bluuebunny/crossref_metadata_2025 huggingface dataset:
Tim23–Tim50 pair coordinates functions of translocators and motor proteins in mitochondrial protein import
Authors: Tamura Yasushi , Harada Yoshihiro , Shiota Takuya , Yamano Koji , Watanabe Kazuaki , Yokota Mihoko , Yamamoto Hayashi , Sesaki Hiromi , Endo Toshiya
Published: January 2009

Mitochondrial protein traffic requires coordinated operation of protein translocator complexes in the mitochondrial membrane. The TIM23 complex translocates and inserts proteins into the mitochondrial inner membrane. Here we analyze the intermembrane space (IMS) domains of Tim23 and Tim50, which are essential subunits of the TIM23 complex, in these functions. We find that interactions of Tim23 and Tim50 in the IMS facilitate transfer of precursor proteins from the TOM40 complex, a general protein translocator in the outer membrane, to the TIM23 complex. Tim23–Tim50 interactions also facilitate a late step of protein translocation across the inner membrane by promoting motor functions of mitochondrial Hsp70 in the matrix. Therefore, the Tim23–Tim50 pair coordinates the actions of the TOM40 and TIM23 complexes together with motor proteins for mitochondrial protein import.
The changing world of modern cell biology
Authors: Misteli Tom
Published: January 2009

Change is always ambiguous. There is the enticing prospect of novelty and better times ahead, but at the same time the concern of losing the good of the past. It is with these sentiments that I take over as the Editor-in-Chief from Ira Mellman who for a decade has cleverly and effectively lead the JCB. During this time he directed and oversaw an extensive modernization of the journal and guided it through dramatic changes in the publishing world. Ira lead the journal with unyielding dedication and enthusiasm and we in the cell biology community must thank him profoundly for his service. It is his work, together with the invaluable contribution of the best editorial board and the most dedicated professional editorial staff in the scientific publishing business, that allows me to now take over the stewardship of the JCB with a tremendous sense of excitement and determination to continue and expand the JCB's role as the leading journal in the cell biology community and as a trendsetter in the rapidly changing world of modern cell biology.
By the scientists, for the scientists
Authors: Mellman Ira
Published: January 2009

My association with the JCB began very early in my scientific career. In fact, it predated my understanding that there would even be a scientific career. In the mid-1970s while still an undergraduate, the JCB published my very first paper, a contribution noted perhaps less so for its reporting the characterization of the first known protein in plant cell walls than for a footnote that called attention to the evolutionary conservation of a relationship between “sex and slime” throughout the plant and animal kingdoms.
The Political Economy of American Transportation
Authors: Rose Mark
Published: January 2009

Throughout its history, the free market system has been held back, not so much by its own economic deficiencies as Marxists would have it, but because of its reliance on political goodwill for its infrastructure.
The recruitment of Atlantic salmon in Europe
Authors: Friedland Kevin D. , MacLean Julian C. , Hansen Lars P. , Peyronnet Arnaud J. , Karlsson Lars , Reddin David G. , Ó Maoiléidigh Niall , McCarthy Jennifer L.
Published: January 2009

Friedland, K. D., MacLean, J. C., Hansen, L. P., Peyronnet, A. J., Karlsson, L., Reddin, D. G., Ó Maoiléidigh, N., and McCarthy, J. L. 2009. The recruitment of Atlantic salmon in Europe. – ICES Journal of Marine Science, 66: 289–304. The stock complex of Atlantic salmon, Salmo salar, in Europe has experienced a multidecadal decline in recruitment, resulting in the lowest stock abundances observed since 1970. Here, physical forcing, biological interactions, and the resultant growth response of post-smolt salmon are examined with a view to understanding the mechanism controlling recruitment. Sea surface temperature (SST) has increased in the Northeast Atlantic, with the pattern and seasonal change in SST negatively correlated with post-smolt survival during summer and in a region that spatially matches the post-smolt nursery. Constituents of the pelagic foodweb, including potential post-smolt food and plankton that may affect post-smolt forage, have changed on a decadal scale and correlate with salmon survival. Retrospective growth analyses of eight stock/sea age components show that post-smolt growth during summer is positively correlated with salmon survival and recruitment. The Atlantic Multidecadal Oscillation appears to be a more closely aligned climate forcing index than the North Atlantic Oscillation with respect to salmon recruitment. European Atlantic salmon recruitment appears to be governed by factors that affect the growth of post-smolts during their first summer at sea, including SST and forage abundances; growth appears to mediate survival by the functional relationship between post-smolts and their predators.
Methionine‐enkephalin secreted by human colorectal cancer cells suppresses T lymphocytes
Authors: Ohmori Hitoshi , Fujii Kiyomu , Sasahira Tomonori , Luo Yi , Isobe Mamoru , Tatsumoto Naokuni , Kuniyasu Hiroki
Published: January 2009

