Phenotypic and Functional Properties of Helios+ Regulatory T Cells

Helios, an Ikaros family transcription factor, is preferentially expressed at the mRNA and protein level in regulatory T cells. Helios expression previously appeared to be restricted to thymic-derived Treg. Consistent with recent data, we show here that Helios expression is inducible in vitro under certain conditions. To understand phenotypic and functional differences between Helios+ and Helios− Treg, we profiled cell-surface markers of FoxP3+ Treg using unmanipulated splenocytes. We found that CD103 and GITR are expressed at high levels on a subset of Helios+ Treg and that a Helios+ Treg population could be significantly enriched by FACS sorting using these two markers. Quantitative real-time PCR (qPCR) analysis revealed increased TGF-β message in Helios+ Treg, consistent with the possibility that this population possesses enhanced regulatory potential. In tumor-bearing mice, we found that Helios+ Treg were relatively over-represented in the tumor-mass, and BrdU studies showed that, in vivo, Helios+ Treg proliferated more than Helios− Treg. We hypothesized that Helios-enriched Treg might exert increased suppressive effects. Using in vitro suppression assays, we show that Treg function correlates with the absolute number of Helios+ cells in culture. Taken together, these data show that Helios+ Treg represent a functional subset with associated CD103 and GITR expression

Treatment outcome and associated factors of severe acute malnutrition among 6–59 months old children in Debre Markos and Finote Selam hospitals, Northwest Ethiopia: a retrospective cohort study

BACKGROUND: In Ethiopia, the health sector has increased its efforts to enhance good nutritional practices through health education, treatment of extremely malnourished children and provision of micronutrients for mothers and children. But, the poor nutritional status of women and children continues to be still a major public health problem. METHODS: A retrospective cohort study was conducted to assess the treatment outcome and associated factors of severe acute malnutrition among a total of 253 children age 6–59 months old. Severe acute malnutrition registration logbook and patient charts were used as a source of data. Data were entered in to Epi-data version 3.1 and exported to SPSS version 20 for analysis. To identify associated factors, Cox proportional hazard analysis was computed and p-value <0.05 at 95% confidence interval was considered as statistically significant. RESULTS: The recovery rate was 77.9% and the overall median recovery time was 11 days. Those children age from 24 to 35 months had 34% lower probability of recovery from SAM compared to 6–11 months old children (AHR = 0.66, 95% CI: 0.35–0.89). Children whose ages from 36 to 59 months had 47% lower probability of recovery from SAM compared to 6–11 months old children (AHR = 0.53, 95% CI: 0.31–0.91). HIV negative children had 2.48 times higher probability of getting recovered from SAM compared to HIV positive children (AHR = 2.48, 95% CI: 1.23–5.01). Children who didn’t take folic acid supplement had 65% lower probability of recovery from SAM compared to children who took folic acid supplement (AHR = 0.35, 95% CI: 0.14–0.89). CONCLUSIONS: This study found that recovery rate of 6–59 months old children treated for severe acute malnutrition in therapeutics units was in acceptable range based on the WHO recommendation. Folic acid supplementation and screening for HIV status should be promoted at all levels of health facilities during early age

Epigenetic biotypes of post-traumatic stress disorder in war-zone exposed veteran and active duty males

Post-traumatic stress disorder (PTSD) is a heterogeneous condition evidenced by the absence of objective physiological measurements applicable to all who meet the criteria for the disorder as well as divergent responses to treatments. This study capitalized on biological diversity observed within the PTSD group observed following epigenome-wide analysis of a well-characterized Discovery cohort (N = 166) consisting of 83 male combat exposed veterans with PTSD, and 83 combat veterans without PTSD in order to identify patterns that might distinguish subtypes. Computational analysis of DNA methylation (DNAm) profiles identified two PTSD biotypes within the PTSD+ group, G1 and G2, associated with 34 clinical features that are associated with PTSD and PTSD comorbidities. The G2 biotype was associated with an increased PTSD risk and had higher polygenic risk scores and a greater methylation compared to the G1 biotype and healthy controls. The findings were validated at a 3-year follow-up (N = 59) of the same individuals as well as in two independent, veteran cohorts (N = 54 and N = 38), and an active duty cohort (N = 133). In some cases, for example Dopamine-PKA-CREB and GABA-PKC-CREB signaling pathways, the biotypes were oppositely dysregulated, suggesting that the biotypes were not simply a function of a dimensional relationship with symptom severity, but may represent distinct biological risk profiles underpinning PTSD. The identification of two novel distinct epigenetic biotypes for PTSD may have future utility in understanding biological and clinical heterogeneity in PTSD and potential applications in risk assessment for active duty military personnel under non-clinician-administered settings, and improvement of PTSD diagnostic markers

Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays

Abstract Background Life science research is moving quickly towards large-scale experimental designs that are comprised of multiple tissues, time points, and samples. Omic time-series experiments offer answers to three big questions: what collective patterns do most analytes follow, which analytes follow an identical pattern or synchronize across multiple cohorts, and how do biological functions evolve over time. Existing tools fall short of robustly answering and visualizing all three questions in a unified interface. Results Functional Heatmap offers time-series data visualization through a Master Panel page, and Combined page to answer each of the three time-series questions. It dissects the complex multi-omics time-series readouts into patterned clusters with associated biological functions. It allows users to identify a cascade of functional changes over a time variable. Inversely, Functional Heatmap can compare a pattern with specific biology respond to multiple experimental conditions. All analyses are interactive, searchable, and exportable in a form of heatmap, line-chart, or text, and the results are easy to share, maintain, and reproduce on the web platform. Conclusions Functional Heatmap is an automated and interactive tool that enables pattern recognition in time-series multi-omics assays. It significantly reduces the manual labour of pattern discovery and comparison by transferring statistical models into visual clues. The new pattern recognition feature will help researchers identify hidden trends driven by functional changes using multi-tissues/conditions on a time-series fashion from omic assays

Minocycline and the SPR741 Adjuvant Are an Efficacious Antibacterial Combination for Acinetobacter baumannii Infections

Antibiotic resistance, when it comes to bacterial infections, is not a problem that is going to disappear anytime soon. With the lack of larger investment in novel antibiotic research and the ever-growing increase of resistant isolates amongst the ESKAPEE pathogens (Enterobacter cloacae, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterococcus sp., and Escherichia coli), it is inevitable that more and more infections caused by extensively drug-resistant (XDR) and pandrug-resistant (PDR) strains will arise. One strategy to counteract the growing threat is to use antibiotic adjuvants, a drug class that on its own lacks significant antibiotic activity, but when mixed with another antibiotic, can potentiate increased killing of bacteria. Antibiotic adjuvants have various mechanisms of action, but polymyxins and polymyxin-like molecules can disrupt the Gram-negative outer membrane and allow other drugs better penetration into the bacterial periplasm and cytoplasm. Previously, we showed that SPR741 had this adjuvant effect with regard to rifampin; however, rifampin is often not used clinically because of easily acquired resistance. To find additional, appropriate clinical partners for SPR741 with respect to pulmonary and wound infections, we investigated tetracyclines and found a previously undocumented synergy with minocycline in vitro and in vivo in murine models of infection

Optomagnetic Imaging Spectroscopy (OMIS) for in situ detection of bacteria in blood – feasibility study

Introduction: Sepsis is one of the leading causes of death in military and civilian hospitals. Rapid identification of involved pathogens is a key step for appropriate diagnosis, treatment and ultimately survival. Current diagnostics tools are either very bulky and not deployment ready, or require a long time to provide results. Given these obstacles, new solutions are urgently needed. Optomagnetic Imaging Spectroscopy (OMIS) is novel technology successfully used for the detection of cancer cells and viruses. OMIS has high sensitivity due to recording the unpaired and paired electrons of sample material. Furthermore, machine learning that uses the algorithms random forest (RF) classifier and artificial neural network (ANN) is integrated into the technology to enhance detection. Here we evaluated the feasibility of OMIS for the detection of bacteria in blood. Methods: We used commercially available human blood spiked with a defined concentration multidrug resistant Staphylococcus aureus derived from a clinical isolate. Final concentrations of bacteria of 1 × 106, 1 × 105 and 1 × 104 CFU/mL corresponding to High (H), Medium (M) and Low (L) concentrations respectively. A total of 240 samples (60 samples per concentration as well as 60 samples of sterile blood (N)) was imaged, and the data were analyzed using random forest classifier and artificial neural network. Images for the training set and validation sets were separately obtained and used for comparison against true positive values (confirmatory plating on the nutrient agar). Results: The average score of classification samples in the correct category (N, L, M, H) one-by-one was 94% for the ANN algorithm, while for the RF algorithm accuracy was 93% (average means that three times different 40 samples (of 240 samples) were chosen, and each prediction test had different sample mixtures). The closeness of the two values of accuracy strongly indicates that the input data (interaction of light with paired and unpaired electrons) and output data (classification N, L, M, H concentration of bacteria) are correlated

Identification and Characterization of vB_PreP_EPr2, a Lytic Bacteriophage of Pan-Drug Resistant <i>Providencia rettgeri</i>

