bluuebunny/crossref_metadata_2025 huggingface dataset:
THE INCREASE IN FRICTIONAL RESISTANCE DUE TO THE ACTION OF WATER ON BOTTOM PAINT
Authors: Stevens E. A.
Published: August 2010

In this brief discussion, Mr. Stevens points out the rather startling effect of the aging of bottom, paints in water on the hull frictional resistance factor of ships. While the data he offers, and the conclusions he reaches are open to attack not only because of the rarity of opportunity to secure such data but because of the confusing factors which affect the results obtained on any full scale ship trial at sea, a brief consideration will convince the most skeptical that some increase from simple roughening of the bottom is to be expected, and Mr. Stevens presents enough points to indicate the trend of the curve. While the curve is presumed to represent naval rather than merchant marine employment, some consideration of the type of employment will indicate how it can be expected to vary.
WELDING ELECTRODES
Authors: Hiemke Hugo W.
Published: August 2010

During the last decade the use of electric arc welding for fabrication of many forms of engineering structures has increased tremendously. This increased use of welding has been augmented by the development of covered welding electrodes which are capable of depositing weld metal as strong and ductile as the metals to be joined.

The purpose of this article is to tabulate available information, and submit a certain amount of new test information. Also, the author classifies the various service requirements for welding electrodes.
SOME OBSERVATIONS CONCERNING METAL CRACKING IN NAVAL BOILERS
Authors: Stewart William C.
Published: August 2010

During the past fifteen years there has been much published concerning the intercrystalline cracking of toiler steel. The volume of published information on this subject has directed thought toward caustic embrittlement whenever cracks are encountered in boiler shells. While the author recognizes the importance of investigative work in this field, he considers other factors which are often responsible for boiler metal failures. Thus, he correlates causes according to their relative importance from his wide experience of phenomena observed and recorded on the subject. He presents his findings and conclusions in an available form.
WATER CIRCULATION IN A‐TYPE MARINE BOILERS
Authors: WORTHEN E. P.
Published: August 2010

Progressive increase in the permissible rating of equipment units follows after the discovery and cure of limiting factors in design. These factors usually appear one at a time in succession as the previous limit is lifted. It is well known that circulation in A‐type boilers has proved adequate for rates of combustion up to about one pound of oil per square foot of boiler water heating surface and to about forty‐five pounds of oil per square foot of radiant surface. Above these rates, circulation tends to become inadequate without special precautions. In the past, factors such as furnace design, burner design, and the type of fuel have all tended to make the limit of forcing come within the rate for which circulation was adequate. At present, these other limitations have been overcome. Efficiency can be obtained with a small boiler at high rates by using economizers and air heaters. Furnaces and burners have ample capacity. But a greater steam output may be obtained only by increased water circulation. The boiler rating is determined by the heat input which the tubes can absorb.
SOME DEVELOPMENTS IN THE REPAIR BY WELDING OF FINISHED‐MACHINED CASTINGS
Authors: Lutts Carlton G. , Ffield. Paul
Published: August 2010

Some “oldtimers” are going to find fault with this article. Eventually, as welding technique improves and the results are definitely proven in service, it is expected that repairs to finished‐machined castings by welding will become a commonplace. In this article, the authors present actual cases where defects in steel castings, practically finished, have been repaired by welding with resultant saving of the casting and of most of the work expended on it.
RUBBER HOSE USED BY THE NAVY
Authors: BUKZIN E. A.
Published: August 2010

Summary. Summary. In summary, this paper attempted to briefly describe some uses the Navy has for the various types of rubber hose. These types encompass all the major hose construction and manufacturing techniques. Some of the immediate needs and programs have been mentioned to point up how applied research and development has and will continue to be of prime importance in this field.
Programmed cell death‐10 enhances proliferation and protects malignant T cells from apoptosis
Authors: LAUENBORG BRITT , KOPP KATHARINA , KREJSGAARD THORBJØRN , ERIKSEN KARSTEN W. , GEISLER CARSTEN , DABELSTEEN SALLY , GNIADECKI ROBERT , ZHANG QIAN , WASIK MARIUSZ A. , WOETMANN ANDERS , ODUM NIELS
Published: August 2010

Lauenborg B, Kopp K, Krejsgaard T, Eriksen KW, Geisler C, Dabelsteen S, Gniadecki R, Zhang Q, Wasik MA, Woetmann A, Odum N. Programmed cell death‐10 enhances proliferation and protects malignant T cells from apoptosis. APMIS 2010; 118: 719–28.

The programmed cell death‐10 (PDCD10; also known as cerebral cavernous malformation‐3 or CCM3) gene encodes an evolutionarily conserved protein associated with cell apoptosis. Mutations in PDCD10 result in cerebral cavernous malformations, an important cause of cerebral hemorrhage. PDCD10 is associated with serine/threonine kinases and phosphatases and modulates the extracellular signal‐regulated kinase pathway suggesting a role in the regulation of cellular growth. Here we provide evidence of a constitutive expression of PDCD10 in malignant T cells and cell lines from peripheral blood of cutaneous T‐cell lymphoma (Sezary syndrome) patients. PDCD10 is associated with protein phosphatase‐2A, a regulator of mitogenesis and apoptosis in malignant T cells. Inhibition of oncogenic signal pathways [Jak3, Notch1, and nuclear factor‐κB (NF‐κB)] partly inhibits the constitutive PDCD10 expression, whereas an activator of Jak3 and NF‐κB, interleukin‐2 (IL‐2), enhances PDCD10 expression. Functional data show that PDCD10 depletion by small interfering RNA induces apoptosis and decreases proliferation of the sensitive cells. To our knowledge, these data provide the first functional link between PDCD10 and cancer.
Therapeutic concepts in mantle cell lymphoma
Authors: Rodriguez Jose , Gutierrez Antonio , Obrador‐Hevia Antonia , Fernandez de Mattos Silvia , Cabanillas Fernando
Published: August 2010

