bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating the Central Metabolism of Clostridium thermosuccinogenes
Authors: Koendjbiharie Jeroen Girwar , Wiersma Kilian , van Kranenburg Richard 
Published: April 2018

ABSTRACT

Clostridium thermosuccinogenes
is a thermophilic anaerobic bacterium able to convert various carbohydrates to succinate and acetate as main fermentation products. Genomes of the four publicly available strains have been sequenced, and the genome of the type strain has been closed. The annotated genomes were used to reconstruct the central metabolism, and enzyme assays were used to validate annotations and to determine cofactor specificity. The genes were identified for the pathways to all fermentation products, as well as for the Embden-Meyerhof-Parnas pathway and the pentose phosphate pathway. Notably, a candidate transaldolase was lacking, and transcriptomics during growth on glucose versus that on xylose did not provide any leads to potential transaldolase genes or alternative pathways connecting the C
5
with the C
3
/C
6
metabolism. Enzyme assays showed xylulokinase to prefer GTP over ATP, which could be of importance for engineering xylose utilization in related thermophilic species of industrial relevance. Furthermore, the gene responsible for malate dehydrogenase was identified via heterologous expression in
Escherichia coli
and subsequent assays with the cell extract, which has proven to be a simple and powerful method for the basal characterization of thermophilic enzymes.

IMPORTANCE
Running industrial fermentation processes at elevated temperatures has several advantages, including reduced cooling requirements, increased reaction rates and solubilities, and a possibility to perform simultaneous saccharification and fermentation of a pretreated biomass. Most studies with thermophiles so far have focused on bioethanol production.
Clostridium thermosuccinogenes
seems an attractive production organism for organic acids, succinic acid in particular, from lignocellulosic biomass-derived sugars. This study provides valuable insights into its central metabolism and GTP and PP
i
cofactor utilization.
LaoABCR, a Novel System for Oxidation of Long-Chain Alcohols Derived from SDS and Alkane Degradation in Pseudomonas aeruginosa
Authors: Panasia Gianna , Philipp Bodo 
Published: April 2018

ABSTRACTThe opportunistic pathogenPseudomonas aeruginosastrain PAO1 is able to use a variety of organic pollutants as growth substrates, including the anionic detergent sodium dodecyl sulfate (SDS) and long-chain alkanes. While the enzymes initiating SDS and alkane degradation are well known, the subsequent enzymatic steps for degradation of the derived primary long-chain alcohols have not yet been identified. By evaluating genes specifically induced during growth with SDS, a gene cluster encoding a putative alcohol dehydrogenase (PA0364/LaoA), a probable inner membrane protein (PA0365/LaoB), and a presumable aldehyde dehydrogenase (PA0366/LaoC) was identified and designated the Lao (long-chain-alcohol/aldehyde-oxidation) system. Growth experiments with deletion mutants with SDS, 1-dodecanol, and alkanes revealed that LaoA and LaoB are involved in the degradation of primary long-chain alcohols. Moreover, detection of 1-dodecanol oxidation in cell extracts by activity staining revealed an interdependency of LaoA and LaoB for efficient 1-dodecanol oxidation. Anin silicoanalysis yielded no well-characterized homologue proteins for LaoA and LaoB. Furthermore, a gene adjacent to thelaogene cluster encodes a putative transcriptional regulator (PA0367/LaoR). AlaoRdeletion mutant exhibited constitutive expression of LaoA and LaoB, indicating that LaoR is a repressor for the expression oflaoABC. Taken together, these results showed that the proteins LaoA and LaoB constitute a novel oxidation system for long-chain alcohols derived from pollutants.IMPORTANCEThe versatile and highly adaptive bacteriumPseudomonas aeruginosa is able to colonize a variety of habitats, including anthropogenic environments, where it is often challenged with toxic compounds. Its ability to degrade such compounds and to use them as growth substrates can significantly enhance spreading of this opportunistic pathogen in hygienic settings, such as clinics or water distribution systems. Thus, knowledge about the metabolism ofP. aeruginosacan contribute to novel approaches for preventing its growth and reducing nosocomial infections. As the Lao system is important for the degradation of two different classes of pollutants, the identification of these novel enzymes can be a useful contribution for developing effective antibacterial strategies.
Draft Genome Sequence of FGL03-6, a Race 1 Strain of Fusarium oxysporum f. sp. conglutinans, the Causal Agent of Cabbage Fusarium Wilt
Authors: Lv Honghao , Yang Yuhong , Liu Xing , Ling Jian , Fang Zhiyuan , Yang Limei , Zhang Yangyong , Wang Yong 
Published: April 2018

