A novel tool for individual haplotype inference using mixed data

Background

In many studies, researchers may recruit samples consisting of independent trios and unrelated individuals. However, most of the currently available haplotype inference methods do not cope well with these kinds of mixed data sets.

Methods

We propose a general and simple methodology using a mixture of weighted multinomial (MIXMUL) approach that combines separate haplotype information from unrelated individuals and independent trios for haplotype inference to the individual level.

Results

The new MIXMUL procedure improves over existing methods in that it can accurately estimate haplotype frequencies from mixed data sets and output probable haplotype pairs in optimized reconstruction outcomes for all subjects that have contributed to estimation. Simulation results showed that this new MIXMUL procedure competes well with the EM-based method, i.e. FAMHAP, under a few assumed scenarios.

Conclusion

The results showed that MIXMUL can provide accurate estimates similar to those haplotype frequencies obtained from FAMHAP and output the probable haplotype pairs in the most optimal reconstruction outcome for all subjects that have contributed to estimation. If available data consist of combinations of unrelated individuals and independent trios, the MIXMUL procedure can be used to estimate the haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.     

Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium Acidovorax ebreus Strain TPSY

Acidovorax ebreus strain TPSY is the first anaerobic nitrate-dependent Fe(II) oxidizer for which there is a completed genome sequence. Preliminary protein annotation revealed an organism optimized for survival in a complex environmental system. Here, we briefly report the completed and annotated genome sequence of strain TPSY.Microorganisms from diverse anoxic environments are capable of nitrate-dependent Fe(II) oxidation at circumneutral pH (4, 11, 17, 18, 20, 21). Despite their geochemical importance (22), little is known of the underlying biochemical and genetic mechanisms. Genome sequencing of several nitrate-dependent Fe(II) oxidizers will provide insight into this process. By comparing Fe(II) oxidation mechanisms in various organisms, we hope to identify both the conserved and disparate aspects of the metabolism. The genome of Acidovorax ebreus strain TPSY is the first of these to be sequenced.Strain TPSY is a motile, Gram-negative facultative anaerobe isolated from groundwater collected from the U.S. Department of Energy Integrated Field Research Challenge site at Oak Ridge, TN. Growth experiments performed as previously described (21) revealed TPSY''s incapacity for lithoautotrophic growth, which was supported by a lack of genes in the genome encoding any known CO₂ fixation pathways. TPSY did grow mixotrophically with Fe(II) as the electron donor and a 0.1 mM acetate carbon source. 16S rRNA gene sequence analysis placed TPSY in the class Betaproteobacteria with 99.8% similarity to Acidovorax sp. strain JS42 in the family Comamonadaceae.The completed genome consisted of a single circular chromosome of 3,796,573 bp with an average 66.8% G+C content. A total of 3,479 protein-encoding genes were predicted, and 34 (0.98%) had no similarity to public database sequences. Sequencing performed at the Department of Energy Joint Genome Institute (JGI) used Sanger sequencing and 454 pyrosequencing to a depth of 20× coverage. All JGI library construction and sequencing techniques can be found at http://www.jgi.doe.gov/. Sequence assembly, quality assessment, and annotation were performed using the software Phred/Phrap/Consed (www.phrap.com) (6-8), Dupfinisher (10), CRITICA (2), GLIMMER, and GENERATION (5) and the JGI Integrated Microbial Genomes site (12). The completed genome sequence contained 33,341 reads and had an average of ninefold coverage per base and an error rate of <1 in 100,000.TPSY was named in part for its meandering motility, and its genome confirmed the twitching phenotype with the presence of pilT, pilU, and a complete set of flagellar and chemotaxis genes. The ability of TPSY to oxidize simple alcohols and acids with oxygen or nitrate respiration was confirmed by the genome. In addition, biosynthetic pathways for all amino acids except tyrosine and phenylalanine were present. No homologues of chorismate mutase (EC 5.4.99.5), an enzyme required for tyrosine and phenylalanine anabolism, were identified. The genome contained both intact Embden-Meyerhof-Parnas and Entner-Doudoroff pathways, in addition to a pentose phosphate pathway and a trichloroacetic acid cycle.In support of its facultative anaerobicity, a complete set of genes for denitrification and three different terminal oxidases (cytochrome aa₃, cbb₃, and cytochrome d quinol oxidase) were present. The cbb₃ and cytochrome d oxidases, with their high oxygen affinity, putatively enable survival in microaerobic environments (14).TPSY had sequences encoding 30 transposases, 11 integrases, and 11 phage/prophage-related genes. A region of particular interest putatively conferred resistance to lead, arsenate, and mercury: pbrRATARTBC, arsRDAB, and merRPCADE. Evidence suggests horizontal transfer and insertion of this region, as it was flanked on the 5′ end by λ prophage-related genes and the 3′ end encoded a putative Tn21 transposase. Phenotypic studies by the method of Wang et al. (19) revealed MICs of 16 μM phenylmercuric acetate and 250 μM MgCl₂. TPSY was also capable of growth in the presence of arsenate (10 mM) but did not use it as an electron acceptor.Related to phage infection, one CRISPR (clustered, regularly interspaced, short palindromic repeats) region (3, 16) was predicted. The core proteins, the cas1 and cas2 genes, and a csn1 gene formed the CRISPR subtype Nmeni, which is associated with vertebrate pathogens and commensals (9). However, the lack of typical pathogenic type I or III secretion systems such as the hec cluster of Dickeya chrysanthemi (15) or the inv/spa system of Salmonella enterica serovar Typhimurium (13) indicated that TPSY would probably not exhibit a pathogenic lifestyle.     

