bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of human-made ecological changes on the genetic architecture of
Daphnia
species
Authors: Brede Nora , Sandrock Christoph , Straile Dietmar , Spaak Piet , Jankowski Thomas , Streit Bruno , Schwenk Klaus
Published: March 2009

The overenrichment (eutrophication) of aquatic ecosystems with nutrients leading to algal blooms and anoxic conditions has been a persistent and widespread environmental problem. Although there are many studies on the ecological impact of elevated phosphorus (P) levels (e.g., decrease in biodiversity and water quality), little is known about the evolutionary consequences for animal species. We reconstructed the genetic architecture of a
Daphnia
species complex in 2 European lakes using diapausing eggs that were isolated from sediment layers covering the past 100 years. Changes in total P were clearly associated with a shift in species composition and the population structure of evolutionary lineages. Although environmental conditions were largely re-established after peak eutrophication during the 1970s and 1980s, original species composition and the genetic architecture of species were not restored but evolved along new evolutionary trajectories. Our data demonstrate that anthropogenically induced temporal alterations of habitats are associated with long-lasting changes in communities and species via interspecific hybridization and introgression.
Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography
Authors: Adachi Motoyasu , Ohhara Takashi , Kurihara Kazuo , Tamada Taro , Honjo Eijiro , Okazaki Nobuo , Arai Shigeki , Shoyama Yoshinari , Kimura Kaname , Matsumura Hiroyoshi , Sugiyama Shigeru , Adachi Hiroaki , Takano Kazufumi , Mori Yusuke , Hidaka Koushi , Kimura Tooru , Hayashi Yoshio , Kiso Yoshiaki , Kuroki Ryota
Published: March 2009

HIV-1 protease is a dimeric aspartic protease that plays an essential role in viral replication. To further understand the catalytic mechanism and inhibitor recognition of HIV-1 protease, we need to determine the locations of key hydrogen atoms in the catalytic aspartates Asp-25 and Asp-125. The structure of HIV-1 protease in complex with transition-state analog KNI-272 was determined by combined neutron crystallography at 1.9-Å resolution and X-ray crystallography at 1.4-Å resolution. The resulting structural data show that the catalytic residue Asp-25 is protonated and that Asp-125 (the catalytic residue from the corresponding diad-related molecule) is deprotonated. The proton on Asp-25 makes a hydrogen bond with the carbonyl group of the allophenylnorstatine (Apns) group in KNI-272. The deprotonated Asp-125 bonds to the hydroxyl proton of Apns. The results provide direct experimental evidence for proposed aspects of the catalytic mechanism of HIV-1 protease and can therefore contribute substantially to the development of specific inhibitors for therapeutic application.
Energy transduction in protein transport and the ATP hydrolytic cycle of SecA
Authors: Robson Alice , Gold Vicki A. M. , Hodson Skye , Clarke Anthony R. , Collinson Ian
Published: March 2009

The motor protein SecA drives the transport of polypeptides through the ubiquitous protein channel SecYEG. Changes in protein-nucleotide binding energy during the hydrolytic cycle of SecA must be harnessed to drive large conformational changes resulting in channel opening and vectorial substrate polypeptide transport. Here, we elucidate the ATP hydrolysis cycle of SecA from
Escherichia coli
by transient and steady-state methods. The basal ATPase activity of SecA is very slow with the release of ADP being some 600-fold slower than hydrolysis. Upon binding to SecYEG the release of ADP is stimulated but remains rate-limiting. ADP release is fastest in the fully coupled system when a substrate protein is being translocated; in this case hydrolysis and ADP release occur at approximately the same rate. The data imply that ADP dissociation from SecA is accompanied by a structural rearrangement that is strongly coupled to the protein interface and protein translocation through SecYEG.
GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent
Authors: Wang Fengping , Zhou Huaiyang , Meng Jun , Peng Xiaotong , Jiang Lijing , Sun Ping , Zhang Chuanlun , Van Nostrand Joy D. , Deng Ye , He Zhili , Wu Liyou , Zhou Jizhong , Xiao Xiang
Published: March 2009

Deep-sea hydrothermal vents are one of the most unique and fascinating ecosystems on Earth. Although phylogenetic diversity of vent communities has been extensively examined, their physiological diversity is poorly understood. In this study, a GeoChip-based, high-throughput metagenomics technology revealed dramatic differences in microbial metabolic functions in a newly grown protochimney (inner section, Proto-I; outer section, Proto-O) and the outer section of a mature chimney (4143-1) at the Juan de Fuca Ridge. Very limited numbers of functional genes were detected in Proto-I (113 genes), whereas much higher numbers of genes were detected in Proto-O (504 genes) and 4143-1 (5,414 genes). Microbial functional genes/populations in Proto-O and Proto-I were substantially different (around 1% common genes), suggesting a rapid change in the microbial community composition during the growth of the chimney. Previously retrieved
cbbL
and
cbbM
genes involved in the Calvin Benson Bassham (CBB) cycle from deep-sea hydrothermal vents were predominant in Proto-O and 4143-1, whereas photosynthetic green-like
cbbL
genes were the major components in Proto-I. In addition, genes involved in methanogenesis, aerobic and anaerobic methane oxidation (e.g., ANME1 and ANME2), nitrification, denitrification, sulfate reduction, degradation of complex carbon substrates, and metal resistance were also detected. Clone libraries supported the GeoChip results but were less effective than the microarray in delineating microbial populations of low biomass. Overall, these results suggest that the hydrothermal microbial communities are metabolically and physiologically highly diverse, and the communities appear to be undergoing rapid dynamic succession and adaptation in response to the steep temperature and chemical gradients across the chimney.
Toxicity of atmospheric aerosols on marine phytoplankton
Authors: Paytan Adina , Mackey Katherine R. M. , Chen Ying , Lima Ivan D. , Doney Scott C. , Mahowald Natalie , Labiosa Rochelle , Post Anton F.
Published: March 2009

