Across lifespan, we observed an increase of the RNA-editing level with advanced age in both brain regions of all three primate species.
SHAPE analysis of the 5′ end of the Mason-Pfizer monkey virus (MPMV) genomic RNA reveals structural elements required for genome dimerization
Authors: Aktar Suriya J. , Jabeen Ayesha , Ali Lizna M. , Vivet-Boudou Valérie , Marquet Roland , Rizvi Tahir A.
Published: October 2013

Earlier genetic and structural prediction analyses revealed that the packaging determinants of Mason Pfizer monkey virus (MPMV) include two discontinuous core regions at the 5′ end of its genomic RNA. RNA secondary structure predictions suggested that these packaging determinants fold into several stem–loops (SLs). To experimentally validate this structural model, we employed selective 2′ hydroxyl acylation analyzed by primer extension (SHAPE), which examines the flexibility of the RNA backbone at each nucleotide position. Our SHAPE data validated several predicted structural motifs, including U5/Gag long-range interactions (LRIs), a stretch of single-stranded purine (ssPurine)-rich region, and a distinctive G-C-rich palindromic (pal) SL. Minimum free-energy structure predictions, phylogenetic, and in silico modeling analyses of different MPMV strains revealed that the U5 and gag sequences involved in the LRIs differ minimally within strains and maintain a very high degree of complementarity. Since the pal SL forms a helix loop containing a canonical “GC” dyad, it may act as a RNA dimerization initiation site (DIS), enabling the virus to package two copies of its genome. Analyses of wild-type and pal mutant RNAs revealed that disruption of pal sequence strongly affected RNA dimerization. However, when in vitro transcribed trans-complementary pal mutants were incubated together showed RNA dimerization was restored authenticating that the pal loop (5′-CGGCCG-3′) functions as DIS.