bluuebunny/crossref_metadata_2025 huggingface dataset:
Self-Criticism, Dependency, and Stress Reactivity: An Experience Sampling Approach to Testing Blatt and Zuroff’s (1992) Theory of Personality Predispositions to Depression in High-Risk Youth
Authors: Adams Philippe , Abela John R. Z. , Auerbach Randy , Skitch Steven
Published: August 2009

S. J. Blatt and D. C. Zuroff’s 1992 theory of personality predispositions to depression posits that individuals who possess high levels of self-criticism and/or dependency are vulnerable to developing depression following negative events. The current study used experience sampling methodology to test this theory in a sample of 49 children ages 7 to 14. Children completed measures of dependency, self-criticism, and depressive symptoms. Subsequently, children were given a handheld computer that signaled them to complete measures of depressive symptoms and negative events at randomly selected times over 2 months. Results of hierarchical linear modeling analyses indicated that higher levels of both self-criticism and dependency were associated with greater elevations in depressive symptoms following negative events. Furthermore, each personality predisposition remained a significant predictor of such elevations after controlling for the interaction between the other personality predisposition and negative events. The results suggest that dependency and self-criticism represent distinct vulnerability factors to depression in youth.
Religious Group Relations Among Christian, Muslim and Nonreligious Early Adolescents in the Netherlands
Authors: Verkuyten Maykel , Thijs Jochem
Published: August 2009

This study conducted among Christian, Muslim, and nonreligious early adolescents living in the Netherlands used intergroup theory for examining religious group evaluations. There was evidence for a religious group divide with a third of the Christian and nonreligious participants explicitly indicating negative feelings toward Muslims, and Muslim children having negative feelings toward Christians, nonbelievers, and Jews. Furthermore, the Muslim early adolescents had high religious in-group identification and higher identification was associated with more negative feelings toward nonbelievers and Jews. In addition, the results show that increased opportunities in school for contact between early adolescents from different religious and nonreligious groups contributes to more positive group relations. It is argued that the pattern of results is in agreement with an intergroup perspective in which the role of the broader social context and the concrete situation is taken into account.
Autonomy in After-School Activity Choice Among Preadolescents From Taiwan and the United States
Authors: Bidjerano Temi , Newman Joan
Published: August 2009

The study examined boys’ and girls’ autonomy of choice of activities in the after-school hours with samples of children from two different countries. Preadolescent children from Taiwan ( n = 289) and the United States ( n = 195) completed a questionnaire on their usual after-school activities indicating who determines the choice of any particular activity and the extent to which the activity engendered positive affect. The two samples of children differed significantly with respect to the proportion of self-chosen time spent in particular activities (educational activities, organized activities, media use, and personal care and household chores) and overall. Patterns for the two genders were largely consistent across the two samples. Girls reported somewhat less choice in activities overall, and hanging out with peers specifically, whereas boys disclosed less choice in academic activities. However, it was found that for both samples and genders, proportion of autonomy in activities was positively related to reported enjoyment and inversely related to anxiety.
The Impact of Relational Factors on Contracting Management in Public Organizations
Authors: Lee Sooho , Kingsley Gordon
Published: August 2009

This study examines how public managers perceive the value of contractors who hire former agency employees. We find that contractors strategically hire former agency employees to ensure the accomplishment of contract work, potential renewal, and extension of the current project. Although it is unclear whether agency managers prefer contractors who are the agency’s former employees to contractors who have no prior connection with the agency, it is clear that they tend to hire contractors who are more familiar with the agency rules, policies, and inside practices rather than those who are not. However, frequency of interaction with current contractors and contract management experience in the private sector do not have any significant effect on the favorable perception of the agency managers toward increasing contracting out. The findings have important implications for human resource managers, particularly when agencies expand and diversify sources of human resources to increase the overall capacity of agencies.
Parenting and Neighborhood Predictors of Youth Problem Behaviors Within Hispanic Families
Authors: Gayles Jochebed G. , Coatsworth J. Douglas , Pantin Hilda M. , Szapocznik José
Published: August 2009

This study examined the influence of family and neighborhood contexts on Hispanic youth problem behavior. The effects of parents' perceptions of neighborhood context and parenting practices on problem behavior were examined in 167 one-parent ( n = 75) and two-parent ( n = 92) families. Results from multigroup path analyses showed significant main effects of perceived neighborhood context on parenting practices and on youth problem behavior and significant main effects of parenting practices on problem behavior in one- and two-parent families. Neighborhood context was indirectly related to problem behavior through positive parenting in one-parent families. The results demonstrate that parenting is embedded within greater ecological contexts and show that their relations with youth can vary across family structure. Implications for further longitudinal investigation and prevention research are discussed.
Dr. Israel Cuéllar (1946-2008)
Authors: Zamarripa Manuel X.
Published: August 2009

