4,409 research outputs found
On limiting cluster size distributions for processes of exceedances for stationary sequences
It is well known that, under broad assumptions, the time-scaled point process
of exceedances of a high level by a stationary sequence converges to a compound
Poisson process as the level grows. The purpose of this note is to demonstrate
that, for any given distribution G on the natural numbers, there exists a
stationary sequence for which the compounding law of this limiting process of
exceedances will coincide with G.Comment: 6 pages, no figure
A General Method for the Calculation of Axis-crossing Moments Technical Report No. 5
Calculating axis-crossing moments by stochastic proces
Analysis of Extensive [FeFe] Hydrogenase Gene Diversity Within the Gut Microbiota of Insects Representing Five Families of Dictyoptera
We have designed and utilized degenerate primers in the phylogenetic analysis of [FeFe] hydrogenase gene diversity in the gut ecosystems of roaches and lower termites. H2 is an important free intermediate in the breakdown of wood by termite gut microbial communities, reaching concentrations in some species exceeding those measured for any other biological system. The primers designed target with specificity the largest group of enzymatic H domain proteins previously identified in a termite gut metagenome. “Family 3” hydrogenase sequences were amplified from the guts of lower termites, Incisitermes minor, Zootermopsis nevadensis, and Reticulitermes hesperus, and two roaches, Cryptocercus punctulatus and Periplaneta americana. Subsequent analyses revealed that all termite and Cryptocercus sequences were phylogenetically distinct from non-termiteassociated hydrogenases available from public databases. The abundance of unique sequence operational taxonomic units (as many as 21 from each species) underscores the previously demonstrated physiological importance of H2 to the gut ecosystems of these wood-feeding insects. The diversity of sequences observed might be reflective of multiple niches that the enzymes have been evolved to accommodate. Sequences cloned from Cryptocercus and the lower termite samples, all of which are wood feeding insects, clustered closely with one another in phylogenetic analyses to the exclusion of alleles from P. americana, an omnivorous cockroach, also cloned during this study. We present primers targeting a family of termite gut [FeFe] hydrogenases and provide results that are consistent with a pivotal role for hydrogen in the termite gut ecosystem and point toward
unique evolutionary adaptations to the gut ecosystem
Diversity of Formyltetrahydrofolate Synthetases in the Guts of the Wood-Feeding Cockroach Cryptocercus punctulatus and the Omnivorous Cockroach Periplaneta americana
We examined the diversity of a marker gene for homoacetogens in two cockroach gut microbial communities. Formyltetrahydrofolate synthetase (FTHFS or fhs) libraries prepared from a wood-feeding cockroach, Cryptocercus punctulatus, were dominated by sequences that affiliated with termite gut treponemes. No spirochete-like sequences were recovered from the omnivorous roach Periplaneta americana, which was dominated by Firmicutes-like sequences
Genes for selenium dependent and independent formate dehydrogenase in the gut microbial communities of three lower, wood-feeding termites and a wood-feeding roach
The bacterial Wood-Ljungdahl pathway for CO_2-reductive acetogenesis is important for the nutritional mutualism occurring between
wood-feeding insects and their hindgut microbiota. A key step in this
pathway is the reduction of CO_2 to formate, catalysed by the enzyme
formate dehydrogenase (FDH). Putative selenocysteine- (Sec) and
cysteine- (Cys) containing paralogues of hydrogenase-linked FDH (FDH_H)
have been identified in the termite gut acetogenic spirochete,
Treponema primitia, but knowledge of their relevance in the termite gut
environment remains limited. In this study, we designed degenerate PCR
primers for FDH_H genes (fdhF) and assessed fdhF diversity in insect gut
bacterial isolates and the gut microbial communities of termites and
cockroaches. The insects examined herein represent three wood-feeding
termite families, Termopsidae, Kalotermitidae and Rhinotermitidae
(phylogenetically 'lower' termite taxa); the wood-feeding roach family
Cryptocercidae (the sister taxon to termites); and the omnivorous roach
family Blattidae. Sec and Cys FDH_H variants were identified in every
wood-feeding insect but not the omnivorous roach. Of 68 novel alleles
obtained from inventories, 66 affiliated phylogenetically with enzymes
from T. primitia. These formed two subclades (37 and 29 phylotypes)
almost completely comprised of Sec-containing and Cys-containing
enzymes respectively. A gut cDNA inventory showed transcription of both
variants in the termite Zootermopsis nevadensis (family Termopsidae).