Mantle cell lymphoma has been considered an incurable disease with current chemotherapy regimens. Recent intense chemoimmunotherapy induction regimens with or without consolidation with autologous stem cell transplantation procedures are showing a potential for cure in a sizable fraction of patients. Similarly, in the salvage setting, preliminary experience with non‐myeloablative allogeneic transplant may cure some patients even after multiple therapeutic failures. However, the recent knowledge of the three basic biologic derangements that are integrated in the disease may change the therapeutic approach of the disease in the near future. In fact, new drugs that target more specifically the major molecular alterations of the disease are being progressively incorporated into the therapeutic armamentarium of the disease. In the near future, more individualized approaches that will take into account not only risk factors present at diagnosis but also biomarkers representative of the molecular alterations present in the disease are foreseen. In this review, we are going to discuss the current therapeutic approaches and the main new drugs that target more specifically the major molecular pathways alterations of the disease.
Diagnosis of leptomeningeal disease in diffuse large B‐cell lymphomas of the central nervous system by flow cytometry and cytopathology
Authors: Schroers Roland , Baraniskin Alexander , Heute Christoph , Vorgerd Matthias , Brunn Anna , Kuhnhenn Jan , Kowoll Annika , Alekseyev Andriy , Schmiegel Wolff , Schlegel Uwe , Deckert Martina , Pels Hendrik
Published: August 2010

Reliable detection of leptomeningeal disease has the potential of facilitating the diagnosis of central nervous system (CNS) lymphoma and is important for therapeutic considerations. Currently, the standard diagnostic procedure for the detection of lymphoma in the cerebrospinal fluid is cytopathology. To improve the limited specificity and sensitivity of cytopathology, flow cytometry has been suggested as an alternative. Here, we evaluated multi‐parameter flow cytometry in combination with conventional cytopathology in cerebrospinal fluid (CSF) samples from 30 patients with primary CNS lymphoma and seven patients with secondary CNS lymphoma. Overall, in 11 of 37 (29.7%) patients with CNS lymphoma, lymphoma cells were detected in CSF by flow cytometry, while cytopathology was less sensitive displaying unequivocally malignant CSF cells in only seven of all 37 (18.9%) patients. Six (16.2%) patients showed cytopathological results suspicious of lymphoma; however, in only one of these patients, the diagnosis of CSF lymphoma cells could be confirmed by flow cytometry. In primary CNS lymphomas (PCNSL), seven of 30 (23.3%) patients were positive for CSF lymphoma cells in flow cytometry, in contrast to four (13.3%) patients with PCNSL with definitely positive cytopathology. In summary, our results suggest that multi‐parameter flow cytometry increases the sensitivity and specificity of leptomeningeal disease detection in CNS lymphomas. Both methods should be applied concurrently for complementary diagnostic assessment in patients with CNS lymphoma.
Subjective Characterization of Nerve Sparing Predicts Recovery of Erectile Function After Radical Prostatectomy: Defining the Utility of a Nerve Sparing Grading System
Authors: Moskovic Daniel J. , Alphs Hannah , Nelson Christian J. , Rabbani Farhang , Eastham James , Touijer Karim , Guillonneau Bertrand , Scardino Peter T. , Mulhall John P.
Published: August 2010

Introduction

Radical prostatectomy (RP) is a common technique for managing prostate cancer. Concern regarding functional outcomes in patients prompted the development of nerve sparing to improve recovery of erectile function.

Aim

To assess if a cumulative nerve damage grading system is a more precise predictor of recovery of erectile function as compared to the current “all-or-none” grading system.

Methods

Baseline demographic, medical history, and International Index of Erectile Function (IIEF)-erectile function domain (EFD) scores were collected. At the time of RP, patients were assigned a nerve sparing score (NSS) by their surgeon for each neurovascular bundle (left and right) to assess the quality of intraoperative nerve sparing (1—complete preservation, 4—complete resection). Patients completed IIEF questionnaires at 24 months after RP.

Main Outcome Measures

Group comparisons and multiple regression analyses were used to test the association between the NSS and IIEF-EFD scores for patients with preoperative EFD scores ≥24.

Results

A total of 173 patients were included in this analysis. Mean age for patients was 59, and 62% of patients had at least one comorbidity. Baseline EFD scores were comparable between all NSS assignments. At 24 months, EFD scores were reduced by 7.2, 11.6, 13.9, and 15.4 points for patients with NSS grades of 2, 3, 4, and 5–8, respectively (P < 0.01). Multivariate analysis demonstrated lower NSS predicted recovery of erectile function at 24 months (P = 0.001), as did age (P = 0.001) and baseline EFD score (P = 0.02).

