bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization and Evolution of Cell Division and Cell Wall Synthesis Genes in the Bacterial Phyla
Verrucomicrobia
,
Lentisphaerae
,
Chlamydiae
, and
Planctomycetes
and Phylogenetic Comparison with rRNA Genes
Authors: Pilhofer Martin , Rappl Kristina , Eckl Christina , Bauer Andreas Peter , Ludwig Wolfgang , Schleifer Karl-Heinz , Petroni Giulio 
Published: March 2008

ABSTRACT

In the past, studies on the relationships of the bacterial phyla
Planctomycetes
,
Chlamydiae
,
Lentisphaerae
, and
Verrucomicrobia
using different phylogenetic markers have been controversial. Investigations based on 16S rRNA sequence analyses suggested a relationship of the four phyla, showing the branching order
Planctomycetes
,
Chlamydiae
,
Verrucomicrobia
/
Lentisphaerae
. Phylogenetic analyses of 23S rRNA genes in this study also support a monophyletic grouping and their branching order—this grouping is significant for understanding cell division, since the major bacterial cell division protein FtsZ is absent from members of two of the phyla
Chlamydiae
and
Planctomycetes
. In
Verrucomicrobia
, knowledge about cell division is mainly restricted to the recent report of
ftsZ
in the closely related genera
Prosthecobacter
and
Verrucomicrobium
. In this study, genes of the conserved division and cell wall (
dcw
) cluster (
ddl
,
ftsQ
,
ftsA
, and
ftsZ
) were characterized in all verrucomicrobial subdivisions (1 to 4) with cultivable representatives (1 to 4). Sequence analyses and transcriptional analyses in
Verrucomicrobia
and genome data analyses in
Lentisphaerae
suggested that cell division is based on FtsZ in all verrucomicrobial subdivisions and possibly also in the sister phylum
Lentisphaerae
. Comprehensive sequence analyses of available genome data for representatives of
Verrucomicrobia
,
Lentisphaerae
,
Chlamydiae
, and
Planctomycetes
strongly indicate that their last common ancestor possessed a conserved, ancestral type of
dcw
gene cluster and an FtsZ-based cell division mechanism. This implies that
Planctomycetes
and
Chlamydiae
may have shifted independently to a non-FtsZ-based cell division mechanism after their separate branchings from their last common ancestor with
Verrucomicrobia
.
Protein Folding by Domain V of
Escherichia coli
23S rRNA: Specificity of RNA-Protein Interactions
Authors: Samanta Dibyendu , Mukhopadhyay Debashis , Chowdhury Saheli , Ghosh Jaydip , Pal Saumen , Basu Arunima , Bhattacharya Arpita , Das Anindita , Das Debasis , DasGupta Chanchal 
Published: March 2008

ABSTRACT

The peptidyl transferase center, present in domain V of 23S rRNA of eubacteria and large rRNA of plants and animals, can act as a general protein folding modulator. Here we show that a few specific nucleotides in
Escherichia coli
domain V RNA bind to unfolded proteins and, as shown previously, bring the trapped proteins to a folding-competent state before releasing them. These nucleotides are the same for the proteins studied so far: bovine carbonic anhydrase, lactate dehydrogenase, malate dehydrogenase, and chicken egg white lysozyme. The amino acids that interact with these nucleotides are also found to be specific in the two cases tested: bovine carbonic anhydrase and lysozyme. They are either neutral or positively charged and are present in random coils on the surface of the crystal structure of both the proteins. In fact, two of these amino acid-nucleotide pairs are identical in the two cases. How these features might help the process of protein folding is discussed.
Biogenesis of the Fraction 1 Capsule and Analysis of the Ultrastructure of
Yersinia pestis
Authors: Runco Lisa M. , Myrczek Selina , Bliska James B. , Thanassi David G. 
Published: March 2008

