The broadly conserved regulator PhoP links pathogen virulence and membrane potential in Escherichia coli

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87159/1/j.1365-2958.2011.07804.x.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/87159/2/MMI_7804_sm_FigS1-4-TabS1.pd

A Framework for Incorporating Dyads in Models of HIV-Prevention

Although HIV is contracted by individuals, it is typically transmitted in dyads. Most efforts to promote safer sex practices, however, focus exclusively on individuals. The goal of this paper is to provide a theoretical framework that specifies how models of dyadic processes and relationships can inform models of HIV-prevention. At the center of the framework is the proposition that safer sex between two people requires a dyadic capacity for successful coordination. According to this framework, relational, individual, and structural variables that affect the enactment of safer sex do so through their direct and indirect effects on that dyadic capacity. This dyadic perspective does not require an ongoing relationship between two individuals; rather, it offers a way of distinguishing between dyads along a continuum from anonymous strangers (with minimal coordination of behavior) to long-term partners (with much greater coordination). Acknowledging the dyadic context of HIV-prevention offers new targets for interventions and suggests new approaches to tailoring interventions to specific populations

Rheumatoid arthritis - treatment: 180. Utility of Body Weight Classified Low-Dose Leflunomide in Japanese Rheumatoid Arthritis

Background: In Japan, more than 20 rheumatoid arthritis (RA) patients died of interstitial pneumonia (IP) caused by leflunomide (LEF) were reported, but many of them were considered as the victims of opportunistic infection currently. In this paper, efficacy and safety of low-dose LEF classified by body weight (BW) were studied. Methods: Fifty-nine RA patients were started to administrate LEF from July 2007 to July 2009. Among them, 25 patients were excluded because of the combination with tacrolimus, and medication modification within 3 months before LEF. Remaining 34 RA patients administered 20 to 50 mg/week of LEF were followed up for 1 year and enrolled in this study. Dose of LEF was classified by BW (50 mg/week for over 50 kg, 40 mg/week for 40 to 50 kg and 20 to 30 mg/week for under 40 kg). The average age and RA duration of enrolled patients were 55.5 years old and 10.2 years. Prednisolone (PSL), methotrexate (MTX) and etanercept were used in 23, 28 and 2 patients, respectively. In case of insufficient response or adverse effect, dosage change or discontinuance of LEF were considered. Failure was defined as dosages up of PSL and MTX, or dosages down or discontinuance of LEF. Last observation carried forward method was used for the evaluation of failed patients at 1 year. Results: At 1 year after LEF start, good/ moderate/ no response assessed by the European League Against Rheumatism (EULAR) response criteria using Disease Activity Score, including a 28-joint count (DAS28)-C reactive protein (CRP) were showed in 14/ 10/ 10 patients, respectively. The dosage changes of LEF at 1 year were dosage up: 10, same dosage: 5, dosage down: 8 and discontinuance: 11 patients. The survival rate of patients in this study was 23.5% (24 patients failed) but actual LEF continuous rate was 67.6% (11 patients discontinued) at 1 year. The major reason of failure was liver dysfunction, and pneumocystis pneumonia was occurred in 1 patient resulted in full recovery. One patient died of sepsis caused by decubitus ulcer infection. DAS28-CRP score was decreased from 3.9 to 2.7 significantly. Although CRP was decreased from 1.50 to 0.93 mg/dl, it wasn't significant. Matrix metalloproteinase (MMP)-3 was decreased from 220.0 to 174.2 ng/ml significantly. Glutamate pyruvate transaminase (GPT) was increased from 19 to 35 U/l and number of leukocyte was decreased from 7832 to 6271 significantly. DAS28-CRP, CRP, and MMP-3 were improved significantly with MTX, although they weren't without MTX. Increase of GPT and leukopenia were seen significantly with MTX, although they weren't without MTX. Conclusions: It was reported that the risks of IP caused by LEF in Japanese RA patients were past IP history, loading dose administration and low BW. Addition of low-dose LEF is a potent safe alternative for the patients showing unsatisfactory response to current medicines, but need to pay attention for liver function and infection caused by leukopenia, especially with MTX. Disclosure statement: The authors have declared no conflicts of interes

A Novel Approach for Transcription Factor Analysis Using SELEX with High-Throughput Sequencing (TFAST)

<div><h3>Background</h3><p>In previous work, we designed a modified aptamer-free SELEX-seq protocol (afSELEX-seq) for the discovery of transcription factor binding sites. Here, we present original software, TFAST, designed to analyze afSELEX-seq data, validated against our previously generated afSELEX-seq dataset and a model dataset. TFAST is designed with a simple graphical interface (Java) so that it can be installed and executed without extensive expertise in bioinformatics. TFAST completes analysis within minutes on most personal computers.</p> <h3>Methodology</h3><p>Once afSELEX-seq data are aligned to a target genome, TFAST identifies peaks and, uniquely, compares peak characteristics between cycles. TFAST generates a hierarchical report of graded peaks, their associated genomic sequences, binding site length predictions, and dummy sequences.</p> <h3>Principal Findings</h3><p>Including additional cycles of afSELEX-seq improved TFAST's ability to selectively identify peaks, leading to 7,274, 4,255, and 2,628 peaks identified in two-, three-, and four-cycle afSELEX-seq. Inter-round analysis by TFAST identified 457 peaks as the strongest candidates for true binding sites. Separating peaks by TFAST into classes of worst, second-best and best candidate peaks revealed a trend of increasing significance (e-values 4.5×10¹², 2.9×10⁻⁴⁶, and 1.2×10⁻⁷³) and informational content (11.0, 11.9, and 12.5 bits over 15 bp) of discovered motifs within each respective class. TFAST also predicted a binding site length (28 bp) consistent with non-computational experimentally derived results for the transcription factor PapX (22 to 29 bp).</p> <h3>Conclusions/Significance</h3><p>TFAST offers a novel and intuitive approach for determining DNA binding sites of proteins subjected to afSELEX-seq. Here, we demonstrate that TFAST, using afSELEX-seq data, rapidly and accurately predicted sequence length and motif for a putative transcription factor's binding site.</p> </div

Schematic of the TFAST workflow.

<p>TFAST analyzes data produced using SELEX and high-throughput sequencing. (<b>A</b>) An overview of SELEX. Members of an input DNA fragment library compete to bind a protein of interest. Out-competed fragments are washed away and removed. Fragments that bind competitively are recovered and separated from the protein (<i>e.g.</i>, by phenol-chloroform extraction). Recovered fragments are amplified using low-cycle PCR, and the resultant library becomes the input for the next cycle. <i>n</i> cycles are repeated to enrich for strongly binding fragments. (<b>B</b>) DNA inputs for each cycle are subjected to high-throughput sequencing. Sequence reads are aligned to the relevant target genome, producing (<b>C</b>) frequency-position plots for each input sequenced. Shown is a magnified example of a region of the chromosome that behaves as a true binding site, enriching in frequency with each cycle. “Cycle 1” refers to the initial DNA library. (<b>D</b>) TFAST identifies and evaluates peaks and compares peak characteristics across all sequenced inputs. TFAST assigns quality scores to peaks and predicts binding site features. TFAST also generates quality scores on randomly selected regions of the chromosome to act as background controls, to improve downstream motif analysis.</p