Fatty acid composition and the classification of the Porifera

The fatty acid content of 30 species of Porifera, including samples of Hexactinellida and Lithistida for which no fatty acid data previously existed, have been examined. The sponges are unique among animal phyla in diversity of fatty acids with generally high levels of long chain fatty acids (LCFAs; C_24–30, high unsaturation (mainly polyunsaturation), high incidence of branched and odd chain fatty acids. Further, peculiarities in proportions of individual acids of particular chain lengths distinguish the phylum. Hexactinellid fatty acid traits corresponded closely to those of Demospongiae while the calcareous species was atypical in exhibiting low levels of LCFAs and unsaturation. Seasonal and geographical influences on components of the fatty acid profile limit the extent to which this information can be utilized in a chemotaxonomic sense.     

Midgut bacterial dynamics in Aedes aegypti

In vector mosquitoes, the presence of midgut bacteria may affect the ability to transmit pathogens. We have used a laboratory colony of Aedes aegypti as a model for bacterial interspecies competition and show that after a blood meal, the number of species (culturable on Luria-Bertani agar) that coexist in the midgut is low and that about 40% of the females do not harbor any cultivable bacteria. We isolated species belonging to the genera Bacillus, Elizabethkingia, Enterococcus, Klebsiella, Pantoea, Serratia, and Sphingomonas, and we also determined their growth rates, antibiotic resistance, and ex vivo inhibition of each other. To investigate the possible existence of coadaptation between midgut bacteria and their host, we fed Ae.?aegypti cohorts with gut bacteria from human, a frog, and two mosquito species and followed the bacterial population growth over time. The dynamics of the different species suggests coadaptation between host and bacteria, and interestingly, we found that Pantoea stewartii isolated from Ae.?aegypti survive better in Ae.?aegypti as compared to P.?stewartii isolated from the malaria mosquito Anopheles gambiae.     

Alternate unstable states: Convergent paths of succession in hydrocarbon-seep tubeworm-associated communities

Previous studies have shown clear, predictable successional trends in habitat characteristics and community structure in tubeworm aggregations at 3 similar hydrocarbon-seep sites on the central upper Louisiana slope of the Gulf of Mexico. In this study, we examine these trends in quantitative community collections from 7 additional hydrocarbon-seep sites widely distributed in the northern Gulf of Mexico. The relative proportions and sizes of Lamellibrachia luymesi and Seepiophila jonesi in tubeworm aggregations were similar at new and central sites, though S. jonesi dominated some collections from new sites, a situation not previously observed at central sites. In general, sulfide declined with increasing aggregation age (average size of tubeworms), but there was more variability in this trend at the new sites. Tubeworm-associated community composition was similar at new and central sites, with only a few rare species collected at the new sites for the first time. The most significant differences in the communities at new sites were the lower relative abundance of various gastropod species, and the absence of gastropods from collections made at the Viosca Knoll site. This community type was largely restricted to young aggregations at new sites that were more isolated from other tubeworm aggregations and consisted of higher proportions of S. jonesi. As succession proceeds from young to old aggregations, many of the previously described processes were apparent at the new sites including a reduction in biomass and a shift in trophic structure from endemic primary consumers to non-endemic higher order predators. Regardless of community composition in young aggregations, succession converges on similar late-stage community types.     

Development of a Two-Color Fluorescence In Situ Hybridization Technique for Species-Level Identification of Human-Infectious Cryptosporidium spp.

A two-color fluorescence in situ hybridization assay that allows for the simultaneous identification of Cryptosporidium parvum and C. hominis was developed. The assay is a simple, rapid, and cost-effective tool for the detection of the major Cryptosporidium species of concern to public health.Cryptosporidium (Apicomplexa) is a genus of protozoan parasites with species and genotypes that infect humans, domesticated livestock, companion animals, and wildlife worldwide (5, 6, 14, 15, 20, 23). The majority of cases of cryptosporidiosis in humans are caused by Cryptosporidium parvum or C. hominis (8, 10, 19, 24), although rare cases due to species such as C. meleagridis, C. felis, or C. canis have been reported (8, 9, 11-13, 17, 18, 22). The specific identification and characterization of Cryptosporidium species are central to the control of this disease in humans and a wide range of animals.One of the most widely adopted techniques for the identification of microorganisms in complex microbial communities is fluorescence in situ hybridization (FISH) using rRNA-targeted oligonucleotide probes (2-4). This method relies on the hybridization of synthetic oligonucleotide probes to specific regions within the rRNA of the organism. While FISH has been applied for the detection of Cryptosporidium oocysts in water samples (21), no FISH probes that successfully differentiate C. hominis from C. parvum have been reported.We have reported previously on the design of a species-specific probe, Cpar677, that detects C. parvum (1). In this study, we report on the design and validation of a C. hominis species-specific probe, Chom253. Together, the two probes were used here for the development of a two-color, microscopy-based FISH assay for the simultaneous detection of C. parvum and C. hominis.     

