Catechol 2,3-dioxygenase-assisted cleavage of aromatics by “anaerobic” termite gut spirochetes and genomic evidence of a complete meta-pathway

The termite hindgut microbial ecosystem functions like a miniature lignocellulose-metabolizing natural bioreactor, has significant implications to nutrient cycling in the terrestrial environment, and represents an array of microbial metabolic diversity. Deciphering the intricacies of this microbial community to obtain as complete a picture as possible of how it functions as a whole, requires a combination of various traditional and cutting-edge bioinformatic, molecular, physiological, and culturing approaches. Isolates from this ecosystem, including Treponema primitia str. ZAS-1 and ZAS-2 as well as T. azotonutricium str. ZAS-9, have been significant resources for better understanding the termite system. While not all functions predicted by the genomes of these three isolates are demonstrated in vitro, these isolates do have the capacity for several metabolisms unique to spirochetes and critical to the termite system’s reliance upon lignocellulose. In this thesis, work culturing, enriching for, and isolating diverse microorganisms from the termite hindgut is discussed. Additionally, strategies of members of the termite hindgut microbial community to defend against O₂-stress and to generate acetate, the “biofuel” of the termite system, are proposed. In particular, catechol 2,3-dioxygenase and other meta-cleavage catabolic pathway genes are described in the “anaerobic” termite hindgut spirochetes T. primitia str. ZAS-1 and ZAS-2, and the first evidence for aromatic ring cleavage in the phylum (division) Spirochetes is also presented. These results suggest that the potential for O₂-dependent, yet nonrespiratory, metabolisms of plant-derived aromatics should be re-evaluated in termite hindgut communities. Potential future work is also illustrated.

Structure theorems for noncommutative complete local rings

If R is a ring with identity, let N(R) denote the Jacobson radical of R. R is local if R/N(R) is an artinian simple ring and ∩N(R)ⁱ = 0. It is known that if R is complete in the N(R)-adic topology then R is equal to (B)_n, the full n by n matrix ring over B where E/N(E) is a division ring. The main results of the thesis deal with the structure of such rings B. In fact we have the following.

If B is a complete local algebra over F where B/N(B) is a finite dimensional normal extension of F and N(B) is finitely generated as a left ideal by k elements, then there exist automorphisms g_i,...,g_k of B/N(B) over F such that B is a homomorphic image of B/N[[x₁,…,x_k;g₁,…,g_k]] the power series ring over B/N(B) in noncommuting indeterminates x_i, where x_ib = g_i(b)x_i for all b ϵ B/N.

Another theorem generalizes this result to complete local rings which have suitable commutative subrings. As a corollary of this we have the following. Let B be a complete local ring with B/N(B) a finite field. If N(B) is finitely generated as a left ideal by k elements then there exist automorphisms g₁,…,g_k of a v-ring V such that B is a homomorphic image of V [[x₁,…,x_k;g₁,…,g_k]].

In both these results it is essential to know the structure of N(B) as a two sided module over a suitable subring of B.

Molecular Phylogeny of Slow Lorises ( Nycticebus) Revealed by D2loop Sequences and Complete Cytochrome bGene Sequences of Mitochondrial DNA

本研究测定了懒猴属( Nycticebus) D 环的部分序列和细胞色素b 基因的全序列(1 140 bp) , 分析了 该属物种之间的系统发育进化关系。在DNA 水平上, 序列分析结果一致地提供了新的分类学证据: 支持Rata2 jszczak 和Groves 的观点, 即N1intermedus 只是N1 pygmaeus 的成体(Ratajszczak , 1998 ; Groves , 1971) 。对两种 序列的数据做了联合及个别分析, 获得相似的系统树, 支持懒猴属由两个单系群组成: 第一群由N1 pygmaeus 聚成, 第二群由N1coucang 聚成。该结果也提供了新的分子遗传证据, 支持懒猴属由N1coucang 和 N1 pygmaeus 两物种组成。

Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation

To determine the origin and genetic diversity of Chinese cattle, we analyzed the complete mtDNA D-loop sequences of 84 cattle from 14 breeds/populations from southwest and west China, together with the available cattle sequences in GenBank. Our results sh

