bluuebunny/crossref_metadata_2025 huggingface dataset:
Homogeneous catalytic hydrogenation of unsaturated fats: Iron Pentacarbonyl
Authors: Frankel E. N. , Peters Helen M. , Jones E. P. , Dutton H. J.
Published: January 2009

Iron pentacarbonyl is an effective homogeneous catalyst for the reduction of polyunsaturated fats. Hydrogenation of soybean oil and its methyl esters has been achieved at 180C, hydrogen pressures of 100‐1,000 psi, and 0.05舑0.5 molar concentrations of catalyst. Analyses of partially reduced products show considerable isomerization of double bonds, reduction of linolenate and linoleate with little or no increase in stearate, and accumulation ofcis,trans‐ andtrans, trans‐conjugated dienes, and isolatedtrans monoenes. The unreduced trienes include diene conjugated fatty esters. The nonconjugated dienes contain large amounts oftrans and nonalkali conjugatable unsaturation. Considerable scattering of double bonds is evident in different fractions between the C4 and C16 positions. Complex formation between iron carbonyl and unsaturated fats is also indicated.

The course of the homogeneous hydrogenation catalyzed by iron pentacarbonyl appears similar to the heterogeneous catalytic reaction. Metal carbonyls are well known for their isomerizing effects and their ability to form stable complexes with olefins. These homogeneous complexes provide suitable model systems to study the mechanism of catalytic hydrogenation of fats.
New nonionic detergents derived from epoxidized oils
Authors: Johnson K. L.
Published: January 2009

A new class of nonionic detergents derived from epoxidized oils having an oxirane oxygen content of 6舑10% is discussed. Their mol wt and micellar wt distributions, as studied in the ultracentrifuge, are presented and cited as partial explanations for their unique properties as compared to conventional nonionic detergents such as ethoxylated alkyl phenols. Critical micelle concentrations (CMC) determined by light scattering data are presented.
Chromatographic analysis of sucrose esters of long chain fatty acids
Authors: Mima Hiroyuki , Kitamori Nobuyuki
Published: January 2009

The procedure of the quantitative analysis of the components of sucrose ester products is described. By thin‐layer chromatography, sucrose ester products have been separated into their components: mono‐,di‐,tri‐, and higher esters. The individual components have been extracted from the plate and determined colorimetrically by using anthrone reagent. Standard substances of monoesters, diesters and triesters, which have been synthesized from gas‐chromatographically pure methyl esters of fatty acids, have been isolated by column chromatography and identified by elemental analysis, colorimetric determination and N.M.R. determination.
Triglyceride composition of native and rearranged butter and coconut oils
Authors: Kuksis A. , Mccarthy M. J. , Beveridge J. M. R.
Published: January 2009

Triglyceride gas chromatography was used for quantitative fractionation by carbon number of native and rearranged butter and coconut oils. Significant differences in the triglyceride type distributions between the corresponding native and chemically modified fats were found. Increased proportions of both short and long chain triglycerides occurred in the rearranged butterfat. In reconstituted coconut oil there was a shift towards the shorter chain length triglycerides. The natural and the rearranged triglyceride distributions of the two oils were shown to differ from the random distributions calculated for the corresponding fatty acid complements. The butterfat triglyceride compositions showed greater deviations from random than did the coconut oils. The modified oils approached random distributions more closely than did the native ones. In both cases the deviations from truly random populations appeared to be in the direction anticipated on the basis of chemical reactivity.
Raney nickel catalyst of improved stability and reactivity in the hydrogenation of triglycerides
Authors: Tɒmer H. V. , Feuge R. O. , Cousins E. R.
Published: January 2009

The degree of activity of Raney nickel catalysts in the hydrogenation of triglycerides has been found to vary considerably with and to depend upon unknown factors in the original alloy. Highly active preparations of Raney nickel rapidly lost their activity when stored in absolute ethanol due to the formation of acetaldehyde. Loss of activity was associated with the amount of residual aluminum in the catalyst. The nickel was found to dissolve to some extent in the acetal‐dehyde‐ethanol solution. Catalysts deactivated by acetaldehyde could be reactivated to a greater degree of activity than that possessed originally by treating with acetic acid. The activity of the original Raney nickel catalyst was preserved to a greater extent by storage in dioxane instead of ethanol.
Factors affecting the rate of deterioration in the frying qualities of fats. 1 i. exposure to air
Authors: Rock S. P. , Roth H.
Published: January 2009

The effect of heating fats in air and the effect of heating fats in an inert atmosphere were compared, and the relationship of air to changes in the frying characteristics of fat studied. The frying characteristics of a fat did not change to an extent that is commercially significant even after 48 hr heating at 375F in the absence of air; fats heated under identical conditions but in the presence of air, changed radically. It was found, also, that fat which had changed appreciably in frying characteristics when heated in air did not continue to change significantly when heated further under nitrogen. Hence, presence of oxygen was shown to be a necessary condition for the deterioration of the frying qualities of fat at frying temp. Rate of change of the frying characteristics was found to be directly proportional to the degree of exposure of fat surface to the oxygen.
Molecular weight distribution of nonionic surfactants. III. Foam, wetting, detergency, emulsification and solubility properties of normal distribution and homogeneous p,t‐octylphenoxyethoxyethanols
Authors: Crook E. H. , Fordyce D. B. , Trebbi G. F.
Published: January 2009

