bluuebunny/crossref_metadata_2025 huggingface dataset:
Causes and consequences of marine mammal population declines in southwest Alaska: a food-web perspective
Authors: Estes J.A. , Doak D.F. , Springer A.M. , Williams T.M.
Published: May 2009

Populations of sea otters, seals and sea lions have collapsed across much of southwest Alaska over the past several decades. The sea otter decline set off a trophic cascade in which the coastal marine ecosystem underwent a phase shift from kelp forests to deforested sea urchin barrens. This interaction in turn affected the distribution, abundance and productivity of numerous other species. Ecological consequences of the pinniped declines are largely unknown. Increased predation by transient (marine mammal-eating) killer whales probably caused the sea otter declines and may have caused the pinniped declines as well. Springer
et al
. proposed that killer whales, which purportedly fed extensively on great whales, expanded their diets to include a higher percentage of sea otters and pinnipeds following a sharp reduction in great whale numbers from post World War II industrial whaling. Critics of this hypothesis claim that great whales are not now and probably never were an important nutritional resource for killer whales. We used demographic/energetic analyses to evaluate whether or not a predator–prey system involving killer whales and the smaller marine mammals would be sustainable without some nutritional contribution from the great whales. Our results indicate that while such a system is possible, it could only exist under a narrow range of extreme conditions and is therefore highly unlikely.
The Epstein–Barr virus lytic cycle activator Zta interacts with methylated ZRE in the promoter of host target gene egr1
Authors: Heather James , Flower Kirsty , Isaac Samine , Sinclair Alison J.
Published: May 2009

Activation of the host geneegr1is essential for the lytic replication of Epstein–Barr virus (EBV).egr1is activated by Zta (BZLF1, ZEBRA). Zta interacts directly with DNA through a series of closely related Zta-response elements (ZREs). Here we dissect the mechanism used by Zta to interact with theegr1promoter and identify a weak interaction withegr1ZRE that is dependent on the distal part ofegr1ZRE. Furthermore, we demonstrate that the ability of Zta to interact withegr1ZRE is enhanced at least tenfold by methylation. The ability of Zta to transactivate a reporter construct driven by theegr1promoter can be enhanced by methylation. As the ability of Zta to interact with a methylated ZRE in the EBV genome correlates with its ability to activate the expression of the endogenous viral geneBRLF1, this suggests that Zta may also have the capability to overturn epigenetic control ofegr1.
Open reading frame structure analysis as a novel genotyping tool for hepatitis E virus and the subsequent discovery of an inter-genotype recombinant
Authors: Fan Jun
Published: May 2009

Accurate viral genotyping is important. Here I investigate genotypes in hepatitis E virus (HEV) and find that the open reading frame (ORF) structure (the lengths of three ORFs and the overlapping relationships among the ORFs) can be a good criterion for genotyping HEV. An inter-genotype recombinant (GenBank accession no. DQ450072) was revealed by analysing the ORF structure and confirmed by phylogenetic analyses. This discovery of the inter-genotype recombinant indicates that genotyping in HEV should be based on full-length sequences. The Mexican strain which is currently classified as a genotype 2 strain also exhibited the mosaic sequence pattern, although without statistical support.
Epstein–Barr virus BDLF2–BMRF2 complex affects cellular morphology
Authors: Loesing Jens-Bernhard , Di Fiore Stefano , Ritter Klaus , Fischer Rainer , Kleines Michael
Published: May 2009

Herpesvirus glycoproteins often form specific heterodimers that can fulfil functions that cannot be carried out by either of the partners acting alone. This study showed that interactions between the Epstein–Barr virus (EBV) multi-spanning transmembrane envelope protein BMRF2 and type II membrane protein BDLF2 influence the way in which these proteins are trafficked in the cell, and hence the subcellular compartment in which they accumulate. When expressed transiently in mammalian cells, BDLF2 accumulated in the endoplasmic reticulum (ER), whereas BMRF2 accumulated in the ER and Golgi apparatus. However, when the two proteins were co-expressed, BDLF2 was transported with BMRF2 to the Golgi apparatus and from there to the plasma membrane, where the proteins co-localized extensively. The distribution of the two proteins at the plasma membrane was reproducibly associated with dramatic changes in cellular morphology, including the formation of enlarged membrane protrusions and cellular processes whose adhesion extremities were organized by the actin cytoskeleton. A dominant-active form of the small GTPase RhoA was epistatic to this morphological phenotype, suggesting that RhoA is a central component of the signalling pathway that reorganizes the cytoskeleton in response to BDLF2–BMRF2. It was concluded that EBV produces a glycoprotein heterodimer that induces changes in cellular morphology through reorganization of the actin cytoskeleton and may facilitate virion spread between cells.
Effective inhibition of infectious bursal disease virus replication by recombinant avian adeno-associated virus-delivered microRNAs
Authors: Wang Yongjuan , Sun Huaichang , Shen Pengpeng , Zhang Xinyu , Xia Xiaoli
Published: May 2009

