bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and x-ray crystal structures of high-potency nonsteroidal glucocorticoid agonists exploiting a novel binding site on the receptor
Authors: Biggadike Keith , Bledsoe Randy K. , Coe Diane M. , Cooper Tony W. J. , House David , Iannone Marie A. , Macdonald Simon J. F. , Madauss Kevin P. , McLay Iain M. , Shipley Tracy J. , Taylor Simon J. , Tran Thuy B. , Uings Iain J. , Weller Victoria , Williams Shawn P.
Published: October 2009

Crystallography and computer modeling have been used to exploit a previously unexplored channel in the glucocorticoid receptor (GR). Highly potent, nonsteroidal indazole amides showing excellent complementarity to the channel were designed with the assistance of the computational technique AlleGrow. The accuracy of the design process was demonstrated through crystallographic structural determination of the GR ligand-binding domain–agonist complex of the D-prolinamide derivative
11
. The utility of the channel was further exemplified through the design of a potent phenylindazole in which structural motifs, seen to interact with the traditional GR ligand pocket, were abandoned and replaced by interactions within the new channel. Occupation of the channel was confirmed with a second GR crystal structure of this truncated D-alaninamide derivative
13
. Compound
11
displays properties compatible with development as an intranasal solution formulation, whereas oral bioavailability has been demonstrated with a related truncated exemplar
14
. Data with the pyrrolidinone amide
12
demonstrate the potential for further elaboration within the “meta” channel to deliver compounds with selectivity for the desired transrepressive activity of glucocorticoids. The discovery of these interactions with this important receptor offers significant opportunities for the design of novel GR modulators.
Multistart simulated annealing refinement of the crystal structure of the 70S ribosome
Authors: Korostelev Andrei , Laurberg Martin , Noller Harry F.
Published: October 2009

A macromolecular X-ray crystal structure is usually represented as a single static model with a single set of temperature factors representing a simple approximation of motion and disorder of the structure. Multiconformer representations of small proteins have been shown to better describe anisotropic motion and disorder and improve the quality of their electron density maps. Here, we apply multistart simulated annealing crystallographic refinement to a 70S ribosome-RF1 translation termination complex that was recently solved at 3.2 Å resolution. The analysis improves the interpretability of the electron density map of this 2.5-MDa ribonucleoprotein complex and provides insights into its structural dynamics. We also used multistart refinement and conventional Fourier difference maps to address a recent study in which cross-crystal averaging between two crystal forms of the 70S ribosome was used to evaluate reported differences between two ribosome crystal structures solved at 2.8 and 3.7 Å resolution. Our analysis suggests that results obtained from cross-crystal averaging are inherently biased toward the higher-resolution dataset.
Glycans on influenza hemagglutinin affect receptor binding and immune response
Authors: Wang Cheng-Chi , Chen Juine-Ruey , Tseng Yung-Chieh , Hsu Che-Hsiung , Hung Yu-Fu , Chen Shih-Wei , Chen Chin-Mei , Khoo Kay-Hooi , Cheng Ting-Jen , Cheng Yih-Shyun E. , Jan Jia-Tsrong , Wu Chung-Yi , Ma Che , Wong Chi-Huey
Published: October 2009

Recent cases of avian influenza H5N1 and the swine-origin 2009 H1N1 have caused a great concern that a global disaster like the 1918 influenza pandemic may occur again. Viral transmission begins with a critical interaction between hemagglutinin (HA) glycoprotein, which is on the viral coat of influenza, and sialic acid (SA) containing glycans, which are on the host cell surface. To elucidate the role of HA glycosylation in this important interaction, various defined HA glycoforms were prepared, and their binding affinity and specificity were studied by using a synthetic SA microarray. Truncation of the N-glycan structures on HA increased SA binding affinities while decreasing specificity toward disparate SA ligands. The contribution of each monosaccharide and sulfate group within SA ligand structures to HA binding energy was quantitatively dissected. It was found that the sulfate group adds nearly 100-fold (2.04 kcal/mol) in binding energy to fully glycosylated HA, and so does the biantennary glycan to the monoglycosylated HA glycoform. Antibodies raised against HA protein bearing only a single N-linked GlcNAc at each glycosylation site showed better binding affinity and neutralization activity against influenza subtypes than the fully glycosylated HAs elicited. Thus, removal of structurally nonessential glycans on viral surface glycoproteins may be a very effective and general approach for vaccine design against influenza and other human viruses.
Mouse neurexin-1α deletion causes correlated electrophysiological and behavioral changes consistent with cognitive impairments
Authors: Etherton Mark R. , Blaiss Cory A. , Powell Craig M. , Südhof Thomas C.
Published: October 2009

Deletions in the neurexin-1α gene were identified in large-scale unbiased screens for copy-number variations in patients with autism or schizophrenia. To explore the underlying biology, we studied the electrophysiological and behavioral phenotype of mice lacking neurexin-1α. Hippocampal slice physiology uncovered a defect in excitatory synaptic strength in neurexin-1α deficient mice, as revealed by a decrease in miniature excitatory postsynaptic current (EPSC) frequency and in the input-output relation of evoked postsynaptic potentials. This defect was specific for excitatory synaptic transmission, because no change in inhibitory synaptic transmission was observed in the hippocampus. Behavioral studies revealed that, compared with littermate control mice, neurexin-1α deficient mice displayed a decrease in prepulse inhibition, an increase in grooming behaviors, an impairment in nest-building activity, and an improvement in motor learning. However, neurexin-1α deficient mice did not exhibit any obvious changes in social behaviors or in spatial learning. Together, these data indicate that the neurexin-1α deficiency induces a discrete neural phenotype whose extent correlates, at least in part, with impairments observed in human patients.
In vitro reconstitution of ER-stress induced ATF6 transport in COPII vesicles
Authors: Schindler Adam J. , Schekman Randy
Published: October 2009