The effect of mol wt distribution on the foaming, wetting, detergency, emulsification and solubility properties of p,t‐octylphenoxyethoxy‐ethanols (OPE's) has been studied by comparing normal distribution and homogeneous compounds: Ross‐Miles foam studies indicate that, although homogeneous OPE7‐10 are higher in initial foam height than normal distribution OPE7‐10, their foam stability is poorer. Hard surface and textile wetting were studied by contact angle determinations and the Draves' skein test, respectively. An exact correlation exists between hard surface wetting by solutions of OPE's of a Teflon surface and surface tension lowering. Normal distribution OPE's are, in general, better hard surface wetting agents than the corresponding homogeneous compounds. In textile wetting, normal distribution OPE5‐10 are approximately equivalent in performance and by implication are probably equivalent in wetting performance to the corresponding homogeneous compounds. Hard surface detergency studies show that normal distribution OPE's are generally slightly superior in detersive power to homogeneous OPE's at corresponding ethylene oxide chain lengths. OPE10 is the best hard surface detergent of the OPE series, there being no distinguishable difference in performance between homogeneous and normal distribution OPE10. Emulsification studies on the system, water‐isooctane, show that only normal distribution OPE5 is capable of forming stable o/w emulsions. Both homogeneous and normal distribution OPE3 and OPE4 form stable w/o (invert) emulsions. Solubility studies in isooctane and Ultrasene show that homogeneous OPE4 is soluble at lower temp than the corresponding normal distribution compound. Studies of aqueous OPE solutions at temp above their cloud points show that solubility of both homogeneous and normal distribution materials is of the same order of magnitude as their critical micelle concn and that homogeneous OPE4 is more soluble than normal distribution OPE4.
The preparation and plasticizing characteristics of pipendides of long chain fatty acids and n‐fatty acyl derivatives of other cyclic imines
Authors: Mod R. R. , Magne F. C. , Skau E. L.
Published: January 2009

Forty‐six N‐acyl derivatives of cyclic imines have been prepared, characterized, and screened as primary plasticizers for poly (vinyl chloridevinyl acetate) copolymer. Among these were the piperidides of decanoic, palmitic, stearic, oleic, erucic, ricinoleic, epoxystearic, epoxyoleic, diepoxystearic, sebacic, pinic, cottonseed, hydrogenated cottonseed, rapeseed,Limnanthes douglasii, animal, 2‐ethylhexanoic, naphthenic, and dimer acids, as well as the N‐oleoyl derivatives of a number of substituted piperidines and other cyclic imines including pyrrolidine, piperazine, hexamethylenimme, tetrahydroquinolme, 3‐azabicyclo [3.2.2] nonane, dipyridylamine, and carbazole.

In general these amides of the 5‐,6‐, and 7‐membered cyclic imines exhibited exceptionally high plasticizing efficiencies. The compatibilities observed were the best to date for fatty acid derivatives on the basis of both individual and ternary fatty acid composition‐compatibility data. Several of these amides exhibited low‐temp characteristics in the adipate plasticizer range without the adverse volatility characteristics of the adipates. There are indications that some of them have appreciable antifungal activity. It has been concluded that cyclic imines will, in general, produce fatty acid derivatives of better than average compatibility as vinyl plasticizers.
Rehabilitation Needs of Combat‐Injured Service Members Admitted to the VA Polytrauma Rehabilitation Centers: The Role of PM&R in the Care of Wounded Warriors
Authors: Sayer Nina A. , Cifu David X. , McNamee Shane , Chiros Christine E. , Sigford Barbara J. , Scott Steve , Lew Henry L.
Published: January 2009

Objective

To describe the rehabilitation course of combat‐injured service members who sustained polytraumatic injuries during the current wars in and around Iraq and Afghanistan.

Design

Retrospective descriptive analysis.

Setting

Department of Veterans Administration Polytrauma Rehabilitation Centers (PRCs).

Participants

One hundred eighty‐eight consecutive, acutely combat‐injured service members suffering polytraumatic injuries requiring inpatient rehabilitation and being treated at PRCs between October 2001 and January 2006.

Interventions

Not applicable.

Main Outcome Measures

Medications prescribed, devices used, injuries and impairment information, and consultative services.

Results

Ninety‐three percent of the patients had sustained a traumatic brain injury (TBI) and more than half of these were incurred secondary to blast explosions. Over half of the patients had infections or surgeries prior to PRC admission that required continued medical attention during their stay. Pain and mental health issues were present in 100% and 39%, respectively, of all patients admitted and added complexity to the brain injury rehabilitation process. Common treatment needs included cognitive‐behavioral interventions, pain care, assistive devices, mental health interventions for both patients and their families, and specialty consultations, in particular to ophthalmology, otolaryngology, and neurology.

Conclusions

Combat‐injured polytrauma patients have complex rehabilitation needs that require a high level of specialized training and skill. Physical medicine and rehabilitation specialists treating war injured service members need a high level of expertise in assessment and treatment of co‐occurring pain, TBI, and stress disorders. Physiatrists are playing an important role in providing and coordinating the rehabilitation care for individuals with significant polytraumatic war injuries from the Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) conflicts.
Practice Parameter: The Evaluation of Distal Symmetric Polyneuropathy: The Role of Laboratory and Genetic Testing (An Evidence‐Based Review)
Authors: England J.D. , Gronseth G.S. , Franklin G. , Carter G.T. , Kinsella L.J. , Cohen J.A. , Asbury A.K. , Szigeti K. , Lupski J.R. , Latov N. , Lewis R.A. , Low P.A. , Fisher M.A. , Herrmann D.N. , Howard J.F. , Lauria G. , Miller R.G. , Polydefkis M. , Sumner A.J.
Published: January 2009

Background

Distal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence‐based guidelines regarding the role of laboratory and genetic tests for the assessment of DSP.