ABSTRACT

We present here the draft genome sequence of FGL03-6, a race 1 strain of
Fusarium oxysporum
f. sp.
conglutinans
, the pathogen causing
Fusarium
yellows of cabbage. The FGL03-6 genome consists of 414 scaffolds with 61,662,789 bp (GC content, 47.9%) and 9,790 predicted genes.
Draft Genome Assembly of the Sheep Scab Mite, Psoroptes ovis
Authors: Burgess Stewart T. G. , Bartley Kathryn , Marr Edward J. , Wright Harry W. , Weaver Robert J. , Prickett Jessica C. , Hughes Margaret , Haldenby Sam , Thi Le Phuong , Rombauts Stephane , Van Leeuwen Thomas , Van de Peer Yves , Nisbet Alasdair J. 
Published: April 2018

ABSTRACT

Sheep scab, caused by infestation with
Psoroptes ovis
, is highly contagious, results in intense pruritus, and represents a major welfare and economic concern. Here, we report the first draft genome assembly and gene prediction of
P. ovis
based on PacBio
de novo
sequencing. The ∼63.2-Mb genome encodes 12,041 protein-coding genes.
Draft Genome Sequence of Mycobacterium porcinum CSURP1564
Authors: Bouam A. , Levasseur A. , Drancourt M. 
Published: April 2018

ABSTRACTMycobacterium porcinumis a rapidly growing environmental mycobacterium responsible for opportunistic infections. The 7,025,616-bp draft genome ofM. porcinumstrain CSURP1564 exhibits a 66.71% G+C content, 6,687 protein-coding genes, and 65 predicted RNA genes.In silicoDNA-DNA hybridization confirms its assignment to theMycobacterium fortuitumcomplex.
Draft Genome Sequence of Pseudomonas sp. Strain LLC-1 (NBRC 111237), Capable of Metabolizing Lignin-Derived Low-Molecular-Weight Compounds
Authors: Hirose Jun , Tsuda Naoki , Miyatake Munetoshi , Yokoi Haruhiko , Shimodaira Jun 
Published: April 2018

ABSTRACT

Pseudomonas
sp. strain LLC-1 (NBRC 111237), isolated from soil, metabolizes lignin-derived low-molecular-weight compounds and utilizes vanillin and vanillic acid as its sole sources of carbon. Here, we report the draft genome sequence of
Pseudomonas
sp. strain LLC-1.
Complete Genome Sequence of a Natural Escherichia coli O145:H11 Isolate That Belongs to Phylogroup A
Authors: Carter Michelle Qiu , Pham Antares 
Published: April 2018

ABSTRACT

Escherichia coli
O145:H11 strain RM14721 was originally isolated from wildlife feces near a leafy greens-growing region in Yuma, AZ. This strain was initially positive for
stx
1
; however, in subsequent cultures,
stx
1
was not detected by PCR. Here, we report the complete genome sequence and annotation of RM14721.
Entamoeba histolytica Alters Ileal Paneth Cell Functions in Intact and Muc2 Mucin Deficiency
Authors: Cobo Eduardo R. , Holani Ravi , Moreau France , Nakamura Kiminori , Ayabe Tokiyoshi , Mastroianni Jennifer R. , Eriguchi Yoshihiro , Ouellette Andre , Chadee Kris 
Published: April 2018

ABSTRACTEnteric α-defensins, termed cryptdins (Crps) in mice, and lysozymes secreted by Paneth cells contribute to innate host defense in the ileum. Antimicrobial factors, including lysozymes and β-defensins, are often embedded in luminal glycosylated colonic Muc2 mucin secreted by goblet cells that form the protective mucus layer critical for gut homeostasis and pathogen invasion. In this study, we investigated ileal innate immunity againstEntamoeba histolytica, the causative agent of intestinal amebiasis, by inoculating parasites in closed ileal loops inMuc2+/+andMuc2−/−littermates and quantifying Paneth cell localization (lysozyme expression) and function (Crp secretion). Relative toMuc2+/+littermates,Muc2−/−littermates showed a disorganized mislocalization of Paneth cells that was diffusely distributed, with elevated lysozyme secretion in the crypts and on villi in response toE. histolytica. Inhibition ofE. histolyticaGal/GalNAc lectin (Gal-lectin) binding with exogenous galactose andEntamoeba histolyticacysteine proteinase 5 (EhCP5)-negativeE. histolyticahad no effect on parasite-induced erratic Paneth cell lysozyme synthesis. Although the basal ileal expression ofCrpgenes was unaffected inMuc2−/−mice in response toE. histolytica, there was a robust release of proinflammatory cytokines and Crp peptide secretions in luminal exudates that was also present in the colon. Interestingly,E. histolytica-secreted cysteine proteinases cleaved the proregion of Crp4 but not the active form. These findings define Muc2 mucin as an essential component of ileal barrier function that regulates the localization and function of Paneth cells critical for host defense against microbes.
Mortality in coeliac disease: a population-based cohort study from a single centre in Southern Derbyshire, UK
Authors: Holmes Geoffrey K T , Muirhead Andrew 
Published: April 2018