The transcription factor ATF6 is held as a membrane precursor in the endoplasmic reticulum (ER), and is transported and proteolytically processed in the Golgi apparatus under conditions of unfolded protein response stress. We show that during stress, ATF6 forms an interaction with COPII, the protein complex required for vesicular traffic of cargo proteins from the ER. Using an in vitro budding reaction that recapitulates the ER-stress induced transport of ATF6, we show that no cytoplasmic proteins other than COPII are necessary for transport. ATF6 is retained in the ER by association with the chaperone BiP (GRP78). In the in vitro reaction, the ATF6-BiP complex disassembles when membranes are treated with reducing agent and ATP. A hybrid protein with the ATF6 cytoplasmic domain replaced by a constitutive sorting signal (Sec22b SNARE) retains stress-responsive transport in vivo and in vitro. These results suggest that unfolded proteins or an ER luminal −SH reactive bond controls BiP-ATF6 stability and access of ATF6 to the COPII budding machinery.
Psychological mindedness and therapist attributes
Authors: Daw Becky , Joseph Stephen
Published: October 2009

Background to study: Psychological Mindedness (PM) involves an interest in and ability to extract and make sense of psychological information (thoughts, feelings and behaviours) from a situation. The nature of the psychotherapeutic role and training demands therapists think about motives, distortions and inner experiences of others. Aims: This study empirically examined the association between PM and adaptive therapist attributes, clinician empathy, self understanding and the therapeutic relationship in practitioners. Method: Forty eight therapists responded to a postal questionnaire. Results: Statistically significant correlations were found between adaptive therapist attributes; empathy, the therapeutic relationship and level of self‐understanding and PM.
The different ties that bind
Authors: Short Ben
Published: October 2009

Two homologues of the cohesin protein Scc3 have specialized roles in chromatid cohesion.
Ubiquilin and p97/VCP bind erasin, forming a complex involved in ERAD
Authors: Lim Precious J. , Danner Rebecca , Liang Jing , Doong Howard , Harman Christine , Srinivasan Deepa , Rothenberg Cara , Wang Hongmin , Ye Yihong , Fang Shengyun , Monteiro Mervyn J.
Published: October 2009

Unwanted proteins in the endoplasmic reticulum (ER) are exported into the cytoplasm and degraded by the proteasome through the ER-associated protein degradation pathway (ERAD). Disturbances in ERAD are linked to ER stress, which has been implicated in the pathogenesis of several human diseases. However, the composition and organization of ERAD complexes in human cells is still poorly understood. In this paper, we describe a trimeric complex that we propose functions in ERAD. Knockdown of erasin, a platform for p97/VCP and ubiquilin binding, or knockdown of ubiquilin in human cells slowed degradation of two classical ERAD substrates. In Caenorhabditis elegans, ubiquilin and erasin are ER stress-response genes that are regulated by the ire-1 branch of the unfolded protein response pathway. Loss of ubiquilin or erasin resulted in activation of ER stress, increased accumulation of polyubiquitinated proteins, and shortened lifespan in worms. Our results strongly support a role for this complex in ERAD and in the regulation of ER stress.
Temporal regulation of Drosophila IAP1 determines caspase functions in sensory organ development
Authors: Koto Akiko , Kuranaga Erina , Miura Masayuki
Published: October 2009

The caspases comprise a family of cysteine proteases that function in various cellular processes, including apoptosis. However, how the balance is struck between the caspases’ role in cell death and their nonapoptotic functions is unclear. To address this issue, we monitored the protein turnover of an endogenous caspase inhibitor, Drosophila IAP1 (DIAP1). DIAP1 is an E3 ubiquitin ligase that promotes the ubiquitination of caspases and thereby prevents caspase activation. For this study, we developed a fluorescent probe to monitor DIAP1 turnover in the external sensory organ precursor (SOP) lineage of living Drosophila. The SOP divides asymmetrically to make the shaft, socket, and sheath cells, and the neuron that comprise each sensory organ. We found that the quantity of DIAP1 changed dramatically depending on the cell type and maturity, and that the temporal regulation of DIAP1 turnover determines whether caspases function nonapoptotically in cellular morphogenesis or cause cell death.
Spred2 interaction with the late endosomal protein NBR1 down-regulates fibroblast growth factor receptor signaling
Authors: Mardakheh Faraz K. , Yekezare Mona , Machesky Laura M. , Heath John K.
Published: October 2009

The potential for modulation of growth factor signaling by endocytic trafficking of receptors is well recognized, but the underlying mechanisms are poorly understood. We examined the regulation of fibroblast growth factor (FGF) signaling by Sprouty related with EVH1 (Ena/VASP homology 1) domain (Spred), a family of signaling inhibitors with proposed tumor-suppressive functions. The inhibitory activity of Spreds has been linked to their N-terminal EVH1 domain, but the molecular mechanism is unknown. In this study, we identify a novel late endosomal protein that directly binds to the EVH1 domain of Spred2. Neighbor of BRCA1 (NBR1) is a highly conserved multidomain protein that interacts and colocalizes with Spred2 in vivo. Attenuation of FGF signaling by Spred2 is dependent on the interaction with NBR1 and is achieved by redirecting the trafficking of activated receptors to the lysosomal degradation pathway. Our findings suggest a critical function for NBR1 in the regulation of receptor trafficking and provide a mechanism for down-regulation of signaling by Spred2 via NBR1.
Therapy of experimental type 1 diabetes by isolated Sertoli cell xenografts alone
Authors: Fallarino Francesca , Luca Giovanni , Calvitti Mario , Mancuso Francesca , Nastruzzi Claudio , Fioretti Maria C. , Grohmann Ursula , Becchetti Ennio , Burgevin Anne , Kratzer Roland , van Endert Peter , Boon Louis , Puccetti Paolo , Calafiore Riccardo
Published: October 2009