Atmospheric aerosol deposition is an important source of nutrients and trace metals to the open ocean that can enhance ocean productivity and carbon sequestration and thus influence atmospheric carbon dioxide concentrations and climate. Using aerosol samples from different back trajectories in incubation experiments with natural communities, we demonstrate that the response of phytoplankton growth to aerosol additions depends on specific components in aerosols and differs across phytoplankton species. Aerosol additions enhanced growth by releasing nitrogen and phosphorus, but not all aerosols stimulated growth. Toxic effects were observed with some aerosols, where the toxicity affected picoeukaryotes and
Synechococcus
but not
Prochlorococcus
. We suggest that the toxicity could be due to high copper concentrations in these aerosols and support this by laboratory copper toxicity tests preformed with
Synechococcus
cultures. However, it is possible that other elements present in the aerosols or unknown synergistic effects between these elements could have also contributed to the toxic effect. Anthropogenic emissions are increasing atmospheric copper deposition sharply, and based on coupled atmosphere–ocean calculations, we show that this deposition can potentially alter patterns of marine primary production and community structure in high aerosol, low chlorophyll areas, particularly in the Bay of Bengal and downwind of South and East Asia.
Iron pnictides as a new setting for quantum criticality
Authors: Dai Jianhui , Si Qimiao , Zhu Jian-Xin , Abrahams Elihu
Published: March 2009

Two major themes in the physics of condensed matter are quantum critical phenomena and unconventional superconductivity. These usually occur in the context of competing interactions in systems of strongly correlated electrons. All this interesting physics comes together in the behavior of the recently discovered iron pnictide compounds that have generated enormous interest because of their moderately high-temperature superconductivity. The ubiquity of antiferromagnetic ordering in their phase diagrams naturally raises the question of the relevance of magnetic quantum criticality, but the answer remains uncertain both theoretically and experimentally. Here, we show that the undoped iron pnictides feature a unique type of magnetic quantum critical point, which results from a competition between electronic localization and itinerancy. Our theory provides a mechanism to understand the experimentally observed variation of the ordered moment among the undoped iron pnictides. We suggest P substitution for As in the undoped iron pnictides as a means to access this example of magnetic quantum criticality in an unmasked fashion. Our findings point to the iron pnictides as a much-needed setting for quantum criticality, one that offers a unique set of control parameters.
PLC-γ2 is essential for formation and maintenance of memory B cells
Authors: Hikida Masaki , Casola Stefano , Takahashi Noriko , Kaji Tomohiro , Takemori Toshitada , Rajewsky Klaus , Kurosaki Tomohiro
Published: March 2009

Resting antigen-experienced memory B cells are thought to be responsible for the more rapid and robust antibody responses after antigen reencounter, which are the hallmark of memory humoral responses. The molecular basis for the development and survival of memory B cells remains largely unknown. We report that phospholipase C (PLC) γ2 is required for efficient formation of germinal center (GC) and memory B cells. Moreover, memory B cell homeostasis is severely hampered by inducible loss of PLC-γ2. Accordingly, mice with a conditional deletion of PLC-γ2 in post-GC B cells had an almost complete abrogation of the secondary antibody response. Collectively, our data suggest that PLC-γ2 conveys a survival signal to GC and memory B cells and that this signal is required for a productive secondary immune response.
Thymus-homing peripheral dendritic cells constitute two of the three major subsets of dendritic cells in the steady-state thymus
Authors: Li JiChu , Park JooHung , Foss Deborah , Goldschneider Irving
Published: March 2009

Many dendritic cells (DCs) in the normal mouse thymus are generated intrathymically from common T cell/DC progenitors. However, our previous work suggested that at least 50% of thymic DCs originate independently of these progenitors. We now formally demonstrate by parabiotic, adoptive transfer, and developmental studies that two of the three major subsets of thymic DCs originate extrathymically and continually migrate to the thymus, where they occupy a finite number of microenvironmental niches. The thymus-homing DCs consisted of immature plasmacytoid DCs (pDCs) and the signal regulatory protein α–positive (Sirpα+) CD11b+ CD8α− subset of conventional DCs (cDCs), both of which could take up and transport circulating antigen to the thymus. The cDCs of intrathymic origin were mostly Sirpα− CD11b− CD8αhi cells. Upon arrival in the thymus, the migrant pDCs enlarged and up-regulated CD11c, major histocompatibility complex II (MHC II), and CD8α, but maintained their plasmacytoid morphology. In contrast, the migrant cDCs proliferated extensively, up-regulated CD11c, MHC II, and CD86, and expressed dendritic processes. The possible functional implications of these findings are discussed.
Prostaglandin E2 regulates Th17 cell differentiation and function through cyclic AMP and EP2/EP4 receptor signaling
Authors: Boniface Katia , Bak-Jensen Kristian S. , Li Ying , Blumenschein Wendy M. , McGeachy Mandy J. , McClanahan Terrill K. , McKenzie Brent S. , Kastelein Robert A. , Cua Daniel J. , de Waal Malefyt René
Published: March 2009

