Optimization of pyrite bioleaching using Sulfolobus acidocaldarius

Optimization of batch pyrite bioleaching with Sulfolobus acidocaldarius was performed using statistical modelling and experimental design. First a screening design was made followed by response surface modelling. The dominating factors identified were pH, pulp density and particle size. The highest batch leaching rate after optimization was 270 mg iron·l^–1·h^–1 for 6% (w/v) pulp density, pH = 1.5 and particle size <20 m. This represents a 3.5-fold increase from the leaching rate of 80 mg iron·l^–1·h^–1 obtained under our standard laboratory conditions. Correspondence to: E. B. Lindström     

WEBnm@: a web application for normal mode analyses of proteins

Background  

Normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channels or virus capsids. NMA relies on the hypothesis that the vibrational normal modes having the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant.     

Typical Danish Caucasian type 2 diabetic patients do not commonly carry genetic variants in GIP and GLP-1 encoding regions of the proGIP and proglucagon genes

BACKGROUND: The enteroinsular-axis is abnormal in type 2 diabetics, which contributes to the diabetic phenotype. The effect of the incretin hormone gastric inhibitory polypeptide (GIP) and the secretion of the incretin hormone glucagon-like peptide-1 (GLP-1) are thus greatly diminished. The explanation for these changes could be changes in the structure of either of the hormones or their receptors. Thus, the aim of this study was to study the occurrence of genetic variants in the GIP and GLP-1 encoding regions of the proGIP and proglucagon genes in type 2 diabetic patients and matched control subjects. METHODS AND RESULTS: Genomic DNA was extracted from buffy coats from 12 Caucasian type 2 diabetics and 12 healthy subjects, matched with respect to sex, age and BMI. The GIP and GLP-1 sequences were amplified using specific primers using the polymerase chain reaction (PCR). The amplified products were then sequenced. No germ-line mutations were identified in the GIP and the GLP-1 encoding regions of the proGIP and proglucagon genes in either the type 2 diabetic or the control subjects. CONCLUSIONS: The perturbed incretin effect in type 2 diabetics is not commonly caused by genetic variants in either the GIP or the GLP-1 encoding genes in type 2 diabetics.     

Exercise Training and Weight Gain in Obese Pregnant Women: A Randomized Controlled Trial (ETIP Trial)

BackgroundThe effectiveness of exercise training for preventing excessive gestational weight gain (GWG) and gestational diabetes mellitus (GDM) is still uncertain. As maternal obesity is associated with both GWG and GDM, there is a special need to assess whether prenatal exercise training programs provided to obese women reduce the risk of adverse pregnancy outcomes. Our primary aim was to assess whether regular supervised exercise training in pregnancy could reduce GWG in women with prepregnancy overweight/obesity. Secondary aims were to examine the effects of exercise in pregnancy on 30 outcomes including GDM incidence, blood pressure, blood measurements, skinfold thickness, and body composition.ConclusionsIn this trial we did not observe a reduction in GWG among overweight/obese women who received a supervised exercise training program during their pregnancy. The incidence of GDM in late pregnancy seemed to be lower in the women randomized to exercise training than in the women receiving standard maternity care only. Systolic blood pressure in late pregnancy was also apparently lower in the exercise group than in the control group. These results indicate that supervised exercise training might be beneficial as a part of standard pregnancy care for overweight/obese women.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01243554","term_id":"NCT01243554"}}NCT01243554     

High Prevalence,Coinfection Rate,and Genetic Diversity of Retroviruses in Wild Red Colobus Monkeys (Piliocolobus badius badius) in Ta? National Park,C?te d'Ivoire

