bluuebunny/crossref_metadata_2025 huggingface dataset:
2D‐DIGE proteomic characterization of head and neck squamous cell carcinoma
Authors: Merkley Mark A. , Weinberger Paul M. , Jackson Lana L. , Podolsky Robert H. , Lee Jeffrey R. , Dynan William S.
Published: October 2009

Objective

Identify proteins that are differentially expressed between head and neck squamous cell cancer (HNSCC) and patient‐matched normal adjacent tissue, and validate findings in a separate patient cohort.

Study Design

Cross‐sectional study of surgical specimens.

Setting

Tertiary care academic medical center.

Subjects and Methods

Laser capture microdissection and two‐dimensional difference gel electrophoresis were used previously to establish proteomic profiles for tumor and normal adjacent tissue from 14 patients. Here, significance analysis of microarray was used to rank candidate biomarkers. Spots meeting statistical and biological criteria of significance were analyzed by liquid chromatography and tandem mass spectrometry to obtain protein identifications. The expression pattern of the highest‐ranked candidate biomarker (cornulin) was validated in a larger, independent patient cohort (n = 68) by immunohistochemical staining of a tissue microarray.

Results

Of 732 spots, 117 (15.9%) met criteria for significance. Identities were obtained for 39 spots, representing 17 different proteins. Four proteins were novel in the context of HNSCC: glutathione synthetase, which was upregulated; and cornulin (squamous epithelial heat shock protein 53), guanylate binding protein 6, and heat shock 70 kDa protein 5 (glucose‐regulated protein, 78 kDa), which were downregulated. Cornulin functions in the stress response in normal squamous epithelium, and reduced expression has been proposed as a marker of susceptibility to laryngopharyngeal reflux and other stressors. Loss of cornulin expression was confirmed in an independent HNSCC patient cohort (P < 0.001).

Conclusions

Downregulation of cornulin is a prominent feature of the molecular signature of HNSCC identified by comparative proteomics. Cornulin may represent a link between HNSCC and other pathologies arising in stratified squamous epithelium.
Volume and distances of the maxillary sinus in craniofacial deformities with midfacial hypoplasia
Authors: Song Seung Yong , Hong Jong Won , Roh Tai Suk , Kim Yong Oock , Kim Deok Won , Park Beyoung Yun
Published: October 2009

Objective

Craniofacial deformities (CFDs) frequently accompany midfacial hypoplasia. The authors evaluated characteristics of maxillary sinuses that had CFDs with variable degrees of midfacial hypoplasia.

Study Design

Cross‐sectional survey with chart review.

Setting

Department of Plastic and Reconstructive Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea.

Subjects and Methods

We investigated 40 patients with CFDs having midfacial hypoplasia. Study group 1 (SG 1) consisted of eight patients with Crouzon syndrome (16 maxillary sinuses). Study group 2 (SG 2) consisted of 10 patients with midfacial hypoplasia after palatoplasty (20 maxillary sinuses). Study group 3 (SG 3) consisted of 22 patients with Pruzansky grade I hemifacial microsomia (22 maxillary sinuses on the affected sides). Data on volume and three‐dimensional distances (height, width, and depth) from computed tomography were collected and compared with each corresponding control group. Correlation coefficient between volume and the three distances was also calculated.

Results

The volume, height, width, and depth of the maxillary sinus were significantly decreased in SG 1 (P < 0.01). In SG 2, only the depth was significantly decreased (P < 0.05). In SG 3, there were no significant differences in any parameters. A multiple‐regression analysis between the volume and the three distances showed a statistically significant relationship for width in SG 1, width and height in SG 2, and all distances in SG 3.

Conclusion

There were differences in the structure of the maxillary sinuses among patients with different CFDs.
In vitro testing of tympanostomy tube occlusion
Authors: Sherman Ethan G. , Antonelli Patrick J. , Tran‐Son‐Tay Roger
Published: October 2009

Objective

Tympanostomy tubes (TTs) are commonly rendered nonfunctional by mucus plug formation. The purpose of this study was to determine whether an in vitro model could be developed to assess TT plug formation with results consistent with human trials.

Study Design

An ear chamber was designed to mimic middle ear air and mucus flow conditions in post‐TT otorrhea. TT occlusion was tested and correlated to published in vivo results.

Methods

TTs that had previously been studied in vivo (Goode “T” and Reuter Bobbin collar buttons) were placed in the model chamber. Pooled, homogenized human middle ear mucus and an analog, egg white, were delivered at 80 μL per hour through the TTs. An air bolus was delivered every two minutes to simulate swallowing. Chamber pressure was monitored over 2.5 hours. Occlusion was determined by a pressure peak and visual confirmation.

Results

Obstruction was found in 60 percent of the Reuter Bobbin and 40 percent of the Goode TTs using the mucus analog. These results are similar to those reported from previous in vivo studies. No plugging was reported for either TT using homogenized human ear mucus.

Conclusions

The in vitro TT chamber simulates the in vivo environment and yields results consistent with in vivo observations. This model system may allow for rapid prototyping and evaluation of new TTs that may be less vulnerable to occlusion.
Pepsin as a causal agent of inflammation during nonacidic reflux
Authors: Samuels Tina L. , Johnston Nikki
Published: October 2009

Objective

To investigate the contribution of pepsin to inflammation attributed to nonacidic gastric reflux via analysis of inflammatory cytokine and cytokine receptor gene expression in pepsin‐treated human hypopharyngeal epithelial cells in vitro.