Methods

A literature review using MEDLINE, EMBASE, Science Citation Index and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four‐tiered level of evidence scheme and recommendations were based upon the level of evidence.

Results and Conclusions

1. Screening laboratory tests may be considered for all patients with polyneuropathy (Level C). Those tests that provide the highest yield of abnormality are blood glucose, serum B12 with metabolites (methylmalonic acid with or without homocysteine) and serum protein immunofixation electrophoresis (Level C). If there is no definite evidence of diabetes mellitus by routine testing of blood glucose, testing for impaired glucose tolerance may be considered in distal symmetric sensory polyneuropathy (Level C). 2. Genetic testing is established as useful for the accurate diagnosis and classification of hereditary neuropathies (Level A). Genetic testing may be considered in patients with cryptogenic polyneuropathy who exhibit a hereditary neuropathy phenotype (Level C). Initial genetic testing should be guided by the clinical phenotype, inheritance pattern, and electrodiagnostic (EDX) features and should focus on the most common abnormalities which are CMT1A duplication/HNPP deletion, Cx32 (GJB1), and MFN2 mutation screening. There is insufficient evidence to determine the usefulness of routine genetic testing in patients with cryptogenic polyneuropathy who do not exhibit a hereditary neuropathy phenotype (Level U).
Insulin levels control female germline stem cell maintenance via the niche in
Drosophila
Authors: Hsu Hwei-Jan , Drummond-Barbosa Daniela
Published: January 2009

Stem cell maintenance depends on local signals provided by specialized microenvironments, or niches, in which they reside. The potential role of systemic factors in stem cell maintenance, however, has remained largely unexplored. Here, we show that insulin signaling integrates the effects of diet and age on germline stem cell (GSC) maintenance through the dual regulation of cap cell number (via Notch signaling) and cap cell–GSC interaction (via E-cadherin) and that the normal process of GSC and niche cell loss that occurs with age can be suppressed by increased levels of insulin-like peptides. These results underscore the importance of systemic factors for the regulation of stem cell niches and, thereby, of stem cell numbers.
PTMap—A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites
Authors: Chen Yue , Chen Wei , Cobb Melanie H. , Zhao Yingming
Published: January 2009

We present sequence alignment software, called PTMap, for the accurate identification of full-spectrum protein post-translational modifications (PTMs) and polymorphisms. The software incorporates several features to improve searching speed and accuracy, including peak selection, adjustment of inaccurate mass shifts, and precise localization of PTM sites. PTMap also automates rules, based mainly on unmatched peaks, for manual verification of identified peptides. To evaluate the quality of sequence alignment, we developed a scoring system that takes into account both matched and unmatched peaks in the mass spectrum. Incorporation of these features dramatically increased both accuracy and sensitivity of the peptide- and PTM-identifications. To our knowledge, PTMap is the first algorithm that emphasizes unmatched peaks to eliminate false positives. The superior performance and reliability of PTMap were demonstrated by confident identification of PTMs on 156 peptides from four proteins and validated by MS/MS of the synthetic peptides. Our results demonstrate that PTMap is a powerful algorithm capable of identification of all possible protein PTMs with high confidence.
Basis for the preferential activation of cardiac sympathetic nerve activity in heart failure
Authors: Ramchandra Rohit , Hood Sally G. , Denton Derek A. , Woods Robin L. , McKinley Michael J. , McAllen Robin M. , May Clive N.
Published: January 2009

In heart failure (HF), sympathetic nerve activity is increased. Measurements in HF patients of cardiac norepinephrine spillover, reflecting cardiac sympathetic nerve activity (CSNA), indicate that it is increased earlier and to a greater extent than sympathetic activity to other organs. This has important consequences because it worsens prognosis, provoking arrhythmias and sudden death. To elucidate the mechanisms responsible for the activation of CSNA in HF, we made simultaneous direct neural recordings of CSNA and renal SNA (RSNA) in two groups of conscious sheep: normal animals and animals in HF induced by chronic, rapid ventricular pacing. In normal animals, the level of activity, measured as burst incidence (bursts of pulse related activity/100 heart beats), was significantly lower for CSNA (30 ± 5%) than for RSNA (94 ± 2%). Furthermore, the resting level of CSNA, relative to its maximum achieved while baroreceptors were unloaded by reducing arterial pressure, was set at a much lower percentage than RSNA. In HF, burst incidence of CSNA increased from 30 to 91%, whereas burst incidence of RSNA remained unaltered at 95%. The sensitivity of the control of both CSNA and RSNA by the arterial baroreflex remained unchanged in HF. These data show that, in the normal state, the resting level of CSNA is set at a lower level than RSNA, but in HF, the resting levels of SNA to both organs are close to their maxima. This finding provides an explanation for the preferential increase in cardiac norepinephrine spillover observed in HF.
Module networks revisited: computational assessment and prioritization of model predictions
Authors: Joshi Anagha , De Smet Riet , Marchal Kathleen , Van de Peer Yves , Michoel Tom
Published: January 2009

Motivation: The solution of high-dimensional inference and prediction problems in computational biology is almost always a compromise between mathematical theory and practical constraints, such as limited computational resources. As time progresses, computational power increases but well-established inference methods often remain locked in their initial suboptimal solution.

