mtDNA diversity in rhesus monkeys reveals overestimates of divergence time and paraphyly with neighboring species

Reconstructions of the human-African great ape phylogeny by using mitochondrial DNA (mtDNA) have been subject to considerable debate. One confounding factor may be the lack of data on intraspecific variation. To test this hypothesis, we examined the effect of intraspecific mtDNA diversity on the phylogenetic reconstruction of another Plio- Pleistocene radiation of higher primates, the fascicularis group of macaque (Macaca) monkey species. Fifteen endonucleases were used to identify 10 haplotypes of 40-47 restriction sites in M. mulatta, which were compared with similar data for the other members of this species group. Interpopulational, intraspecific mtDNA diversity was large (0.5%- 4.5%), and estimates of divergence time and branching order incorporating this variation were substantially different from those based on single representatives of each species. We conclude that intraspecific mtDNA diversity is substantial in at least some primate species. Consequently, without prior information on the extent of genetic diversity within a particular species, intraspecific variation must be assessed and accounted for when reconstructing primate phylogenies. Further, we question the reliability of hominoid mtDNA phylogenies, based as they are on one or a few representatives of each species, in an already depauperate superfamily of primates.      

A novel bacterium carrying out anaerobic ammonium oxidation in a reactor for biological treatment of the filtrate of wastewater fermented sludge

A new genus and species of bacteria capable of ammonium oxidation under anaerobic conditions in the presence of nitrite is described. The enrichment culture was obtained from the Moscow River silt by sequential cultivation in reactors with selective conditions for anaerobic ammonium oxidation. Bacterial cells were coccoid, ～0.4 × 0.7 μm, with the intracellular membrane structures typical of bacteria capable of anaerobic ammonium oxidation (anammoxosome and paryphoplasm). The cells formed aggregates 5–25 μm in diameter (10 μm on average). They were readily adhered to solid surfaces. The cells were morphologically labile: they easily lost their content and changed their morphology during fixation for electron microscopy. The organism was capable of ammonium oxidation with nitrite. The semisaturation constants Ks for nitrite and ammonium were 0.38 mg N-NO₂/L and 0.41 mg N-NH₄/L, respectively. The maximal nitrite concentrations for growth were 90 and 75 mg N-NO₂/L for single and continuous application, respectively. The doubling time was 32 days, μ_max = 0.022 day^?1, the optimal temperature and pH were 20°C and 7.8–8.3, respectively. According to the results of 16S rRNA gene sequencing, the bacterium was assigned to a new genus and species within the phylum Planctomycetes. The proposed name for the new bacterium is Candidatus Anammoximicrobium moscowii gen. nov., sp. nov. (a microorganism carrying out anaerobic ammonium oxidation, isolated in the Moscow region).     

Growth of mesophilic methanotrophs at low temperatures

The optimal growth of mesophilic methanotrophic bacteria (collection strains of the genera Methylocystis, Methylomonas, Methylosinus, and Methylobacter) occurred within temperature ranges of 31-34 degrees C and 23-25 degrees C. None of the strains studied were able to grow at 1.5 or 4 degrees C. Representatives of six methanotrophic species (strains Mcs. echinoides 2, Mm. methanica 12, Mb. bovis 89, Mcs. pyriformis 14, Mb. chroococcum 90, and Mb. vinelandii 87) could grow at 10 degrees C (with a low specific growth rate). The results obtained suggest that some mesophilic methane-oxidizing bacteria display psychrotolerant (psychrotrophic) but not psychrophilic properties. In general, the Rosso model, which describes bacterial growth rate as a function of temperature, fits well the experimental data, although, for most methanotrophs, with symmetrical approximations for optimal temperature.     

