Mitotic deacetylase complex (MiDAC) recognizes the HIV-1 core promoter to control activated viral gene expression

The human immunodeficiency virus (HIV) integrates into the host genome forming latent cellular reservoirs that are an obstacle for cure or remission strategies. Viral transcription is the first step in the control of latency and depends upon the hijacking of the host cell RNA polymerase II (Pol II) machinery by the 5' HIV LTR. Consequently, "block and lock" or "shock and kill" strategies for an HIV cure depend upon a full understanding of HIV transcriptional control. The HIV trans-activating protein, Tat, controls HIV latency as part of a positive feed-forward loop that strongly activates HIV transcription. The recognition of the TATA box and adjacent sequences of HIV essential for Tat trans-activation (TASHET) of the core promoter by host cell pre-initiation complexes of HIV (PICH) has been shown to be necessary for Tat trans-activation, yet the protein composition of PICH has remained obscure. Here, DNA-affinity chromatography was employed to identify the mitotic deacetylase complex (MiDAC) as selectively recognizing TASHET. Using biophysical techniques, we show that the MiDAC subunit DNTTIP1 binds directly to TASHET, in part via its CTGC DNA motifs. Using co-immunoprecipitation assays, we show that DNTTIP1 interacts with MiDAC subunits MIDEAS and HDAC1/2. The Tat-interacting protein, NAT10, is also present in HIV-bound MiDAC. Gene silencing revealed a functional role for DNTTIP1, MIDEAS, and NAT10 in HIV expression in cellulo. Furthermore, point mutations in TASHET that prevent DNTTIP1 binding block the reactivation of HIV by latency reversing agents (LRA) that act via the P-TEFb/7SK axis. Our data reveal a key role for MiDAC subunits DNTTIP1, MIDEAS, as well as NAT10, in Tat-activated HIV transcription and latency. DNTTIP1, MIDEAS and NAT10 emerge as cell cycle-regulated host cell transcription factors that can control activated HIV gene expression, and as new drug targets for HIV cure strategies.

Identification of aryl hydrocarbon receptor as a barrier to HIV-1 infection and outgrowth in CD4+ T cells

The aryl hydrocarbon receptor (AhR) regulates Th17-polarized CD4+ T cell functions, but its role in HIV-1 replication/outgrowth remains unknown. Genetic (CRISPR-Cas9) and pharmacological inhibition reveal AhR as a barrier to HIV-1 replication in T cell receptor (TCR)-activated CD4+ T cells in vitro. In single-round vesicular stomatitis virus (VSV)-G-pseudotyped HIV-1 infection, AhR blockade increases the efficacy of early/late reverse transcription and subsequently facilitated integration/translation. Moreover, AhR blockade boosts viral outgrowth in CD4+ T cells of people living with HIV-1 (PLWH) receiving antiretroviral therapy (ART). Finally, RNA sequencing reveals genes/pathways downregulated by AhR blockade in CD4+ T cells of ART-treated PLWH, including HIV-1 interactors and gut-homing molecules with AhR-responsive elements in their promoters. Among them, HIC1, a repressor of Tat-mediated HIV-1 transcription and a tissue-residency master regulator, is identified by chromatin immunoprecipitation as a direct AhR target. Thus, AhR governs a T cell transcriptional program controlling viral replication/outgrowth and tissue residency/recirculation, supporting the use of AhR inhibitors in "shock and kill" HIV-1 remission/cure strategies.

1182 THE PREVALENCE OF ORAL FRAILTY AND ITS ASSOCIATION WITH DYSPHAGIA, FRAILTY AND FORMAL CARE NEEDS

Introduction

Oral frailty (OF), gradual loss of oral function combined associated with presbyphagia often in conjunction with cognitive and physical decline, has been recommended to be considered as a geriatric giant. DENTAL has been suggested as a possible screening tool for OF. We have looked at the prevalence of OF and its association with dysphagia, frailty and formal care, amongst people admitted acutely to the acute medical/frailty wards in our hospital.