On September 7th, 2008, the mental health field lost a trailblazing researcher and clinician as he lost his battle with amyotrophic lateral sclerosis (ALS), commonly referred to as Lou Gehrig's disease. Dr. Israel Cuéllar made significant contributions to the study of acculturation including its importance in delivering appropriate mental health services to diverse populations. In particular, the construction of the Acculturation Scale for Mexican Americans-II (Cuéllar, Arnold, & Maldonado, 1995) has been and continues to be one of the most important instruments in the measurement of the acculturation process. It remains the most utilized instrument for measuring acculturation for Mexican Americans. For many of us in the mental health field, particularly those of us with an interest and passion to find ways to best serve the Latina/o population, he will remain an inspiration.
Social Environment and Problem Behavior
Authors: March Alice L. , Serdar Atav A.
Published: August 2009

In 2007, 48% of U.S. students of grades 9 to 12 had experienced sexual debut, 7% before the age of 13 years. Preventing early intercourse, sexually transmitted diseases, adolescent pregnancy, and the loss of educational opportunity are important concerns for nurses and educators. A secondary data analysis of the Youth Risk Behavior Survey (YRBS) 2003 provided data identifying the relationships among age at sexual debut, gender, location of residence, and perceived school safety (PSS) as framed by the theory of problem behavior. Mean age at sexual debut was 14.4 years. Males were younger at sexual debut than females. Students reporting positive PSS were older at sexual debut. Age at sexual debut was significantly associated with PSS, gender, and location of residence. School nurses are positioned to identify evidence-based programs, facilitate the development of collaborative interventions to improve PSS, and change trajectories of sexual activity leading to poor health outcomes in adolescents and health risk behaviors in adults.
Tourette Syndrome: Information for School Nurses
Authors: Golder Tracy
Published: August 2009

Tourette syndrome (TS) is a neurobehavioral disorder that consists of simple and complex tics. This disorder can significantly affect a child’s self-esteem and academic success. Although some believe that only adults are affected, this disorder occurs most frequently in early childhood and symptoms decrease with age. Diagnosis of this disorder can be difficult due to the high incidence of comorbidity of other psychiatric illnesses, such as attention-deficit hyperactivity disorder (ADHD), obsessive-compulsive disorder (OCD), bipolar disease, and depression. Early recognition of the disorder allows positive interventions geared toward controlling tics and provides an outlet for tic release. Children and families who are affected by the disorder may attempt to hide the behaviors due to embarrassment of tics. The school nurse is instrumental in working with parents, staff, and other children to assure understanding of the disorder, provide coordination of care, and provide a safe outlet for the child to release the stress of tics during the school day.
Clopidogrel Provides Significantly Greater Inhibition of Platelet Activity Than Aspirin When Combined With Atorvastatin After Coronary Artery Bypass Grafting: A Prospective Randomized Study
Authors: Tetik Sermin , Ak Koray , Isbir Selim , Eksioglu-Demiralp Emel , Arsan Sinan , Iqbal Omer , Yardimci Turay
Published: August 2009

Objective: We aimed to compare the effects of 2 different antiplatelet agents on platelet activity in patients receiv- ing atorvastatin after coronary artery bypass grafting (CABG). Methods: We prospectively randomized 50 patients undergoing CABG into 2 groups; group 1 started to receive atorvastatin (10 mg) plus clopidogrel (75 mg; C + A, n = 25) and group 2 atorvastatin (10 mg) and acetylsalicylic acid (ASA; 300 mg, ASA + A, n = 25) daily on postoperative day 1 and continued for 6 months after operation. Adenosine diphosphate (ADP)–induced pla- telet aggregation and the expressions of glycoprotein (Gp) IIb, GpIIIa, P-selectin, and fibrinogen (Fg) and low-density lipoprotein (LDL) binding to platelets were assessed preoperatively and at postoperative days 7, 90, and 180. Results: The mean age of the patients was 59.6 ± 7.6 years, and 82% of the patients were males. The combination of C + A markedly inhibited ADP-induced platelet aggregation compared with ASA + A at postoperative days 90 and 180 (52% ± 6.0% vs 56% ± 7.25% and 19.6% ± 3.2% vs 37% ± 4.1%, P = .039 and P = .0001, respectively). The therapy of C + A significantly suppressed the expressions of GpIIIa at postoperative days 7, 90, and 180 (P = .0001, P = .0001, and P = .0001, respectively) and P-selectin at postoperative days 90 and 180 (P = .035 and P = .002, respectively) when compared to ASA + A. The expression of GpIIb was also significantly depressed at postoperative day 180 in group 1 when compared to group 2 (P = .0001). Low-density lipoprotein binding was significantly increased at day 180 postoperatively in both the groups (basal: 42.9% ± 5.6% vs 45.3% ± 4.4% and day 180: 60.3% ± 4.6% vs 61.8% ± 5.7%, P = .0001). Conclusions: Our results demonstrate that the combination of C + A is more effective than that of ASA + A in inhibiting ADP-mediated platelet aggregation and expression of major platelet receptors after CABG.
Measuring Homeland Security Innovation in Small Municipal Agencies
Authors: Schafer Joseph A. , Burruss George W. , Giblin Matthew J.
Published: August 2009