Results: We revisit the approach of Segal et al. to infer regulatory modules and their condition-specific regulators from gene expression data. In contrast to their direct optimization-based solution, we use a more representative centroid-like solution extracted from an ensemble of possible statistical models to explain the data. The ensemble method automatically selects a subset of most informative genes and builds a quantitatively better model for them. Genes which cluster together in the majority of models produce functionally more coherent modules. Regulators which are consistently assigned to a module are more often supported by literature, but a single model always contains many regulator assignments not supported by the ensemble. Reliably detecting condition-specific or combinatorial regulation is particularly hard in a single optimum but can be achieved using ensemble averaging.

Availability: All software developed for this study is available from http://bioinformatics.psb.ugent.be/software.

Contact:  tom.michoel@psb.ugent.be

Supplementary information:  Supplementary data and figures are available from http://bioinformatics.psb.ugent.be/supplementary_data/anjos/module_nets_yeast/.
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
Authors: Davey Norman E. , Shields Denis C. , Edwards Richard J.
Published: January 2009

Motivation: Short linear motifs (SLiMs) are important mediators of protein–protein interactions. Their short and degenerate nature presents a challenge for computational discovery. We sought to improve SLiM discovery by incorporating evolutionary information, since SLiMs are more conserved than surrounding residues.

Results: We have developed a new method that assesses the evolutionary signal of a residue in its sequence and structural context. Under-conserved residues are masked out prior to SLiM discovery, allowing incorporation into the existing statistical model employed by SLiMFinder. The method shows considerable robustness in terms of both the conservation score used for individual residues and the size of the sequence neighbourhood. Optimal parameters significantly improve return of known functional motifs from benchmarking data, raising the return of significant validated SLiMs from typical human interaction datasets from 20% to 60%, while retaining the high level of stringency needed for application to real biological data. The success of this regime indicates that it could be of general benefit to computational annotation and prediction of protein function at the sequence level.

Availability: All data and tools in this article are available at http://bioware.ucd.ie/~slimdisc/slimfinder/conmasking/.

Contact:  r.edwards@southampton.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies
Authors: Anandam Parvez , Torarinsson Elfar , Ruzzo Walter L.
Published: January 2009

Summary: Assessing the statistical significance of structured RNA predicted from multiple sequence alignments relies on the existence of a good null model. We present here a random shuffling algorithm, Multiperm, that preserves not only the gap and local conservation structure in alignments of arbitrarily many sequences, but also the approximate dinucleotide frequencies. No shuffling algorithm that simultaneously preserves these three characteristics of a multiple (beyond pairwise) alignment has been available to date. As one benchmark, we show that it produces shuffled exonic sequences having folding free energy closer to native sequences than shuffled alignments that do not preserve dinucleotide frequencies.

Availability: The Multiperm GNU Cb++ source code is available at http://www.anandam.name/multiperm

Contact:  anandam@u.washington.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Profiling model T-cell metagenomes with short reads
Authors: Warren René L. , Nelson Brad H. , Holt Robert A.
Published: January 2009

Motivation: T-cell receptor (TCR) diversity in peripheral blood has not yet been fully profiled with sequence level resolution. Each T-cell clonotype expresses a unique receptor, generated by somatic recombination of TCR genes and the enormous potential for T-cell diversity makes repertoire analysis challenging. We developed a sequencing approach and assembly software (immuno-SSAKE or iSSAKE) for profiling T-cell metagenomes using short reads from the massively parallel sequencing platforms.

Results: Models of sequence diversity for the TCR β-chain CDR3 region were built using empirical data and used to simulate, at random, distinct TCR clonotypes at 1–20 p.p.m. Using simulated TCRβ (sTCRβ) sequences, we randomly created 20 million 36 nt reads having 1–2% random error, 20 million 42 or 50 nt reads having 1% random error and 20 million 36 nt reads with 1% error modeled on real short read data. Reads aligning to the end of known TCR variable (V) genes and having consecutive unmatched bases in the adjacent CDR3 were used to seed iSSAKE de novo assemblies of CDR3. With assembled 36 nt reads, we detect over 51% and 63% of rare (1 p.p.m.) clonotypes using a random or modeled error distribution, respectively. We detect over 99% of more abundant clonotypes (6 p.p.m. or higher) using either error distribution. Longer reads improve sensitivity, with assembled 42 and 50 nt reads identifying 82.0% and 94.7% of rare 1 p.p.m. clonotypes, respectively. Our approach illustrates the feasibility of complete profiling of the TCR repertoire using new massively parallel short read sequencing technology.

