bluuebunny/crossref_metadata_2025 huggingface dataset:
Retrograde Shiga Toxin Trafficking Is Regulated by ARHGAP21 and Cdc42
Authors: Hehnly Heidi , Longhini Katrina Marie , Chen Ji-Long , Stamnes Mark
Published: August 2009

Shiga-toxin–producing Escherichia coli remain a food-borne health threat. Shiga toxin is endocytosed by intestinal epithelial cells and transported retrogradely through the secretory pathway. It is ultimately translocated to the cytosol where it inhibits protein translation. We found that Shiga toxin transport through the secretory pathway was dependent on the cytoskeleton. Recent studies reveal that Shiga toxin activates signaling pathways that affect microtubule reassembly and dynein-dependent motility. We propose that Shiga toxin alters cytoskeletal dynamics in a way that facilitates its transport through the secretory pathway. We have now found that Rho GTPases regulate the endocytosis and retrograde motility of Shiga toxin. The expression of RhoA mutants inhibited endocytosis of Shiga toxin. Constitutively active Cdc42 or knockdown of the Cdc42-specific GAP, ARHGAP21, inhibited the transport of Shiga toxin to the juxtanuclear Golgi apparatus. The ability of Shiga toxin to stimulate microtubule-based transferrin transport also required Cdc42 and ARHGAP21 function. Shiga toxin addition greatly decreases the levels of active Cdc42-GTP in an ARHGAP21-dependent manner. We conclude that ARHGAP21 and Cdc42-based signaling regulates the dynein-dependent retrograde transport of Shiga toxin to the Golgi apparatus.
CP250, a Novel Acidic Coiled Coil Protein of theDictyosteliumcentrosome, Affects Growth, Chemotaxis, and the Nuclear Envelope
Authors: Blau-Wasser Rosemarie , Euteneuer Ursula , Xiong Huajiang , Gassen Berthold , Schleicher Michael , Noegel Angelika A.
Published: August 2009

The Dictyostelium centrosome is a nucleus associated body consisting of a box-shaped core surrounded by the corona, an amorphous matrix functionally equivalent to the pericentriolar material of animal centrosomes which is responsible for the nucleation and anchoring of microtubules. Here we describe CP250 a component of the corona, an acidic coiled coil protein that is present at the centrosome throughout interphase while disappearing during prophase and reappearing at the end of late telophase. Amino acids 756-1148 of the 2110 amino acids are sufficient for centrosomal targeting and cell cycle–dependent centrosome association. Mutant cells lacking CP250 are smaller in size, growth on bacteria is delayed, chemotaxis is altered, and development is affected, which, in general, are defects observed in cytoskeletal mutants. Furthermore, loss of CP250 affected the nuclear envelope and led to reduced amounts and altered distribution of Sun-1, a conserved nuclear envelope protein that connects the centrosome to chromatin.
AP180-Mediated Trafficking of Vamp7B Limits Homotypic Fusion ofDictyosteliumContractile Vacuoles
Authors: Wen Yujia , Stavrou Irene , Bersuker Kirill , Brady Rebecca J. , De Lozanne Arturo , O'Halloran Theresa J.
Published: August 2009

Clathrin-coated vesicles play an established role in endocytosis from the plasma membrane, but they are also found on internal organelles. We examined the composition of clathrin-coated vesicles on an internal organelle responsible for osmoregulation, the Dictyostelium discoideum contractile vacuole. Clathrin puncta on contractile vacuoles contained multiple accessory proteins typical of plasma membrane–coated pits, including AP2, AP180, and epsin, but not Hip1r. To examine how these clathrin accessory proteins influenced the contractile vacuole, we generated cell lines that carried single and double gene knockouts in the same genetic background. Single or double mutants that lacked AP180 or AP2 exhibited abnormally large contractile vacuoles. The enlarged contractile vacuoles in AP180-null mutants formed because of excessive homotypic fusion among contractile vacuoles. The SNARE protein Vamp7B was mislocalized and enriched on the contractile vacuoles of AP180-null mutants. In vitro assays revealed that AP180 interacted with the cytoplasmic domain of Vamp7B. We propose that AP180 directs Vamp7B into clathrin-coated vesicles on contractile vacuoles, creating an efficient mechanism for regulating the internal distribution of fusion-competent SNARE proteins and limiting homotypic fusions among contractile vacuoles. Dictyostelium contractile vacuoles offer a valuable system to study clathrin-coated vesicles on internal organelles within eukaryotic cells.
TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples
Authors: Bandyopadhyay Sanghamitra , Mitra Ramkrishna
Published: August 2009

Motivation: Prediction of microRNA (miRNA) target mRNAs using machine learning approaches is an important area of research. However, most of the methods suffer from either high false positive or false negative rates. One reason for this is the marked deficiency of negative examples or miRNA non-target pairs. Systematic identification of non-target mRNAs is still not addressed properly, and therefore, current machine learning approaches are compelled to rely on artificially generated negative examples for training.

Results: In this article, we have identified ∼300 tissue-specific negative examples using a novel approach that involves expression profiling of both miRNAs and mRNAs, miRNA–mRNA structural interactions and seed-site conservation. The newly generated negative examples are validated with pSILAC dataset, which elucidate the fact that the identified non-targets are indeed non-targets.These high-throughput tissue-specific negative examples and a set of experimentally verified positive examples are then used to build a system called TargetMiner, a support vector machine (SVM)-based classifier. In addition to assessing the prediction accuracy on cross-validation experiments, TargetMiner has been validated with a completely independent experimental test dataset. Our method outperforms 10 existing target prediction algorithms and provides a good balance between sensitivity and specificity that is not reflected in the existing methods. We achieve a significantly higher sensitivity and specificity of 69% and 67.8% based on a pool of 90 feature set and 76.5% and 66.1% using a set of 30 selected feature set on the completely independent test dataset.

