bluuebunny/crossref_metadata_2025 huggingface dataset:
A Comparison of Handwritten to Computerised Urological Operative Notes
Authors: Dukic Ivo , Shaw Greg , Dukic Marko , Hussain Mahreen , Al-Buheissi Salah , Maraj Barry
Published: November 2009

Introduction:

Operative notes are traditionally handwritten and are essential for providing optimal postoperative care and planning the future management of patients. This study compares handwritten to computerised operative notes using a common standard.

Method:

One hundred handwritten urological operative notes were compared to 97 urological database printed notes using the Royal College of Surgeons' of England (RCSEng) guidelines for Good Surgical Practice.

Results:

There was an overall improvement in the quality of documentation, excluding the recording of tissue removed and the presence of a signature. The recording of parameters in the printed operative database notes was greater than 95% in 16 out of 18 parameters assessed.

Conclusion:

We strongly recommend the use of an operative database to raise the standard of operative notes in order to improve patient care and to provide a robust medico-legal record.
Beyond ribosome rescue: tmRNA and co‐translational processes
Authors: Hayes Christopher S. , Keiler Kenneth C.
Published: November 2009

tmRNA is a unique bi‐functional RNA that acts as both a tRNA and an mRNA to enter stalled ribosomes and direct the addition of a peptide tag to the C terminus of nascent polypeptides. Despite a reasonably clear understanding of tmRNA activity, the reason for its absolute conservation throughout the eubacteria is unknown. Although tmRNA plays many physiological roles in different bacterial systems, recent studies suggest a general role for trans‐translation in monitoring protein folding and perhaps other co‐translational processes. This review will focus on these new hypotheses and the data that support them.
c‐Abl tyrosine kinase interacts with MAVS and regulates innate immune response
Authors: Song Ting , Wei Congwen , Zheng Zirui , Xu Yang , Cheng Xiaozhong , Yuan Yuan , Guan Kai , Zhang Yanhong , Ma Qingjun , Shi Wei , Zhong Hui
Published: November 2009

MINT‐7297498, MINT‐7297511, MINT‐7297557, MINT‐7297574: MAVS (uniprotkb:Q7Z434) physically interacts (MI:0915) with c‐Abl (uniprotkb:P00519) by anti tag coimmunoprecipitation (MI:0007)MINT‐7297542: c‐Abl (uniprotkb:P00519) physically interacts (MI:0915) with MAVS (uniprotkb:Q7Z434) by anti bait coimmunoprecipitation (MI:0006)MINT‐7297526: c‐Abl (uniprotkb:P00519) physically interacts (MI:0915) with MAVS (uniprotkb:Q7Z434) by far western blotting (MI:0047)
Structural activity relationship of flavonoids with estrogen‐related receptor gamma
Authors: Huang Zhiyan , Fang Fang , Wang Junjian , Wong Chi-Wai
Published: November 2009

MINT‐7297297, MINT‐7297435: PGC‐1 alpha NR2 (uniprotkb:Q9UBK2) binds (MI:0407) to ERR gamma (uniprotkb:P62508) by surface plasmon resonance (MI:0107)
Processivity of translation in the eukaryote cell: Role of aminoacyl‐tRNA synthetases
Authors: Mirande Marc
Published: November 2009

Several lines of evidence led to the conclusion that mammalian ribosomal protein synthesis is a highly organized biological process in vivo. A wealth of data support the concept according to which tRNA aminoacylation, formation of the ternary complex on EF1A and delivery of aminoacyl‐tRNA to the ribosome is a processive mechanism where tRNA is vectorially transferred from one component to another. Polypeptide extensions, referred to as tRBDs (tRNA binding domains), are appended to mammalian and yeast aminoacyl‐tRNA synthetases. The involvement of these domains in the capture of deacylated tRNA and in the sequestration of aminoacylated tRNA, suggests that cycling of tRNA in translation is mediated by the processivity of the consecutive steps. The possible origin of the tRBDs is discussed.
Cell signaling: What is the signal and what information does it carry?
Authors: Brent Roger
Published: November 2009

This paper reviews key findings from quantitative study of the yeast pheromone response system. Most come from single cell experiments that quantify molecular events the system uses to operate. After induction, signal propagation is relatively slow; peak activity takes minutes to reach the nucleus. At each measurement point along the transmission chain, signal rises, overshoots, peaks, and declines toward steady state. At at least one measurement point, this decline depends on negative feedback. The system senses and relays percent receptor occupancy, and one effect of the feedback is to maximize precision of this transmitted information. Over time, the system constantly adjusts quantitative behaviors to convey extracellular ligand concentration faithfully. These behaviors and mechanisms that control them are likely to be general for metazoan signaling systems.
Differential functions of genes regulated by VEGF–NFATc1 signaling pathway in the migration of pulmonary valve endothelial cells
Authors: Jang Gun Hyuk , Park In-Sook , Yang Jeong Hee , Bischoff Joyce , Lee You Mie
Published: November 2009

We have reported that vascular endothelial growth factor (VEGF)‐A induces the proliferation of human pulmonary valve endothelial cells (HPVECs) through nuclear factor in activated T cells (NFAT)c1 activation [1]. Here we show that VEGF‐A increases the migration of HPVECs through NFATc1 activation, suggesting that VEGF‐A/NFATc1 regulates the migration of HPVECs. To learn how this pathway may be involved in post‐natal valvular repair, HPVECs were treated with VEGF‐A, with or without cyclosporine A to selectively block VEGF–NFATc1 signaling. Down Syndrome critical region 1 (DSCR1) and heparin‐binding EGF‐like growth factor (HB‐EGF) are two genes identified by DNA microarray as being up‐regulated by VEGF‐A in a cyclosporine‐A‐sensitive manner. DSCR1 silencing increased the migration of ovine valve endothelial cells, whereas HB‐EGF silencing inhibited migration. This differential effect suggests that VEGF‐A/NFATc1 signaling might be a crucial coordinator of endothelial cell migration in post‐natal valves.
Fungal regulatory evolution: cis and trans in the balance
Authors: Thompson Dawn Anne , Regev Aviv
Published: November 2009