Methods

OF, dysphagia and frailty were screened for as part of the routine clinical assessment of patients during the usual clinical ward round. Screening tools used were DENTAL for OF, Rockwood Score for frailty and 4QT for dysphagia. Age, sex comorbidities and the need for formal care was documented.

Results

101 people were assessed over a 4-week period. Mean age was 84 years (65-99), 58 (57.4%) were female, 31(30.7%) were independent, 33 (32.6%) dementia, 57 (56.4%) frail, 54 (53.4%) had swallowing problems, and 34 (33.6%) OF. Of those with OF 97% had dysphagia, 88% were frail and 85% required formal care support (85%). OF was associated with dysphagia (p<0.0001), frailty (p< 0.0001), formal care support (p<0.05) and dementia (p<0.05). There was an association between needing care and frailty (p<0.01).

Conclusions

OF is associated with dysphagia, frailty and the need for formal care. OF may result in poor oral health and contribute to dysphagia and frailty, conversely frailty and dysphagia may result in poor oral health due to dependency and poor nutrition and dehydration. The associations are most likely be bidirectional. Further work is required to elucidate this. Clinical staff need to be aware of OF and oral health and include oral screening in their clinical assessment of an older adult.

Treatment of pulmonary artery pseudoaneurysms and stenosis with balloon-expandable stents

We describe our use of balloon-expandable stents in pulmonary arteries for a variety of indications. This is an endovascular technique that provides an alternative treatment option to treat some forms of complex pulmonary artery disease when standard surgical or other endovascular options are not possible. This case series describes the successful treatment of four patients with different pulmonary artery diseases. Indications for stent placement include multiple broad-necked pulmonary artery pseudoaneurysms, symptomatic malignant pulmonary artery narrowing and post-surgical iatrogenic pulmonary artery stenosis. No stent-related complication had been identified from 3 months to 4 years of follow-up. All surviving patients have experienced sustained symptomatic improvement.

Opposing roles of CLK SR kinases in controlling HIV-1 gene expression and latency

BACKGROUND

The generation of over 69 spliced HIV-1 mRNAs from one primary transcript by alternative RNA splicing emphasizes the central role that RNA processing plays in HIV-1 replication. Control is mediated in part through the action of host SR proteins whose activity is regulated by multiple SR kinases (CLK1-4, SRPKs).

METHODS

Both shRNA depletion and small molecule inhibitors of host SR kinases were used in T cell lines and primary cells to evaluate the role of these factors in the regulation of HIV-1 gene expression. Effects on virus expression were assessed using western blotting, RT-qPCR, and immunofluorescence.

RESULTS

The studies demonstrate that SR kinases play distinct roles; depletion of CLK1 enhanced HIV-1 gene expression, reduction of CLK2 or SRPK1 suppressed it, whereas CLK3 depletion had a modest impact. The opposing effects of CLK1 vs. CLK2 depletion were due to action at distinct steps; reduction of CLK1 increased HIV-1 promoter activity while depletion of CLK2 affected steps after transcript initiation. Reduced CLK1 expression also enhanced the response to several latency reversing agents, in part, by increasing the frequency of responding cells, consistent with a role in regulating provirus latency. To determine whether small molecule modulation of SR kinase function could be used to control HIV-1 replication, we screened a GSK library of protein kinase inhibitors (PKIS) and identified several pyrazolo[1,5-b] pyridazine derivatives that suppress HIV-1 gene expression/replication with an EC₅₀ ~ 50 nM. The compounds suppressed HIV-1 protein and viral RNA accumulation with minimal impact on cell viability, inhibiting CLK1 and CLK2 but not CLK3 function, thereby selectively altering the abundance of individual CLK and SR proteins in cells.