Prostaglandins, particularly prostaglandin E2 (PGE2), play an important role during inflammation. This is exemplified by the clinical use of cyclooxygenase 2 inhibitors, which interfere with PGE2 synthesis, as effective antiinflammatory drugs. Here, we show that PGE2 directly promotes differentiation and proinflammatory functions of human and murine IL-17–producing T helper (Th17) cells. In human purified naive T cells, PGE2 acts via prostaglandin receptor EP2- and EP4-mediated signaling and cyclic AMP pathways to up-regulate IL-23 and IL-1 receptor expression. Furthermore, PGE2 synergizes with IL-1β and IL-23 to drive retinoic acid receptor–related orphan receptor (ROR)-γt, IL-17, IL-17F, CCL20, and CCR6 expression, which is consistent with the reported Th17 phenotype. While enhancing Th17 cytokine expression mainly through EP2, PGE2 differentially regulates interferon (IFN)-γ production and inhibits production of the antiinflammatory cytokine IL-10 in Th17 cells predominantly through EP4. Furthermore, PGE2 is required for IL-17 production in the presence of antigen-presenting cells. Hence, the combination of inflammatory cytokines and noncytokine immunomodulators, such as PGE2, during differentiation and activation determines the ultimate phenotype of Th17 cells. These findings, together with the altered IL-12/IL-23 balance induced by PGE2 in dendritic cells, further highlight the crucial role of the inflammatory microenvironment in Th17 cell development and regulation.
Effects of climate control on air pollution: Coupling an energy-environment-economy global model (E3MG) and atmospheric chemistry model (p-TOMCAT) in decarbonising international transport
Authors: O Dessens  , T Barker  , H Rogers  , Annela Anger  , R Jones  , J Pyle
Published: March 2009

This article was submitted without an abstract, please refer to the full-text PDF file.
Increased activity of indoleamine 2,3-dioxygenase in serum from acutely infected dengue patients linked to gamma interferon antiviral function
Authors: Becerra Aniuska , Warke Rajas V. , Xhaja Kris , Evans Barbara , Evans James , Martin Katherine , de Bosch Norma , Rothman Alan L. , Bosch Irene
Published: March 2009

The depletion ofl-tryptophan (L-Trp) has been associated with the inhibition of growth of micro-organisms and also has profound effects on T cell proliferation and immune tolerance. The enzyme indoleamine 2,3-dioxygenase (IDO) catalyses the rate-limiting step in the catabolic pathway of L-Trp. Gene expression analysis has shown upregulation of genes involved in L-Trp catabolism inin vitromodels of dengue virus (DENV) infection. To understand the role of IDO during DENV infection, we measured IDO activity in sera from control and DENV-infected patients. We found increased IDO activity, lower levels of L-Trp and higher levels ofl-kynurenine in sera from DENV-infected patients during the febrile days of the disease compared with patients with other febrile illnesses and healthy donors. Furthermore, we confirmed upregulation of IDO mRNA expression in response to DENV infectionin vitro, using a dendritic cell (DC) model of DENV infection. We found that the antiviral effect of gamma interferon (IFN-γ) in DENV-infected DCsin vitrowas partially dependent on IDO activity. Our results demonstrate that IDO plays an important role in the antiviral effect of IFN-γagainst DENV infectionin vitroand suggest that it has a role in the immune response to DENV infectionsin vivo.
Macaca fascicularis papillomavirus type 1: a non-human primate betapapillomavirus causing rapidly progressive hand and foot papillomatosis
Authors: Joh Joongho , Hopper Kelly , Van Doorslaer Koenraad , Sundberg John P. , Jenson Alfred B. , Ghim Shin-Je
Published: March 2009

Papillomaviruses (PVs) are a group of small, non-enveloped DNA viruses that cause mucosal or cutaneous neoplasia in a variety of animals. Whilst most papillomas will regress spontaneously, some may persist or undergo malignant transformation. In this study, aggressive, persistent and extensive warts were observed on the hands and feet of a cynomolgus macaque (Macaca fascicularis). The presence of PV in the wart biopsies was identified by immunohistochemistry and PCR amplification of PV DNA. The genomic DNA of this PV was cloned and sequenced, and the PV was designated M. fascicularis papillomavirus type 1 (MfPV-1). Its genome was 7588 bp in length and the organization of its putative open reading frames (E1, E2, E6, E7, L1, L2 and E4) was similar to that of other PVs. MfPV-1 had a short non-coding region (NCR) of 412 bp. Molecular analysis of MfPV-1 genomic DNA classified it into the genus Betapapillomavirus, to which all epidermodysplasia verruciformis (EV)-type PVs belong. Diseases caused by PVs of the genus Betapapillomavirus are usually associated with natural or iatrogenic immunosuppression. The genomic characterization performed in this study showed that MfPV-1 clustered within the genus Betapapillomavirus and also contained EV-type-specific motifs in its NCR. Further characterization of this virus and its host interactions may allow us to develop a non-human primate model for human betapapillomaviruses, a genus populated by human PV types causing EV.
Evolutionary history and dynamics of dog rabies virus in western and central Africa
Authors: Talbi Chiraz , Holmes Edward C. , de Benedictis Paola , Faye Ousmane , Nakouné Emmanuel , Gamatié Djibo , Diarra Abass , Elmamy Bezeid Ould , Sow Adama , Adjogoua Edgard Valery , Sangare Oumou , Dundon William G. , Capua Ilaria , Sall Amadou A. , Bourhy Hervé
Published: March 2009