The role of methionine‐enkephalin (MENK) as an immunomodulator in colorectal carcinomas (CRC) was examined. MENK was produced in CT26, IEC6A, Colo320, and HT29 CRC cell lines but not in IEC6 intestinal cells. MENK secretion was associated with tumorigenicity and metastasis of CRC cells in syngeneic rodent models. The MENK concentration in subcutaneous tumors of CT26 and IEC6A CRC cells exhibited an inverse correlation with the number of tumor‐infiltrating T lymphocytes. MENK inhibited the growth of MOLT‐4 T‐lymphoblastic cells in a dose‐dependent manner. Furthermore, it increased the phosphorylation level of c‐Jun N‐terminal kinase and induced apoptosis in MOLT‐4 cells. MENK‐induced apoptosis was abrogated by a c‐Jun N‐terminal kinase inhibitor. Immunohistochemical analysis revealed moderate to strong expression of MENK in 33 (54%) of 61 CRC. MENK expression was associated with Dukes’ staging, nodal metastasis, and liver metastasis. The MENK concentration in tumor tissues was higher in Dukes’ C cases than in Dukes’ B cases. MENK expression was associated with tumor‐infiltrating T lymphocytes, especially those belonging to the CD4+ subset. These findings suggest that MENK secreted by CRC cells caused escape of the host from the effects of immunity. (Cancer Sci 2009; 100: 497–502)
Features of basal and race‐specific defences in photosynthetic Arabidopsis thaliana suspension cultured cells
Authors: CECCHINI NICOLÁS MIGUEL , MONTEOLIVA MARIELA INÉS , BLANCO FRANCISCA , HOLUIGUE LORETO , ÁLVAREZ MARÍA ELENA
Published: January 2009

Plant suspension cell cultures display many features of the innate immune responses observed in planta and have been extensively applied to the study of basal and race‐specific defences. However, no single model including photosynthetic cultured cells has been used for the exhaustive characterization of both basal and race‐specific defences to date. In this article, we report the activation of basal and race‐specific defences in green cultured cells from Arabidopsis thaliana. Inoculation of cultured cells with isogenic virulent or avirulent strains of Pseudomonas syringae pv. tomato DC3000 (Pst) was used to evaluate race‐specific defences. The proliferation of avirulent Pst was found to be lower than that of virulent Pst in the inoculated cultures. Extracellular pH changes, sustained oxidative burst (5–13 h post‐inoculation), enhancement of salicylic acid, and massive cell death were specifically stimulated by the avirulent bacterium. Neither avirulent nor virulent Pst induced markers of basal resistance, such as callose deposition or early oxidative burst (1–5 h post‐inoculation). However, both basal defences were activated when cells were exposed to Pseudomonas syringae pv. phaseolicola or to the Pst mutant defective in the type III secretion system (TTSS), Pst‐hrpL−. Thus, in these cells, basal defences may be inhibited by Pst in a TTSS‐dependent manner. Recapitulation of classical defence features demonstrates the usefulness of this system for the fine characterization of plant innate immune components.
Effect‐site concentration of remifentanil for laryngeal mask airway insertion during target‐controlled infusion of propofol
Authors: Kim M. K. , Lee J. W. , Jang D. J. , Shin O. Y. , Nam S. B.
Published: January 2009

The purpose of this study was to determine the effect‐site concentration of remifentanil that would provide optimal conditions for successful laryngeal mask airway insertion during a target‐controlled infusion (TCI) of propofol at 3.5 μg.ml−1 without the use of neuromuscular blockade. Five minutes after propofol infusion, remifentanil was infused at a dose determined by a modified Dixon’s up‐and‐down method. Five minutes after remifentanil infusion, the laryngeal mask was inserted. The effect‐site concentration of remifentanil for successful laryngeal mask insertion in 50% of adults (EC50) was 3.04 (SD 0.49) ng.ml−1 during a TCI of 3.5 μg.ml−1 propofol without neuromuscular blockade. From the probit analysis, the EC50 and EC95 of remifentanil were 2.84 ng.ml−1 (95% CI 2.09–3.57 ng.ml−1) and 3.79 ng.ml−1 (95% CI 3.26–9.25 ng.ml−1), respectively.
The effect of grade of anaesthetist on outcome after day surgery*
Authors: Hanousek J. , Stocker M. E. , Montgomery J. E.
Published: January 2009

We conducted a retrospective survey to investigate if the grade of anaesthetist was a significant factor in determining outcome after day surgery in a district general hospital. All day surgery procedures performed between 1996 and 2006 were included except those under surgically administered local anaesthetic. The outcome measures assessed were unplanned admissions and symptoms reported after discharge. The overall admission rate was 2.6%, the admission rate for anaesthetic‐related reasons was 1.5%, and 49% of patients reported some symptoms after discharge. Over the period studied the admission rate fell from 4.2% to 2.0%, admissions for anaesthetic‐related reasons fell from 3.0% to 0.7% and reported symptoms fell from 67% to 37%. Consultants anaesthetists were associated with the lowest unplanned admission rate (consultants 2.3%, staff grade and associate specialists 3.1%, and trainees 3.3%), the lowest admission rate for anaesthetic reasons (consultants 1.2%, staff and associate specialists 2.0%, and trainees 1.8%), lower than expected specialty‐weighted admissions and the lowest number of reported symptoms (consultants 47.3%, staff grade and associate specialists 52.6%, trainees 49.0%) (p < 0.001). We conclude that there was an improvement in outcome over the period of study and that the grade of anaesthetist is associated with outcome after day surgery.
Pumpless extracorporeal removal of carbon dioxide combined with ventilation using low tidal volume and high positive end‐expiratory pressure in a patient with severe acute respiratory distress syndrome
Authors: Bein T. , Zimmermann M. , Hergeth K. , Ramming M. , Rupprecht L. , Schlitt H. J. , Slutsky A. S.
Published: January 2009