RNA interference (RNAi) is a novel antiviral strategy against a variety of virus infections. Infectious bursal disease virus (IBDV) causes an economically important disease in young chickens. This study demonstrated efficient inhibition of IBDV replication by recombinant avian adeno-associated virus (rAAAV)-delivered anti-VP1 and anti-VP2 microRNAs (miRNAs). In the viral vector-transduced cells, sequence-specific miRNA expression was detected by poly(A)-tailed RT-PCR. Reporter assays using a pVP2-EGFP vector showed significant and long-lasting inhibition of VP2–EGFP expression in cells transduced with anti-VP2 miRNA-expressing rAAAV-RFPmiVP2E, but not with the control miRNA-expressing rAAAV-RFPmiVP2con or anti-VP1 miRNA-expressing rAAAV-RFPmiVP1. Semi-quantitative RT-PCR and/or virus titration assays showed a significant inhibitory effect on homologous IBDV replication in cells transduced with rAAAV-RFPmiVP1 or rAAAV-RFPmiVP2E. For two heterologous IBDV isolates, transduction with rAAAV-RFPmiVP1 led to slightly weaker but similar inhibitory effects, whereas transduction with rAAAV-RFPmiVP2E resulted in significantly weaker and different inhibitory effects. These results suggest that rAAAV could act as an efficient vector for miRNA delivery into avian cells and that VP1 is the more suitable target for interfering with IBDV replication using RNAi technology.
The role of RNAi and microRNAs in animal virus replication and antiviral immunity
Authors: Umbach Jennifer L. , Cullen Bryan R.
Published: May 2009

The closely related microRNA (miRNA) and RNAi pathways have emerged as important regulators of virus–host cell interactions. Although both pathways are relatively well conserved all the way from plants to invertebrates to mammals, there are important differences between these systems. A more complete understanding of these differences will be required to fully appreciate the relationship between these diverse host organisms and the various viruses that infect them. Insights derived from this research will facilitate a better understanding of viral pathogenesis and the host innate immune response to viral infection.
Initiating chromosome replication in E. coli: it makes sense to recycle
Authors: Leonard Alan C. , Grimwade Julia E.
Published: May 2009

Initiating new rounds of Escherichia coli chromosome replication requires DnaA-ATP to unwind the replication origin, oriC, and load DNA helicase. In this issue of Genes & Development, Fujimitsu and colleagues (pp. 1221–1233) demonstrate that two chromosomal sites, termed DARS (DnaA-reactivating sequences), recycle inactive DnaA-ADP into DnaA-ATP. Fujimitsu and colleagues propose these sites are necessary to attain the DnaA-ATP threshold during normal growth and are important regulators of initiation timing in bacteria.
Histone demethylase JMJD3 contributes to epigenetic control of INK4a/ARF by oncogenic RAS
Authors: Barradas Marta , Anderton Emma , Acosta Juan Carlos , Li SiDe , Banito Ana , Rodriguez-Niedenführ Marc , Maertens Goedele , Banck Michaela , Zhou Ming-Ming , Walsh Martin J. , Peters Gordon , Gil Jesús
Published: May 2009

The INK4a/ARF tumor suppressor locus, a key executor of cellular senescence, is regulated by members of the Polycomb group (PcG) of transcriptional repressors. Here we show that signaling from oncogenic RAS overrides PcG-mediated repression of INK4a by activating the H3K27 demethylase JMJD3 and down-regulating the methyltransferase EZH2. In human fibroblasts, JMJD3 activates INK4a, but not ARF, and causes p16INK4a-dependent arrest. In mouse embryo fibroblasts, Jmjd3 activates both Ink4a and Arf and elicits a p53-dependent arrest, echoing the effects of RAS in this system. Our findings directly implicate JMJD3 in the regulation of INK4a/ARF during oncogene-induced senescence and suggest that JMJD3 has the capacity to act as a tumor suppressor.
The PRC1 Polycomb group complex interacts with PLZF/RARA to mediate leukemic transformation
Authors: Boukarabila Hanane , Saurin Andrew J. , Batsché Eric , Mossadegh Noushine , van Lohuizen Maarten , Otte Arie P. , Pradel Jacques , Muchardt Christian , Sieweke Michael , Duprez Estelle
Published: May 2009

Ectopic repression of retinoic acid (RA) receptor target genes by PML/RARA and PLZF/RARA fusion proteins through aberrant recruitment of nuclear corepressor complexes drives cellular transformation and acute promyelocytic leukemia (APL) development. In the case of PML/RARA, this repression can be reversed through treatment with all-trans RA (ATRA), leading to leukemic remission. However, PLZF/RARA ectopic repression is insensitive to ATRA, resulting in persistence of the leukemic diseased state after treatment, a phenomenon that is still poorly understood. Here we show that, like PML/RARA, PLZF/RARA expression leads to recruitment of the Polycomb-repressive complex 2 (PRC2) Polycomb group (PcG) complex to RA response elements. However, unlike PML/RARA, PLZF/RARA directly interacts with the PcG protein Bmi-1 and forms a stable component of the PRC1 PcG complex, resulting in PLZF/RARA-dependent ectopic recruitment of PRC1 to RA response elements. Upon treatment with ATRA, ectopic recruitment of PRC2 by either PML/RARA or PLZF/RARA is lost, whereas PRC1 recruited by PLZF/RARA remains, resulting in persistent RA-insensitive gene repression. We further show that Bmi-1 is essential for the PLZF/RARA cellular transformation property and implicates a central role for PRC1 in PLZF/RARA-mediated myeloid leukemic development.
Translational reprogramming following UVB irradiation is mediated by DNA-PKcs and allows selective recruitment to the polysomes of mRNAs encoding DNA repair enzymes
Authors: Powley Ian R. , Kondrashov Alexander , Young Lucy A. , Dobbyn Helen C. , Hill Kirsti , Cannell Ian G. , Stoneley Mark , Kong Yi-Wen , Cotes Julia A. , Smith Graeme C.M. , Wek Ron , Hayes Christopher , Gant Timothy W. , Spriggs Keith A. , Bushell Martin , Willis Anne E.
Published: May 2009