Type I diabetes mellitus is caused by autoimmune destruction of pancreatic β cells, and effective treatment of the disease might require rescuing β cell function in a context of reinstalled immune tolerance. Sertoli cells (SCs) are found in the testes, where their main task is to provide local immunological protection and nourishment to developing germ cells. SCs engraft, self-protect, and coprotect allogeneic and xenogeneic grafts from immune destruction in different experimental settings. SCs have also been successfully implanted into the central nervous system to create a regulatory environment to the surrounding tissue which is trophic and counter-inflammatory. We report that isolated neonatal porcine SC, administered alone in highly biocompatible microcapsules, led to diabetes prevention and reversion in the respective 88 and 81% of overtly diabetic (nonobese diabetic [NOD]) mice, with no need for additional β cell or insulin therapy. The effect was associated with restoration of systemic immune tolerance and detection of functional pancreatic islets that consisted of glucose-responsive and insulin-secreting cells. Curative effects by SC were strictly dependent on efficient tryptophan metabolism in the xenografts, leading to TGF-β–dependent emergence of autoantigen-specific regulatory T cells and recovery of β cell function in the diabetic recipients.
Variants of CTGF are associated with hepatic fibrosis in Chinese, Sudanese, and Brazilians infected with Schistosomes
Authors: Dessein Alain , Chevillard Christophe , Arnaud Violaine , Hou Xunya , Hamdoun Anas Ahmed , Dessein Helia , He Hongbin , Abdelmaboud Suzan A. , Luo Xinsong , Li Jun , Varoquaux Arthur , Mergani Adil , Abdelwahed Mohammed , Zhou Jie , Monis Ahmed , Pitta Maira G.R. , Gasmelseed Nagla , Cabantous Sandrine , Zhao Yaqing , Prata Aluizio , Brandt Carlos , Elwali Nasr Eldin , Argiro Laurent , Li Yuesheng
Published: October 2009

Abnormal fibrosis occurs during chronic hepatic inflammations and is the principal cause of death in hepatitis C virus and schistosome infections. Hepatic fibrosis (HF) may develop either slowly or rapidly in schistosome-infected subjects. This depends, in part, on a major genetic control exerted by genes of chromosome 6q23. A gene (connective tissue growth factor [CTGF]) is located in that region that encodes a strongly fibrogenic molecule. We show that the single nucleotide polymorphism (SNP) rs9402373 that lies close to CTGF is associated with severe HF (P = 2 × 10−6; odds ratio [OR] = 2.01; confidence interval of OR [CI] = 1.51–2.7) in two Chinese samples, in Sudanese, and in Brazilians infected with either Schistosoma japonicum or S. mansoni. Furthermore, SNP rs12526196, also located close to CTGF, is independently associated with severe fibrosis (P = 6 × 10−4; OR = 1.94; CI = 1.32–2.82) in the Chinese and Sudanese subjects. Both variants affect nuclear factor binding and may alter gene transcription or transcript stability. The identified variants may be valuable markers for the prediction of disease progression, and identify a critical step in the development of HF that could be a target for chemotherapy.
Id2-, RORγt-, and LTβR-independent initiation of lymphoid organogenesis in ocular immunity
Authors: Nagatake Takahiro , Fukuyama Satoshi , Kim Dong-Young , Goda Kaoru , Igarashi Osamu , Sato Shintaro , Nochi Tomonori , Sagara Hiroshi , Yokota Yoshifumi , Jetten Anton M. , Kaisho Tsuneyasu , Akira Shizuo , Mimuro Hitomi , Sasakawa Chihiro , Fukui Yoshinori , Fujihashi Kohtaro , Akiyama Taishin , Inoue Jun-ichiro , Penninger Josef M. , Kunisawa Jun , Kiyono Hiroshi
Published: October 2009

The eye is protected by the ocular immunosurveillance system. We show that tear duct–associated lymphoid tissue (TALT) is located in the mouse lacrimal sac and shares immunological characteristics with mucosa-associated lymphoid tissues (MALTs), including the presence of M cells and immunocompetent cells for antigen uptake and subsequent generation of mucosal immune responses against ocularly encountered antigens and bacteria such as Pseudomonas aeruginosa. Initiation of TALT genesis began postnatally; it occurred even in germ-free conditions and was independent of signaling through organogenesis regulators, including inhibitor of DNA binding/differentiation 2, retinoic acid–related orphan receptor γt, lymphotoxin (LT) α1β2–LTβR, and lymphoid chemokines (CCL19, CCL21, and CXCL13). Thus, TALT shares immunological features with MALT but has a distinct tissue genesis mechanism and plays a key role in ocular immunity.
Activation and desensitization of the olfactory cAMP-gated transduction channel: identification of functional modules
Authors: Waldeck Clemens , Vocke Kerstin , Ungerer Nicole , Frings Stephan , Möhrlen Frank
Published: October 2009