Conclusions

Our data support the adoption of a subjectively assigned NSS to more precisely predict erectile function outcomes and suggest that even minor nerve trauma significantly impairs the recovery of erectile function after procedures classically regarded as having achieved bilateral nerve sparing. Further studies are needed to identify the optimal NSS system.
Land trust defense and enforcement of conserved areas
Authors: Rissman Adena R. , Butsic Van
Published: August 2010

Achieving conservation goals in protected areas hinges on continual monitoring, enforcement, and legal defense. In an era of devolved governance, nonprofit land trusts have become increasingly important. Yet, their approaches to legal defense of conserved areas are relatively unknown. A national survey of 205 land trusts provides the first quantitative data on the types, costs, and outcomes of major legal challenges. Half of land trusts reported a legal challenge, and one‐quarter of those land trusts were hindered by financial barriers in pursuing a legal challenge. Interviews with land trust staff revealed the necessary conditions for pursuing legal defense including organizational capacity, community support, and persuasive property claims. Results indicate the importance of stewardship endowments and the need for greater land trust capacity and accountability. Donors, agency funders, and the public should support thoughtful, contextually appropriate, and powerful enforcement actions to ensure conservation objectives over the long term.
Constructing Semantic Representations From a Gradually Changing Representation of Temporal Context
Authors: Howard Marc W. , Shankar Karthik H. , Jagadisan Udaya K. K.
Published: August 2010

Computational models of semantic memory exploit information about co‐occurrences of words in naturally occurring text to extract information about the meaning of the words that are present in the language. Such models implicitly specify a representation of temporal context. Depending on the model, words are said to have occurred in the same context if they are presented within a moving window, within the same sentence, or within the same document. The temporal context model (TCM), which specifies a particular definition of temporal context, has proved useful in the study of episodic memory. The predictive temporal context model (pTCM) uses the same definition of temporal context to generate semantic memory representations. Taken together pTCM and TCM may prove to be part of a general model of declarative memory.
Microbial metacommunities in the lichen–rock habitat
Authors: Bjelland Torbjørg , Grube Martin , Hoem Solveig , Jorgensen Steffen L. , Daae Frida Lise , Thorseth Ingunn H. , Øvreås Lise
Published: August 2010

Lichens are common as colonizers of bare rocks and contribute to weathering, but their associated bacterial communities have been poorly studied. In this study Hydropunctaria maura, Ophioparma ventosa, Pertusaria corallina and Rhizocarpon geographicum were analysed to determine the influence of lichens on lichen–rock‐associated microbial metacommunities. For the first time, Archaea were documented to be associated with rock‐inhabiting lichens. All the archaeal sequences obtained were affiliated with Crenarchaeota. The Bacteria detected in the lichen–rock samples were affiliated with the major lineages Acidobacteria, Actinobacteria, Alpha‐, Beta‐, Gammaproteobacteria, Bacteriodetes, Chloroflexi, Deinococcus, Firmicutes, Planctomycetes, Tenericutes and Cyanobacteria. The microbial communities of O. ventosa, P. corallina and R. geographicum were more similar to each other both terms of the number and types of different sequences, than to H. maura. A higher bacterial diversity was observed endolithically than within the epilithic lichen thalli directly above. The abundance of Archaea were also generally higher endolithically than in the epilithic lichen thalli, while the abundance of Bacteria was higher in the lichen thalli compared with within the rock. These results demonstrated that the lichen–rock interfaces are complex habitats, where the macroscopic lichens influence the composition of microbial metacommunities.
Non‐autonomous transposable elements associated with inactivation of microcystin gene clusters in strains of the genus Anabaena isolated from the Baltic Sea
Authors: Fewer David P. , Halinen Katrianna , Sipari Hanna , Bernardová Kateřina , Mänttäri Mia , Eronen Eeva , Sivonen Kaarina
Published: August 2010

Microcystins are potent peptide toxins produced by a range of distantly related cyanobacteria. They are assembled on a large enzyme complex encoded by the 55 kb microcystin synthetase (mcy) gene cluster. Here we report two strains of the genus Anabaena isolated from the Baltic Sea, which contain the entire mcy gene cluster but do not produce microcystins. Transcription analysis demonstrated that mcy genes were not expressed in these strains. We identified short insertion elements interrupting the mcyA, mcyD and mcyE genes in the two strains isolated in different years from different parts of the Baltic Sea. The 126–207 bp insertion elements encoded both terminal inverted repeats and direct repeats but lacked transposases. However, we found evidence for transposition of these elements despite the absence of genes encoding transposases, suggesting that they are non‐autonomous mobile miniature inverted‐repeat transposable elements (MITEs) recently described from cyanobacteria. The MITE insertion elements were present in mcyD genes amplified directly from the cyanobacterial community present in the Baltic Sea blooms from 2005. The results demonstrate that mcy gene cluster mutants can make up a stable proportion of the mcy gene pool in the Baltic Sea population.
A simple and efficient method for concentration of ocean viruses by chemical flocculation
Authors: John Seth G. , Mendez Carolina B. , Deng Li , Poulos Bonnie , Kauffman Anne Kathryn M. , Kern Suzanne , Brum Jennifer , Polz Martin F. , Boyle Edward A. , Sullivan Matthew B.
Published: August 2010

Ocean viruses alter ecosystems through host mortality, horizontal gene transfer and by facilitating remineralization of limiting nutrients. However, the study of wild viral populations is limited by inefficient and unreliable concentration techniques. Here, we develop a new technique to recover viruses from natural waters using iron‐based flocculation and large‐pore‐size filtration, followed by resuspension of virus‐containing precipitates in a pH 6 buffer. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered. This Fe‐based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research.
The viscerosympathetic response in rabbits is mediated by GABAergic and glutamatergic inputs into the sympathetic premotor neurons of the rostral ventrolateral medulla
Authors: Koganezawa Tadachika , Shimomura Yuri , Terui Naohito
Published: August 2010