UVB-induced lesions in mammalian cellular DNA can, through the process of mutagenesis, lead to carcinogenesis. However, eukaryotic cells have evolved complex mechanisms of genomic surveillance and DNA damage repair to counteract the effects of UVB radiation. We show that following UVB DNA damage, there is an overall inhibition of protein synthesis and translational reprogramming. This reprogramming allows selective synthesis of DDR proteins, such as ERCC1, ERCC5, DDB1, XPA, XPD, and OGG1 and relies on upstream ORFs in the 5′ untranslated region of these mRNAs. Experiments with DNA-PKcs-deficient cell lines and a specific DNA-PKcs inhibitor demonstrate that both the general repression of mRNA translation and the preferential translation of specific mRNAs depend on DNA-PKcs activity, and therefore our data establish a link between a key DNA damage signaling component and protein synthesis.
Quantitative proteomics using formalin‐fixed paraffin‐embedded tissues of oral squamous cell carcinoma
Authors: Negishi Ayako , Masuda Mari , Ono Masaya , Honda Kazufumi , Shitashige Miki , Satow Reiko , Sakuma Tomohiro , Kuwabara Hideya , Nakanishi Yukihiro , Kanai Yae , Omura Ken , Hirohashi Setsuo , Yamada Tesshi
Published: May 2009

Clinical proteomics using a large archive of formalin‐fixed paraffin‐embedded (FFPE) tissue blocks has long been a challenge. Recently, a method for extracting proteins from FFPE tissue in the form of tryptic peptides was developed. Here we report the application of a highly sensitive mass spectrometry (MS)‐based quantitative proteome method to a small amount of samples obtained by laser microdissection from FFPE tissues. Cancerous and adjacent normal epithelia were microdissected from FFPE tissue blocks of 10 squamous cell carcinomas of the tongue. Proteins were extracted in the form of tryptic peptides and analyzed by 2‐dimensional image‐converted analysis of liquid chromatography and mass spectrometry (2DICAL), a label‐free quantitative proteomics method developed in our laboratory. From a total of 25 018 peaks we selected 72 mass peaks whose expression differed significantly between cancer and normal tissues (P < 0.001, paired t‐test). The expression of transglutaminase 3 (TGM3) was significantly down‐regulated in cancer and correlated with loss of histological differentiation. Hypermethylation of TGM3 gene CpG islands was observed in 12 oral squamous cell carcinoma (OSCC) cell lines with reduced TGM3 expression. These results suggest that epigenetic silencing of TGM3 plays certain roles in the process of oral carcinogenesis. The method for quantitative proteomic analysis of FFPE tissue described here offers new opportunities to identify disease‐specific biomarkers and therapeutic targets using widely available archival samples with corresponding detailed pathological and clinical records. (Cancer Sci 2009; 100: 1605–1611)
[13C]‐pantoprazole breath test to predict CYP2C19 phenotype and efficacy of a proton pump inhibitor, lansoprazole
Authors: FURUTA T. , KODAIRA C. , NISHINO M. , YAMADE M. , SUGIMOTO M. , IKUMA M. , HISHIDA A. , WATANABE H. , UMEMURA K.
Published: May 2009

Background  13CO2 is produced on metabolism of 13C‐labelled‐pantoprazole ([13C]‐pantoprazole) by CYP2C19.

Aim  To investigate whether the [13C]‐pantoprazole breath test can predict CYP2C19 status and efficacy of proton pump inhibitors (PPIs) in Japanese.

Methods  We classified 110 healthy volunteers as rapid metabolizers (RM), intermediate metabolizers (IM) or poor metabolizers (PM) of CYP2C19 by genotyping. Breath samples were collected at 10‐min intervals for 60 min after dosing with 100 mg [13C]‐pantoprazole. Changes in the carbon isotope ratios (13CO2/12CO2) in carbon dioxide in breath samples were measured and expressed as a delta‐over‐baseline (DOB) ratio (‰). Of the 110 subjects, twenty‐two randomly selected subjects underwent intragastric pH monitoring on day 7 of dosing with 30 mg of lansoprazole.

Results  The DOB values of RMs were the highest and those of PMs the lowest of the three groups. Statistically significant differences were observed in the area‐under‐the‐curve (AUC)20–60 min of DOB among the three groups. The mean 24‐h intragastric pHs attained by lansoprazole 30 mg for 7 days were inversely correlated with the AUC20–60 min of DOB.

Conclusions  [13C]‐pantoprazole breath test can easily estimate the individual activity of CYP2C19 and predict the efficacy of a PPI (i.e. lansoprazole). This test would be useful for individualized medicine with a PPI.
Neonatal hyperthyrotropinemia: population characteristics, diagnosis, management and outcome after cessation of therapy
Authors: Zung Amnon , Tenenbaum‐Rakover Yardena , Barkan Shiri , Hanukoglu Aaron , Hershkovitz Eli , Pinhas‐Hamiel Orit , Bistritzer Tzvy , Zadik Zvi
Published: May 2009

Introduction  Neonatal hyperthyrotropinaemia (HT), defined by elevated TSH and normal T4, is either transient or persistent. The eventual outcome of neonatal HT is unpredictable and the management of HT patients is controversial. We assessed perinatal parameters and diagnostic measures that may distinguish between transient and persistent HT, compared with congenital hypothyroidism (CH). We also aimed to recommend optimal treatment in these forms of thyroid impairment.

Design and patients  A multi‐centre, retrospective study was conducted in six paediatric endocrinology units. Forty‐three HT patients and 83 CH patients were included in the study.

Measurements  We evaluated differences in birth weight (BW), gestational age (GA), modes of diagnosis, screening and confirmatory T4 and TSH levels, thyroid imaging results and optimal thyroxine doses between HT and CH and between the two forms of HT.