Regulatory divergence is likely a major driving force in evolution. Comparative genomics is being increasingly used to infer the evolution of gene regulation. Ascomycota fungi are uniquely suited among eukaryotes for regulatory evolution studies, due to broad phylogenetic scope, many sequenced genomes, and tractability of genomic analysis. Here we review recent advances in the identification of the contribution of cis‐ and trans‐factors to expression divergence. Whereas current strategies have led to the discovery of surprising signatures and mechanisms, we still understand very little about the adaptive role of regulatory evolution. Empirical studies including experimental evolution, comparative functional genomics and hybrid and engineered strains are showing early promise toward deciphering the contribution of regulatory divergence to adaptation.
Serine 62 is a phosphorylation site in folliculin, the Birt–Hogg–Dubé gene product
Authors: Wang Lu , Kobayashi Toshiyuki , Piao Xianghua , Shiono Masatoshi , Takagi Yumiko , Mineki Reiko , Taka Hikari , Zhang Danqing , Abe Masaaki , Sun Guodong , Hagiwara Yoshiaki , Okimoto Kazuo , Matsumoto Izumi , Kouchi Mami , Hino Okio
Published: November 2009

MINT‐7298229: FNIPL (uniprotkb:Q9P278) physically interacts (MI:0915) with Flcn (uniprotkb:Q76JQ2) by anti tag coimmunoprecipitation (MI:0007)
Functional interactions by transfer RNAs in the ribosome
Authors: Khade Prashant , Joseph Simpson
Published: November 2009

Recent X‐ray crystal structures of the ribosome have revolutionized the field by providing a much‐needed structural framework to understand ribosome function. Indeed, the crystal structures rationalize much of the genetic and biochemical data that have been meticulously gathered over 50 years. Here, we focus on the interactions between tRNAs and the ribosome and describe some of the insights that the structures provide about the mechanism of translation. Both high‐resolution structures and functional studies are essential for fully appreciating the complex process of protein synthesis.
Numerical modeling of valley glacier stagnation as a paleoclimatic indicator
Authors: Vacco David A. , Alley Richard B. , Pollard David , Reusch David B.
Published: November 2009

Stagnation of the terminal region of a glacier occurs in response to sufficiently large and rapid climatic warming, so the presence of stagnation deposits provides quantitative information on the climate change that forced retreat. Here we use a simple flow-line glacier model to investigate the relationship between stagnation, climate forcing and aspects of the glacier bed. For climatic warming greater than the threshold to cause stagnation, larger or faster warming events cause longer regions of a glacier to stagnate. Smaller or slower warming episodes, below the threshold for stagnation, cause retreat while active flow persists along the entire glacier length. The threshold for stagnation depends not only on the climatic forcing but also on many other aspects of the glacier, with stagnation favored by factors including a lower mean bed slope with greater roughness. Quantitative determination of the climatic forcing consistent with the occurrence or absence of stagnation deposits requires that these site-specific characteristics be incorporated in modeling.
Age of road-killed common brushtail possums (Trichosurus vulpecula) and common ringtail possums (Pseudocheirus peregrinus) in an urban environment
Authors: Giffney R. A. , Russell T. , Kohen J. L.
Published: November 2009

Road-associated mortality has been identified as having major ecological effects on small, fragmented and declining populations. Both the common brushtail possum (Trichosurus vulpecula) and common ringtail possum (Pseudocheirus peregrinus) appear to be in decline in some regions across their natural ranges. Urban populations may be an exception; however, little is known of their population ecology. This study investigates age trends in a subset of road-killed brushtail and ringtail possums collected along eight northern Sydney roads between March 2004 and March 2006. From a total of 591 recorded road-killed possums, 86 were collected for use in this study (36 brushtails, 50 ringtails). Age was estimated using tooth wear patterns on cleaned skulls. Both species showed trends associated with age, and younger possums of both species were more likely to be killed on roads than older animals. Male-biased dispersal of subadult possums is considered a major contributing factor to the over-representation of young brushtail possums in this road-kill sample.
Ephrin-B1 and ephrin-B2 mediate EphB-dependent presynaptic development via syntenin-1
Authors: McClelland Andrew C. , Sheffler-Collins Sean I. , Kayser Matthew S. , Dalva Matthew B.
Published: November 2009

The development of central nervous system synapses requires precise coordination between presynaptic and postsynaptic components. The EphB family controls postsynaptic development by interacting with glutamate receptors and regulating dendritic filopodia motility, but how EphBs induce the formation of presynaptic specializations is less well understood. Here, we show that knockdown of presynaptic ephrin-B1, ephrin-B2, or syntenin-1, but not ephrin-B3, prevents EphB-dependent presynaptic development. Ephrin-B1, ephrin-B2, and syntenin-1 are clustered together with presynaptic markers, suggesting that these molecules function jointly in presynaptic development. Knockdown of ephrin-B1 or ephrin-B2 reduces the number of synaptic specializations and the colocalization of syntenin-1 with synaptic markers. Simultaneous knockdown of ephrin-B1 and ephrin-B2 suggests that they function independently in the formation of synaptic contacts, but act together to recruit syntenin-1 to presynaptic terminals. Taken together, these results demonstrate that ephrin-B1 and ephrin-B2 function with EphB to mediate presynaptic development via syntenin-1.
Regulation of Class IA PI 3-kinases: C2 domain-iSH2 domain contacts inhibit p85/p110α and are disrupted in oncogenic p85 mutants
Authors: Wu Haiyan , Shekar S. Chandra , Flinn Rory J. , El-Sibai Mirvat , Jaiswal Bijay S. , Sen K. Ilker , Janakiraman Vasantharajan , Seshagiri Somasekar , Gerfen Gary J. , Girvin Mark E. , Backer Jonathan M.
Published: November 2009

