bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of Salicylic Acid and Fatty Acid Desaturation Pathways in ssi2-Mediated Signaling
Authors: Kachroo Pradeep , Venugopal Srivathsa C. , Navarre Duroy A. , Lapchyk Ludmila , Kachroo Aardra 
Published: November 2005

Abstract
Stearoyl-acyl carrier protein desaturase-mediated conversion of stearic acid to oleic acid (18:1) is the key step that regulates the levels of unsaturated fatty acids (FAs) in cells. Our previous work with the Arabidopsis (Arabidopsis thaliana) ssi2/fab2 mutant and its suppressors demonstrated that a balance between glycerol-3-phosphate (G3P) and 18:1 levels is critical for the regulation of salicylic acid (SA)- and jasmonic acid-mediated defense signaling in the plant. In this study, we have evaluated the role of various genes that have an impact on SA, resistance gene-mediated, or FA desaturation (FAD) pathways on ssi2-mediated signaling. We show that ssi2-triggered resistance is dependent on EDS1, PAD4, EDS5, SID2, and FAD7 FAD8 genes. However, ssi2-triggered defects in the jasmonic acid pathway, morphology, and cell death phenotypes are independent of the EDS1, EDS5, PAD4, NDR1, SID2, FAD3, FAD4, FAD5, DGD1, FAD7, and FAD7 FAD8 genes. Furthermore, the act1-mediated rescue of ssi2 phenotypes is also independent of the FAD2, FAD3, FAD4, FAD5, FAD7, and DGD1 genes. Since exogenous application of glycerol converts wild-type plants into ssi2 mimics, we also studied the effect of exogenous application of glycerol on mutants impaired in resistance-gene signaling, SA, or fad pathways. Glycerol increased SA levels and induced pathogenesis-related gene expression in all but sid2, nahG, fad7, and fad7 fad8 plants. Furthermore, glycerol-induced phenotypes in various mutant lines correlate with a concomitant reduction in 18:1 levels. Inability to convert glycerol into G3P due to a mutation in the nho1-encoded glycerol kinase renders plants tolerant to glycerol and unable to induce the SA-dependent pathway. A reduction in the NHO1-derived G3P pool also results in a partial age-dependent rescue of the ssi2 morphological and cell death phenotypes in the ssi2 nho1 plants. The glycerol-mediated induction of defense was not associated with any major changes in the lipid profile and/or levels of phosphatidic acid. Taken together, our results suggest that glycerol application and the ssi2 mutation in various mutant backgrounds produce similar effects and that restoration of ssi2 phenotypes is not associated with the further desaturation of 18:1 to linoleic or linolenic acids in plastidal or extraplastidal lipids.
Molecular predictors of clinical outcome in patients with head and neck squamous cell carcinoma
Authors: Thomas Giovana R. , Nadiminti Hari , Regalado Jacinto 
Published: November 2005

SummaryHead and neck squamous cell carcinoma (HNSCC) involves the upper aerodigestive tract and can destroy the structure and function of organs involved in voice, speech, taste, smell and hearing, as well as vital structures necessary for survival. HNSCC has long been a treatment challenge because of the high rate of recurrences and of advanced disease at the time of diagnosis. Molecular identification of tissue biomarkers in diagnostic biopsy specimens may not only identify patients at risk for developing HNSCC but may also select patients that may benefit from more aggressive treatment modalities. Several biomarkers studied to date such as the proteins p53, cyclin D1, p16, Cox‐2 enzyme, epidermal growth factor and vascular endothelial growth factor receptors, matrix metalloproteinases and the Fhit marker for genomic instability could be manipulated for the therapeutic benefit of these patients. This review presents the most updated information on molecular biomarkers with the greatest prognostic potential in HNSCC and discusses some factors that contribute to the controversy concerning their prognostic importance.
On the lack of good scientific reasons for the growing phylogeny/classification gap
Authors: Franz Nico M. 
Published: November 2005