Though homeland security has been the focus of ample rhetoric since the 9/11 attacks, empirical accounts of actual innovations in local American policing have been lacking. This study considers the measurement of homeland security innovations within small municipal departments in the state of Illinois. Using survey data, the analysis examines perceptions of risk, engagement in preparatory measures, and perceptions of response capacities within these small agencies. The analysis also considers whether innovation and associated issues are influenced by being located in the Chicago metropolitan area, an urban county, or a rural county. Results suggest limited differences across these regions, with most differences likely emerging due to variation in respondent’s proximity to larger peer agencies. The results are discussed within the context of extant literature on policing in small agencies and rural communities.
Creating Blind Photoarrays Using Virtual Human Technology
Authors: Cutler Brian L. , Daugherty Brent , Babu Sabarish , Hodges Larry , Van Wallendael Lori
Published: August 2009

This article examined the feasibility of a computer-based program that alleviates the human resource challenge associated with blind photoarrays (photoarrays in which the investigator is blind to the suspect’s identity). Students watched videotaped crimes and attempted to identify the perpetrators from photoarays conducted by a “virtual officer” who responds to simple voice commands or by research assistants playing the role of investigators. The student investigators and virtual officer produced comparable identification performance and student reactions to the photoarray procedures. Results of this evaluation study are encouraging, and the authors recommend further laboratory and field testing of the virtual officer technology for conducting blind lineups.
Practitioner Perspectives on the Gap Between Research and Practice: What Gap?
Authors: Keefer Jeffrey M. , Stone Sophia J.
Published: August 2009

The problem and the solution. The research-to-practice gap within HRD is an increasingly important focus of research.This study empirically investigates this issue from the perspective of practitioners, who are directly asked about their use of research. Results suggest that practitioners use “research,” though the term is not used in the same way that those who engage in academic and scholarly research use it. This peer-reviewed research is perceived to not be reaching practitioners, who instead turn to their own communities of practice to meet their research needs.
Renal-Splanchnic Steal Syndrome: The Treatment of Chronic Mesenteric Ischemia With Renal Angioplasty and Stenting
Authors: Joseph deFreitas Dorian , Stoner Michael , Powell Steven , Parker Frank
Published: August 2009

The clinical syndrome of chronic mesenteric ischemia classically presents with a combination of involuntary weight loss, post prandial abdominal pain, and food fear. With occlusion or stenosis of the celiac and superior mesenteric arteries (SMA) collateral blood flow between mesenteric vessels is common and frequently act as the sole blood supply to the intestine. We present a rare case of chronic mesenteric ischemia in which the main blood supply to the celiac and SMA were collaterals coming off the right renal artery resulting in renal-splachnic steal. After an unsuccessful attempt to cannulate the SMA and celiac vessels it was possible to relieve this patient’s symptoms with renal artery stenting.
Harnessing the physiology of lymphopenia to support adoptive immunotherapy in lymphoreplete hosts
Authors: Cui Yongzhi , Zhang Hua , Meadors Joanna , Poon Rita , Guimond Martin , Mackall Crystal L.
Published: August 2009

Lymphopenia enhances the effectiveness of adoptive immunotherapy by facilitating expansion of transferred T cells but also limits the T-cell repertoire available to mediate immune responses and, in humans, is associated with chronic immune dysfunction. Previous studies concluded that lymphopenia augments adoptive immunotherapy by diminishing Tregs and increasing homeostatic cytokines. We sought to determine whether targeted therapies that replicate the physiology of lymphopenia in lymphoreplete hosts could provide a similarly supportive milieu. Pmel-1 T cells were transferred to B16-bearing lymphopenic versus lymphoreplete mice receiving αCD25 and/or recombinant human interleukin-7. Although CD25-based Treg depletion was inefficient because of peripheral expansion of CD4+CD25−FOXP3+ cells, outcomes were better in αCD25-treated lymphoreplete hosts than in lymphopenic hosts, and adoptive immunotherapy was most effective in lymphoreplete hosts receiving αCD25 plus recombinant human interleukin-7. Lymphopenic hosts supported increased proliferation of adoptively transferred antigen-specific T cells, but cells transferred to lymphoreplete recipients receiving targeted therapies showed superior function. Further, determinant spreading was substantial in lymphoreplete hosts but absent in lymphopenic hosts. These results demonstrate that targeted therapies delivered to mimic the “physiology of lymphopenia” enhance the efficacy of adoptive immunotherapy in lymphoreplete hosts and provide a potentially superior alternative to the induction of lymphopenia.
MYC gene rearrangements are associated with a poor prognosis in diffuse large B-cell lymphoma patients treated with R-CHOP chemotherapy
Authors: Savage Kerry J. , Johnson Nathalie A. , Ben-Neriah Susana , Connors Joseph M. , Sehn Laurie H. , Farinha Pedro , Horsman Douglas E. , Gascoyne Randy D.
Published: August 2009