Providencia rettgeri is an emerging opportunistic Gram-negative pathogen with reports of increasing antibiotic resistance. Pan-drug resistant (PDR) P. rettgeri infections are a growing concern, demonstrating a need for the development of alternative treatment options which is fueling a renewed interest in bacteriophage (phage) therapy. Here, we identify and characterize phage vB_PreP_EPr2 (EPr2) with lytic activity against PDR P. rettgeri MRSN 845308, a clinical isolate that carries multiple antibiotic resistance genes. EPr2 was isolated from an environmental water sample and belongs to the family Autographiviridae, subfamily Studiervirinae and genus Kayfunavirus, with a genome size of 41,261 base pairs. Additional phenotypic characterization showed an optimal MOI of 1 and a burst size of 12.3 ± 3.4 PFU per bacterium. EPr2 was determined to have a narrow host range against a panel of clinical P. rettgeri strains. Despite this fact, EPr2 is a promising lytic phage with potential for use as an alternative therapeutic for treatment of PDR P. rettgeri infections

A role for the transcription factor Helios in human CD4+CD25+ regulatory T cells

Gyotaejeon (Queen's Quarters), detail of stone pylons and raised base with ondol (underfloor heating); The largest of the Five Grand Palaces built by the Joseon dynasty, Gyeongbokgung served as the home of Kings of the Joseon [Chosŏn (medieval to modern) also known as Yi] dynasty, the Kings' households, as well as the government. The Yi dynasty ruled the Korean peninsula from 1392 to 1910, founded by Yi Sŏng-gye, posthumously known as King T’aejo (reigned 1392-1398). The palace was burnt and abandoned for three centuries following the Imjin War (1592-1598). In 1865-1872, all 7,700 rooms were restored along with 500 buildings over a 40 hectare site. In the early 20th century, much of the palace was systematically destroyed (all but 10 buildings) by Imperial Japan. Since the 1990s, the walled palace complex is gradually being reconstructed to its original form, with buildings built during Japanese occupation being pulled down, including the Japanese Government-General Building (removed 1996). By the end of 2009, it was estimated that approximately 40 percent of the structures that were standing before the Japanese occupation of Korea were restored or reconstructed; another 20 years of rebuilding is planned. Source: Wikipedia; http://en.wikipedia.org/wiki/Main_Page (accessed 6/29/2015

Brain proteomics of anopheles gambiae

Anopheles gambiae has a well-adapted system for host localization, feeding, and mating behavior, which are all governed by neuronal processes in the brain. However, there are no published reports characterizing the brain proteome to elucidate neuronal signaling mechanisms in the vector. To this end, a large-scale mapping of the brain proteome of An. gambiae was carried out using high resolution tandem mass spectrometry, revealing a repertoire of \u3e1800 proteins, of which 15% could not be assigned any function. A large proportion of the identified proteins were predicted to be involved in diverse biological processes including metabolism, transport, protein synthesis, and olfaction. This study also led to the identification of 10 GPCR classes of proteins, which could govern sensory pathways in mosquitoes. Proteins involved in metabolic and neural processes, chromatin modeling, and synaptic vesicle transport associated with neuronal transmission were predominantly expressed in the brain. Proteogenomic analysis expanded our findings with the identification of 15 novel genes and 71 cases of gene refinements, a subset of which were validated by RT-PCR and sequencing. Overall, our study offers valuable insights into the brain physiology of the vector that could possibly open avenues for intervention strategies for malaria in the future. © Copyright 2014, Mary Ann Liebert, Inc. 2014

Sequencing CTLA-4 blockade with cell-based immunotherapy for prostate cancer Open Access

Background: The FDA recently approved an anti-CTLA-4 antibody (Iplimumab) for the treatment of metastatic melanoma. This decision was based on Phase III results, which demonstrate that blocking this immune checkpoint provides a survival advantage in patients with advanced disease. As a single agent, ipilimumab is also being clinically evaluated in advanced (metastatic, castrate-resistant) prostate cancer and two randomized, placebocontrolled Phase III studies have recently completed accrual. Methods: We used a well-described genetically engineered mouse (GEM), autochronous prostate cancer model (Pro-TRAMP) to explore the relative sequencing and dosing of anti-CTLA-4 antibody when combined with a cellbased, GM-CSF-secreting vaccine (GVAX). Results: Our results show that combined treatment results in a dramatic increase in effector CD8 T cells in the prostate gland, and enhanced tumor-antigen directed lytic function. These effects are maximized when CTLA-4 blockade is applied after, but not before, vaccination. Additional experiments, using models of metastatic disease, show that incorporation of low-dose cyclophosphamide into this combined treatment regimen results in an additional pre-clinical benefit. Conclusions: Together these studies define a combination regimen using anti-CTLA-4/GVAX immunotherapy and low-dose chemotherapy for potential translation to a clinical trial setting