Availability:  ftp://ftp.bcgsc.ca/supplementary/iSSAKE

Contact:  rwarren@bcgsc.ca

Supplementary information:  Supplementary methods and data are available at Bioinformatics online.
Beam equations for multi-walled carbon nanotubes derived from Flügge shell theory
Authors: Usuki Tsuneo , Yogo Kiyoshi
Published: January 2009

The Flügge shell theory is frequently used for the analysis of carbon nanotubes (CNTs) due to the relatively accurate results it provides in spite of its theoretical simplicity. Based on the Flügge shell theory, a tubular beam theory was established by considering non-locality. In order to convert a cylindrical shell theory for a curved plate per unit width into a tubular beam theory by contour integration, the longitudinal coordinate that passes through the centre of the circular contour was defined, and, based on this, the radial coordinate was defined. In this way, a generalized beam theory (GBT) was obtained as a further refined form of the Flügge theory. This GBT coincides with the Flügge theory, if the refined form and the non-locality are ignored. After obtaining the phase-velocity curve and the group-velocity curve with respect to single- to triple-walled CNTs, the influences of multiplicity, reduction of the plate-bending stiffness and the stiffness of the surrounding matrix were investigated.
Tyrosine and Phenylalanine Are Synthesized within the Plastids in Arabidopsis
Authors: Rippert Pascal , Puyaubert Juliette , Grisollet Delphine , Derrier Laure , Matringe Michel
Published: January 2009

While the presence of a complete shikimate pathway within plant plastids is definitively established, the existence of a cytosolic postchorismate portion of the pathway is still debated. This question is alimented by the presence of a chorismate mutase (CM) within the cytosol. Until now, the only known destiny of prephenate, the product of CM, is incorporation into tyrosine (Tyr) and/or phenylalanine (Phe). Therefore, the presence of a cytosolic CM suggests that enzymes involved downstream of CM in Tyr or Phe biosynthesis could be present within the cytosol of plant cells. It was thus of particular interest to clarify the subcellular localization of arogenate dehydrogenases (TYRAs) and arogenate dehydratases (ADTs), which catalyze the ultimate steps in Tyr and Phe biosynthesis, respectively. The aim of this study was to address this question in Arabidopsis (Arabidopsis thaliana) by analysis of the subcellular localization of the two TYRAAts and the six AtADTs. This article excludes the occurrence of a spliced TYRAAt1 transcript encoding a cytosolic TYRA protein. Transient expression analyses of TYRA- and ADT-green fluorescent protein fusions reveal that the two Arabidopsis TYRA proteins and the six ADT proteins are all targeted within the plastid. Accordingly, TYRA and ADT proteins were both immunodetected in the chloroplast soluble protein fraction (stroma) of Arabidopsis. No TYRA or ADT proteins were immunodetected in the cytosol of Arabidopsis cells. Taken together, all our data exclude the possibility of Tyr and/or Phe synthesis within the cytosol, at least in green leaves and Arabidopsis cultured cells.
Rearrangement of Actin Cytoskeleton Mediates Invasion ofLotus japonicusRoots byMesorhizobium loti
Authors: Yokota Keisuke , Fukai Eigo , Madsen Lene H. , Jurkiewicz Anna , Rueda Paloma , Radutoiu Simona , Held Mark , Hossain Md Shakhawat , Szczyglowski Krzysztof , Morieri Giulia , Oldroyd Giles E.D. , Downie J. Allan , Nielsen Mette W. , Rusek Anna Maria , Sato Shusei , Tabata Satoshi , James Euan K. , Oyaizu Hiroshi , Sandal Niels , Stougaard Jens
Published: January 2009

Infection thread–dependent invasion of legume roots by rhizobia leads to internalization of bacteria into the plant cells, which is one of the salient features of root nodule symbiosis. We found that two genes, Nap1 (for Nck-associated protein 1) and Pir1 (for 121F-specific p53 inducible RNA), involved in actin rearrangements were essential for infection thread formation and colonization of Lotus japonicus roots by its natural microsymbiont, Mesorhizobium loti. nap1 and pir1 mutants developed an excess of uncolonized nodule primordia, indicating that these two genes were not essential for the initiation of nodule organogenesis per se. However, both the formation and subsequent progression of infection threads into the root cortex were significantly impaired in these mutants. We demonstrate that these infection defects were due to disturbed actin cytoskeleton organization. Short root hairs of the mutants had mostly transverse or web-like actin filaments, while bundles of actin filaments in wild-type root hairs were predominantly longitudinal. Corroborating these observations, temporal and spatial differences in actin filament organization between wild-type and mutant root hairs were also observed after Nod factor treatment, while calcium influx and spiking appeared unperturbed. Together with various effects on plant growth and seed formation, the nap1 and pir1 alleles also conferred a characteristic distorted trichome phenotype, suggesting a more general role for Nap1 and Pir1 in processes establishing cell polarity or polar growth in L. japonicus.
Disruption of the Ao
pex11-1
Gene Involved in Peroxisome Proliferation Leads to Impaired Woronin Body Formation in
Aspergillus oryzae
Authors: Escaño Cristopher Salazar , Juvvadi Praveen Rao , Jin Feng Jie , Takahashi Tadashi , Koyama Yasuji , Yamashita Shuichi , Maruyama Jun-ichi , Kitamoto Katsuhiko
Published: January 2009