In order to establish the effectiveness of the systematically generated negative examples, the SVM is trained using a different set of negative data generated using the method in Yousef et al. A significantly higher false positive rate (70.6%) is observed when tested on the independent set, while all other factors are kept the same. Again, when an existing method (NBmiRTar) is executed with the our proposed negative data, we observe an improvement in its performance. These clearly establish the effectiveness of the proposed approach of selecting the negative examples systematically.

Availability: TargetMiner is now available as an online tool at www.isical.ac.in/∼bioinfo_miu

Contact:  sanghami@isical.ac.in; rmitra_t@isical.ac.in

Supplementary information:  Supplementary data are available at Bioinformatics online.
Treatment of Idiopathic Parkinson′s Disease with Traditional Chinese Herbal Medicine: A Randomized Placebo‐Controlled Pilot Clinical Study
Authors: Kum Wan Fung , Durairajan Siva Sundara Kumar , Bian Zhao Xiang , Man Sui Cheung , Lam Yuen Chi , Xie Li Xia , Lu Jia Hong , Wang Yan , Huang Xian Zhang , Li Min
Published: August 2009

The objective of this clinical study is to examine the effects of a Chinese herbal medicine formula (Jia Wei Liu Jun Zi Tang: JWLJZT) on motor and non‐motor symptoms, and on complications of conventional therapy in idiopathic Parkinson′s disease (PD), using an add‐on design. Fifty‐five patients with PD were randomly allocated to receive either Chinese herbal medicine or placebo for 24 weeks. Primary outcome measure was the 39‐item Parkinson′s Disease Questionnaire (PDQ‐39). Secondary outcome measures included the Unified Parkinson′s Disease Rating Scale (UPDRS), Short‐Form‐36 Health Survey (SF‐36), Geriatric Depression Scale (GDS), home diaries, and a range of category rating scales. JWLJZT resulted in a significant improvement in the UPDRS IVC when compared with placebo at 12 weeks (P = .039) and 24 weeks (P = .034). In addition, patients in the Chinese herbal medicine group also showed significant improvement in PDQ‐39 communication scores at 12 weeks (P = .024) and 24 weeks (P = .047) when compared with the placebo group. There were no significant differences between treatment and control groups for SF‐36 variables, GDS score or the mean daily “on‐off” time. One case of mild diarrhea was noted in the treatment group. The findings suggest that JWLJZT can relieve some non‐motor complications of conventional therapy and improve the communication ability in patients with PD. The results of this pilot study warrant larger multi‐center clinical studies to assess long‐term efficacy and tolerability of JWLJZT, and to elucidate the mechanisms by which it affects PD function.
Utilization of 3‐Month Yoga Program for Adults at High Risk for Type 2 Diabetes: A Pilot Study
Authors: Yang Kyeongra , Bernardo Lisa M. , Sereika Susan M. , Conroy Molly B. , Balk Judy , Burke Lora E.
Published: August 2009

Various modes of physical activity, combined with dieting, have been widely recommended to prevent or delay type 2 diabetes. Among these, yoga holds promise for reducing risk factors for type 2 diabetes by promoting weight loss, improving glucose levels and reducing blood pressure and lipid levels. This pilot study aimed to assess the feasibility of implementing a 12‐week yoga program among adults at high risk for type 2 diabetes. Twenty‐three adults (19 Whites and 4 non‐Whites) were randomly assigned to the yoga intervention group or the educational group. The yoga group participated in a 3‐month yoga intervention with sessions twice per week and the educational group received general health educational materials every 2 weeks. All participants completed questionnaires and had blood tests at baseline and at the end of 3 months. Effect sizes were reported to summarize the efficacy of the intervention. All participants assigned to the yoga intervention completed the yoga program without complication and expressed high satisfaction with the program (99.2%). Their yoga session attendance ranged from 58.3 to 100%. Compared with the education group, the yoga group experienced improvements in weight, blood pressure, insulin, triglycerides and exercise self‐efficacy indicated by small to large effect sizes. This preliminary study indicates that a yoga program would be a possible risk reduction option for adults at high risk for type 2 diabetes. In addition, yoga holds promise as an approach to reducing cardiometabolic risk factors and increasing exercise self‐efficacy for this group.
Both in‐ and out‐hospital worsening of renal function predict outcome in patients with heart failure: results from the Coordinating Study Evaluating Outcome of Advising and Counseling in Heart Failure (COACH)
Authors: Damman Kevin , Jaarsma Tiny , Voors Adriaan A. , Navis Gerjan , Hillege Hans L. , van Veldhuisen Dirk J. ,   on behalf of the COACH investigators
Published: August 2009

Aims

The effect of worsening renal function (WRF) after discharge on outcome in patients with heart failure is unknown.

Methods and results

We assessed estimated glomerular filtration rate (eGFR) and serum creatinine at admission, discharge, and 6 and 12 months after discharge, in 1023 heart failure patients. Worsening renal function was defined as an increase in serum creatinine of >26.5 µmol/L and >25%. The primary endpoint was a composite of all‐cause mortality and heart failure admissions. The mean age of patients was 71 ± 11 years, and 62% was male. Mean eGFR at admission was 55 ± 21 mL/min/1.73 m2. In‐hospital WRF occurred in 11% of patients, while 16 and 9% experienced WRF from 0 to 6, and 6 to 12 months after discharge, respectively. In multivariate landmark analysis, WRF at any point in time was associated with a higher incidence of the primary endpoint: hazard ratio (HR) 1.63 (1.10–2.40), P = 0.014 for in‐hospital WRF, HR 2.06 (1.13–3.74), P = 0.018 for WRF between 0–6 months, and HR 5.03 (2.13–11.88), P < 0.001 for WRF between 6–12 months.