Approximately 5% to 10% of diffuse large B-cell lymphomas (DLBCLs) harbor an MYC oncogene rearrangement (MYC+). The prognostic significance of MYC+ DLBCL was determined in an unselected population of patients with newly diagnosed DLBCL treated with rituximab in combination with cyclophosphamide, doxorubicin, vincristine, and prednisone chemotherapy (R-CHOP). Using a Vysis break-apart fluorescence in situ hybridization probe, 12 of 135 (8.8%) cases of MYC+ DLBCL were identified that had no defining high-risk features. MYC+ DLBCL was associated with an inferior 5-year progression-free survival (66% vs 31%, P = .006) and overall survival (72% vs 33%, P = .016). Multivariate analysis confirmed the prognostic importance of MYC for both progression-free survival (hazard ratio = 3.28; 95% confidence interval, 1.49-7.21, P = .003) and overall survival (hazard ratio = 2.98; 95% confidence interval, 1.28-6.95, P = .011). Cases of MYC+ DLBCL also had a higher risk of central nervous system relapse (P = .023), independent of other risk factors. The diagnosis of MYC+ DLBCL is likely underappreciated; and given the lack of defining risk factors, fluorescence in situ hybridization for MYC rearrangements should be performed in all patients with DLBCL. In the R-CHOP treatment era, MYC+ DLBCLs have an inferior prognosis. Treatment regimens similar to those used in Burkitt lymphoma may be more appropriate in this patient population and need to be prospectively tested.
ABO blood group glycans modulate sialic acid recognition on erythrocytes
Authors: Cohen Miriam , Hurtado-Ziola Nancy , Varki Ajit
Published: August 2009

ABH(O) blood group polymorphisms are based on well-known intraspecies variations in structures of neutral blood cell surface glycans in humans and other primates. Whereas natural antibodies against these glycans can act as barriers to blood transfusion and transplantation, the normal functions of this long-standing evolutionary polymorphism remain largely unknown. Although microbial interactions have been suggested as a selective force, direct binding of lethal pathogens to ABH antigens has not been reported. We show in this study that ABH antigens found on human erythrocytes modulate the specific interactions of 3 sialic acid-recognizing proteins (human Siglec-2, 1918SC influenza hemagglutinin, and Sambucus nigra agglutinin) with sialylated glycans on the same cell surface. Using specific glycosidases that convert A and B glycans to the underlying H(O) structure, we show ABH antigens stabilize sialylated glycan clusters on erythrocyte membranes uniquely for each blood type, generating differential interactions of the 3 sialic acid-binding proteins with erythrocytes from each blood type. We further show that by stabilizing such structures ABH antigens can also modulate sialic acid-mediated interaction of pathogens such as Plasmodium falciparum malarial parasite. Thus, ABH antigens can noncovalently alter the presentation of other cell surface glycans to cognate-binding proteins, without themselves being a direct ligand.
Escalated regeneration in sciatic nerve crush injury by the combined therapy of human amniotic fluid mesenchymal stem cells and fermented soybean extracts, Natto
Authors: Pan Hung-Chuan , Yang Dar-Yu , Ho Shu-Peng , Sheu Meei-Ling , Chen Chung-Jung , Hwang Shiaw-Min , Chang Ming-Hong , Cheng Fu-Chou
Published: August 2009

Attenuation of inflammatory cell deposits and associated cytokines prevented the apoptosis of transplanted stem cells in a sciatic nerve crush injury model. Suppression of inflammatory cytokines by fermented soybean extracts (Natto) was also beneficial to nerve regeneration. In this study, the effect of Natto on transplanted human amniotic fluid mesenchymal stem cells (AFS) was evaluated. Peripheral nerve injury was induced in SD rats by crushing a sciatic nerve using a vessel clamp. Animals were categorized into four groups: Group I: no treatment; Group II: fed with Natto (16 mg/day for 7 consecutive days); Group III: AFS embedded in fibrin glue; Group IV: Combination of group II and III therapy. Transplanted AFS and Schwann cell apoptosis, inflammatory cell deposits and associated cytokines, motor function, and nerve regeneration were evaluated 7 or 28 days after injury. The deterioration of neurological function was attenuated by AFS, Natto, or the combined therapy. The combined therapy caused the most significantly beneficial effects. Administration of Natto suppressed the inflammatory responses and correlated with decreased AFS and Schwann cell apoptosis. The decreased AFS apoptosis was in line with neurological improvement such as expression of early regeneration marker of neurofilament and late markers of S-100 and decreased vacuole formation. Administration of either AFS, or Natto, or combined therapy augmented the nerve regeneration. In conclusion, administration of Natto may rescue the AFS and Schwann cells from apoptosis by suppressing the macrophage deposits, associated inflammatory cytokines, and fibrin deposits.
Characterization of a novel Nav1.5 channel mutation, A551T, associated with Brugada syndrome
Authors: Chiang Kun-Chi , Lai Ling-Ping , Shieh Ru-Chi
Published: August 2009