The Woronin body, a unique organelle found in the
Pezizomycotina
, plugs the septal pore upon hyphal damage to prevent excessive cytoplasmic bleeding. Although it was previously shown that the Woronin body buds out from the peroxisome, the relationship between peroxisomal proliferation/division and Woronin body differentiation has not been extensively investigated. In this report, we examined whether Pex11 required for peroxisomal proliferation participates in Woronin body formation in
Aspergillus oryzae. A. oryzae
contained two orthologous
PEX11
genes that were designated Ao
pex11-1
and Ao
pex11-2
. Deletion of Ao
pex11
genes revealed that only the ΔAo
pex11-1
strain showed reduced growth and enlarged peroxisomes in the presence of oleic acid as a sole carbon source, indicating a defect in peroxisomal function and proliferation. Disruption of Ao
pex11-1
gene impaired the Woronin body function, leading to excessive loss of the cytosol upon hyphal injury. Dual localization analysis of the peroxisome and Woronin body protein AoHex1 demonstrated that Woronin bodies fail to fully differentiate from peroxisomes in the ΔAo
pex11-1
strain. Furthermore, distribution of AoHex1 was found to be peripheral in the enlarged peroxisome or junctional in dumbbell-shaped peroxisomes. Electron microscopy of the ΔAo
pex11-1
strain revealed the presence of Woronin bodies that remained associated with organelles resembling peroxisomes, which was supported from the sucrose gradient centrifugation confirming that the Woronin body protein AoHex1 overlapped with the density-shifted peroxisome in the ΔAo
pex11-1
strain. In conclusion, the present study describes the role of Pex11 in Woronin body differentiation for the first time.
Flagellar Biogenesis of
Xanthomonas campestris
Requires the Alternative Sigma Factors RpoN2 and FliA and Is Temporally Regulated by FlhA, FlhB, and FlgM
Authors: Yang Tsuey-Ching , Leu Yu-Wei , Chang-Chien Hui-Chen , Hu Rouh-Mei
Published: January 2009

In prokaryotes, flagellar biogenesis is a complicated process involving over 40 genes. The phytopathogen
Xanthomonas campestris
pv. campestris possesses a single polar flagellum, which is essential for the swimming motility. A σ
54
activator, FleQ, has been shown to be required for the transcriptional activation of the flagellar type III secretion system (F-T3SS), rod, and hook proteins. One of the two
rpoN
genes,
rpoN2
, encoding σ
54
, is essential for flagellation. RpoN2 and FleQ direct the expression of a second alternative sigma FliA (σ
28
) that is essential for the expression of the flagellin FliC. FlgM interacts with FliA and represses the FliA regulons. An
flgM
mutant overexpressing FliC generates a deformed flagellum and displays an abnormal motility. Mutation in the two structural genes of F-T3SS,
flhA
and
flhB
, suppresses the production of FliC. Furthermore, FliA protein levels are decreased in an
flhB
mutant. A mutant defective in
flhA
, but not
flhB
, exhibits a decreased infection rate. In conclusion, the flagellar biogenesis of
Xanthomonas campestris
requires alternative sigma factors RpoN2 and FliA and is temporally regulated by FlhA, FlhB, and FlgM.
Functional Analysis of Insertion Sequence IS
Aba1
, Responsible for Genomic Plasticity of
Acinetobacter baumannii
Authors: Mugnier Pauline D. , Poirel Laurent , Nordmann Patrice
Published: January 2009

IS
Aba1
is an insertion sequence that is widely distributed in
Acinetobacter baumannii
. We demonstrated here that IS
Aba1
and the composite transposon Tn
2006
are capable of transposition, generating 9-bp target site duplications. The expression of the IS
Aba1
transposase-encoding gene was downregulated by translational frameshifting.
The Atypical Hybrid Histidine Protein Kinase RodK in
Myxococcus xanthus
: Spatial Proximity Supersedes Kinetic Preference in Phosphotransfer Reactions
Authors: Wegener-Feldbrügge Sigrun , Søgaard-Andersen Lotte
Published: January 2009

Many proteins of two-component signal transduction systems (TCS) have domain structures that do not comply with a phosphate flow as observed in linear TCS, phosphorelays, or simple branched pathways. An example is RodK, which is essential for fruiting body formation in
Myxococcus xanthus
and, in addition to a sensor domain, consists of a kinase domain and three receiver domains (RodK-R1, -R2, and -R3), all of which are functionally important. We identified the RokA response regulator as part of the RodK pathway. In vitro the isolated RodK kinase domain engages in phosphotransfer to RodK-R3 and RokA, with a kinetic preference for RokA. However, in the context of the full-length protein, the RodK kinase domain has a preference for phosphotransfer to RodK-R3 over RokA. We suggest that in full-length RodK, the spatial proximity of the RodK kinase domain and RodK-R3 compensate for the kinetic preference of the isolated kinase domain for RokA. Thus, the kinetic preference observed using an isolated kinase domain of a hybrid kinase does not necessarily reflect the phosphotransfer preference of the full-length protein. We speculate that the phosphorylation status of RodK-R1 and RodK-R2 determines whether RodK engages in phosphotransfer to RodK-R3 or RokA in vivo.
Isolation and Characterization of Superdormant Spores of
Bacillus
Species
Authors: Ghosh Sonali , Setlow Peter
Published: January 2009

