bluuebunny/crossref_metadata_2025_split huggingface dataset:
ppGpp Conjures Bacterial Virulence
Authors: Dalebroux Zachary D. , Svensson Sarah L. , Gaynor Erin C. , Swanson Michele S. 
Published: May 2010

SUMMARYLike for all microbes, the goal of every pathogen is to survive and replicate. However, to overcome the formidable defenses of their hosts, pathogens are also endowed with traits commonly associated with virulence, such as surface attachment, cell or tissue invasion, and transmission. Numerous pathogens couple their specific virulence pathways with more general adaptations, like stress resistance, by integrating dedicated regulators with global signaling networks. In particular, many of nature's most dreaded bacteria rely on nucleotide alarmones to cue metabolic disturbances and coordinate survival and virulence programs. Here we discuss how components of the stringent response contribute to the virulence of a wide variety of pathogenic bacteria.
Two new dothideomycetous endoconidial genera from declining larch
Authors: Tsuneda A. , Davey M. L. , Tsuneda I. , Currah R. S. 
Published: May 2010

Two endoconidial, black meristematic fungi, Celosporium larixicolum gen. et sp. nov. (Dothideales) and Hispidoconidioma alpina gen. et sp. nov. (Capnodiales) are described from black subicula on twigs of declining larch ( Larix lyallii Parl) trees in Alberta, Canada. Conidioma morphology and phylogenetic analysis of LSU and ITS regions indicate that these taxa are both distinct from each other and from previously described endoconidial genera. Conidiomata of C. larixicolum consist of black cellular clumps (aggregated conidiogenous cells) that are either naked or enveloped by scant to dense mycelium that sometimes organizes into a cupulate peridium. Endoconidia are 1–3 celled, hyaline when released but become pigmented as they age, and very variable in size and shape, e.g., globose, pear-shaped, osteoid, or discoid with an irregular flange. In H. alpina, colonies are three-layered, consisting of a central pseudoparenchymatous layer sandwiched between an upper and a basal hyphal layers, and conidiogenesis occurs in sporadic areas of the central layer. Endoconidia are unicellular, hyaline, and subglobose to ellipsoid. The strong phylogenetic affinities between these newly described taxa and slow-growing, melanized fungi isolated from rocks suggest individual black meristematic fungus lineages may have broad habitat ranges.
Characterization of expressed sequence tag-derived simple sequence repeat markers for 17 Linum species
Authors: Fu Yong-Bi , Peterson Gregory W. 
Published: May 2010

One major challenge in genetic and evolutionary studies of wild flax species is the lack of informative molecular markers. A set of 100 informative expressed sequence tag-derived simple sequence repeat (EST-SSR) primer pairs developed in cultivated flax ( Linum usitatissimum L.) were characterized on 35 Linum accessions representing 17 Linum species for their transferability to other Linum species. Ninety-nine primer pairs displayed scorable polymorphisms across 35 Linum samples and generated 627 bands likely from 121 loci. About 50% of the detected bands occurred only in three or fewer samples. A total of 393 bands, likely from 116 loci, were detected by 97 primer pairs in Linum bienne Mill. samples, but only up to 60 bands, likely from up to 39 loci, were revealed by 6 to 37 primer pairs in the samples of the other 15 Linum species. The L. bienne samples displayed 23.7% more EST-SSR variation than the L. usitatissimum samples. These characterized EST-SSR markers should be useful for future genetic diversity and evolutionary studies of Linum species, particularly for the progenitor of cultivated flax.
Ultrastructure of pit membrane dissolution and movement of Xylella fastidiosa through pit membranes in petioles of Vitis vinifera
Authors: Ellis E. Ann , McEachern George Ray , Clark Samantha , Cobb B. Greg 
Published: May 2010

Xylella fastidiosa is the causative agent in Pierce’s disease (PD) in Vitis vinifera L. (grape) vines. Xylella fastidiosa colonizes and disseminates itself from one xylem element to another by dissolution and breach of pit membranes. These studies on naturally infected V. vinifera grown under vineyard conditions document by transmission electron microscopy that there is dissolution and breach of pit membranes by X. fastidiosa in vertical and lateral colonization in PD. These processes were documented in two cultivars of V. vinifera: ‘Syrah’ and ‘Cabernet Sauvignon.’
Drought-triggered false ring formation in a Mediterranean shrub
Authors: Copenheaver Carolyn A. , Gärtner Holger , Schäfer Isabelle , Vaccari Francesco P. , Cherubini Paolo 
Published: May 2010