AbstractAn increasing number of phylogenetic analyses is no longer translated into classifications. The resulting phylogeny/classification gap is undesirable because the precise transmission of phylogenetic insights depends on the frequent revision of Linnaean names. The move away from classifying has numerous correlates. These include: an expanded pool of researchers who are able to produce phylogenetic estimates, a mismatch between the properties of molecular phylogenies and the requirements for verbal Linnaean definitions, the emphasis of statistical representations over the creation and evaluation of scientific terms, and a partial disconnect between the processes of nomenclature and taxonomy. The “taxonomic concept” approach allows systematists to express their varying perspectives with a high precision and can therefore help reduce the aforementioned gap. The phylogeny/classification link must persist in order to ensure community‐wide access to, and continued testing of, the products of systematic research.© The Willi Hennig Society 2005.
Conflict and congruence in a combined DNA–morphology analysis of megachiropteran bat relationships (Mammalia: Chiroptera: Pteropodidae)
Authors: Giannini Norberto P. , Simmons Nancy B. 
Published: November 2005

AbstractThe phylogeny of megabats (Mammalia: Chiroptera: Megachiroptera) has been addressed only on molecular grounds, as little effort has previously been made to describe the impressive morphological variation of the group in terms of phylogenetically informative characters. Here we provide a morphological matrix of 236 characters from the integument, dentition, cranial and post‐cranial skeleton, digestive apparatus and urogenital system. This data set covers most characters discussed previously in more restricted taxonomic contexts, as well a large number of new characters. Our aim was to generate a phylogenetic hypothesis for megabats based on a combined analysis of morphological characters and available gene sequence data from four mitochondrial and one nuclear loci. We used direct optimization under conventional equal costs, as well as under a cost ratio that maximizes homology when inapplicables (gaps) are present. Our results contradict the allegedly high level of conflict between the molecular and morphological partitions. We found that, although morphology alone recovered trees different and to some extent incompatible with those from previous molecular analyses, the combination of the two sources of evidence easily accommodated the morphological and molecular signals, yielding a resolved and relatively well‐supported phylogeny of Megachiroptera that is in reasonable agreement with the current morphology‐based taxonomy of the group. Overall congruence favored the maximization of homology by a narrow margin. In addition, partial analyses showed that implied weighting of morphology performed slightly better than equal weighting with respect to the combined analyses.© The Willi Hennig Society 2005.
Spreading of methylation within RUNX3 CpG island in gastric cancer
Authors: Homma Naoyuki , Tamura Gen , Honda Teiichiro , Matsumoto Yutaka , Nishizuka Satoshi , Kawata Sumio , Motoyama Teiichi 
Published: November 2005

RUNX3 is a novel tumor suppressor gene that is frequently silenced by promoter hypermethylation in gastric cancer. The methylation status of multiple regions within the RUNX3 promoter CpG island (3478 bp) was examined in gastric cancer cell lines, primary gastric cancers and non‐neoplastic gastric mucosa to clarify how methylation spreads within the CpG island. The critical regions for RUNX3 silencing were evaluated by analysis of cell lines. The most 5′ region of the CpG island was methylated in 90% (9/10) of gastric cancer cell lines, 96% (43/45) of primary gastric cancers and in 96% (43/45) of non‐neoplastic gastric mucosa. The frequencies of methylation were less near the transcription start site and were 40% (4/10) in cell lines, 53% (24/45) in primary gastric cancers and 11% (5/45) in non‐neoplastic gastric mucosa, where methylation was proven to be critical for gene silencing. Thus, hypermethylation initially occurs at the most 5′ region of the RUNX3 CpG island and spreads to the transcription start site before ultimately shutting down RUNX3 mRNA expression. The detection of hypermethylation at multiple regions within the RUNX3 CpG island may be useful in the diagnosis and risk assessment of gastric cancer. (Cancer Sci 2005)
The role of alcohol and drugs in triggering criminal violence: a case‐crossover study*
Authors: Haggård‐Grann Ulrika , Hallqvist Johan , Långström Niklas , Möller Jette 
Published: November 2005