We previously proposed a model of Class IA PI3K regulation in which p85 inhibition of p110α requires (
i
) an inhibitory contact between the p85 nSH2 domain and the p110α helical domain, and (
ii
) a contact between the p85 nSH2 and iSH2 domains that orients the nSH2 so as to inhibit p110α. We proposed that oncogenic truncations of p85 fail to inhibit p110 due to a loss of the iSH2-nSH2 contact. However, we now find that within the context of a minimal regulatory fragment of p85 (the nSH2-iSH2 fragment, termed p85ni), the nSH2 domain rotates much more freely (τ
c
≈12.7 ns) than it could if it were interacting rigidly with the iSH2 domain. These data are not compatible with our previous model. We therefore tested an alternative model in which oncogenic p85 truncations destabilize an interface between the p110α C2 domain (residue N345) and the p85 iSH2 domain (residues D560 and N564). p85ni-D560K/N564K shows reduced inhibition of p110α, similar to the truncated p85ni-572
STOP
. Conversely, wild-type p85ni poorly inhibits p110αN345K. Strikingly, the p110αN345K mutant is inhibited to the same extent by the wild-type or truncated p85ni, suggesting that mutation of p110α-N345 is not additive with the p85ni-572
STOP
mutation. Similarly, the D560K/N564K mutation is not additive with the p85ni-572
STOP
mutant for downstream signaling or cellular transformation. Thus, our data suggests that mutations at the C2-iSH2 domain contact and truncations of the iSH2 domain, which are found in human tumors, both act by disrupting the C2-iSH2 domain interface.
Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival
Authors: Bogunovic Dusan , O'Neill David W. , Belitskaya-Levy Ilana , Vacic Vladimir , Yu Yi-Lo , Adams Sylvia , Darvishian Farbod , Berman Russell , Shapiro Richard , Pavlick Anna C. , Lonardi Stefano , Zavadil Jiri , Osman Iman , Bhardwaj Nina
Published: November 2009

Although remission rates for metastatic melanoma are generally very poor, some patients can survive for prolonged periods following metastasis. We used gene expression profiling, mitotic index (MI), and quantification of tumor infiltrating leukocytes (TILs) and CD3+ cells in metastatic lesions to search for a molecular basis for this observation and to develop improved methods for predicting patient survival. We identified a group of 266 genes associated with postrecurrence survival. Genes positively associated with survival were predominantly immune response related (e.g.,ICOS,CD3d,ZAP70,TRAT1,TARP,GZMK,LCK,CD2,CXCL13,CCL19,CCR7,VCAM1) while genes negatively associated with survival were cell proliferation related (e.g.,PDE4D,CDK2,GREF1,NUSAP1,SPC24). Furthermore, any of the 4 parameters (prevalidated gene expression signature, TILs, CD3, and in particular MI) improved the ability of Tumor, Node, Metastasis (TNM) staging to predict postrecurrence survival; MI was the most significant contributor (HR = 2.13,P= 0.0008). An immune response gene expression signature and presence of TILs and CD3+ cells signify immune surveillance as a mechanism for prolonged survival in these patients and indicate improved patient subcategorization beyond current TNM staging.
Nogo receptor 1 regulates formation of lasting memories
Authors: Karlén Alexandra , Karlsson Tobias E. , Mattsson Anna , Lundströmer Karin , Codeluppi Simone , Pham Therese M. , Bäckman Cristina M. , Ögren Sven Ove , Åberg Elin , Hoffman Alexander F. , Sherling Michael A. , Lupica Carl R. , Hoffer Barry J. , Spenger Christian , Josephson Anna , Brené Stefan , Olson Lars
Published: November 2009

Formation of lasting memories is believed to rely on structural alterations at the synaptic level. We had found that increased neuronal activity down-regulates Nogo receptor-1 (NgR1) in brain regions linked to memory formation and storage, and postulated this to be required for formation of lasting memories. We now show that mice with inducible overexpression of NgR1 in forebrain neurons have normal long-term potentiation and normal 24-h memory, but severely impaired month-long memory in both passive avoidance and swim maze tests. Blocking transgene expression normalizes these memory impairments. Nogo, Lingo-1, Troy, endogenous NgR1, and BDNF mRNA expression levels were not altered by transgene expression, suggesting that the impaired ability to form lasting memories is directly coupled to inability to down-regulate NgR1. Regulation of NgR1 may therefore serve as a key regulator of memory consolidation. Understanding the molecular underpinnings of synaptic rearrangements that carry lasting memories may facilitate development of treatments for memory dysfunction.
Refolding dynamics of stretched biopolymers upon force quench
Authors: Hyeon Changbong , Morrison Greg , Pincus David L. , Thirumalai D.
Published: November 2009

Single-molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse of RNA and proteins upon force quench by using simulations of an RNA hairpin and theory based on the de Gennes model for homopolymer collapse. The folding time, τ

F

, depends asymmetrically on δ
f

S

=
f

S

−
f

m

and δ
f

Q

=
f

m

−
f

Q

where
f

S

(
f

Q

) is the stretch (quench) force and
f

m

is the transition midforce of the RNA hairpin. In accord with experiments, the relaxation kinetics of the molecular extension,
R
(
t
), occurs in three stages: A rapid initial decrease in the extension is followed by a plateau and finally, an abrupt reduction in
R
(
t
) occurs as the native state is approached. The duration of the plateau increases as λ = τ

