HAPLOFREQ--estimating haplotype frequencies efficiently.

A commonly used tool in disease association studies is the search for discrepancies between the haplotype distribution in the case and control populations. In order to find this discrepancy, the haplotypes frequency in each of the populations is estimated from the genotypes. We present a new method HAPLOFREQ to estimate haplotype frequencies over a short genomic region given the genotypes or haplotypes with missing data or sequencing errors. Our approach incorporates a maximum likelihood model based on a simple random generative model which assumes that the genotypes are independently sampled from the population. We first show that if the phased haplotypes are given, possibly with missing data, we can estimate the frequency of the haplotypes in the population by finding the global optimum of the likelihood function in polynomial time. If the haplotypes are not phased, finding the maximum value of the likelihood function is NP-hard. In this case, we define an alternative likelihood function which can be thought of as a relaxed likelihood function. We show that the maximum relaxed likelihood can be found in polynomial time and that the optimal solution of the relaxed likelihood approaches asymptotically to the haplotype frequencies in the population. In contrast to previous approaches, our algorithms are guaranteed to converge in polynomial time to a global maximum of the different likelihood functions. We compared the performance of our algorithm to the widely used program PHASE, and we found that our estimates are at least 10% more accurate than PHASE and about ten times faster than PHASE. Our techniques involve new algorithms in convex optimization. These algorithms may be of independent interest. Particularly, they may be helpful in other maximum likelihood problems arising from survey sampling.     

Yeasts in the gastrointestinal tract of preweaned calves and possible involvement of Candida glabrata in neonatal calf diarrhea

To examine the possibility of a mycotic involvement in neonatal calf diarrhea (NCD) the presence of fungi was assessed in (a) the intestinal contents of dead calves and fecal samples submitted for routine laboratory examination, (b) fecal specimens, sampled once in winter and once in summer, of calves raised on 2 farms with different management systems, and (c) mucosal scrapings of various segments of the digestive tract of a diarrheic calf, massively shedding Candida glabrata.C. glabrata was the most prevalent fungal species isolated from the routine samples. It was the only fungus which was shed by the calves on the 2 farms, for continuous, more or less prolonged periods, but exclusively in the winter months. Diarrhea and C. glabrata shedding seemed to be associated. C. glabrata colonized the abomasum (the functional equivalent of the monogastric stomach) but not the other segments of the digestive tract of the euthanized calfBased on the findings of this study it seems that while some yeast species may be considered as commensals of the digestive tract of calves, and consequently their isolation from intestinal contents or fecal samples has no clinical significance, others, such as C. glabrata may be involved in enteric pathogenic processes. Moreover, characteristics of the culture, previous chemotherapeutic treatments, the animal's age and possibly climatic conditions should be taken into account before deciding on the fungal isolate's clinical relevance. Determination of mycotic involvement in NCD by routine mycological examination of intestinal contents and fecal samples of diarrheic calves may be useful to avoid unnecessary and potentially harmful antibacterial therapy.This revised version was published online in October 2005 with corrections to the Cover Date.     

An exceptional family: Ophiocordyceps‐allied fungus dominates the microbiome of soft scale insects (Hemiptera: Sternorrhyncha: Coccidae)

Hemipteran insects of the suborder Sternorrhyncha are plant sap feeders, where each family is obligately associated with a specific bacterial endosymbiont that produces essential nutrients lacking in the sap. Coccidae (soft scale insects) is the only major sternorrhynchan family in which obligate symbiont(s) have not been identified. We studied the microbiota in seven species from this family from Israel, Spain and Cyprus, by high‐throughput sequencing of ribosomal genes, and found that no specific bacterium was prevalent and abundant in all the tested species. In contrast, an Ophiocordyceps‐allied fungus sp.—a lineage widely known as entomopathogenic—was highly prevalent. All individuals of all the tested species carried this fungus. Phylogenetic analyses showed that the Ophiocordyceps‐allied fungus from the coccids is closely related to fungi described from other hemipterans, and they appear to be monophyletic, although the phylogenies of the Ophiocordyceps‐allied fungi and their hosts do not appear to be congruent. Microscopic observations show that the fungal cells are lemon‐shaped, are distributed throughout the host's body and are present in the eggs, suggesting vertical transmission. Taken together, the results suggest that the Ophiocordyceps‐allied fungus may be a primary symbiont of Coccidae—a major evolutionary shift from bacteria to fungi in the Sternorrhyncha, and an important example of fungal evolutionary lifestyle switch.     

Type 4 pili are dispensable for biofilm development in the cyanobacterium Synechococcus elongatus

The hair‐like cell appendages denoted as type IV pili are crucial for biofilm formation in diverse eubacteria. The protein complex responsible for type IV pilus assembly is homologous with the type II protein secretion complex. In the cyanobacterium Synechococcus elongatus PCC 7942, the gene Synpcc7942_2071 encodes an ATPase homologue of type II/type IV systems. Here, we report that inactivation of Synpcc7942_2071 strongly affected the suite of proteins present in the extracellular milieu (exo‐proteome) and eliminated pili observable by electron microscopy. These results support a role for this gene product in protein secretion as well as in pili formation. As we previously reported, inactivation of Synpcc7942_2071 enables biofilm formation and suppresses the planktonic growth of S. elongatus. Thus, pili are dispensable for biofilm development in this cyanobacterium, in contrast to their biofilm‐promoting function in type IV pili‐producing heterotrophic bacteria. Nevertheless, pili removal is not required for biofilm formation as evident by a piliated mutant of S. elongatus that develops biofilms. We show that adhesion and timing of biofilm development differ between the piliated and non‐piliated strains. The study demonstrates key differences in the process of biofilm formation between cyanobacteria and well‐studied type IV pili‐producing heterotrophic bacteria.     