Study Design

Translational research.

Setting

This study was performed in an academic research laboratory.

Subjects and Methods

Human hypopharyngeal epithelial cells were incubated with or without pepsin (0.1 mg/mL) at pH 7.4, 37°C, overnight. Expression of 84 inflammatory cytokines and cytokine receptors was analyzed via RT2 qPCR array.

Results

Expression of a number of inflammatory cytokines and receptors was altered in human hypopharyngeal epithelial cells following overnight treatment with pepsin at neutral pH. Greater than 1.5‐fold change in gene expression was detected for CCL20, CCL26, IL8, IL1F10, IL1A, IL5, BCL6, CCR6, and CXCL14 (P < 0.05).

Conclusion

Exposure of hypopharyngeal cells to pepsin in a nonacidic environment induces the expression of several pro‐inflammatory cytokines and receptors, including those known to be involved in inflammation of esophageal epithelium in response to reflux and which contribute to the pathophysiology of reflux esophagitis. These data indicate that refluxed pepsin may contribute to laryngeal inflammation associated with nonacidic gastric reflux, including that experienced by patients despite maximal acid suppression therapy.
Unexpected consequences of proton pump inhibitor use
Authors: Altman Kenneth W. , Radosevich James A.
Published: October 2009

Proton pump inhibitors (PPIs) are among the most widely prescribed classes of medications for gastroesophageal and laryngopharyngeal reflux diseases. There is emerging evidence that the pathogenesis of disease in laryngeal mucosa is not just related to refluxed acid, but also the presence of pepsin and acidic microenvironments. The widespread use of PPIs is also calling into question potential complications of PPI use. This commentary expands upon these issues with other potential unexpected consequences, and considers the importance of determining a proper approach to patient management.
A Systematic Approach to Clinical Determinations of Causation in Symptomatic Spinal Disk Injury Following Motor Vehicle Crash Trauma
Authors: Freeman Michael D. , Centeno Christopher J. , Kohles Sean S.
Published: October 2009

Clinical determinations of causation in cases of intervertebral disk (IVD) injury after a motor vehicle crash (MVC) are often disputed in medicolegal settings. No published systematic guidelines exist for making such determinations, which has resulted in infringement by nonclinical personnel into injury causation evaluations, a traditionally clinical activity. The result is causal determinations that are potentially disconnected from clinical observations of injury. The purpose of this review was to evaluate the current literature on causation, causal determinations after trauma and IVD injury after MVC, and to develop a practicable, logical, and literature‐based approach to causation determinations of symptomatic IVD injury after MVC. The results of the review indicate IVD injury can result from any MVC regardless of magnitude, thus meeting the first criteria of causation, biologic plausibility. Individual determinations of causation depend entirely on the temporal association between the collision and the symptom onset (the second criterion) and a lack of a more probable explanation for the symptoms (the third). When these causal elements are met, clinicians can assert causation on a “more probable than not” or “reasonable probability” basis. Because of a lack of an established or reliable relationship between collision force and the probability of IVD injury the investigation of collision parameters is not a useful adjunct to causal determinations.
Effects of Exercise Training on Calf Tissue Oxygenation in Men With Intermittent Claudication
Authors: Figoni Stephen F. , Kunkel Charles F. , Scremin A.M. Erika , Asher Arash , Banks Norman L. , Rivera Anthony , Tin John K. , Cohen Babak
Published: October 2009

Objective

To determine the effects of exercise training on calf tissue oxygenation in men with peripheral arterial disease and intermittent calf claudication.

Design

This pilot study was prospective and longitudinal and used a one‐group, pretest‐posttest design.

Setting

Tertiary care medical center for veterans.

Participants

Fifteen male veterans (mean age 69 years) with Fontaine stage IIa peripheral arterial disease and classic intermittent claudication.

Main Outcome Measurements

Before and after intervention, participants performed graded treadmill exercise tests while medial calf tissue oxygenation (StO2, % oxyhemoglobin saturation) was monitored continuously with near‐infrared spectroscopy.

Intervention

The intervention consisted of a 3‐month exercise training program involving 3 sessions per week at the clinic (treadmill walking, calf ergometry) and 2 sessions per week at home (free walking, standing heel raises).

Results

After completion of the intervention, participants significantly increased their maximal treadmill exercise time from 7.19 to 11.27 minutes. Mean exercise StO2 decreased from 29% to 19% saturation, StO2 × time area increased from 421% · min to 730% · min StO2 nadir, and StO2 recovery time did not change significantly.

Conclusions

After the exercise intervention, the improved treadmill walking performance was accompanied by greater calf tissue deoxygenation during exercise. Given the continued presence of ischemia, this finding may represent increased capillarization and diffusion‐based enhancement of arteriovenous O2 extraction.
Sonographically Guided Posterior Subtalar Joint Injections: Anatomic Study and Validation of 3 Approaches
Authors: Henning Troy , Finnoff Jonathan T. , Smith Jay
Published: October 2009

Objective

To describe and validate 3 different approaches to perform sonographically guided posterior subtalar joint (PSTJ) injections.

Design

Sonographically guided procedures performed on cadaveric specimens.

Setting

Procedural skills lab at a tertiary medical facility.

