bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lysine acetylation can generate highly charged enzymes with increased resistance toward irreversible inactivation
Authors: Shaw Bryan F. , Schneider Gregory F. , Bilgiçer Başar , Kaufman George K. , Neveu John M. , Lane William S. , Whitelegge Julian P. , Whitesides George M. 
Published: May 2008

AbstractThis paper reports that the acetylation of lysine ε‐NH3+ groups of α‐amylase—one of the most important hydrolytic enzymes used in industry—produces highly negatively charged variants that are enzymatically active, thermostable, and more resistant than the wild‐type enzyme to irreversible inactivation on exposure to denaturing conditions (e.g., 1 h at 90°C in solutions containing 100‐mM sodium dodecyl sulfate). Acetylation also protected the enzyme against irreversible inactivation by the neutral surfactant TRITON X‐100 (polyethylene glycol p‐(1,1,3,3‐tetramethylbutyl)phenyl ether), but not by the cationic surfactant, dodecyltrimethylammonium bromide (DTAB). The increased resistance of acetylated α‐amylase toward inactivation is attributed to the increased net negative charge of α‐amylase that resulted from the acetylation of lysine ammonium groups (lysine ε‐NH3+ → ε‐NHCOCH3). Increases in the net negative charge of proteins can decrease the rate of unfolding by anionic surfactants, and can also decrease the rate of protein aggregation. The acetylation of lysine represents a simple, inexpensive method for stabilizing bacterial α‐amylase against irreversible inactivation in the presence of the anionic and neutral surfactants that are commonly used in industrial applications.
Use of Laser Microdissection for Phylogenetic Characterization of Polyphosphate-Accumulating Bacteria
Authors: Gloess Stefanie , Grossart Hans-Peter , Allgaier Martin , Ratering Stefan , Hupfer Michael 
Published: May 2008

ABSTRACT
Our novel approach for taxonomic identification of uncultured bacteria harboring specific physiological features in complex environmental samples combines cell collection by laser microdissection and subsequent DNA analysis. The newly developed approach was successfully tested for collection and phylogenetic characterization of polyphosphate-accumulating bacteria in activated sludge and lake sediment.
The Two-Component System CesRK Controls the Transcriptional Induction of Cell Envelope-Related Genes in
Listeria monocytogenes
in Response to Cell Wall-Acting Antibiotics
Authors: Gottschalk Sanne , Bygebjerg-Hove Iver , Bonde Mette , Nielsen Pia Kiil , Nguyen Thanh Ha , Gravesen Anne , Kallipolitis Birgitte H. 
Published: May 2008

ABSTRACT

The two-component system CesRK of
Listeria monocytogenes
responds to cell wall-acting antibiotics. We show here that CesRK controls the transcription of several cell envelope-related genes. The CesRK-dependent induction of these genes may be viewed as an attempt by
L. monocytogenes
to protect itself against the damaging effects of cell wall-acting antibiotics.
Temperature Sensitivity and Cell Division Defects in an
Escherichia coli
Strain with Mutations in
yghB
and
yqjA
, Encoding Related and Conserved Inner Membrane Proteins
Authors: Thompkins Kandi , Chattopadhyay Ballari , Xiao Ying , Henk Margaret C. , Doerrler William T. 
Published: May 2008