Results  Newborns with HT had lower BW and GA than those with CH. Transient (n = 18) and persistent HT (n = 25) patients were indistinguishable by most parameters, but those with persistent HT had a higher prevalence of abnormal thyroid imaging (69%vs 8%; P = 0·005). During treatment, 79% and 55% of transient and persistent HT patients respectively experienced elevated levels of free T4. Although most HT patients were reevaluated after 2·5 years, six transient HT patients stopped therapy and showed full recovery within the first year of life.

Conclusions  We recommend obtaining thyroid imaging to distinguish between the two forms of HT. Adherence to recommended doses of thyroxine and probably early cessation of therapy in transient HT can prevent iatrogenic hyperthyroidism in these patients.
Randomized study comparing endoscopic ultrasound‐guided Trucut biopsy and fine needle aspiration with high suction
Authors: Gerke H. , Rizk M. K. , Vanderheyden A. D. , Jensen C. S.
Published: May 2009

H. Gerke, M. K. Rizk, A. D. Vanderheyden and C. S. Jensen Randomized study comparing endoscopic ultrasound‐guided Trucut biopsy and fine needle aspiration with high suction

Objectives:  Endoscopic ultrasound (EUS)‐guided Trucut biopsy (TCB) enables acquisition of tissue cores for histological assessment. Because of the rigid needle and the spring mechanism, tissue acquisition can be difficult from regions that require sharp angulation of the echoendoscope. Fine needle aspiration with high suction (FNAHS) has been proposed as a method to obtain histological tissue cores while affording the flexibility to obtain specimens even with extreme endoscope angulation. The objective was to compare prospectively these two methods in their ability to obtain specimens for histological assessment and in their diagnostic accuracy, including cytological diagnosis when achieved.

Methods:  Eighty lesions in 77 patients were amenable to transoesophageal, transgastric or transrectal biopsy and were randomized to TCB (n = 44) or FNAHS (n = 36). Each specimen was assessed for adequacy (scoring system where a score of 0 was no material, 1–2 was considered cytological, and 3–5 was considered histological). Follow‐up information was obtained to establish a gold standard final diagnosis.

Results:  The median histological scores for FNAHS and TCB were 2 and 5, respectively. Histological cores were obtained in 95.3% of TCB, as opposed to 27.8% in the FNAHS group (P < 0.0001). Although the diagnostic accuracy for TCB was greater than that for FNAHS (88.3% and 77.8%, respectively), this was not statistically significant (P = 0.24).

Conclusion:  If histological information is required, TCB is superior to FNAHS. The difference in diagnostic accuracy did not reach statistical significance due to low numbers and the fact that FNAHS often enabled a cytological diagnosis.
Subsistence fishing in two communities of the Lacandon Forest, Mexico
Authors: INDA‐DIAZ E. , RODILES‐HERNÁNDEZ R. , NARANJO E. J. , MENDOZA‐CARRANZA M.
Published: May 2009

Abstract  Subsistence fishing was surveyed in the communities of Nueva Esperanza and Loma Bonita of the Lacandon Forest in the Usumacinta River Basin of Chiapas, Mexico from March to August 2005. Thirty fish species, four turtles and two crustaceans were harvested. The most prevalent species in terms of biomass extracted were the pantano cichlid, Herichthys pearsei (Hubbs), grass carp, Ctenopharyngodon idella (Valenciennes), northern checkmark cichlid, Vieja intermedia (Günther), bigmouth sleeper, Gobiomorus dormitor Lacepède, machaca, Brycon guatemalensis Regan, and blue catfish, Ictalurus furcatus (Lesueur). Ten fishing gears were employed in four habitat types. Fishing patterns, fishing gears employed, species harvested, biomass extracted and catch rates differed between localities. The uniqueness of local fisheries should be considered in further studies and management policies for conservation of fish populations.
Can the Nomura lens be free of spherical aberration?
Authors: HAWKES P.W.
Published: May 2009

Nomura has recently claimed that a combination of magnetic lenses can be found that is free of spherical aberration. Doubt is cast on this claim.
Image analysis and automatic classification of transformed foci
Authors: URANI C. , STEFANINI F.M. , BUSSINELLI L. , MELCHIORETTO P. , CROSTA G.F.
Published: May 2009

Carcinogenesis is a multi‐step process involving genetic alterations and non‐genotoxic mechanisms. The in vitro cell transformation assay allows the monitoring of the neoplastic phenotype by foci formation in suitable cells (e.g. C3H10T1/2 mouse embryo fibroblasts) showing aberrant morphology of massive build‐up, polar and multi‐layered densely stained cells. The classification of transformed foci in C3H cells relies on light microscopy scoring by a trained human expert based on standard rules. This procedure is time‐consuming and prone, in some cases, to subjectivity, thereby leading to possible over‐ or under‐estimation of the carcinogenic potential of tested compounds. Herewith we describe the in vitro neoplastic transformation induced by B[a]P and CdCl2, and the development of a foci classifier based on image analysis and statistical classification. The image analysis system, which relies on ‘spectrum enhancement’, is quantitative and extracts descriptors of foci texture and structure. The statistical classification method is based on the Random Forest algorithm. We obtained a classifier trained by using expert's supervision with a 20% classification error. The proposed method could serve as a basis to automate the in vitro cell transformation assay.
Real‐time data acquisition incorporating high‐speed software correlator for single‐molecule spectroscopy
Authors: YANG L.‐L. , LEE H.‐Y. , WANG M.‐K. , LIN X.‐Y. , HSU K.‐H. , CHANG Y.‐R. , FANN W. , WHITE J.D.
Published: May 2009