ABSTRACT

Analysis of a
Yersinia pestis
Δ
caf1A
mutant demonstrated that the Caf1A usher is required for the assembly and secretion of the fraction 1 capsule. The capsule assembled into thin fibrils and denser aggregates on the bacterial surface. Pilus-like fibers were also detected on the surface of
Y. pestis
. The capsule occasionally coated these fibers, suggesting how the capsule may cloak surface features to prevent host recognition.
Molecular Analysis of Three
Aeromonas hydrophila
AH-3 (Serotype O34) Lipopolysaccharide Core Biosynthesis Gene Clusters
Authors: Jimenez Natalia , Canals Rocío , Lacasta Anna , Kondakova Anna N. , Lindner Buko , Knirel Yuriy A. , Merino Susana , Regué Miguel , Tomás Juan M. 
Published: March 2008

ABSTRACT

By the isolation of three different
Aeromonas hydrophila
strain AH-3 (serotype O34) mutants with an altered lipopolysaccharide (LPS) migration in gels, three genomic regions encompassing LPS core biosynthesis genes were identified and characterized. When possible, mutants were constructed using each gene from the three regions, containing seven, four, and two genes (regions 1 to 3, respectively). The mutant LPS core structures were elucidated by using mass spectrometry, methylation analysis, and comparison with the full core structure of an O-antigen-lacking AH-3 mutant previously established by us. Combining the gene sequence and complementation test data with the structural data and phenotypic characterization of the mutant LPSs enabled a presumptive assignment of all LPS core biosynthesis gene functions in
A. hydrophila
AH-3. The three regions and the genes contained are in complete agreement with the recently sequenced genome of
A. hydrophila
ATCC 7966. The functions of the
A. hydrophila
genes
waaC
in region 3 and
waaF
in region 2 were completely established, allowing the genome annotations of the two heptosyl transferase products not previously assigned. Having the functions of all genes involved with the LPS core biosynthesis and most corresponding single-gene mutants now allows experimental work on the role of the LPS core in the virulence of
A. hydrophila
.
Atlantic Dominance of the Meridional Overturning Circulation
Authors: de Boer A. M. , Toggweiler J. R. , Sigman D. M. 
Published: February 2008

Abstract
North Atlantic (NA) deep-water formation and the resulting Atlantic meridional overturning cell is generally regarded as the primary feature of the global overturning circulation and is believed to be a result of the geometry of the continents. Here, instead, the overturning is viewed as a global energy–driven system and the robustness of NA dominance is investigated within this framework. Using an idealized geometry ocean general circulation model coupled to an energy moisture balance model, various climatic forcings are tested for their effect on the strength and structure of the overturning circulation. Without winds or a high vertical diffusivity, the ocean does not support deep convection. A supply of mechanical energy through winds or mixing (purposefully included or due to numerical diffusion) starts the deep-water formation. Once deep convection and overturning set in, the distribution of convection centers is determined by the relative strength of the thermal and haline buoyancy forcing. In the most thermally dominant state (i.e., negligible salinity gradients), strong convection is shared among the NA, North Pacific (NP), and Southern Ocean (SO), while near the haline limit, convection is restricted to the NA. The effect of a more vigorous hydrological cycle is to produce stronger salinity gradients, favoring the haline state of NA dominance. In contrast, a higher mean ocean temperature will increase the importance of temperature gradients because the thermal expansion coefficient is higher in a warm ocean, leading to the thermally dominated state. An increase in SO winds or global winds tends to weaken the salinity gradients, also pushing the ocean to the thermal state. Paleoobservations of more distributed sinking in warmer climates in the past suggest that mean ocean temperature and winds play a more important role than the hydrological cycle in the overturning circulation over long time scales.
Response of Knee Ligaments to Prolotherapy in a Rat Injury Model
Authors: Jensen Kristina T. , Rabago David P. , Best Thomas M. , Patterson Jeffrey J. , Vanderby Ray 
Published: March 2008