ABSTRACT

Ludox density gradients were used to enrich for
Escherichia coli
mutants with conditional growth defects and alterations in membrane composition. A temperature-sensitive mutant named Lud135 was isolated with mutations in two related, nonessential genes:
yghB
and
yqjA
.
yghB
harbors a single missense mutation (G203D) and
yqjA
contains a nonsense mutation (W92TGA) in Lud135. Both mutations are required for the temperature-sensitive phenotype: targeted deletion of both genes in a wild-type background results in a strain with a similar phenotype and expression of either gene from a plasmid restores growth at elevated temperatures. The mutant has altered membrane phospholipid levels, with elevated levels of acidic phospholipids, when grown under permissive conditions. Growth of Lud135 under nonpermissive conditions is restored by the presence of millimolar concentrations of divalent cations Ca
2+
, Ba
2+
, Sr
2+
, or Mg
2+
or 300 to 500 mM NaCl but not 400 mM sucrose. Microscopic analysis of Lud135 demonstrates a dramatic defect at a late stage of cell division when cells are grown under permissive conditions.
yghB
and
yqjA
belong to the conserved and widely distributed
dedA
gene family, for which no function has been reported. The two open reading frames encode predicted polytopic inner membrane proteins with 61% amino acid identity. It is likely that YghB and YqjA play redundant but critical roles in membrane biology that are essential for completion of cell division in
E. coli
.
Use of organophilic clay in sand-bentonite as a barrier to diesel fuel
Authors: Boldt-Leppin Brigitte EJ , Haug Moir D , Headley John V 
Published: May 2008

A laboratory research program was conducted to evaluate the long-term hydraulic performance of sandbentonite liners augmented with organophilic clay and permeated with diesel fuel. This program was also designed to establish guidelines for the incorporation of organophilic clay in sandbentonite liners. The study involved three areas of testing. The first was to characterize the materials. The second was to evaluate various combinations of materials and preparation techniques through hydraulic conductivity tests. The third area involved unconfined infiltration tests. The primary hydraulic conductivity testing was broken into three phases. These investigated the hydraulic conductivity of organophilic sandbentonite liners using various percentages of organophilic clay and evaluated the hydraulic performance of these specimens when permeated with distilled water and diesel fuel. Hydraulic conductivity was measured in specially designed low gradient, low effective stress stainless-steel triaxial permeameters. The results of this test program indicated that small percentages (3%) of organophilic clay in a sandbentonite liner material could effectively be used to avoid desiccation cracking in a liner permeated with petroleum products. High percentages (7.5%) of organophilic clay in a sandbentonite mixture resulted in a liner permeable to water, but reduced permeability to diesel fuel. Key words: organophilic clay, diesel fuel, bentonite, liners, hydraulic conductivity, triaxial permeability testing.
Eighteenth Canadian Geotechnical Colloquium: Limit States Design For Foundations. Part II. Development for the National Building Code of Canada
Authors: Becker Dennis E 
Published: May 2008

The geotechnical engineering profession in Canada is in the process of evaluating limit states design (LSD) for its incorporation into codes of practice for foundation engineering to provide a consistent design approach between geotechnical and structural engineers. This paper describes the work carried out for the initial development of LSD for foundations in the National Building Code of Canada. A load and resistance factor design approach, based on a factored overall geotechnical resistance, is used. The resistance factors for the ultimate limit states of bearing capacity and sliding of shallow and deep foundations are derived from a direct calibration with working stress design (WSD) and from a reliability analysis. The resistance factors derived from both approaches are consistent with each other and provide a reasonably constant reliability index of about 3.0 to 3.5. A relationship is presented that relates the reliability index to a global factor of safety and resistance factor. Design examples are provided that show that the proposed LSD produces designs that are comparable with those produced by traditional WSD. The importance of serviceability limits states is discussed, and the items that require further study and research work to refine code calibration are identified. Key words: limit states design, reliability index, code calibration, resistance factors, foundations, ultimate limit states.
Osteolineage niche cells initiate hematopoietic stem cell mobilization
Authors: Mayack Shane R. , Wagers Amy J. 
Published: May 2008