Neurons in the rostral ventrolateral medulla (RVLM) receive inputs from various sources, including baroreceptors, and then regulate the activity of sympathetic preganglionic neurons in the spinal cord. Whether RVLM neurons mediate the viscerosympathetic reflex has yet to be clarified. In the present study, we investigated the role of RVLM neurons in the viscerosympathetic reflex in anaesthetized and vagotomized rabbits. Electrical stimulation of the greater splanchnic nerve (SplN) evoked reflex responses in renal sympathetic activity that were composed of inhibitory and/or excitatory components. Bilateral microinjection of muscimol, a GABAA receptor agonist, into the RVLM blocked the reflex responses. Bilateral microinjection of bicuculline, a GABAA receptor antagonist, largely attenuated the inhibitory component, whereas kynurenic acid, a glutamate receptor antagonist, eliminated the excitatory component. The activities of 21 RVLM barosensitive bulbospinal neurons were recorded. Twenty of the neurons responded to the SplN stimulation. The responses also consisted of inhibitory and/or excitatory components. The excitatory component of these neurons preceded that of the renal sympathetic nerve activity by about 100 ms. This latency difference was almost the same as that of the inhibitory responses evoked by aortic nerve stimulation. Therefore, the renal sympathetic reflex responses evoked by SplN stimulation are mediated by RVLM neurons, and GABAergic and glutamatergic transmission in the RVLM are related to this reflex.
Horizon-Specific Bacterial Community Composition of German Grassland Soils, as Revealed by Pyrosequencing-Based Analysis of 16S rRNA Genes
Authors: Will Christiane , Thürmer Andrea , Wollherr Antje , Nacke Heiko , Herold Nadine , Schrumpf Marion , Gutknecht Jessica , Wubet Tesfaye , Buscot François , Daniel Rolf
Published: August 2010

The diversity of bacteria in soil is enormous, and soil bacterial communities can vary greatly in structure. Here, we employed a pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to characterize the overall and horizon-specific (A and B horizons) bacterial community compositions in nine grassland soils, which covered three different land use types. The entire data set comprised 752,838 sequences, 600,544 of which could be classified below the domain level. The average number of sequences per horizon was 41,824. The dominant taxonomic groups present in all samples and horizons were the
Acidobacteria
,
Betaproteobacteria
,
Actinobacteria
,
Gammaproteobacteria
,
Alphaproteobacteria
,
Deltaproteobacteria
,
Chloroflexi
,
Firmicutes
, and
Bacteroidetes
. Despite these overarching dominant taxa, the abundance, diversity, and composition of bacterial communities were horizon specific. In almost all cases, the estimated bacterial diversity (
H
′) was higher in the A horizons than in the corresponding B horizons. In addition, the
H
′ was positively correlated with the organic carbon content, the total nitrogen content, and the C-to-N ratio, which decreased with soil depth. It appeared that lower land use intensity results in higher bacterial diversity. The majority of sequences affiliated with the
Actinobacteria
,
Bacteroidetes
,
Cyanobacteria
,
Fibrobacteres
,
Firmicutes
,
Spirochaetes
,
Verrucomicrobia
,
Alphaproteobacteria
,
Betaproteobacteria
, and
Gammaproteobacteria
were derived from A horizons, whereas the majority of the sequences related to
Acidobacteria
,
Chloroflexi
,
Gemmatimonadetes
,
Nitrospira
, TM7, and WS3 originated from B horizons. The distribution of some bacterial phylogenetic groups and subgroups in the different horizons correlated with soil properties such as organic carbon content, total nitrogen content, or microbial biomass.
Inhibition of the Activity of Both Domains of Lysostaphin through Peptidoglycan Modification by the Lysostaphin Immunity Protein
Authors: Gargis Shaw R. , Heath Harry E. , LeBlanc Paul A. , Dekker Linda , Simmonds Robin S. , Sloan Gary L.
Published: August 2010

Resistance to lysostaphin, a staphylolytic glycylglycine endopeptidase, is due to a FemABX-like immunity protein that inserts serines in place of some glycines in peptidoglycan cross bridges. These modifications inhibit both binding of the recombinant cell wall targeting domain and catalysis by the recombinant catalytic domain of lysostaphin.
Significant Association between Sulfate-Reducing Bacteria and Uranium-Reducing Microbial Communities as Revealed by a Combined Massively Parallel Sequencing-Indicator Species Approach
Authors: Cardenas Erick , Wu Wei-Min , Leigh Mary Beth , Carley Jack , Carroll Sue , Gentry Terry , Luo Jian , Watson David , Gu Baohua , Ginder-Vogel Matthew , Kitanidis Peter K. , Jardine Philip M. , Zhou Jizhong , Criddle Craig S. , Marsh Terence L. , Tiedje James M.
Published: August 2010

Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 μM and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions.CastellaniellaandRhodanobactercharacterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio,Anaeromyxobacter, andDesulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducerGeobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.
Transmission of Plant-Pathogenic Bacteria by Nonhost Seeds without Induction of an Associated Defense Reaction at Emergence
Authors: Darrasse Armelle , Darsonval Arnaud , Boureau Tristan , Brisset Marie-Noëlle , Durand Karine , Jacques Marie-Agnès
Published: August 2010