Q

/τ

F

decreases (where τ

Q

is the time in which the force is reduced from
f

S

to
f

Q

). Variations in the mechanisms of force-quench relaxation as λ is altered are reflected in the experimentally measurable time-dependent entropy, which is computed directly from the folding trajectories. An analytical solution of the de Gennes model under tension reproduces the multistage stage kinetics in
R
(
t
). The prediction that the initial stages of collapse should also be a generic feature of polymers is validated by simulation of the kinetics of toroid (globule) formation in semiflexible (flexible) homopolymers in poor solvents upon quenching the force from a fully stretched state. Our findings give a unified explanation for multiple disparate experimental observations of protein folding.
MEK1 mutations confer resistance to MEK and B-RAF inhibition
Authors: Emery Caroline M. , Vijayendran Krishna G. , Zipser Marie C. , Sawyer Allison M. , Niu Lili , Kim Jessica J. , Hatton Charles , Chopra Rajiv , Oberholzer Patrick A. , Karpova Maria B. , MacConaill Laura E. , Zhang Jianming , Gray Nathanael S. , Sellers William R. , Dummer Reinhard , Garraway Levi A.
Published: November 2009

Genetic alterations that activate the mitogen-activated protein kinase (MAP kinase) pathway occur commonly in cancer. For example, the majority of melanomas harbor mutations in the
BRAF
oncogene, which are predicted to confer enhanced sensitivity to pharmacologic MAP kinase inhibition (e.g., RAF or MEK inhibitors). We investigated the clinical relevance of MEK dependency in melanoma by massively parallel sequencing of resistant clones generated from a
MEK1
random mutagenesis screen in vitro, as well as tumors obtained from relapsed patients following treatment with AZD6244, an allosteric MEK inhibitor. Most mutations conferring resistance to MEK inhibition in vitro populated the allosteric drug binding pocket or α-helix C and showed robust (≈100-fold) resistance to allosteric MEK inhibition. Other mutations affected MEK1 codons located within or abutting the N-terminal negative regulatory helix (helix A), which also undergo gain-of-function germline mutations in cardio-facio-cutaneous (CFC) syndrome. One such mutation, MEK1(P124L), was identified in a resistant metastatic focus that emerged in a melanoma patient treated with AZD6244. Both MEK1(P124L) and MEK1(Q56P), which disrupts helix A, conferred cross-resistance to PLX4720, a selective B-RAF inhibitor. However, exposing
BRAF
-mutant melanoma cells to AZD6244 and PLX4720 in combination prevented emergence of resistant clones. These results affirm the importance of MEK dependency in
BRAF
-mutant melanoma and suggest novel mechanisms of resistance to MEK and B-RAF inhibitors that may have important clinical implications.
Design and construction of diverse mammalian prion strains
Authors: Colby David W. , Giles Kurt , Legname Giuseppe , Wille Holger , Baskakov Ilia V. , DeArmond Stephen J. , Prusiner Stanley B.
Published: November 2009

Prions are infectious proteins that encipher biological information within their conformations; variations in these conformations dictate different prion strains. Toward elucidating the molecular language of prion protein (PrP) conformations, we produced an array of recombinant PrP amyloids with varying conformational stabilities. In mice, the most stable amyloids produced the most stable prion strains that exhibited the longest incubation times, whereas more labile amyloids generated less stable strains and shorter incubation times. The direct relationship between stability and incubation time of prion strains suggests that labile prions are more fit, in that they accumulate more rapidly and thus kill the host faster. Although incubation times can be changed by altering the PrP expression level, PrP sequence, prion dose, or route of inoculation, we report here the ability to modify the incubation time predictably in mice by modulating the prion conformation.
Induction of a MT1-MMP and MT2-MMP-dependent basement membrane transmigration program in cancer cells by Snail1
Authors: Ota Ichiro , Li Xiao-Yan , Hu Yuexian , Weiss Stephen J.
Published: November 2009

The ability of carcinoma cells arising at primary sites to cross their underlying basement membrane (BM), a specialized form of extracellular matrix that subtends all epithelial cells, and to access the host vasculature are central features of the malignant phenotype. The initiation of the invasive phenotype has been linked to the aberrant expression of zinc-finger transcriptional repressors, like Snail1, which act by triggering an epithelial-mesenchymal cell-like transformation (EMT-like) via the regulation of largely undefined, downstream effectors. Herein, we find that Snail1 induces cancer cells to (
i
) degrade and perforate BM barriers, (
ii
) initiate angiogenesis, and (
iii
) and intravasate vascular networks in vivo via a matrix metalloproteinase (MMP)-dependent process. Unexpectedly, the complete Snail1 invasion program can be recapitulated by expressing directly either of the membrane-anchored metalloproteinases, MT1-MMP or MT2-MMP. The pro-invasive, angiogenic, and metastatic activities of MT1-MMP and MT2-MMP are unique relative to all other metalloproteinase family members and cannot be mimicked in vivo by the secreted MMPs, MMP-1, MMP-2, MMP-3, MMP-7, MMP-9, or MMP-13. Further, siRNA-specific silencing of MT1-MMP and MT2-MMP ablates completely the ability of Snail1 to drive cancer cell BM invasion, induce angiogenesis, or trigger intravasation. Taken together, these data demonstrate that MT1-MMP and MT2-MMP cooperatively function as direct-acting, pro-invasive factors that confer Snail1-triggered cells with the key activities most frequently linked to morbidity and mortality in cancer.
Markedly enhanced colon tumorigenesis inApcMinmice lacking glutathione S-transferase Pi
Authors: Ritchie Kenneth J. , Walsh Shaun , Sansom Owen J. , Henderson Colin J. , Wolf C. Roland
Published: November 2009