The effects of the combination of a ‘lowest’ lung ventilation with extracorporeal elimination of carbon dioxide by interventional lung assist are described in a patient presenting with severe acute respiratory distress syndrome due to fulminant pneumonia. Reducing tidal volume to 3 ml.kg−1 together with interventional lung assist resulted in a decrease in severe hypercapnia without alveolar collapse or hypoxaemia but with a decrease in serum levels of interleukin‐6. This approach was applied for 12 days with recovery of the patient, without complications. Extracorporeal removal of carbon dioxide by interventional lung assist may be a useful tool to enable ‘ultraprotective’ ventilation in severe acute respiratory distress syndrome.
Triggering of systolic arterial pressure alarms using statistics‐based versus threshold alarms*
Authors: Connor C. W. , Gohil B. , Harrison M. J.
Published: January 2009

Threshold systolic arterial pressure alarms often use pre‐operative values as a guide for intra‐operative values. Recently, two systems (normalisation and principal component analysis) have been described that use the ‘current’ systolic arterial pressure and the change in systolic arterial pressure over a preceding time interval to generate an alarm based on units of standard deviation. Normalisation and principal component analysis techniques should prioritise alarms for clinically significant changes and hence reduce overall activation of alarms. Our aim was to measure the change in alarm activation using these techniques compared with standard threshold alarms. Systolic blood pressure data, collected from 10 patients (a total of 2177 min at 100 Hz), were cleaned and submitted to analysis using threshold alarms, normalisation and principal component analysis. With the threshold alarms set at 100 mmHg (low) and 140 mmHg (high), and a 5‐min window, the alarms were activated for 557 min; using statistics‐based thresholds the alarms were activated for 169 min (normalisation) and 155 min (principal component analysis), a reduction of approximately 70–72%.
Early treatment of a quetiapine and sertraline overdose with Intralipid®*
Authors: Finn S. D. H. , Uncles D. R. , Willers J. , Sable N.
Published: January 2009

We describe the initial management and subsequent recovery of a 61 year‐old male patient following attempted suicide by oral ingestion of a potentially fatal overdose of quetiapine and sertraline. Intravenous Intralipid® was given soon after initiation of basic resuscitation. There was a rapid improvement in the patient’s level of consciousness. No other clinical signs of drug toxicity were observed. Intralipid may have reversed the deep coma associated with ingestion and prevented other manifestations of drug toxicity occurring, thus expediting this patient's recovery.
The TEG® vs the ROTEM® thromboelastography/thromboelastometry systems
Authors: Jackson G. N. B. , Ashpole K. J. , Yentis S. M.
Published: January 2009

We have evaluated the TEG® thromboelastograph and the ROTEM® thromboelastometer, two point‐of‐care devices that measure blood coagulation. During a one‐week period, seven consultant anaesthetists, one consultant haematologist, one associate specialist anaesthetist and two senior trainee anaesthetists were trained by the manufacturers and set up, calibrated and used both systems, after which their views were obtained and specific technical/support information was sought from the manufacturers using a questionnaire. Although the devices shared common features, they differed in complexity and aspects of ease of use, and in their purchase and running costs.
Ease of intubation with the GlideScope or Airway Scope by novice operators in simulated easy and difficult airways – a manikin study*
Authors: Tan B. H. , Liu E. H. C. , Lim R. T. C. , Liow L. M. H. , Goy R. W. L.
Published: January 2009

The GlideScope and Airway Scope are video laryngoscopes that have been found to be useful in difficult airway situations. With the GlideScope, there are frequently problems associated with insertion of the tracheal tube despite the ability to view the glottis. The Airway Scope’s imaging system and disposable PBlade aid alignment of the PBlade with the glottis and guide insertion of the tracheal tube. We performed a randomised crossover study of 20 medical students using both videolaryngoscopes in a manikin, with simulated normal and difficult airway scenarios. We found that the students required less time for tracheal intubation with the Airway Scope and reported greater ease of intubation with the Airway Scope in both scenarios. A greater number of students chose the Airway Scope as their device of choice. Our results suggest that the Airway Scope’s features may improve the ease of tracheal intubation compared with the GlideScope.
Guidelines and the adoption of ‘lipid rescue’ therapy for local anaesthetic toxicity
Authors: Picard J. , Ward S. C. , Zumpe R. , Meek T. , Barlow J. , Harrop‐Griffiths W.
Published: January 2009

Gathering evidence from animal experiments, an editorial in this journal and published human case reports culminated in the Association of Anaesthetists of Great Britain and Ireland recommending in August 2007 that lipid emulsion be immediately available to all patients given potentially cardiotoxic doses of local anaesthetic drugs. This development offered an opportunity to track the adoption of an innovation by anaesthetists in the UK and to gauge the effects of guidelines. Two surveys, each of 66 NHS hospitals delivering acute care within London and its penumbra, examined the adoption of lipid emulsion therapy. After the publication of the editorial in autumn 2006, the spread of ‘lipid rescue’ was rapid. The timing of the adoption and the impetus for innovation varied substantially between the sampled hospitals. When the formal guidelines were published, approximately half of the hospitals surveyed did not have lipid rescue. Of those that subsequently adopted it, half attributed their decision to the guidelines. At the end of 2007, there remained a small number of hospitals that had yet to adopt lipid rescue. Lipid rescue’s adoption by anaesthetists in the UK offers a rare example of swift uptake of an innovation. National guidelines accelerated the adoption of innovation by some hospitals.
Serial chimerism analyses indicate that mixed haemopoietic chimerism influences the probability of graft rejection and disease recurrence following allogeneic stem cell transplantation (SCT) for severe aplastic anaemia (SAA): indication for routine assessment of chimerism post SCT for SAA
Authors: Lawler Mark , McCann Shaun R. , Marsh Judith C. W. , Ljungman Per , Hows Jill , Vandenberghe Elisabeth , O’Riordan Joan , Locasciulli Anna , Socié Gérard , Kelly Alan , Schrezenmeier Hubert , Marin Pedro , Tichelli André , Passweg Jakob R. , Dickenson Anne , Ryan Jacqueline , Bacigalupo Andrea ,   from the Severe Aplastic Anaemia Working Party of the European Blood and Marrow Transplant Group
Published: January 2009

