R-body-producing bacteria.

Until 10 years ago, R bodies were known only as diagnostic features by which endosymbionts of paramecia were identified as kappa particles. They were thought to be limited to the cytoplasm of two species in the Paramecium aurelia species complex. Now, R bodies have been found in free-living bacteria and other Paramecium species. The organisms now known to form R bodies include the cytoplasmic kappa endosymbionts of P. biaurelia and P. tetraurelia, the macronuclear kappa endosymbionts of P. caudatum, Pseudomonas avenae (a free-living plant pathogen), Pseudomonas taeniospiralis (a hydrogen-oxidizing soil microorganism), Rhodospirillum centenum (a photosynthetic bacterium), and a soil bacterium, EPS-5028, which is probably a pseudomonad. R bodies themselves fall into five distinct groups, distinguished by size, the morphology of the R-body ribbons, and the unrolling behavior of wound R bodies. In recent years, the inherent difficulties in studying the organization and assembly of R bodies by the obligate endosymbiont kappa, have been alleviated by cloning and expressing genetic determinants for these R bodies (type 51) in Escherichia coli. Type 51 R-body synthesis requires three low-molecular-mass polypeptides. One of these is modified posttranslationally, giving rise to 12 polypeptide species, which are the major structural subunits of the R body. R bodies are encoded in kappa species by extrachromosomal elements. Type 51 R bodies, produced in Caedibacter taeniospiralis, are encoded by a plasmid, whereas bacteriophage genomes probably control R-body synthesis in other kappa species. However, there is no evidence that either bacteriophages or plasmids are present in P. avenae or P. taeniospiralis. No sequence homology was detected between type 51 R-body-encoding DNA and DNA from any R-body-producing species, except C. varicaedens 1038. The evolutionary relatedness of different types of R bodies remains unknown.     

Seasonal and sex differences in the structure and chemical composition of adipose tissue in wild polar bears (Ursus maritimus)

Biopsy samples of adipose tissue from the upper thigh were collected in spring and in late summer/autumn from 370 wild polar bears ( Ursus maritimus ), including adult females with and without cubs, adult males and juveniles. Mean adipocyte volume was measured from all samples and chemical assays of the lipid, total protein and collagen were also performed on samples from 53 bears. Mean adipocyte volume was smaller in all specimens in spring than in late summer/autumn, but the differences were greatest for solitary adult females. The range of adipocyte volumes was much greater for adult females than for adult males, and in females only, mean adipocyte volume correlated significantly with total body mass. Therefore, adipocyte volume measurements from biopsy samples provide some information about fatness in adult females, but are worthless as an indicator of body composition in males and juveniles. In juveniles and females, but not adult males, the lipid content of the adipose tissue was up to 18% lower in autumn than in spring. The collagen content was significantly higher in autumn than in spring in all bears except females with cubs. We suggest that these differences in chemical composition arise from accumulation of water within and between the adipocytes, which would minimize tissue shrinkage, and from changes in the vascularization of the adipose tissue. These properties may be adaptations to rapid fattening and prolonged fasting and the sex differences may reflect the contrasting reproductive strategy of female and male polar bears.     

On the Validity of Evolutionary Models with Site-Specific Parameters

Evolutionary models that make use of site-specific parameters have recently been criticized on the grounds that parameter estimates obtained under such models can be unreliable and lack theoretical guarantees of convergence. We present a simulation study providing empirical evidence that a simple version of the models in question does exhibit sensible convergence behavior and that additional taxa, despite not being independent of each other, lead to improved parameter estimates. Although it would be desirable to have theoretical guarantees of this, we argue that such guarantees would not be sufficient to justify the use of these models in practice. Instead, we emphasize the importance of taking the variance of parameter estimates into account rather than blindly trusting point estimates – this is standardly done by using the models to construct statistical hypothesis tests, which are then validated empirically via simulation studies.     

Effect of obesity per se on plasma lipid and aortic responses to diet in swine

Thirty-two genetically lean and obese Yorkshire X Duroc crossbred castrated male pigs were divided within genetic line into two groups at 7 weeks of age. Eight pigs within each line were fed a diet low in fat and cholesterol (maize-soybean meal diet fortified with minerals and vitamins). The other group was fed a similar diet containing added beef tallow (11%) and dried egg yolk (1%). All pigs were fed ad libitum for 4 months when one-half of each group was slaughtered. All other pigs were continued on their respective diets at a restricted level of intake for an additional 5 months at which time the protein source of two pigs in each diet group within each genetic line was changed from soybean meal to casein. After an additional 6 months on their respective diets (16 months total duration of experiment) these pigs were slaughtered. Blood samples were taken monthly or bimonthly for total plasma cholesterol and triglycerides. At slaughter, the aorta was opened, stained with Sudan IV, and the stained area traced and measured planimetrically. Only a moderate rise occurred in plasma cholesterol and triglycerides of pigs fed high fat-high cholesterol diets. Genetically obese pigs were no more susceptible to diet-induced hypercholesterolemia and to the percentage of the surface area of the aorta stained with Sudan IV than were lean pigs. It is concluded that obesity per se is not necessarily associated with development of atherosclerosis in pigs and that innate ability to metabolize high dietary cholesterol is of greater importance than body fatness in determining the response to diet.     