Methods

Three ultrasound‐guided approaches to inject the PSTJ: anterolateral, posteromedial, and posterolateral were derived based on anatomic review, published fluoroscopic and computed tomography (CT) techniques, and clinical experience. Three separate unembalmed cadaveric ankle‐foot specimens were injected by a single, experienced operator using a 25‐gauge, 38‐mm stainless steel needle. A different approach was used on each specimen. The needles were left in place and each specimen was subsequently dissected by co‐investigators to confirm accurate needle placement and determine the proximity of each needle to local tendons and neurovascular structures.

Main Outcome Measurements

Direct assessment of needle placement within posterior subtalar joint.

Results

All 3 approaches provided accurate needle placement into the posterior subtalar joint while avoiding nearby tendinous and neurovascular structures.

Conclusions

Sonographically guided PSTJ injections are technically feasible. All 3 approaches provide accurate needle placement while minimizing the risk of needle entry into adjacent soft tissue structures not visualized by other modalities such as fluoroscopy or CT.
Prospective Pilot Study of Painful Lumbar Facet Joint Arthropathy after Intra‐articular Injection of Hylan G‐F 20
Authors: DePalma Michael J. , Ketchum Jessica M. , Queler Evan D. , Trussell Brian S.
Published: October 2009

Objective

To examine changes in pain, disability, and medication usage over time from baseline to up to 12 months after facet joint injection of hylan G‐F 20.

Design

Prospective, uncontrolled, pilot study.

Setting

University spine center.

Participants

Fifteen patients (12 females), mean age of 57 years (standard deviation = 12.5), with a median duration of low back pain of 24 months (interquartile range = 11‐66).

Methods

Patients who fulfilled inclusion criteria underwent diagnostic blocks with local comparative anesthetics at one unilateral facet joint (FJ). Those with a true positive response underwent 2 1.0‐mL intra‐articular hylan G‐F 20 injections, 10 days apart, into the painful FJ. A third hylan G‐F 20 injection was offered to patients dissatisfied with the results obtained with the first 2 injections.

Main Outcome Measures

Visual analog scale (VAS) (average, standing, walking), Oswestry Disability Index (ODI), SF‐36, finger to floor distance (FTF), tolerance (standing, sitting, walking), analgesic usage, and patient satisfaction collected at baseline, 7‐10 days, and at 1‐, 3‐, 6‐, and 12‐months follow‐up.

Results

Repeated measures mixed‐models indicated that VAS (average, standing, walking [P all < .005]), ODI (P = .029), SF‐36 (P = .013), FTF (P = .032), and sitting tolerance (P = .020) all showed significant changes from baseline up to 6 months and were not sustained at 12 months; with the exception of the baseline to 12‐month difference for FTF. There was not evidence of changes over time in standing (P = .085) or walking (P = .084) tolerance. Satisfaction initially increased from baseline (0%) to 7‐10 days (64%) but declined over time (36% at 12 months). As compared with baseline (80%), analgesic usage decreased nominally over time showing significant decreases at 6 months (33%, P = .0253) and increased slightly at 12 months (45%).

Conclusions

Viscosupplementation for lumbar FJ arthropathy with hylan G‐F 20 is associated with modest efficacy that predominately lasts up to 6 months. Limitations include a small sample size and lack of both a control and blinding. Larger, randomized, controlled studies are indicated to better clarify its clinical safety, efficacy, and utility.
Trunk Muscle Attributes Are Associated With Balance and Mobility in Older Adults: A Pilot Study
Authors: Suri Pradeep , Kiely Dan K. , Leveille Suzanne G. , Frontera Walter R. , Bean Jonathan F.
Published: October 2009

Objective

To determine whether trunk muscle attributes are associated with balance and mobility performance among mobility‐limited older adults.

Design

Cross‐sectional analysis of data from a randomized clinical trial.

Setting

Outpatient rehabilitation research center.

Participants

Community‐dwelling older adults (N = 70; mean age 75.9 years) with mobility limitations as defined by the Short Physical Performance Battery (SPPB).

Methods

Independent variables included physiologic measures of trunk extension strength, trunk flexion strength, trunk extension endurance, trunk extension endurance, and leg press strength. All measures were well tolerated by the study subjects without the occurrence of any associated injuries or adverse events. The association of each physiologic measure with each outcome was examined by the use of separate multivariate models to calculate the partial variance (R2) of each trunk and extremity measure.

Main Outcome Measurements

Balance measured by the Berg Balance Scale and Unipedal Stance Test and mobility performance as measured by the SPPB.

Results

Trunk extension endurance (partialR2= .14,P= .02), and leg press strength (partialR2= .14,P= .003) accounted for the greatest amount of the variance in SPPB performance. Trunk extension endurance (partialR2= .17,P= .007), accounted for the greatest amount of the variance in BBS performance. Trunk extension strength (R2= .09,P= .03), accounted for the greatest amount of the variance in UST performance. The variance explained by trunk extension endurance equaled or exceeded the variance explained by limb strength across all three performance outcomes.

