Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast

Genetic analysis of phenotypic differences between species is typically limited to interfertile species. Here, we conducted a genome-wide noncomplementation screen to identify genes that contribute to a major difference in thermal growth profile between two reproductively isolated yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum. The screen identified only a single nuclear-encoded gene with a moderate effect on heat tolerance, but, in contrast, revealed a large effect of mitochondrial DNA (mitotype) on both heat and cold tolerance. Recombinant mitotypes indicate that multiple genes contribute to thermal divergence, and we show that protein divergence in COX1 affects both heat and cold tolerance. Our results point to the yeast mitochondrial genome as an evolutionary hotspot for thermal divergence.This work was supported by the NIH (grant GM080669) to J.C.F. Additional support to C.T.H. was provided by the USDA National Institute of Food and Agriculture (Hatch project 1003258), the National Science Foundation (DEB-1253634), and the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-SC0018409 and DE-FC02-07ER64494 to T. J. Donohue). C.T.H. is a Pew Scholar in the Biomedical Sciences and a Vilas Faculty Early Career Investigator, supported by the Pew Charitable Trusts and the Vilas Trust Estate, respectively. D.P. is a Marie Sklodowska-Curie fellow of the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 747775).Peer reviewe

Niobium-based superconducting nano-devices fabrication using all-metal suspended masks

We report a novel method for the fabrication of superconducting nanodevices based on niobium. The well-known difficulties of lithographic patterning of high-quality niobium are overcome by replacing the usual organic resist mask by a metallic one. The quality of the fabrication procedure is demonstrated by the realization and characterization of long and narrow superconducting lines and niobium-gold-niobium proximity SQUIDs

Modeling of Laser Vaporization and Plume Chemistry in a Boron Nitride Nanotube Production Rig

Flow in a pressurized, vapor condensation (PVC) boron nitride nanotube (BNNT) production rig is modeled. A laser provides a thermal energy source to the tip of a boron ber bundle in a high pressure nitrogen chamber causing a plume of boron-rich gas to rise. The buoyancy driven flow is modeled as a mixture of thermally perfect gases (B, B2, N, N2, BN) in either thermochemical equilibrium or chemical nonequilibrium assuming steady-state melt and vaporization from a 1 mm radius spot at the axis of an axisymmetric chamber. The simulation is intended to define the macroscopic thermochemical environment from which boron-rich species, including nanotubes, condense out of the plume. Simulations indicate a high temperature environment (T > 4400K) for elevated pressures within 1 mm of the surface sufficient to dissociate molecular nitrogen and form BN at the base of the plume. Modifications to Program LAURA, a finite-volume based solver for hypersonic flows including coupled radiation and ablation, are described to enable this simulation. Simulations indicate that high pressure synthesis conditions enable formation of BN vapor in the plume that may serve to enhance formation of exceptionally long nanotubes in the PVC process

A Fish Farmer’s Role in Sustainable Aquaculture: An Overview of Philippine Aquaculture

The expansion of Philippine aquaculture is essential to addressing poverty and food insecurity in the midst of a seemingly irreversible decline in national capture fisheries. Concomitant with its rise, however, are compounding environmental problems caused by climate change, lackluster governance and irresponsible farming practices. It is equally important to ensure aquaculture sustainability so that fish demand from a rapidly growing population is continually met and that fish farmers’ socioeconomic well-being is secured. As such, programs have been developed that aim to enjoin the government and private sectors with fishing communities to realize this goal

Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase.

Plant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant-microbe interaction. However, very few complete genomes exist for plant cyanobionts, and therefore little is known about their genomic and functional diversity. Here, we present four complete genomes of cyanobacteria isolated from bryophytes. Nanopore long-read sequencing allowed us to obtain circular contigs for all the main chromosomes and most of the plasmids. We found that despite having a low 16S rRNA sequence divergence, the four isolates exhibit considerable genome reorganizations and variation in gene content. Furthermore, three of the four isolates possess genes encoding vanadium (V)-nitrogenase (vnf), which is uncommon among diazotrophs and has not been previously reported in plant cyanobionts. In two cases, the vnf genes were found on plasmids, implying possible plasmid-mediated horizontal gene transfers. Comparative genomic analysis of vnf-containing cyanobacteria further identified a conserved gene cluster. Many genes in this cluster have not been functionally characterized and would be promising candidates for future studies to elucidate V-nitrogenase function and regulation