Supplementing Exposure to Hypoxia with a Copper Depleted Diet Does Not Exacerbate Right Ventricular Remodeling in Mice

Background

Pulmonary hypertension and subsequent right ventricular (RV) failure are associated with high morbidity and mortality. Prognosis is determined by occurrence of RV failure. Currently, adequate treatment for RV failure is lacking. Further research into the molecular basis for the development of RV failure as well as the development of better murine models of RV failure are therefore imperative. We hypothesize that adding a low-copper diet to chronic hypoxia in mice reinforces their individual effect and that the combination of mild pulmonary vascular remodeling and capillary rarefaction, induces RV failure.

Methods

Six week old mice were subjected to normoxia (N; 21% O₂) or hypoxia (H; 10% O₂) during a period of 8 weeks and received either a normal diet (Cu+) or a copper depleted diet (Cu-). Cardiac function was assessed by echocardiography and MRI analysis.

Results and Conclusion

Here, we characterized a mouse model of chronic hypoxia combined with a copper depleted diet and demonstrate that eight weeks of chronic hypoxia (10%) is sufficient to induce RV hypertrophy and subsequent RV failure. Addition of a low copper diet to hypoxia did not have any further deleterious effects on right ventricular remodeling.     

Adaptive Resistance Mutations at Suprainhibitory Concentrations Independent of SOS Mutagenesis

Emergence of resistant bacteria during antimicrobial treatment is one of the most critical and universal health threats. It is known that several stress-induced mutagenesis and heteroresistance mechanisms can enhance microbial adaptation to antibiotics. Here, we demonstrate that the pathogen Bartonella can undergo stress-induced mutagenesis despite the fact it lacks error-prone polymerases, the rpoS gene and functional UV-induced mutagenesis. We demonstrate that Bartonella acquire de novo single mutations during rifampicin exposure at suprainhibitory concentrations at a much higher rate than expected from spontaneous fluctuations. This is while exhibiting a minimal heteroresistance capacity. The emerged resistant mutants acquired a single rpoB mutation, whereas no other mutations were found in their whole genome. Interestingly, the emergence of resistance in Bartonella occurred only during gradual exposure to the antibiotic, indicating that Bartonella sense and react to the changing environment. Using a mathematical model, we demonstrated that, to reproduce the experimental results, mutation rates should be transiently increased over 1,000-folds, and a larger population size or greater heteroresistance capacity is required. RNA expression analysis suggests that the increased mutation rate is due to downregulation of key DNA repair genes (mutS, mutY, and recA), associated with DNA breaks caused by massive prophage inductions. These results provide new evidence of the hazard of antibiotic overuse in medicine and agriculture.     

Tube law for the intrapulmonary airway

A semiempirical model of a pressure-area relationship for the bronchial airways is developed. It is described by a single similarity law consistent in form with the nonlinear elastic behavior of biological tissue. The tethering effect of the parenchyma is lumped into the wall properties of the bronchi and is included in an effective wall stiffness. The model, which is fitted to the experimental data of Takishima and his associates (J. Appl. Physiol. 38: 875-881, 1975), is lung-volume dependent and is therefore suitable for the analyses of airflow at different lung volumes, especially for modeling of forced expiration.     

Translocation from nuclei to cytoplasm is necessary for anti A‐PCD activity and turnover of the Type II IAP BcBir1

Type II inhibitors of apoptosis (IAPs) belong to a subgroup of IAP‐related proteins. While IAPs are restricted to animals, Type II IAPs are found in other phyla, including fungi. BcBir1, a Type II IAP from Botrytis cinerea has anti apoptotic‐like programmed cell death (A‐PCD) activity, which is important for pathogenicity of this fungus. Here we report on the role of sub‐cellular localization of BcBir1 in protein turnover and anti A‐PCD activity. Expression of BcBir1 in Saccharomyces cerevisiae had no effect on sensitivity of the yeast cells to A‐PCD‐inducing conditions, whereas expression of a truncated N' part reduced sensitivity of the cells to these conditions. The full‐length BcBir1 protein was detected only in the yeast nucleus, whereas the N' part was observed both in the nucleus and cytoplasm. In B. cinerea, BcBir1 was mainly nuclear under optimal conditions, whereas under A‐PCD‐inducing conditions it shuttled to the cytoplasm and then it was completely degraded. Collectively, our results show that anti A‐PCD activity of BcBir1 occurs in the cytoplasm, the C′ end mediates regulation of steady state level of BcBir1 in the nucleus, and the N' end mediates anti A‐PCD activity as well as fast degradation of BcBir1 in the cytoplasm.