Rapid purification method for the 26S proteasome from the filamentous fungus Trichoderma reesei

We have developed a fast and simple two column chromatographic method for the purification of the 26S proteasome from the filamentous fungus Trichoderma reesei that simplifies the overall procedure and reduces the purification time from 5 to 2.5 days. The combination of only the anionic exchange POROS^® HQ column (Applied Biosystems) together with a size exclusion column has not been used previously for proteasome purification. The purified complex was analysed further by two-dimensional electrophoresis (2DE) and examined by transmission electron microscopy (TEM). A total of 102 spots separated by 2DE were identified by mass spectrometry using cross-species identification (CSI) or an in-house custom-made protein database derived from the T. reesei sequencing project. Fifty-one spots out of 102 represented unique proteins. Among them, 30 were from the 20S particle and eight were from the 19S particle. In addition, seven proteasome-interacting proteins as well as several non-proteasome related proteins were identified. Co-purification of the 19S regulatory particle was confirmed by TEM and Western blotting. The rapidity of the purification procedure and largely intact nature of the complex suggest that similar procedure may be applicable to the isolation and purification of the other protein complexes.     

Assessment of the partitioning capacity of high abundant proteins in human cerebrospinal fluid using affinity and immunoaffinity subtraction spin columns

The performance of three different affinity and immunoaffinity subtraction spin columns was investigated for the removal of the most abundant proteins in human cerebrospinal fluid (CSF). A pool of human CSF was processed with the spin columns and both the bound and flow through fractions were compared with each other and with intact CSF using 1D gel electrophoresis and nanoLC–MALDI-TOF/TOF-MS analysis. MASCOT MS/MS ionscores were compared before and after processing with the columns. The non-specific co-removal of proteins bound to the high abundant proteins, so called “sponge effect” was also examined for each spin column. The reproducibility of one of the spin columns, ProteomeLab IgY-12 proteome partitioning spin column, was further investigated by isobaric tags for relative and absolute quantification (iTRAQ) labeling and MS/MS analysis. Overall, 173 unique proteins were identified on a 95% MudPIT confidence scoring level. For all three spin columns, the number of proteins identified and their MASCOT scores were increased up to 10 times. The largest degree of non-specific protein removal was observed for a purely affinity based albumin removal column, where 28 other proteins also were present. The ProteomeLab IgY-12 proteome partitioning spin column showed very high reproducibility when combined with iTRAQ labeling and MS/MS analysis. The combined relative standard deviation (R.S.D.) for the high abundant protein removal, iTRAQ labeling and nanoLC–MALDI-TOF/TOF-MS analysis was less than 17.5%.     

Genetic diversity of Clostridium perfringens type A isolates from animals, food poisoning outbreaks and sludge

Background  

Clostridium perfringens, a serious pathogen, causes enteric diseases in domestic animals and food poisoning in humans. The epidemiological relationship between C. perfringens isolates from the same source has previously been investigated chiefly by pulsed-field gel electrophoresis (PFGE). In this study the genetic diversity of C. perfringens isolated from various animals, from food poisoning outbreaks and from sludge was investigated.     

Methodologic aspects of evaluating brush samples from biliary strictures by cytology and DNA flow cytometry

OBJECTIVE: To present a method of increasing the cell yield from brush samples of the biliary tree for measurement of DNA content by flow cytometry (FCM). STUDY DESIGN: One hundred eight cell specimens from 86 patients were studied by FCM for DNA ploidy and cell cycle composition. All specimens were cytologically classified into benign, suspicious for malignancy and malignant. Two methods for preparation of the cell material were compared. RESULTS: Enzymatic treatment of formalin-fixed brushes for release of cell nuclei was superior to mechanical removal of the cells. The fraction of samples not possible to assess was reduced from 27% to 4%, and good quality histograms increased from 21% to 62%. Aneuploidy was detected in 7% of benign and 57% of suspicious malignant samples. Using DNA analysis in addition to cytology as a diagnostic marker for cancer, the sensitivity increased from 12% to 31%. CONCLUSION: FCM of cells from biliary strictures can be used routinely as an adjunct to cytology for DNA analysis.