Single‐molecule spectroscopy and detection are powerful techniques for the study of single fluorescent particles and their interaction with their environment. We present a low‐cost system for simultaneous real‐time acquisition, storage of inter‐photon arrival times and the calculation and display of the fluorescence time trace, autocorrelation function and distribution of delays histogram for single‐molecule experiments. From a hardware perspective, in addition to a multi‐core computer, only a standard low‐cost counting board is required as processing is software‐based. Software is written in a parallel programming environment with time crucial operations coded in ANSI‐C. Crucial to system performance is a simple and efficient real‐time autocorrelation algorithm (acf) optimized for the count rates (approximately 104 cps) encountered in single‐molecule experiments. The algorithm's time complexity is independent of temporal resolution, which is maintained at all time delays. The system and algorithm's performance was validated by duplicating the signal from the photon detector and sending it to both the ordinary counter board and a commercial correlator simultaneously. The data acquisition system's robustness under typical single‐molecule experimental conditions was tested by observing the diffusion of Rhodamine 6G molecules in deionized water.
Comparison of applying particulate demineralized bone matrix (DBM), putty DBM and open flap debridement in periodontal horizontal bone defects. A 12‐month longitudinal, multi‐center, triple‐blind, split‐mouth, randomized, controlled clinical study. Part 1 – clinical and radiographic evaluation
Authors: KAYA Y. , YALIM M. , BAHÇECITAPAR M. , BALOŞ K.
Published: May 2009

Summary  Putty form graft materials may have additional favourable effects when compared with particulate ones in periodontal bone defects. The purpose of this study was to assess clinical and also radiographic changes following application of (i) putty form demineralized bone matrix (DBM), (ii) particulate form DBM and (iii) open flap debridement (control), using modified curtain suturing technique in the treatment of interproximal suprabony (horizontal) defects. Twenty‐five chronic periodontitis patients with 125 sites (radiologically ≥4 mm horizontal bone defect) were selected to participate in this triple‐blind, split mouth, randomized, controlled clinical trial. Putty and particulate form DBM grafts were placed at experimental sites. Clinical measurements included probing depth (PD), relative attachment level (RAL), gingival recession and bone probing depth (BPD) were made at baseline and repeated 12 months after the operations. Standardized digital radiographs were also taken to measure radiographic bone level (RBL) at baseline and 12 months later to be compared in a software. Probing depth reductions and RAL gains were significantly improved in all treatment groups (P < 0·001). No significant differences in soft tissue parameters were found among three groups (P > 0·05). Bone probing depth measurements indicated comparable significant bone gain in graft applied groups (P < 0·01) and a significant bone resorption in open flap debridement group (P < 0·01). Radiographic evaluation did not show any significant bone gain or resorption in all treatment groups (P > 0·05). The results of this study indicate that either putty or particulate DBM demonstrates similar enhancements in soft and hard tissue parameters. Applying putty or particulate form DBM results with slight bone formation when compared with open flap debridement in horizontal bone defects at 1‐year post‐operative examination according to BPD measurements.
Pharmacokinetics of voriconazole after single dose intravenous and oral administration to alpacas
Authors: CHAN H. M. , DURAN S. H. , WALZ P. H. , RAVIS W. R.
Published: May 2009

Voriconazole is a new antifungal drug that has shown effectiveness in treating serious fungal infections and has the potential for being used in large animal veterinary medicine. The objective of this study was to determine the plasma concentrations and pharmacokinetic parameters of voriconazole after single‐dose intravenous (i.v.) and oral administration to alpacas. Four alpacas were treated with single 4 mg/kg i.v. and oral administrations of voriconazole. Plasma voriconazole concentrations were measured by a high‐performance liquid chromatography method. The terminal half‐lives following i.v. and oral administration were 8.01 ± 2.88 and 8.75 ± 4.31 h, respectively; observed maximum plasma concentrations were 5.93 ± 1.13 and 1.70 ± 2.71 μg/mL, respectively; and areas under the plasma concentration vs. time curve were 38.5 ± 11.1 and 9.48 ± 6.98 mg·h/L, respectively. The apparent systemic oral availability was low with a value of 22.7 ± 9.5%. The drug plasma concentrations remained above 0.1 μg/mL for at least 24 h after single i.v. dosing. The i.v. administration of 4 mg/kg/day voriconazole may be a safe and appropriate option for antifungal treatment of alpacas. Due to the low extent of absorption in alpacas, oral voriconazole doses of 20.4 to 33.9 mg/kg/day may be needed.
Genetic differentiation and reproductive isolation of a naturally occurring floral homeotic mutant within a wild‐type population of Capsella bursa‐pastoris (Brassicaceae)
Authors: HAMEISTER STEFFEN , NEUFFER BARBARA , BLEEKER WALTER
Published: May 2009

Apart from the common floral architecture in Brassicaceae, variation in flower morphology occurs in several genera within the family and is considered to affect speciation processes. We analysed genetic differentiation and flowering time variation of two floral variants of Capsella bursa‐pastoris, the Spe variant and the wild‐type, which occur sympatrically in a vineyard in southwest Germany. The Spe variant is characterized by an additional whorl of stamens instead of petals and was formerly classified as an independent taxon ‘Capsella apetala’ Opiz. Amplified fragment length polymorphism and allozyme analysis revealed a substantial genetic differentiation of the two floral variants and a higher genetic variation within the wild‐type subpopulation compared with the Spe subpopulation. The low genetic variation in the mutant provided evidence of a recent local origin or recent introduction. Flowering time analysis indicated that, within the analysed population, the Spe variant flowers significantly later than the wild‐type (P < 0.001). We conclude that the evolution and persistence of Spe within a wild‐type population is facilitated by high selfing rates and been enhanced by a shift in flowering phenology. Hence, our data provide substantial evidence that the Spe phenotype has established itself as an isolated entity within a wild‐type population and may thus serve as a model for the analysis of the evolutionary significance of homeotic mutants in wild populations.
Dbf2 is essential for cytokinesis and correct mitotic spindle formation in Candida albicans
Authors: González‐Novo Alberto , Labrador Leticia , Pablo‐Hernando M. Evangelina , Correa‐Bordes Jaime , Sánchez Miguel , Jiménez Javier , De Aldana Carlos R. Vázquez
Published: May 2009