Conclusion

Both in‐ and out‐hospital worsening of renal function are independently related to poor prognosis in patients with heart failure, suggesting that renal function in heart failure patients should be monitored long after discharge.
Comparison of four right ventricular systolic echocardiographic parameters to predict adverse outcomes in chronic heart failure
Authors: Damy Thibaud , Viallet Caroline , Lairez Olivier , Deswarte Guillaume , Paulino Alexandra , Maison Patrick , Vermes Emmanuelle , Gueret Pascal , Adnot Serge , Dubois‐Randé Jean‐Luc , Hittinger Luc
Published: August 2009

Aims

Heart failure (HF) has a poor prognosis. Several right ventricular (RV) echocardiographic parameters have been proposed as sensitive markers to detect patients at risk. Our objective was to compare the predictive value of four RV systolic echocardiographic parameters for outcomes in patients with HF.

Methods and results

One hundred and thirty‐six patients with stable HF and a left ventricular ejection fraction <35% were assessed for the following: (i) RV fractional area (RVFA), (ii) tricuspid annular plane systolic excursion (TAPSE), (iii) integral of the systolic wave (ISWtdi), and (iv) peak systolic velocity (PSVtdi). ISWtdi and PSVtdi were measured using tissue Doppler imaging at the tricuspid annulus. The primary endpoint was death, urgent transplantation, urgent ventricular assist device implantation, or an acute HF episode. During a mean follow‐up of 295 days, 33 patients reached the primary endpoint. The cut‐off thresholds for RVFA, TAPSE, PSVtdi, and ISWtdi defined using receiver‐operating characteristic curves were 36.8%, 13.5 mm, 9.5 cm s−1, and 1.75 cm, respectively. On Cox multivariate analysis, NYHA, log BNP, and only PSVtdi from the RV systolic parameters were found to be independent predictors of outcome.

Conclusion

PSVtdi is a strong independent predictor of outcome in HF at a threshold value of 9.5 cm s−1 and appears to be superior to other RV systolic echocardiographic parameters.
Characterization of Kafirins in Algerian Sorghum Cultivars
Authors: Mokrane Hind , Lagrain Bert , Gebruers Kurt , Courtin Christophe M. , Brijs Kristof , Proost Paul , Delcour Jan A.
Published: August 2009

The prolamins in seven Algerian Sahara sorghum cultivars of varying seed shape and color were investigated. Protein contents ranged from 12 to 16%. Prolamins were the major protein fraction. They could be separated according to degree of disulfide cross‐linking. Kafirin monomers and low molecular weight polymers could be extracted with 70% ethanol, whereas highly cross‐linked kafirins additionally needed a reducing agent to become extractable. Kafirin monomers of α‐, β‐ and γ‐type were purified and N‐terminally sequenced. For the first time, δ‐kafirin was identified at the protein level. The study clearly revealed intercultivar differences between protein levels. The joint use of SDS‐PAGE, SE‐HPLC, and RP‐HPLC allowed discriminating among cultivars based on the differences in prolamin levels and composition.
Does segregating variation in sexual or microhabitat preferences lead to non-random mating within a population of
Drosophila melanogaster
?
Authors: Foley Brad R. , Genissel Anne , Kristy Harmon L. , Nuzhdin Sergey V.
Published: August 2009

Variation in female choice for mates has implications for the maintenance of genetic variation and the evolution of male traits. Yet, estimates of population-level variation in male mating success owing to female genotype are rare. Here, we used a panel of recombinant inbred lines to estimate the strength of selection at many genetic loci in a single generation and attempt to assess differences between females with respect to the males they mated with. We performed selection assays in a complex environment to allow differences in habitat or social group preference to be expressed. We detected directional selection at loci across the genome, but are unable to provide support for differential male success because of variation in female genotype.
Henri Paul Cartan. 8 July 1904 — 13 August 2008
Authors: Serre Jean-Pierre
Published: August 2009

Henri Cartan, Professor of Mathematics in Paris, was, for many of the younger generation, the symbol of the resurgence of French mathematics after World War II. He died in 2008 at the age of 104 years.
The unmaking of an anthropologist: Wallace returns from the field, 1862–70
Authors: Vetter Jeremy
Published: August 2009

This essay follows Alfred Russel Wallace back from the field in 1862, tracing how his views on human evolution developed after his field experiences in the East Indies and how he articulated them within the social structure of British science during the 1860s. It analyses his involvement in the metropolitan scientific institutions dedicated to the study of man, the Ethnological Society of London and its breakaway counterpart, the Anthropological Society of London, which offered differing visions for a science of man and its intersection with political commitments. Using evidence from his participation in society meetings, the reception of his own anthropological papers, and the responses to the views he expressed in his field travel narrative,
The Malay Archipelago
, I show that although Wallace's involvement was initially enthusiastic, over time his views came into conflict with both groups. His involvement in established human science institutions declined, and Wallace turned towards other social locations for cultivating his knowledge of and engagement with questions involving the study of humanity.
Invasive plant integration into native plant–pollinator networks across Europe
Authors: Vilà Montserrat , Bartomeus Ignasi , Dietzsch Anke C. , Petanidou Theodora , Steffan-Dewenter Ingolf , Stout Jane C. , Tscheulin Thomas
Published: August 2009

The structure of plant–pollinator networks has been claimed to be resilient to changes in species composition due to the weak degree of dependence among mutualistic partners. However, detailed empirical investigations of the consequences of introducing an alien plant species into mutualistic networks are lacking. We present the first cross-European analysis by using a standardized protocol to assess the degree to which a particular alien plant species (i.e.
Carpobrotus
affine
acinaciformis
,
Impatiens glandulifera
,
Opuntia stricta
,
Rhododendron ponticum
and
Solanum elaeagnifolium
) becomes integrated into existing native plant–pollinator networks, and how this translates to changes in network structure.