ObjectiveWith the advent of screening tests, it was hypothesised that milder cases of coeliac disease coming to diagnosis might have reduced risk of mortality. An earlier publication did not support this view. We have re-examined this issue employing a larger number of patients followed for a further 8 years.DesignPatients with coeliac disease from Southern Derbyshire, UK, were followed prospectively from 1978 to 2014 and included those diagnosed by biopsy and serology. Causes of death were ascertained. Standardised mortality ratios were calculated for all deaths, cardiovascular disease, malignancy, accidents and suicides, respiratory and digestive disease. Ratios were calculated for individual causes. Analysis centred on the postdiagnosis period that included follow-up time beginning 2 years from the date of coeliac disease diagnosis to avoid ascertainment bias. Patients were stratified according to date of diagnosis to reflect increasing use of serological methods.ResultsAll-cause mortality increase was 57%. Mortality in the serology era declined overall. Mortality from cardiovascular disease, specifically, decreased significantly over time. Death from respiratory disease significantly increased in the postdiagnosis period. The standardised mortality ratio for non-Hodgkin’s lymphoma was 6.32, for pneumonia 2.58, for oesophageal cancer 2.80 and for liver disease 3.10. Survival in those who died after diagnosis increased by three times over the past three decades.ConclusionsSerological testing has impacted on the risk of mortality in coeliac disease. There is an opportunity to improve survival by implementing vaccination programmes for pneumonia and more prompt, aggressive treatments for liver disease.
Uniform zinc thioporphyrazine nanosphere by self-assembly and the photocatalytic performance
Authors: Yang Changjun , Gao Lanchang , Zhang Bingguang , Zhang Zehui , Deng Kejian 
Published: April 2018

A novel strategy for the synthesis of zinc thioporphyrazine nanospheres is presented. The uniform spheres were fabricated through a polymerization reaction without using any template or emulsifier, which result from the covalent links between zinc tetra(2,3-bis(pentenylthio)porphyrazine (ZnPz) possessing eight long flexible chains in periphery and each with one terminal olefin group. A possible mechanism to explain the self-assembly of ZnPz nanospheres was also illuminated through monitoring nanosphere formation by means of transmission electron microscopy (TEM). More importantly, ZnPz nanospheres can effectively activate dioxygen in aqueous media under simulated sunlight irradiation, and showed significantly improved photocatalytic activity for the degradation of Rhodamine B (RhB) as compared to monomeric ZnPz. Furthermore, the reactive oxygen species derived from ZnPz nanospheres under light irradiation were determined by electron paramagnetic resonance (EPR) technology, indicating that singlet oxygen ([Formula: see text]O[Formula: see text] and hydroxyl radical (•OH) are the major reactive oxygen species. The facile synthetic methodology and the enhanced photocatalytic performance of the ZnPz nanospheres endow this novel material with the potential of being an efficient biomimetic photocatalyst for wastewater treatment.
Hexahedral-Dominant Meshing
Authors: Sokolov Dmitry , Ray Nicolas , Untereiner Lionel , Lévy Bruno 
Published: April 2018

This article introduces a method that generates a hexahedral-dominant mesh from an input tetrahedral mesh. It follows a three-step pipeline similar to the one proposed by Carrier Baudoin et al.: (1) generate a frame field, (2) generate a pointset
P
that is mostly organized on a regular grid locally aligned with the frame field, and (3) generate the hexahedral-dominant mesh by recombining the tetrahedra obtained from the constrained Delaunay triangulation of
P
.