Ninety‐one patients were studied serially for chimeric status following allogeneic stem cell transplantation (SCT) for severe aplastic anaemia (SAA) or Fanconi Anaemia (FA). Short tandem repeat polymerase chain reaction (STR‐PCR) was used to stratify patients into five groups: (A) complete donor chimeras (n = 39), (B) transient mixed chimeras (n = 15) (C) stable mixed chimeras (n = 18), (D) progressive mixed chimeras (n = 14) (E) recipient chimeras with early graft rejection (n = 5). As serial sampling was not possible in Group E, serial chimerism results for 86 patients were available for analysis. The following factors were analysed for association with chimeric status: age, sex match, donor type, aetiology of aplasia, source of stem cells, number of cells engrafted, conditioning regimen, graft‐versus‐host disease (GvHD) prophylaxis, occurrence of acute and chronic GvHD and survival. Progressive mixed chimeras (PMCs) were at high risk of late graft rejection (n = 10, P < 0·0001). Seven of these patients lost their graft during withdrawal of immunosuppressive therapy. STR‐PCR indicated an inverse correlation between detection of recipient cells post‐SCT and occurrence of acute GvHD (P = 0·008). PMC was a bad prognostic indicator of survival (P = 0·003). Monitoring of chimeric status during cyclosporin withdrawal may facilitate therapeutic intervention to prevent late graft rejection in patients transplanted for SAA.
Rediscovering alemtuzumab: current and emerging therapeutic roles
Authors: Gribben John G. , Hallek Michael
Published: January 2009

The humanized anti‐CD52 monoclonal antibody alemtuzumab belongs to the family of Campath‐1 antibodies, which were initially developed for their ability to prevent graft‐versus‐host disease (GVHD) and graft rejection in stem cell transplantation. Alemtuzumab is indicated for the treatment of chronic lymphocytic leukaemia (CLL) and has demonstrated considerable activity in relapsed/refractory disease and in previously untreated disease. It has been shown to induce minimal residual disease‐negative responses as a single agent or as part of consolidation therapy in a meaningful proportion of patients with CLL and has shown promising activity in patients with high‐risk cytogenetic markers. Alemtuzumab may also have significant activity in T‐cell malignancies, such as mycosis fungoides and T‐cell prolymphocytic leukaemia. Recent studies also have evaluated alemtuzumab as part of a conditioning regimen to prevent GVHD in stem cell transplantation. This article reviews our current understanding of alemtuzumab and discusses its emerging role in the treatment of CLL and other haematological malignancies.
Gene expression of anti‐ and pro‐apoptotic proteins in malignant and normal plasma cells
Authors: Jourdan Michel , Reme Thierry , Goldschmidt Hartmut , Fiol Geneviève , Pantesco Véronique , De Vos John , Rossi Jean‐François , Hose Dirk , Klein Bernard
Published: January 2009

The survival of malignant plasma cells is a key event in disease occurrence, progression and chemoresistance. Using DNA‐microarrays, we analysed the expression of genes coding for 58 proteins linked with extrinsic and intrinsic apoptotic pathways, caspases and inhibitor of apoptosis proteins. We considered six memory B cells (MBC), seven plasmablasts (PPC), seven bone marrow plasma cells (BMPC) and purified myeloma cells (MMC) from 92 newly‐diagnosed patients. Forty out of the 58 probe sets enabled the separation of MBC, PPC and BMPC in three homogeneous clusters, characterized by an elevated expression of TNFRSF10A, TNFRSF10B, BCL2A1, CASP8, CASP9 and PMAIP1 genes for MBC, of FAS, FADD, AIFM1, BIRC5, CASP CASP2, CASP3 and CASP6 for PPC and of BCL2, MCL1, BID, BIRC3 and XIAP for BMPC. Thus, B cell differentiation was associated with change of expression of pro‐apoptotic and anti‐apoptotic genes. Regarding MMC, the major finding was TRAIL upregulation that might be counteracted by a high osteoprotegerin production by BM stromal cells and a decreased expression of FAS, APAF1 and BNIP3 compared to normal BMPC. Out of the 40 genes, CASP2 and BIRC5 expression in MMC had adverse prognosis in two independent series of previously‐untreated patients.
Plankton metabolic balance at the margins of very large lakes: temporal variability and evidence for dominance of autochthonous processes
Authors: BOCANIOV SERGHEI A. , SMITH RALPH E. H.
Published: January 2009

1. Planktonic metabolic balance (PMBm) of the surface mixed layer (SML) was measured as the ratio of areal rates of gross photosynthesis (AGP) to community respiration (AR) to test the idea that previously neglected allochthonous inputs of organic matter may support chronic excess respiration relative to photosynthesis even in very large lakes during the summer (May–October) season. Four Laurentian Great Lakes coastal sites of varying trophic status, physical structure and dissolved organic carbon (DOC) concentration were studied with oxygen light‐and dark bottle and 14C methods, with excess respiration anticipated in the higher DOC sites.