The burden of rabies in Africa is estimated at 24 000 human deaths year−1, almost all of which result from infection with dog rabies viruses (RABV). To investigate the evolutionary dynamics of RABV in western and central Africa, 92 isolates sampled from 27 African countries over 29 years were collected and sequenced. This revealed that RABV currently circulating in dogs in this region fell into a single lineage designated ‘Africa 2’. A detailed analysis of the phylogeographical structure of this Africa 2 lineage revealed strong population subdivision at the country level, with only limited movement of virus among localities, including a possible east-to-west spread across Africa. In addition, Bayesian coalescent analysis suggested that the Africa 2 lineage was introduced into this region of Africa only recently (probably <200 years ago), in accordance with the timescale of expanding European colonial influence and urbanization, and then spread relatively slowly, perhaps occupying the entire region in a 100 year period.
Japanese encephalitis virus produces a CD4+ Th2 response and associated immunoprotection in an adoptive-transfer murine model
Authors: Biswas S. M. , Ayachit V. M. , Sapkal G. N. , Mahamuni S. A. , Gore M. M.
Published: March 2009

Japanese encephalitis is an acute infection of the central nervous system caused by Japanese encephalitis virus (JEV). The importance of an effective humoral response in preventing JEV infection has already been established, although the contribution of cellular immunity remains unclear. This study used an experimental murine model to understand the protective effects of cell-mediated immunity in JEV infection. Fourteen-day-old mice adoptively transferred with JEV-immune splenocytes were found to be protected from peripheral JEV challenge. The survival rate was reduced when transferred cells were depleted of their CD4+ T-cell population. Correspondingly, increased protection was observed when JEV-primed isolated CD4+ T cells were transferred compared with isolated CD8+ T cells. Mice protected from JEV infection by the adoptive transfer of JEV-immune splenocytes had higher levels of immunomodulatory cytokines and decreased expression of pro-inflammatory cytokines. Concurrent with the increase in Th2 cytokines, JEV-specific IgM and IgG1 antibody titres were found to be elevated in protected mice. Taken together, these data indicate a definite role for CD4+ T cells in protection from lethal JEV infection in naïve 14-day-old mice. Induction of a Th2 cytokine response and IgG1 antibody probably achieves an immunomodulatory effect that results in the enhanced survival of these animals.
Roles and interactions of begomoviruses and satellite DNAs associated with okra leaf curl disease in Mali, West Africa
Authors: Kon Tatsuya , Rojas Maria R. , Abdourhamane Issoufou K. , Gilbertson Robert L.
Published: March 2009

Okra leaf curl disease (OLCD) is a major constraint on okra (Abelmoschus esculentus) production in West Africa. Two monopartite begomoviruses (okra virus-1 and okra virus-2), a betasatellite and a DNA1 satellite are associated with OLCD in Mali. Okra virus-1 is an isolate of okra yellow crinkle virus (OYCrV), okra virus-2 is a recombinant isolate of cotton leaf curl Gezira virus (CLCuGV) and the betasatellite is a variant of cotton leaf curl Gezira betasatellite (CLCuGB). Cloned DNA of OYCrV and CLCuGV were infectious and induced leaf curl symptoms in Nicotiana benthamiana plants, but did not induce OLCD in okra. However, when these clones were individually co-inoculated with the cloned CLCuGB DNA, symptom severity and viral DNA levels were increased in N. benthamiana plants and typical OLCD symptoms were induced in okra. The CLCuGB was also replicated by, and increased symptom severity of, three monopartite tomato-infecting begomoviruses, including two from West Africa. The sequence of the DNA1 satellite was highly divergent, indicating that it represents a distinct West African lineage. DNA1 replicated autonomously, and replication required the DNA1-encoded Rep protein. Although DNA1 reduced helper begomovirus DNA levels, symptoms were not attenuated. In the presence of CLCuGB, DNA levels of the helper begomoviruses and DNA1 were substantially increased. Together, these findings establish that OLCD in Mali is caused by a complex of monopartite begomoviruses and a promiscuous betasatellite with an associated parasitic DNA1 satellite. These findings are discussed in terms of the aetiology of OLCD and the evolution of new begomovirus/satellite DNA complexes.
Variability in the level of RNA silencing suppression caused by triple gene block protein 1 (TGBp1) from various potexviruses during infection
Authors: Senshu Hiroko , Ozeki Johji , Komatsu Ken , Hashimoto Masayoshi , Hatada Kouji , Aoyama Michiko , Kagiwada Satoshi , Yamaji Yasuyuki , Namba Shigetou
Published: March 2009

RNA silencing is an important defence mechanism against virus infection, and many plant viruses encode RNA silencing suppressors as a counter defence. In this study, we analysed the RNA silencing suppression ability of multiple virus species of the genus Potexvirus. Nicotiana benthamiana plants exhibiting RNA silencing of a green fluorescent protein (GFP) transgene showed reversal of GFP fluorescence when systemically infected with potexviruses. However, the degree of GFP fluorescence varied among potexviruses. Agrobacterium-mediated transient expression assay in N. benthamiana leaves demonstrated that the triple gene block protein 1 (TGBp1) encoded by these potexviruses has drastically different levels of silencing suppressor activity, and these differences were directly related to variations in the silencing suppression ability during virus infection. These results suggest that suppressor activities differ even among homologous proteins encoded by viruses of the same genus, and that TGBp1 contributes to the variation in the level of RNA silencing suppression by potexviruses. Moreover, we investigated the effect of TGBp1 encoded by Plantago asiatica mosaic virus (PlAMV), which exhibited a strong suppressor activity, on the accumulation of microRNA, virus genomic RNA and virus-derived small interfering RNAs.
Stimulation of hepatitis B virus genome replication by HBx is linked to both nuclear and cytoplasmic HBx expression
Authors: Cha Man-Young , Ryu Dong-Kyun , Jung Hyeon-Sik , Chang Ho-Eun , Ryu Wang-Shick
Published: March 2009