ABSTRACTAims  To investigate the triggering effects of alcohol, illegal substances and major classes of prescribed psychotropic drugs on criminal violence.Design  A case‐crossover design, using each subject as its own control.Setting and participants  A consecutive sample of 133 violent offenders was recruited from a forensic psychiatric evaluation unit and a national prison evaluation unit in Sweden during 2002–03.Measurements  Offenders were assessed with structured interviews. Risk estimates were based on hazard periods of 24 hours. We used standard Mantel–Haenszel methods for statistical analyses.Findings  A 13.2‐fold increase of risk of violence [95% confidence interval (CI): 8.2–21.2] was found within 24 hours of alcohol consumption. This increase in violence risk was similar among individuals combining alcohol with benzodiazepines [Relative risk (RR) = 13.2, 95% CI: 4.9–35.3]. Use of benzodiazepines alone in regular doses (RR = 0.4, 95% CI: 0.2–0.5) or antidepressants [selective serotonin reuptake inhibitors (SSRIs) or tricyclics] (RR = 0.4, 95% CI: 0.3–0.8) was associated with a lowered risk for violence.Conclusions  This study confirmed that alcohol is a strong trigger of criminal violence. Benzodiazepines in combination with alcohol caused no further increase of violence risk. Benzodiazepines in regular doses and antidepressants may inhibit violence, but further studies are needed to verify causality. The case‐crossover method can contribute to research on the proximal causes of criminal violence.
The role of gemtuzumab ozogamicin in acute leukaemia therapy
Authors: Tsimberidou Apostolia‐Maria , Giles Francis J. , Estey Elihu , O'Brien Susan , Keating Michael J. , Kantarjian Hagop M. 
Published: November 2005

AbstractGemtuzumab ozogamicin (GO) is an immunoconjugate that binds to CD33 on the surface of acute myeloid leukaemia (AML) blasts and, after internalisation, releases a cytotoxic drug, calicheamicin. GO is approved by the US Food and Drug Administration for the treatment of CD33‐positive AML at first relapse in patients 60 years and older who are not candidates for other cytotoxic therapy. GO as a single agent has low antileukaemic activity. When given to patients meeting the criteria noted above, it produces a complete response (CR) rate of only 12%, with another 12% achieving CR with inadequate platelet recovery (CRp). The median survival of patients treated with GO monotherapy is 11·2 months. GO therapy at 9 mg/m2 is complicated with hepatic veno‐occlusive disease in 5–10% of patients, particularly prior to or following stem cell transplantation. GO at lower doses combined with chemotherapy as induction or postremission therapy is promising, however, and phase III trials are ongoing. GO is probably most active in acute promyelocytic leukaemia (APL). It is used for induction regimens in high‐risk APL and for the elimination of minimal residual APL. Case reports suggest that GO also has activity in CD33‐positive acute lymphoblastic leukaemia. In conclusion, single agent GO can induce responses in patients with CD33‐positive AML in first recurrence. The future of GO is its use in combination with other cytotoxic agents. Ongoing clinical trials may better define the role of GO combinations, particularly in untreated AML.
Growth, demography and carbon relations ofPolylepistrees at the world's highest treeline
Authors: HOCH G. , KÖRNER C. 
Published: November 2005

SummaryGrowth, reproductive success and non‐structural carbon pools inPolylepis tarapacanaPhilippi trees were examined across a transect between 4360 and 4810 m altitude on Nevado Sajama, Bolivia.The mean −10‐cm soil temperature of 5·4 °C under trees at the treeline during the 265‐day growing season matched the threshold temperature found at other subtropical and tropical treelines. Beyond 4400 mPolylepisis restricted to the warmer and drier equator‐facing slopes, suggesting a direct thermal limitation of tree growth.Maximum tree height, annual shoot increment and mean tree‐ring width decreased with altitude. Trees near the upper range limit reached a maximum tree height of 3·3 m and a maximum stem diameter of 34 cm.The smallest tree‐height classes dominated populations at all altitudes, and the uppermost site revealed the highest proportion of seedlings. Tree‐size demography indicates a critical phase for tree establishment during the sapling stage, when trees emerge from sheltered niches near the ground.No evidence of a depletion of mobile C stores (sugars, starch and lipids) was found in any tissue type with increasing elevation, suggesting a limitation of C investment (growth) rather than C acquisition (photosynthesis) at treeline.
The influence of reproductive state on cardiac parameters and hypoxia tolerance in the Grass Shrimp, Palaemonetes pugio
Authors: GUADAGNOLI J. A. , JONES L. A. , REIBER C. L. 
Published: November 2005