We have characterized the DBF2 gene, encoding a protein kinase of the NDR family in Candida albicans, and demonstrate that this gene is essential for cell viability. Conditional mutants were constructed by using the MET3 promoter to analyse the phenotype of cells lacking this kinase. The absence of Dbf2 resulted in cells arrested as large‐budded pairs that failed to contract the actomyosin ring, a function similar to that described for its Saccharomyces cerevisiae orthologue. In addition to its role in cytokinesis, Dbf2 regulates mitotic spindle organization and nuclear segregation as Dbf2‐depleted cells have abnormal microtubules and severe defects in nuclear migration to the daughter cell, which results in a cell cycle block during mitosis. Taken together, these results imply that Dbf2 performs several functions during exit from mitosis and cytokinesis. Consistent with a role in spindle organization, the protein localizes to the mitotic spindle during anaphase, and it interacts physically with tubulin, as indicated by immunoprecipitation experiments. Finally, DBF2 depletion also resulted in impaired true hyphal growth.
The crenarchaeal DNA damage‐inducible transcription factor B paralogue TFB3 is a general activator of transcription
Authors: Paytubi Sonia , White Malcolm F.
Published: May 2009

Transcription initiation factor B (TFB) is conserved in eukaryotes and archaea and has an essential role in the recruitment of RNA polymerase to the promoter and the initiation of transcription. The genome of Sulfolobus solfataricus and related crenarchaea contain three paralogues of the tfb gene. Two of them (tfb1 and tfb2) encode full‐length TFB proteins. The third (tfb3) is significantly shorter than the other two, possessing an N‐terminal Zn ribbon domain but lacking the B‐finger and DNA binding domains. In S. solfataricus and Sulfolobus acidocaldarius, tfb3 is one of the most highly upregulated transcripts following exposure to UV irradiation. We demonstrate that S. solfataricus TFB3 binds to the RpoK subunit of RNA polymerase, an interaction dependent on the Zn ribbon motif of TFB3. TFB3 can also interact with the ternary complex of TBP and TFB1 bound to a DNA promoter. TFB3 stimulates transcription in vitro from several promoters in the presence of TFB1 and TBP. These observations are consistent with a model whereby TFB3 activates general transcription in trans, via an interaction with RNA polymerase in the pre‐initiation complex. This could provide a mechanism for the modulation of transcription initiation in response to environmental stresses, such as DNA damage.
Borrelia burgdorferi bb0426 encodes a 2′‐deoxyribosyltransferase that plays a central role in purine salvage
Authors: Lawrence Kevin A. , Jewett Mollie W. , Rosa Patricia A. , Gherardini Frank C.
Published: May 2009

Borrelia burgdorferi is an obligate parasite with a limited genome that severely narrows its metabolic and biosynthetic capabilities. Thus survival of this spirochaete in an arthropod vector and mammalian host requires that it can scavenge amino acids, fatty acids and nucleosides from a blood meal or various host tissues. Additionally, the utilization of ribonucleotides for DNA synthesis is further complicated by the lack of a ribonucleotide reductase for the conversion of nucleoside‐5′‐diphosphates to deoxynucleosides‐5′‐diphosphates. The data presented here demonstrate that B. burgdorferi must rely on host‐derived sources of purine bases, deoxypurines and deoxypyrimidines for the synthesis of DNA. However, if deoxyguanosine (dGuo) is limited in host tissue, the enzymatic activities of a 2′‐deoxyribosyltransferase (DRTase, encoded by bb0426), IMP dehydrogenase (GuaB) and GMP synthase (GuaA) catalyse the multistep conversion of hypoxanthine (Hyp) to dGMP for DNA synthesis. This pathway provides additional biochemical flexibility for B. burgdorferi when it colonizes and infects different host tissues.
BNR – a LINE family from Beta vulgaris– contains a RRM domain in open reading frame 1 and defines a L1 sub‐clade present in diverse plant genomes
Authors: Heitkam Tony , Schmidt Thomas
Published: May 2009

We characterized a novel type of plant non‐LTR retrotransposons, identified as the BNR family, in sugar beet (Beta vulgaris) genomes. Although their ORF2 sequences were similar to those of previously analysed LINEs (long interspersed nuclear elements) of the L1 clade, their ORF1 sequences differ strongly from those of most plant LINEs. Two novel domains were identified, containing a conserved secondary motif, known as the RNA recognition motif (RRM). ORF1 lacks the zinc finger motif that is typical of plant LINEs, but has an RRM that is likely to have a RNA‐binding function. BNR LINEs are highly diverse, and were characterized by gel‐blot and fluorescent in situ hybridization, showing a widespread occurrence and clustering along chromosome arms. Insertion of BNR1 into a well‐described satellite repeat was detected in two cultivars only, indicating recent activity. Database searches revealed the existence of LINE families possessing an ORF1 sequence similar to that of BNR in the genomes of higher plants such as poplar, lotus and soybean. Comparing their reverse transcriptase regions with those of other retrotransposons, these LINEs were assigned to the L1 clade, but form a distinct group, providing evidence of a major separation of L1 elements in plants. This indicates a common origin of BNR‐like LINEs, suggesting that these elements form a sub‐clade designated as the BNR sub‐clade.
A rapid wound signal activates the systemic synthesis of bioactive jasmonates in Arabidopsis
Authors: Koo Abraham J.K. , Gao Xiaoli , Daniel Jones A. , Howe Gregg A.
Published: May 2009