HBx, a small regulatory protein of hepatitis B virus, plays an important role in stimulating viral genome replication. HBx was shown to be associated with diverse subcellular locations, such as the nucleus, cytoplasm and mitochondria. Some studies have linked the stimulation of genome replication by HBx to its cytoplasmic function, while other reports have attributed this function to its nuclear component. To clarify this discrepancy, we measured viral genome replication by complementing an HBx-null replicon in two different ways: by (i) co-transfecting with an increasing amount of HBx expression plasmid and (ii) co-transfecting with re-targeted variants of HBx that are confined to either the nucleus or the cytoplasm due to either the nuclear localization signal (NLS) or the nuclear export signal (NES) tags, respectively. Intriguingly, immunostaining analysis indicated that the subcellular localization of HBx is primarily influenced by its abundance; HBx is confined to the nucleus at low levels but is usually detected in the cytoplasm at high levels. Importantly, HBx, whether re-targeted by either the NLS or NES tag, stimulates viral genome replication to a level comparable to that of the wild-type. Furthermore, similar to the wild-type, the stimulation of viral genome replication by the re-targeted HBx occurred at the transcription level. Thus, we concluded that the stimulation of viral genome replication by HBx is linked to both nuclear and cytoplasmic HBx, although the underlying mechanism of stimulation most likely differs.
Identification and characterization of a new Kaposi's sarcoma-associated herpesvirus replication and transcription activator (RTA)-responsive element involved in RTA-mediated transactivation
Authors: Wen Hui-Ju , Minhas Veenu , Wood Charles
Published: March 2009

Kaposi's sarcoma-associated herpesvirus (KSHV) replication and transcription activator (RTA) is well established as a key transcriptional activator that regulates the KSHV life cycle from latency to lytic replication. It is expressed immediately after infection and activates a number of viral genes leading to virus replication. The RTA-responsive element (RRE) in the RTA target gene promoters is critical for RTA to mediate this transactivation. A number of non-conserved RREs have been identified in various RTA-responsive promoters, and AT-rich sequences have been proposed to serve as RTA targets, but no consensus RRE sequence has been identified so far. Two non-conserved RREs (RRE1 and RRE2) containing AT-rich sequences have been identified previously in the promoter of one of the KSHV lytic genes, ORF57, which can be strongly activated by RTA. Based on homology with the consensus sequence of the Epstein–Barr virus Rta RRE, this study identified a third RTA-responsive element (RRE3) in the ORF57 promoter. This RRE comprised a GC-rich sequence that could bind RTA both in vitro and in vivo, and plays a role in RTA-mediated transactivation of the ORF57 promoter. The presence of two of the three RREs in close proximity to each other was required for optimal RTA-mediated transactivation of the ORF57 promoter, even though the presence of only one RRE is needed for RTA binding. These results suggest that the ability of RTA to mediate transcriptional activation is distinct from its ability to bind to its target elements.
Finding the fifth base: Genome-wide sequencing of cytosine methylation
Authors: Lister Ryan , Ecker Joseph R.
Published: March 2009

Complete sequences of myriad eukaryotic genomes, including several human genomes, are now available, and recent dramatic developments in DNA sequencing technology are opening the floodgates to vast volumes of sequence data. Yet, despite knowing for several decades that a significant proportion of cytosines in the genomes of plants and animals are present in the form of methylcytosine, until very recently the precise locations of these modified bases have never been accurately mapped throughout a eukaryotic genome. Advanced “next-generation” DNA sequencing technologies are now enabling the global mapping of this epigenetic modification at single-base resolution, providing new insights into the regulation and dynamics of DNA methylation in genomes.
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
Authors: Brunner Alayne L. , Johnson David S. , Kim Si Wan , Valouev Anton , Reddy Timothy E. , Neff Norma F. , Anton Elizabeth , Medina Catherine , Nguyen Loan , Chiao Eric , Oyolu Chuba B. , Schroth Gary P. , Absher Devin M. , Baker Julie C. , Myers Richard M.
Published: March 2009

To investigate the role of DNA methylation during human development, we developed Methyl-seq, a method that assays DNA methylation at more than 90,000 regions throughout the genome. Performing Methyl-seq on human embryonic stem cells (hESCs), their derivatives, and human tissues allowed us to identify several trends during hESC and in vivo liver differentiation. First, differentiation results in DNA methylation changes at a minimal number of assayed regions, both in vitro and in vivo (2%–11%). Second, in vitro hESC differentiation is characterized by both de novo methylation and demethylation, whereas in vivo fetal liver development is characterized predominantly by demethylation. Third, hESC differentiation is uniquely characterized by methylation changes specifically at H3K27me3-occupied regions, bivalent domains, and low density CpG promoters (LCPs), suggesting that these regions are more likely to be involved in transcriptional regulation during hESC differentiation. Although both H3K27me3-occupied domains and LCPs are also regions of high variability in DNA methylation state during human liver development, these regions become highly unmethylated, which is a distinct trend from that observed in hESCs. Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation.
Estrogenic G protein‐coupled receptor 30 signaling is involved in regulation of endometrial carcinoma by promoting proliferation, invasion potential, and interleukin‐6 secretion via the MEK/ERK mitogen‐activated protein kinase pathway
Authors: He Yin‐Yan , Cai Bin , Yang Yi‐Xia , Liu Xue‐Lian , Wan Xiao‐Ping
Published: March 2009