CONCLUSIONS

These findings demonstrate the unique roles played by individual SR kinases in regulating HIV-1 gene expression, validating the targeting of these functions to either enhance latency reversal, essential for "Kick-and-Kill" strategies, or to silence HIV protein expression for "Block-and-Lock" strategies.

The novel Mechanical Ventilator Milano for the COVID-19 pandemic

This paper presents the Mechanical Ventilator Milano (MVM), a novel intensive therapy mechanical ventilator designed for rapid, large-scale, low-cost production for the COVID-19 pandemic. Free of moving mechanical parts and requiring only a source of compressed oxygen and medical air to operate, the MVM is designed to support the long-term invasive ventilation often required for COVID-19 patients and operates in pressure-regulated ventilation modes, which minimize the risk of furthering lung trauma. The MVM was extensively tested against ISO standards in the laboratory using a breathing simulator, with good agreement between input and measured breathing parameters and performing correctly in response to fault conditions and stability tests. The MVM has obtained Emergency Use Authorization by U.S. Food and Drug Administration (FDA) for use in healthcare settings during the COVID-19 pandemic and Health Canada Medical Device Authorization for Importation or Sale, under Interim Order for Use in Relation to COVID-19. Following these certifications, mass production is ongoing and distribution is under way in several countries. The MVM was designed, tested, prepared for certification, and mass produced in the space of a few months by a unique collaboration of respiratory healthcare professionals and experimental physicists, working with industrial partners, and is an excellent ventilator candidate for this pandemic anywhere in the world.

Instrument flight to the inner ear

Surgical robot systems can work beyond the limits of human perception, dexterity and scale making them inherently suitable for use in microsurgical procedures. However, despite extensive research, image-guided robotics applications for microsurgery have seen limited introduction into clinical care to date. Among others, challenges are geometric scale and haptic resolution at which the surgeon cannot sufficiently control a device outside the range of human faculties. Mechanisms are required to ascertain redundant control on process variables that ensure safety of the device, much like instrument-flight in avionics. Cochlear implantation surgery is a microsurgical procedure, in which specific tasks are at sub-millimetric scale and exceed reliable visuo-tactile feedback. Cochlear implantation is subject to intra- and inter-operative variations, leading to potentially inconsistent clinical and audiological outcomes for patients. The concept of robotic cochlear implantation aims to increase consistency of surgical outcomes such as preservation of residual hearing and reduce invasiveness of the procedure. We report successful image-guided, robotic CI in human. The robotic treatment model encompasses: computer-assisted surgery planning, precision stereotactic image-guidance, in-situ assessment of tissue properties and multipolar neuromonitoring (NM), all based on in vitro, in vivo and pilot data. The model is expandable to integrate additional robotic functionalities such as cochlear access and electrode insertion. Our results demonstrate the feasibility and possibilities of using robotic technology for microsurgery on the lateral skull base. It has the potential for benefit in other microsurgical domains for which there is no task-oriented, robotic technology available at present.