Conclusions

Trunk endurance and strength can be safely measured in mobility‐limited older adults and are associated with both balance and mobility performance. Trunk endurance and trunk strength are physiologic attributes worthy of targeting in the rehabilitative care of mobility‐limited older adults.
Classifying biotechnology-related policy, regulatory and innovation regimes: A framework for the comparative analysis of genomics policy-making
Authors: Migone Andrea , Howlett Michael
Published: October 2009

An important part of the study of the policy response of government in the area of a novel technology, such as genomics, lies in identifying the technological trajectory followed in the sector and how it intersects or impacts upon existing policy, regulatory and innovation regimes. Part of the challenge in studying the impacts and outcomes of such trajectories, therefore, is their multilayered nature. This has led to the proliferation of different models or frameworks for the analysis of many sectors, each one tackling a specific level and obscuring the linkages between levels and units of analysis. Research into innovations, however, benefits from an understanding of the overall policy and regulatory regimes present in a sector while an understanding of regulatory behaviour is in turn linked to the overall policy framework set up to govern a sector. As such, analyses of both regulation and innovation in a sector such as genomics can profit from an integrated, multi-level approach grounded in the overall nature of the policy regime present in the sphere of activity under examination. We offer such an approach by synthesizing four existing models of policy, regulatory and innovation behaviour that fit the three levels of analysis – the policy regime, regulatory regime and the innovation regime – in the sphere of biotechnology.
Post-communist regime types: Hierarchies across attributes and space
Authors: Møller Jørgen , Skaaning Svend-Erik
Published: October 2009

In this article we order the 28 post-communist countries in a theoretically informed typology of political regime forms. Our theoretical expectation is that a hierarchy exists in the extent to which the post-communist countries fulfill democratic criteria concerning electoral rights, civil liberties, and the rule of law. More particularly, we expect that the countries are doing better with respect to electoral rights than civil liberties and that they fare worst regarding the rule of law. The analyses confirm three — ever stricter — versions of this hypothesis, in the end establishing the presence of an almost perfect hierarchy across the attributes in the form of a Guttman scale. Furthermore, a systematic cross-spatial distribution is identified, which lends support to the notion that the present political differences must be traced back to structural constraints and are, therefore, likely to subsist.
Notch1 signaling plays a role in regulating precursor differentiation during CNS remyelination
Authors: Zhang Yueting , Argaw Azeb Tadesse , Gurfein Blake T. , Zameer Andleeb , Snyder Brian J. , Ge Changhui , Lu Q. Richard , Rowitch David H. , Raine Cedric S. , Brosnan Celia F. , John Gareth R.
Published: October 2009

In the developing CNS, Notch1 and its ligand, Jagged1, regulate oligodendrocyte differentiation and myelin formation, but their role in repair of demyelinating lesions in diseases such as multiple sclerosis remains unresolved. To address this question, we generated a mouse model in which we targeted Notch1 inactivation to oligodendrocyte progenitor cells (OPCs) using Olig1
Cre
and a floxed
Notch1
allele,

Notch1
12f

. During CNS development, OPC differentiation was potentiated in Olig1

Cre:Notch1
12f/12f

mice. Importantly, in adults, remyelination of demyelinating lesions was also accelerated, at the expense of proliferation within the progenitor population. Experiments in vitro confirmed that Notch1 signaling was permissive for OPC expansion but inhibited differentiation and myelin formation. These studies also revealed that astrocytes exposed to TGF-β1 restricted OPC maturation via Jagged1-Notch1 signaling. These data suggest that Notch1 signaling is one of the mechanisms regulating OPC differentiation during CNS remyelination. Thus, Notch1 may represent a potential therapeutical avenue for lesion repair in demyelinating disease.
Elevating the frequency of chromosome mis-segregation as a strategy to kill tumor cells
Authors: Janssen Aniek , Kops Geert J. P. L. , Medema René H.
Published: October 2009

The mitotic checkpoint has evolved to prevent chromosome mis-segregations by delaying mitosis when unattached chromosomes are present. Inducing severe chromosome segregation errors by ablating the mitotic checkpoint causes cell death. Here we have analyzed the consequences of gradual increases in chromosome segregation errors on the viability of tumor cells and normal human fibroblasts. Partial reduction of essential mitotic checkpoint components in four tumor cell lines caused mild chromosome mis-segregations, but no lethality. These cells were, however, remarkably more sensitive to low doses of taxol, which enhanced the amount and severity of chromosome segregation errors. Sensitization to taxol was achieved by reducing levels of Mps1 or BubR1, proteins having dual roles in checkpoint activation and chromosome alignment, but not by reducing Mad2, functioning solely in the mitotic checkpoint. Moreover, we find that untransformed human fibroblasts with reduced Mps1 levels could not be sensitized to sublethal doses of taxol. Thus, targeting the mitotic checkpoint and chromosome alignment simultaneously may selectively kill tumor cells by enhancing chromosome mis-segregations.
Pdx1 (
MODY4
) regulates pancreatic beta cell susceptibility to ER stress
Authors: Sachdeva Mira M. , Claiborn Kathryn C. , Khoo Cynthia , Yang Juxiang , Groff David N. , Mirmira Raghavendra G. , Stoffers Doris A.
Published: October 2009

Type 2 diabetes mellitus (T2DM) results from pancreatic β cell failure in the setting of insulin resistance. Heterozygous mutations in the gene encoding the β cell transcription factor pancreatic duodenal homeobox 1 (Pdx1) are associated with both T2DM and maturity onset diabetes of the young (MODY4), and low levels of Pdx1 accompany β cell dysfunction in experimental models of glucotoxicity and diabetes. Here, we find that Pdx1 is required for compensatory β cell mass expansion in response to diet-induced insulin resistance through its roles in promoting β cell survival and compensatory hypertrophy. Pdx1-deficient β cells show evidence of endoplasmic reticulum (ER) stress both in the complex metabolic milieu of high-fat feeding as well as in the setting of acutely reduced Pdx1 expression in the Min6 mouse insulinoma cell line. Further, Pdx1 deficiency enhances β cell susceptibility to ER stress-associated apoptosis. The results of high throughput expression microarray and chromatin occupancy analyses reveal that Pdx1 regulates a broad array of genes involved in diverse functions of the ER, including proper disulfide bond formation, protein folding, and the unfolded protein response. These findings suggest that Pdx1 deficiency leads to a failure of β cell compensation for insulin resistance at least in part by impairing critical functions of the ER.
Allosteric control of catalysis by the F loop of RNA polymerase
Authors: Miropolskaya Nataliya , Artsimovitch Irina , Klimašauskas Saulius , Nikiforov Vadim , Kulbachinskiy Andrey
Published: October 2009