Alien species were visited by almost half of the pollinator species present, accounting on average for 42 per cent of the visits and 24 per cent of the network interactions. Furthermore, in general, pollinators depended upon alien plants more than on native plants. However, despite the fact that invaded communities received more visits than uninvaded communities, the dominant role of alien species over natives did not translate into overall changes in network connectance, plant linkage level and nestedness. Our results imply that although supergeneralist alien plants can play a central role in the networks, the structure of the networks appears to be very permeable and robust to the introduction of invasive alien species into the network.
Does coevolution promote species richness in parasitic cuckoos?
Authors: Krüger Oliver , Sorenson Michael D. , Davies Nicholas B.
Published: August 2009

Why some lineages have diversified into larger numbers of species than others is a fundamental but still relatively poorly understood aspect of the evolutionary process. Coevolution has been recognized as a potentially important engine of speciation, but has rarely been tested in a comparative framework. We use a comparative approach based on a complete phylogeny of all living cuckoos to test whether parasite–host coevolution is associated with patterns of cuckoo species richness. There are no clear differences between parental and parasitic cuckoos in the number of species per genus. However, a cladogenesis test shows that brood parasitism is associated with both significantly higher speciation and extinction rates. Furthermore, subspecies diversification rate estimates were over twice as high in parasitic cuckoos as in parental cuckoos. Among parasitic cuckoos, there is marked variation in the severity of the detrimental effects on host fitness; chicks of some cuckoo species are raised alongside the young of the host and others are more virulent, with the cuckoo chick ejecting or killing the eggs/young of the host. We show that cuckoos with a more virulent parasitic strategy have more recognized subspecies. In addition, cuckoo species with more recognized subspecies have more hosts. These results hold after controlling for confounding geographical effects such as range size and isolation in archipelagos. Although the power of our analyses is limited by the fact that brood parasitism evolved independently only three times in cuckoos, our results suggest that coevolutionary arms races with hosts have contributed to higher speciation and extinction rates in parasitic cuckoos.
An Rrf2-Type Transcriptional Regulator Is Required for Expression of psaAB Genes in the Cyanobacterium Synechocystis sp. PCC 6803
Authors: Midorikawa Takafumi , Matsumoto Koji , Narikawa Rei , Ikeuchi Masahiko
Published: August 2009

Photosynthetic organisms must regulate photosystem stoichiometry (photosystem I-to-photosystem II ratio) under various light conditions. Transcriptional regulation of the psaAB genes is a critical process for this photoacclimation in cyanobacteria. In the course of our screening of transcriptional regulators in the cyanobacterium Synechocystis sp. PCC 6803, we found that chlorophyll accumulation was impaired in an Rrf2-type regulator Slr0846 mutant. DNA microarray and primer extension analyses showed that the expression of psaAB genes was markedly decreased in the mutant. Consistently, the mutant exhibited lower photosystem I-to-photosystem II ratio under normal light conditions, suggestive of decreased accumulation of the photosystem I reaction center. Gel-shift assay confirmed that the Slr0846 protein bound to a far upstream promoter region of psaAB. These phenotypes of the mutant varied substantially with light conditions. These results suggest that Slr0846 is a novel transcriptional regulator for optimal expression of psaAB.
Gene Content and Virtual Gene Order of Barley Chromosome 1H
Authors: Mayer Klaus F.X. , Taudien Stefan , Martis Mihaela , Šimková Hana , Suchánková Pavla , Gundlach Heidrun , Wicker Thomas , Petzold Andreas , Felder Marius , Steuernagel Burkhard , Scholz Uwe , Graner Andreas , Platzer Matthias , Doležel Jaroslav , Stein Nils
Published: August 2009

Chromosome 1H (approximately 622 Mb) of barley (Hordeum vulgare) was isolated by flow sorting and shotgun sequenced by GSFLX pyrosequencing to 1.3-fold coverage. Fluorescence in situ hybridization and stringent sequence comparison against genetically mapped barley genes revealed 95% purity of the sorted chromosome 1H fraction. Sequence comparison against the reference genomes of rice (Oryza sativa) and sorghum (Sorghum bicolor) and against wheat (Triticum aestivum) and barley expressed sequence tag datasets led to the estimation of 4,600 to 5,800 genes on chromosome 1H, and 38,000 to 48,000 genes in the whole barley genome. Conserved gene content between chromosome 1H and known syntenic regions of rice chromosomes 5 and 10, and of sorghum chromosomes 1 and 9 was detected on a per gene resolution. Informed by the syntenic relationships between the two reference genomes, genic barley sequence reads were integrated and ordered to deduce a virtual gene map of barley chromosome 1H. We demonstrate that synteny-based analysis of low-pass shotgun sequenced flow-sorted Triticeae chromosomes can deliver linearly ordered high-resolution gene inventories of individual chromosomes, which complement extensive Triticeae expressed sequence tag datasets. Thus, integration of genomic, transcriptomic, and synteny-derived information represents a major step toward developing reference sequences of chromosomes and complete genomes of the most important plant tribe for mankind.
Complexation and Toxicity of Copper in Higher Plants. II. Different Mechanisms for Copper versus Cadmium Detoxification in the Copper-Sensitive Cadmium/Zinc Hyperaccumulator Thlaspi caerulescens (Ganges Ecotype)
Authors: Mijovilovich Ana , Leitenmaier Barbara , Meyer-Klaucke Wolfram , Kroneck Peter M.H. , Götz Birgit , Küpper Hendrik
Published: August 2009