2. Planktonic metabolic balance was net autotrophic in 73% of the observations. The calculated mixing depth at which respiration would predominate over photosynthesis was greater than typically observed mixing depths, varying from 11 to 25 m in the more transparent, low DOC (<3 g m−3) sites to 8–15 m in the higher DOC (4–6 g m−3) sites. Biweekly measurements at one higher and one lower DOC site over two successive summer seasons showed that seasonal gross photosynthesis (ΣAGP) exceeded seasonal community respiration (ΣAR). Despite the location of the sites at the periphery of the lakes, where allochthonous influences should be strongest, the measurements indicated prevailing conditions of net autotrophy in the SML.

3. Individual measurements of AR from this study and the literature were correlated with AGP but season average values were more tightly correlated, suggesting a tighter coupling of metabolic rates on a larger scale and a looser coupling on a shorter scale. The observed temporal variability was variable in pattern among years, and likely to confound inferences based on limited sampling.

4. It is shown that accepted formulations for AGP and AR lead to the conclusion that PMBm should be largely predictable from knowledge of a biological properties ratio (light‐saturated gross photosynthesis to plankton community respiration, Pmax/R) and a physical properties ratio (euphotic to mixing depths, Zeu/Zm) and this prediction was confirmed using data from this study and from the literature. The evident success of this model points to the pre‐eminent importance of plankton biomass and physical conditions in determining metabolic balance. Variation in these fundamental factors appears capable of explaining the diversity of PMBm reported for different Great Lakes.
Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus
Authors: Hirano Yasuhiro , Ishii Kohei , Kumeta Masahiro , Furukawa Kazuhiro , Takeyasu Kunio , Horigome Tsuneyoshi
Published: January 2009

The nuclear matrix has classically been assumed to be a solid structure coherently aligning nuclear components, but its real nature remains obscure. We separated the proteins in a ribonucleoprotein‐containing nuclear matrix fraction of HeLa cells by reversed‐phase HPLC followed by SDS‐PAGE, and identified 83 proteins through peptide mass fingerprint (PMF) analysis. Many nucleolar proteins, classical nuclear matrix proteins, RNA binding proteins, cytoskeletal proteins and five uncharacterized proteins were identified in this fraction. Four of the latter proteins were localized to the cell nucleus, BXDC1 and EBNA1BP2 being especially localized to the nucleolus. Fluorescence recovery after photobleaching and RNAi knockdown analyses suggested that BXDC1 and EBNA1BP2 function in a dynamic scaffold for ribosome biogenesis.
Localization of gene products using a chromosomally tagged GFP‐fusion library in the fission yeast Schizosaccharomyces pombe
Authors: Hayashi Aki , Da‐Qiao Ding , Tsutsumi Chihiro , Chikashige Yuji , Masuda Hirohisa , Haraguchi Tokuko , Hiraoka Yasushi
Published: January 2009

We constructed a library of chromosomally‐tagged green fluorescent protein (GFP) fusions in the fission yeast Schizosaccharomyces pombe. This library contains 1058 strains. In each strain, the coding sequence of GFP is integrated at the 3′‐end of a particular chromosomal ORF such that the full‐length GFP fusion construct is expressed under the control of the original promoter. Integration of the GFP coding sequence at the authentic chromosomal location of each gene was confirmed by PCR. Microscopic screening of these strains detected sufficient levels of GFP signal in 710 strains and allowed assignment of these GFP‐fusion gene products with their intracellular localization: 374 proteins were localized in the nucleus, 65 proteins in the nucleolus, 34 proteins at the nuclear periphery, 27 proteins at the plasma membrane and cytoplasmic membranous structures, 24 proteins at the spindle pole body and microtubules, 92 proteins at cytoplasmic structures, and 94 proteins were uniformly distributed throughout the cytoplasm.
Focal adhesion‐localization of START‐GAP1/DLC1 is essential for cell motility and morphology
Authors: Kawai Katsuhisa , Iwamae Yui , Yamaga Masaki , Kiyota Minoru , Ishii Hiroko , Hirata Hajime , Homma Yoshimi , Yagisawa Hitoshi
Published: January 2009

There is a class of GTPase activating proteins for the Rho family GTPases (RhoGAPs) that contain the steroidogenic acute regulatory protein (STAR)‐related lipid transfer (START) domain. In mammals three genes encode such proteins and they are designated START‐GAP1–3 or deleted in liver cancer 1–3 (DLC1–3). In this study, we examined the intracellular localization and roles of START‐GAP1/DLC1 in cell motility. Immunofluorescence microscopic analysis of NRK cells and HeLa cells revealed that START‐GAP1 was localized in focal adhesions. Amino acid residues 265–459 of START‐GAP1 were found to be necessary for focal adhesion targeting and we name the region “the focal adhesion‐targeting (FAT) domain.” It was previously known that ectopic expression of START‐GAP1 induced cell rounding. We demonstrated that the FAT domain of START‐GAP1 was partially required for this morphological change. Furthermore, expression of this domain in HeLa cells resulted in dissociation of endogenous START‐GAP1 from focal adhesions as a dominant negative modulator, reducing cell migration and spreading. Taken together, START‐GAP1 is targeted to focal adhesions via the FAT domain and regulates actin rearrangement through down‐regulation of active RhoA and Cdc42. Its absence from focal adhesions could, therefore, cause abnormal cell motility and spreading.
Long‐term fire frequency variability in the eastern Canadian boreal forest: the influences of climate vs. local factors
Authors: ALI ADAM A. , CARCAILLET CHRISTOPHER , BERGERON YVES
Published: January 2009