Glutathione transferases are a multigene family of proteins that catalyze the conjugation of toxic electrophiles and carcinogens to glutathione. Glutathione transferase Pi (GSTP) is commonly overexpressed in human tumors and there is emerging evidence that the enzyme has additional cellular functions in addition to its role in drug and carcinogen detoxification. To investigate the unique functions of this enzyme, we have crossedGstpnull mice with an initiated model of colon cancer, theApcMinmouse. In contrast to theApcMin/+Gstp1/p2+/+(Gstp-wtApcMin) mice, which rarely develop colonic tumours,ApcMin/+Gstp1/p2−/−(Gstp-nullApcMin) mice had a 6-fold increase in colon adenoma incidence, and a 50-fold increase in colorectal adenoma multiplicity, relative toGstp-wtApcMin. This increase was associated with early tumor onset and decreased survival. Analysis of the biochemical changes in the colon tissue ofGstp-nullApcMinmice demonstrated a marked induction of many inflammatory genes, including IL-6, IL-4, IFN-γ, and inducible nitric oxide synthase. In support of the induction of inducible nitric oxide synthase, a profound induction of nitrotyrosine adducts was observed.Gstptherefore appears to play a role in controlling inflammatory responses in the colon, which would explain the change in tumor incidence observed. These data also suggest that individual variation in GSTP levels may be a factor in colon cancer susceptibility.
GroEL/GroES cycling: ATP binds to an open ring before substrate protein favoring protein binding and production of the native state
Authors: Tyagi Navneet K. , Fenton Wayne A. , Horwich Arthur L.
Published: November 2009

The GroEL/GroES reaction cycle involves steps of ATP and polypeptide binding to an open GroEL ring before the GroES encapsulation step that triggers productive folding in a sequestered chamber. The physiological order of addition of ATP and nonnative polypeptide, typically to the open
trans
ring of an asymmetrical GroEL/GroES/ADP complex, has been unknown, although there have been assumptions that polypeptide binds first, allowing subsequent ATP-mediated movement of the GroEL apical domains to exert an action of forceful unfolding on the nonnative polypeptide. Here, using fluorescence measurements, we show that the physiological order of addition is the opposite, involving rapid binding of ATP, accompanied by nearly as rapid apical domain movements, followed by slower binding of nonnative polypeptide. In order-of-addition experiments, approximately twice as much Rubisco activity was recovered when nonnative substrate protein was added after ATP compared with it being added before ATP, associated with twice as much Rubisco protein recovered with the chaperonin. Furthermore, the rate of Rubisco binding to an ATP-exposed ring was twice that observed in the absence of nucleotide. Finally, when both ATP and Rubisco were added simultaneously to a GroEL ring, simulating the physiological situation, the rate of Rubisco binding corresponded to that observed when ATP had been added first. We conclude that the physiological order, ATP binding before polypeptide, enables more efficient capture of nonnative substrate proteins, and thus allows greater recovery of the native state for any given round of the chaperonin cycle.
Inducible costimulator promotes helper T-cell differentiation through phosphoinositide 3-kinase
Authors: Gigoux Mathieu , Shang Jijun , Pak Youngshil , Xu Minghong , Choe Jongseon , Mak Tak W. , Suh Woong-Kyung
Published: November 2009

The T-cell costimulatory receptors, CD28 and the inducible costimulator (ICOS), are required for the generation of follicular B helper T cells (TFH) and germinal center (GC) reaction. A common signal transducer used by CD28 and ICOS is the phosphoinositide 3-kinase (PI3K). Although it is known that CD28-mediated PI3K activation is dispensable for GC reaction, the role of ICOS-driven PI3K signaling has not been defined. We show here that knock-in mice that selectively lost the ability to activate PI3K through ICOS had severe defects in TFHgeneration, GC reaction, antibody class switch, and antibody affinity maturation. In preactivated CD4+T cells, ICOS delivered a potent PI3K signal that was critical for the induction of the key TFHcytokines, IL-21 and IL-4. Under the same settings, CD28 was unable to activate PI3K but supported a robust secondary expansion of T cells. Thus, our results demonstrate a nonredundant function of ICOS-PI3K pathway in the generation of TFHand suggest that CD28 and ICOS play differential roles during a multistep process of TFHdifferentiation.
Proteiniclasticum ruminis gen. nov., sp. nov., a strictly anaerobic proteolytic bacterium isolated from yak rumen
Authors: Zhang Kegui , Song Lei , Dong Xiuzhu
Published: November 2009

Two strictly anaerobic, proteolytic bacterial strains, designated strain D3RC-2Tand D3RC-3r, were isolated from a cellulose-degrading mixed culture enriched from yak rumen content. The strains were Gram-stain negative and non-spore-forming with cell sizes of 0.5–0.8×0.6–2.0 μm. The temperature range for growth was 24–46 °C (optimum 38–39 °C) and the pH range was between 5.6 and 8.7 (optimum 7.0–7.3). Both strains used soya peptone, tryptone,l-phenylalanine,l-leucine,l-methionine,l-serine,l-valine,l-threonine andl-histidine as carbon and nitrogen sources, but did not use any of the saccharides tested. The major fermentation products from PY medium were acetate, propionate and iso-butyrate. The DNA G+C contents of strains D3RC-2Tand D3RC-3r were 41.0±0.1 mol% and 41.3±0.1 mol% (HPLC), respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two strains represented a new phyletic sublineage within the familyClostridiaceae, with <93.8 % 16S rRNA gene sequence similarity to recognized species. On the basis of the phenotypic, genotypic and physiological evidence, strains D3RC-2Tand D3RC-3r are proposed as representing a novel species of a new genus, for which the nameProteiniclasticum ruminisgen. nov., sp. nov. is proposed. The type strain of the type species is D3RC-2T(=AS 1.5057T=JCM 14817T).
Laceyella tengchongensis sp. nov., a thermophile isolated from soil of a volcano
Authors: Zhang Jing , Tang Shu-Kun , Zhang Yu-Qin , Yu Li-Yan , Klenk Hans-Peter , Li Wen-Jun
Published: November 2009

