Circulating angiogenic factors in patients with thromboangiitis obliterans

Background

Thromboangiitis obliterans (TAO, also known as Buerger''s disease) is a non-atherosclerotic inflammatory vascular disease that primarily affects arteries in the extremities of young adult smokers. Since the etiology of TAO is still unknown, therapeutic options are limited. Recent attempts in therapeutic angiogenesis have been promising. Therefore, the aim of our study was to evaluate angiogenic processes and factors including circulating progenitor cells in TAO.

Methodology/Principal Findings

TAO patients with critical limb ischemia and age- and gender-matched nonsmokers and smokers without cardiovascular disease (n = 12 in each group) were enrolled in the study. Flow cytometric analysis of peripheral blood showed significantly decreased levels of circulating CD45^dimCD34⁺ progenitor cells in TAO patients and in smokers compared to nonsmokers. In contrast to both control groups, the proportion of CD45^dimCD34⁺ progenitor cells co-expressing VEGF receptor-2 (VEGFR2) was significantly elevated in TAO patients. Enzyme-linked immunosorbent assay (ELISA) of common angiogenic factors (such as VEGF) did not clearly point to pro- or antiangiogenic conditions in serum or plasma of TAO patients. Serum of TAO patients and controls was evaluated in proliferation, migration (scratch assay) and spheroid sprouting assays using human umbilical vein endothelial cells (HUVECs). Serum of TAO patients exhibited a diminished sprouting capacity of HUVECs compared to both control groups. Proliferation and migration of endothelial cells were impaired after treatment with serum of TAO patients.

Conclusion

Levels of circulating progenitor cells were altered in TAO patients compared to healthy nonsmokers and smokers. Furthermore, serum of TAO patients exhibited an antiangiogenic activity (impaired endothelial cell sprouting, migration and proliferation) on endothelial cells, which may contribute to vascular pathology in this patient population.     

The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process

With the availability of next-generation sequencing (NGS) technology, it is expected that sequence variants may be called on a genomic scale. Here, we demonstrate that a deeper understanding of the distribution of the variant call frequencies at heterozygous loci in NGS data sets is a prerequisite for sensitive variant detection. We model the crucial steps in an NGS protocol as a stochastic branching process and derive a mathematical framework for the expected distribution of alleles at heterozygous loci before measurement that is sequencing. We confirm our theoretical results by analyzing technical replicates of human exome data and demonstrate that the variance of allele frequencies at heterozygous loci is higher than expected by a simple binomial distribution. Due to this high variance, mutation callers relying on binomial distributed priors are less sensitive for heterozygous variants that deviate strongly from the expected mean frequency. Our results also indicate that error rates can be reduced to a greater degree by technical replicates than by increasing sequencing depth.     

The aggressiveness of murine lymphomas selected in vivo by growth rate correlates with galectin-1 expression and response to cyclophosphamide

Although lymphomas account for almost half of blood-derived cancers that are diagnosed each year, the causes of new cases are poorly understood, as reflected by the relatively few risk factors established. Galectin-1, an immunoregulatory ?-galactoside-binding protein, has been widely associated with tumor-immune escape. The aim of the present work was to study the relationship between tumor growth rate, aggressiveness, and response to cyclophosphamide (Cy) therapy with regard to Gal-1 expression in murine T-cell lymphoma models. By means of a disruptive selection process for tumor growth rate, we generated two lymphoma variants from a parental T-cell lymphoma, which have unique characteristics in terms of tumor growth rate, spontaneous regression, metastatic capacity, Gal-1 expression and sensitivity to Cy therapy. Here, we show that Gal-1 expression strongly correlates with tumor growth rate, metastatic capacity and response to single-dose Cy therapy in T-cell lymphoma models; this association might have important consequences for evaluating prognosis and treatments of this type of tumors.     

Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions

Regulatory small RNAs (sRNAs) have crucial roles in the adaptive responses of bacteria to changes in the environment. Thus far, potential regulatory RNAs have been studied mainly in marine picocyanobacteria in genetically intractable Prochlorococcus, rendering their molecular analysis difficult. Synechococcus sp. WH7803 is a model cyanobacterium, representative of the picocyanobacteria from the mesotrophic areas of the ocean. Similar to the closely related Prochlorococcus it possesses a relatively streamlined genome and a small number of genes, but is genetically tractable. Here, a comparative genome analysis was performed for this and four additional marine Synechococcus to identify the suite of possible sRNAs and other RNA elements. Based on the prediction and on complementary microarray profiling, we have identified several known as well as 32 novel sRNAs. Some sRNAs overlap adjacent coding regions, for instance for the central photosynthetic gene psbA. Several of these novel sRNAs responded specifically to environmentally relevant stress conditions. Among them are six sRNAs changing their accumulation level under cold stress, six responding to high light and two to iron limitation. Target predictions suggested genes encoding components of the light-harvesting apparatus as targets of sRNAs originating from genomic islands and that one of the iron-regulated sRNAs might be a functional homolog of RyhB. These data suggest that marine Synechococcus mount adaptive responses to these different stresses involving regulatory sRNAs.     

