Do Iron Curtains Happen More than Once?

Two separations significant for World Christendom commemorated their 50th birthdays on 13 August: the construction of the Berlin Wall and the splitting up of the “All-Union Council of Evangelical Christians-Baptists”. On 18 August, in one of two major Russian-language commentaries on the second event, Moscow’s Mikhail Cherenkov celebrated in the news service “Protestant” the maverick and courageous spirit of the underground, “Initiativniki” Baptist movement. He described them as a “mighty spiritual” and “radical reformist” movement and exclaimed: No one could have expected that an “anti-church directive” put out by the All-Union Council could “invoke such massive resistance on the local-church level”. Who would have reckoned that “simple, uneducated, inexperienced pastors from the most remote of provinces could organise a resistance movement capable of engulfing the entire Soviet Union?” Cherenkov compares its martyrs to the early church fathers who died with “For Christ alone!” on their lips. The Initiativniki were in any case also part of the “down with Moscow” sentiment still alive in the wide expanses of Russia. The author also compares three of Moscow’s newest Baptist congregations. Finally, he discusses the rehabilitation of large numbers of addicts by Protestant churches in Russia

Biofilm Associated Staphylococcus Aureus Viability is Altered By Burkholderia Cenocepacia

Respiratory failure caused by chronic and recurrent microbial infections is the most common cause of death for people with cystic fibrosis (CF)1, a disease causing the formation of thick mucus in the lungs2. Most bacteria can form biofilms, collections of sessile cells adhered to a surface by a secreted substance. Biofilm-associated cells develop antibiotic resistance at higher rates3. The thicker mucus in CF lungs is extremely difficult to clear via action of the mucociliary escalator and its presence fosters the formation of bacterial biofilms. Staphylococcus aureus and Burkholderia cenocepacia are two pathogens commonly found in the CF lung. Previous work in the Yoder-Himes laboratory established an antagonistic relationship between members of the B. cepacia complex and S. aureus biofilms4. To understand this antagonism, it is crucial to identify the biofilm changes occurring when S. aureus and B. cenocepacia interact. This work provides insight into the changes that may be responsible for the reduced viability of S. aureus in biofilms. Using crystal violet to measure biofilm biomass, confocal laser scanning microscopy, and assessing differences in antibiotic susceptibility, S. aureus and B. cenocepacia were examined in both monoculture and co-culture conditions. The results of this experiment indicate S. aureus and B. cenocepacia biofilm formation increases over time and is greater in nutrient-rich media. Additionally, B. cenocepacia inhibits biofilm formation of S. aureus. These findings provide information that can be used for understanding the interactions between pathogenic bacteria in the lungs of CF patients, leading to the development of more effective therapeutics.https://ir.library.louisville.edu/uars/1038/thumbnail.jp

Development and quantitative analyses of a universal rRNA-subtraction protocol for microbial metatranscriptomics

Metatranscriptomes generated by pyrosequencing hold significant potential for describing functional processes in complex microbial communities. Meeting this potential requires protocols that maximize mRNA recovery by reducing the relative abundance of ribosomal RNA, as well as systematic comparisons to identify methodological artifacts and test for reproducibility across data sets. Here, we implement a protocol for subtractive hybridization of bacterial rRNA (16S and 23S) that uses sample-specific probes and is applicable across diverse environmental samples. To test this method, rRNA-subtracted and unsubtracted transcriptomes were sequenced (454 FLX technology) from bacterioplankton communities at two depths in the oligotrophic open ocean, yielding 10 data sets representing ~350 Mbp. Subtractive hybridization reduced bacterial rRNA transcript abundance by 40–58%, increasing recovery of non-rRNA sequences up to fourfold (from 12% to 20% of total sequences to 40–49%). In testing this method, we established criteria for detecting sequences replicated artificially via pyrosequencing errors and identified such replicates as a significant component (6–39%) of total pyrosequencing reads. Following replicate removal, statistical comparisons of reference genes (identified via BLASTX to NCBI-nr) between technical replicates and between rRNA-subtracted and unsubtracted samples showed low levels of differential transcript abundance (<0.2% of reference genes). However, gene overlap between data sets was remarkably low, with no two data sets (including duplicate runs from the same pyrosequencing library template) sharing greater than 17% of unique reference genes. These results indicate that pyrosequencing captures a small subset of total mRNA diversity and underscores the importance of reliable rRNA subtraction procedures to enhance sequencing coverage across the functional transcript pool.Agouron InstituteGordon and Betty Moore FoundationUnited States. Dept. of Energy. Office of ScienceNational Science Foundation (U.S.) (NSF Science and Technology Center Award EF0424599