Olfactory receptor neurons respond to odor stimulation with a receptor potential that results from the successive activation of cyclic AMP (cAMP)-gated, Ca2+-permeable channels and Ca2+-activated chloride channels. The cAMP-gated channels open at micromolar concentrations of their ligand and are subject to a Ca2+-dependent feedback inhibition by calmodulin. Attempts to understand the operation of these channels have been hampered by the fact that the channel protein is composed of three different subunits, CNGA2, CNGA4, and CNGB1b. Here, we explore the individual role that each subunit plays in the gating process. Using site-directed mutagenesis and patch clamp analysis, we identify three functional modules that govern channel operation: a module that opens the channel, a module that stabilizes the open state at low cAMP concentrations, and a module that mediates rapid Ca2+-dependent feedback inhibition. Each subunit could be assigned to one of these functions that, together, define the gating logic of the olfactory transduction channel.
Genetic Effects of FTO and MC4R Polymorphisms on Body Mass in Constitutional Types
Authors: Cha Seongwon , Koo Imhoi , Park Byung L. , Jeong Sangkyun , Choi Sun M. , Kim Kil S. , Shin Hyoung D. , Kim Jong Y.
Published: October 2009

Sasang constitutional medicine (SCM), a Korean tailored medicine, categorizes human beings into four types through states of physiological imbalances and responsiveness to herbal medicine. One SCM type susceptible to obesity seems sensitive to energy intake due to an imbalance toward preserving energy. Common variants of fat mass and obesity associated (FTO) and melanocortin 4 receptor (MC4R) genes have been associated with increased body mass index (BMI) by affecting energy intake. Here, we statistically examined the association of FTO and MC4R polymorphisms with BMI in two populations with 1370 Koreans before and after SCM typing, and with the lowering of BMI in 538 individuals who underwent a 1‐month lifestyle intervention. The increased BMI replicated the association with FTO haplotypes (effect size ≃ 1.1 kg/m2) and MC4R variants (effect size ≃ 0.64 kg/m2). After the lifestyle intervention, the carriers of the haplotype represented by the minor allele of rs1075440 had a tendency to lose more waist‐to‐hip ratio (0.76%) than non‐carriers. The constitutional discrepancy for the accumulation of body mass by the effects of FTO and/or MC4R variants seemed to reflect the physique differences shown in each group of SCM constitutional types. In conclusion, FTO and MC4R polymorphisms appear to play an important role in weight gain, while only FTO variants play a role in weight loss after lifestyle intervention. Different trends were observed among individuals of SCM types, especially for weight gain. Therefore, classification of individuals based on physiological imbalance would offer a good genetic stratification system in assessing the effects of obesity genes.
XAF1 as a prognostic biomarker and therapeutic target in pancreatic cancer
Authors: Huang Jia , Yao Wei‐yan , Zhu Qi , Tu Shui‐ping , Yuan Fei , Wang Hua‐feng , Zhang Yong‐ping , Yuan Yao‐zong
Published: October 2009

XAF1 (X chromosome‐linked inhibitor of apoptosis [XIAP]‐associated factor 1) is a novel XIAP modulator that negatively regulates the anti‐apoptotic effects of XIAP and sensitizes cells to other cell death triggers. It has been reported to be downregulated in a variety of human cancer cell lines. However, the role of XAF1 in pancreatic carcinogenesis remains unclear. In the present study, we investigated the prognostic values of XAF1 expression and its regulation in cancer cell growth and apoptosis both in vitro and in vivo. From the immunohistochemistry staining of tissue microarray, 40 of 89 (44.9%) pancreatic specimens showed low levels of XAF1 expression. Statistical analysis suggested the downregulation of XAF1 was significantly correlated with tumor staging (P = 0.047) and those patients with low XAF1 levels had shorter survival times (P = 0.0162). Multivariate analysis indicated that XAF1 expression was an independent prognostic indicator of the survival of patients with pancreatic cancer (P = 0.007). Furthermore, we found that restoration of XAF1 expression mediated by Ad5/F35 virus suppressed cell proliferation and induced cell cycle arrest and apoptosis, accompanied by the activation of caspases 3, 8, and 9 and poly(ADP‐ribose) polymerase as well as increased level of cytochrome c and Bid cleavage. Notably, XAF1 restoration robustly decreased survivin expression rather than XIAP. In addition, in vivo s.c. xenografts from Ad5/F35‐XAF1 treatment, which showed less cellular proliferation and enhanced apoptosis, were significantly smaller than those from control groups. Our findings document that XAF1 is a valuable prognostic marker in pancreatic cancer and could be a potential candidate for cancer gene therapy. (Cancer Sci 2009)
LIM domain‐containing adaptor, leupaxin, localizes in focal adhesion and suppresses the integrin‐induced tyrosine phosphorylation of paxillin
Authors: Tanaka Toshiyuki , Moriwaki Kazumasa , Murata Shinsuke , Miyasaka Masayuki
Published: October 2009

Focal adhesion (FA) consists of multiple cellular proteins including paxillin and serves as a center for adhesion‐mediated signaling. The assembly and disassembly of FAs is regulated by locally produced intracellular signals, and tyrosine phosphorylation of paxillin has been implicated in this process. A Lin‐11 Isl‐1 Mec‐3 (LIM) domain‐containing adaptor protein, leupaxin, a member of the paxillin family, is expressed in leukocytes as well as in certain cancer cells, and shares overall structural characteristics with paxillin. However, it remains unknown whether leupaxin and paxillin cooperate with or antagonize each other in integrin signaling. Here we show that leupaxin potently represses the tyrosine phosphorylation of paxillin. When expressed in mouse thymoma BW5147 cells bound to ICAM‐1, leupaxin accumulated in FA‐like patches in the cell periphery. When expressed in NIH3T3 and HEK293T cells, leupaxin localized to FAs upon cell adhesion to fibronectin and strongly suppressed the integrin‐induced tyrosine phosphorylation of paxillin. In integrin‐stimulated HEK293T cells, leupaxin’s LIM3 domain appeared essential for selective FA localization and the suppression of paxillin tyrosine phosphorylation. Leupaxin’s LD3 motif, which is critical for stable association with FAK, was dispensable for leupaxin’s suppressive ability. In addition, leupaxin reduced the spreading of NIH3T3 cells on fibronectin, which required both the LD3 motif and LIM3 domain. When expressed in human leukocytic K562 cells, leupaxin significantly suppressed integrin α5β1‐mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin functions as a paxillin counterpart that potently suppresses the tyrosine phosphorylation of paxillin during integrin signaling. (Cancer Sci 2009)
Enhanced tumor growth in the NaS1 sulfate transporter null mouse
Authors: Dawson Paul Anthony , Choyce Allison , Chuang Christine , Whitelock John , Markovich Daniel , Leggatt Graham Robert
Published: October 2009