Cancerpedia: A Framework for Implementing Comprehensive Cancer Centres

Background and context: Comprehensive cancer centers or programs form a nucleus of cancer care delivery. Although there are frameworks for population cancer control, no similar published framework exists for cancer centers. Aim: We sought to develop a framework for designing and implementing a comprehensive cancer center or program within the context of a population-based model of cancer control that spans diagnosis, treatment, supportive care, and palliative care as well as integration with primary care and the community. Strategy/Tactics: The framework was constructed with the patient at the center and provides a system-level perspective as well as a granular view of the fundamental resources and structures needed to build and maintain individual cancer centers and programs. Due to its breadth, we focused the framework on essential information while linking to a wide range of vetted publications that detail additional standards, guidelines and best practices. Program/Policy process: “Cancerpedia” emerged as a cohesive framework for the delivery of high-quality cancer care within and beyond the cancer center. It provides an overview of the cancer control and care delivery framework, describes cancer care services (e.g., radiotherapy, chemotherapy, palliative care) and details infrastructure and core services (e.g., physical facilities, human resources). In addition to these services, the framework presents guidelines for governance that ensure oversight and quality, describes the critical need for integrating education and research and presents the best practices for engaging in philanthropy. Cancerpedia also outlines the role of the comprehensive cancer center in integration with the community and influencing policy and regulation. Over 30 chapters provide a detailed description of each element and include a description of the service or function, resources requirements such as people, equipment and facilities, management structures, quality performance guidelines and future trends in innovation. Outcomes: To our knowledge, no comparable published framework exists as a reference for developing comprehensive cancer centers. Cancerpedia was designed to serve as a global public good and is adaptable and applicable to diverse contexts and healthcare environments. It is relevant to high-, middle- and low-income countries alike and provides a reference point from which to structure a plan for growth. What was learned: While it is important to describe the various elements required for cancer care delivery, it is critical to consider and address the integration and interdependencies of these various elements. Future opportunities for learning include seeking input from a global audience to gauge the utility and applicability of Cancerperdia to local contexts.

Mortality in acute non-invasive ventilation

A prospective study of non-invasive ventilation at The Prince Charles Hospital outside of the intensive care unit from March 2015 to March 2016 was performed. Overall 69 patients were included. Acute hypercapnic respiratory failure was the most common indication (n = 59; 85%). 49 (71%) had multifactorial respiratory failure. 15 (22%) patients died. Premorbid inability to perform self-care (P = 0.001) and the combination of mean pH < 7.25 and mean PaCO₂ ≥ 75 mmHg within 2 h of NIV initiation (P = 0.037) were significantly associated with mortality. There was a non-significant association between older age and mortality.

Inhibition of NF-κB-dependent HIV-1 replication by the marine natural product bengamide A

HIV-1 inhibitors that act by mechanisms distinct from existing antiretrovirals can provide novel insights into viral replication and potentially inform development of new therapeutics. Using a multi-cycle HIV-1 replication assay, we screened 252 pure compounds derived from marine invertebrates and microorganisms and identified 6 (actinomycin Z₂, bastadin 6, bengamide A, haliclonacyclamine A + B, keramamine C, neopetrosiamide B) that inhibited HIV-1 with 50% effective concentrations (EC₅₀s) of 3.8 μM or less. The most potent inhibitor, bengamide A, blocked HIV-1 in a T cell line with an EC₅₀ of 0.015 μM and in peripheral blood mononuclear cells with an EC₅₀ of 0.032 μM. Bengamide A was previously described to inhibit NF-κB signaling. Consistent with this mechanism, bengamide A suppressed reporter expression from an NF-κB-driven minimal promoter and an HIV-1 long terminal repeat (LTR) with conserved NF-κB response elements, but lacked activity against an LTR construct with mutation of these elements. In single-cycle HIV-1 infection assays, bengamide A also suppressed viral protein expression when viruses encoded an intact LTR but exhibited minimal activity against those with mutated NF-κB elements. Finally, bengamide A did not inhibit viral DNA accumulation, indicating that it likely acts downstream of this step in HIV-1 replication. Our study identifies multiple new antiviral compounds including an unusually potent inhibitor of HIV-1 gene expression.

Modulation of the splicing regulatory function of SRSF10 by a novel compound that impairs HIV-1 replication

We recently identified the 4-pyridinone-benzisothiazole carboxamide compound 1C8 as displaying strong anti-HIV-1 potency against a variety of clinical strains in vitro. Here we show that 1C8 decreases the expression of HIV-1 and alters splicing events involved in the production of HIV-1 mRNAs. Although 1C8 was designed to be a structural mimic of the fused tetracyclic indole compound IDC16 that targets SRSF1, it did not affect the splice site shifting activity of SRSF1. Instead, 1C8 altered splicing regulation mediated by SRSF10. Depleting SRSF10 by RNA interference affected viral splicing and, like 1C8, decreased expression of Tat, Gag and Env. Incubating cells with 1C8 promoted the dephosphorylation of SRSF10 and increased its interaction with hTra2β, a protein previously implicated in the control of HIV-1 RNA splicing. While 1C8 affects the alternative splicing of cellular transcripts controlled by SRSF10 and hTra2β, concentrations greater than those needed to inhibit HIV-1 replication were required to elicit significant alterations. Thus, the ability of 1C8 to alter the SRSF10-dependent splicing of HIV-1 transcripts, with minor effects on cellular splicing, supports the view that SRSF10 may be used as a target for the development of new anti-viral agents.