An invisible ubiquitin conformation is required for efficient phosphorylation by PINK1

The Ser/Thr protein kinase PINK1 phosphorylates the well‐folded, globular protein ubiquitin (Ub) at a relatively protected site, Ser65. We previously showed that Ser65 phosphorylation results in a conformational change in which Ub adopts a dynamic equilibrium between the known, common Ub conformation and a distinct, second conformation wherein the last β‐strand is retracted to extend the Ser65 loop and shorten the C‐terminal tail. We show using chemical exchange saturation transfer (CEST) nuclear magnetic resonance experiments that a similar, C‐terminally retracted (Ub‐CR) conformation also exists at low population in wild‐type Ub. Point mutations in the moving β5 and neighbouring β‐strands shift the Ub/Ub‐CR equilibrium. This enabled functional studies of the two states, and we show that while the Ub‐CR conformation is defective for conjugation, it demonstrates improved binding to PINK1 through its extended Ser65 loop, and is a superior PINK1 substrate. Together our data suggest that PINK1 utilises a lowly populated yet more suitable Ub‐CR conformation of Ub for efficient phosphorylation. Our findings could be relevant for many kinases that phosphorylate residues in folded protein domains.     

From recommendation to action: psychosocial factors influencing physician intention to use Health Technology Assessment (HTA) recommendations

Background

The Evidence-Based Practice (EBP) Project has been investigating the implementation of evidence-based mental health practices (Assertive Community Treatment, Family Psychoeducation, Integrated Dual Diagnosis Treatment, Illness Management and Recovery, and Supported Employment) in state public mental health systems in the United States since 2001. To date, Project findings have yielded valuable insights into implementation strategy characteristics and effectiveness. This paper reports results of an effort to identify and classify state-level implementation activities and strategies employed across the eight states participating in the Project.

Methods

Content analysis and Greenhalgh et al's (2004) definition of innovation were used to identify and classify state-level activities employed during three phases of EBP implementation: Pre-Implementation, Initial Implementation and Sustainability Planning. Activities were coded from site visit reports created from documents and notes from key informant interviews conducted during two periods, Fall 2002 – Spring 2003, and Spring 2004. Frequency counts and rank-order analyses were used to examine patterns of implementation activities and strategies employed across the three phases of implementation.

Results

One hundred and six discreet implementation activities and strategies were identified as innovative and were classified into five categories: 1) state infrastructure building and commitment, 2) stakeholder relationship building and communications, 3) financing, 4) continuous quality management, and 5) service delivery practices and training. Implementation activities from different categories were employed at different phases of implementation.

Conclusion

Insights into effective strategies for implementing EBPs in mental health and other health sectors require qualitative and quantitative research that seeks to: a) empirically test the effects of tools and methods used to implement EBPs, and b) establish a stronger evidence-base from which to plan, implement and sustain such efforts. This paper offers a classification scheme and list of innovative implementation activities and strategies. The classification scheme offers potential value for future studies that seek to assess the effects of various implementation processes, and helps establish widely accepted standards and criteria that can be used to assess the value of innovative activities and strategies.     

PARTAKE Survey of Public Knowledge and Perceptions of Clinical Research in India

Background

A public that is an informed partner in clinical research is important for ethical, methodological, and operational reasons. There are indications that the public is unaware or misinformed, and not sufficiently engaged in clinical research but studies on the topic are lacking. PARTAKE – Public Awareness of Research for Therapeutic Advancements through Knowledge and Empowerment is a program aimed at increasing public awareness and partnership in clinical research. The PARTAKE Survey is a component of the program.

Objective

To study public knowledge and perceptions of clinical research.

Methods

A 40-item questionnaire combining multiple-choice and open-ended questions was administered to 175 English- or Hindi-speaking individuals in 8 public locations representing various socioeconomic strata in New Delhi, India.

Results

Interviewees were 18–84 old (mean: 39.6, SD±16.6), 23.6% female, 68.6% employed, 7.3% illiterate, 26.3% had heard of research, 2.9% had participated and 58.9% expressed willingness to participate in clinical research. The following perceptions were reported (% true/% false/% not aware): ‘research benefits society’ (94.1%/3.5%/2.3%), ‘the government protects against unethical clinical research’ (56.7%/26.3%/16.9%), ‘research hospitals provide better care’ (67.2%/8.7%/23.9%), ‘confidentiality is adequately protected’ (54.1%/12.3%/33.5%), ‘participation in research is voluntary’ (85.3%/5.8%/8.7%); ‘participants treated like ‘guinea pigs’’ (20.7%/53.2%/26.0%), and ‘compensation for participation is adequate’ (24.7%/12.9%/62.3%).