Abstract
Recent studies have implicated bone-lining osteoblasts as important regulators of hematopoietic stem cell (HSC) self-renewal and differentiation; however, because much of the evidence supporting this notion derives from indirect in vivo experiments, which are unavoidably complicated by the presence of other cell types within the complex bone marrow milieu, the sufficiency of osteoblasts in modulating HSC activity has remained controversial. To address this, we prospectively isolated mouse osteoblasts, using a novel flow cytometry–based approach, and directly tested their activity as HSC niche cells and their role in cyclophosphamide/granulocyte colony-stimulating factor (G-CSF)–induced HSC proliferation and mobilization. We found that osteoblasts expand rapidly after cyclophosphamide/G-CSF treatment and exhibit phenotypic and functional changes that directly influence HSC proliferation and maintenance of reconstituting potential. Effects of mobilization on osteoblast number and function depend on the function of ataxia telangiectasia mutated (ATM), the product of the Atm gene, demonstrating a new role for ATM in stem cell niche activity. These studies demonstrate that signals from osteoblasts can directly initiate and modulate HSC proliferation in the context of mobilization. This work also establishes that direct interaction with osteolineage niche cells, in the absence of additional environmental inputs, is sufficient to modulate stem cell activity.
Precision-mapping and statistical validation of quantitative trait loci by machine learning
Authors: Bedo Justin , Wenzl Peter , Kowalczyk Adam , Kilian Andrzej 
Published: May 2008

Abstract

Background
We introduce a QTL-mapping algorithm based on Statistical Machine Learning (SML) that is conceptually quite different to existing methods as there is a strong focus on generalisation ability. Our approach combines ridge regression, recursive feature elimination, and estimation of generalisation performance and marker effects using bootstrap resampling. Model performance and marker effects are determined using independent testing samples (individuals), thus providing better estimates. We compare the performance of SML against Composite Interval Mapping (CIM), Bayesian Interval Mapping (BIM) and single Marker Regression (MR) on synthetic datasets and a multi-trait and multi-environment dataset of the progeny for a cross between two barley cultivars.

Results
In an analysis of the synthetic datasets, SML accurately predicted the number of QTL underlying a trait while BIM tended to underestimate the number of QTL. The QTL identified by SML for the barley dataset broadly coincided with known QTL locations. SML reported approximately half of the QTL reported by either CIM or MR, not unexpected given that neither CIM nor MR incorporates independent testing. The latter makes these two methods susceptible to producing overly optimistic estimates of QTL effects, as we demonstrate for MR. The QTL resolution (peak definition) afforded by SML was consistently superior to MR, CIM and BIM, with QTL detection power similar to BIM. The precision of SML was underscored by repeatedly identifying, at ≤ 1-cM precision, three QTL for four partially related traits (heading date, plant height, lodging and yield). The set of QTL obtained using a 'raw' and a 'curated' version of the same genotypic dataset were more similar to each other for SML than for CIM or MR.

Conclusion
The SML algorithm produces better estimates of QTL effects because it eliminates the optimistic bias in the predictive performance of other QTL methods. It produces narrower peaks than other methods (except BIM) and hence identifies QTL with greater precision. It is more robust to genotyping and linkage mapping errors, and identifies markers linked to QTL in the absence of a genetic map.
Circadian genomics of the chick pineal gland in vitro
Authors: Karaganis Stephen P , Kumar Vinod , Beremand Phillip D , Bailey Michael J , Thomas Terry L , Cassone Vincent M 
Published: May 2008

Abstract

Background
Chick pinealocytes exhibit all the characteristics of a complete circadian system, comprising photoreceptive inputs, molecular clockworks and an easily measured rhythmic output, melatonin biosynthesis. These properties make the in vitro pineal a particularly useful model for exploring circadian control of gene transcription in a pacemaker tissue, as well as regulation of the transcriptome by primary inputs to the clock (both photic and noradrenergic).

Results
We used microarray analysis to investigate the expression of approximately 8000 genes within cultured pinealocytes subjected to both LD and DD. We report that a reduced subset of genes was rhythmically expressed in vitro compared to those previously published in vivo, and that gene expression rhythms were lower in amplitude, although the functional distribution of the rhythmic transcriptome was largely similar. We also investigated the effects of 6-hour pulses of light or of norepinephrine on gene expression in free-running cultures during both subjective day and night. As expected, both light and norepinephrine inhibited melatonin production; however, the two treatments differentially enhanced or suppressed specific sets of genes in a fashion that was dependent upon time of day.