Sulfate plays an important role in maintaining normal structure and function of tissues, and its content is decreased in certain cancers including lung carcinoma. In this study, we investigated tumor growth in a mouse model of hyposulfatemia (Nas1−/−) and compared it to wild‐type (Nas1+/+) mice. Lung epithelial tumor cells (TC‐1 cell line) were injected subcutaneously into male Nas1−/− and Nas1+/+ mice on a mixed 129Sv and C57BL/6 genetic background. Tumor sections were stained with anti‐glycosaminoglycan antibodies to assess the distribution of proteoglycans and Gomori’s trichrome to detect collagen. After 14 days, tumor weights were markedly increased (by ∼12‐fold) in Nas1−/− mice when compared with Nas1+/+ mice. Histological analyses of tumors revealed increased (by ≈2.4‐fold) vessel content, as well as markedly reduced collagen and immunoreactivity against glycosaminoglycan structural epitopes in the tumors from Nas1−/− mice. No significant differences were found for the growth of cultured TC‐1 cells supplemented with Nas1−/− or Nas1+/+ serum, as determined by 3H‐thymidine incorporation, implying that the cell culture conditions may not reflect the in vivo situation of enhanced tumor growth. This study has revealed increased tumor growth and an altered extracellular tumor matrix in hyposulfatemic Nas1−/− mice. These findings highlight the importance of blood sulfate levels as a possible modulator of tumor growth, and could lead to future cancer studies in humans with altered sulfate homeostasis. (Cancer Sci 2009; 00: 000–000)
Woody biomass estimation of Tarchonanthus camphoratus in three woodland stands at Naivasha, Kenya
Authors: Kiruki Harun , Njung’e Joseph , Kiyiapi James
Published: October 2009

L’on a développé des équations individuelles pour la biomasse des arbres d’une forêt de Tarchonanthus et on a testé leur applicabilité dans trois bosquets de Tarchonanthusà Naivasha, au Kenya, en se basant sur les mesures d’arbres abattus. Trois forêts homogènes identifiées au moyen d’une classification automatique (cluster analysis) ont constitué les unités d’échantillonnage de base. Quarante‐cinq T. camphoratus de diverses classes de diamètre (de 2 à 28 cm) ont été sélectionnés et coupés dans les trois types de bosquets. Les relations alternatives ont été analysées et l’on a présenté les quatre meilleurs modèles (Tableaux 1 & 2). Pour tester l’exactitude des modèles développés, 15 arbres supplémentaires ont été coupés dans chaque bosquet et l’on a calculé leur poids sec que l’on a comparé avec le poids sec estimé. Pour chaque modèle, une validation fut faite par bosquet dans le but de déterminer si chaque modèle particulier s’appliquait à un bosquet spécifique ou à tous les types de bosquets. Le meilleur modèle, basé sur un R2; ajusté, une erreur standard de l’estimation et une distribution des résidus, est présenté et comparé avec les équations qui existaient au préalable. Le modèle utilise la transformation racine carrée de la biomasse. On en conclut que le modèle présenté ici peut être utilisé pour estimer la biomasse des arbres dans toutes les forêts dominées par T. camphoratus, qui, en de nombreux endroits, produisent des bosquets quasi purs, excluant toute autre espèce ligneuse. Le fait que l’exactitude de l’estimation ait eu tendance à varier légèrement d’un bosquet à l’autre suggère que le modèle ne peut s’appliquer qu’à cette forêt et à d’autres dont la structure n’est pas significativement différente.
Daily and hourly movement of male desert‐dwelling elephants
Authors: Leggett Keith
Published: October 2009

The daily and hourly movements of eight male desert‐dwelling elephants of various ages (12–45 years old) were determined hourly by global positioning system (GPS)/telemetry collars during the wet, cold dry and hot dry seasons of 2006 in northwest Namibia. The average daily movement in the wet season was greater than that observed during either the cold dry or the hot dry seasons. A similar difference was also observed for the movement rates, with the highest average rate of hourly movement recorded during the wet season. The diurnal movements (both distance and rate) were greater than those in the nocturnal hours during the wet season, whilst during the cold dry and hot dry season the reverse was true. The daily cycle of movement also changed seasonally, with greatest movement rates observed during the wet season between 11.00–20.00 hours, during the cold dry season between 14.00–21.00 hours; and between 04.00–11.00 hours during the hot dry season. Periods of decreased movement rates were observed between 09.00–10.00 and 02.00–03.00 hours in the wet season; 03.00–06.00 and 11.00–13.00 hours in the cold dry season; and 01.00–03.00 and 12.00–14.00 hours during the hot dry season.
Participatory wildlife surveys in communal lands: a case study from Simanjiro, Tanzania
Authors: Msoffe Fortunata U. , Ogutu Joseph O. , Kaaya John , Bedelian Claire , Said Mohammed Y. , Kifugo Shem C. , Reid Robin S. , Neselle Moses , Van Gardingen Paul , Thirgood Simon
Published: October 2009