A thermophilic strain, designated YIM 10002T, was isolated from a soil sample of Big Empty Volcano in Tengchong county, Yunnan province, south-west China, and a polyphasic approach was used to investigate its taxonomic position. Strain YIM 10002T formed endospores on both aerial and substrate mycelia. Whole-cell hydrolysates contained meso-diaminopimelic acid, ribose, xylose and glucose. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The predominant menaquinone was MK-9. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides, together with some unknown phospholipids. The G+C content of its genomic DNA was 48.6 mol%. All of these chemotaxonomic data together with morphological characters consistently assigned strain YIM 10002T to the genus Laceyella. 16S rRNA gene sequence analysis showed that strain YIM 10002T was most closely related to Laceyella sacchari KCTC 9790T and Laceyella putida KCTC 3666T (99.9 and 98.0 % 16S rRNA gene sequence similarity, respectively). However, strain YIM 10002T showed relatively low DNA–DNA relatedness (34.0 and 39.0 %, respectively) with the above strains. Therefore, strain YIM 10002T represents a novel species of the genus Laceyella, for which the name Laceyella tengchongensis sp. nov. is proposed. The type strain is YIM 10002T (=DSM 45262T =CCTCC AA 208050T).
Clostridium arbusti sp. nov., an anaerobic bacterium isolated from pear orchard soil
Authors: Jung Min Young , Park In-Soon , Kim Wonyong , Kim Hong Lim , Paek Woon Kee , Chang Young-Hyo
Published: November 2009

An obligately anaerobic, Gram-positive, spore-forming bacterial strain, designated SL206T, was isolated from pear orchard soils. Strain SL206T cells were straight or slightly curved rods, with motility by peritrichate flagella. Cell walls contained meso-diaminopimelic acid; wall sugars were glucose, rhamnose and mannose. The major fatty acids were C16 : 0, C18 : 1
ω9c and summed feature 10 (containing C18 : 1
ω11c/9t/6t). API 20A reactions were negative for oxidase, catalase and acid production from l-rhamnose, sucrose, trehalose, d-xylose, melezitose, salicin and d-sorbitol, and positive for acid production from d-glucose, sucrose, maltose, d-mannose and raffinose. Glucose was fermented to acetate, butyrate, CO2, H2 and ethanol in culture. The G+C content of the genomic DNA was 31.1 mol%. Based on comparative 16S rRNA gene sequence analysis, the isolate belonged to the genus Clostridium and formed a clade with Clostridium pasteurianum. The species most closely related to strain SL206T were C. pasteurianum (98.6 % similarity) and Clostridium acidisoli (97.8 % similarity). In DNA–DNA relatedness studies, the isolate had 59.5 % relatedness with C. pasteurianum and thus represented a unique species. On the basis of these studies, strain SL206T (=KCTC 5449T =JCM 14858T) is proposed to represent the type strain of a novel species, Clostridium arbusti sp. nov.
Haloterrigena daqingensis sp. nov., an extremely haloalkaliphilic archaeon isolated from a saline–alkaline soil
Authors: Wang Shuang , Yang Qian , Liu Zhi-Hua , Sun Lei , Wei Dan , Zhang Jun-Zheng , Song Jin-Zhu , Yuan Hai-Feng
Published: November 2009

A haloalkaliphilic archaeon, strain JX313T, was isolated from a saline–alkaline soil from Daqing, Heilongjiang Province, China. Its morphological, physiological and biochemical features and 16S rRNA gene sequence were determined. Colonies of the strain were orange–red and cells were non-motile cocci and Gram-stain-variable. The strain required at least 1.7 M NaCl for growth, with optimal growth occurring in 2.0–2.5 M NaCl. Growth was observed at 20–50 °C and pH 8.0–10.5, with optimal growth at 35 °C and pH 10.0. The G+C content of its genomic DNA was 59.3 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain JX313T is associated with the genera Haloterrigena and Natrinema and is most closely related to Haloterrigena salina XH-65T (96.2 % sequence similarity) and Haloterrigena hispanica FP1T (96.2 %). DNA–DNA hybridization experiments revealed that the relatedness of strain JX313T to type strains of related species of the genus Haloterrigena or Natrinema was less than 50 %. Furthermore, the cellular polar lipids of strain JX313T, identified as phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and mannose-2,6-disulfate (1→2)-glucose glycerol diether (S2-DGD), were consistent with the polar lipid characteristics of the genus Haloterrigena. Therefore, phylogenetic analysis, phenotypic assessment and chemotaxonomic data showed that JX313T represents a novel species within the genus Haloterrigena, for which the name Haloterrigena daqingensis sp. nov. is proposed. The type strain is JX313T (=CGMCC 1.8909T =NBRC 105739T).
Nocardia mikamii sp. nov., isolated from human pulmonary infections in the USA
Authors: Jannat-Khah Deanna , Kroppenstedt Reiner M. , Klenk Hans-Peter , Spröer Cathrin , Schumann Peter , Lasker Brent A. , Steigerwalt Arnold G. , Hinrikson Hans P. , Brown June M.
Published: November 2009