The regulatory mechanism of endometrial carcinoma and the signal transduction pathways involved in hormone action are poorly defined. It has become apparent that the G protein‐coupled receptor (GPR) 30 mediates the non‐genomic signaling of 17β‐estradiol (E2). Here we show that GPR30 is highly expressed in endometrial cancer tissues and cancer cell lines and positively regulates cell proliferation and invasion. GPR30 expression was detected in 50 human endometrial carcinomas. The transcription level of GPR30 was significantly higher in the tissue of endometrial carcinoma than in normal endometrium (P < 0.05). Immunohistochemical assays revealed that the positive expression rate of GPR30 protein in endometrial carcinoma tissue (35/50, 70%) was statistically higher than in normal endometrium tissue (8/30, 26.67%) (χ2 = 14.16, P = 0.0002). GPR30 overexpression was correlated with high‐grade endometrial carcinoma. GPR30 expression was also found in two human endometrial cancer cell lines: RL95‐2 (estrogen receptor positive) and KLE (estrogen receptor negative). The roles of GPR30 in proliferative and invasive responses to E2 and G1, a non‐steroidal GPR30‐specific agonist, in RL95‐2 and KLE cell lines were then explored. We showed that E2 and G1 could initiate the MAPK/ERK mitogen‐activated protein kinase pathway in both cell lines. What's more, E2 and G1 promoted KLE and RL95‐2 proliferation and stimulated matrix metalloproteinase production and activity via the GPR30‐mediated MEK/ERK mitogen‐activated protein kinase pathway, as well as increased interleukin‐6 secretion. These findings suggest that GPR30‐mediated non‐genomic signaling could play an important role in endometrial cancer. (Cancer Sci 2009; 100: 1051–1061)
Personal use of hair dye and cancer risk in a prospective cohort of Chinese women
Authors: Mendelsohn Julie Bloch , Li Qi‐Zhai , Ji Bu‐Tian , Shu Xiao‐Ou , Yang Gong , Li Hong‐Lan , Lee Kyoung‐Mu , Yu Kai , Rothman Nathaniel , Gao Yu‐Tang , Zheng Wei , Chow Wong‐Ho
Published: March 2009

Although widely studied over the past 40 years, personal use of hair dye generally has not been associated with overall cancer risk. The association between hair dye use and risk of bladder and hematopoietic cancers has been less conclusive. Most hair dye studies have been case‐control studies conducted in Caucasian populations. We examined the relationship between personal hair dye use and cancer risk in a prospective cohort of 70 366 Chinese women. After an average of 7 years of follow up, 2437 women were newly diagnosed with cancer by 31 December 2005. Cox proportional hazard models were used to estimate relative risks (RR) and 95% confidence intervals (CI) of cancer risk associated with hair dye use, adjusting for potential confounding factors. Compared with women who reported no hair dye use, ever users had an overall cancer risk of 0.89 (95% CI 0.82, 0.97). No significant association was observed for several common cancers, including cancers of the breast (RR 0.93, 95% CI 0.78, 1.09), lung (RR 0.81, 95% CI 0.62, 1.09), stomach (RR 0.90, 95% CI 0.66, 1.21), and colorectum (RR 1.04, 95% CI 0.84, 1.28). We also found no significant association with most other cancers, including bladder cancer (RR 1.14, 95% CI 0.56, 2.35) and hematopoietic cancers overall (RR 0.89, 95% CI 0.59, 1.35) or their subtypes, including non‐Hodgkin lymphoma, multiple myeloma, and leukemia. We generally found no evidence of an association between personal use of hair dye and cancer risk, although our study is limited by small numbers for certain cancer types. (Cancer Sci 2009; 100: 1088–1091)
Determination of the soil organic carbon, nitrogen, available phosphorus and the combined aboveground plant materials in the semi‐arid Mbulu District, Tanzania
Authors: Cosmas Mligo
Published: March 2009

Soil of the semi‐arid Mbulu District is part of the tropical soils, covered with sparse trees, shrubs or grasses in which domestic grazing animals have prevented the wide spread of vegetation cover. The study aimed at determining soil organic carbon (OC), total nitrogen (N), available phosphorus (P) and the combined aboveground plant materials. Six study sites were established in which soil samples were collected at the depths of 0–5, 6–10 and 11–20 cm. Soil samples were analysed for OC, N and P as well as the levels of N and P in the combined aboveground materials of Panicum coloratum and Hyparrhenia filipendula. The percentage concentrations of OC, N and P were high in the top soil than in the deeper soil horizons. However, analysis of variance showed significant differences of OC in some sites whereas no difference for N and P between soil depth classes. OC was highly related with N and P along soil depth classes. It was concluded that the availability of N and P was because of the decomposition of organic matter in the soil. Soil N and P were highly related with the same in the combined aboveground plant materials. It was concluded that the increased concentration of N and P in the soil resulted into availability of the same in P. coloratum and H. filipendula. There was a very high variation in N and P among sites with different levels of intensity of grazing. It was concluded that grazing animals contributes to the redistribution of soil elements in the rangelands because they graze upon plant parts but the excreta are dropped away from the grazed spot.
Wind erosion of the wind‐deposited Navajo Sandstone, USA
Authors: Loope David B. , Mason Joseph A.
Published: March 2009