Jasmonic acid (JA) and its biologically active derivatives (bioactive JAs) perform a critical role in regulating plant responses to wound stress. The perception of bioactive JAs by the F‐box protein COI1 triggers the SCFCOI1/ubiquitin‐dependent degradation of JASMONATE ZIM‐DOMAIN (JAZ) proteins that repress the expression of JA‐response genes. JA is required for many wound‐inducible systemic defense responses, but little is known about the role of the hormone in long‐distance signal relay between damaged and undamaged leaves. Here, we show that the wounding of Arabidopsis thaliana leaves results in the rapid (<5 min) accumulation of jasmonoyl‐l‐isoleucine (JA‐Ile), the bioactive form of JA, in leaves distal to the wound site. The rapid systemic increase in JA‐Ile preceded the onset of early transcriptional responses, and was associated with JAZ degradation. Wound‐induced systemic production of JA‐Ile required the JA biosynthetic enzyme 12‐oxo‐phytodienoic acid (OPDA) reductase 3 (OPR3) in undamaged responding leaves, but not in wounded leaves, and was largely dependent on the JA‐conjugating enzyme JAR1. Interestingly, the wound‐induced synthesis of JA/JA‐Ile in systemic leaves was correlated with a rapid decline in OPDA levels. These results are consistent with a model in which a rapidly transmitted wound signal triggers the systemic synthesis of JA, which, upon conversion to JA‐Ile, activates the expression of early response genes by the SCFCOI1/JAZ pathway.
Transplantation of high‐risk donor organs: a survey of US solid organ transplant center practices as reported by transplant infectious diseases physicians
Authors: Ison Michael G. , Stosor Valentina
Published: May 2009

Abstract:  Public Health Service (PHS) guidelines developed in 1994 provide guidance to minimize the risk of HIV transmission and to monitor recipients following the transplantation of “high‐risk” organs. There are no data on current practices or opinions of these policies by transplant infectious diseases (TID) physicians. An electronic survey was sent to all US solid organ transplatation centers with identified TID expertise as self‐reported to the American Society of Transplantation and Infectious Diseases Society of America. A total of 108 surveys were sent in December 2007 and 32 responses were received (30%). Thirty‐three percent of centers obtain only verbal, 52% verbal and written, and 14% do not obtain any special consent from recipients of organs from high‐risk donors (ROHRD). Post‐solid organ transplantation serologies for HIV, hepatitis B (HBV), and hepatitis C virus (HCV) are obtained at 40% of centers in ROHRD only, 20% in all recipients, and not performed in 40%; post‐solid organ transplantation nucleic acid testing (NAT) testing is carried out in 36–45% of centers in ROHRD, 11% in all recipients, and not performed in approximately 50% of centers. Only 22.7% of respondents believed current guidelines accurately represent what they consider to be high‐risk donors. There is significant variability in the acceptance and management of ROHRD in the US. Most TID experts do not feel that the current PHS guidelines accurately define high‐risk donors.
Performance of Agricultural Systems under Contrasting Growing Season Conditions in South‐western Quebec
Authors: Almaraz J. J. , Mabood F. , Zhou X. , Strachan I. , Ma B. , Smith D. L.
Published: May 2009

Climate change will alter temperature and rainfall patterns over North American agricultural regions and there will be a need to adapt crop production systems to the altered conditions. A set of field experiments were conducted in south‐western Quebec, Canada, with soybean (Glycine max L.), corn (Zea mays L.), sorghum (Sorghum bicolor L.) × sudangrass (Sorghum sudanense Piper) hybrid and switchgrass (Panicum virgatum L.) under two tillage and three nitrogen fertility regimes, to study their performance in three successive growing seasons (2001–2003), two of them with unusually warm and dry conditions. The annual crops were established in two tillage systems: conventional and no‐till (NT). All crops except soybean were fertilized with three levels of nitrogen: corn – 0, 90 and 180 kg N ha−1, sorghum‐sudangrass – 0, 75 and 150 kg N ha−1, switchgrass – 0, 30 and 60 kg N ha−1. The 2001 and 2002 seasons were hotter and drier than the 2003 season, which was the most favourable for crop growth. The capacity of the crops to yield in dry seasons was as follow: switchgrass > sorghum‐sudangrass > corn > soybean. The corn and sorghum‐sudangrass responses to nitrogen fertilizer were low in 2001 due to the combined effect of dry growing season and coarse soil texture. Soybean did not perform well under NT. Corn yielded better at the highest nitrogen fertilizer rate under NT when the early season was warmer than the normal. Our results show that switchgrass and sorghum‐sudangrass could be an option in south‐western Quebec if the frequency of hot and dry seasons increase in the future, because of climate change.
Cryotop Vitrification of Buffalo (Bubalus Bubalis) In Vitro Matured Oocytes: Effects of Cryoprotectant Concentrations and Warming Procedures
Authors: Attanasio L , Boccia L , Vajta G , Kuwayama M , Campanile G , Zicarelli L , Neglia G , Gasparrini B
Published: May 2009