Precise manipulation of biophysical particle parameters enables control of proinflammatory cytokine production in presence of TLR 3 and 4 ligands

The biophysical parameters governing nanoparticle (NP)-cell interactions significantly affect biological responses, particularly in the application of NP-based immunotherapeutics. Modulation of the surface biophysical character of NPs can be achieved via introduction of amino acids, which offer the ability to fine tune a range of biophysical parameters of interest. We employed this approach using monodisperse silica NPs coated with numerous poly(amino acid)s (PAAs). The NPs were incubated with dendritic cells (DCs) in conjunction with TLR ligands and production of IL-1β from DCs and IFNγ from T cells primed by these DCs were measured. These key cytokines can prognosticate the efficacy of the NP platform as a potential vaccine or active cellular immunotherapy carrier. IL-1β production showed a correlation with both NP size and degree of hydrophobicity. High IFNγ secretion from T cells was shown to be correlated with both the hydrophobicity and charge of the NPs used to activate the DCs. Other cytokines were also screened in order to compare the immune responses. The results of this study highlight the importance of nanoparticle biophysical parameters and the selection of TLR ligands to the rational design of nanoparticle-based vaccines and immunotherapies.

STATEMENT OF SIGNIFICANCE

The manuscript describes a systematic investigation into the effects of biophysical parameters of nanoparticles (NPs) on immune cells. Modulation of the biophysical character of the NP surface can be achieved by introduction of amino acids on monodisperse silica NPs, introducing a range of tunable biophysical parameters of interest, i.e. distinct sizes, different surface charges and varying degrees of surface hydrophobicity. We examine internalization of the NP in dendritic cells (DCs) and measure a myriad of cytokines, including IL-1β and IFNγ, which prognosticate the efficacy of the NPs as a potential vaccine (IL-1β metric) or active cellular immunotherapy carrier (IFNγ metric). Two different TLR ligands (a viral TLR3 ligand and a bacterial TLR4 ligand) were used along with the PAA NPs to compare their costimulatory immunogenicity. We strongly believe that this study will provide crucial information to many readers of Acta Biomaterialia and further drive the use of nanoparticle platforms in modulating immune responses.

Alternative splicing of TAF6: downstream transcriptome impacts and upstream RNA splice control elements

The TAF6δ pathway of apoptosis can dictate life versus death decisions independently of the status of p53 tumor suppressor. TAF6δ is an inducible pro-apoptotic subunit of the general RNA polymerase II (Pol II) transcription factor TFIID. Alternative splice site choice of TAF6δ has been shown to be a pivotal event in triggering death via the TAF6δ pathway, yet nothing is currently known about the mechanisms that promote TAF6δ splicing. Furthermore the transcriptome impact of the gain of function of TAF6δ versus the loss of function of the major TAF6α splice form remains undefined. Here we employ comparative microarray analysis to show that TAF6δ drives a transcriptome profile distinct from that resulting from depletion of TAF6α. To define the cis-acting RNA elements responsible for TAF6δ alternative splicing we performed a mutational analysis of a TAF6 minigene system. The data point to several new RNA elements that can modulate TAF6δ and also reveal a role for RNA secondary structure in the selection of TAF6δ.