Brugada syndrome is a life-threatening, inherited arrhythmia disorder associated with autosomal dominant mutations in SCN5A, the gene encoding the human cardiac Na+ channel α subunit (Nav1.5). Here, we characterized the biophysical properties of a novel Brugada syndrome-associated Nav1.5 mutation, A551T, identified in a proband who was successfully resuscitated from an episode of ventricular fibrillation with sudden collapse. Whole-cell currents through wild-type (WT) Nav1.5 and mutant (A551T) channels were recorded and compared in the human embryonic kidney cell line HEK293T transfected with SCN5A cDNA and SCN1B cDNA, using the patch-clamp technique. Current density was decreased in the A551T mutant compared to the WT. In addition, the A551T mutation reduced Nav1.5 activity by promoting entry of the channel into fast inactivation from the closed state, thereby shifting the steady-state inactivation curve by -5 mV. Furthermore, when evaluated at -90 mV, the resting membrane potential, but not at the conventionally used -120 mV, both the percentage, and rate, of channel recovery from inactivation were reduced in the mutant. These results suggest that the DI-DII linker may be involved in the stability of inactivation gating process. This study supports the notion that a reduction in Nav1.5 channel function is involved in the pathogenesis of Brugada syndrome. The structural-functional study of the Nav1.5 channel advances our understanding of its pathophysiolgocial function.
Comparison of exhaled breath condensate pH using two commercially available devices in healthy controls, asthma and COPD patients
Authors: Koczulla Rembert , Dragonieri Silvano , Schot Robert , Bals Robert , Gauw Stefanie A , Vogelmeier Claus , Rabe Klaus F , Sterk Peter J , Hiemstra Pieter S
Published: August 2009

Background

Analysis of exhaled breath condensate (EBC) is a non-invasive method for studying the acidity (pH) of airway secretions in patients with inflammatory lung diseases.

Aim

To assess the reproducibility of EBC pH for two commercially available devices (portable RTube and non-portable ECoScreen) in healthy controls, patients with asthma or COPD, and subjects suffering from an acute cold with lower-airway symptoms. In addition, we assessed the repeatability in healthy controls.

Methods

EBC was collected from 40 subjects (n = 10 in each of the above groups) using RTube and ECoScreen. EBC was collected from controls on two separate occasions within 5 days. pH in EBC was assessed after degasification with argon for 20 min.

Results

In controls, pH-measurements in EBC collected by RTube or ECoScreen showed no significant difference between devices (p = 0.754) or between days (repeatability coefficient RTube: 0.47; ECoScreen: 0.42) of collection. A comparison between EBC pH collected by the two devices in asthma, COPD and cold patients also showed good reproducibility. No differences in pH values were observed between controls (mean pH 8.27; RTube) and patients with COPD (pH 7.97) or asthma (pH 8.20), but lower values were found using both devices in patients with a cold (pH 7.56; RTube, p < 0.01; ECoScreen, p < 0.05).

Conclusion

We conclude that pH measurements in EBC collected by RTube and ECoScreen are repeatable and reproducible in healthy controls, and are reproducible and comparable in healthy controls, COPD and asthma patients, and subjects with a common cold.
Effects of intratracheal administration of nuclear factor-kappaB decoy oligodeoxynucleotides on long-term cigarette smoke-induced lung inflammation and pathology in mice
Authors: Li Yu-Tao , He Bei , Wang Yu-Zhu , Wang Jing
Published: August 2009

To determine if nuclear factor-κB (NF-κB) activation may be a key factor in lung inflammation and respiratory dysfunction, we investigated whether NF-κB can be blocked by intratracheal administration of NF-κB decoy oligodeoxynucleotides (ODNs), and whether decoy ODN-mediated NF-κB inhibition can prevent smoke-induced lung inflammation, respiratory dysfunction, and improve pathological alteration in the small airways and lung parenchyma in the long-term smoke-induced mouse model system. We also detected changes in transcriptional factors. In vivo, the transfection efficiency of NF-κB decoy ODNs to alveolar macrophages in BALF was measured by fluorescein isothiocyanate (FITC)-labeled NF-κB decoy ODNs and flow cytometry post intratracheal ODN administration. Pulmonary function was measured by pressure sensors, and pathological changes were assessed using histology and the pathological Mias software. NF-κB and activator protein 1(AP-1) activity was detected by the electrophoretic motility shift assay (EMSA). Mouse cytokine and chemokine pulmonary expression profiles were investigated by enzyme-linked immunosorbent assay (ELISA) in bronchoalveolar lavage fluid (BALF) and lung tissue homogenates, respectively, after repeated exposure to cigarette smoke. After 24 h, the percentage of transfected alveolar macrophages was 30.00 ± 3.30%. Analysis of respiratory function indicated that transfection of NF-κB decoy ODNs significantly impacted peak expiratory flow (PEF), and bronchoalveolar lavage cytology displayed evidence of decreased macrophage infiltration in airways compared to normal saline-treated or scramble NF-κB decoy ODNs smoke exposed mice. NF-κB decoy ODNs inhibited significantly level of macrophage inflammatory protein (MIP) 1α and monocyte chemoattractant protein 1(MCP-1) in lung homogenates compared to normal saline-treated smoke exposed mice. In contrast, these NF-κB decoy ODNs-treated mice showed significant increase in the level of tumor necrosis factor-α(TNF-α) and pro-MMP-9(pro-matrix metalloproteinase-9) in mice BALF. Further measurement revealed administration of NF-κB decoy ODNs did not prevent pathological changes. These findings indicate that NF-κB activation play an important role on the recruitment of macrophages and pulmonary dysfunction in smoke-induced chronic lung inflammation, and with the exception of NF-κB pathway, there might be complex mechanism governing molecular dynamics of pro-inflammatory cytokines expression and structural changes in small airways and pulmonary parenchyma in vivo.
Identification of a nuclear localization motif in the serine/arginine protein kinase PSRPK of physarum polycephalum
Authors: Liu Shide , Zhou Zhuolong , Lin Ziyang , Ouyang Qiuling , Zhang Jianhua , Tian Shengli , Xing Miao
Published: August 2009

Background

Serine/arginine (SR) protein-specific kinases (SRPKs) are conserved in a wide range of organisms, from humans to yeast. Studies showed that SRPKs can regulate the nuclear import of SR proteins in cytoplasm, and regulate the sub-localization of SR proteins in the nucleus. But no nuclear localization signal (NLS) of SRPKs was found. We isolated an SRPK-like protein PSRPK (GenBank accession No. DQ140379) from Physarum polycephalum previously, and identified a NLS of PSRPK in this study.