The influence of climatic and local nonclimatic factors on the fire regime of the eastern Canadian boreal forest over the last 8000 years is investigated by examining charred particles preserved in four lacustrine deposits. Herein, we compare the distribution of fire‐free intervals (FFIs) and the synchronicity of fire events among sites, using Ripley'sK‐function to determine the extent of the role of local‐scale vs. large‐scale processes with respect to fire control. Between 8000 and 5800 cal.bp(calibrated years before present) the climatic and ecological conditions were less conducive to fire events than after this date. After 5800 cal.bp, the number of fires per 1000 years (fire frequency) progressively increased, reaching a maximum ca. 3400 cal.bp. There was a sharp decrease in fire frequency during the last 800 years. Between 8000 and 4000 cal.bp, comparable FFIs and synchronous fire episodes were determined for the study sites. During this period, the fire frequency was predominantly controlled by climate. After 4000 cal.bp, two sites displayed independent fire histories (different FFI distributions or asynchronous fire events), underlining the important influence of local factors, including short‐term fuel wetness, characteristics of the watershed and landscape connectivity, in determining fire occurrence. We conclude that climatic changes occurred during the last 4000 years that induced a rise in the water table; this may explain the high spatial heterogeneity in fire history. Current and projected global climatic changes may cause similar spatial variability in fire frequency.
Stimulation of microbial extracellular enzyme activities by elevated CO2 depends on soil aggregate size
Authors: DORODNIKOV MAXIM , BLAGODATSKAYA EVGENIA , BLAGODATSKY SERGEY , MARHAN SVEN , FANGMEIER ANDREAS , KUZYAKOV YAKOV
Published: January 2009

Increased belowground carbon (C) transfer by plant roots at elevated CO2 may change properties of the microbial community in the rhizosphere. Previous investigations that focused on total soil organic C or total microbial C showed contrasting results: small increase, small decrease or no changes. We evaluated the effect of 5 years of elevated CO2 (550 ppm) on four extracellular enzymes: β‐glucosidase, chitinase, phosphatase, and sulfatase. We expected microorganisms to be differently localized in aggregates of various sizes and, therefore analyzed microbial biomass (Cmic by SIR) and enzyme activities in three aggregate‐size classes: large macro‐ (> 2 mm), small macro‐ (0.25–2 mm), and microaggregates (< 0.25 mm). To estimate the potential enzyme production, we activated microorganisms by substrate (glucose and nutrients) amendment. Although Ctotal and Cmic as well as the activities of β‐glucosidase, phosphatase, and sulfatase were unaffected in bulk soil and in aggregate‐size classes by elevated CO2, significant changes were observed in potential enzyme production after substrate amendment. After adding glucose, enzyme activities under elevated CO2 were 1.2–1.9‐fold higher than under ambient CO2. This indicates the increased activity of microorganisms, which leads to accelerated C turnover in soil under elevated CO2. Significantly higher chitinase activity in bulk soil and in large macroaggregates under elevated CO2 revealed an increased contribution of fungi to turnover processes. At the same time, less chitinase activity in microaggregates underlined microaggregate stability and the difficulties for fungal hyphae penetrating them. We conclude that quantitative and qualitative changes of C input by plants into the soil at elevated CO2 affect microbial community functioning, but not its total content. Future studies should therefore focus more on the changes of functions and activities, but less on the pools.
Effect of ecosystem warming on boreal black spruce bud burst and shoot growth
Authors: BRONSON DUSTIN R. , GOWER STITH T. , TANNER MYRON , VAN HERK INGRID
Published: January 2009

The boreal forest is predicted to experience the greatest warming of any forest biome during the next 50–100 years, but the effects of warming on vegetation phenology are not well known. The objectives of this study were to (1) examine the effects of whole ecosystem warming on bud burst and annual shoot growth of black spruce trees in northern Manitoba, Canada and (2) correlate bud burst to cumulative degree‐days (CDD). The experimental design was a complete randomized block design that consisted of four replicated blocks. Each replicate block contained four treatments: soil warming only (heated outside, HO), soil and air warming (heated inside, HI), control outside (no chamber, no heating, CO), and inside a chamber maintained at ambient conditions (no soil or air warming, control inside, CI). Bud burst was measured during the first and second years of the experiment, starting in 2004, and annual shoot growth was measured for the first 3 years (2004–2006) of the study. On average, shoot bud burst occurred 11 and 9 days earlier in 2004 and 2005, respectively, for HI than for other treatments. However, mean CDD required for bud burst for HI was within the standard deviation of CO for both years. In year 1 of the treatments, shoot bud burst occurred earlier for HI than other treatments (CI, CO, HO), but final shoot length of HI trees was less than in CO trees. In the second year of warming, final shoot length was not different for HI than CO. By the third year of warming final shoot length was significantly greater for HI than all other treatments. Empirical results from this study suggest that soil and air warming causes an earlier bud burst for all years of observation and greater shoot lengths by the third season of warming. A longer growing season and greater annual shoot growth should increase carbon uptake by boreal black spruce trees in a warmer climate.
Climate‐induced changes in the small mammal communities of the Northern Great Lakes Region
Authors: MYERS PHILIP , LUNDRIGAN BARBARA L. , HOFFMAN SUSAN M. G. , HARAMINAC ALLISON POOR , SETO STEPHANIE H.
Published: January 2009