Chameleon radiation by oceanic dispersal

Historical biogeography is dominated by vicariance methods that search for a congruent pattern of fragmentation of ancestral distributions produced by shared Earth history(1-3). A focus of vicariant studies has been austral area relationships and the break-up of the supercontinent Gondwana(3-5). Chameleons are one of the few extant terrestrial vertebrates thought to have biogeographic patterns that are congruent with the Gondwanan break-up of Madagascar and Africa(6,7). Here we show, using molecular and morphological evidence for 52 chameleon taxa, support for a phylogeny and area cladogram that does not fit a simple vicariant history. Oceanic dispersal-not Gondwanan breakup-facilitated species radiation, and the most parsimonious biogeographic hypothesis supports a Madagascan origin for chameleons, with multiple 'out-of-Madagascar' dispersal events to Africa, the Seychelles, the Comoros archipelago, and possibly Reunion Island. Although dispersal is evident in other Indian Ocean terrestrial animal groups(8-16), our study finds substantial out-of-Madagascar species radiation, and further highlights the importance of oceanic dispersal as a potential precursor for speciation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62614/1/415784a.pd

Significance of Cuscutain, a cysteine protease from Cuscuta reflexa, in host-parasite interactions

<p>Abstract</p> <p>Background</p> <p>Plant infestation with parasitic weeds like <it>Cuscuta reflexa </it>induces morphological as well as biochemical changes in the host and the parasite. These modifications could be caused by a change in protein or gene activity. Using a comparative macroarray approach <it>Cuscuta </it>genes specifically upregulated at the host attachment site were identified.</p> <p>Results</p> <p>One of the infestation specific <it>Cuscuta </it>genes encodes a cysteine protease. The protein and its intrinsic inhibitory peptide were heterologously expressed, purified and biochemically characterized. The haustoria specific enzyme was named cuscutain in accordance with similar proteins from other plants, e.g. papaya. The role of cuscutain and its inhibitor during the host parasite interaction was studied by external application of an inhibitor suspension, which induced a significant reduction of successful infection events.</p> <p>Conclusions</p> <p>The study provides new information about molecular events during the parasitic plant - host interaction. Inhibition of cuscutain cysteine proteinase could provide means for antagonizing parasitic plants.</p

A resampling-based meta-analysis for detection of differential gene expression in breast cancer

<p>Abstract</p> <p>Background</p> <p>Accuracy in the diagnosis of breast cancer and classification of cancer subtypes has improved over the years with the development of well-established immunohistopathological criteria. More recently, diagnostic gene-sets at the mRNA expression level have been tested as better predictors of disease state. However, breast cancer is heterogeneous in nature; thus extraction of differentially expressed gene-sets that stably distinguish normal tissue from various pathologies poses challenges. Meta-analysis of high-throughput expression data using a collection of statistical methodologies leads to the identification of robust tumor gene expression signatures.</p> <p>Methods</p> <p>A resampling-based meta-analysis strategy, which involves the use of resampling and application of distribution statistics in combination to assess the degree of significance in differential expression between sample classes, was developed. Two independent microarray datasets that contain normal breast, invasive ductal carcinoma (IDC), and invasive lobular carcinoma (ILC) samples were used for the meta-analysis. Expression of the genes, selected from the gene list for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes were tested on 10 independent primary IDC samples and matched non-tumor controls by real-time qRT-PCR. Other existing breast cancer microarray datasets were used in support of the resampling-based meta-analysis.</p> <p>Results</p> <p>The two independent microarray studies were found to be comparable, although differing in their experimental methodologies (Pearson correlation coefficient, R = 0.9389 and R = 0.8465 for ductal and lobular samples, respectively). The resampling-based meta-analysis has led to the identification of a highly stable set of genes for classification of normal breast samples and breast tumors encompassing both the ILC and IDC subtypes. The expression results of the selected genes obtained through real-time qRT-PCR supported the meta-analysis results.</p> <p>Conclusion</p> <p>The proposed meta-analysis approach has the ability to detect a set of differentially expressed genes with the least amount of within-group variability, thus providing highly stable gene lists for class prediction. Increased statistical power and stringent filtering criteria used in the present study also make identification of novel candidate genes possible and may provide further insight to improve our understanding of breast cancer development.</p

Socio-economic differences and health seeking behaviour for the diagnosis and treatment of malaria: a case study of four local government areas operating the Bamako initiative programme in south-east Nigeria

BACKGROUND: Malaria is one of the leading causes of mortality and morbidity in Nigeria. It is not known how user fees introduced under the Bamako Initiative (BI) system affect healthcare seeking among different socio-economic groups in Nigeria for diagnosis and treatment of malaria. Reliable information is needed to initiate new policy thrusts to protect the poor from the adverse effect of user fees. METHODS: Structured questionnaires were used to collect information from 1594 female household primary care givers or household head on their socio-economic and demographic status and use of malaria diagnosis and treatment services. Principal components analysis was used to create a socio-economic status index which was decomposed into quartiles and chi-square for trends was used to calculate for any statistical difference. RESULTS: The study showed that self diagnosis was the commonest form of diagnosis by the respondents. This was followed by diagnosis through laboratory tests, community health workers, family members and traditional healers. The initial choice of care for malaria was a visit to the patent medicine dealers for most respondents. This was followed by visit to the government hospitals, the BI health centres, traditional medicine healers, private clinics, community health workers and does nothing at home. Furthermore, the private health facilities were the initial choice of treatment for the majority with a decline among those choosing them as a second source of care and an increase in the utilization of public health facilities as a second choice of care. Self diagnosis was practiced more by the poorer households while the least poor used the patent medicine dealers and community health workers less often for diagnosis of malaria. The least poor groups had a higher probability of seeking treatment at the BI health centres (creating equity problem in BI), hospitals, and private clinics and in using laboratory procedures. The least poor also used the patent medicine dealers and community health workers less often for the treatment of malaria. The richer households complained more about poor staff attitude and lack of drugs as their reasons for not attending the BI health centres. The factors that encourage people to use services in BI health centres were availability of good services, proximity of the centres to the homes and polite health workers. CONCLUSIONS: Factors deterring people from using BI centres should be eliminated. The use of laboratory services for the diagnosis of malaria by the poor should be encouraged through appropriate information, education and communication which at the long run will be more cost effective and cost saving for them while devising means of reducing the equity gap created. This could be done by granting a properly worked out and implemented fee exemptions to the poor or completely abolishing user fees for the diagnosis and treatment of malaria in BI health centres