Estimation of genotyping error rate from repeat genotyping,unintentional recaptures and known parent–offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus)

Genotyping errors are present in almost all genetic data and can affect biological conclusions of a study, particularly for studies based on individual identification and parentage. Many statistical approaches can incorporate genotyping errors, but usually need accurate estimates of error rates. Here, we used a new microsatellite data set developed for brown rockfish (Sebastes auriculatus) to estimate genotyping error using three approaches: (i) repeat genotyping 5% of samples, (ii) comparing unintentionally recaptured individuals and (iii) Mendelian inheritance error checking for known parent–offspring pairs. In each data set, we quantified genotyping error rate per allele due to allele drop‐out and false alleles. Genotyping error rate per locus revealed an average overall genotyping error rate by direct count of 0.3%, 1.5% and 1.7% (0.002, 0.007 and 0.008 per allele error rate) from replicate genotypes, known parent–offspring pairs and unintentionally recaptured individuals, respectively. By direct‐count error estimates, the recapture and known parent–offspring data sets revealed an error rate four times greater than estimated using repeat genotypes. There was no evidence of correlation between error rates and locus variability for all three data sets, and errors appeared to occur randomly over loci in the repeat genotypes, but not in recaptures and parent–offspring comparisons. Furthermore, there was no correlation in locus‐specific error rates between any two of the three data sets. Our data suggest that repeat genotyping may underestimate true error rates and may not estimate locus‐specific error rates accurately. We therefore suggest using methods for error estimation that correspond to the overall aim of the study (e.g. known parent–offspring comparisons in parentage studies).     

Caregiver recognition of childhood diarrhea, care seeking behaviors and home treatment practices in rural Burkina Faso: a cross-sectional survey

Introduction

To design effective national diarrhea control programs, including oral rehydration solution (ORS) and therapeutic zinc supplementation, information is needed on local perceptions of illness, external care seeking behaviors, and home treatment practices.

Methods

A cross-sectional, community-based household survey was conducted in the Orodara Health District, Burkina Faso. Caregivers of 10,490 children <27 months were interviewed to assess child diarrhea prevalence and related care practices. Characteristics of households, caregivers, children, and reported illnesses were compared for those caregivers who did or did not recognize the presence of diarrhea, as defined according to clinical criteria (≥3 liquid or semi-liquid stools/day). Multiple logistic regression models were used to examine factors associated with illness recognition and treatment.

Results

Clinically defined diarrhea was present in 7.6% (95% CI: 7.1–8.1%) of children during the 24 hours preceding the survey but recognized by only 55% of caregivers. Over half (55%) of the caregivers of 1,067 children with a clinically defined diarrhea episode in the past 14 days sought care outside the home; 78% of those seeking care attended a public sector clinic. Care was sought and treatment provided more frequently for children with fever, vomiting, anorexia, longer illness duration, and those living closer to the health center; and care was sought more frequently for male children. 80% of children with recent diarrhea received some form of treatment; only 24% received ORS, whereas 14% received antibiotics. Zinc was not yet available in the study area.

Conclusions

Caregivers frequently fail to recognize children''s diarrhea, especially among younger infants and when illness signs are less severe. Treatment practices do not correspond with international recommendations in most cases, even when caregivers consult with formal health services. Child caregivers need additional assistance to recognize diarrhea correctly, and both caregivers and health care providers need updated training on current diarrhea treatment recommendations.     

Molecular analysis of hemolysin-mediated secretion of a human interleukin-6 fusion protein in Salmonella typhimurium

Previously, we reported a plasmid-bearing Salmonella typhimurium strain capable of secreting human interleukin-6 (hIL-6) when genetically fused to the Escherichia coli hemolysin transport signal (HlyA(S)). Stationary phase culture supernatants of this strain revealed three major forms of hIL-6-HlyA(S) fusion protein (apparent molecular masses 32.4, 30.3, 27.0 kDa), at which the largest protein presumably represented full-length hIL-6-HlyA(S). The biological activity of the hIL-6-HlyA(S) protein mixture was similar to that of mature hIL-6. Accumulation of hIL-6-HlyA(S) in the culture supernatant occurred only during the initial growth phase, whereas in stationary phase and under in vitro conditions successive cleavage into the two truncated forms was observed. On the other hand, in whole cell lysates only full-length hIL-6-HlyA(S) could be detected, accounting for more than 50% of the totally synthesized protein. Upon cell fractionation, cellular hIL-6-HlyA(S) was exclusively found in the membrane fraction. These results suggest, that in S. typhimurium production and secretion of hIL-6-HlyA(S) is restricted to growing cells. A specific processing by a Salmonella-derived protease did not affect the biological activity of the fusion protein.     

Use of Stochastic Models To Assess the Effect of Environmental Factors on Microbial Growth

We present a novel application of a stochastic ecological model to the study and analysis of microbial growth dynamics as influenced by environmental conditions in an extensive experimental data set. The model proved to be useful in bridging the gap between theoretical ideas in ecology and an applied problem in microbiology. The data consisted of recorded growth curves of Escherichia coli grown in triplicate in a base medium with all 32 possible combinations of five supplements: glucose, NH₄Cl, HCl, EDTA, and NaCl. The potential complexity of 2⁵ experimental treatments and their effects was reduced to 2² as just the metal chelator EDTA, the presumed osmotic pressure imposed by NaCl, and the interaction between these two factors were enough to explain the variability seen in the data. The statistical analysis showed that the positive and negative effects of the five chemical supplements and their combinations were directly translated into an increase or decrease in time required to attain stationary phase and the population size at which the stationary phase started. The stochastic ecological model proved to be useful, as it effectively explained and summarized the uncertainty seen in the recorded growth curves. Our findings have broad implications for both basic and applied research and illustrate how stochastic mathematical modeling coupled with rigorous statistical methods can be of great assistance in understanding basic processes in microbial ecology.