Four nocardioform bacterial strains isolated from clinical respiratory sources were characterized using a polyphasic taxonomic approach. On the basis of 16S rRNA gene sequence analyses, these strains were found to be 100 % similar to each other and were shown to belong to the genus Nocardia. Chemotaxonomic data [major menaquinone: ω-cyclic isoprene side chain MK-8(H4cycl
); major polar lipids: diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides; major fatty acids: monounsaturated fatty acids with a considerable amount of tuberculostearic acid; and mycolic acids (52–62 carbon atoms)] were consistent with the assignment of the novel strains to the genus Nocardia. Comparative phylogenetic analysis of the 16S rRNA gene sequences showed that the novel strains were related to Nocardia cerradoensis DSM 44546T (99.8 %) and Nocardia aobensis JCM 12352T (99.6 %). Analysis of gyrB gene sequences showed these strains were related to N. aobensis (96.6 %) and to N. cerradoensis (96.3 %). The results suggest that gyrB gene sequencing is a more powerful tool than 16S rRNA gene sequencing for taxonomic identification within the genus Nocardia. DNA–DNA hybridization and physiological and biochemical tests supported the genotypic and phenotypic differentiation of the novel strains from related species. These data indicated that the new strains represent a novel species within the genus Nocardia, for which the name Nocardia mikamii sp. nov. is proposed, with strain W8061T (=DSM 45174T=JCM 15508T) as the type strain.
Shewanella corallii sp. nov., a marine bacterium isolated from a Red Sea coral
Authors: Shnit-Orland Maya , Sivan Alex , Kushmaro Ariel
Published: November 2009

A marine bacterial strain, designated fav-2-10-05T, was isolated from the mucus layer of a coral of the genus Favia, collected from the coral reef in the Gulf of Eilat, Israel (29.5 ° N 34.9 ° E). On the basis of 16S rRNA gene sequence comparisons, strain fav-2-10-05T was affiliated with the family Shewanellaceae. The closest relatives of strain fav-2-10-05T were Shewanella marisflavi SW-117T (96.0 % 16S rRNA gene sequence similarity) and Shewanella haliotis DW-1T (95.9 %). Strain fav-2-10-05T was Gram-negative, rod-shaped and motile by means of a single polar flagellum and formed yellow–brownish colonies within 2 days of incubation at 26 °C. Strain fav-2-10-05T demonstrated antibacterial activity against indicator strains and grew in the presence of 0.5–8.0 % (w/v) NaCl and at 10–37 °C. The major fatty acids were C17 : 1
ω8c (21.6 %), iso-C15 : 0 (18.6 %), C15 : 0 (9.1 %) and iso-C13 : 0 (8.9 %). The DNA G+C content was 49.1 mol%. The phylogenetic and phenotypic analyses of strain fav-2-10-05T suggested that it belongs to a novel species of the genus Shewanella, for which the name Shewanella corallii sp. nov. is proposed. The type strain is fav-2-10-05T (=LMG 24563T =DSM 21332T).
Cohnella thailandensis sp. nov., a xylanolytic bacterium from Thai soil
Authors: Khianngam Saowapar , Tanasupawat Somboon , Akaracharanya Ancharida , Kim Kwang Kyu , Lee Keun Chul , Lee Jung-Sook
Published: November 2009

A xylanolytic bacterium, strain S1-3T, was isolated from soil collected in Nan province, Thailand. It was characterized taxonomically based on phenotypic characteristics and 16S rRNA gene sequence comparison. The strain was a Gram-stain-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium. It contained meso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-7. Iso-C16 : 0 (39.5 %) and anteiso-C15 : 0 (26.8 %) were predominant cellular fatty acids. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and lysyl-phosphatidylglycerol were the major polar lipids. The DNA G+C content was 53.3 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain S1-3T was affiliated to the genus Cohnella, and was closely related to Cohnella ginsengisoli GR21-5T and Cohnella thermotolerans CCUG 47242T with 95.7 and 95.3 % sequence similarity, respectively. Strain S1-3T could be clearly distinguished from related species of the genus Cohnella by its physiological and biochemical characteristics as well as by its phylogenetic position. Therefore, the strain represents a novel species of the genus Cohnella, for which the name Cohnella thailandensis sp. nov. is proposed. The type strain is S1-3T (=KCTC 22296T =TISTR 1890T =PCU 306T).
Rhodotorula rosulata sp. nov., Rhodotorula silvestris sp. nov. and Rhodotorula straminea sp. nov., novel myo-inositol-assimilating yeast species in the Microbotryomycetes
Authors: Golubev Wladyslav I. , Scorzetti Gloria
Published: November 2009

Three novel species are described as Rhodotorula rosulata sp. nov. (type strain VKM Y-2962T =CBS 10977T), Rhodotorula silvestris sp. nov. (type strain VKM Y-2971T =CBS 11420T) and Rhodotorula straminea sp. nov. (type strain VKM Y-2964T =CBS 10976T) based on the study of eight isolates from needle litter. The new species, phylogenetically located within the Microbotryomycetes, are related to glucuronate-assimilating species of the genus Rhodotorula. Sequencing of the D1/D2 domains of the LSU rDNA gene and the internal transcribed spacer (ITS) region, as well as physiological characterization, revealed their distinct taxonomic positions.
Euzebya tangerina gen. nov., sp. nov., a deeply branching marine actinobacterium isolated from the sea cucumber Holothuria edulis, and proposal of Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov.
Authors: Kurahashi Midori , Fukunaga Yukiyo , Sakiyama Yayoi , Harayama Shigeaki , Yokota Akira
Published: November 2009