Superdormant spores of
Bacillus subtilis
and
Bacillus megaterium
were isolated in 4 to 12% yields following germination with high nutrient levels that activated one or two germinant receptors. These superdormant spores did not germinate with the initial nutrients or those that stimulated other germinant receptors, and the superdormant spores' defect was not genetic. The superdormant spores did, however, germinate with Ca
2+
-dipicolinic acid or dodecylamine. Although these superdormant spores did not germinate with high levels of nutrients that activated one or two nutrient germinant receptors, they germinated with nutrient mixtures that activated more receptors, and using high levels of nutrient mixtures activating more germinant receptors decreased superdormant spore yields. The use of moderate nutrient levels to isolate superdormant spores increased their yields; the resultant spores germinated poorly with the initial moderate nutrient concentrations, but they germinated well with high nutrient concentrations. These findings suggest that the levels of superdormant spores in populations depend on the germination conditions used, with fewer superdormant spores isolated when better germination conditions are used. These findings further suggest that superdormant spores require an increased signal for triggering spore germination compared to most spores in populations. One factor determining whether a spore is superdormant is its level of germinant receptors, since spore populations with higher levels of germinant receptors yielded lower levels of superdormant spores. A second important factor may be heat activation of spore populations, since yields of superdormant spores from non-heat-activated spore populations were higher than those from optimally activated spores.
In
Bacillus subtilis
, the Sirtuin Protein Deacetylase, Encoded by the
srtN
Gene (Formerly
yhdZ
), and Functions Encoded by the
acuABC
Genes Control the Activity of Acetyl Coenzyme A Synthetase
Authors: Gardner Jeffrey G. , Escalante-Semerena Jorge C.
Published: January 2009

This report provides in vivo evidence for the posttranslational control of the acetyl coenzyme A (Ac-CoA) synthetase (AcsA) enzyme of
Bacillus subtilis
by the
acuA
and
acuC
gene products. In addition, both in vivo and in vitro data presented support the conclusion that the
yhdZ
gene of
B. subtilis
encodes a NAD
+
-dependent protein deacetylase homologous to the yeast Sir2 protein (also known as sirtuin). On the basis of this new information, a change in gene nomenclature, from
yhdZ
to
srtN
(for sirtuin), is proposed to reflect the activity associated with the YdhZ protein. In vivo control of
B. subtilis
AcsA function required the combined activities of AcuC and SrtN. Inactivation of
acuC
or
srtN
resulted in slower growth and cell yield under low-acetate conditions than those of the wild-type strain, and the
acuC srtN
strain grew under low-acetate conditions as poorly as the
acsA
strain. Our interpretation of the latter result was that both deacetylases (AcuC and SrtN) are needed to maintain AcsA as active (i.e., deacetylated) so the cell can grow with low concentrations of acetate. Growth of an
acuA acuC srtN
strain on acetate was improved over that of the
acuA
+
acuC srtN
strain, indicating that the AcuA acetyltransferase enzyme modifies (i.e., inactivates) AcsA in vivo, a result consistent with previously reported in vitro evidence that AcsA is a substrate of AcuA.
Polymorphisms in the IGF1 signalling pathway including the myostatin gene are associated with left ventricular mass in male athletes
Authors: Karlowatz Ruth-Jessica , Scharhag Jürgen , Rahnenführer Jörg , Schneider Ulrich , Jakob Ernst , Kindermann Wilfried , Zang Klaus Dieter
Published: January 2009

Background

Athlete's heart as an adaptation to long-time and intensive endurance training can vary considerably between individuals. Genetic polymorphisms in the cardiological relevant insulin-like growth factor 1 (IGF1) signalling pathway seem to have an essential influence on the extent of physiological hypertrophy.

Objective

Analysis of polymorphisms in the genes of IGF1, IGF1 receptor (IGF1R) and the negative regulator of the cardiac IGF1 signalling pathway, myostatin (MSTN), and their relation to left ventricular mass (LVM) of endurance athletes.

Methods

In 110 elite endurance athletes or athletes with a high amount of endurance training (75 males and 35 females) and 27 male controls, which were examined by echocardiographic imaging methods and ergometric exercise-testing, the genotypes of a cytosine–adenine repeat polymorphism in the promoter region of the IGF1 gene and a G/A substitution at position 3174 in the IGF1R gene were determined. Additionally, a mutation screen of the MSTN gene was performed.

Results

The polymorphisms in the IGF1 and the IGF1R gene showed a significant relation to the LVM for male (IGF1: p=0.003; IGF1R: p=0.01), but not for female athletes. The same applies to a previously unnoticed polymorphism in the 1 intron of the MSTN gene, whose deletion allele (AAA→AA) appears to increase the myostatic effect (p=0.015). Moreover, combinations of the polymorphisms showed significant synergistic effects on the LVM of the male athletes.

Conclusions

The authors' results argue for the importance of polymorphisms in the IGF1 signalling pathway in combination with MSTN on the variant degree of physiological hypertrophy of male athletes.
Alterations to cell metabolism in connective tissues of the knee after ovariohysterectomy in a rabbit model: are there implications for the postmenopausal athlete?: Table 1
Authors: Hart D A , Achari Y
Published: January 2009

Background

Participation in regular exercise and athletic activities across the lifespan is encouraged to maintain the cardiovascular and musculoskeletal systems and general wellbeing. Before the menopause there is an increased risk of anterior cruciate ligament (ACL) injuries in female athletes, whereas there is an increased risk of joint diseases such as knee osteoarthritis after the menopause. Although there are few data regarding alterations in individual connective tissues of the knee in humans either before, during or after the menopause, it is possible to assess changes in experimental models following surgical menopause.

Objective

To assess changes in cell metabolism in the medial collateral ligament, ACL, patellar tendon, lateral and medial menisci, tibial plateau and femoral condyle articular cartilage and the synovium after surgical menopause in an experimental model system.