An integrated 2-D model of a lithium ion battery: The effect of material parameters and morphology on storage particle stress

An integrated 2-D model of a lithium ion battery is developed to study the mechanical stress in storage particles as a function of material properties. A previously developed coupled stress-diffusion model for storage particles is implemented in 2-D and integrated into a complete battery system. The effect of morphology on the stress and lithium concentration is studied for the case of extraction of lithium in terms of previously developed non-dimensional parameters. These non-dimensional parameters include the material properties of the storage particles in the system, among other variables. We examine particles functioning in isolation as well as in closely-packed systems. Our results show that the particle distance from the separator, in combination with the material properties of the particle, is critical in predicting the stress generated within the particle. © 2012 Springer-Verlag.

The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): Unusual features of its control region and the phylogenetic position of the Sciaenidae

To understand the systematic status of Larimichthys crocea in the Percoidei, we determined the complete mitochondrial (mt) genome sequence using 454 sequencing-by-synthesis technology. The complete mt genome is 16,466 bp in length including the typical structure of 22 tRNAs, 2 rRNAs, 13 protein-coding genes and the noncoding control region (CR). Further sequencing for the complete CR was performed using the primers Cyt b-F and 12S-R on six L crocea individuals and two L polyactis individuals. Interestingly, all seven CR sequences from L crocea were identical while the three sequences from L polyactis were distinct (including one from GenBank). Although the conserved blocks such as TAS and CSB-1, -2, and -3 are readily identifiable in the control regions of the two species, the typical central conserved blocks CSB-D, -E, and -F could not be detected, while they are found in Cynoscion acoupa of Sciaenidae and other Percoidei species. Phylogenetic analysis shows that L crocea is a relatively recently emerged species in Sciaenidae and this family is closely related to family Pomacanthidae within the Percoidei. L crocea, as the first species of Sciaenidae with complete mitochondrial genome available, will provide important information on the molecular evolution of the group. Moreover, the genus-specific pair of primers designed in this study for amplifying the complete mt control region will be very useful in studies on the population genetics and conservation biology of Larimichthys. (c) 2008 Elsevier B.V. All rights reserved.

The complete mitochondrial genome of the mantid shrimp Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda): Novel non-coding regions features and phylogenetic implications of the Stomatopoda

The complete mitochondrial (mt) genome sequence of Oratosquilla oratoria (Crustacea: Malacostraca: Stomatopoda) was determined; a circular molecule of 15,783 bp in length. The gene content and arrangement are consistent with the pancrustacean ground pattern. The mt control region of O. oratoria is characterized by no GA-block near the 3' end and different position of [TA(A)]n-blocks compared with other reported Stomatopoda species. The sequence of the second hairpin structure is relative conserved which suggests this region may be a synapomorphic character for the Stomatopoda. In addition, a relative large intergenic spacer (101 bp) with higher A + T content than that in control region was identified between the tRNA(Glu) and tRNA(Phe) genes. Phylogenetic analyses based on the current dataset of complete mt genomes strongly support the Stomatopoda is closely related to Euphausiacea. They in turn cluster with Penaeoidea and Caridea clades while other decapods form a separate group, which rejects the monophyly of Decapoda. This challenges the suitability of Stomatopoda as an outgroup of Decapoda in phylogenetic analyses. The basal position of Stomatopoda within Eumalacostraca according to the morphological characters is also questioned. (C) 2010 Elsevier Inc. All rights reserved.

Computing 3-D Motion in Custom Analog and Digital VLSI

This thesis examines a complete design framework for a real-time, autonomous system with specialized VLSI hardware for computing 3-D camera motion. In the proposed architecture, the first step is to determine point correspondences between two images. Two processors, a CCD array edge detector and a mixed analog/digital binary block correlator, are proposed for this task. The report is divided into three parts. Part I covers the algorithmic analysis; part II describes the design and test of a 32$\time $32 CCD edge detector fabricated through MOSIS; and part III compares the design of the mixed analog/digital correlator to a fully digital implementation.