Summary

In many crustaceans, female reproduction represents a time of increased metabolic demand. Palaemonetes pugio are typically hypoxia tolerant; but the energetic demands of reproduction may compromise their ability to tolerate hypoxic conditions. Given the correlation between cardiac output and metabolic demand, we used cardiac output (CO) to measure differences in metabolic demand in the life‐history stages of P. pugeo.
We hypothesized that (1) the cost of egg production would result in an increased CO for gravid females compared with non‐gravid females; (2) those females that were both ovigerous and gravid would have an additional metabolic demand due to brooding behaviour (pleopod fanning) and hence an even greater CO; and (3) hypoxia tolerance would decrease with increasing reproductive demand. To test these hypotheses, we compared cardiac output across three reproductive states and at decreasing water oxygen tensions.
Ovigerous females had significantly greater pleopod fanning frequency than non‐ovigerous females at all oxygen tensions. Additionally, ovigerous/gravid females had significantly higher cardiac output at all oxygen tensions than gravid only or non‐gravid females.
Changes in cardiac output indicate that females became more sensitive to environmental oxygen tension with increasing reproductive demand. Non‐gravid females were able to maintain cardiac output down to 15 mm Hg O2, whereas gravid and ovigerous/gravid females maintained cardiac output down to 50 mm Hg and 75 mm Hg O2, respectively.
These differences in CO suggest that metabolic demands of females change with reproductive state and, while gravid and ovigerous/gravid females appear more sensitive to low oxygen tensions, they are able to physiologically tolerate low environmental oxygen conditions.
Mate location tactics in garter snakes: effects of rival males, interrupted trails and non‐pheromonal cues
Authors: SHINE R. , WEBB J. K. , LANE A. , MASON R. T. 
Published: November 2005

Summary

The ability to follow substrate‐deposited scent trails using sophisticated vomeronasal abilities is a key feature of snake biology. However, previous research on this topic has derived mostly from a highly artificial test situation: captive snakes following continuous trails over structurally simple homogeneous substrates, in the absence of any other cues (e.g. visual or olfactory) either from the target of that search or from other snakes.
Our field experimental trials with Red‐Sided Garter Snakes (Thamnophis sirtalis parietalis) at a communal den in Manitoba explored wider issues in mate location.
Males followed a female's trail less successfully if she had recently been followed by rival males, suggesting that trailing males obscured the cues left by the female.
Males that lost contact with a female's trail exhibited stereotyped, spatially extensive and prolonged circling behaviour centred on the last point at which the trail was detectable; in nature, this behaviour would maximize the male's ability to relocate a discontinuous trail.
Trail‐following males switched from chemical to visual cues as soon as they were close to a female, enhancing speed but decreasing the accuracy of mate location (because males could distinguish between females and other males based on either visual or airborne olfactory cues).
Incorporating additional cues and broader spatial scales can clarify aspects of trail‐following behaviour not evident from studies in small, highly simplified laboratory situations.
Bud‐burst modelling in Siberia and its impact on quantifying the carbon budget
Authors: PICARD GHISLAIN , QUEGAN SHAUN , DELBART NICOLAS , LOMAS MARK R. , LE TOAN THUY , WOODWARD F. IAN 
Published: November 2005

AbstractVegetation phenology is affected by climate change and in turn feeds back on climate by affecting the annual carbon uptake by vegetation. To quantify the impact of phenology on terrestrial carbon fluxes, we calibrate a bud‐burst model and embed it in the Sheffield dynamic global vegetation model (SDGVM) in order to perform carbon budget calculations.Bud‐burst dates derived from the VEGETATION sensor onboard the SPOT‐4 satellite are used to calibrate a range of bud‐burst models. This dataset has been recently developed using a new methodology based on the normalized difference water index, which is able to distinguish snowmelt from the onset of vegetation activity after winter. After calibration, a simple spring warming model was found to perform as well as more complex models accounting for a chilling requirement, and hence it was used for the carbon flux calculations. The root mean square difference (RMSD) between the calibrated model and the VEGETATION dataset was 6.5 days, and was 6.9 days between the calibrated model and independent ground observations of bud‐burst available at nine locations over Siberia.The effects of bud‐burst model uncertainties on the carbon budget were evaluated using the SDGVM. The 6.5 days RMSD in the bud‐burst date (a 6% variation in the growing season length), treated as a random noise, translates into about 41 g cm−2 yr−1 in net primary production (NPP), which corresponds to 8% of the mean NPP. This is a moderate impact and suggests the calibrated model is accurate enough for carbon budget calculations.In addition to random differences between the calibrated model and VEGETATION data, systematic errors between the calibrated bud‐burst model and true ground behaviour may occur, because of bias in the temperature dataset or because the bud‐burst detected by VEGETATION is because of some other phenological indicator. A systematic error of 1 day in bud‐burst translates into a 10 g cm−2 yr−1 error in NPP (about 2%). Based on the limited available ground data, any systematic error because of the use of VEGETATION data should not lead to significant errors in the calculated carbon flux. In contrast, widely used methods based on the normalized difference vegetation index from the advanced very high resolution radiometer satellite are likely to confuse snowmelt and vegetation greening, leading to errors of up to 15 days in bud‐burst date, with consequent large errors in carbon flux calculations.
Model‐data synthesis of diurnal and seasonal CO2fluxes at Niwot Ridge, Colorado
Authors: SACKS WILLIAM J. , SCHIMEL DAVID S. , MONSON RUSSELL K. , BRASWELL BOBBY H. 
Published: November 2005