Contents

The aim of the work was to evaluate the in vitro developmental competence of in vitro‐matured buffalo oocytes after Cryotop vitrification (CTV) and in vitro fertilization (IVF). To optimize parameters, two cryoprotectant (CP) concentrations and two warming–dilution procedures were applied. Oocytes were vitrified in 16.5% ethylene glycol (EG), 16.5% dimethylsulphoxide (DMSO) and 0.5 m sucrose in Groups A and C, and in higher CP concentrations (20% EG, 20% DMSO and 0.5 m sucrose) in Groups B and D. Warming was performed in 1.25 m sucrose for 1 min, then in 0.62, 0.42 and 0.31 m sucrose, 30 s each (Groups A and B), or in 0.25 m sucrose for 1 min and in 0.15 m sucrose for 5 min (Groups C and D). After warming, the oocytes were fertilized and cultured in vitro. Survival rate post‐warming was lower in Group D (83.6%) than in Groups A and B (92.4 and 92.8%, respectively), while intermediate values were found in Group C (85.7%). Survival rates at 24 h decreased in Groups C and D (52.0% and 50%, respectively) and remained high in Groups A and B (84.0% and 85.6%, respectively), thus indicating that the dilution of CP after warming is critical for buffalo oocyte cryopreservation. Similar differences were also observed in cleavage rates (42.7%, 55.3%, 28.4% and 36.3% for Groups A, B, C and D, respectively) whereas no differences in blastocyst rates were found among groups (6.4%, 7.8%, 5.9% and 6.9% for Groups A, B, C and D, respectively). Blastocyst production after IVF of vitrified oocytes proves the feasibility of CTV in buffalo species.
Prevention of hepatocellular carcinoma in nonviral‐related liver diseases
Authors: Fan Jian‐Gao , Farrell Geoffrey C ,   the Asia‐Pacific Working Party for Prevention of Hepatocellular Carcinoma
Published: May 2009

Although chronic infection with hepatitis B virus and/or hepatitis C virus are the most important risk factors for hepatocellular carcinoma (HCC) worldwide, other causes of cirrhosis can also lead to HCC. Given the high prevalence of alcoholism and the worldwide obesity epidemic, the relevant importance of nonviral liver disease‐related HCC is expected to increase in the future. Some evidence supports mechanistic interactions between host or environmental factors and chronic viral hepatitis in the development of HCC. For example, food‐ and water‐borne carcinogens have contributed to unusually high rates of HCC in parts of China and sub‐Saharan Africa. With some of these conditions, appropriate public health measures to reduce the population's exposure to known etiologic agents, or early therapeutic intervention for ‘at‐risk’ individuals before development of cirrhosis (e.g. hereditary hemochromatosis) can prevent HCC. Community‐based programs to discourage and deal with excessive alcohol intake, to promote tobacco smoking awareness, to avoid exposure to aflatoxin and other food toxins, and measures to reduce the pandemic of obesity and diabetes are vital for effective interruption of the rising tide of HCC from nonviral liver disease.
Coagulation dynamics and platelet functions in obstructive jaundiced patients
Authors: Çakır Tebessüm , Cingi Asım , Yeğen Cumhur
Published: May 2009

Background:  All of the body systems are affected by increased levels of bilirubin. The aim of this study is to investigate the function of platelets and clotting dynamics in patients with obstructive jaundice.

Methods:  Liver function tests, serum CRP, PT, PTT and hemogram were measured in 23 patients with obstructive jaundice. Thromboelastography (TEG) was done for the evaluation of coagulation dynamics, while platelet function assay (PFA 100) was used to evaluate platelet functions. Blood samples were obtained at two occasions, before the drainage and 3 weeks after the relief of the obstruction.

Results:  Hypercoagulation was detected in 80% of patients. Maximum strength, elasticity, coagulation indices of the clot were correlated with increased concentrations of direct bilirubin. Although maximum strength of coagulum usually represents increased activity of platelet function, membrane closure times with PFA 100 were found to be prolonged in 30% of patients, reduced values were determined in 17% of patients. No demonstrable effect on coagulation parameters and platelet function were detected after drainage procedures regardless of modality.

Conclusions:  Even though there is a general assumption about the increased bleeding tendency in obstructive jaundiced patients, we could not demonstrate reduced clotting activity by measuring with either PFA or TEG. On the contrary we observed tendency for hypercoagulation independent of increased prothrombin times. The most probable cause of this effect is the increased activity of fibrin polymers on platelet membrane.
Revision of the genusChalcasthenesArrow (Coleoptera: Scarabaeidae: Dynastinae: Oryctoderini) from the Solomon Islands
Authors: Jameson Mary Liz , Ratcliffe Brett C
Published: May 2009

The genusChalcasthenesArrow (Dynastinae: Oryctoderini), a scarab beetle genus endemic to the Solomon Islands, is reviewed. Based on examination of type specimens, the genusStrehliaFrey (Rutelinae: Rutelini: Parastasiina) is a new junior synonym ofChalcasthenes. The historical classification of these genera (either in the subfamily Dynastinae or Rutelinae) and character‐based criteria for assigning the taxa to the Dynastinae are provided. We discuss character states that support the monophyly of members of the genusChalcasthenes,comment on the distribution and biogeography of species in the genus and provide a key to species. The genus includes four species:Chalcasthenes divinusEndrödi,Chalcasthenes pulcherArrow,Chalcasthenes squamigerusFreynew combinationandChalcasthenes styracocerosJameson and Ratcliffe n. sp. Species hypotheses are corroborated based on evidence from Pleistocene geological reconstructions of the Solomon Islands, geographic variation of bird species in the region and development in scarab beetles.