Simian retroviruses are precursors of all human retroviral pathogens. However, little is known about the prevalence and coinfection rates or the genetic diversity of major retroviruses—simian immunodeficiency virus (SIV), simian T-cell lymphotropic virus type 1 (STLV-1), and simian foamy virus (SFV)—in wild populations of nonhuman primates. Such information would contribute to the understanding of the natural history of retroviruses in various host species. Here, we estimate these parameters for wild West African red colobus monkeys (Piliocolobus badius badius) in the Taï National Park, Côte d''Ivoire. We collected samples from a total of 54 red colobus monkeys; samples consisted of blood and/or internal organs from 22 monkeys and additionally muscle and other tissue samples from another 32 monkeys. PCR analyses revealed a high prevalence of SIV, STLV-1, and SFV in this population, with rates of 82%, 50%, and 86%, respectively. Forty-five percent of the monkeys were coinfected with all three viruses while another 32% were coinfected with SIV in combination with either STLV or SFV. As expected, phylogenetic analyses showed a host-specific pattern for SIV and SFV strains. In contrast, STLV-1 strains appeared to be distributed in genetically distinct and distant clades, which are unique to the Taï forest and include strains previously described from wild chimpanzees in the same area. The high prevalence of all three retroviral infections in P. b. badius represents a source of infection to chimpanzees and possibly to humans, who hunt them.Lentiviruses and deltaretroviruses that infect African nonhuman primates have received considerable attention as they are the precursors of all pathogenic human retroviruses: human immunodeficiency virus types 1 and 2 (HIV-1/HIV-2) and human T-cell lymphotropic virus type 1 (HTLV-1). These human infections are the results of past zoonotic transfers of simian immunodeficiency virus (SIV) and simian T-cell lymphotropic viruses type 1 (STLV-1) from wild monkeys and apes into local human populations, presumably through primate hunting and handling of primate bushmeat (13, 19, 43, 46, 55, 58, 59). Via the same route, zoonotic transmission of simian foamy virus (SFV), a spumaretrovirus whose exact pathogenicity in human hosts is still unknown, has also been shown (64). The increasing contact between humans and wild primates implies that further zoonotic transmission of retroviruses is likely to happen (42, 63). Studying the occurrence and circulation of simian retroviruses such as SIV, STLV-1, and SFV in wild primate populations enables us to better understand retrovirus evolution in primates and also provides tools for monitoring possible future retroviral zoonotic events.Systematic studies of SIV, STLV-1, and SFV in wild primates are relatively rare. Many use bushmeat samples, which can vary in their quality and are prone to cross-contamination from butchering and storage with other carcasses. Confiscated primates are also not representative of the situation in the wild since the animals are caught at a young age when the occurrence of different retroviruses may be extremely low (24). The technical possibilities for the detection of various pathogens in noninvasive samples such as urine and feces have greatly improved and are frequently used; however, in general, the sensitivity of detection methods is higher when blood and tissue samples are used (25, 32, 47). Such samples can be collected if fresh carcasses are found, or they can be collected by anesthetizing live primates for sampling purpose, animal translocation, or medical intervention, such as snare removal. The practical and ethical issues of each of the sampling methods have been discussed elsewhere (12, 14).Red colobus monkeys [Procolobus (Piliocolobus)] are interesting subjects for retroviral infection studies for a number of reasons. First, they are widely distributed (yet in a fragmented manner) from East to West Africa, which suggests that red colobus species and subspecies, or more likely ancestor(s) of these, could have been key hosts in transmitting retroviruses across tropical Africa (4, 54). Second, as they are herbivore primates, the hunting of other primates can be excluded as a route of infection. Finally, these monkeys are frequently hunted by humans and chimpanzees and represent a possibly large reservoir for retroviruses and other pathogens that ought to be investigated further (2, 45).Very little information is available about the prevalence and coinfection of SIV, STLV-1, and SFV in wild red colobus monkeys across Africa. In other colobine monkeys only SIV has been documented: in olive colobus (Procolobus verus) in Côte d''Ivoire and in black and white colobus (Colobus guereza) in Cameroon (7, 8). Based on fecal samples from habituated adult individuals, the prevalence of SIV in West African red colobus monkeys (SIVwrc; local subspecies, Piliocolobus badius badius) has been estimated to a minimum of 26% in the Taï National Park, Côte d''Ivoire, but the authors recognized the low sensitivity of viral RNA detection in fecal samples (34). Another study conducted on the same population revealed that 5 out of 10 blood samples were SIV positive (7). These results highlight that the most reliable prevalence data are based on analyses of blood/tissue samples although such sampling is not always feasible for reasons discussed above. Published prevalence information concerning STLV-1 and SFV in wild red colobus monkeys (STLV-1wrc and SFVwrc) in the same area is restricted to results obtained from analyses of a limited number of blood and necropsy samples collected as a part of studies whose focus was on cross-species transmission of these two viruses to chimpanzees (27, 28). However, these samples indicated a high prevalence of STLV-1wrc and SFVwrc in the red colobus monkey population (56% and 90%, respectively). A recent study from Uganda, East Africa, estimated the prevalence of SIV, STLV-1, and SFV in another red colobus species (Piliocolobus rufomitratus tephrosceles) to be 22.6%, 6.4%, and 97%, respectively (15). The study was performed using blood samples collected from anesthetized wild red colobus monkeys living in their natural habitat, which allowed reliable assessment of the prevalence and genetic diversity of these three retroviruses.The preliminary data from the Taï National Park indicate that there might be great variation in the prevalence of retroviruses across the African continent, even in closely related species of wild primates. Here, we aimed at generating reliable prevalence and coinfection data for SIVwrc, STLV-1wrc, and SFVwrc based on the analysis of blood and tissue samples from wild Western red colobus monkeys. We expected that this would allow for proper comparison of retroviral prevalence in the allied species P. b. badius and P. r. tephrosceles.     