For step (1), we use a state-of-the-art algorithm to generate a smooth frame field. For step (2), we introduce an extension of Periodic Global Parameterization to the volumetric case. As compared with other global parameterization methods (such as CubeCover), our method relaxes some global constraints to avoid creating degenerate elements, at the expense of introducing some singularities that are meshed using non-hexahedral elements. For step (3), we build on the formalism introduced by Meshkat and Talmor, fill in a gap in their proof, and provide a complete enumeration of all the possible recombinations, as well as an algorithm that efficiently detects all the matches in a tetrahedral mesh.
The method is evaluated and compared with the state of the art on a database of examples with various mesh complexities, varying from academic examples to real industrial cases. Compared with the method of Carrier-Baudoin et al., the method results in better scores for classical quality criteria of hexahedral-dominant meshes (hexahedral proportion, scaled Jacobian, etc.). The method also shows better robustness than CubeCover and its derivatives when applied to complicated industrial models.
Network Structure Inference, A Survey
Authors: Brugere Ivan , Gallagher Brian , Berger-Wolf Tanya Y. 
Published: April 2018

Networks represent relationships between entities in many complex systems, spanning from online social interactions to biological cell development and brain connectivity. In many cases, relationships between entities are unambiguously known: are two users “friends” in a social network? Do two researchers collaborate on a published article? Do two road segments in a transportation system intersect? These are directly observable in the system in question. In most cases, relationships between nodes are not directly observable and must be inferred: Does one gene regulate the expression of another? Do two animals who physically co-locate have a social bond? Who infected whom in a disease outbreak in a population?
Existing approaches for inferring networks from data are found across many application domains and use specialized knowledge to infer and measure the quality of inferred network for a specific task or hypothesis. However, current research lacks a rigorous methodology that employs standard statistical validation on inferred models. In this survey, we examine (1) how network representations are constructed from underlying data, (2) the variety of questions and tasks on these representations over several domains, and (3) validation strategies for measuring the inferred network’s capability of answering questions on the system of interest.
Approximation Algorithms for Minimum-Load
k
-Facility Location
Authors: Ahmadian Sara , Behsaz Babak , Friggstad Zachary , Jorati Amin , Salavatipour Mohammad R. , Swamy Chaitanya 
Published: April 2018

We consider a facility-location problem that abstracts settings where the cost of serving the clients assigned to a facility is incurred by the facility. Formally, we consider the
minimum-load k-facility location
(ML
k
FL) problem, which is defined as follows. We have a set
F
of facilities, a set
C
of clients, and an integer
k
≥ 0. Assigning client
j
to a facility
f
incurs a connection cost
d
(
f
,
j
). The goal is to open a set
F
⊆
F
of
k
facilities and assign each client
j
to a facility
f
(
j
)∈
F
so as to minimize max

f
∈

F
∑

j
∈
C
:
f
(
j
)=
f

d
(
f
,
j
); we call ∑

j
∈
C
:
f
(
j
)=
f

d
(
f
,
j
) the
load
of facility
f
. This problem was studied under the name of min-max star cover in References [3, 7], who (among other results) gave bicriteria approximation algorithms for ML
k
FL for when
F
=
C
. ML
k
FL is rather poorly understood, and only an
O
(
k
)-approximation is currently known for ML
k
FL,
even for line metrics
.

Our main result is the
first polytime approximation scheme
(PTAS) for ML
k
FL on line metrics (note that no non-trivial true approximation of any kind was known for this metric). Complementing this, we prove that ML
k
FL is strongly
NP
-hard on line metrics. We also devise a quasi-PTAS for ML
k
FL on tree metrics. ML
k
FL turns out to be surprisingly challenging even on line metrics and resilient to attack by a variety of techniques that have been successfully applied to facility-location problems. For instance, we show that (a) even a configuration-style LP-relaxation has a bad integrality gap and (b) a multi-swap
k
-median style local-search heuristic has a bad locality gap. Thus, we need to devise various novel techniques to attack ML
k
FL.