The cadmium/zinc hyperaccumulator Thlaspi caerulescens is sensitive toward copper (Cu) toxicity, which is a problem for phytoremediation of soils with mixed contamination. Cu levels in T. caerulescens grown with 10 μ  m Cu2+ remained in the nonaccumulator range (<50 ppm), and most individuals were as sensitive toward Cu as the related nonaccumulator Thlaspi fendleri. Obviously, hyperaccumulation and metal resistance are highly metal specific. Cu-induced inhibition of photosynthesis followed the “sun reaction” type of damage, with inhibition of the photosystem II reaction center charge separation and the water-splitting complex. A few individuals of T. caerulescens were more Cu resistant. Compared with Cu-sensitive individuals, they recovered faster from inhibition, at least partially by enhanced repair of chlorophyll-protein complexes but not by exclusion, since the content of Cu in their shoots was increased by about 25%. Extended x-ray absorption fine structure (EXAFS) measurements on frozen-hydrated leaf samples revealed that a large proportion of Cu in T. caerulescens is bound by sulfur ligands. This is in contrast to the known binding environment of cadmium and zinc in the same species, which is dominated by oxygen ligands. Clearly, hyperaccumulators detoxify hyperaccumulated metals differently compared with nonaccumulated metals. Furthermore, strong features in the Cu-EXAFS spectra ascribed to metal-metal contributions were found, in particular in the Cu-resistant specimens. Some of these features may be due to Cu binding to metallothioneins, but a larger proportion seems to result from biomineralization, most likely Cu(II) oxalate and Cu(II) oxides. Additional contributions in the EXAFS spectra indicate complexation of Cu(II) by the nonproteogenic amino acid nicotianamine, which has a very high affinity for Cu(II) as further characterized here.
Contributions of the effector gene hopQ1‐1 to differences in host range between Pseudomonas syringae pv. phaseolicola and P. syringae pv. tabaci
Authors: FERRANTE PATRIZIA , CLARKE CHRISTOPHER R. , CAVANAUGH KERI A. , MICHELMORE RICHARD W. , BUONAURIO ROBERTO , VINATZER BORIS A.
Published: August 2009

To study the role of type III‐secreted effectors in the host adaptation of the tobacco (Nicotiana sp.) pathogen Pseudomonas syringae pv. tabaci, a selection of seven strains was first characterized by multilocus sequence typing (MLST) to determine their phylogenetic affinity. MLST revealed that all strains represented a tight phylogenetic group and that the most closely related strain with a completely sequenced genome was the bean (Phaseolus vulgaris) pathogen P. syringae pv. phaseolicola 1448A. Using primers designed to 21 P. syringae pv. phaseolicola 1448A effector genes, it was determined that P. syringae pv. phaseolicola 1448A shared at least 10 effectors with all tested P. syringae pv. tabaci strains. Six of the 11 effectors that failed to amplify from P. syringae pv. tabaci strains were individually expressed in one P. syringae pv. tabaci strain. Although five effectors had no effect on phenotype, growth in planta and disease severity of the transgenic P. syringae pv. tabaci expressing hopQ1‐1Pph1448A were significantly increased in bean, but reduced in tobacco. We conclude that hopQ1‐1 has been retained in P. syringae pv. phaseolicola 1448A, as this effector suppresses immunity in bean, whereas hopQ1‐1 is missing from P. syringae pv. tabaci strains because it triggers defences in Nicotiana spp. This provides evidence that fine‐tuning effector repertoires during host adaptation lead to a concomitant reduction in virulence in non‐host species.
Incidence and severity of marine borer attack at different depths at Mtongwe Jetty Pontoon Mombasa, Kenya
Authors: Sirmah P. K. , Mburu F. G. , Muisu F. N. , Wahungu G. M. , Waweru C. W.
Published: August 2009

The activity of marine borers was investigated at Mtongwe Jetty Pontoon, Mombasa, Kilindini harbour using untreated panels of Pinus patula (Schlecht) submerged to different depths. Twenty test panels replicated over 7 months were each strung in three ladder‐like frames using nylon twine and suspended vertically, in such a way that the top most panels were 25 cm below the water surface at low and high tide. Monthly observations were made between January and July for the vertical incidence and extent of marine borer attack following the technique of Bobat (1995). Marine borers were collected from test panels, identified and counted. In addition, the percentage weight loss for panels at different depths was determined at the end of 7 months. Teredo fulleri (Clapp) was dominant on panels near water surface while Martesia striata (Linne) and Lyrodus pedicellatus (Quatrefages) were predominant at the bottom. The results showed that attack began within the first month of exposure and was severest by the seventh month. The vertical incidence and extent of attack decreased with increasing depth of panel exposure and was negatively correlated with depth. This is attributed to changes in hydrographic conditions.
Herbaceous phytomass and nutrient concentrations of four grass species in Sudanian savanna woodland subjected to recurrent early fire
Authors: Savadogo Patrice , Tigabu Mulualem , Sawadogo Louis , Odén Per Christer
Published: August 2009