Organization of white adipose tissue in lemuridae

The gross anatomy of white adipose tissue was studied in seven carcasses representing three lemurid species (Lemur catta, Eulemur fulvus, E. mongoz) to validate in vivo methods of assessing fatness, and to contribute to a comprehensive database on the organization of adipose tissue in Mammalia. During the years preceding their deaths, subjects had been either caged or semi-provisioned under semi-captive conditions, and their body masses had been recorded several times annually. All specimens were as fat or fatter than anthropoid primates maintained for long periods under comparable conditions. At least eight superficial, four intra-abdominal, and two intermuscular adipose depots were described, all of which were comparable to those described previously for macaques and humans. All typical mammalian depots were present. Many superficial depots adhered tightly to the skin and/or underlying muscles. The superficial “paunch” depot on the outer ventral wall of the abdomen, characteristic of anthropoid primates, was found in all specimens. The existence of this depot in lemurs suggests that it evolved early in Primates. As in monkeys and humans, the paunch was very variable in size, massive in obese specimens but almost absent in moderately lean ones, confirming that extensive accumulation and selective depletion of adipose tissue at this depot is a special feature of Primates. In some obese specimens, adipose tissue on the ventral and lateral thorax and on the inner dorsal wall of the abdomen, extending around the kidneys and into the pelvic canal, was also massive. The investigation allowed for improvement of protocols for external measurement in ongoing research on growth, mass, and fatness in ringtailed and redfronted lemurs. Comparisons of subjects' ranges of body mass change during adult life with masses of adipose tissue found upon dissection suggested that much of lemurs' predictable seasonal change in body mass is due to changes in the mass of white adipose tissue. © 1995 Wiley-Liss, Inc.     

Antimicrobial susceptibility patterns,emm type distribution and genetic diversity of Streptococcus pyogenes recovered in Brazil

Streptococcus pyogenes is responsible for a variety of infectious diseases and immunological complications. In this study, 91 isolates of S. pyogenes recovered from oropharynx secretions were submitted to antimicrobial susceptibility testing, emm typing and pulsed-field gel electrophoresis (PFGE) analysis. All isolates were susceptible to ceftriaxone, levofloxacin, penicillin G and vancomycin. Resistance to erythromycin and clindamycin was 15.4%, which is higher than previous reports from this area, while 20.9% of the isolates were not susceptible to tetracycline. The macrolide resistance phenotypes were cMLSB (10) and iMLSB (4). The ermB gene was predominant, followed by the ermA gene. Thirty-two emm types and subtypes were found, but five (emm1, emm4, emm12, emm22, emm81) were detected in 48% of the isolates. Three new emm subtypes were identified (emm1.74, emm58.14, emm76.7). There was a strong association between emm type and PFGE clustering. A variety of PFGE profiles as well as emm types were found among tetracycline and erythromycin-resistant isolates, demonstrating that antimicrobial resistant strains do not result from the expansion of one or a few clones. This study provides epidemiological data that contribute to the development of suitable strategies for the prevention and treatment of such infections in a poorly studied area.     

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform

Since its identification in 1983, HIV-1 has been the focus of a research effort unprecedented in scope and difficulty, whose ultimate goals — a cure and a vaccine – remain elusive. One of the fundamental challenges in accomplishing these goals is the tremendous genetic variability of the virus, with some genes differing at as many as 40% of nucleotide positions among circulating strains. Because of this, the genetic bases of many viral phenotypes, most notably the susceptibility to neutralization by a particular antibody, are difficult to identify computationally. Drawing upon open-source general-purpose machine learning algorithms and libraries, we have developed a software package IDEPI (IDentify EPItopes) for learning genotype-to-phenotype predictive models from sequences with known phenotypes. IDEPI can apply learned models to classify sequences of unknown phenotypes, and also identify specific sequence features which contribute to a particular phenotype. We demonstrate that IDEPI achieves performance similar to or better than that of previously published approaches on four well-studied problems: finding the epitopes of broadly neutralizing antibodies (bNab), determining coreceptor tropism of the virus, identifying compartment-specific genetic signatures of the virus, and deducing drug-resistance associated mutations. The cross-platform Python source code (released under the GPL 3.0 license), documentation, issue tracking, and a pre-configured virtual machine for IDEPI can be found at https://github.com/veg/idepi.

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