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.      

Study of the NADH and NADPH-ferredoxin oxidoreductase activities in Clostridium acetobutylicum]

The NADH and NADPH-ferredoxin oxidoreductase have been studied in Clostridium acetobutylicum. Acetyl-CoA is an obligatory activator of NADH-ferredoxin reductase activity and NADH a competitive inhibitor of ferredoxin-NAD+ reductase activity. These regulations are the same when C. acetoburylicum moves from 'butylic-type metabolism' to 'butyric-type metabolism'; this demonstrates that NADH-ferredoxin oxidoreductase cna, through its reversible action, meet the very different cell needs imposed by these two types of culture. The physiological function of the clostridial NADPH-ferredoxin oxidoreductase was anabolic as it has been with other clostridia.     

A randomized trial of cognitive rehabilitation in cancer survivors

Aims

The second most frequently reported post-treatment symptom in cancer survivors are concerns about impaired cognition. Despite numerous studies demonstrating significant impairments in a portion of survivors, information on effective treatments remains an emerging area of research. This study examined the effectiveness of a group-based cognitive rehabilitation intervention in cancer survivors.

Main methods

This study was a randomized, controlled study of a 7-week cognitive rehabilitation intervention delivered in group format. Participants were evaluated with subjective symptom questionnaires and objective neurocognitive tests prior to and following treatment.

Key findings

Twenty-eight participants (mean age 58 years) with a median of 3 years (± 6 years) post-primary/adjuvant treatment and various cancer sites (breast, bladder, prostate, colon, uterine) completed the study. Compared to baseline, the treatment group demonstrated improvements in symptoms of perceived cognitive impairments (p < .01), cognitive abilities (p < .01) and overall quality of life with regard to cognitive symptoms (p < .01) as measured by the FACT-Cog. The treatment group also improved on objective measures of attention (p < .05) and a trend toward improvement on verbal memory. Significant improvement was not observed on all cognitive tests.

Significance

A group based cognitive rehabilitation intervention in cancer survivors was effective for improving attention abilities and overall quality of life related to cognition. Results suggest that group based cognitive rehabilitation may be an effective intervention for treating cognitive dysfunction in cancer patients and should be further studied in a larger trial with an active control condition.     

Phenanthrene Emulsification and Biodegradation Using Rhamnolipid Biosurfactants and Acinetobacter calcoaceticus In Vitro

The ability of biosurfactants and Acinetobacter calcoaceticus to enhance the emulsification and biodegradation of phenanthrene was investigated. Phenanthrene is a polycyclic aromatic hydrocarbon that may be derived from various sources, for example incomplete combustion of petroleum fuel, and thus it occurs ubiquitously throughout the environment. In order to assess the efficacy of a biosurfactant microparticle system, emulsification assays and in vitro biodegradation studies were conducted. Emulsification assays were carried out to assess the stability of phenanthrene emulsions. Emulsion stability was determined by the height of the emulsion layer (Emulsification Index) and turbidity. In vitro biodegradation tests were done to estimate phenanthrene degradation from an aqueous system by A. calcoaceticus supplemented with encapsulated (ERhBS) and nonencapsulated biosurfactants (NERhBS). Results show that phenanthrene emulsifications were stabilized after 48 h with NERhBS and remained stable for 72 additional hours. Phenanthrene emulsifications were stabilized with ERhBS after 216 h and remained stable for an additional 96 h. A. calcoaceticus alone and supplemented with rhamnolipid biosurfactant were able to biodegrade 10 to 50 mg L^?1 of phenanthrene within 250 h. When supplemented with NERhBS, A. calcoaceticus degraded phenanthrene significantly faster than when nonsupplemented or supplemented with ERhBS. Addition of exogenous biosurfactants was considered to be a major factor driving the direct correlation between decreasing phenanthrene concentration in the system and increasing bacterial biomass.     

Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA

Escherichia coli and related bacteria require nickel for the synthesis of hydrogenases, enzymes involved in hydrogen oxidation and proton reduction. Nickel transport to the cytoplasm depends on five proteins, NikA-E. We have previously reported the three-dimensional structure of the soluble periplasmic nickel transporter NikA in a complex with FeEDTA(H 2O) (-). We have now determined the structure of EDTA-free NikA and have found that it binds a small organic molecule that contributes three ligands to the coordination of a transition metal ion. Unexpectedly, His416, which was far from the metal-binding site in the FeEDTA(H 2O) (-)-NikA complex, becomes the fourth observed ligand to the metal. The best match to the omit map electron density is obtained for butane-1,2,4-tricarboxylate (BTC). Our attempts to obtain a BTC-Ni-NikA complex using apo protein and commercial reagents resulted in nickel-free BTC-NikA. Overall, our results suggest that nickel transport in vivo requires a specific metallophore that may be BTC.     

Low ratios of silica to dissolved nitrogen supplied to rivers arise from agriculture not reservoirs

Coastal marine systems are greatly altered by toxic marine algae, eutrophication and hypoxia. These problems have been linked to decreased ratios of dissolved silica to inorganic nitrogen (Si : DIN) delivered from land. Two mechanisms for this decline under consideration are enhanced nitrogen (N) fertiliser losses from agricultural lands or Si sequestration in reservoirs. Here we examine these mechanisms via nutrient concentrations in impoundments receiving water from 130 watersheds in a landscape representative of the agriculture that often dominates coastal nutrient inputs. Decreased Si : DIN was correlated with agriculture, not impoundment. Watersheds with > 60% agricultural land yielded highest DIN, whereas Si was uncorrelated with agricultural intensity. Furthermore, eutrophic lakes were dominated by Cyanobacteria that use little Si, so reservoirs did not diminish Si : DIN. Instead, Si : DIN increased slightly as reservoir residence time increased. These data suggest that impoundments in agricultural watersheds may enhance the water quality of coastal ecosystems, whereas fertiliser losses are detrimental.     

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.