Conclusion
Our combined approach of utilizing a temporal, photic and pharmacological microarray experiment allowed us to identify novel genes linking clock input to clock function within the pineal. We identified approximately 30 rhythmic, light-responsive, NE-insensitive genes with no previously known clock function, which may play a role in circadian regulation of the pineal. These are candidates for future functional genomics experiments to elucidate their potential role in circadian physiology. Further, we hypothesize that the pineal circadian transcriptome is reduced but functionally conserved in vitro, and supports an endogenous role for the pineal in regulating local rhythms in metabolism, immune function, and other conserved pathways.
The Burdens — pioneers in mental health
Authors: Jancar J. 
Published: May 2008

Rarely in a lifetime do three people contribute to society in so many ways as the Burdens in Bristol. Here are some of their major achievements.The Reverend Burden and his wifw Katharine opened ‘The Royal Victoria Home’, near Horfield Prison, for the care of inebriate women and girls in moral danger in 1895.
Referrals to an out-patient forensic psychology service
Authors: Hambridge J. A. 
Published: May 2008

Following the recommendations of the Butler Report (Home Office, 1975), there has been a slow growth in the number of Regional Secure Units (RSUs) (Snowden, 1985), which aim to assess and treat mentally disordered offenders in England and Wales in conditions of “medium security”. One particular recommendation of the Butler Report was that:“The main emphasis in forensic psychiatric services … should be on community care and out-patient work.” (paragraph 20.14)
North West Division Trainees Day
Authors: Craufurd D. , Davidson I. A. , Simpson N. 
Published: May 2008

The 1984 North West Division Trainees Day took place at Prestwich Hospital on 29 February 1984. This was the first occasion on which it was held at a peripheral hospital.Dr A. A. Campbell (Chairman, NW Division) welcomed trainees to the meeting. He outlined the current programme of the division and encouraged greater trainee participation. This was followed by an explanation of the structure and function of trainee representation, both centrally and locally, from Dr N. Simpson (Honorary Secretary, CTC), who also included a brief report on activities in the past year.
Synaptic transmission in neurons that express theDrosophilaatypical soluble guanylyl cyclases, Gyc-89Da and Gyc-89Db, is necessary for the successful completion of larval and adult ecdysis
Authors: Morton David B. , Stewart Judith A. , Langlais Kristofor K. , Clemens-Grisham Rachel A. , Vermehren Anke 
Published: May 2008

SUMMARYInsect ecdysis is a precisely coordinated series of behavioral and hormonal events that occur at the end of each molt. A great deal is known about the hormonal events that underlie this process, although less is known about the neuronal circuitry involved. In this study we identified two populations of neurons that are required for larval and adult ecdyses in the fruit fly, Drosophila melanogaster (Meigen). These neurons were identified by using the upstream region of two genes that code for atypical soluble guanylyl cyclases to drive tetanus toxin in the neurons that express these cyclases to block their synaptic activity. Expression of tetanus toxin in neurons that express Gyc-89Da blocked adult eclosion whereas expression of tetanus toxin in neurons that express Gyc-89Db prevented the initiation of the first larval ecdysis. Expression of tetanus toxin in the Gyc-89Da neurons also resulted in about 50% lethality just prior to pupariation; however, this was probably due to suffocation in the food as lethality was prevented by stopping the larvae from burrowing deep within the food. This result is consistent with our model that the atypical soluble guanylyl cyclases can act as molecular oxygen detectors. The expression pattern of these cyclases did not overlap with any of the neurons containing peptides known to regulate ecdysis and eclosion behaviors. By using the conditional expression of tetanus toxin we were also able to demonstrate that synaptic activity in the Gyc-89Da and Gyc-89Db neurons is required during early adult development for adult eclosion.
Numerical investigation of the hydrodynamics of carangiform swimming in the transitional and inertial flow regimes
Authors: Borazjani Iman , Sotiropoulos Fotis 
Published: May 2008