Bacterial RNA polymerases (RNAPs) undergo coordinated conformational changes during catalysis. In particular, concerted folding of the trigger loop and rearrangements of the bridge helix at the RNAP active center have been implicated in nucleotide addition and RNAP translocation. At moderate temperatures, the rate of catalysis by RNAP from thermophilic
Thermus aquaticus
is dramatically reduced compared with its closest mesophilic relative,
Deinococcus radiodurans
. Here, we show that a part of this difference is conferred by a third element, the F loop, which is adjacent to the N terminus of the bridge helix and directly contacts the folded trigger loop. Substitutions of amino acid residues in the F loop and in an adjacent segment of the bridge helix in
T. aquaticus
RNAP for their
D. radiodurans
counterparts significantly increased the rate of catalysis (up to 40-fold at 20 °C). A deletion in the F loop dramatically impaired the rate of nucleotide addition and pyrophosphorolysis, but it had only a moderate effect on intrinsic RNA cleavage. Streptolydigin, an antibiotic that blocks folding of the trigger loop, did not inhibit nucleotide addition by the mutant enzyme. The resistance to streptolydigin likely results from the loss of its functional target, the folding of the trigger loop, which is already impaired by the F-loop deletion. Our results demonstrate that the F loop is essential for proper folding of the trigger loop during nucleotide addition and governs the temperature adaptivity of RNAPs in different bacteria.
Shifting the genomic gold standard for the prokaryotic species definition
Authors: Richter Michael , Rosselló-Móra Ramon
Published: October 2009

DNA-DNA hybridization (DDH) has been used for nearly 50 years as the gold standard for prokaryotic species circumscriptions at the genomic level. It has been the only taxonomic method that offered a numerical and relatively stable species boundary, and its use has had a paramount influence on how the current classification has been constructed. However, now, in the era of genomics, DDH appears to be an outdated method for classification that needs to be substituted. The average nucleotide identity (ANI) between two genomes seems the most promising method since it mirrors DDH closely. Here we examine the work package JSpecies as a user-friendly, biologist-oriented interface to calculate ANI and the correlation of the tetranucleotide signatures between pairwise genomic comparisons. The results agreed with the use of ANI to substitute DDH, with a narrowed boundary that could be set at ≈95–96%. In addition, the JSpecies package implemented the tetranucleotide signature correlation index, an alignment-free parameter that generally correlates with ANI and that can be of help in deciding when a given pair of organisms should be classified in the same species. Moreover, for taxonomic purposes, the analyses can be produced by simply randomly sequencing at least 20% of the genome of the query strains rather than obtaining their full sequence.
Exon sequences at the splice junctions affect splicing fidelity and alternative splicing
Authors: Crotti Luciana B. , Horowitz David S.
Published: October 2009

Identification of splice sites is essential for the expression of most eukaryotic genes, allowing accurate splicing of pre-mRNAs. The splice sites are recognized by the splicing machinery based on sequences within the pre-mRNA. Here, we show that the exon sequences at the splice junctions play a significant, previously unrecognized role in the selection of 3′ splice sites during the second step of splicing. The influence of the exon sequences was enhanced by the Prp18 mutant Prp18ΔCR, and the strength of an exon sequence in Prp18ΔCR splicing predicted its effect in wild-type splicing. Analysis of the kinetics of splicing in vitro demonstrated that 3′ splice sites were chosen competitively during the second step, likely at the same time as exon ligation. In wild-type yeast, splice site selection for two genes studied was altered by point mutations in their exon bases, affecting splicing fidelity and alternative splicing. Finally, we note that the degeneracy of the genetic code allows competing 3′ splice sites to be eliminated from coding regions, and we suggest that the evolution of the splicing signals and the genetic code are connected.
Fibulin-4 conducts proper elastogenesis via interaction with cross-linking enzyme lysyl oxidase
Authors: Horiguchi Masahito , Inoue Tadashi , Ohbayashi Tetsuya , Hirai Maretoshi , Noda Kazuo , Marmorstein Lihua Y. , Yabe Daisuke , Takagi Kyoko , Akama Tomoya O. , Kita Toru , Kimura Takeshi , Nakamura Tomoyuki
Published: October 2009

Great arteries, as well as lungs and skin, contain elastic fibers as important components to maintain their physiological functions. Although recent studies have revealed that a glycoprotein fibulin-4 (FBLN4) is indispensable for the assembly of mature elastic fibers, it remains to be elucidated how FBLN4 takes part in elastogenesis. Here, we report a dose-dependent requirement for FBLN4 in the development of the elastic fibers in arteries, and a specific role of FBLN4 in recruiting the elastin-cross-linking enzyme, lysyl oxidase (LOX). Reduced expression of
Fbln4
, which was achieved with a smooth muscle-specific Cre-mediated gene deletion, caused arterial stiffness. Electron-microscopic examination revealed disorganized thick elastic laminae with aberrant deposition of elastin. Aneurysmal dilation of the ascending aorta was found when the
Fbln4
expression level was reduced to an even lower level, whereas systemic
Fbln4
null mice died perinatally from rupture of the diaphragm. We also found a specific interaction between FBLN4 and the propeptide of LOX, which efficiently promotes assembly of LOX onto tropoelastin. These data suggest a mechanism of elastogenesis, in which a sufficient amount of FBLN4 is essential for tethering LOX to tropoelastin to facilitate cross-linking.
Finding of residues crucial for supersecondary structure formation
Authors: Kister Alexander E. , Gelfand Israel
Published: October 2009