Recently, the Mediterranean region has experienced unprecedented drought. Climate models continue to predict an increase in drought frequency and duration, which increases the importance of quantifying the response of already drought-tolerant Mediterranean plants to increased drought. We examined the wood anatomy and dendroecological features of a Mediterranean shrub, Arbutus unedo L., at a xeric and a mesic site on the Italian island of Elba to identify shrub growth response to drought. Cross-sectional microsections of A. unedo stems were stained, described, and crossdated. Annual ring widths of radial microsections were measured and compared with regional climatic variables. False rings (intra-annual bands of latewood typically formed in response to a specific stressor) were visible in the wood samples when viewing radial microsections under high magnification. False ring formation coincided with below-average rainfall in late summer at the xeric site, and below-average rainfall and high temperatures in spring and summer at the mesic site. If increased drought occurs in the Mediterranean region, it is likely that plants in this region will experience a drought-induced growth response similar to that seen in A. unedo, and slight differences in drought tolerance may become more important as plants compete for moisture under drier conditions.
Virulence and molecular polymorphisms of the wheat leaf rust fungus Puccinia triticina in Canada from 1997 to 2007
Authors: Wang Xiben , Bakkeren Guus , McCallum Brent 
Published: May 2010

Populations of Puccinia triticina , one of the casual agents of wheat leaf rust disease, in the pacific (British Columbia and Alberta), prairie (Manitoba and Saskatchewan), and eastern regions (Quebec and Ontario) of Canada from 1997 to 2007 were analyzed for virulence and genetic diversity by revealing expressed sequence tag derived simple sequence repeat (EST-SSR) polymorphisms. Since 1997, a significant shift in the virulence of P. triticina occurred across Canada. The diversity of P. triticina virulence phenotypes in Manitoba and Saskatchewan, as measured by Shannon and Simpson indexes, decreased due to the directional selection toward predominant virulence phenotypes, whereas it remained relatively constant in Quebec and Ontario. The clustering of P. triticina virulence phenotypes from 1997 to 2007 was similar to that found in previous years, and was correlated with virulence to leaf rust resistance genes Lr2a, Lr2c, and Lr17a. Distinct EST-SSR profiles were found in different groups of P. triticina virulence phenotypes based on virulence to Lr2a, Lr2c, and Lr17a. In addition, the population of P. triticina in Manitoba and Saskatchewan was different from that in Quebec and Ontario from 1997 to 2007, based on both virulence characteristics and EST-SSR genotypes.
Fatal End of a Safety Algorithm for Pulmonary Vein Isolation With Use of High-Intensity Focused Ultrasound
Authors: Neven Kars , Schmidt Boris , Metzner Andreas , Otomo Kiyoshi , Nuyens Dieter , De Potter Tom , Chun K.R. Julian , Ouyang Feifan , Kuck Karl-Heinz 
Published: May 2010

Background—
High-intensity focused ultrasound (HIFU) can achieve pulmonary vein isolation (PVI), but there are safety concerns after severe complications. Therefore, we evaluated an esophageal temperature (ET)-guided safety algorithm to apply HIFU safely.

Methods and Results—

After standard left atrial access, HIFU was repeatedly applied until PVI was complete. A safety algorithm was used: ≤3 complete ablations per pulmonary vein (PV), early abortion when no effect after 50%of programmed time or when ET was ≥40.0°C, use of power modulation (PM) at ET 39.0°C: to reduce ablation temperature in surrounding tissue, acoustic power is switched on/off at 1 Hz; in all first ablations, use of PM after 50% of programmed time. Touch-up radiofrequency ablation was used when PVI failed. Periprocedural ET monitoring and endoscopy 2 days after ablation were performed. Twenty-eight patients (18 males; mean age at enrollment, 63 years), with paroxysmal atrial fibrillation (AF; n=19) and persistent AF (n=9) were included. In 84 of 109 PV (9 of 25 patients), PVI was achieved using HIFU only. In 9 of 109 PV, HIFU was aborted because of high ET. Mean ET at the end of the ablations with and without use of PM were 38.1±2.0°C and 37.4±1.0°C (
P
=0.0002). During endoscopy in 2 of 26 patients, a small thermal lesion was found. Other complications included 2 persistent phrenic nerve palsies, 1 ischemic stroke, 1 pericardial effusion 48 days after ablation, 1 unexplained death 49 days after ablation, and 1 lethal atrial-to-esophageal fistula 31 days after ablation.