It is widely accepted that protected areas alone are not sufficient to conserve wildlife populations particularly for migratory or wide‐ranging species. In this study, we assess the population density of migratory species in the Tarangire–Simanjiro Ecosystem by conducting a ground census using DISTANCE sampling. We focus on the Simanjiro Plains which are used as a dispersal area by wildebeest (Connochaetes taurinus) and zebra (Equus burchellii). We demonstrate that DISTANCE sampling can provide precise estimates of population density and is an affordable method for monitoring wildlife populations over time. We stress the importance of involving local communities in monitoring programmes across landscapes that incorporate communal lands as well as protected areas.
Home range, core areas and movement in the ‘critically endangered’ kipunji (Rungwecebus kipunji) in southwest Tanzania
Authors: De Luca Daniela W. , Picton Phillipps Guy , Machaga Sophy J. , Davenport Tim R. B.
Published: October 2009

Understanding how threatened forest primates use a heterogeneous landscape is essential to ensuring their survival. Kipunji (Rungwecebus kipunji) are ‘critically endangered’, arboreal monkeys restricted to two sites in Tanzania. Over 90% of the population lives in the degraded Rungwe‐Kitulo forests of the Southern Highlands. In this study, we present the first comprehensive investigation into daily path length and home range size of kipunji, based on data from four groups followed simultaneously over 70 consecutive days on Mt. Rungwe. The mean daily distance travelled was 1293 m (SE 150.82), and daily distance was not significantly correlated to group size. Using fixed kernel density estimation, an area enclosing 90% of the home range calculated using the ‘reference’ method as a smoothing parameter, measured a mean of 306.18 ha (SE 67), and the core area (50% use) was 86.55 ha (SE 18.73). Using the ‘least‐squares cross validation’ method, the mean home range and core area were 205.45 ha (SE 57.02) and 55.45 ha (SE 14.23) respectively. Home range overlap was extensive, although contact between groups was rare, with >97.30% of all observations within 20 min separated by >250 m. The data strongly suggest that kipunji are not territorial.
Insights in the exhumation history of the NW Zagros from bedrock and detrital apatite fission‐track analysis: evidence for a long‐lived orogeny
Authors: Homke Stéphane , Vergés Jaume , Van Der Beek Peter , Fernàndez Manel , Saura Eduard , Barbero Luis , Badics Balazs , Labrin Erika
Published: October 2009

We present the first fission‐track (FT) thermochronology results for the NW Zagros Belt (SW Iran) in order to identify denudation episodes that occurred during the protracted Zagros orogeny. Samples were collected from the two main detrital successions of the NW Zagros foreland basin: the Palaeocene–early Eocene Amiran–Kashkan succession and the Miocene Agha Jari and Bakhtyari Formations. In situ bedrock samples were furthermore collected in the Sanandaj‐Sirjan Zone. Only apatite fission‐track (AFT) data have been successfully obtained, including 26 ages and 11 track‐length distributions. Five families of AFT ages have been documented from analyses of in situ bedrock and detrital samples: pre‐middle Jurassic at ∼171 and ∼225 Ma, early–late Cretaceous at ∼91 Ma, Maastrichtian at ∼66 Ma, middle–late Eocene at ∼38 Ma and Oligocene–early Miocene at ∼22 Ma. The most widespread middle–late Eocene cooling phase, around ∼38 Ma, is documented by a predominant grain‐age population in Agha Jari sediments and by cooling ages of a granitic boulder sample. AFT ages document at least three cooling/denudation periods linked to major geodynamic events related to the Zagros orogeny, during the late Cretaceous oceanic obduction event, during the middle and late Eocene and during the early Miocene. Both late Cretaceous and early Miocene orogenic processes produced bending of the Arabian plate and concomitant foreland deposition. Between the two major flexural foreland episodes, the middle–late Eocene phase mostly produced a long‐lasting slow‐ or nondepositional episode in the inner part of the foreland basin, whereas deposition and tectonics migrated to the NE along the Sanandaj‐Sirjan domain and its Gaveh Rud fore‐arc basin. As evidenced in this study, the Zagros orogeny was long‐lived and multi‐episodic, implying that the timing of accretion of the different tectonic domains that form the Zagros Mountains requires cautious interpretation.
Advances in the understanding of cobalamin assimilation and metabolism
Authors: Quadros Edward V.
Published: October 2009

The haematological and neurological consequences of cobalamin deficiency define the essential role of this vitamin in key metabolic reactions. The identification of cubilin‐amnionless as the receptors for intestinal absorption of intrinsic factor‐bound cobalamin and the plasma membrane receptor for cellular uptake of transcobalamin bound cobalamin have provided a clearer understanding of the absorption and cellular uptake of this vitamin. As the genes involved in the intracellular processing of cobalamins and genetic defects of these pathways are identified, the metabolic disposition of cobalamins and the proteins involved are being recognized. The synthesis of methylcobalamin and 5′‐deoxyadenosylcobalamin, their utilization in conjunction with methionine synthase and methylmalonylCoA mutase, respectively, and the metabolic consequences of defects in these pathways could provide insights into the clinical presentation of cobalamin deficiency.
Genome wide DNA‐profiling of HIV‐related B‐cell lymphomas
Authors: Capello Daniela , Scandurra Marta , Poretti Giulia , Rancoita Paola M. V. , Mian Michael , Gloghini Annunziata , Deambrogi Clara , Martini Maurizio , Rossi Davide , Greiner Timothy C. , Chan Wing C. , Ponzoni Maurilio , Moreno Santiago M. , Piris Miguel A. , Canzonieri Vincenzo , Spina Michele , Tirelli Umberto , Inghirami Giorgio , Rinaldi Andrea , Zucca Emanuele , Favera Riccardo D. , Cavalli Franco , Larocca Luigi Maria , Kwee Ivo , Carbone Antonino , Gaidano Gianluca , Bertoni Francesco
Published: October 2009

