Kaposi's Sarcoma-Associated Herpesvirus Latency Locus Compensates for Interleukin-6 in Initial B Cell Activation

Interleukin 6 (IL-6) is considered a proliferation and survival factor for B cells. To assess the role of IL-6 in Kaposi sarcoma-associated herpesvirus (KSHV) latency, KSHV latency locus-transgenic mice (referred to as latency mice) lacking IL-6 were evaluated. IL-6 −/− latency mice had the same phenotypes as the latency mice, i.e., increased frequency of marginal zone B cells, hyperplasia, and hyperglobulinemia, indicating that the KSHV latency locus, which includes all viral microRNAs (miRNAs), can compensate for lack of IL-6 in premalignant B cell activation

Suppression of HBV by Tenofovir in HBV/HIV coinfected patients : a systematic review and meta-analysis

Background: Hepatitis B coinfection is common in HIV-positive individuals and as antiretroviral therapy has made death due to AIDS less common, hepatitis has become increasingly important. Several drugs are available to treat hepatitis B. The most potent and the one with the lowest risk of resistance appears to be tenofovir (TDF). However there are several questions that remain unanswered regarding the use of TDF, including the proportion of patients that achieves suppression of HBV viral load and over what time, whether suppression is durable and whether prior treatment with other HBV-active drugs such as lamivudine, compromises the efficacy of TDF due to possible selection of resistant HBV strains. Methods: A systematic review and meta-analysis following PRISMA guidelines and using multilevel mixed effects logistic regression, stratified by prior and/or concomitant use of lamivudine and/or emtricitabine. Results: Data was available from 23 studies including 550 HBV/HIV coinfected patients treated with TDF. Follow up was for up to seven years but to ensure sufficient power the data analyses were limited to three years. The overall proportion achieving suppression of HBV replication was 57.4%, 79.0% and 85.6% at one, two and three years, respectively. No effect of prior or concomitant 3TC/FTC was shown. Virological rebound on TDF treatment was rare. Interpretation: TDF suppresses HBV to undetectable levels in the majority of HBV/HIV coinfected patients with the proportion fully suppressed continuing to increase during continuous treatment. Prior treatment with 3TC/FTC does not compromise efficacy of TDF treatment. The use of combination treatment with 3TC/FTC offers no significant benefit over TDF alone

Quantitative Excited State Spectroscopy of a Single InGaAs Quantum Dot Molecule through Multi-million Atom Electronic Structure Calculations

Atomistic electronic structure calculations are performed to study the coherent inter-dot couplings of the electronic states in a single InGaAs quantum dot molecule. The experimentally observed excitonic spectrum [12] is quantitatively reproduced, and the correct energy states are identified based on a previously validated atomistic tight binding model. The extended devices are represented explicitly in space with 15 million atom structures. An excited state spectroscopy technique is presented in which the externally applied electric field is swept to probe the ladder of the electronic energy levels (electron or hole) of one quantum dot through anti-crossings with the energy levels of the other quantum dot in a two quantum dot molecule. This technique can be applied to estimate the spatial electron-hole spacing inside the quantum dot molecule as well as to reverse engineer quantum dot geometry parameters such as the quantum dot separation. Crystal deformation induced piezoelectric effects have been discussed in the literature as minor perturbations lifting degeneracies of the electron excited (P and D) states, thus affecting polarization alignment of wave function lobes for III-V Heterostructures such as single InAs/GaAs quantum dots. In contrast this work demonstrates the crucial importance of piezoelectricity to resolve the symmetries and energies of the excited states through matching the experimentally measured spectrum in an InGaAs quantum dot molecule under the influence of an electric field. Both linear and quadratic piezoelectric effects are studied for the first time for a quantum dot molecule and demonstrated to be indeed important. The net piezoelectric contribution is found to be critical in determining the correct energy spectrum, which is in contrast to recent studies reporting vanishing net piezoelectric contributions.Comment: Accepted for publication in IOP Nanotechnology Journa

Holographic Charged Fluid with Anomalous Current at Finite Cutoff Surface in Einstein-Maxwell Gravity

The holographic charged fluid with anomalous current in Einstein-Maxwell gravity has been generalized from the infinite boundary to the finite cutoff surface by using the gravity/fluid correspondence. After perturbing the boosted Reissner-Nordstrom (RN)-AdS black brane solution of the Einstein-Maxwell gravity with the Chern-Simons term, we obtain the first order perturbative gravitational and Maxwell solutions, and calculate the stress tensor and charged current of the dual fluid at finite cutoff surfaces which contains undetermined parameters after demanding regularity condition at the future horizon. We adopt the Dirichlet boundary condition and impose the Landau frame to fix these parameters, finally obtain the dependence of transport coefficients in the dual stress tensor and charged current on the arbitrary radical cutoff $r_c$. We find that the dual fluid is not conformal, but it has vanishing bulk viscosity, and the shear viscosity to entropy density ratio is universally $1/4\pi$. Other transport coefficients of the dual current turns out to be cutoff-dependent. In particular, the chiral vortical conductivity expressed in terms of thermodynamic quantities takes the same form as that of the dual fluid at the asymptotic AdS boundary, and the chiral magnetic conductivity receives a cutoff-dependent correction which vanishes at the infinite boundary.Comment: 19 pages, v2: references added, v3: typos corrected, v5: typos corrected, version accepted for publication in JHE

The use of multi-omics data and approaches in breast cancer immunotherapy: a review

Breast cancer is projected to be the most common cancer in women in 2020 in the USA. Despite high remission rates treatment side effects remain an issue, hence the interest in novel approaches such as immunotherapies which aim to utilize patients’ immune systems to target cancer cells. This review summarizes the basics of breast cancer including staging and treatment options, followed by a discussion on immunotherapy, including immune checkpoint blockade. After this, examples of the role of omics-type data and computational biology/bioinformatics in breast cancer are explored. Ultimately, there are several promising areas to investigate such as the prediction of neoantigens and the use of multi-omics data to direct research, with noted appropriate in clinical trial design in terms of end points

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

Background Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction. Results Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia. Conclusion We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer

Innate Immune Responses of Pulmonary Epithelial Cells to Burkholderia pseudomallei Infection

10.1371/journal.pone.0007308PLoS ONE410

The synthesis of chalcones as anticancer prodrugs and their bioactivation in CYP1 expressing breast cancer cells

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI linkAbstract: Background: Although the expression levels of many P450s differ between tumour and corresponding normal tissue, CYP1B1 is one of the few CYP subfamilies which is significantly and consistently overexpressed in tumours. CYP1B1 has been shown to be active within tumours and is capable of metabolising a structurally diverse range of anticancer drugs. Because of this, and its role in the activation of procarcinogens, CYP1B1 is seen as an important target for anticancer drug development. Objectives: To synthesise a series of chalcone derivatives based on the chemopreventative agent DMU-135 and investigate their antiproliferative activities in human breast cancer cell lines which express CYP1B1 and CYP1A1. Method: A series of chalcones were synthesised in yields of 43-94% using the Claisen-Schmidt condensation reaction. These were screened using a MTT assay against a panel of breast cancer cell lines which have been characterised for CYP1 expression. Results: A number of derivatives showed promising antiproliferative activities in human breast cancer cell lines which express CYP1B1 and CYP1A1, while showing significantly lower toxicity towards a non-tumour breast cell line with no CYP expression. Experiments using the CYP1 inhibitors acacetin and -naphthoflavone provided supporting evidence for the involvement of CYP1 enzymes in the bioactivation of these compounds. Conclusions: Chalcones show promise as anticancer agents with evidence suggesting that CYP1 activation of these compounds may be involved

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types