Two-photon interference between disparate sources for quantum networking

Quantum networks involve entanglement sharing between multiple users. Ideally, any two users would be able to connect regardless of the type of photon source they employ, provided they fulfill the requirements for two-photon interference. From a theoretical perspective, photons coming from different origins can interfere with a perfect visibility, provided they are made indistinguishable in all degrees of freedom. Previous experimental demonstrations of such a scenario have been limited to photon wavelengths below 900 nm, unsuitable for long distance communication, and suffered from low interference visibility. We report two-photon interference using two disparate heralded single photon sources, which involve different nonlinear effects, operating in the telecom wavelength range. The measured visibility of the two-photon interference is 80 ± 4%, which paves the way to hybrid universal quantum networks.

Abstract P3-08-04: Survivorship care involving a nurse-led survivorship consultation, community support and shared care with primary practitioners

Background

Survivorship care (SC) has gained prominence as the number of patients disease free after breast cancer treatment increases, the specific needs of those patients become recognised, and funding to meet these demands is constrained. Involvement of Primary Care Practitioners in SC is seen as a solution, but models of Shared Care have met varying degrees of success. We report on a model that involves Specialist centres, Primary Care Practitioners and organisations, and a community based patient support organisation.

Patients and Methods

A consortium comprising two hospital based breast services – the Royal Melbourne/Royal Women's and Western Hospitals – a regional consortium of Primary Care Physicians, and BreaCan, a non-government peer support organisation for women diagnosed with breast cancer, collaborated to obtain and implement a government-supported Survivorship Care Program. Patients completing definitive treatment for early breast cancer were invited to a Nurse-led consultation where the disease, its pathology, treatment and follow-up were reviewed. Psychosocial and other issues were explored and a personalised SC plan was devised and agreed upon. This plan included Shared Care with the Primary Care Practitioner in the majority of cases. Unmet needs were identified and addressed. The SC plan was signed off by a senior breast cancer clinician and forwarded to the primary care physician for ratification. Evaluation included satisfaction surveys and interviews with patients and primary care physicians. Intensity of use of hospital based services was calculated and compared to a previous cohort of early breast cancer patients.

Results

282 patients completing definitive treatment were offered Nurse-led survivorship consultation. 29 declined, and 28 cancelled. At 31 May 2013, 148 care plans were completed, 38 were in preparation and 39 appointments were booked. Response to this initiative from hospital based specialists was positive. All believed that this program would reduce the amount of routine consultations and increase capacity for new or returning patients requiring specialist care. Primary care doctors overwhelmingly believed the survivorship care plan contained information needed to allow them to manage breast cancer survivors, and gave them confidence to take on this role, although there was some uncertainty regarding role delineation between Primary Care and hospital. Patient evaluation of the Nurse-led clinics was strongly positive. All reported finding out something during the consultation, and 94% said they considered the hospital and GP to be partners in their on-going follow-up care. Modelling suggests that about 5 fewer hospital appointments will be required for each patient managed under this program compared to routine hospital-based care.

Conclusions

Hospital based specialists embrace Survivorship care including shared care and patients expect it, while Primary physicians will participate if offered education, support and specific direction. A model including an end-of –treatment consultation and Shared care with Primary Practitioners appears to address many of the requirements for a successful Survivorship program.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-08-04.

HMGA1 directly interacts with TAR to modulate basal and Tat-dependent HIV transcription

The transactivating response element (TAR) of human immunodeficiency virus 1 (HIV-1) is essential for promoter transactivation by the viral transactivator of transcription (Tat). The Tat-TAR interaction thereby recruits active positive transcription elongation factor b (P-TEFb) from its inactive, 7SK/HEXIM1-bound form, leading to efficient viral transcription. Here, we show that the 7SK RNA-associating chromatin regulator HMGA1 can specifically bind to the HIV-1 TAR element and that 7SK RNA can thereby compete with TAR. The HMGA1-binding interface of TAR is located within the binding site for Tat and other cellular activators, and we further provide evidence for competition between HMGA1 and Tat for TAR-binding. HMGA1 negatively influences the expression of a HIV-1 promoter-driven reporter in a TAR-dependent manner, both in the presence and in the absence of Tat. The overexpression of the HMGA1-binding substructure of 7SK RNA results in a TAR-dependent gain of HIV-1 promoter activity similar to the effect of the shRNA-mediated knockdown of HMGA1. Our results support a model in which the HMGA1/TAR interaction prevents the binding of transcription-activating cellular co-factors and Tat, subsequently leading to reduced HIV-1 transcription.