An understanding of the mechanisms involved in the different steps of bacterial disease epidemiology is essential to develop new control strategies. Seeds are the passive carriers of a diversified microbial cohort likely to affect seedling physiology. Among seed-borne plant-pathogenic bacteria, seed carriage in compatible situations is well evidenced. The aims of our work are to determine the efficiency of pathogen transmission to seeds of a nonhost plant and to evaluate bacterial and plant behaviors at emergence. Bacterial transmission from flowers to seeds and from seeds to seedlings was measured forXanthomonas campestrispv. campestris in incompatible interactions with bean. Transmissions from seeds to seedlings were compared forX. campestrispv. campestris, forXanthomonas citripv. phaseoli var. fuscans in compatible interactions with bean, and forEscherichia coli, a human pathogen, in null interactions with bean. The induction of defense responses was monitored by using reverse transcription and quantitative PCR (RT-qPCR) of genes representing the main signaling pathways and assaying defense-related enzymatic activities. Flower inoculations resulted in a high level of bean seed contamination byX. campestrispv. campestris, which transmitted efficiently to seedlings. Whatever the type of interaction tested, dynamics of bacterial population sizes were similar on seedlings, and no defense responses were induced evidencing bacterial colonization of seedlings without any associated defense response induction. Bacteria associated with the spermosphere multiply in this rich environment, suggesting that the colonization of seedlings relies mostly on commensalism. The transmission of plant-pathogenic bacteria to and by nonhost seeds suggests a probable role of seeds of nonhost plants as an inoculum source.
Association of
Campylobacter jejuni
Cj0859c Gene (
fspA
) Variants with Different
C. jejuni
Multilocus Sequence Types
Authors: de Haan C. P. A. , Kivistö R. , Hänninen M. L.
Published: August 2010

Cj0859c variants
fspA1
and
fspA2
from 669 human, poultry, and bovine
Campylobacter jejuni
strains were associated with certain hosts and multilocus sequence typing (MLST) types. Among the human and poultry strains,
fspA1
was significantly (
P
< 0.001) more common than
fspA2
. FspA2 amino acid sequences were the most diverse and were often truncated.
A Mutation within the β Subunit ofEscherichia coliRNA Polymerase Impairs Transcription from Bacteriophage T4 Middle Promoters
Authors: James Tamara D. , Cashel Michael , Hinton Deborah M.
Published: August 2010

During infection ofEscherichia coli, bacteriophage T4 usurps the host transcriptional machinery, redirecting it to the expression of early, middle, and late phage genes. Middle genes, whose expression begins about 1 min postinfection, are transcribed both from the extension of early RNA into middle genes and by the activation of T4 middle promoters. Middle-promoter activation requires the T4 transcriptional activator MotA and coactivator AsiA, which are known to interact with σ70, the specificity subunit of RNA polymerase. T4motAamber [motA(Am)] orasiA(Am) phage grows poorly in wild-typeE. coli. However, previous work has found that T4motA(Am)does not grow in theE. colimutant strain TabG. We show here that the RNA polymerase in TabG contains two mutations within its β-subunit gene:rpoB(E835K) andrpoB(G1249D). We find that the G1249D mutation is responsible for restricting the growth of either T4motA(Am)orasiA(Am) and for impairing transcription from MotA/AsiA-activated middle promotersin vivo. With one exception, transcription from tested T4 early promoters is either unaffected or, in some cases, even increases, and there is no significant growth phenotype for therpoB(E835K G1249D) strain in the absence of T4 infection. In reported structures of thermophilic RNA polymerase, the G1249 residue is located immediately adjacent to a hydrophobic pocket, called the switch 3 loop. This loop is thought to aid in the separation of the RNA from the DNA-RNA hybrid as RNA enters the RNA exit channel. Our results suggest that the presence of MotA and AsiA may impair the function of this loop or that this portion of the β subunit may influence interactions among MotA, AsiA, and RNA polymerase.
Orientations of theBacteroides fragilisCapsular Polysaccharide Biosynthesis Locus Promoters during Symbiosis and Infection
Authors: Troy Erin B. , Carey Vincent J. , Kasper Dennis L. , Comstock Laurie E.
Published: August 2010

Orientations of the seven invertible polysaccharide biosynthesis locus promoters ofBacteroidesfragiliswere determined from bacteria grownin vitro, from feces of monoassociated and complex colonized mice, and fromB. fragilis-induced murine abscesses. Bacteria grownin vivohave greater variability in orientation of polysaccharide locus promoters than culture-grown organisms.
Characterization of the CDP-2-Glycerol Biosynthetic Pathway in
Streptococcus pneumoniae
Authors: Wang Quan , Xu Yanli , Perepelov Andrei V. , Xiong Wei , Wei Dongmei , Shashkov Alexander S. , Knirel Yuriy A. , Feng Lu , Wang Lei
Published: August 2010