This work evaluates the hypothesis that proteins with an identical supersecondary structure (SSS) share a unique set of residues—SSS-determining residues—even though they may belong to different protein families and have very low sequence similarities. This hypothesis was tested on two groups of sandwich-like proteins (SPs). Proteins in each group have an identical SSS, but their sequence similarity is below the “twilight zone.” To find the SSS-determining residues specific to each group, a unique structure-based algorithm of multiple sequences alignment was developed. The units of alignment are individual strands and loops rather than whole sequences. The algorithm is based on the alignment of residues that form hydrogen bonds between corresponding strands. Structure-based alignment revealed that 30–35% of the positions in the sequences in each group of proteins are “conserved positions” occupied either by hydrophobic-only or hydrophilic-only residues. Moreover, each group of SPs is characterized by a unique set of SSS-determining residues found at the conserved positions. The set of SSS-determining residues has very high sensitivity and specificity for identifying proteins with a corresponding SSS: It is an “amino acid tag” that brands a sequence as having a particular SSS. Thus, the sets of SSS-determining residues can be used to classify proteins and to predict the SSS of a query amino acid sequence.
Murine hematopoietic blast colony-forming cells and their progeny have distinctive membrane marker profiles
Authors: Metcalf Donald , Ng Ashley P. , Loughran Stephen J. L. , Phipson Belinda , Smyth Gordon K. , Di Rago Ladina , Mifsud Sandra
Published: October 2009

Two distinct bone marrow-derived blast colony-forming cells can generate colonies of lineage-restricted progenitor cells in agar cultures of murine bone marrow. Both cell types selectively had a Kit
+
ScaI
+
phenotype distinguishing them from most lineage-restricted progenitor cells. Multicentric blast colony-forming cells stimulated by stem cell factor plus interleukin-6 (IL-6) (BL-CFC-S) were separable from most dispersed blast colony-forming cells stimulated by Flt3 ligand and IL-6 (BL-CFC-F) using CD34 and Flt3R probes. Multicentric BL-CFC-S cofractionated with colony-forming units, spleen (CFU-S) supporting the possibility that the 2 cells may be identical. The colony populations generated by BL-CFC-S were similar in their phenotype and proliferative capacity to progenitor cells in whole bone marrow but the progeny of BL-CFC-F were skewed with an abnormally high proportion of Kit
−
Flt3R
+
cells whose clonogenic cells tended to generate only macrophage progeny. Both blast colony populations had a high percentage of GR1
+
and Mac1
+
cells but BL-CFC-F colonies also contained a significant population of B220
+
and IL-7R
+
cells relevant to the superior ability of BL-CFC-F colony cells to generate B lymphocytes and the known dependency of this process on Flt3 ligand and IL-7. The commitment events and phenotypic changes during the generation of differing progenitor cells in blast colonies can now be clonally analyzed in a convenient in vitro culture system.
NGSView: an extensible open source editor for next-generation sequencing data
Authors: Arner Erik , Hayashizaki Yoshihide , Daub Carsten O.
Published: October 2009

Summary:High-throughput sequencing technologies introduce novel demands on tools available for data analysis. We have developed NGSView (Next Generation Sequence View), a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. NGSView is available under an open source license and can be extended through a well documented API.

Availability:  http://ngsview.sourceforge.net

Contact:  arner@gsc.riken.jp
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Authors: Wang Likun , Feng Zhixing , Wang Xi , Wang Xiaowo , Zhang Xuegong
Published: October 2009

Summary: High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform. Here, we present DEGseq, an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples. In this package, we integrated three existing methods, and introduced two novel methods based on MA-plot to detect and visualize gene expression difference.

Availability: The R package and a quick-start vignette is available at http://bioinfo.au.tsinghua.edu.cn/software/degseq

Contact:  xwwang@tsinghua.edu.cn; zhangxg@tsinghua.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
GTP Is Required for the Microtubule Catastrophe-Inducing Activity of MAP200, a Tobacco Homolog of XMAP215
Authors: Hamada Takahiro , Itoh Tomohiko J. , Hashimoto Takashi , Shimmen Teruo , Sonobe Seiji
Published: October 2009