Background Prolotherapy is an alternative therapy for chronic musculoskeletal injury including joint laxity. The commonly used injectant, D-glucose (dextrose), is hypothesized to improve ligament mechanics and decrease pain through an inflammatory mechanism. No study has investigated the mechanical effects of prolotherapy on stretch-injured ligaments. Hypotheses Dextrose injections will enlarge cross-sectional area, decrease laxity, strengthen, and stiffen stretch-injured medial collateral ligaments (MCLs) compared with controls. Dextrose prolotherapy will increase collagen fibril diameter and density of stretch-injured MCLs. Study Design Controlled laboratory study. Methods Twenty-four rats were bilaterally MCL stretch-injured, and the induced laxity was measured. After 2 weeks, 32 MCLs Were injected twice, 1 week apart, with either dextrose or saline control; 16 MCLs received no injection. Seven uninjured rats (14 MCLs) were additional controls. Two weeks after the second injection, ligament laxity, mechanical properties (n = 8), and collagen fibril diameter and density (n = 3) were assessed. Results The injury model created consistent ligament laxity ( P < .05) that was not altered by dextrose injections. Cross-sectional area of dextrose-injected MCLs was increased 30% and 90% compared with saline and uninjured controls, respectively ( P < .05). Collagen fibril diameter and density were decreased in injured ligaments compared with uninjured controls ( P < .05), but collagen fibril characteristics were not different between injured groups. Conclusion Dextrose injections increased the cross-sectional area of MCLs compared with saline-injected and uninjured controls. Dextrose injections did not alter other measured properties in this model. Clinical Relevance Our results suggest that clinical improvement from prolotherapy may not result from direct effects on ligament biomechanics.
Optimization of Graft Fixation at the Time of Anterior Cruciate Ligament Reconstruction
Authors: Mae Tatsuo , Shino Konsei , Nakata Ken , Toritsuka Yukiyoshi , Otsubo Hidenori , Fujie Hiromichi 
Published: March 2008

Background Although anterior cruciate ligament (ACL) reconstructions are frequently performed, little is known about the effect of initial tension on an ACL graft at the time of its fixation. Purpose The objective of this study was to evaluate the effects of initial tension on the relative position and the load between femur and tibia during passive motion. Study Design Controlled laboratory study. Methods Seven cadaveric knees underwent a passive flexion-extension movement from 0° to 90° with a robotic system developed in the authors’ laboratory under 6 degrees of freedom, while their 3-dimensional paths were recorded. A single-socket ACL reconstruction was performed with an autogenous quadrupled hamstring tendon graft, while the knees underwent the same movement as before with the initial graft tension of 22 N (group A), 44 N (group B), or 88 N (group C) at 20°. The relative position between the femur and the tibia was recorded, and the load in the femorotibial joint was calculated using the principle of superposition. Results The tibia in group C was most posteriorly positioned among the 3 groups (an average posterior translation of 0.6, 1.3, and 2.6 mm in groups A, B, and C, respectively). The tibia also moved proximally and laterally with external and valgus rotation with an increase in initial tension, and consequently the load in the femorotibial joint increased at ail flexion angles. Conclusion With an increase in initial tension, the tibia moved posterolaterally with external and valgus rotation, and consequently the contact force in the femorotibial joint increased. Clinical Relevance Excessive initial tension at the time of ACL reconstruction may potentially bring deleterious effects to the articular surface, leading to cartilage degeneration.
Characterization of primitive hematopoietic cells from patients with dyskeratosis congenita
Authors: Goldman Frederick D. , Aubert Geraldine , Klingelhutz Al J. , Hills Mark , Cooper Sarah R. , Hamilton Wendy S. , Schlueter Annette J. , Lambie Karen , Eaves Connie J. , Lansdorp Peter M. 
Published: March 2008

Abstract
Dyskeratosis congenita (DC) is an inherited bone marrow (BM) failure syndrome associated with mutations in telomerase genes and the acquisition of shortened telomeres in blood cells. To investigate the basis of the compromised hematopoiesis seen in DC, we analyzed cells from granulocyte colony-stimulating factor mobilized peripheral blood (mPB) collections from 5 members of a family with autosomal dominant DC with a hTERC mutation. Premobilization BM samples were hypocellular, and percentages of CD34+ cells in marrow and mPB collections were significantly below values for age-matched controls in 4 DC subjects. Directly clonogenic cells, although present at normal frequencies within the CD34+ subset, were therefore absolutely decreased. In contrast, even the frequency of long-term culture-initiating cells within the CD34+ DC mPB cells was decreased, and the telomere lengths of these cells were also markedly reduced. Nevertheless, the different lineages of mature cells were produced in normal numbers in vitro. These results suggest that marrow failure in DC is caused by a reduction in the ability of hematopoietic stem cells to sustain their numbers due to telomere impairment rather than a qualitative defect in their commitment to specific lineages or in the ability of their lineage-restricted progeny to execute normal differentiation programs.
Identification of a fibrin-independent platelet contractile mechanism regulating primary hemostasis and thrombus growth
Authors: Ono Akiko , Westein Erik , Hsiao Sarah , Nesbitt Warwick S. , Hamilton Justin R. , Schoenwaelder Simone M. , Jackson Shaun P. 
Published: March 2008