Our PTAS for line metrics consists of two main ingredients. First, we prove that there always exists a near-optimal solution possessing some nice structural properties. A novel aspect of this proof is that we first move to a mixed-integer LP (MILP) encoding of the problem and argue that a MILP-solution minimizing a certain potential function possesses the desired structure and then use a rounding algorithm for the generalized-assignment problem to “transfer” this structure to the rounded integer solution. Complementing this, we show that these structural properties enable one to find such a structured solution via dynamic programming.
Choosing a foveal goal recruits the saccadic system during smooth pursuit
Authors: Heinen Stephen J. , Badler Jeremy B. , Watamaniuk Scott N. J. 
Published: April 2018

Models of smooth pursuit eye movements stabilize an object’s retinal image, yet pursuit is peppered with small, destabilizing “catch-up” saccades. Catch-up saccades might help follow a small, spot stimulus used in most pursuit experiments, since fewer of them occur with large stimuli. However, they can return when a large stimulus has a small central feature. It may be that a central feature on a large object automatically recruits the saccadic system. Alternatively, a cognitive choice is made that the feature is the pursuit goal, and the saccadic system is then recruited to pursue it. Observers pursued a 5-dot stimulus composed of a central dot surrounded by four peripheral dots arranged as a diamond. An attention task specified the pursuit goal as either the central element, or the diamond gestalt. Fewer catch-up saccades occurred with the Gestalt goal than with the central goal, although the additional saccades with the central goal neither enhanced nor impeded pursuit. Furthermore, removing the central element from the diamond goal further reduced catch-up saccade frequency, indicating that the central element automatically triggered some saccades. Higher saccade frequency was not simply due to narrowly focused attention, since attending a small peripheral diamond during pursuit elicited fewer saccades than attending the diamond positioned foveally. The results suggest some saccades are automatically elicited by a small central element, but when it is chosen as the pursuit goal the saccadic system is further recruited to pursue it. NEW & NOTEWORTHY Smooth-pursuit eye movements stabilize retinal image motion to prevent blur. Curiously, smooth pursuit is frequently supplemented by small catchup saccades that could reduce image clarity. Catchup saccades might only be needed to pursue small laboratory stimuli, as they are infrequent during large object pursuit. Yet large objects with central features revive them. Here, we show that voluntarily selecting a feature as the pursuit goal elicits saccades that do not help pursuit.
Pulsed infrared releases Ca2+from the endoplasmic reticulum of cultured spiral ganglion neurons
Authors: Barrett John N. , Rincon Samantha , Singh Jayanti , Matthewman Cristina , Pasos Julio , Barrett Ellen F. , Rajguru Suhrud M. 
Published: April 2018

Inner ear spiral ganglion neurons were cultured from day 4 postnatal mice and loaded with a fluorescent Ca2+indicator (fluo-4, -5F, or -5N). Pulses of infrared radiation (IR; 1,863 nm, 200 µs, 200–250 Hz for 2–5 s, delivered via an optical fiber) produced a rapid, transient temperature increase of 6–12°C (above a baseline of 24–30°C). These IR pulse trains evoked transient increases in both nuclear and cytosolic Ca2+concentration ([Ca2+]) of 0.20–1.4 µM, with a simultaneous reduction of [Ca2+] in regions containing endoplasmic reticulum (ER). IR-induced increases in cytosolic [Ca2+] continued in medium containing no added Ca2+(±Ca2+buffers) and low [Na+], indicating that the [Ca2+] increase was mediated by release from intracellular stores. Consistent with this hypothesis, the IR-induced [Ca2+] response was prolonged and eventually blocked by inhibition of ER Ca2+-ATPase with cyclopiazonic acid, and was also inhibited by a high concentration of ryanodine and by inhibitors of inositol (1,4,5)-trisphosphate (IP3)-mediated Ca2+release (xestospongin C and 2-aminoethoxydiphenyl borate). The thermal sensitivity of the response suggested involvement of warmth-sensitive transient receptor potential (TRP) channels. The IR-induced [Ca2+] increase was inhibited by TRPV4 inhibitors (HC-067047 and GSK-2193874), and immunostaining of spiral ganglion cultures demonstrated the presence of TRPV4 and TRPM2 that colocalized with ER marker GRP78. These results suggest that the temperature sensitivity of IR-induced [Ca2+] elevations is conferred by TRP channels on ER membranes, which facilitate Ca2+efflux into the cytosol and thereby contribute to Ca2+-induced Ca2+-release via IP3and ryanodine receptors.NEW & NOTEWORTHY Infrared radiation-induced photothermal effects release Ca2+from the endoplasmic reticulum of primary spiral ganglion neurons. This Ca2+release is mediated by activation of transient receptor potential (TRPV4) channels and involves amplification by Ca2+-induced Ca2+-release. The neurons immunostained for warmth-sensitive channels, TRPV4 and TRPM2, which colocalize with endoplasmic reticulum. Pulsed infrared radiation provides a novel experimental tool for releasing intracellular Ca2+, studying Ca2+regulatory mechanisms, and influencing neuronal excitability.