Fire is an integral ecological factor in African savanna ecosystems, but its effects on savanna productivity are highly variable and less understood. We conducted a field experiment to quantify changes in herbaceous phytomass and nutrient composition in a Sudanian savanna woodland subjected to annual early fire from 1993 to 2004. Fire effects were also assessed on two perennial and two annual grass species during the following growing season. Early fire significantly reduced above‐ground phytomass of the studied species (P = 0.03), their crude protein (P = 0.022), neutral detergent insoluble crude protein (P = 0.016) and concentrations of Ca, Fe and Mn (P < 0.05). Perennial grasses had higher above‐ground phytomass but lower total crude protein and fat than annual grasses. Nonstructural carbohydrates tended to be higher for annuals, while fibre and lignin contents were high for perennials. Except Na and Fe, the concentration of mineral elements varied between species. Fire did not affect measures of digestibility and metabolizable energy, but its effect differed significantly among species. In conclusion, the results illustrate that long‐term frequent fire will counterbalance the short‐term increase in soil fertility and plant nutrient concentrations claimed to be accrued from single or less frequent fire.
Clinical trial: the impact of cyclooxygenase inhibitors on gastrointestinal recovery after major surgery – a randomized double blind controlled trial of celecoxib or diclofenac vs. placebo
Authors: WATTCHOW D. A. , DE FONTGALLAND D. , BAMPTON P. A. , LEACH P. L. , MCLAUGHLIN K. , COSTA M.
Published: August 2009

Background  Ileus occurs after abdominal surgery and may be severe. Inhibition of prostaglandin release reduces post‐operative ileus in a rat model.

Aim  To determine whether prostaglandin inhibition by cyclooxygenase inhibitors, celecoxib or diclofenac, could enhance gastrointestinal recovery and reduce post‐operative ileus in humans.

Methods  Two hundred and ten patients undergoing elective major abdominal surgery were randomized to receive twice daily placebo (n = 67), celecoxib (100 mg, n = 74) or diclofenac (50 mg, n = 69), preoperatively and continuing for up to 7 days. Primary outcomes were hallmarks of gut recovery. Secondary outcomes were paralytic ileus, pain and complications.

Results  There was no clinically significant difference between the groups for restoration of bowel function. There was a significant reduction in paralytic ileus in the celecoxib‐treated group (n = 1, 1%) compared with diclofenac (n = 7, 10%) and placebo (n = 9, 13%); P = 0.025, RR 0.20, CI 0.01–0.77. Pain scores, analgesia, transfusion requirements and adverse event rates were similar between study groups.

Conclusions  Perioperative low dose celecoxib, but not diclofenac, markedly reduced the development of paralytic ileus following major abdominal surgery, but did not accelerate early recovery of bowel function. This was independent of narcotic use and had no increase in post‐operative complications.
A SNP/microsatellite genetic linkage map of the Atlantic cod (Gadus morhua)
Authors: Moen T. , Delghandi M. , Wesmajervi M. S. , Westgaard J.‐I. , Fjalestad K. T.
Published: August 2009

A first genetic linkage map of the Atlantic cod (Gadus morhua) was produced, based on segregation data from 12 full‐sib families of Norwegian origin. The map contained 174 single nucleotide polymorphism markers and 33 microsatellites, distributed on 25 linkage groups and had a length of 1225 cM. A significant difference in recombination rates between sexes was found, the average ratio of female:male recombination rates being 1.78 ± 1.62 (SD).
Marrow repopulation in mice treated with busulphan or isopropyl methane sulphonate and bone marrow
Authors: Massa G. , Wyllie J. P. , Pratt A. M. , Molineux G. , Schofield R.
Published: August 2009

By using karyotypic analysis of female mice treated with (a) busulphan or (b) isopropyl methane sulphonate (IMS), and injected with male bone marrow the donor contribution to both total marrow cellularity and spleen colony forming cells (CFU‐S) was assessed for up to 6 months after transplant. In the mice treated with busulphan the marrow cells yielded metaphases of which between 40% and 83% were of donor type. Between 60% and 97% of metaphases in spleen colonies formed in irradiated mice were of donor type during the 24‐week study period. In contrast, mice prepared for the transplant with IMS showed no cells of donor type at any time after transplant, neither did they possess CFU‐S of donor type. We were therefore led to conclude that the donor cells made no contribution to long‐term engraftment in mice prepared with IMS, whilst in those prepared with busulphan they were the predominantly active haemopoietic cells.

These results are consistent with a model of haemopoiesis in which the most primitive cells reside in a ‘niche’where they are resistant to the effects of IMS but susceptible to the action of busulphan. Busulphan may vacate some niches to allow engraftment by transplanted marrow, whilst IMS yields no unoccupied niches for grafted cells to occupy, and cannot therefore lead to a stable chimaerism.
Erythrokinetics and iron status in heterozygous β thalassaemia, and the effect of interaction with α thalassaemia
Authors: Pippard M. J. , Wainscoat J. S.
Published: August 2009