Conclusions—
The safety algorithm failed to prevent lethal complications. Currently HIFU does not meet the safety standards required for treatment of atrial fibrillation.
Effect of Femoral Tunnel Length on the Safety of Anterior Cruciate Ligament Graft Fixation Using Cross-Pin Technique
Authors: Gelber Pablo Eduardo , Reina Francisco , Torres Raúl , Monllau Juan Carlos 
Published: May 2010

Background: A more oblique placement of the anterior cruciate ligament (ACL) graft has been related to better control of rotatory knee stability. Femoral fixation with a transverse system might injure its posterolateral structures. Hypothesis: A cross-pin system, originally developed for transtibial reconstruction of the ACL, can safely be used when creating a lower femoral tunnel through the anteromedial portal. However, a long femoral tunnel must be created to protect the posterolateral structures of the knee. Study Design: Controlled laboratory study. Methods: An ACL was arthroscopically reconstructed with a hamstring graft in 22 fresh cadaveric knees. The femoral tunnel was anatomically drilled in all cases. Knee flexion angle was set at 110°. Femoral fixation was performed with a cross-pin system. A 30-mm-long femoral tunnel was created in 11 knees (group A). In the remaining 11 knees, the femoral tunnel was drilled as long as each lateral condyle permitted (group B). For both groups, the relationships were compared between the cross-pin and the lateral collateral ligament (LCL), popliteus tendon, articular cartilage, and peroneal nerve. Results: In 5 cases of group A, the cross-pin was placed either through the LCL or between the LCL and popliteus tendon, whereas in group B it was always posterior to the LCL ( P = .035). The cross-pin was closer to the articular cartilage in group A than in group B (7.14 mm versus 16.9 mm; P < .001). The minimal distance to the peroneal nerve in all specimens was 23.89 mm. Conclusion: Hamstring graft fixation with a cross-pin system from the anteromedial portal with a 30-mm femoral tunnel presents a higher risk of injury to the LCL. The femoral tunnel should be drilled as long as possible. Clinical Relevance: A long femoral tunnel is required for safe transverse femoral fixation in an anatomical ACL reconstruction.
JCoDA: a tool for detecting evolutionary selection
Authors: Steinway Steven N , Dannenfelser Ruth , Laucius Christopher D , Hayes James E , Nayak Sudhir 
Published: May 2010

Abstract

Background
The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences.

Results
JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway.

Conclusions
JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at http://www.tcnj.edu/~nayaklab/jcoda.
Functional characterization of the vertebrate primary ureter: Structure and ion transport mechanisms of the pronephric duct in axolotl larvae (Amphibia)
Authors: Haugan Birgitte M , Halberg Kenneth A , Jespersen Åse , Prehn Lea R , Møbjerg Nadja 
Published: May 2010

Abstract

Background
Three kidney systems appear during vertebrate development: the pronephroi, mesonephroi and metanephroi. The pronephric duct is the first or primary ureter of these kidney systems. Its role as a key player in the induction of nephrogenic mesenchyme is well established. Here we investigate whether the duct is involved in urine modification using larvae of the freshwater amphibian Ambystoma mexicanum (axolotl) as model.

Results
We investigated structural as well as physiological properties of the pronephric duct. The key elements of our methodology were: using histology, light and transmission electron microscopy as well as confocal laser scanning microscopy on fixed tissue and applying the microperfusion technique on isolated pronephric ducts in combination with single cell microelectrode impalements. Our data show that the fully differentiated pronephric duct is composed of a single layered epithelium consisting of one cell type comparable to the principal cell of the renal collecting duct system. The cells are characterized by a prominent basolateral labyrinth and a relatively smooth apical surface with one central cilium. Cellular impalements demonstrate the presence of apical Na+ and K+ conductances, as well as a large K+ conductance in the basolateral cell membrane. Immunolabeling experiments indicate heavy expression of Na+/K+-ATPase in the basolateral labyrinth.

Conclusions
We propose that the pronephric duct is important for the subsequent modification of urine produced by the pronephros. Our results indicate that it reabsorbs sodium and secretes potassium via channels present in the apical cell membrane with the driving force for ion movement provided by the Na+/K+ pump. This is to our knowledge the first characterization of the pronephric duct, the precursor of the collecting duct system, which provides a model of cell structure and basic mechanisms for ion transport. Such information may be important in understanding the evolution of vertebrate kidney systems and human diseases associated with congenital malformations.
Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae)
Authors: Yuan Qing-Jun , Zhang Zhi-Yong , Hu Juan , Guo Lan-Ping , Shao Ai-Juan , Huang Lu-Qi 
Published: May 2010