Results

We carried out a thorough molecular dissection of the different domains of the PSRPK protein involved in its nuclear localization. By truncation of PSRPK protein, deletion of and single amino acid substitution in a putative NLS and transfection of mammalian cells, we observed the distribution of PSRPK fluorescent fusion protein in mammalian cells using confocal microscopy and found that the protein was mainly accumulated in the nucleus; this indicated that the motif contained a nuclear localization signal (NLS). Further investigation with truncated PSPRK peptides showed that the NLS (318PKKGDKYDKTD328) was localized in the alkaline Ω-loop of a helix-loop-helix motif (HLHM) of the C-terminal conserved domain. If the 318PKKGDK322 sequence was deleted from the loop or K320 was mutated to T320, the PSRPK fluorescent fusion protein could not enter and accumulate in the nucleus.

Conclusion

This study demonstrated that the 318PKKGDKYDKTD328 peptides localized in the C-terminal conserved domain of PSRPK with the Ω-loop structure could play a crucial role in the NLS function of PSRPK.
GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction
Authors: Yu Yao , Tu Kang , Zheng Siyuan , Li Yun , Ding Guohui , Ping Jie , Hao Pei , Li Yixue
Published: August 2009

Background

In the post-genomic era, the development of high-throughput gene expression detection technology provides huge amounts of experimental data, which challenges the traditional pipelines for data processing and analyzing in scientific researches.

Results

In our work, we integrated gene expression information from Gene Expression Omnibus (GEO), biomedical ontology from Medical Subject Headings (MeSH) and signaling pathway knowledge from sigPathway entries to develop a context mining tool for gene expression analysis – GEOGLE. GEOGLE offers a rapid and convenient way for searching relevant experimental datasets, pathways and biological terms according to multiple types of queries: including biomedical vocabularies, GDS IDs, gene IDs, pathway names and signature list. Moreover, GEOGLE summarizes the signature genes from a subset of GDSes and estimates the correlation between gene expression and the phenotypic distinction with an integrated p value.

Conclusion

This approach performing global searching of expression data may expand the traditional way of collecting heterogeneous gene expression experiment data. GEOGLE is a novel tool that provides researchers a quantitative way to understand the correlation between gene expression and phenotypic distinction through meta-analysis of gene expression datasets from different experiments, as well as the biological meaning behind. The web site and user guide of GEOGLE are available at: http://omics.biosino.org:14000/kweb/workflow.jsp?id=00020
Genoviz Software Development Kit: Java tool kit for building genomics visualization applications
Authors: Helt Gregg A , Nicol John W , Erwin Ed , Blossom Eric , Blanchard Steven G , Chervitz Stephen A , Harmon Cyrus , Loraine Ann E
Published: August 2009

Background

Visualization software can expose previously undiscovered patterns in genomic data and advance biological science.

Results

The Genoviz Software Development Kit (SDK) is an open source, Java-based framework designed for rapid assembly of visualization software applications for genomics. The Genoviz SDK framework provides a mechanism for incorporating adaptive, dynamic zooming into applications, a desirable feature of genome viewers. Visualization capabilities of the Genoviz SDK include automated layout of features along genetic or genomic axes; support for user interactions with graphical elements (Glyphs) in a map; a variety of Glyph sub-classes that promote experimentation with new ways of representing data in graphical formats; and support for adaptive, semantic zooming, whereby objects change their appearance depending on zoom level and zooming rate adapts to the current scale. Freely available demonstration and production quality applications, including the Integrated Genome Browser, illustrate Genoviz SDK capabilities.

Conclusion

Separation between graphics components and genomic data models makes it easy for developers to add visualization capability to pre-existing applications or build new applications using third-party data models. Source code, documentation, sample applications, and tutorials are available athttp://genoviz.sourceforge.net/.
Molecular phylogeny of beetle associated diplogastrid nematodes suggests host switching rather than nematode-beetle coevolution
Authors: Mayer Werner E , Herrmann Matthias , Sommer Ralf J
Published: August 2009

Background

Nematodes are putatively the most species-rich animal phylum. They have various life styles and occur in a variety of habitats, ranging from free-living nematodes in aquatic or terrestrial environments to parasites of animals and plants. The rhabditid nematode Caenorhabditis elegans is one of the most important model organisms in modern biology. Pristionchus pacificus of the family of the Diplogastridae has been developed as a satellite model for comparison to C. elegans. The Diplogastridae, a monophyletic clade within the rhabditid nematodes, are frequently associated with beetles. How this beetle-association evolved and whether beetle-nematode coevolution occurred is still elusive. As a prerequisite to answering this question a robust phylogeny of beetle-associated Diplogastridae is needed.