Conclusions

Results suggest the Indian public is aware of some key features of clinical research (e.g., purpose, value, voluntary nature of participation), and supports clinical research in general but is unaware of other key features (e.g., compensation, confidentiality, protection of human participants) and exhibits some distrust in the conduct and reporting of clinical trials. Larger, cross-cultural surveys are required to inform educational programs addressing these issues.     

Approaches to cultivation of “nonculturable” bacteria: Cyclic cultures

The work deals with more efficient procedures for the isolation and cultivation of “nonculturable” microorganisms (NM) from environmental sources. The techniques for NM cultivation in situ and under laboratory conditions are discussed. A new approach is considered, viz., cultivation under cyclically varying conditions with the cycle duration comparable to the duration of the cell cycle. Cyclic cultivation implies sequential changes of several cultivation phases with different growth conditions. An established sequence of growth phases provides for the competitiveness of the target microorganisms and for accumulation of their biomass. Cultivation of phosphate-accumulating bacteria, nonculturable microorganisms which have not been previously isolated in pure culture, in an SBR reactor is discussed as an example of cyclic cultures.     

Methane Oxidation in Landfill Cover Soil

Methane oxidation in the cover soil of the Khmet'evo municipal landfill in Moscow oblast was investigated. Methane emission from the experimental site of the landfill was highly heterogeneous. At a depth of 45–60 cm, the pore gas mainly consisted of CH₄ (60–70%) and CO₂ (30–40%). In the upper layers of the cover soil, the concentration of these gases sharply decreased. Methods for estimation of the methane-oxidizing activity in the cover soil of the landfill were tested. The rate of methane oxidation in the soil correlated with the cell number of culturable methanotrophic bacteria and was the factor limiting methane emission from the surface of the landfill. The method of indirect immunofluorescence revealed ten known species of methanotrophic bacteria in enrichment cultures obtained from samples of the cover soil. Our results also indicate the presence of unknown psychrotolerant methanotrophs that are active at the low temperatures characteristic of Moscow oblast.     

Dynamics of the composition of a microbial consortium during start-up of a single-stage constant flow laboratory nitritation/anammox setup

Dynamics of the composition of the microbial community was studied during start-up of a single-stage completely mixed constant flow laboratory setup for ammonium removal by the nitritation/anammox process from the filtrate of digested sludge of the Kuryanovo wastewater treatment plant (KWTP), Moscow. To decrease the period of the start-up, the setup was initially inoculated with two types of activated sludge (nitrifying sludge from a KWTP aeration tank and sludge from a sequencing batch reactor enriched with anammox bacteria). The start-up and adjustment stage was therefore decreased to 35–40 days, and nitrogen removal efficiency reached 80% after 120 days of the setup operation. Taxonomic analysis of the composition of the microbial community was carried out by pyrosequencing of the 16S rRNA fragments obtained using the universal and planctomycetes-specific primers. In the course of adaptation of activated sludge to increasing nitrogen load, microbial community of the setup became less diverse and more specialized. The contribution of anammox bacteria of the family Brocadiaceae, closely related to Candidatus “Brocadia caroliniensis,” increased gradually. Members of the order Nitrosomonadales were involved in ammonium oxidation to nitrite. While nitrite-oxidizing bacteria of the genus Nitrospira were also detected, their share decreased with accumulation of the activated sludge. The contribution of other bacteria varied as well: the shares of the phyla Ignavibacteria, Chloroflexi, and Acidobacteria increased significantly (up to 13, 12, and 10%, respectively of the total number of reads), while relative abundance of the Proteobacteria, Bacteroidetes, Actinobacteria, Firmicutes, Synergistetes, Aminicenantes, Thermotogae, and Cloacimonetes decreased. Thus, application of pyrosequencing made it possible to monitor succession of the bacterial community involved in nitrogen removal by nitritation/anammox process.