AbstractBackgroundCultivation of medicinal plants is not only a means for meeting current and future demands for large volume production of plant-based drug and herbal remedies, but also a means of relieving harvest pressure on wild populations.Scutellaria baicalensisGeorgi (Huang-qin or Chinese skullcap) is a very important medicinal plant in China. Over the past several decades, wild resource of this species has suffered rapid declines and large-scale cultivation was initiated to meet the increasing demand for its root. However, the genetic impacts of recent cultivation onS. baicalensishave never been evaluated. In this study, the genetic diversity and genetic structure of 28 wild and 22 cultivated populations were estimated using three polymorphic chloroplast fragments. The objectives of this study are to provide baseline data for preserving genetic resource ofS. baicalensisand to evaluate the genetic impacts of recent cultivation on medicinal plants, which may be instructive to future cultivation projects of traditional Chinese medicinal plants.ResultsThirty-two haplotypes ofS. baicalensis(HapA-Y and Hap1-7) were identified when three chloroplast spacers were combined. These haplotypes constituted a shallow gene tree without obvious clusters for cultivated populations, suggesting multiple origins of cultivatedS. baicalensis. Cultivated populations (hT= 0.832) maintained comparable genetic variation with wild populations (hT= 0.888), indicating a slight genetic bottleneck due to multiple origins of cultivation. However, a substantial amount of rare alleles (10 out of 25 haplotypes within wild populations) lost during the course ofS. baicalensiscultivation. The genetic differentiation for cultivated group (GST= 0.220) was significantly lower than that of wild group (GST= 0.701). Isolation by distance analysis showed that the effect of geographical isolation on genetic structure was significant in wild populations (r= 0.4346,P< 0.0010), but not in cultivated populations (r =0.0599,P= 0.2710). These genetic distribution patterns suggest that a transient cultivation history and the extensive seed change among different geographical areas during the course ofS. baicalensiscultivation.ConclusionsAlthough cultivatedS. baicalensismaintains comparable genetic diversity relative to wild populations, recent cultivation has still imposed profound impacts on genetic diversity patterns of the cultivatedS. baicalensispopulations, i.e., the loss of rare alleles and homogenization of cultivated populations. This study suggests that conservation-by-cultivation is an effective means for protecting genetic resources ofS. baicalensis, however, the wild resources still need to be protectedin situand the evolutionary consequences of extensive seed exchange mediated by human being should be monitored carefully.
Differential cytokine regulation by NF-κB and AP-1 in Jurkat T-cells
Authors: Khalaf Hazem , Jass Jana , Olsson Per-Erik 
Published: May 2010

AbstractBackgroundActivator protein (AP)-1 and nuclear factor (NF)-κB largely control T-cell activation, following binding of foreign antigens to the T-cell receptor leading to cytokine secretion. Elevated levels of pro-inflammatory cytokines and chemokines such as TNF, IL-6 and CXCL8 are associated with several human diseases including cystic fibrosis, pulmonary fibrosis and AIDS. The aim of this study was to investigate the role of the transcription factors, AP-1 and NF-κB, in IL-6 and CXCL8 regulation in Jurkat T-cells.ResultsPhorbol myristate acetate (PMA) exposure resulted in an up-regulation of AP-1 and down-regulation of NF-κB activity, however, exposure to heat killed (HK)Escherichia. coliMG1655 resulted in a dose-dependent increase in NF-κB activity without affecting AP-1. The cytokine profile revealed an up-regulation of the chemokine CXCL8 and the pro-inflammatory cytokines TNF, IL-2 and IL-6 following treatment with both PMA and HKE. coli, while the levels of the anti-inflammatory cytokine IL-10 were not affected by PMA but were significantly down-regulated by HKE. coli. AP-1 activation was significantly increased 2 h after PMA exposure and continued to increase thereafter. In contrast, NF-κB responded to PMA exposure by a rapid up-regulation followed by a subsequent down-regulation. Increased intracellular Ca2+concentrations countered the down-regulation of NF-κB by PMA, while similar treatment with calcium ionophore resulted in a reduced NF-κB activity following induction with HKE. coli. In order to further study NF-κB activation, we considered two up-stream signalling proteins, PKC and Bcl10. Phosphorylated-PKC levels increased in response to PMA and HKE. coli, while Bcl10 levels significantly decreased following PMA treatment. Using an NF-κB activation inhibitor, we observed complete inhibition of IL-6 expression while CXCL8 levels only decreased by 40% at the highest concentration. Treatment of Jurkat T-cells with PMA in the presence of JNK-inhibitor suppressed both CXCL8 and IL-6 while PKC-inhibitor primarily decreased CXCL8 expression.ConclusionThe present study shows that NF-κB regulated IL-6 but not CXCL8. This complex regulation of CXCL8 suggests that there is a need to further evaluate the signalling pathways in order to develop new treatment for diseases with elevated CXCL8 levels, such as AIDS and autoimmune diseases.