AbstractEddy covariance records hold great promise for understanding the processes controlling the net ecosystem exchange of CO2(NEE). However, NEE is the small difference between two large fluxes: photosynthesis and ecosystem respiration. Consequently, separating NEE into its component fluxes, and determining the process‐level controls over these fluxes, is a difficult problem. In this study, we used a model‐data synthesis approach with the Simplified PnET (SIPNET) flux model to extract process‐level information from 5 years of eddy covariance data at an evergreen forest in the Colorado Rocky Mountains. SIPNET runs at a twice‐daily time step, and has two vegetation carbon pools, a single aggregated soil carbon pool, and a soil moisture submodel that models both evaporation and transpiration. By optimizing the model parameters before evaluating model‐data mismatches, we were able to probe the model structure independent of any arbitrary parameter set. In doing so, we were able to learn about the primary controls over NEE in this ecosystem, and in particular the respiration component of NEE. We also used this parameter optimization, coupled with a formal model selection criterion, to investigate the effects of making hypothesis‐driven changes to the model structure. These experiments lent support to the hypotheses that (1) photosynthesis, and possibly foliar respiration, are down‐regulated when the soil is frozen and (2) the metabolic processes of soil microbes vary in the summer and winter, possibly because of the existence of distinct microbial communities at these two times. Finally, we found that including water vapor fluxes, in addition to carbon fluxes, in the parameter optimization did not yield significantly more information about the partitioning of NEE into gross photosynthesis and ecosystem respiration.
Variation of carbon isotope fractionation in hydrogenotrophic methanogenic microbial cultures and environmental samples at different energy status
Authors: PENNING HOLGER , PLUGGE CAROLINE M. , GALAND PIERRE E. , CONRAD RALF 
Published: November 2005

AbstractMethane is a major product of anaerobic degradation of organic matter and an important greenhouse gas. Its stable carbon isotope composition can be used to reveal active methanogenic pathways, if associated isotope fractionation factors are known. To clarify the causes that lead to the wide variation of fractionation factors of methanogenesis from H2 plus CO2 (), pure cultures and various cocultures were grown under different thermodynamic conditions. In syntrophic and obligate syntrophic cocultures thriving on different carbohydrate substrates, fermentative bacteria were coupled to three different species of hydrogenotrophic methanogens of the families Methanobacteriaceae and Methanomicrobiaceae. We found that C‐isotope fractionation was correlated to the Gibbs free energy change (ΔG) of CH4 formation from H2 plus CO2 and that the relation can be described by a semi‐Gauss curve. The derived relationship was used to quantify the average ΔG that is available to hydrogenotrophic methanogenic archaea in their habitat, thus avoiding the problems encountered with measurement of low H2 concentrations on a microscale. Boreal peat, rice field soil, and rumen fluid, which represent major sources of atmospheric CH4, exhibited increasingly smaller , indicating that thermodynamic conditions for hydrogenotrophic methanogens became increasingly more favourable. Vice versa, we hypothesize that environments with similar energetic conditions will also exhibit similar isotope fractionation. Our results, thus, provide a mechanistic constraint for modelling the 13C flux from microbial sources of atmospheric CH4.