Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave,Northern Sweden

Speleothems are secondary mineral deposits normally formed by water supersaturated with calcium carbonate percolating into underground caves, and are often associated with low-nutrient and mostly non-phototrophic conditions. Tjuv-Ante’s cave is a shallow-depth cave formed by the action of waves, with granite and dolerite as major components, and opal-A and calcite as part of the speleothems, making it a rare kind of cave. We generated two DNA shotgun sequencing metagenomic datasets from the interior of a speleothem from Tjuv-Ante’s cave representing areas of old and relatively recent speleothem formation. We used these datasets to perform i) an evaluation of the use of these speleothems as past biodiversity archives, ii) functional and taxonomic profiling of the speleothem’s different formation periods, and iii) taxonomic comparison of the metagenomic results to previous microscopic analyses from a nearby speleothem of the same cave. Our analyses confirm the abundance of Actinobacteria and fungi as previously reported by microscopic analyses on this cave, however we also discovered a larger biodiversity. Interestingly, we identified photosynthetic genes, as well as genes related to iron and sulphur metabolism, suggesting the presence of chemoautotrophs. Furthermore, we identified taxa and functions related to biomineralization. However, we could not confidently establish the use of this type of speleothems as biological paleoarchives due to the potential leaching from the outside of the cave and the DNA damage that we propose has been caused by the fungal chemical etching.     

Effects of pregnancy on the extrinsic innervation of the guinea pig uterus. A histochemical, immunohistochemical and ultrastructural study

Summary The extrinsic innervation of the guinea pig uterus was studied by immunohistochemical, ultrastructural and enzyme histochemical methods.The extrinsic innervation was organized in two major ways. One consisted of nerve trunks and non-varicose nerve fibres running in the suspensory ligament, and the other of a plexus of varicose nerve fibres surrounding vessels, and non-vessel-related non-varicose nerve fibres in the mesouterus. The use of different neuronal and Schwann cell markers showed that the extrinsic innervation was predominantly adrenergic and contained only few peptidergic nerves. Acetylcholinesterase-positive (cholinergic) nerves were only found around the uterine artery.In late pregnancy, the extrinsic nerves of the mesouterus adjacent to foetus-containing uterine horns underwent pronounced degenerative changes comprising both Schwann cell and axonal structures. In comparison, no changes were found in extrinsic nerves of mesouteri adjacent to non-foetus-bearing uterine horns or in extrinsic nerves in the suspensory ligaments. Further, chemical sympathectomy produced axonal degeneration but no changes in the Schwann cells.In conclusion, the pregnancy-induced nerve degeneration is of a very special type different from that following chemical sympathectomy and represents a local phenomenon related to the conceptus. Hypothetically, this could be of importance for counteracting disturbances in placental blood flow.     

Intratumour Diversity of Chromosome Copy Numbers in Neuroblastoma Mediated by On-Going Chromosome Loss from a Polyploid State

Neuroblastomas (NBs) are tumours of the sympathetic nervous system accounting for 8–10% of paediatric cancers. NBs exhibit extensive intertumour genetic heterogeneity, but their extent of intratumour genetic diversity has remained unexplored. We aimed to assess intratumour genetic variation in NBs with a focus on whole chromosome changes and their underlying mechanism. Allelic ratios obtained by SNP-array data from 30 aneuploid primary NBs and NB cell lines were used to quantify the size of clones harbouring specific genomic imbalances. In 13 cases, this was supplemented by fluorescence in situ hybridisation to assess copy number diversity in detail. Computer simulations of different mitotic segregation errors, single cell cloning, analysis of mitotic figures, and time lapse imaging of dividing NB cells were used to infer the most likely mechanism behind intratumour variation in chromosome number. Combined SNP array and FISH analyses showed that all cases exhibited higher inter-cellular copy number variation than non-neoplastic control tissue, with up to 75% of tumour cells showing non-modal chromosome copy numbers. Comparisons of copy number profiles, resulting from simulations of different segregation errors to genomic profiles of 120 NBs indicated that loss of chromosomes from a tetraploid state was more likely than other mechanisms to explain numerical aberrations in NB. This was supported by a high frequency of lagging chromosomes at anaphase and polyploidisation events in growing NB cells. The dynamic nature of numerical aberrations was corroborated further by detecting substantial copy number diversity in cell populations grown from single NB cells. We conclude that aneuploid NBs typically show extensive intratumour chromosome copy number diversity, and that this phenomenon is most likely explained by continuous loss of chromosomes from a polyploid state.     

The transthyretin-related protein family.