Ferrokinetic studies, α globin gene mapping, and assessment of iron status have been carried out in 16 healthy subjects with heterozygous β thalassaemia. Six subjects had coinherited α thalassaemia and had more balanced α/β globin chain synthesis ratios than the remaining 10 subjects with uncomplicated heterozygous β thalassaemia. The overall efficiency of erythropoiesis was significantly reduced in the latter group (mean 76 ± 17 (SD)% of normal), but was indistinguishable from normal in subjects with coexistent α thalassaemia. Red cell survival was unimpaired in both groups, indicating that the defect was one of mild ineffective erythropoiesis rather than peripheral haemolysis. Values for total plasma iron turnover were normal or only slightly increased. This suggests a lack of any additional stimulus to erythropoiesis, which might normally be expected to compensate easily for the mild degree of anaemia. Uncomplicated heterozygous β thalassaemia produces an extremely mild disorder of erythropoiesis, which is dependent on the inbalance between α and β globin chain synthesis, and is not associated with a risk of serious iron overload.
Lactoferrin uptake and iron processing into macrophages: a study in familial haemochromatosis
Authors: Moguilevsky Nicole , Masson Pierre‐L. , Courtoy Pierre‐J.
Published: August 2009

Various properties of lactoferrin from neutrophils of normal individuals and patients with familial haemochromatosis were compared. No difference was found with respect to (1) the lactoferrin content of neutrophils, (2) the molecular weight and isoelectric point of the protein, (3) the dissociation of its complex with iron at acidic pH, (4) its binding to isolated monocytes, and (5) its uptake by the mouse reticulo‐endothelial system. Macrophages from patients and controls were also found to be similar in their ability to bind and ingest lactoferrin and to process the iron provided by the protein. Therefore a defect in the interaction of lactoferrin with the reticulo‐endothelial system, related either to the protein itself or to the cells, seems unlikely. A comparison of the lactoferrin‐ and the transferrin‐mediated iron processing by monocytes is finally presented.
Interleukin‐4 distinctively modifies responses of germinal centre‐like and activated B‐cell‐like diffuse large B‐cell lymphomas to immuno‐chemotherapy
Authors: Sarosiek Kristopher A. , Nechushtan Hovav , Lu Xiaoqing , Rosenblatt Joseph D. , Lossos Izidore S.
Published: August 2009

Diffuse large B‐cell lymphomas (DLBCLs) can be classified into two subtypes: germinal‐centre B‐cell (GCB)‐like and Activated B‐cell (ABC)‐like tumours, which are associated with longer or shorter patient overall survival, respectively. In our previous studies, we have shown that, although DLBCL tumours of GCB‐like and ABC‐like subtypes express similar levels of IL4 mRNA, they exhibit distinct patterns of IL‐4‐induced intracellular signalling and different expression of IL‐4 target genes. We hypothesized that these differences may contribute to the different clinical behaviour and outcome of DLBCL subtypes. Herein, we demonstrated that IL‐4 increased the sensitivity of GCB‐like DLBCL to doxorubicin‐induced apoptosis and complement‐dependent rituximab cell killing. In contrast, IL‐4 protected ABC‐like DLBCL from the cytotoxic effects of doxorubicin and rituximab. The distinct effects of IL‐4 on doxorubicin sensitivity in GCB‐like and ABC‐like DLBCL cells may be partially attributed to the contrasting effects of the cytokine on Bcl‐2 and Bad protein levels in the DLBCL subtypes. These findings suggest that the different effects of IL‐4 on chemotherapy and immunotherapy‐induced cytotoxicity of GCB‐ and ABC‐like DLBCL could contribute to the different clinical outcomes exhibited by patients with these two subtypes of DLBCL.
On the propagation characteristics of tunnel surface‐waves for seismic prediction
Authors: Jetschny Stefan , Bohlen Thomas , De Nil Denise
Published: August 2009

To increase the safety and efficiency of tunnel constructions, online seismic exploration ahead of a tunnel has become a valuable tool. One recent successful forward looking approach is based on the excitation and registration of tunnel surface‐waves. For further development and for finding optimal acquisition geometries it is important to study the propagation characteristics of tunnel surface‐waves. 3D seismic finite difference modelling and analytic solutions of the wave equation in cylindrical coordinates reveal that at higher frequencies, i.e., if the tunnel‐diameter is significantly larger than the wavelength of surface‐waves, these surface‐waves can be regarded as Rayleigh‐waves confined to the tunnel wall and following helical paths along the tunnel axis. For lower frequencies, i.e., when the tunnel surface‐wavelength approaches the tunnel‐diameter, the propagation characteristics of these surface‐waves are similar to S‐waves. We define the surface‐wave wavelength‐to‐tunnel diameter ratio w to be a gauge for separating Rayleigh‐ from S‐wave excitation. For w > 1.2 tunnel surface‐waves behave like S‐waves, i.e. their velocity approaches the S‐wave velocity and the particle motion is linear and perpendicular to the ray direction. For w < 0.6 they behave like Rayleigh‐waves, i.e., their velocity approaches the Rayleigh‐wave velocity and they exhibit elliptical particle motion. For 0.6 < w < 1.2 a mixture of both types is observed. Field data from the Gotthard Base Tunnel (Switzerland) show both types of tunnel surface‐waves and S‐waves propagating along the tunnel.
Characterization of Pasteurized Fluid Milk Shelf‐life Attributes
Authors: Fromm H.I. , Boor K.J.
Published: August 2009

ABSTRACT: Pasteurized fluid milk samples were systematically collected from 3 commercial dairy plants. Samples were evaluated for microbial, chemical, and sensory attributes throughout shelf life. In general, product shelf lives were limited by multiplication of heat‐resistant psychrotrophic organisms that caused undesirable flavors in milk. The predominant microorganisms identified were Gram‐positive rods including Paenibacillus, Bacillus, and Microbacterium. Principal component analysis of sensory data collected using quantitative descriptive analysis showed that attributes related to milk flavor defects explained the largest amount of variance. These findings highlight the need to develop specific strategies for excluding bacterial contaminants from milk to further extend product shelf lives.
Malolactic Activity of Lactic Acid Bacteria during Sauerkraut Fermentation
Authors: Johanningsmeier S.D. , Fleming H.P. , Breidt R
Published: August 2009