Recognizing 3-D Objects Using 2-D Images

We discuss a strategy for visual recognition by forming groups of salient image features, and then using these groups to index into a data base to find all of the matching groups of model features. We discuss the most space efficient possible method of representing 3-D models for indexing from 2-D data, and show how to account for sensing error when indexing. We also present a convex grouping method that is robust and efficient, both theoretically and in practice. Finally, we combine these modules into a complete recognition system, and test its performance on many real images.

Non-Markovian decoherence: complete positivity and decomposition

In this work, the non-Markovian decoherence is considered in two ways. Firstly, an effective Hamiltonian approach is demonstrated to investigate the decoherence of a quantum system in a non-Markovian environment, in which complete positivity of the reduced dynamics is achieved. This method uses the notion of an effective environment, that is a subsystem of the environment that causes the decoherence. Secondly, the evolution of the system and environment is decomposed, thus partially illuminating how they would interact given that memory effects are allowed. It should be noted that beam splitters and rotators are sufficient to explain this decomposition.

Conformations, vibrational frequencies and Raman intensities of short-chain fatty acid methyl esters using DFT with 6-31G(d) and Sadlej pVTZ basis sets

Density functional calculations, using B3LPY/6-31G(d) methods, have been used to investigate the conformations and vibrational (Raman) spectra of three short-chain fatty acid methyl esters (FAMEs) with the formula CnH2nO2 (n = 3-5). In all three FAMEs, the lowest energy conformer has a simple 'all-trans' structure but there are other conformers, with different torsions about the backbone, which lie reasonably close in energy to the global minimum. One result of this is that the solid samples we studied do not appear to consist entirely of the lowest energy conformer. Indeed, to account for the 'extra' bands that were observed in the Raman data but were not predicted for the all-trans conformer, it was necessary to add-in contributions from other conformers before a complete set of vibrational assignments could be made. Provided this was done, the agreement between experimental Raman frequencies and 6-31G(d) values (after scaling) was excellent, RSD = 12.6 cm(-1). However, the agreement between predicted and observed intensities was much less satisfactory. To confirm the validity of the approach followed by the 6-3 1 G(d) basis set, we used a larger basis set, Sadlej pVTZ, and found that these calculations gave accurate Raman intensities and simulated spectra (summed from two different conformers) that were in quantitative agreement with experiment. In addition, the unscaled Sadlej pVTZ, and the scaled 6-3 1 G(d) calculations gave the same vibrational mode assignments for all bands in the experimental data. This work provides the foundation for calculations on longer-chain FAMEs (which are closer to those found as triglycerides in edible fats and oils) because it shows that scaled 6-3 1 G(d) calculations give equally accurate frequency predictions, and the same vibrational mode assignments, as the much more CPU-expensive Sadlej pVTZ basis set calculations.

An ingress and a complete transit of HD80606 b

We have used four telescopes at different longitudes to obtain near-continuous light-curve coverage of the star HD80606 as it was transited by its ~4-MJup planet. The observations were performed during the predicted transit windows around 2008 October 25 and 2009 February 14. Our data set is unique in that it simultaneously constrains the duration of the transit and the planet's period. Our Markov Chain Monte Carlo analysis of the light curves, combined with constraints from radial-velocity data, yields system parameters consistent with previously reported values. We find a planet-to-star radius ratio marginally smaller than previously reported, corresponding to a planet radius of Rp = 0.921 +/- 0.036RJup.

Analysis of Degradation Data of Poly(L-lactide-co-L,D-lactic actide) and Poly(L-lactide) Obtained at Elevated and Physiological Temperatures Using Mathematical Models

The degradation of resorbable polymeric devices often takes months to years. Accelerated testing at elevated temperatures is an attractive but controversial technique. The purposes of this paper include: (a) to provide a summary of the mathematical models required to analyse accelerated degradation data and to indicate the pitfalls of using these models; (b) to improve the model previously developed by Han and Pan; (c) to provide a simple version of the model of Han and Pan with an analytical solution that is convenient to use; (d) to demonstrate the application of the improved model in two different poly(lactic acid) systems. It is shown that the simple analytical relations between molecular weight and degradation time widely used in the literature can lead to inadequate conclusions. In more general situations the rate equations are only part of a complete degradation model. Together with previous works in the literature, our study calls for care in using the accelerated testing technique.