Theoretical analysis of noncanonical base pairing interactions in RNA molecules

Noncanonical base pairs in RNA have strong structural and functional implications but are currently not considered for secondary structure predictions. We present results of comparative ab initio studies of stabilities and interaction energies for the three standard and 24 selected unusual RNA base pairs reported in the literature. Hydrogen added models of isolated base pairs, with heavy atoms frozen in their 'away from equilibrium' geometries, built from coordinates extracted from NDB, were geometry optimized using HF/6-31G** basis set, both before and after unfreezing the heavy atoms. Interaction energies, including BSSE and deformation energy corrections, were calculated, compared with respective single point MP2 energies, and correlated with occurrence frequencies and with types and geometries of hydrogen bonding interactions. Systems having two or more N-H...O/N hydrogen bonds had reasonable interaction energies which correlated well with respective occurrence frequencies and highlighted the possibility of some of them playing important roles in improved secondary structure prediction methods. Several of the remaining base pairs with one N-H...O/N and/or one C-H...O/N interactions respectively, had poor interaction energies and negligible occurrences. High geometry variations on optimization of some of these were suggestive of their conformational switch like characteristics.     

Testing the Reproducibility of Multiple Displacement Amplification on Genomes of Clonal Endosymbiont Populations

The multiple displacement amplification method has revolutionized genomic studies of uncultured bacteria, where the extraction of pure DNA in sufficient quantity for next-generation sequencing is challenging. However, the method is problematic in that it amplifies the target DNA unevenly, induces the formation of chimeric reads and also amplifies contaminating DNA. Here, we have tested the reproducibility of the multiple displacement amplification method using serial dilutions of extracted genomic DNA and intact cells from the cultured endosymbiont Bartonella australis. The amplified DNA was sequenced with the Illumina sequencing technology, and the results were compared to sequence data obtained from unamplified DNA in this study as well as from a previously published genome project. We show that artifacts such as the extent of the amplification bias, the percentage of chimeric reads and the relative fraction of contaminating DNA increase dramatically for the smallest amounts of template DNA. The pattern of read coverage was reproducibly obtained for samples with higher amounts of template DNA, suggesting that the bias is non-random and genome-specific. A re-analysis of previously published sequence data obtained after amplification from clonal endosymbiont populations confirmed these predictions. We conclude that many of the artifacts associated with the use of the multiple displacement amplification method can be alleviated or much reduced by using multiple cells as the template for the amplification. These findings should be particularly useful for researchers studying the genomes of endosymbionts and other uncultured bacteria, for which a small clonal population of cells can be isolated.     

Sleep deprivation sensitizes human craniofacial muscles

It is unknown whether and how sleep deprivation influences craniofacial muscle sensitivity in healthy humans. We investigated whether total sleep deprivation (TSD) and one night of recovery sleep (RS) can alter mechanical pain sensitivity in temporal and masseter muscles. Fifteen healthy volunteers participated in three consecutive sessions. Pressure pain thresholds were measured on the temporal and masseter muscles. Both temporal and masseter muscles became sensitized after 24?h of TSD. RS reversed the muscle sensitization.