Anterior ECG changes following iatrogenic dissection of the right coronary artery into the aortic root: exclusion of left coronary obstruction with transoesophageal echocardiography

One of the most troublesome complications of percutaneous coronary intervention (PCI) or angiography is retrograde dissection of the artery into the aortic root. We report a case involving the right coronary artery (RCA) which was treated with prompt deployment of stents. Recurrent chest pain and ST segment elevation in V(2-4) mimicked the ECG appearance of acute anterior infarction and prompted concern that the dissection had extended to impair flow in the left coronary artery (LCA). Transoesophageal echocardiography (TOE) demonstrated that the aortic root dissection had been contained and that the LCA was not compromised.

CTGC motifs within the HIV core promoter specify Tat-responsive pre-initiation complexes

Background

HIV latency is an obstacle for the eradication of HIV from infected individuals. Stable post-integration latency is controlled principally at the level of transcription. The HIV trans-activating protein, Tat, plays a key function in enhancing HIV transcriptional elongation. The HIV core promoter is specifically required for Tat-mediated trans-activation of HIV transcription. In addition, the HIV core promoter has been shown to be a potential anti-HIV drug target. Despite the pivotal role of the HIV core promoter in the control of HIV gene expression, the molecular mechanisms that couple Tat function specifically to the HIV core promoter remain unknown.

Results

Using electrophoretic mobility shift assays (EMSAs), the TATA box and adjacent sequences of HIV essential for Tat trans-activation were shown to form specific complexes with nuclear extracts from peripheral blood mononuclear cells, as well as from HeLa cells. These complexes, termed pre-initiation complexes of HIV (PICH), were distinct in composition and DNA binding specificity from those of prototypical eukaryotic TATA box regions such as Adenovirus major late promoter (AdMLP) or the hsp70 promoter. PICH contained basal transcription factors including TATA-binding protein and TFIIA. A mutational analysis revealed that CTGC motifs flanking the HIV TATA box are required for Tat trans-activation in living cells and correct PICH formation in vitro. The binding of known core promoter binding proteins AP-4 and USF-1 was found to be dispensable for Tat function. TAR RNA prevented stable binding of PICH-2, a complex that contains the general transcription factor TFIIA, to the HIV core promoter. The impact of TAR on PICH-2 specifically required its bulge sequence that is also known to interact with Tat.

Conclusion

Our data reveal that CTGC DNA motifs flanking the HIV TATA box are required for correct formation of specific pre-initiation complexes in vitro and that these motifs are also required for Tat trans-activation in living cells. The impact of TAR RNA on PICH-2 stability provides a mechanistic link by which pre-initiation complex dynamics could be coupled to the formation of the nascent transcript by the elongating transcription complex. Together, these findings shed new light on the mechanisms by which the HIV core promoter specifically responds to Tat to activate HIV gene expression.