Widely conserved among eukaryotes, the microtubule-associated protein 215 (MAP215) family enhances microtubule dynamic instability. The family member studied most extensively, Xenopus laevis XMAP215, has been reported to enhance both assembly and disassembly parameters, although the mechanism whereby one protein can exert these apparently contradictory effects has not been clarified. Here, we analyze the activity of a plant MAP215 homolog, tobacco (Nicotiana tabacum) MAP200 on microtubule behavior in vitro. We show that, like XMAP215, MAP200 promotes both assembly and disassembly parameters, including microtubule growth rate and catastrophe frequency. When MAP200 is added to tubulin and taxol, strikingly long-coiled structures form. When GDP partially replaces GTP, the increase of catastrophe frequency by MAP200 is strongly diminished, even though this replacement stimulates catastrophe in the absence of MAP200. This implies that MAP200 induces catastrophes by a specific, GTP-requiring pathway. We hypothesize that, in the presence of MAP200, a catastrophe-prone microtubule lattice forms occasionally when elongated but nonadjacent protofilaments make lateral contacts.
The Ectomycorrhizal FungusLaccaria bicolorStimulates Lateral Root Formation in Poplar and Arabidopsis through Auxin Transport and Signaling
Authors: Felten Judith , Kohler Annegret , Morin Emmanuelle , Bhalerao Rishikesh P. , Palme Klaus , Martin Francis , Ditengou Franck A. , Legué Valérie
Published: October 2009

The early phase of the interaction between tree roots and ectomycorrhizal fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We aimed to identify gene networks that regulate LR development during the early signal exchanges between poplar (Populus tremula × Populus alba) and the ectomycorrhizal fungus Laccaria bicolor with a focus on auxin transport and signaling pathways. Our data demonstrated that increased LR development in poplar and Arabidopsis (Arabidopsis thaliana) interacting with L. bicolor is not dependent on the ability of the plant to form ectomycorrhizae. LR stimulation paralleled an increase in auxin accumulation at root apices. Blocking plant polar auxin transport with 1-naphthylphthalamic acid inhibited LR development and auxin accumulation. An oligoarray-based transcript profile of poplar roots exposed to molecules released by L. bicolor revealed the differential expression of 2,945 genes, including several components of polar auxin transport (PtaPIN and PtaAUX genes), auxin conjugation (PtaGH3 genes), and auxin signaling (PtaIAA genes). Transcripts of PtaPIN9, the homolog of Arabidopsis AtPIN2, and several PtaIAAs accumulated specifically during the early interaction phase. Expression of these rapidly induced genes was repressed by 1-naphthylphthalamic acid. Accordingly, LR stimulation upon contact with L. bicolor in Arabidopsis transgenic plants defective in homologs of these genes was decreased or absent. Furthermore, in Arabidopsis pin2, the root apical auxin increase during contact with the fungus was modified. We propose a model in which fungus-induced auxin accumulation at the root apex stimulates LR formation through a mechanism involving PtaPIN9-dependent auxin redistribution together with PtaIAA-based auxin signaling.
Uncovering Small RNA-Mediated Responses to Phosphate Deficiency in Arabidopsis by Deep Sequencing
Authors: Hsieh Li-Ching , Lin Shu-I. , Shih Arthur Chun-Chieh , Chen June-Wei , Lin Wei-Yi , Tseng Ching-Ying , Li Wen-Hsiung , Chiou Tzyy-Jen
Published: October 2009

Recent studies have demonstrated the important role of plant microRNAs (miRNAs) under nutrient deficiencies. In this study, deep sequencing of Arabidopsis (Arabidopsis thaliana) small RNAs was conducted to reveal miRNAs and other small RNAs that were differentially expressed in response to phosphate (Pi) deficiency. About 3.5 million sequence reads corresponding to 0.6 to 1.2 million unique sequence tags from each Pi-sufficient or Pi-deficient root or shoot sample were mapped to the Arabidopsis genome. We showed that upon Pi deprivation, the expression of miR156, miR399, miR778, miR827, and miR2111 was induced, whereas the expression of miR169, miR395, and miR398 was repressed. We found cross talk coordinated by these miRNAs under different nutrient deficiencies. In addition to miRNAs, we identified one Pi starvation-induced DICER-LIKE1-dependent small RNA derived from the long terminal repeat of a retrotransposon and a group of 19-nucleotide small RNAs corresponding to the 5′ end of tRNA and expressed at a high level in Pi-starved roots. Importantly, we observed an increased abundance of TAS4-derived trans-acting small interfering RNAs (ta-siRNAs) in Pi-deficient shoots and uncovered an autoregulatory mechanism of PAP1/MYB75 via miR828 and TAS4-siR81(−) that regulates the biosynthesis of anthocyanin. This finding sheds light on the regulatory network between miRNA/ta-siRNA and its target gene. Of note, a substantial amount of miR399* accumulated under Pi deficiency. Like miR399, miR399* can move across the graft junction, implying a potential biological role for miR399*. This study represents a comprehensive expression profiling of Pi-responsive small RNAs and advances our understanding of the regulation of Pi homeostasis mediated by small RNAs.
An ABC Transporter Mutation Alters Root Exudation of Phytochemicals That Provoke an Overhaul of Natural Soil Microbiota
Authors: Badri Dayakar V. , Quintana Naira , El Kassis Elie G. , Kim Hye Kyong , Choi Young Hae , Sugiyama Akifumi , Verpoorte Robert , Martinoia Enrico , Manter Daniel K. , Vivanco Jorge M.
Published: October 2009