Episodic Evolution and Adaptation of Chloroplast Genomes in Ancestral Grasses

It has been suggested that the chloroplast genomes of the grass family, Poaceae, have undergone an elevated evolutionary rate compared to most other angiosperms, yet the details of this phenomenon have remained obscure. To know how the rate change occurred during evolution, estimation of the time-scale with reliable calibrations is needed. The recent finding of 65 Ma grass phytoliths in Cretaceous dinosaur coprolites places the diversification of the grasses to the Cretaceous period, and provides a reliable calibration in studying the tempo and mode of grass chloroplast evolution.By using chloroplast genome data from angiosperms and by taking account of new paleontological evidence, we now show that episodic rate acceleration both in terms of non-synonymous and synonymous substitutions occurred in the common ancestral branch of the core Poaceae (a group formed by rice, wheat, maize, and their allies) accompanied by adaptive evolution in several chloroplast proteins, while the rate reverted to the slow rate typical of most monocot species in the terminal branches.Our finding of episodic rate acceleration in the ancestral grasses accompanied by adaptive molecular evolution has a profound bearing on the evolution of grasses, which form a highly successful group of plants. The widely used model for estimating divergence times was based on the assumption of correlated rates between ancestral and descendant lineages. However, the assumption is proved to be inadequate in approximating the episodic rate acceleration in the ancestral grasses, and the assumption of independent rates is more appropriate. This finding has implications for studies of molecular evolutionary rates and time-scale of evolution in other groups of organisms

The Formation of Collective Silk Balls in the Spider Mite Tetranychus urticae Koch

Tetranychus urticae is a phytophagous mite that forms colonies of several thousand individuals. These mites construct a common web to protect the colony. When plants become overcrowded and food resources become scarce, individuals gather at the plant apex to form a ball composed of mites and their silk threads. This ball is a structure facilitating group dispersal by wind or animal transport. Until now, no quantitative study had been done on this collective form of migration. This is the first attempt to understand the mechanisms that underlie the emergence and growth of the ball. We studied this collective behaviour under laboratory conditions on standardized infested plants. Our results show that the collective displacement and the formation of balls result from a recruitment process: by depositing silk threads on their way up to the plant apex, mites favour and amplify the recruitment toward the balls. A critical threshold (quorum response) in the cumulative flow of mites must be reached to observe the emergence of a ball. At the beginning of the balls formation, mites form an aggregate. After 24 hours, the aggregated mites are trapped inside the silk balls by the complex network of silk threads and finally die, except for recently arrived individuals. The balls are mainly composed of immature stages. Our study reconstructs the key events that lead to the formation of silk balls. They suggest that the interplay between mites' density, plant morphology and plant density lead to different modes of dispersions (individual or collective) and under what conditions populations might adopt a collective strategy rather than one that is individually oriented. Moreover, our results lead to discuss two aspects of the cooperation and altruism: the importance of Allee effects during colonization of new plants and the importance of the size of a founding group

The role of unintegrated DNA in HIV infection

Integration of the reverse transcribed viral genome into host chromatin is the hallmark of retroviral replication. Yet, during natural HIV infection, various unintegrated viral DNA forms exist in abundance. Though linear viral cDNA is the precursor to an integrated provirus, increasing evidence suggests that transcription and translation of unintegrated DNAs prior to integration may aid productive infection through the expression of early viral genes. Additionally, unintegrated DNA has the capacity to result in preintegration latency, or to be rescued and yield productive infection and so unintegrated DNA, in some circumstances, may be considered to be a viral reservoir. Recently, there has been interest in further defining the role and function of unintegrated viral DNAs, in part because the use of anti-HIV integrase inhibitors leads to an abundance of unintegrated DNA, but also because of the potential use of non-integrating lentiviral vectors in gene therapy and vaccines. There is now increased understanding that unintegrated viral DNA can either arise from, or be degraded through, interactions with host DNA repair enzymes that may represent a form of host antiviral defence. This review focuses on the role of unintegrated DNA in HIV infection and additionally considers the potential implications for antiviral therapy