Non‐Hodgkin lymphomas (NHL) represent a frequent complication of human immunodeficiency virus (HIV) infection. To elucidate HIV‐NHL pathogenesis, we performed a genome‐wide DNA profiling based on a single nucleotide polymorphism‐based microarray comparative genomic hybridization in 57 HIV‐lymphomas and, for comparison, in 105 immunocompetent diffuse large B‐cell lymphomas (IC‐DLBCL). Genomic complexity varied across HIV‐NHL subtypes. HIV‐Burkitt lymphoma showed a significantly lower number of lesions than HIV‐DLBCL (P = 0·032), whereas the median number of copy number changes was significantly higher in Epstein–Barr virus negative (EBV‐) HIV‐DLBCL (42·5, range 8–153) compared to EBV+ cases (22; range 3–41; P = 0·029). Compared to IC‐DLBCL, HIV‐DLBCL displayed a distinct genomic profile with no gains of 18q and specific genetic lesions. Fragile sites‐associated genes, including FHIT (FRA3B), WWOX (FRA16D), DCC (FRA18B) and PARK2 (FRA6E) were frequently inactivated in HIV‐NHL by interstitial deletions, and a significantly higher prevalence of FHIT alterations was observed in HIV‐DLBCL compared to IC‐DLBCL. The same genes involved by fragile site deletions were also frequently affected by aberrant methylation of regulative regions.
Zinc-ion binding and cytokine activity regulation pathways predicts outcome in relapsing–remitting multiple sclerosis
Authors: Achiron A , Gurevich M , Snir Y , Segal E , Mandel M
Published: October 2009

Multiple sclerosis (MS) is a demyelinating disease characterized by an unpredictable clinical course with intermittent relapses that lead over time to significant neurological disability. Clinical and radiological variables are limited in the ability to predict disease course. Peripheral blood genome scale analyses were used to characterize MS patients with different disease types, but not for prediction of outcome. Using complementary-DNA microarrays we studied peripheral-blood gene expression patterns in 53 relapsing–remitting MS patients. Patients were classified into good, intermediate and poor clinical outcome established after 2-year follow-up. A training set of 26 samples was used to identify clinical outcome differentiating gene-expression signature. Supervised learning and feature selection algorithms were applied to identify a predictive signature that was validated in an independent group of 27 patients. Key genes within the predictive signature were confirmed by quantitative reverse transcription–polymerase chain reaction in an additional 10 patients. The analysis identified 431 differentiating genes between patients with good and poor clinical outcome (change in neurological disability by the expanded disability status scale was −0·33 ± 0·24 and 1·6 ± 0·35, P = 0·0002, total number of relapses were 0 and 1·80 ± 0·35, P = 0·00009, respectively). An optimal set of 29 genes was depicted as a clinical outcome predictive gene expression signature and classified appropriately 88·9% of patients. This predictive signature was enriched by genes related biologically to zinc-ion binding and cytokine activity regulation pathways involved in inflammation and apoptosis. Our findings provide a basis for monitoring patients by prediction of disease outcome and can be incorporated into clinical decision-making in relapsing–remitting MS.
Evaluation of T cell immune responses in multi-drug-resistant tuberculosis (MDR-TB) patients toMycobacterium tuberculosistotal lipid antigens
Authors: Shahemabadi A S , Hosseini A Zavaran , Shaghsempour S , Masjedi M R , Rayani M , Pouramiri M
Published: October 2009

Mycobacterium tuberculosis lipid antigens produce significant T cell responses in healthy tuberculin reactor [purified protein derivative (PPD-positive] individuals. In the present study, proliferation and interferon (IFN)-γ/interleukin (IL)-4 responses were analysed to M. tuberculosis total lipid antigens in T lymphocytes from 25 patients with multi-drug-resistant tuberculosis (MDR-TB). The obtained results were compared with those of 30 asymptomatic healthy PPD-positive and 30 healthy tuberculin skin test negative (PPD-negative) subjects. Peripheral blood mononuclear cells (PBMCs) and T cells (CD4+ and CD8+) were stimulated using autologous immature dendritic cells. Proliferation responses were assessed using 3–{4,5-dimethylthiazol-2-yl}–2,5 diphenyl tetrazolium bromide (MTT). IFN-γ/IL-4 concentrations in the supernatant of the CD4+ and CD8+T cells were measured by enzyme-linked immunosorbent assay. Proliferation assay showed that the peripheral blood mononuclear cells and CD4+ T cells from the MDR-TB patients responded significantly less to the M. tuberculosis total lipid antigens than to the CD4+ T cells in the PPD-positive subjects. Total lipid antigen-specific proliferative responses in the CD8+ T cells from the MDR-TB patients were minimally detected and the responses were similar to those of the PPD-positive subjects. IFN-γ production by the CD4+ T cells stimulated by total lipid antigens from the MDR-TB patients was decreased significantly compared with the PPD-positive individuals, whereas IL-4 production in the patients was elevated. IFN-γ and IL-4 production in the CD8+ T cells of the MDR-TB patients was similar to those of the PPD-positive subjects. In conclusion, it is suggested that stimulated CD4+ T cells by M. tuberculosis total lipid antigens may be shifted to T helper 2 responses in MDR-TB patients.
Internal prostaglandin synthesis augments osteoprotegerin production in human gingival fibroblasts stimulated by lipopolysaccharide
Authors: Kiji M , Nagasawa T , Hormdee D , Yashiro R , Kobayashi H , Noguchi K , Nitta H , Izumi Y , Ishikawa I
Published: October 2009