The gene patterns suggest that FDH_H enzymes are important for the
CO_2-reductive metabolism of uncultured acetogenic treponemes and imply
that the availability of selenium, a trace element, shaped microbial
gene content in the last common ancestor of dictyopteran, wood-feeding
insects, and continues to shape it to this day
Development of reliability methodology for systems engineering. Volume III - Theoretical investigations - An approach to a class of reliability problems Final report
Random quantities from continuous time stochastic process with application to reliability and probabilit
On certain functionals of normal processes Technical report no. 1
Probabilistic modeling and stochastic process investigations to provide measures of quality of performance and reliability for systems engineering - Chebyshev approximatio
Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones
LuxR-type transcriptional regulators play key roles in quorum-sensing systems that employ acyl-homoserine lactones (acyl-HSLs) as signal molecules. These proteins mediate quorum control by changing their interactions with RNA polymerase and DNA in response to binding their cognate acyl-HSL. The evolutionarily related LuxR-type proteins exhibit considerable diversity in primary sequence and in their response to acyl-HSLs having acyl groups of differing length and composition. Little is known about which residues determine acyl-HSL specificity, and less about the evolutionary time scales required to forge new ones. To begin to examine such issues, we have focused on the LuxR protein from Vibrio fischeri, which activates gene transcription in response to binding its cognate quorum signal, 3-oxohexanoyl-homoserine lactone (3OC6HSL). Libraries of luxR mutants were screened for variants exhibiting increased gene activation in response to octanoyl-HSL (C8HSL), with which wild-type LuxR interacts only weakly. Eight LuxR variants were identified that showed a 100-fold increase in sensitivity to C8HSL; these variants also displayed increased sensitivities to pentanoyl-HSL and tetradecanoyl-HSL, while maintaining a wild-type or greater response to 3OC6HSL. The most sensitive variants activated gene transcription as strongly with C8HSL as the wild type did with 3OC6HSL. With one exception, the amino acid residues involved were restricted to the N-terminal, 'signal-binding' domain of LuxR. These residue positions differed from critical positions previously identified via 'loss-of-function' mutagenesis. We have demonstrated that acyl-HSL-dependent quorum-sensing systems can evolve rapidly to respond to new acyl-HSLs, suggesting that there may be an evolutionary advantage to maintaining such plasticity
Description of Treponema azotonutricium sp. nov. and Treponema primitia sp. nov., the First Spirochetes Isolated from Termite Guts
Long after their original discovery, termite gut spirochetes were recently isolated in pure culture for the first time. They revealed metabolic capabilities hitherto unknown in the Spirochaetes division of the Bacteria, i.e., H2 plus CO2 acetogenesis (J. R. Leadbetter, T. M. Schmidt, J. R. Graber, and J. A. Breznak, Science 283:686-689, 1999) and dinitrogen fixation (T. G. Lilburn, K. S. Kim, N. E. Ostrom, K. R. Byzek, J. R. Leadbetter, and J. A. Breznak, Science 292:2495-2498, 2001). However, application of specific epithets to the strains isolated (Treponema strains ZAS-1, ZAS-2, and ZAS-9) was postponed pending a more complete characterization of their phenotypic properties. Here we describe the major properties of strain ZAS-9, which is readily distinguished from strains ZAS-1 and ZAS-2 by its shorter mean cell wavelength or body pitch (1.1 versus 2.3 µm), by its nonhomoacetogenic fermentation of carbohydrates to acetate, ethanol, H2, and CO2, and by 7 to 8% dissimilarity between its 16S rRNA sequence and those of ZAS-1 and ZAS-2. Strain ZAS-9 is proposed as the type strain of the new species, Treponema azotonutricium. Strains ZAS-1 and ZAS-2, which are H2-consuming, CO2-reducing homoacetogens, are proposed here to be two strains of the new species Treponema primitia. Apart from the salient differences mentioned above, the genomes of all three strains were similar in size (3,461 to 3,901 kb), in G+C content (50.0 to 51.0 mol%), and in possession of 2 copies of the gene encoding 16S rRNA (rrs). For comparison, the genome of the free-living spirochete Spirochaeta aurantia strain J1 was analyzed by the same methods and found to have a size of 3,719 kb, to contain 65.6 mol% G+C, and also to possess 2 copies of the rrs gene
Maximizing Productivity and Quality in Senior Thesis Writing with Artificial Intelligence and Natural Language Processing Driven Tools
This project is a Python program designed to generate a senior thesis on a user-inputted topic using natural language processing techniques. The program takes in atopic from the user and then uses OpenAI API to deploy text models for text genera-tion and evaluation, such as GPT-3 and Davinci-003. The resulting output is in .texformat and includes a first-draft outline and paper, followed by self-generated assessment, with scoring, revisions, and feedback comments instructing manual revisions.
This submission is a sample using one available model of the project, meant todemonstrate it’s functionality and limitations. Further model versions are availablein the project repository: https://github.com/laurenleadbetter/senior_thesis_generator
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