Phylogeny based discovery of regulatory elements

BACKGROUND: Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advantage of an explicit model for the constrained evolution of functional DNA sequences. RESULTS: We developed a probabilistic framework that combines an HKY85 model, which assigns probabilities to different base substitutions between species, and weight matrix models of transcription factor binding sites, which describe the probabilities of observing particular nucleotides at specific positions in the binding site. The method incorporates the phylogenies of the species under consideration and takes into account the position specific variation of transcription factor binding sites. Using our framework we assessed the suitability of alignments of genomic sequences from commonly used species as substrates for comparative genomic approaches to regulatory motif finding. We then applied this technique to Saccharomyces cerevisiae and related species by examining all possible six base pair DNA sequences (hexamers) and identifying sequences that are conserved in a significant number of promoters. By combining similar conserved hexamers we reconstructed known cis-regulatory motifs and made predictions of previously unidentified motifs. We tested one prediction experimentally, finding it to be a regulatory element involved in the transcriptional response to glucose. CONCLUSION: The experimental validation of a regulatory element prediction missed by other large-scale motif finding studies demonstrates that our approach is a useful addition to the current suite of tools for finding regulatory motifs

Feasibility and cost of converting oil- and coal-fired utility boilers to intermittent use of natural gas

The continuous or intermittent use of natural gas in place of oil or coal in existing utility boilers would reduce emissions of sulfur and thereby the concentration of sulfate ions in precipitation. This report examines the technological feasibility and capital cost of retrofitting oil and coal fired utility boilers to burn intermittently natural gas and the parent fuel. Using extensive studies of the retrofitting of such boilers to burn synthetic gas of low to moderate heating value (LBG), it is found that natural gas closely simulates the combustion properties of LBG of medium heating value. Based upon this comparison, it is concluded that little or no modifications to the boiler are required to achieve the same boiler rating as when burning the original fuel, and that only a small efficiency penalty must be paid. Examination of the history of four eastern utility boiler conversions from oil to natural gas confirms these performance estimates, and shows that conversion costs for in-plant equipment are very small, less than 19 $(1985)/KW in all instances, while conversion times are less than one year (with little down time beyond that required for annual maintenance). Pipelining costs will vary with the local conditions.American Gas Associatio

Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae

Saccharomyces cerevisiae is predominantly found in association with human activities, particularly the production of alcoholic beverages. S. paradoxus, the closest known relative of S. cerevisiae, is commonly found on exudates and bark of deciduous trees and in associated soils. This has lead to the idea that S. cerevisiae is a domesticated species, specialized for the fermentation of alcoholic beverages, and isolates of S. cerevisiae from other sources simply represent migrants from these fermentations. We have surveyed DNA sequence diversity at five loci in 81 strains of S. cerevisiae that were isolated from a variety of human and natural fermentations as well as sources unrelated to alcoholic beverage production, such as tree exudates and immunocompromised patients. Diversity within vineyard strains and within saké strains is low, consistent with their status as domesticated stocks. The oldest lineages and the majority of variation are found in strains from sources unrelated to wine production. We propose a model whereby two specialized breeds of S. cerevisiae have been created, one for the production of grape wine and one for the production of saké wine. We estimate that these two breeds have remained isolated from one another for thousands of years, consistent with the earliest archeological evidence for winemaking. We conclude that although there are clearly strains of S. cerevisiae specialized for the production of alcoholic beverages, these have been derived from natural populations unassociated with alcoholic beverage production, rather than the opposite

The structure and diversity of strain-level variation in vaginal bacteria

The vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain-level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core genomes for six species of vaginal bacteria

On the numerical evaluation of algebro-geometric solutions to integrable equations

Physically meaningful periodic solutions to certain integrable partial differential equations are given in terms of multi-dimensional theta functions associated to real Riemann surfaces. Typical analytical problems in the numerical evaluation of these solutions are studied. In the case of hyperelliptic surfaces efficient algorithms exist even for almost degenerate surfaces. This allows the numerical study of solitonic limits. For general real Riemann surfaces, the choice of a homology basis adapted to the anti-holomorphic involution is important for a convenient formulation of the solutions and smoothness conditions. Since existing algorithms for algebraic curves produce a homology basis not related to automorphisms of the curve, we study symplectic transformations to an adapted basis and give explicit formulae for M-curves. As examples we discuss solutions of the Davey-Stewartson and the multi-component nonlinear Schr\"odinger equations.Comment: 29 pages, 20 figure