Hacking anthropology

This essay outlines how the ‘hack’ might offer a model for anthropological research in the face of the distributed relations evidenced by digital data. The argument builds on fieldwork with citizens and activists and looks at their attempts to understand and make use of the data produced by energy sensors and monitors. Drawing on their experiences, I suggest that ‘the hack’ emerges as an important form of practice that helps people navigate the place of data in social relations. Taking the hack not just as ethnographic observation but also as a methodological proposition, I use my ethnographic material on the practice of the hack to reconsider the anthropological challenge of doing ethnography of processes that are only perceptible through numerical or digital data. To explore the value of the hack for anthropology, I introduce an example of an attempt to do ethnography in the mode of the hack. The essay ends with reflections on how the hack might provide us with new ways of getting to grips with the anthropological implications of systemic and emergent relations that are both brought to light and remade through data.     

Temperature dependence of tryptophan fluorescence lifetime in aqueous glycerol and trehalose solutions

The temperature dependences of tryptophan fluorescence decay kinetics in aqueous glycerol and 1 M trehalose solutions were examined. The fluorescence decay kinetics were recorded in the spectral region of 292.5–417.5 nm with nanosecond time resolution. The kinetics curves were approximated by the sum of three exponential terms, and the spectral distribution (DAS) of these components was determined. An antisymbatic course of fluorescence decay times of two (fast and medium) components in the temperature range from –60 to +10°C was observed. The third (slow) component showed only slight temperature dependence. The antisymbatic behavior of fluorescence lifetimes of the fast and medium components was explained on the assumption that some of the excited tryptophan molecules are transferred from a short-wave-length B-form with short fluorescence lifetime to a long-wavelength R-form with an intermediate fluorescence lifetime. This transfer occurred in the indicated temperature range.     

The Benzidine Staining Method for Blood Vessels

Two modifications of the method are described: A. Living specimens of sabellid and serpluid polychaetes, earthworms, small tadpoles, or fish larvae are immersed in an approximately saturated solution of benzidine for 30 minutes and then 3% hydrogen peroxide is added until bubbles of gas appear. When the blood vessels appear dark blue, the specimens are fixed in acidified 70% alcohol, dehydrated, cleared and either mounted in Canada balsam as whole mounts, or embedded in paraffin, sectioned at 100 to 250µ and mounted. B. Material fixed in 10% formalin in sea-water, or in formalin hypertonic saline, is incubated at 37°C. for one hour in an aqueous mixture containing sodium nitroprusside, 0.1%; benzidine, acetic acid 0.5%, followed by a weak (0.01-0.02%) hydrogen peroxide solution for a further hour, embedded in paraffin, cut into thick sections and mounted.     

Effect of osmolality on renal medullary Na-K-ATPase activity in the postobstructive kidney.

The aim of this study was to determine the effect of changes in osmolality on the reduced renal medullary Na-K-ATPase (EC 3.6.1.3) activity of the postobstructive kidney. The effect of osmolality on renal medullary Na-K-ATPase activity was studied by incubating tissue slices from sham-operated and bilaterally obstructed rats in media with osmolality varied before enzyme isolation using sodium chloride, choline chloride, or sucrose. Both sham-operated and bilaterally obstructed rat renal medullary enzyme showed a similar increase in activity with increased osmolality due to sodium chloride. Medullary Na-K-ATPase from the postobstructive kidney also showed increased activity with osmotic changes induced by choline chloride or sucrose. It is proposed that the decrease of Na-K-ATPase activity observed after bilateral ureteral obstruction is due, at least in part, to the loss of the solute concentration gradient in the kidney.