SUMMARYWe employ numerical simulation to investigate the hydrodynamics of carangiform locomotion as the relative magnitude of viscous and inertial forces, i.e. the Reynolds number (Re), and the tail-beat frequency,i.e. the Strouhal number (St), are systematically varied. The model fish is a three-dimensional (3D) mackerel-like flexible body undulating with prescribed experimental kinematics of carangiform type. Simulations are carried out for three Re spanning the transitional and inertial flow regimes, Re=300 and 4000 (viscous flow), and ∞ (inviscid flow). For each Re there is a critical Strouhal number, St*, at which the net mean force becomes zero, making constant-speed self-propulsion possible. St* is a decreasing function of Re and approaches the range of St at which most carangiform swimmers swim in nature (St∼0.25) only as Re approaches infinity. The propulsive efficiency at St* is an increasing function of Re while the power required for swimming is decreasing with Re. For all Re, however, the swimming power is shown to be significantly greater than that required to tow the rigid body at the same speed. We also show that the variation of the total drag and its viscous and form components with St depend on the Re. For Re=300, body undulations increase the drag over the rigid body level, while significant drag reduction is observed for Re=4000. This difference is shown to be due to the fact that at sufficiently high Re the drag force variation with St is dominated by its form component variation, which is reduced by undulatory swimming for St&gt;0.2. Finally, our simulations clarify the 3D structure of various wake patterns observed in experiments –single and double row vortices – and suggest that the wake structure depends primarily on the St. Our numerical findings help elucidate the results of previous experiments with live fish, underscore the importance of scale (Re) effects on the hydrodynamic performance of carangiform swimming, and help explain why in nature this mode of swimming is typically preferred by fast swimmers.
Size matters: diversity in swimbladders and Weberian ossicles affects hearing in catfishes
Authors: Lechner Walter , Ladich Friedrich 
Published: May 2008

SUMMARYOtophysine fish possess Weberian ossicles, which connect the swimbladder to the inner ear and improve hearing ability. There is a high diversity in the morphology of the swimbladder and Weberian apparatus in catfishes, which might affect hearing. We have examined these structures in representatives of six families with large, single bladders (Ariidae, Auchenipteridae, Heptapteridae,Malapteruridae, Mochokidae, Pseudopimelodidae) and five subfamilies from two families (Callichthyidae, Loricariidae) having small, paired, encapsulated bladders. We tested their hearing abilities utilizing the non-invasive auditory evoked potential recording technique. Species with single,non-encapsulated, free airbladders possess one, three or four ossicles,whereas species with encapsulated bladders possess one or two. The relative sizes of the bladders and ossicles were significantly smaller in the latter group. All species were able to detect sound stimuli between 50 Hz and 5 kHz. Interspecific differences in hearing sensitivity varied at most by 24 dB below 1 kHz, whilst this variation increased to more than 50 dB at higher frequencies. Catfishes with free bladders had lower thresholds above 1 kHz than those having encapsulated ones. The relative lengths of swimbladders and of ossicular chains were correlated with hearing sensitivity above 1 and 2 kHz, respectively. The number of ossicles affected hearing at 4 and 5 kHz. These results indicate that larger bladders and ossicles as well as higher ossicle numbers improve hearing ability at higher frequencies in catfishes. We furthermore assume that the tiny bladders have minimized their hydrostatic function but were not completely lost because of their auditory function.
Proposed procedure and trial simulation of rail profile evolution due to uniform wear
Authors: Enblom R , Berg M 
Published: May 2008

A procedure for numerical simulation of rail wear and the corresponding profile evolution has been formulated. The wear is assumed to be uniform in the sense that the profiles remain constant along the track portion to be investigated. A simulation set is selected defining the vehicles running on the track, their operating conditions, and contact parameters. Several variations of input data may be included together with the corresponding occurrence probability. Simulation of multi-body dynamics is used to calculate contact forces and positions, and Archard's wear equation is applied for the calculation of wear depth. Wear coefficients as a function of contact pressure and relative sliding velocity are collected from different test results. Trial calculations of four non-lubricated and two lubricated curves with radii from 303 to 802m show qualitatively reasonable results in terms of profile shape development and difference in wear mechanisms between gauge corner and rail head. The wear rates related to traffic tonnage are, however, overestimated and the lubrication efficiency underestimated. It is expected that model refinements in terms of environmental influence and contact stress calculation are useful to improve the quantitative results.