ABSTRACT: The frequency of lactic acid bacteria (LAB) involved in sauerkraut fermentation with (MDC+) or without (MDC‐) the ability to decarboxylate malic acid was determined. The MDC+ phenotype was found in > 99% of homofermentative LAB isolated from commercial fermentations. In contrast, heterofermentative LAB isolates from 0.25, 3, 7, and 10 d had only 53%, 54%, 15%, and 11% MDC+ phenotype, respectively, indicating that more than 1 strain or species was involved. The malolactic reaction was demonstrated in cabbage juice with known strains of Leuconostoc mesenteroides, raising the question of desirability of such activity in cultures selected for the controlled fermentation of cabbage.
Pulsed Electric Field Processing of Beer: Microbial, Sensory, and Quality Analyses
Authors: Evrendilek G.A. , Li S. , Dantzer W.R. , Zhang Q.H.
Published: August 2009

ABSTRACT: In this study, pulsed electric field (PEF) treatment of beer, effectiveness of PEF treatment on microbial inactivation, effects of PEF treatment on sensory properties, and detection of electrode material migration were explored. Beer samples were treated by PEF for the inactivation of natural flora and inoculated cultures of Saccaromyces uvarum, Rhodotorula rubra, Lactobacillus plantarum, Pediococcus damnosus, and Bacillus subtilis. Inactivation induced by the PEF treatment was 0.5, 4.1, 4.3, 4.7, 5.8, and 4.8 log10 colony‐forming units/mL in the above microorganisms, respectively (P < 0.05). There was a significant increase in the amount of Cr, Zn, Fe, and Mn ions in the beer samples after PEF treatment (P < 0.05) leading to a statistically significant degradation in flavor and mouth feel. Further studies are needed to optimize electrode materials and PEF treatment to minimize or eliminate this degradation.
Morphological Changes in Autolytic Wine Yeast during Aging in Two Model Systems
Authors: Martinez‐Rodriguez A.J. , Gonzalez R. , Carrascosa A.V.
Published: August 2009

ABSTRACT: Morphological changes produced in Saccharomyces cerevisiae IFI473 and 2 autolytic mutants derived from it (M1 and M2 mutants) were studied during yeast aging in 2 model systems (rich medium and model wine). Different conditions affecting autolysis, including temperature, culture media, nitrogen starvation, or phenyl‐methylsulfonylfluoride addition, were analyzed. In rich medium, morphological changes mainly consisted in variation of cell size, presence of autophagic bodies inside the cytoplasm, detachment of the cytoplasm from the cell wall, spore formation, and loss of cytoplasmic material. Morphological changes were greater for mutant M2 than for the rest of the strains studied. In the wine medium, a decrease in cell size was the most relevant feature and the morphological changes observed were similar for all strains. Results obtained show morphological differences between autophagy and autolysis suggesting that yeast cells with accelerated autolysis could also present accelerated autophagy.
Video Analysis to Monitor Rigor Mortis in Cultured Gulf of Mexico Sturgeon (Ancipenser oxyrynchus desotoi)
Authors: Oliveira A.C.M. , O'Keefe S.F. , Balaban M.O.
Published: August 2009

ABSTRACT: A subjective method was used to evaluate rigor mortis in 50 Gulf sturgeons distributed into 5 weight categories. Duration of rigor increased with fish weight. Onset of rigor ranged from 12 to 24 h. A new method to determine onset and resolution of rigor in cultured Gulf sturgeon was studied using analysis of video images. Insight on the progress of rigor through the fish body is provided. In 10 different time intervals from 0 to 67 h after death, fish were temporarily secured to the edge of a table by the head, with the body free to droop, and video images were taken. Rulers in the background allowed quantification of body position. The extent of deflection of various points along the body length was analyzed. New parameters based on maximum deflection and integral deflections were developed. Rigor in Gulf sturgeon took an average of 24 h to onset and 67 h to resolve and was not a uniform process: the tail reached maximum rigor later than the middle of the fish.
Effect of Ultra‐high Temperature Treatment on the Enzymatic Cross‐linking of Micellar Casein and Sodium Caseinate by Transglutaminase
Authors: Bönisch M.P. , Lauber S. , Kulozik U.
Published: August 2009

ABSTRACT: It was found that ultra‐high temperature (UHT) treatment of sodium caseinate and native whey protein‐depleted micellar casein drastically increases the protein polymerization effect of an enzymatic treatment by microbial transglutaminase (TG). As a result the concentration of the isopeptide ε‐(γ‐glutamyl)lysine was increased significantly in UHT‐treated micellar casein solutions after TG incubation compared with the unheated casein solution. Sodium caseinate was more susceptible to the cross‐linking reaction as compared with the native casein micelles. The results demonstrate that the protein structure significantly affects the TG cross‐linking reaction. The effect of an UHT treatment was considered to be related to a better TG accessibility due to a more open casein micelle structure and to the inactivation of a TG inhibitor substance. The results demonstrate that an unidentified component in the natural milk serum inhibits the TG reaction. The thermal inactivation of a TG inhibitor is the dominant effect explaining the improved cross‐linking of UHT‐treated casein micelles as well as sodium caseinate.