Root exudates influence the surrounding soil microbial community, and recent evidence demonstrates the involvement of ATP-binding cassette (ABC) transporters in root secretion of phytochemicals. In this study, we examined effects of seven Arabidopsis (Arabidopsis thaliana) ABC transporter mutants on the microbial community in native soils. After two generations, only the Arabidopsis abcg30 (Atpdr2) mutant had significantly altered both the fungal and bacterial communities compared with the wild type using automated ribosomal intergenic spacer analysis. Similarly, root exudate profiles differed between the mutants; however, the largest variance from the wild type (Columbia-0) was observed in abcg30, which showed increased phenolics and decreased sugars. In support of this biochemical observation, whole-genome expression analyses of abcg30 roots revealed that some genes involved in biosynthesis and transport of secondary metabolites were up-regulated, while some sugar transporters were down-regulated compared with genome expression in wild-type roots. Microbial taxa associated with Columbia-0 and abcg30 cultured soils determined by pyrosequencing revealed that exudates from abcg30 cultivated a microbial community with a relatively greater abundance of potentially beneficial bacteria (i.e. plant-growth-promoting rhizobacteria and nitrogen fixers) and were specifically enriched in bacteria involved in heavy metal remediation. In summary, we report how a single gene mutation from a functional plant mutant influences the surrounding community of soil organisms, showing that genes are not only important for intrinsic plant physiology but also for the interactions with the surrounding community of organisms as well.
Protein Phosphatases 2C Regulate the Activation of the Snf1-Related Kinase OST1 by Abscisic Acid inArabidopsis
Authors: Vlad Florina , Rubio Silvia , Rodrigues Americo , Sirichandra Caroline , Belin Christophe , Robert Nadia , Leung Jeffrey , Rodriguez Pedro L. , Laurière Christiane , Merlot Sylvain
Published: October 2009

The plant hormone abscisic acid (ABA) orchestrates plant adaptive responses to a variety of stresses, including drought. This signaling pathway is regulated by reversible protein phosphorylation, and genetic evidence demonstrated that several related protein phosphatases 2C (PP2Cs) are negative regulators of this pathway in Arabidopsis thaliana. Here, we developed a protein phosphatase profiling strategy to define the substrate preferences of the HAB1 PP2C implicated in ABA signaling and used these data to screen for putative substrates. Interestingly, this analysis designated the activation loop of the ABA activated kinase OST1, related to Snf1 and AMPK kinases, as a putative HAB1 substrate. We experimentally demonstrated that HAB1 dephosphorylates and deactivates OST1 in vitro. Furthermore, HAB1 and the related PP2Cs ABI1 and ABI2 interact with OST1 in vivo, and mutations in the corresponding genes strongly affect OST1 activation by ABA. Our results provide evidence that PP2Cs are directly implicated in the ABA-dependent activation of OST1 and further suggest that the activation mechanism of AMPK/Snf1-related kinases through the inhibition of regulating PP2Cs is conserved from plants to human.
Cotranslational Proteolysis Dominates Glutathione Homeostasis to Support Proper Growth and Development
Authors: Frottin Frédéric , Espagne Christelle , Traverso José A. , Mauve Caroline , Valot Benoît , Lelarge-Trouverie Caroline , Zivy Michel , Noctor Graham , Meinnel Thierry , Giglione Carmela
Published: October 2009

The earliest proteolytic event affecting most proteins is the excision of the initiating Met (NME). This is an essential and ubiquitous cotranslational process tightly regulated in all eukaryotes. Currently, the effects of NME on unknown complex cellular networks and the ways in which its inhibition leads to developmental defects and cell growth arrest remain poorly understood. Here, we provide insight into the earliest molecular mechanisms associated with the inhibition of the NME process in Arabidopsis thaliana. We demonstrate that the developmental defects induced by NME inhibition are caused by an increase in cellular proteolytic activity, primarily induced by an increase in the number of proteins targeted for rapid degradation. This deregulation drives, through the increase of the free amino acids pool, a perturbation of the glutathione homeostasis, which corresponds to the earliest limiting, reversible step promoting the phenotype. We demonstrate that these effects are universally conserved and that the reestablishment of the appropriate glutathione status restores growth and proper development in various organisms. Finally, we describe a novel integrated model in which NME, protein N-α-acylation, proteolysis, and glutathione homeostasis operate in a sequentially regulated mechanism that directs both growth and development.
ARABIDOPSIS TRITHORAX-RELATED7 Is Required for Methylation of Lysine 4 of Histone H3 and for Transcriptional Activation of FLOWERING LOCUS C
Authors: Tamada Yosuke , Yun Jae-Young , Woo Seung chul , Amasino Richard M.
Published: October 2009

In the winter-annual accessions of Arabidopsis thaliana, presence of an active allele of FRIGIDA (FRI) elevates expression of FLOWERING LOCUS C (FLC), a repressor of flowering, and thus confers a vernalization requirement. FLC activation by FRI involves methylation of Lys 4 of histone H3 (H3K4) at FLC chromatin. Many multicellular organisms that have been examined contain two classes of H3K4 methylases, a yeast (Saccharomyces cerevisiae) Set1 class and a class related to Drosophila melanogaster Trithorax. In this work, we demonstrate that ARABIDOPSIS TRITHORAX-RELATED7 (ATXR7), a putative Set1 class H3K4 methylase, is required for proper FLC expression. The atxr7 mutation partially suppresses the delayed flowering of a FRI-containing line. The rapid flowering of atxr7 is associated with reduced FLC expression and is accompanied by decreased H3K4 methylation and increased H3K27 methylation at FLC. Thus, ATXR7 is required for the proper levels of these histone modifications that set the level of FLC expression to create a vernalization requirement in winter-annual accessions. Previously, it has been reported that lesions in ATX1, which encodes a Trithorax class H3K4 methylase, partially suppress the delayed flowering of winter-annual Arabidopsis. We show that the flowering phenotype of atx1 atxr7 double mutants is additive relative to those of single mutants. Therefore, both classes of H3K4 methylases appear to be required for proper regulation of FLC expression.