Outcrops of the Early Jurassic Navajo Sandstone in southern Utah and northern Arizona, south‐western USA are being actively eroded by sand‐laden, south‐westerly winds. Small‐scale stepped topography with risers facing into the wind develops even on steep canyon walls when wind‐swept grains strike the rock at a low angle. Photosynthetic, endolithic microbes directly underlie most outcrop surfaces; the crusts formed by these organisms are essential to formation of the small‐scale steps. Wind erosion of highlands also forms troughs and pits that are tens of metres across. The pits have deeply scalloped, overhanging walls, and contain central domes surrounded by ‘moats’ filled with dune sand. Wind erosion of aeolian sandstone is favoured by a positive feedback mechanism in which grains that are liberated from outcrops by impacting particles become a fresh supply of pre‐sorted abrasive particles for further attack.
Possible role for TRPV1 in neomycin‐induced inhibition of visceral hypersensitivity in rat
Authors: Van Den Wijngaard R. M. , Welting O. , Bulmer D. C. , Wouters M. M. , Lee K. , De Jonge W. J. , Boeckxstaens G. E.
Published: March 2009

Abstract  Transient receptor ion channel 1 (TRPV1) is a nociceptor involved in visceral hypersensitivity. Aminoglycosides like neomycin are not only potent antibiotics but in vitro data suggest that neomycin also acts as a TRPV1‐antagonist and alleviates somatic pain responses. To what extent neomycin reduces visceral hypersensitivity remains unknown. Therefore, we aimed to investigate whether neomycin can inhibit in vivo TRPV1‐dependent hypersensitivity responses in two rat models of visceral pain. In the first model rats were pretreated with intraperitoneal (i.p.) capsazepine, the selective TRPV1 antagonist SB‐705498, neomycin or vehicle alone and 30 min later instilled with intracolonic TRPV1‐activating capsaicin. Likewise, rats were pretreated with 10 days oral neomycin and then subjected to intracolonic capsaicin. The visceromotor response (VMR) to distension was measured before and after capsaicin application. In addition, the VMR to distension was measured in adult maternal separated rats before and after acute stress. Before the 2nd distension protocol these rats were treated with i.p. neomycin, amoxycillin or vehicle alone. Our results showed that capsaicin administration induced an enhanced VMR to distension that was prevented by i.p. capsazepine, SB‐705498 and neomycin. Oral neomycin treatment changed bacterial faecal content but could not inhibit capsaicin induced visceral hypersensitivity. In maternal separated rats acute stress induced an enhanced response to distension that was reversed by i.p. neomycin, but not amoxycillin. These data indicate that (i.p.) neomycin can inhibit visceral hypersensitivity to distension in a nonbactericidal manner and suggest that TRPV1‐modulation may be involved.
Evaluation of T cell responses in healing and nonhealing leishmaniasis reveals differences in T helper cell polarization ex vivo and in vitro
Authors: CHOI B.‐S. , KROPF P.
Published: March 2009

Experimental leishmaniasis is widely used to study the effector functions of T helper cell subsets in vivo. Healing and nonhealing Leishmania major infections have been correlated with T helper 1 and T helper 2 responses, respectively. In the present study, we determined T cell effector functions ex vivo, without any further restimulation and compared them to those obtained following antigen‐specific restimulation in vitro. Our results show that T helper cell responses are significantly less polarized when determined ex vivo as compared to those measured after restimulation in vitro. Moreover, the differences in CD4+ T cell proliferation observed between healer and nonhealer strains of mice differed ex vivo and in vitro. Our results suggest that determination of both ex vivo as well as in vitro T cell responses is crucial to characterize immune responses during experimental leishmaniasis.
The turkey, compared to the chicken, fails to mount an effective early immune response to Histomonas meleagridis in the gut
Authors: POWELL F. L. , ROTHWELL L. , CLARKSON M. J. , KAISER P.
Published: March 2009

Histomonosis is a disease of poultry caused by Histomonas meleagridis. Chickens usually recover while the mortality rate in turkeys is high. The immunological response of both species towards H. meleagridis was investigated. Parasites migrated in greater numbers to the turkey liver compared with that of chicken. Chicken mounted an effective caecal innate response, with increased expression of IL‐1β, CXCLi2 and IL‐6 mRNA, resulting in control of parasite numbers. The turkey failed to mount such an effective innate response in the caecal tonsil, allowing greater numbers to migrate to the liver, where a sustained, uncontrolled immune response was mounted, evidenced by the upregulation of mRNA for IL‐1β, CXCLi2, IFN‐γ, IL‐13, IL‐4 and IL‐10. Expression levels of mRNA of the chicken and turkey β‐defensin AvBD2 suggest that this response was not limited to the cytokines. There was an influx of CD4+, CD8α+, CD28+ and CD44+ cells into the livers of both species, coinciding with parasite movement. These influxes were more pronounced in the turkey, correlating with a decrease in numbers of the same cells in the spleen, which was not observed in the chicken. Antibody levels in the chicken increased more than those in the turkey, supporting evidence of an adaptive response.
Infectious complications after allogeneic stem cell transplantation: incidence in matched‐related and matched‐unrelated transplant settings
Authors: Rieger C.T. , Rieger H. , Kolb H.J. , Peterson L. , Huppmann S. , Fiegl M. , Ostermann H.
Published: March 2009

Abstract: Background. Bacterial, viral, and fungal pathogens frequently cause severe, life‐threatening infections in immunocompromised patients after allogeneic hematopoietic stem cell transplantation (SCT).