A number of proteins related to the homotetrameric transport protein transthyretin (TTR) forms a highly conserved protein family, which we present in an integrated analysis of data from different sources combined with an initial biochemical characterization. Homologues of the transthyretin-related protein (TRP) can be found in a wide range of species including bacteria, plants and animals, whereas transthyretins have so far only been identified in vertebrates. A multiple sequence alignment of 49 TRP sequences from 47 species to TTR suggests that the tertiary and quaternary features of the three-dimensional structure are most likely preserved. Interestingly, while some of the TRP orthologues show as little as 30% identity, the residues at the putative ligand-binding site are almost entirely conserved. RT/PCR analysis in Caenorhabditis elegans confirms that one TRP gene is transcribed, spliced and predominantly expressed in the worm, which suggests that at least one of the two C. elegans TRP genes encodes a functional protein. We used double-stranded RNA-mediated interference techniques in order to determine the loss-of-function phenotype for the two TRP genes in C. elegans but detected no apparent phenotype. The cloning and initial characterization of purified TRP from Escherichia coli reveals that, while still forming a homotetramer, this protein does not recognize thyroid hormones that are the natural ligands of TTR. The ligand for TRP is not known; however, genomic data support a functional role involving purine catabolism especially linked to urate oxidase (uricase) activity.     

Gender-Based Comorbidity in Benign Paroxysmal Positional Vertigo

It has been noted that benign paroxysmal positional vertigo (BPPV) may be associated with certain disorders and medical procedures. However, most studies to date were done in Europe, and epidemiological data on the United States (US) population are scarce. Gender-based information is even rarer. Furthermore, it is difficult to assess the relative prevalence of each type of association based solely on literature data, because different comorbidities were reported by various groups from different countries using different patient populations and possibly different inclusion/exclusion criteria. In this study, we surveyed and analyzed a large adult BPPV population (n = 1,360 surveyed, 227 completed, most of which were recurrent BPPV cases) from Omaha, NE, US, and its vicinity, all diagnosed at Boys Town National Research Hospital (BTNRH) over the past decade using established and consistent diagnostic criteria. In addition, we performed a retrospective analysis of patients’ diagnostic records (n = 1,377, with 1,360 adults and 17 children). The following comorbidities were found to be significantly more prevalent in the BPPV population when compared to the age- and gender-matched general population: ear/hearing problems, head injury, thyroid problems, allergies, high cholesterol, headaches, and numbness/paralysis. There were gender differences in the comorbidities. In addition, familial predisposition was fairly common among the participants. Thus, the data confirm some previously reported comorbidities, identify new ones (hearing loss, thyroid problems, high cholesterol, and numbness/paralysis), and suggest possible predisposing and triggering factors and events for BPPV.     

Decisions among the Undecided: Implicit Attitudes Predict Future Voting Behavior of Undecided Voters

Implicit attitudes have been suggested as a key to unlock the hidden preferences of undecided voters. Past research, however, offered mixed support for this hypothesis. The present research used a large nationally representative sample and a longitudinal design to examine the predictive utility of implicit and explicit attitude measures in the 2008 U.S. presidential election. In our analyses, explicit attitudes toward candidates predicted voting better for decided than undecided voters, but implicit candidate attitudes were predictive of voting for both decided and undecided voters. Extending our examination to implicit and explicit racial attitudes, we found the same pattern. Taken together, these results provide convergent evidence that implicit attitudes predict voting about as well for undecided as for decided voters. We also assessed a novel explanation for these effects by evaluating whether implicit attitudes may predict the choices of undecided voters, in part, because they are neglected when people introspect about their confidence. Consistent with this idea, we found that the extremity of explicit but not implicit attitudes was associated with greater confidence. These analyses shed new light on the utility of implicit measures in predicting future behavior among individuals who feel undecided. Considering the prior studies together with this new evidence, the data seem to be consistent that implicit attitudes may be successful in predicting the behavior of undecided voters.     

Effects of pH, Nitrite, and Ascorbic Acid on Nonenzymatic Nitric Oxide Generation and Bacterial Growth in Urine

Nitrite may be generated by bacteria in urine during urinary tract infections. Acidification of nitrite results in the formation of nitric oxide (NO) and other reactive nitrogen oxides, which are toxic to a variety of microorganisms. We have studied NO formation and bacterial growth in mildly acidified human urine containing nitrite and the reducing agent vitamin C. Urine collected from healthy subjects was incubated in closed syringes at different pH values with varying amounts of nitrite and/or ascorbic acid added. NO generation was measured in headspace gas using a chemiluminescence technique. A similar setup was also used to study the growth of three strains of bacteria in urine. Mildly acidified nitrite-containing urine generated large amounts of NO and this production was greatly potentiated by ascorbic acid. The growth of Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus saprophyticus was markedly reduced by the addition of nitrite to acidified urine. This inhibition was enhanced by ascorbic acid. In conclusion, we show that the growth of three common urinary pathogens is markedly inhibited in mildly acidified urine when nitrite is present. The bacteriostatic effect of acidified nitrite is likely related to the release of NO and other toxic reactive nitrogen intermediates. These results may help to explain the well-known beneficial effects of urinary acidification with, e.g., vitamin C in treatment and prevention of urinary tract infection.