Results

Sequences for the nuclear small subunit ribosomal RNA and for 12 ribosomal protein encoding nucleotide sequences were collected for 14 diplogastrid taxa yielding a dataset of 5996 bp of concatenated aligned sequences. A molecular phylogeny of beetle-associated diplogastrid nematodes was established by various algorithms. Robust subclades could be demonstrated embedded in a phylogenetic tree topology with short internal branches, indicating rapid ancestral divergences. Comparison of the diplogastrid phylogeny to a comprehensive beetle phylogeny revealed no major congruence and thus no evidence for a long-term coevolution.

Conclusion

Reconstruction of the phylogenetic history of beetle-associated Diplogastridae yields four distinct subclades, whose deep phylogenetic divergence, as indicated by short internal branch lengths, shows evidence for evolution by successions of ancient rapid radiation events. The stem species of the Diplogastridae existed at the same time period when the major radiations of the beetles occurred. Comparison of nematode and beetle phylogenies provides, however, no evidence for long-term coevolution of diplogastrid nematodes and their beetle hosts. Instead, frequent host switching is observed. The molecular phylogeny of the Diplogastridae provides a framework for further examinations of the evolution of these associations, for the study of interactions within the ecosystems, and for investigations of diplogastrid genome evolution.
Erratum To: Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair
Authors: Wu Dong-Dong , Irwin David M , Zhang Ya-Ping
Published: August 2009

Correction to Wu DD, Irwin DM, Zhang YP: Molecular evolution of the keratin associated protein gene family in mammals, role in the evolution of mammalian hair. BMC Evol Biol 2008, 8:241.
Rice sHsp genes: genomic organization and expression profiling under stress and development
Authors: Sarkar Neelam K , Kim Yeon-Ki , Grover Anil
Published: August 2009

Background

Heat shock proteins (Hsps) constitute an important component in the heat shock response of all living systems. Among the various plant Hsps (i.e. Hsp100, Hsp90, Hsp70 and Hsp20), Hsp20 or small Hsps (sHsps) are expressed in maximal amounts under high temperature stress. The characteristic feature of the sHsps is the presence of α-crystallin domain (ACD) at the C-terminus. sHsps cooperate with Hsp100/Hsp70 and co-chaperones in ATP-dependent manner in preventing aggregation of cellular proteins and in their subsequent refolding. Database search was performed to investigate the sHsp gene family across rice genome sequence followed by comprehensive expression analysis of these genes.

Results

We identified 40 α-crystallin domain containing genes in rice. Phylogenetic analysis showed that 23 out of these 40 genes constitute sHsps. The additional 17 genes containing ACD clustered with Acd proteins of Arabidopsis. Detailed scrutiny of 23 sHsp sequences enabled us to categorize these proteins in a revised scheme of classification constituting of 16 cytoplasmic/nuclear, 2 ER, 3 mitochondrial, 1 plastid and 1 peroxisomal genes. In the new classification proposed herein nucleo-cytoplasmic class of sHsps with 9 subfamilies is more complex in rice than in Arabidopsis. Strikingly, 17 of 23 rice sHsp genes were noted to be intronless. Expression analysis based on microarray and RT-PCR showed that 19 sHsp genes were upregulated by high temperature stress. Besides heat stress, expression of sHsp genes was up or downregulated by other abiotic and biotic stresses. In addition to stress regulation, various sHsp genes were differentially upregulated at different developmental stages of the rice plant. Majority of sHsp genes were expressed in seed.

Conclusion

We identified twenty three sHsp genes and seventeen Acd genes in rice. Three nucleocytoplasmic sHsp genes were found only in monocots. Analysis of expression profiling of sHsp genes revealed that these genes are differentially expressed under stress and at different stages in the life cycle of rice plant.
A genome-wide analysis of nonribosomal peptide synthetase gene clusters and their peptides in a Planktothrix rubescens strain
Authors: Rounge Trine B , Rohrlack Thomas , Nederbragt Alexander J , Kristensen Tom , Jakobsen Kjetill S
Published: August 2009

Background

Cyanobacteria often produce several different oligopeptides, with unknown biological functions, by nonribosomal peptide synthetases (NRPS). Although some cyanobacterial NRPS gene cluster types are well described, the entire NRPS genomic content within a single cyanobacterial strain has never been investigated. Here we have combined a genome-wide analysis using massive parallel pyrosequencing ("454") and mass spectrometry screening of oligopeptides produced in the strain Planktothrix rubescens NIVA CYA 98 in order to identify all putative gene clusters for oligopeptides.

Results

Thirteen types of oligopeptides were uncovered by mass spectrometry (MS) analyses. Microcystin, cyanopeptolin and aeruginosin synthetases, highly similar to already characterized NRPS, were present in the genome. Two novel NRPS gene clusters were associated with production of anabaenopeptins and microginins, respectively. Sequence-depth of the genome and real-time PCR data revealed three copies of the microginin gene cluster. Since NRPS gene cluster candidates for microviridin and oscillatorin synthesis could not be found, putative (gene encoded) precursor peptide sequences to microviridin and oscillatorin were found in the genes mdn A and osc A, respectively. The genes flanking the microviridin and oscillatorin precursor genes encode putative modifying enzymes of the precursor oligopeptides. We therefore propose ribosomal pathways involving modifications and cyclisation for microviridin and oscillatorin. The microviridin, anabaenopeptin and cyanopeptolin gene clusters are situated in close proximity to each other, constituting an oligopeptide island.