Objective. To compare the frequency of infections in patients with matched‐related (Group A) or with human leukocyte antigen (HLA)‐matched‐unrelated donors (Group B).

Patients and methods. Patients treated at our transplantation unit between April 2004 and April 2005 were enrolled into this analysis. Documentation comprised demographic data, conditioning treatment, stem cell source, clinical course, as well as microbiological and clinical data and mortality.

Results. We analyzed 59 patients, 22 in Group A and 37 in Group B. Both groups were well balanced regarding demographic data. Diagnoses were acute myeloid leukemia (30 of 59 patients, 50.8%), multiple myeloma (15.2%), acute lymphoblastic leukemia (11.9%), and chronic myeloid leukemia (10.2%). Patients in Group A developed infections in 95.5% of the cases compared with 97.3% in patients in Group B. Most frequently detected pathogens were Staphylococcus species, human herpesvirus‐6, and Epstein–Barr virus. Three proven fungal infections were detected in Group A compared with 9 proven fungal infections in Group B. Lung infiltrations were observed in equivalent incidence in both groups. Two years after transplantation, 55.9% of patients were alive (Group A: 68.2%; Group B: 48.6%, not significant).

Conclusion. Allogeneic SCT from HLA‐matched‐unrelated donors does not have a higher infection risk than patients transplanted from matched‐related donors.
Histopathological changes and tumour necrosis factor‐α, transforming growth factor‐β and tenascin expression in patients with primary type I membranoproliferative glomerulonephritis in remission
Authors: ARIKAN HAKKI , KOC MEHMET , CAKALAGAOGLU FULYA , TUGLULAR SERHAN , OZENER CETIN , AKOGLU EMEL
Published: March 2009

Aim:  Primary type I membranoproliferative glomerulonephritis (MPGN) is a rare cause of glomerular disease with a high relapse rate and poor prognosis. The aim of this study was: (i) to evaluate the histopathological findings associated with remission; and (ii) to document the possible clinical and histopathological factors predicting relapses.

Methods:  Eleven type I MPGN patients (five men, six women; mean age, 38.8 ± 13.5 years) who were in remission for at least 1 year after the cessation of immunosuppressive drugs were re‐biopsied. The intensity of immunostaining for tumor necrosis factor (TNF)‐α, transforming growth factor (TGF)‐β1, and tenascin was graded from 0 (no staining) to 3+ (maximum staining).

Results:  Mean baseline mesangial cellularity score and tubulointerstitial infiltration score were reduced and mesangial matrix expansion score was increased at protocol re‐biopsies compared to baseline. The glomerular and tubulointerstitial staining scores for TGF‐β1 and tenascin were higher than that of baseline. Reduced tubulointerstitial TNF‐α expression was found in re‐biopsy specimens compared to baseline. Patients have been followed for a mean time of 51.5 ± 22.2 months after the protocol biopsy. Eight patients had a relapse. Mesangial cellularity score and glomerular tenascin expression at re‐biopsy specimens were higher in relapsed patients compared to those without a relapse.

Conclusion:  Our study shows that mesangial cellularity and tubulointerstitial cell infiltration are reducing whereas mesangial matrix expansion, glomerular and tubulointerstitial TGF‐β1 and tenascin expression are increasing with remission. The higher mesangial cell proliferation and glomerular tenascin scores in remission are associated with the development of relapse.
Intravenous calcitriol versus paricalcitol in haemodialysis patients with severe secondary hyperparathyroidism
Authors: ABDUL GAFOR ABDUL HALIM , SAIDIN RASHIDI , LOO CHEE YEAN , MOHD ROZITA , ZAINUDIN SOEHARDY , SHAH SHAMSUL AZHAR , NORELLA KONG CHIEW TONG
Published: March 2009

Aim: Secondary hyperparathyroidism (SHPT) is common among haemodialysis patients. Intensive treatment with calcitriol is often complicated by hypercalcaemia, hyperphosphataemia and elevated calcium phosphorus (Ca X PO4) product. Paricalcitol is a vitamin D analogue developed to overcome some of the limitations of calcitriol therapy. The study objectives were to compare the response of intact parathyroid hormone (iPTH) and the incidence of hypercalcaemia, hyperphosphataemia and elevated Ca X PO4product in patients with severe SHPT treated with either i.v. calcitriol or i.v. paricalcitol.

Methods: This was a single centre randomized open label study. Patients with serum intact iPTH of 50 pmol/L or more were randomized to receive either i.v. calcitriol (0.01 ug/kg) or i.v. paricalcitol (0.04 ug/kg) during every haemodialysis treatment. Serum iPTH, calcium, phosphorus and alkaline phosphatase were measured at the beginning of the study and every 3 weeks for 12 weeks.

Results: Twenty‐five patients were enrolled into the study – 12 were randomized into the calcitriol group and 13 into the paricalcitol group. There were no differences in the baseline study parameters between both groups. Serum iPTH levels were significantly reduced (P = 0.003) only in the paricalcitol group but not in the calcitriol group (P = 0.101). On the other hand, serum calcium levels were significantly increased only in the calcitriol group (P = 0.004 vsP = 0.242). Serum phosphorus, alkaline phosphatase and Ca X PO4product were not different.

Conclusion: Intravenous paricalcitol may be superior to i.v. calcitriol for the treatment of severe SHPT in our chronic haemodialysis population. A larger randomized controlled trial is indicated to confirm these initial findings.