Periodontitis is an inflammatory bone disease caused by Gram-negative anaerobic bacteria. Osteoclast differentiation is regulated by the balance between receptor activator of nuclear factor kappa B ligand (RANKL) and osteoprotegerin (OPG). The purpose of this study was to examine the mechanism of OPG production in human gingival fibroblasts (HGF) stimulated by lipopolysaccharide (LPS) from periodontopathic bacteria. The expressions of Toll-like receptor 2 (TLR-2) and TLR-4 in HGF were examined using flow-cytometry. HGF were stimulated with whole cell extracts or LPS from Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis with or without polymyxin B, a LPS inhibitor. In addition, HGF were stimulated with LPS, prostaglandin E2 (PGE2), various agonists of PGE receptors (EP1, EP2, EP3 and EP4 agonists) with or without indomethacin (IND), a prostaglandin synthesis inhibitor. OPG and PGE2 production was measured using an enzyme-linked immunosorbent assay (ELISA). HGF expressed both TLR-2 and TLR-4. Both A. actinomycetemcomitans and P. gingivalis LPS augmented OPG expression in HGF. Whole cell extracts from A. actinomycetemcomitans and P. gingivalis augmented OPG production by HGF; the augmentation was suppressed by polymyxin B. IND suppressed OPG production in LPS-stimulated HGF. PGE2 stimulated HGF to produce OPG. EP1 and EP2 agonists, but not EP3 and EP4 agonists, increased OPG production by HGF. These results suggest that LPS-induced OPG production by HGF is regulated via EP1 and/or EP2 receptors by endogenously generated PGE2.
Identification of prediabetes in first-degree relatives at intermediate risk of type I diabetes
Authors:   Belgian Diabetes Registry, Truyen I , De Grijse J , Weets I , Kaufman L , Pipeleers L , Nanos N , Decochez K , Hilbrands R , Kaufman J-M , Keymeulen B , Mathieu C , Van Gaal L , Pipeleers D G , Gorus F K
Published: October 2009

Prevention trials of type I diabetes are limited by recruitment of individuals at high risk of the disease. We investigated whether demographic and biological characteristics can identify rapid progressors among first-degree relatives of known patients at intermediate (< 10%) 5-year risk. Diabetes-associated antibodies, random proinsulin : C-peptide (PI/C) ratio and HLA DQ genotype were determined (repeatedly) in 258 islet antibody-positive IA-2Antibody-negative (Abpos/IA-2Aneg) normoglycaemic first-degree relatives. During follow-up (median 81 months), 14 of 258 Abpos/IA-2Aneg relatives developed type I diabetes; 13 (93%) of them had persistent antibodies conferring a 12% [95% confidence interval (CI): 5–19%] 5-year risk of diabetes. In Abpos/IA-2Aneg relatives with persistent antibodies (n = 126), the presence of ≥ 1 HLA DQ susceptibility haplotype in the absence of a protective haplotype (P = 0·033) and appearance on follow-up of a high PI/C ratio (P = 0·007) or IA-2A-positivity (P = 0·009) were identified as independent predictors of diabetes. In persistently antibody-positive relatives with HLA DQ risk a recurrently high PI/C ratio or development of IA-2A identified a subgroup (n = 32) comprising 10 of 13 (77%) prediabetic relatives and conferred a 35% (95% CI: 18–53%) 5-year risk. Under age 15 years, 5-year progression (95% CI) was 57% (30–84%) and sensitivity 62%. In the absence of IA-2A, the combination of antibody persistence, HLA DQ risk and elevated PI/C ratio or later development of IA-2A and young age defines a subgroup of relatives with a high risk of type I diabetes (≥ 35% in 5 years). Together with initially IA-2A-positive relatives these individuals qualify for standardized beta cell function tests in view of prevention trials.
Hypothermic preservation of lung allograft inhibits cytokine-induced chemoattractant-1, endothelial leucocyte adhesion molecule, vascular cell adhesion molecule-1 and intracellular adhesion molecule-1 expression
Authors: Hanusch C , Nowak K , Gill I S , Törlitz P , Rafat N , Mueller A M , Van Ackern K C , Yard B , Beck G C
Published: October 2009

Organ dysfunction is a major clinical problem after lung transplantation. Prolonged cold ischaemia and reperfusion injury are believed to play a central role in this complication. The influence of cold preservation on subsequent warm reperfusion was studied in an isolated, ventilated and perfused rat lung. Rat lungs were flushed with cold Perfadex-solution and stored at 4°C for different time periods. Thereafter lungs were perfused and ventilated for up to 3 h. Physiological parameters, production of inflammatory mediators and leucocyte infiltration were measured before and after perfusion. Lungs subjected to a cold ischaemia time of up to 6 h showed stable physiological conditions when perfused for 3 h. However, cold-ischaemia time beyond 6 h resulted in profound tissue oedema, thereby impairing ventilation and perfusion. Warm reperfusion and ventilation per se induced a strong inflammatory response, as demonstrated by a significant up-regulation of chemokines and adhesion molecules (cytokine-induced chemoattractant-1, intracellular adhesion molecule and endothelial leucocyte adhesion molecule), accompanied by enhanced leucocyte infiltration. Although the up-regulation of inflammatory mediators was blunted in lungs that were subjected to cold ischaemia, this did not influence leucocyte infiltration. In fact, cold ischaemia time correlated with leucocyte sequestration. Although cold preservation inhibits the expression of inflammatory mediators it does not affect leucocyte sequestration during warm reperfusion. Cold preservation might cause impairment of the endothelial barrier function, as evidenced by tissue oedema and profound leucocyte infiltration.