We use museum and other collection records to document large and extraordinarily rapid changes in the ranges and relative abundance of nine species of mammals in the northern Great Lakes region (white‐footed mice, woodland deer mice, southern red‐backed voles, woodland jumping mice, eastern chipmunks, least chipmunks, southern flying squirrels, northern flying squirrels, common opossums). These species reach either the southern or the northern limit of their distributions in this region. Changes consistently reflect increases in species of primarily southern distribution (white‐footed mice, eastern chipmunks, southern flying squirrels, common opossums) and declines by northern species (woodland deer mice, southern red‐backed voles, woodland jumping mice, least chipmunks, northern flying squirrels). White‐footed mice and southern flying squirrels have extended their ranges over 225 km since 1980, and at particularly well‐studied sites in Michigan's Upper Peninsula, small mammal assemblages have shifted from numerical domination by northern species to domination by southern species. Repeated resampling at some sites suggests that southern species are replacing northern ones rather than simply being added to the fauna. Observed changes are consistent with predictions from climatic warming but not with predictions based on recovery from logging or changes in human populations. Because of the abundance of these focal species (the eight rodent species make up 96.5% of capture records of all forest‐dwelling rodents in the region and 70% of capture records of all forest‐dwelling small mammals) and the dominating ecological roles they play, these changes substantially affect the composition and structure of forest communities. They also provide an unusually clear example of change that is likely to be the result of climatic warming in communities that are experienced by large numbers of people.
Climate‐induced changes in high elevation stream nitrate dynamics
Authors: BARON JILL S. , SCHMIDT TRAVIS M. , HARTMAN MELANNIE D.
Published: January 2009

Mountain terrestrial and aquatic ecosystems are responsive to external drivers of change, especially climate change and atmospheric deposition of nitrogen (N). We explored the consequences of a temperature‐warming trend on stream nitrate in an alpine and subalpine watershed in the Colorado Front Range that has long been the recipient of elevated atmospheric N deposition. Mean annual stream nitrate concentrations since 2000 are higher by 50% than an earlier monitoring period of 1991–1999. Mean annual N export increased by 28% from 2.03 kg N ha−1 yr−1 before 2000 to 2.84 kg N ha−1 yr−1 in Loch Vale watershed since 2000. The substantial increase in N export comes as a surprise, since mean wet atmospheric N deposition from 1991 to 2006 (3.06 kg N ha−1 yr−1) did not increase. There has been a period of below average precipitation from 2000 to 2006 and a steady increase in summer and fall temperatures of 0.12 °C yr−1 in both seasons since 1991. Nitrate concentrations, as well as the weathering products calcium and sulfate, were higher for the period 2000–2006 in rock glacier meltwater at the top of the watershed above the influence of alpine and subalpine vegetation and soils. We conclude the observed recent N increases in Loch Vale are the result of warmer summer and fall mean temperatures that are melting ice in glaciers and rock glaciers. This, in turn, has exposed sediments from which N produced by nitrification can be flushed. We suggest a water quality threshold may have been crossed around 2000. The phenomenon observed in Loch Vale may be indicative of N release from ice features such as rock glaciers worldwide as mountain glaciers retreat.
Rapid biogeographical plankton shifts in the North Atlantic Ocean
Authors: GREGORY BEAUGRAND , CHRISTOPHE LUCZAK , MARTIN EDWARDS
Published: January 2009

Large‐scale biogeographical changes in the biodiversity of a key zooplankton group (calanoid copepods) were detected in the north‐eastern part of the North Atlantic Ocean and its adjacent seas over the period 1960–1999. These findings provided key empirical evidence for climate change impacts on marine ecosystems at the regional to oceanic scale. Since 1999, global temperatures have continued to rise in the region. Here, we extend the analysis to the period 1958–2005 using all calanoid copepod species assemblages (nine species assemblages based on an analysis including a total of 108 calanoid species or taxa) and show that this phenomenon has been reinforced in all regions. Our study reveals that the biodiversity of calanoid copepods are responding quickly to sea surface temperature (SST) rise by moving geographically northward at a rapid rate up to about 23.16 km yr−1. Our analysis suggests that nearly half of the increase in sea temperature in the northeast Atlantic and adjacent seas is related to global temperature rises (46.35% of the total variance of temperature) while changes in both natural modes of atmospheric and oceanic circulation explain 26.45% of the total variance of temperature. Although some SST isotherms have moved northwards by an average rate of up to 21.75 km yr−1 (e.g. the North Sea), their movement cannot fully quantify all species assemblage shifts. Furthermore, the observed rates of biogeographical movements are far greater than those observed in the terrestrial realm. Here, we discuss the processes that may explain such a discrepancy and suggest that the differences are mainly explained by the fluid nature of the pelagic domain, the life cycle of the zooplankton and the lesser anthropogenic influence (e.g. exploitation, habitat fragmentation) on these organisms. We also hypothesize that despite changes in the path and intensity of the oceanic currents that may modify quickly and greatly pelagic zooplankton species, these organisms may reflect better the current impact of climate warming on ecosystems as terrestrial organisms are likely to significantly lag the current impact of climate change.
Sources of plant‐derived carbon and stability of organic matter in soil: implications for global change
Authors: CROW SUSAN E. , LAJTHA KATE , FILLEY TIMOTHY R. , SWANSTON CHRISTOPHER W. , BOWDEN RICHARD D. , CALDWELL BRUCE A.
Published: January 2009