AbstractA fundamental property of platelets is their ability to transmit cytoskeletal contractile forces to extracellular matrices. While the importance of the platelet contractile mechanism in regulating fibrin clot retraction is well established, its role in regulating the primary hemostatic response, independent of blood coagulation, remains ill defined. Real-time analysis of platelet adhesion and aggregation on a collagen substrate revealed a prominent contractile phase during thrombus development, associated with a 30% to 40% reduction in thrombus volume. Thrombus contraction developed independent of thrombin and fibrin and resulted in the tight packing of aggregated platelets. Inhibition of the platelet contractile mechanism, with the myosin IIA inhibitor blebbistatin or through Rho kinase antagonism, markedly inhibited thrombus contraction, preventing the tight packing of aggregated platelets and undermining thrombus stability in vitro. Using a new intravital hemostatic model, we demonstrate that the platelet contractile mechanism is critical for maintaining the integrity of the primary hemostatic plug, independent of thrombin and fibrin generation. These studies demonstrate an important role for the platelet contractile mechanism in regulating primary hemostasis and thrombus growth. Furthermore, they provide new insight into the underlying bleeding diathesis associated with platelet contractility defects.
Interventional microadhesiolysis: A new nonsurgical release technique for adhesive capsulitis of the shoulder
Authors: Ahn Kang , Lee Young-Jin , Kim Eun-Ha , Yang Seung-Min , Lim Tae-Kyun , Kim Yong-Soo , Jhun Hyung-Joon 
Published: February 2008

Abstract

Background
A nonsurgical intervention, interventional microadhesiolysis, was developed to release adhesions in joints and soft tissues. This paper introduces the procedure and evaluates the efficacy of the intervention for adhesive capsulitis of the shoulder.

Methods
Ten patients (five men and five women) with primary adhesive capsulitis of the shoulder were treated at a chronic pain management center in Korea. Three specially made needles are used in interventional microadhesiolysis: the Round, Flexed Round, and Ahn's needles. A Round Needle is inserted on the skin over middle of supraspinatus and advanced under the acromion and acromioclavicular joint (subacromial release). A Flexed Round Needle is inserted two-fingers caudal to the inferior border of the scapular spine and advanced over the capsule sliding on the surface of infraspinatus muscle-tendon fascia. The capsule is released while an assistant simultaneously passively abducts the shoulder to full abduction (posteroinferior capsule release). An Ahn's Needle is inserted on the skin over the lesser tubercle and advanced under the coracoid process sliding on the surface of the subscapularis muscle (subcoracoid release).

Results
After the patients underwent interventional microadhesiolysis, the self-rated pain score or severity declined significantly (p < .01), the shoulder range of motion increased significantly (p < .01), and joint effusion in the affected shoulder decreased or disappeared in nine of ten patients on magnetic resonance imaging compared to their initial status.

Conclusion
Our findings suggest that interventional microadhesiolysis is effective for managing adhesive capsulitis of the shoulder.
Animal model ofMycobacterium abscessuslung infection
Authors: Ordway Diane , Henao-Tamayo Marcela , Smith Erin , Shanley Crystal , Harton Marisa , Troudt JoLynn , Bai Xiyuan , Basaraba Randall J , Orme Ian M , Chan Edward D 
Published: March 2008