Capsule polysaccharide (CPS) plays an important role in the virulence of
Streptococcus pneumoniae
and is usually used as the pneumococcal vaccine target. Glycerol-2-phosphate is found in the CPS of
S. pneumoniae
types 15A and 23F and is rarely found in the polysaccharides of other bacteria. The biosynthetic pathway of the nucleotide-activated form of glycerol-2-phosphate (NDP-2-glycerol) has never been identified. In this study, three genes (
gtp1
,
gtp2
, and
gtp3
) from
S. pneumoniae
23F that have been proposed to be involved in the synthesis of NDP-2-glycerol were cloned and the enzyme products were expressed, purified, and assayed for their respective activities. Capillary electrophoresis was used to detect novel products from the enzyme-substrate reactions, and the structure of the product was elucidated using electrospray ionization mass spectrometry and nuclear magnetic resonance spectroscopy. Gtp1 was identified as a reductase that catalyzes the conversion of 1,3-dihydroxyacetone to glycerol, Gtp3 was identified as a glycerol-2-phosphotransferase that catalyzes the conversion of glycerol to glycerol-2-phosphate, and Gtp2 was identified as a cytidylyltransferase that transfers CTP to glycerol-2-phosphate to form CDP-2-glycerol as the final product. The kinetic parameters of Gtp1 and Gtp2 were characterized in depth, and the effects of temperature, pH, and cations on these two enzymes were analyzed. This is the first time that the biosynthetic pathway of CDP-2-glycerol has been identified biochemically; this pathway provides a method to enzymatically synthesize this compound.
Characterization of the RNA Degradosome ofPseudoalteromonas haloplanktis: Conservation of the RNase E-RhlB Interaction in the Gammaproteobacteria
Authors: Aït-Bara Soraya , Carpousis Agamemnon J.
Published: August 2010

The degradosome is a multienzyme complex involved in mRNA degradation inEscherichia coli. The essential endoribonuclease RNase E contains a large noncatalytic region necessary for protein-protein interactions with other components of the RNA degradosome. Interacting proteins include the DEAD-box RNA helicase RhlB, the glycolytic enzyme enolase, and the exoribonuclease PNPase.Pseudoalteromonas haloplanktis, a psychrotolerant gammaproteobacterium distantly related toE. coli, encodes homologs of each component of the RNA degradosome. InP. haloplanktis, RNase E associates with RhlB and PNPase but not enolase. Plasmids expressingP. haloplanktisRNase E (Ph-RNase E) can complementE. colistrains lackingE. coliRNase E (Ec-RNase E). Ph-RNase E, however, does not confer a growth advantage toE. coliat low temperature. Ph-RNase E has a heterologous protein-protein interaction with Ec-RhlB but not with Ec-enolase or Ec-PNPase. The Ph-RNase E binding sites for RhlB and PNPase were mapped by deletion analysis. The PNPase binding site is located at the C-terminal end of Ph-RNase E at the same position as that in Ec-RNase E, but the sequence of the site is not conserved. The sequence of the RhlB binding site in Ph-RNase E is related to the sequence in Ec-RNase E. Together with the heterologous interaction between Ph-RNase E and Ec-RhlB, our results suggest that the underlying structural motif for the RNase E-RhlB interaction is conserved. Since the activity of Ec-RhlB requires its physical interaction with Ec-RNase E, conservation of the underlying structural motif over a large evolutionary distance could be due to constraints involved in the control of RhlB activity.
An Extreme Thermophile,Thermus thermophilus, Is a Polyploid Bacterium
Authors: Ohtani Naoto , Tomita Masaru , Itaya Mitsuhiro
Published: August 2010

An extremely thermophilic bacterium,Thermus thermophilusHB8, is one of the model organisms for systems biology. Its genome consists of a chromosome (1.85 Mb), a megaplasmid (0.26 Mb) designated pTT27, and a plasmid (9.3 kb) designated pTT8, and the complete sequence is available. We show here thatT. thermophilusis a polyploid organism, harboring multiple genomic copies in a cell. In the case of the HB8 strain, the copy number of the chromosome was estimated to be four or five, and the copy number of the pTT27 megaplasmid seemed to be equal to that of the chromosome. It has never been discussed whetherT. thermophilusis haploid or polyploid. However, the finding that it is polyploid is not surprising, asDeinococcus radiodurans, an extremely radioresistant bacterium closely related toThermus, is well known to be a polyploid organism. As is the case forD. radioduransin the radiation environment, the polyploidy ofT. thermophilusmight allow for genomic DNA protection, maintenance, and repair at elevated growth temperatures. Polyploidy often complicates the recognition of an essential gene inT. thermophilusas a model organism for systems biology.
The Flagellar Basal Body-Associated Protein FlgT Is Essential for a Novel Ring Structure in the Sodium-Driven
Vibrio
Motor
Authors: Terashima Hiroyuki , Koike Masafumi , Kojima Seiji , Homma Michio
Published: August 2010

In
Vibrio alginolyticus
, the flagellar motor can rotate at a remarkably high speed, ca. three to four times faster than the
Escherichia coli
or
Salmonella
motor. Here, we found a
Vibrio
-specific protein, FlgT, in the purified flagellar basal body fraction. Defects of FlgT resulted in partial Fla
−
and Mot
−
phenotypes, suggesting that FlgT is involved in formation of the flagellar structure and generating flagellar rotation. Electron microscopic observation of the basal body of Δ
flgT
cells revealed a smaller LP ring structure compared to the wild type, and most of the T ring was lost. His
6
-tagged FlgT could be coisolated with MotY, the T-ring component, suggesting that FlgT may interact with the T ring composed of MotX and MotY. From these lines of evidence, we conclude that FlgT associates with the basal body and is responsible to form an outer ring of the LP ring, named the H ring, which can be distinguished from the LP ring formed by FlgH and FlgI.
Vibrio
-specific structures, e.g., the T ring and H ring might contribute the more robust motor structure compared to that of
E. coli
and
Salmonella
.
Enterococcus faecalis rnjB
Is Required for Pilin Gene Expression and Biofilm Formation
Authors: Gao Peng , Pinkston Kenneth L. , Nallapareddy Sreedhar R. , van Hoof Ambro , Murray Barbara E. , Harvey Barrett R.
Published: August 2010