Alterations in forest productivity and changes in the relative proportion of above‐ and belowground biomass may have nonlinear effects on soil organic matter (SOM) storage. To study the influence of plant litter inputs on SOM accumulation, the Detritus Input Removal and Transfer (DIRT) Experiment continuously alters above‐ and belowground plant inputs to soil by a combination of trenching, screening, and litter addition. Here, we used biogeochemical indicators [i.e., cupric oxide extractable lignin‐derived phenols and suberin/cutin‐derived substituted fatty acids (SFA)] to identify the dominant sources of plant biopolymers in SOM and various measures [i.e., soil density fractionation, laboratory incubation, and radiocarbon‐based mean residence time (MRT)] to assess the stability of SOM in two contrasting forests within the DIRT Experiment: an aggrading deciduous forest and an old‐growth coniferous forest. In the deciduous forest, removal of both above‐ and belowground inputs increased the total amount of SFA over threefold compared with the control, and shifted the SFA signature towards a root‐dominated source. Concurrently, light fraction MRT increased by 101 years and C mineralization during incubation decreased compared with the control. Together, these data suggest that root‐derived aliphatic compounds are a source of SOM with greater relative stability than leaf inputs at this site. In the coniferous forest, roots were an important source of soil lignin‐derived phenols but needle‐derived, rather than root‐derived, aliphatic compounds were preferentially preserved in soil. Fresh wood additions elevated the amount of soil C recovered as light fraction material but also elevated mineralization during incubation compared with other DIRT treatments, suggesting that not all of the added soil C is directly stabilized. Aboveground needle litter additions, which are more N‐rich than wood debris, resulted in accelerated mineralization of previously stored soil carbon. In summary, our work demonstrates that the dominant plant sources of SOM differed substantially between forest types. Furthermore, inputs to and losses from soil C pools likely will not be altered uniformly by changes in litter input rates.
Long‐term temporal changes of plant phenology in the Western Mediterranean
Authors: GORDO OSCAR , SANZ JUAN JOSÉ
Published: January 2009

Plants are altering their life cycles in response to current climatic change around the globe. More than 200 000 records for six phenological events (leaf unfolding, flowering, fruit ripening, fruit harvesting, leaf falling and growing season) of 29 perennial species for the period 1943–2003 recorded throughout Spain provide the longest temporal and the broadest spatial assessment of plant phenology changes in the Mediterranean region. The overwhelming majority of the 118 studied phenophases shifted their dates in recent decades. Such changes differed among phenological events. Leaf unfolding, flowering and fruiting are markedly advancing (−0.48, −0.59 and −0.32 days yr−1, respectively), but only since the mid‐1970s. Anemophilous have advanced more days their flowering than entomophilous. However, some species have delayed and others have advanced their leaf falling dates and as a result only a weak shift was observed in this event for the whole of the studied species (+0.12 days yr−1). The growing season lengthened by 18 days, which implies an increase of 8% in the life of annual leaves. Such an increase was achieved mainly through the advance of leaf unfolding dates in the spring, one of the most productive times of year for vegetation in the Mediterranean. Shifts in the plant calendar were accompanied as well by long‐term changes in the range of onset dates in 39% of studied phenophases. Leaf unfolding, flowering and growing season tended to reduce spatial variability, reflecting a faster and more synchronized onset (or duration) of phenophases across the study area. Changes in spatial variability may aggravate calendar mismatching with other trophic levels resulting from changes in dates. Because temporal responses differed markedly among species, calendar guilds of plants have changed, which suggests alterations of interspecific relationships in plant communities from Mediterranean ecosystems.
Long‐term transpiration change with rainfall decline in a Mediterranean Quercus ilex forest
Authors: LIMOUSIN J. M. , RAMBAL S. , OURCIVAL J. M. , ROCHETEAU A. , JOFFRE R. , RODRIGUEZ‐CORTINA R.
Published: January 2009

In the Mediterranean basin, precipitation is expected to decline as a consequence of climate change. The response of a Quercus ilex forest in southern France to such a decline in water availability was studied using a 4‐year throughfall exclusion experiment. Seasonal courses of sap flow and leaf water potential were obtained from 2004 to 2007 and used to characterize tree water relations in a control and a dry treatment. The experiment reduced the average precipitation input to the soil by 29%, and resulted in a 23% reduction in annual transpiration. Soil water potential was significantly lower in the dry treatment only during summer drought, but transpiration was reduced all year round even during well‐watered periods. Despite a tight stomatal control over transpiration, whole‐tree hydraulic conductance was found to be lower in the trees growing in the driest conditions. This reduction in water transport capacity was observed jointly with a reduction in leaf transpiring area. Canopy leaf area decreased by 18% in the dry treatment as a consequence of the throughfall exclusion, which was found to validate the ecohydrological equilibrium theory.
Domain analyses of the Runx1 transcription factor responsible for modulating T‐cell receptor‐β/CD4 and interleukin‐4/interferon‐γ expression in CD4+ peripheral T lymphocytes
Authors: Uchino Ryuji
Published: January 2009

The Runx1 transcription factor is one of the master regulators of T‐lymphocyte differentiation. There have been several reports trying to assign a domain within the Runx1 protein that is responsible for gene expression in thymocytes. The Runx1 domains involved in regulating the expression of several genes in peripheral CD4+ T cells were analysed. It was observed that Runx1 over‐expression enhanced the surface expression of CD4 and CD69 molecules via its activation domain and VWRPY domain, and decreased that of T‐cell receptor‐β via its activation domain. Runx1 over‐expression enhanced interferon‐γ expression via its activation and VWRPY domains, and abolished interleukin‐4 expression through its activation domain. Transduction of Runx1 did not down‐regulate CD4 expression until 72 hr of culture, but the repression of CD4 expression became evident after 96 hr. The main region responsible for repressing CD4 expression was the inhibitory domain of Runx1. Taken together, these results lead to a proposal that the regions in Runx1 responsible for modulating gene expression are distinct in thymocytes and in peripheral CD4+ T cells.