AbstractChronic lung disease as a result of Mycobacterium abscessus is an emerging infection in the United States. We characterized the lung immune responses in mice and guinea pigs infected with M. abscessus. C57BL/6 and leptin-deficient ob/ob mice challenged with a low-dose aerosol (LDA) of M. abscessus did not develop an infection. However, when challenged with a high-dose aerosol (HDA), C57BL/6 and ob/ob mice developed an established infection and a pulmonary immune response consisting of an early influx of IFN-γ+ CD4+ T cells; this immune response preceded the successful clearance of M. abscessus in both strains of mice, although mycobacterial elimination was delayed in the ob/ob mice. Infected guinea pigs showed an increased influx of lymphocytes into the lungs with bacterial clearance by Day 60. In contrast to the C57BL/6 and ob/ob mice and guinea pigs, IFN-γ knockout (GKO) mice challenged with a LDA or HDA of M. abscessus showed a progressive lung infection despite a robust influx of T cells, macrophages, and dendritic cells, culminating in extensive lung consolidation. Furthermore, with HDA challenge of the GKO mice, emergence of IL-4- and IL-10-producing CD4+ and CD8+ T cells was seen in the lungs. In conclusion, IFN-γ is critically important in the host defense against M. abscessus. As the number of effective drugs against M. abscessus is limited, the GKO mice provide a model for in vivo testing of novel drugs.
Childhood sexual abuse and non-suicidal self-injury: meta-analysis
Authors: Klonsky E. David , Moyer Anne 
Published: March 2008

BackgroundMany theorists posit that childhood sexual abuse has a central role in the aetiology of self-injurious behaviour. Studies that report statistically significant associations between a history of such abuse and self-injury are cited to support this view.AimsA meta-analysis was conducted to determine systematically the magnitude of the association between childhood sexual abuse and self-injurious behaviour.MethodForty-five analyses of the association were identified. Effect sizes were converted to a standard metric and aggregated.ResultsThe relationship between childhood sexual abuse and self-injurious behaviour is relatively small (mean weighted aggregateϕ=0.23). This figure may be inflated owing to publication bias. In studies that statistically controlled for psychiatric risk factors, childhood sexual abuse explained little or no unique variance in self-injurious behaviour.ConclusionsTheories that childhood sexual abuse has a central or causal role in the development of self-injurious behaviour are not supported by the available empirical evidence. Instead, it appears that the two are modestly related because they are correlated with the same psychiatric risk factors.
Self-harm in first-episode psychosis
Authors: Harvey Samuel B. , Dean Kimberlie , Morgan Craig , Walsh Elizabeth , Demjaha Arsime , Dazzan Paola , Morgan Kevin , Lloyd Tuhina , Fearon Paul , Jones Peter B. , Murray Robin M. 
Published: March 2008

BackgroundLittle is known about self-harm occurring during the period of untreated first-episode psychosis.AimsTo establish the prevalence, nature, motivation and risk factors for self-harm occurring during the untreated phase of first-episode psychosis.MethodAs part of the æSOP (Aetiology and Ethnicity in Schizophrenia and Other Psychoses) study, episodes of self-harm were identified among all incident cases of psychosis presenting to services in south-east London and Nottingham over a 2-year period.ResultsOf the 496 participants, 56 (11.3%) had engaged in self-harm between the onset of psychotic symptoms and first presentation to services. The independent correlates of self-harm were: male gender, belonging to social class I/II, depression and a prolonged period of untreated psychosis. Increased insight was also associated with risk of self-harm.ConclusionsSelf-harm is common during the pre-treatment phase of first-episode psychosis. A unique set of fixed and malleable risk factors appear to operate in those with first-episode psychosis. Reducing treatment delay and modifying disease attitudes may be key targets for suicide prevention.
Cognitive-behavioural intervention for self-harm: randomised controlled trial
Authors: Slee Nadja , Garnefski Nadia , van der Leeden Rien , Arensman Ella , Spinhoven Philip 
Published: March 2008

BackgroundSelf-harm by young people is occurring with increasing frequency. Conventional in-patient and out-patient treatment has yet to be proved efficacious.AimsTo investigate the efficacy of a short cognitive-behavioural therapy intervention with 90 adolescents and adults who had recently engaged in self-harm.MethodParticipants (aged 15–35 years) were randomly assigned to treatment as usual plus the intervention, or treatment as usual only. Assessments were completed at baseline and at 3 months, 6 months and 9 months follow-up.ResultsPatients who received cognitive-behavioural therapy in addition to treatment as usual were found to have significantly greater reductions in self-harm, suicidal cognitions and symptoms of depression and anxiety, and significantly greater improvements in self-esteem and problem-solving ability, compared with the control group.ConclusionsThese findings extend the evidence that a time-limited cognitive-behavioural intervention is effective for patients with recurrent and chronic self-harm.