Pili in Gram-positive bacteria play a major role in the colonization of host tissue and in the development of biofilms. They are promising candidates for vaccines or drug targets since they are highly immunogenic and share common structural and functional features among various Gram-positive pathogens. Numerous publications have helped build a detailed understanding of pilus surface assembly, yet regulation of pilin gene expression has not been well defined. Utilizing a monoclonal antibody developed against the
Enterococcus faecalis
major pilus protein EbpC, we identified mutants from a transposon (Tn) insertion library which lack surface-exposed Ebp pili. In addition to insertions in the
ebp
regulon, an insertion in
ef1184
(
dapA
) significantly reduced levels of EbpC. Analysis of in-frame
dapA
deletion mutants and mutants with the downstream gene
rnjB
deleted further demonstrated that
rnjB
was responsible for the deficiency of EbpC. Sequence analysis revealed that
rnjB
encodes a putative RNase J2. Subsequent quantitative real-time PCR (qRT-PCR) and Northern blotting demonstrated that the
ebpABC
mRNA transcript level was significantly decreased in the
rnjB
deletion mutant. In addition, using a reporter gene assay, we confirmed that
rnjB
affects the expression of the
ebpABC
operon. Functionally, the
rnjB
deletion mutant was attenuated in its ability to produce biofilm, similar to that of an
ebpABC
deletion mutant which lacks Ebp pili. Together, these results demonstrate the involvement of
rnjB
in
E. faecalis
pilin gene expression and provide insight into a novel mechanism of regulation of pilus production in Gram-positive pathogens.
Genetics and Regulation of the Major Enzymes of Alanine Synthesis inEscherichia coli
Authors: Kim Sok Ho , Schneider Barbara L. , Reitzer Larry
Published: August 2010

Genetic analysis of alanine synthesis in the model genetic organismEscherichia colihas implicatedavtA, the still uncharacterizedalaAandalaBgenes, and probably other genes. We identifiedalaAasyfbQ. We then transferred mutations in several transaminase genes into ayfbQmutant and isolated a mutant that required alanine for optimal growth. For cells grown with carbon sources other than pyruvate, the major alanine-synthesizing transaminases are AvtA, YfbQ (AlaA), and YfdZ (which we designate AlaC). Growth with pyruvate as the carbon source and multicopy suppression suggest that several other transaminases can contribute to alanine synthesis. Expression studies showed that alanine modestly repressedavtAandyfbQbut had no effect onyfdZ. The leucine-responsive regulatory protein (Lrp) mediated control by alanine. We purified YfbQ and YfdZ and showed that both are dimers withKms for pyruvate within the intracellular range of pyruvate concentration.
Deficiency inl-Serine Deaminase Interferes with One-Carbon Metabolism and Cell Wall Synthesis inEscherichia coliK-12
Authors: Zhang Xiao , El-Hajj Ziad W. , Newman Elaine
Published: August 2010

Escherichia coliK-12 provided with glucose and a mixture of amino acids depletesl-serine more quickly than any other amino acid even in the presence of ammonium sulfate. A mutant without three 4Fe4Sl-serine deaminases (SdaA, SdaB, and TdcG) ofE. coliK-12 is unable to do this. The high level ofl-serine that accumulates when such a mutant is exposed to amino acid mixtures starves the cells for C1units and interferes with cell wall synthesis. We suggest that at high concentrations,l-serine decreases synthesis of UDP-N-acetylmuramate-l-alanine by themurC-encoded ligase, weakening the cell wall and producing misshapen cells and lysis. The inhibition by highl-serine is overcome in several ways: by a large concentration ofl-alanine, by overproducing MurC together with a low concentration ofl-alanine, and by overproducing FtsW, thus promoting septal assembly and also by overexpression of the glycine cleavage operon.S-Adenosylmethionine reduces lysis and allows an extensive increase in biomass without improving cell division. This suggests thatE. colihas a metabolic trigger for cell division. Without that reaction, if no other inhibition occurs, other metabolic functions can continue and cells can elongate and replicate their DNA, reaching at least 180 times their usual length, but cannot divide.
The N-Terminal Domain of
Aliivibrio fischeri
LuxR Is a Target of the GroEL Chaperonin
Authors: Manukhov Ilya V. , Melkina Ol'ga E. , Goryanin Ignatii I. , Baranova Ancha V. , Zavilgelsky Gennadii B.
Published: August 2010

Here we show that the C-terminal domain of LuxR activates the transcription of
Aliivibrio fischeri luxICDABEG
in
Escherichia coli
SKB178
gro
+
and
E. coli
OFB1111
groEL673
strains to the same level. Using affinity chromatography, we showed that GroEL binds to the N-terminal domain of LuxR, pointing to a GroEL/GroES requirement for the folding of the N-terminal domain of LuxR.
Inactivation of a Heterocyst-Specific Invertase Indicates a Principal Role of Sucrose Catabolism in Heterocysts of
Anabaena
sp
Authors: López-Igual Rocío , Flores Enrique , Herrero Antonia
Published: August 2010