Conclusion

Altogether seven nonribosomal peptide synthetase (NRPS) gene clusters and two gene clusters putatively encoding ribosomal oligopeptide biosynthetic pathways were revealed. Our results demonstrate that whole genome shotgun sequencing combined with MS-directed determination of oligopeptides successfully can identify NRPS gene clusters and the corresponding oligopeptides. The analyses suggest independent evolution of all NRPS gene clusters as functional units. Our data indicate that the Planktothrix genome displays evolution of dual pathways (NRPS and ribosomal) for production of oligopeptides in order to maximize the diversity of oligopeptides with similar but functional discrete bioactivities.
Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli
Authors: Vázquez Carlos Daniel , Freyre-González Julio A , Gosset Guillermo , Loza José Antonio , Gutiérrez-Ríos Rosa María
Published: August 2009

Background

Glucose is the preferred carbon and energy source for Bacillus subtilis and Escherichia coli. A complex regulatory network coordinates gene expression, transport and enzymatic activities, in response to the presence of this sugar. We present a comparison of the cellular response to glucose in these two model organisms, using an approach combining global transcriptome and regulatory network analyses.

Results

Transcriptome data from strains grown in Luria-Bertani medium (LB) or LB+glucose (LB+G) were analyzed, in order to identify differentially transcribed genes in B. subtilis. We detected 503 genes in B. subtilis that change their relative transcript levels in the presence of glucose. A similar previous study identified 380 genes in E. coli, which respond to glucose. Catabolic repression was detected in the case of transport and metabolic interconversion activities for both bacteria in LB+G. We detected an increased capacity for de novo synthesis of nucleotides, amino acids and proteins. A comparison between orthologous genes revealed that global regulatory functions such as transcription, translation, replication and genes relating to the central carbon metabolism, presented similar changes in their levels of expression. An analysis of the regulatory network of a subset of genes in both organisms revealed that the set of regulatory proteins responsible for similar physiological responses observed in the transcriptome analysis are not orthologous. An example of this observation is that of transcription factors mediating catabolic repression for most of the genes that displayed reduced transcript levels in the case of both organisms. In terms of topological functional units in both these bacteria, we found interconnected modules that cluster together genes relating to heat shock, respiratory functions, carbon and peroxide metabolism. Interestingly, B. subtilis functions not found in E. coli, such as sporulation and competence were shown to be interconnected, forming modules subject to catabolic repression at the level of transcription.

Conclusion

Our results demonstrate that the response to glucose is partially conserved in model organisms E. coli and B. subtilis, including genes encoding basic functions such as transcription, translation, replication and genes involved in the central carbon metabolism.
Regulation of Neph3 gene in podocytes – key roles of transcription factors NF-κB and Sp1
Authors: Ristola Mervi , Arpiainen Satu , Saleem Moin A , Mathieson Peter W , Welsh Gavin I , Lehtonen Sanna , Holthöfer Harry
Published: August 2009

Background

Neph3 (filtrin) is expressed in the glomerular podocytes where it localizes at the specialized cell adhesion structures of the foot processes called slit diaphragms which form the outermost layer of the glomerular filtration barrier. Neph3 protein shows homology and structural similarity to Neph1, Neph2 and nephrin, which all are crucial for maintaining the normal glomerular ultrafiltration function. The exact function of Neph3 in the kidney is not known but we have previously shown that the level of Neph3 mRNA is decreased in proteinuric diseases. This suggests that Neph3 may play a role in the pathogenesis of kidney damage, and emphasizes the need to analyze the regulatory mechanisms of Neph3 gene. In this study we investigated the transcriptional regulation of Neph3 gene by identifying transcription factors that control Neph3 expression.

Results

We cloned and characterized approximately 5 kb fragment upstream of the Neph3 gene. Neph3 proximal promoter near the transcription start site was found to be devoid of TATA and CAAT boxes, but to contain a highly GC-rich area. Using promoter reporter gene constructs, we localized the main activating regulatory region of Neph3 gene in its proximal promoter region from -105 to -57. Within this region, putative transcription factor binding sites for NF-κB and Sp1 were found by computational analysis. Mutational screening indicated that NF-κB and Sp1 response elements are essential for the basal transcriptional activity of the Neph3 promoter. Co-transfection studies further showed that NF-κB and Sp1 regulate Neph3 promoter activity. In addition, overexpression of NF-κB increased endogenous Neph3 gene expression. Chromatin immunoprecipitation assay using cultured human podocytes demonstrated that both NF-κB and Sp1 interact with the Neph3 promoter.

Conclusion

Our results show that NF-κB and Sp1 are key regulators of Neph3 expression at the basal level in podocytes, therefore providing new insight into the molecular mechanisms that contribute to the expression of Neph3 gene.