Methods

Panels of rabbits were subjected to ovariohysterectomy or sham operations, and RNA from each tissue was assessed for collagen, proteoglycan, proteinase, growth factor, sex hormone receptor and inflammatory mediator messenger RNA levels by reverse transcribed PCR.

Results

Unique alterations in cell metabolism were detected 2 months after surgical menopause and the pattern of significant changes was tissue specific (number of mRNA species altered, extent of changes, elevation/depression of changes).

Conclusions

Changes in cell metabolism may alter the set point for the tissues of the knee and subsequently the functioning of the knee after the menopause. Such changes may contribute to an increased risk of injury and/or degenerative conditions. Further studies in pre and postmenopausal women athletes may also shed light on whether the present findings can be extrapolated to human populations.
Echocardiographic deformation imaging reveals preserved regional systolic function in endurance athletes with left ventricular hypertrophy
Authors: Teske A J , Prakken N H , De Boeck B W , Velthuis B K , Doevendans P A , Cramer M J
Published: January 2009

Background

Left ventricular hypertrophy (LVH) is often observed in athletes, which should be differentiated from hypertrophic cardiomyopathy. The aim of the study was to explore the functional changes measured using tissue Doppler imaging (TDI) deformation analysis in athletes fulfilling LVH criteria participating in different endurance sports.

Methods

Healthy controls (n = 62, 58% men) and endurance athletes (n = 120, 62% men) aged 18–40 years were prospectively enrolled and underwent both standard echocardiography as well as TDI. Longitudinal TDI-derived strain and strain rate (SR) were calculated in the septal and posterior wall in three segments. LVH was defined as a left ventricular mass (LVM) over 132 g/m2in men and over 109 g/m2in women.

Results

Echocardiographic LVH was observed in 33 athletes (67% men). LVM was significantly increased in both athlete groups (102.6 g/m2(SD 16.0) and 135.7 g/m2(SD 15.9) vs 88.0 g/m2(SD 16.5) in controls, p<0.001). Diastolic parameters were not significantly different between groups. Athletes with LVH showed no significant difference in strain and SR values in any segment of the septal or posterior wall compared with controls or those without LVH. A weak but significant correlation (also after multivariate analysis) was found for septal wall thickness and LVM in peak systolic strain (r = 0.26, p<0.01 and 0.23, p<0.01) and SR (r = 0.27, p<0.01 and 0.29, p<0.01). Nevertheless, strain and SR values were still within normal limits in all athletes.

Conclusion

Athletes with LVH overall show normal deformation values in the left ventricle. These data suggest that a moderate reduction in regional septal deformation should not be considered as pathological when evaluating the endurance athlete with echocardiographic LVH of unknown origin.
Creating active environments across the life course: “thinking outside the square”
Authors: Giles-Corti B , King A C
Published: January 2009

The built environment and physical activity agenda provides a unique opportunity for public health, physical activity and planning researchers to be front and centre of a movement aimed at creating healthier and more sustainable environments. However, in order to optimise environments that encourage physical activity across the life course, researchers in this field need to think beyond their “square” —that is, the target group, setting and physical activity behaviour with which they work. We suggest that researchers working in this field need a better understanding of systems theory to appreciate that a change to one part of a complex system can positively and negatively influence other parts of the system. An understanding of systems theory would help minimise unintended negative consequences to other population subgroups or to other types of physical activity from the implementation of our research findings. In this way, a more comprehensive set of research, practice and programme-related activities may emerge, which will advance physical activity research and practice, and improve population health across the life course.
Adaptive response of the heart to long-term anemia induced by iron deficiency
Authors: Naito Yoshiro , Tsujino Takeshi , Matsumoto Mika , Sakoda Tsuyoshi , Ohyanagi Mitsumasa , Masuyama Tohru
Published: January 2009

Anemia is common in patients with chronic heart failure and an independent predictor of poor prognosis. Chronic anemia leads to left ventricular (LV) hypertrophy and heart failure, but its molecular mechanisms remain largely unknown. We investigated the mechanisms, including the molecular signaling pathway, of cardiac remodeling induced by iron deficiency anemia (IDA). Weanling Sprague-Dawley rats were fed an iron-deficient diet for 20 wk to induce IDA, and the molecular mechanisms of cardiac remodeling were evaluated. The iron-deficient diet initially induced severe anemia, which resulted in LV hypertrophy and dilation with preserved systolic function associated with increased serum erythropoietin (Epo) concentration. Cardiac STAT3 phosphorylation and VEGF gene expression increased by 12 wk of IDA, causing angiogenesis in the heart. Thereafter, sustained IDA induced upregulation of cardiac hypoxia inducible factor-1α gene expression and maintained upregulation of cardiac VEGF gene expression and cardiac angiogenesis; however, sustained IDA promoted cardiac fibrosis and lung congestion, with decreased serum Epo concentration and cardiac STAT3 phosphorylation after 20 wk of IDA compared with 12 wk. Upregulation of serum Epo concentration and cardiac STAT3 phosphorylation is associated with a beneficial adaptive mechanism of anemia-induced cardiac hypertrophy, and later decreased levels of these molecules may be critical for the transition from adaptive cardiac hypertrophy to cardiac dysfunction in long-term anemia. Understanding the mechanism of cardiac maladaptation to anemia may lead to a new strategy for treatment of chronic heart failure with anemia.