Anabaena
sp. strain PCC 7120 is a filamentous cyanobacterium that carries out N
2
fixation in specialized cells called heterocysts, which exchange nutrients and regulators with the filament's vegetative cells that perform the photosynthetic fixation of CO
2
. The
Anabaena
genome carries two genes coding for alkaline/neutral invertases,
invA
and
invB
. As shown by Northern analysis, both genes were expressed monocistronically and induced under nitrogen deprivation, although induction was stronger for
invB
than for
invA
. Whereas expression of an InvA-N-GFP fusion (green fluorescent protein [GFP] fused to the N terminus of the InvA protein [InvA-N]) was homogeneous along the cyanobacterial filament, consistent with the lack of dependence on HetR, expression of an InvB-N-GFP fusion upon combined nitrogen deprivation took place mainly in differentiating and mature heterocysts. In an
hetR
genetic background, the InvB-N-GFP fusion was strongly expressed all along the filament. An insertional mutant of
invA
could grow diazotrophically but was impaired in
nifHDK
induction and exhibited an increased frequency of heterocysts, suggesting a regulatory role of the invertase-mediated carbon flux in vegetative cells. In contrast, an
invB
mutant was strongly impaired in diazotrophic growth, showing a crucial role of sucrose catabolism mediated by the InvB invertase in the heterocysts.
Mutational Analysis of
Bacillus megaterium
QM B1551 Cortex-Lytic Enzymes
Authors: Christie Graham , Üstok Fatma Isık , Lu Qiaozhi , Packman Len C. , Lowe Christopher R.
Published: August 2010

Molecular-genetic and muropeptide analysis techniques have been applied to examine the function
in vivo
of the
Bacillus megaterium
QM B1551 SleB and SleL proteins. In common with
Bacillus subtilis
and
Bacillus anthracis
, the presence of anhydromuropeptides in
B. megaterium
germination exudates, which is indicative of lytic transglycosylase activity, is associated with an intact
sleB
structural gene.
B. megaterium sleB cwlJ
double mutant strains complemented with engineered SleB variants in which the predicted N- or C-terminal domain has been deleted (SleB-ΔN or SleB-ΔC) efficiently initiate and hydrolyze the cortex, generating anhydromuropeptides in the process. Additionally,
sleB cwlJ
strains complemented with SleB-ΔN or SleB-ΔC, in which glutamate and aspartate residues have individually been changed to alanine, all retain the ability to hydrolyze the cortex to various degrees during germination, with concomitant release of anhydromuropeptides to the surrounding medium. These data indicate that while the presence of either the N- or C-terminal domain of
B. megaterium
SleB is sufficient for initiation of cortex hydrolysis and the generation of anhydromuropeptides, the perceived lytic transglycosylase activity may be derived from an enzyme(s), perhaps exclusively or in addition to SleB, which has yet to be identified.
B. megaterium
SleL appears to be associated with the epimerase-type activity observed previously in
B. subtilis
, differing from the glucosaminidase function that is apparent in
B. cereus
/
B. anthracis
.
Genome Sequences of
Pelagibaca bermudensis
HTCC2601
T
and
Maritimibacter alkaliphilus
HTCC2654
T
, the Type Strains of Two Marine
Roseobacter
Genera
Authors: Thrash J. Cameron , Cho Jang-Cheon , Ferriera Steve , Johnson Justin , Vergin Kevin L. , Giovannoni Stephen J.
Published: August 2010

Pelagibaca bermudensis
HTCC2601
T
and
Maritimibacter alkaliphilus
HTCC2654
T
represent two marine genera in the globally significant
Roseobacter
clade of the
Alphaproteobacteria
. Here, we present the genome sequences of these organisms, isolated from the Sargasso Sea using dilution-to-extinction culturing, which offer insight into the genetic basis for the metabolic and ecological diversity of this important group.
A day in the life of a junior doctor: everyday ethical encounters
Authors: Quarini Catherine J
Published: August 2010

This paper presents a hypothetical ‘day in the life’ of junior doctors working on a busy hospital ward. It illustrates the fact that, although the everyday ethical encounters faced by doctors are generally not as dramatic as some of the ethical issues discussed at medical school, the underlying principles, such as consent, confidentiality and resource allocation, are highly relevant to daily practice. After presenting some of the ethical challenges faced by junior doctors, from patients confused by poor explanations to inadequate consent procedures, the paper ends with suggestions on how to improve the situation.
CASCADING FAILURES IN CONGESTED SCALE-FREE NETWORKS
Authors: ZHENG JIAN-FENG , YANG LING-XIAO , GAO ZI-YOU , FU BAI-BAI
Published: August 2010

In this work, we study the effect of congestion on the behavior of cascading failures in scale-free networks, where a capacity is assigned on each node (controlled by a tolerance parameter α), and traffic flows are governed by user equilibrium instead of going along the shortest paths. The effect of congestion can be described by link cost function, which denotes the time needed to travel along the link. Here we focus on studying the effect of link's practical capacity, which is a parameter in link cost function. Two different kinds of link's practical capacity are investigated, i.e. uniform case and nonuniform case. In the uniform case, each link has the same value of practical capacity. While in the nonuniform case, we assume that link's practical capacity and degrees of the link's endpoints are correlated (controlled by parameter θ, which governs the heterogeneity of link's practical capacity). Simulation results show that, in the uniform case, scale-free networks are more prone to cascading failures when increasing the value of link's practical capacity. In the nonuniform case, cascading failures in scale-free networks are very sensitive to α when θ > 0; while θ < 0, scale-free networks may suffer from serious cascading failures, regardless of α.