Development of an Evidence biochip array kit for the multiplex screening of more than 20 anthelmintic drugs

Anthelmintic drugs are used in clinical and veterinary practice for the treatment of infections caused by parasitic worms. Their extensive use in food-producing animals can cause the presence of residues in food. For consumer protection it is necessary to monitor the levels of anthelmintic residues to ensure that they remain within the legally permitted maximum acceptable concentrations. For this purpose, the use of multiplex screening methods is advantageous. Biochip array technology allows the simultaneous determination of multiple analytes from a single sample at a single point in time. This study reports the development of an Evidence biochip array for the multiplex screening of anthelmintic drugs. Simultaneous competitive chemiluminescent immunoassays are employed. The solid support and vessel is the biochip, which contains an array of discrete test sites. The assays were applied to the semiautomated bench-top analyser Evidence Investigator. The aminobenzimidazoles assay detected aminomebendazole, albendazole 2-aminosulphone and aminoflubendazole, the avermectins assay detected emamectin benzoate, eprinomectin, abamectin, ivermectin and doramectin, the benzimidazoles assay detected albendazole sulphone, albendazole, albendazole sulphoxide, oxibendazole, oxfendazole and flubendazole, the thiabendazole assay detected cambendazole, thiabendazole and 5-hydroxythiabendazole and the triclabendazole assay detected ketotriclabendazole, triclabendazole and triclabendazole sulphoxide. The limits of detection ranged from 0.3 ppb (aminobenzimidazoles) to 2.0 ppb (levamisole) in milk and from 0.15 ppb (aminobenzimidazoles) to 6.5 ppb (levamisole) in tissue. The average recovery range was 71-135 %. This multianalytical approach on a biochip platform is applicable to the screening of more than 20 anthelmintic drugs in different food matrices, leading to consolidation of tests and enhancement of the test result output.

Probing endogenous RNA polymerase II pre-initiation complexes by electrophoretic mobility shift assay

RNA polymerase II (Pol II) plays a crucial role in eukaryotic biology since it is necessary for the expression of all protein-coding genes as well as most microRNAs and several small nuclear RNAs. Pol II is specifically recruited to core promoter DNA via its association with general transcription factors (GTFs) that possess DNA binding activity such as TFIID, TFIIA, and TFIIB. The large multi-protein assemblies of Pol II together with the GTFs required for productive transcription are termed pre-initiation complexes (PICs). To date, studies of the interaction of PICs with promoter DNA have relied on the use of purified or recombinant GTFs. Recent findings have demonstrated an astonishing diversity in the function of core promoters as well as in the protein composition of PICs. The currently known subset of GTFs alone cannot account for observed PIC and core promoter diversity. In order to identify the full complement of factors that impart PIC specificity, techniques to analyze the DNA binding of endogenous PIC are essential. Analysis of endogenous PIC formation has remained out of reach due to technical hurdles presumably including the large size of endogenous PIC, their highly dynamic association with core promoters, and the complex topology of DNA bound to PIC. We have optimized electrophoretic mobility shift assays (EMSAs) to achieve the detection of endogenous Pol II PIC from nuclear extracts of human cells. Here, we provide a robust and sensitive EMSA method for the analysis of endogenous Pol II PICs.

Review of the carriage of zoonotic bacteria by arthropods, with special reference to Salmonella in mites, flies and litter beetles

This systematic review considers the relationship between arthropods commonly found in and around livestock premises and zoonotic bacteria. The principal focus is upon insects and arachnids on poultry units, where houses, litter and manure provide good conditions for the growth, multiplication and protection of flies, beetles and mites, and where zoonotic pathogens such as Salmonella and Campylobacter are prevalent. Other members of the Enterobacteriaceae and the taxa Clostridium, Helicobacter, Erysipelas and Chlamydiaceae are also discussed. Salmonella is widely distributed in the flies of affected livestock units and is detectable to a lesser degree in beetles and mites. Persistent carriage appears to be common and there is some field and experimental evidence to support arthropod-mediated transmission between poultry flocks, particularly carry-over from one flock to the next. Campylobacter may readily be isolated from arthropods in contact with affected poultry flocks, although carriage is short-lived. There appears to be a role for flies, at least, in the breaching of biosecurity around Campylobacter-negative flocks. The carriage of other zoonotic bacteria by arthropods has been documented, but the duration and significance of such associations remain uncertain in the context of livestock production.