A tangerine-coloured, Gram-positive actinobacterial strain, designated F10T, was isolated from the abdominal epidermis of a sea cucumber, Holothuria edulis, collected in seawater off the coast of Japan. A 16S rRNA gene sequence analysis indicated that strain F10T was a member of the class Actinobacteria and was most closely related to Nitriliruptor alkaliphilus ANL-iso2T (87.4 % sequence similarity). Phylogenetic analyses showed that strain F10T represented a novel, deep-rooted, and distinct phylogenetic lineage within the class Actinobacteria and clustered with N. alkaliphilus and uncultured bacteria. The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and rhamnose and galactose as the diagnostic cell-wall sugars. Strain F10T contained C16 : 1
ω7c, C16 : 0 and C17 : 1
ω8c as the major cellular fatty acids. The predominant isoprenoid quinone was MK-9 (H4). The G+C content of the DNA was 68.3 mol%. Based on data from the current polyphasic study, it is proposed that the new marine isolate be placed in a novel genus and be considered a novel species designated Euzebya tangerina gen. nov., sp. nov. within the new family, order and subclass Euzebyaceae fam. nov., Euzebyales ord. nov. and Nitriliruptoridae subclassis nov. in the class Actinobacteria. The type strain of Euzebya tangerina is F10T (=NBRC 105439T =KCTC 19736T).
Revival and emended description of ‘Mycobacterium paraffinicum’ Davis, Chase and Raymond 1956 as Mycobacterium paraffinicum sp. nov., nom. rev.
Authors: Toney Nadege , Adekambi Toidi , Toney Sean , Yakrus Mitchell , Butler W. Ray
Published: November 2009

The omission of the name ‘Mycobacterium paraffinicum’ from the Approved Lists of Bacterial Names was due to phenotypic confusion surrounding a close relationship with Mycobacterium scrofulaceum. Correspondingly, ‘M. paraffinicum’ strains grew slowly in >7 days, stained acid–alcohol-fast and produced yellow-pigmented, smooth, waxy colonies in the dark at an optimal temperature of 35 °C. However, ‘M. paraffinicum’ strains demonstrated no activity for urease, nicotinamidase or pyrazinamidase and lacked growth at 42 °C, unlike M. scrofulaceum. The mycolic acid pattern, as determined by HPLC, clustered ‘M. paraffinicum’ with M. scrofulaceum, Mycobacterium avium and Mycobacterium parascrofulaceum. Strains were fully susceptible to linezolid, rifabutin, clarithromycin and amikacin. Examination of the historical reference strain of ‘M. paraffinicum’, ATCC 12670, and five additional isolates using comparative studies with 16S rRNA, hsp65 and rpoB gene and concatenated sequences showed that they formed a tight taxonomic group that was distinct from similar non-tuberculous mycobacteria. Multilocus enzyme electrophoresis (MEE) analysis confirmed a close association of the five additional isolates with the reference strain of ‘M. paraffinicum’ with a genetic distance of 0.12 and showed that all six strains were distinct from other closely related species. These genetic results provided unambiguous evidence of the uniqueness of this slowly growing, scotochromogenic species and supported the revival of the name as Mycobacterium paraffinicum (ex Davis, Chase and Raymond 1956) sp. nov., nom. rev. We propose the previously deposited reference strain ATCC 12670T =DSM 44181T =NCIMB 10420T, located in collections worldwide, as the type strain.
Listeria rocourtiae sp. nov.
Authors: Leclercq Alexandre , Clermont Dominique , Bizet Chantal , Grimont Patrick A. D. , Le Flèche-Matéos Anne , Roche Sylvie M. , Buchrieser Carmen , Cadet-Daniel Véronique , Le Monnier Alban , Lecuit Marc , Allerberger Franz
Published: November 2009

A Listeria-like strain isolated in Austria from pre-cut lettuce fitted the description of the genus Listeria although it could not be assigned to any of the known species. Comparison of the rrs gene (encoding 16S rRNA) sequence and gene content by DNA-array indicated affiliation to the genus Listeria. Phylogenetic distance from known species of the genus Listeria indicated that it represents a novel species. Since it can be differentiated from all other known species of the genus Listeria by using phenotypic tests, the name Listeria rocourtiae sp. nov. is proposed for the novel species. The type strain is CIP 109804T (=DSM 22097T =Allerberger 700284/02T). The type strain is avirulent as assessed by cell culture assays and inoculation of mice.
Phylogeny and differentiation of species of the genus Gluconacetobacter and related taxa based on multilocus sequence analyses of housekeeping genes and reclassification of Acetobacter xylinus subsp. sucrofermentans as Gluconacetobacter sucrofermentans (Toyosaki et al. 1996) sp. nov., comb. nov.
Authors: Cleenwerck Ilse , De Vos Paul , De Vuyst Luc
Published: November 2009

Three housekeeping genes (dnaK, groEL and rpoB) of strains belonging to the genus Gluconacetobacter (37 strains) or related taxa (38 strains) were sequenced. Reference strains of the 15 species of the genus Gluconacetobacter were included. Phylogenetic trees generated using these gene sequences confirmed the existence of two phylogenetic groups within the genus Gluconacetobacter. These groups clustered separately in trees constructed using concatenated sequences of the three genes, indicating that the genus Gluconacetobacter should not remain a single genus and should be split, as suggested previously. Multilocus sequence analysis (MLSA) of the three housekeeping genes also proved useful for species differentiation in the family Acetobacteraceae. It also suggested that Gluconacetobacter xylinus LMG 18788, better known as the type and only strain of Acetobacter xylinus subsp. sucrofermentans, represents a distinct species in the genus Gluconacetobacter, and is not a true G. xylinus strain. In previous studies, this strain showed less than 70 % DNA relatedness to the type strains of G. xylinus and Gluconacetobacter nataicola, the phylogenetically nearest relatives, and could be distinguished from them phenotypically. Additionally, AFLP and (GTG)5-PCR DNA fingerprinting data supported its reclassification within a distinct species. The name Gluconacetobacter sucrofermentans (Toyosaki et al. 1996) sp. nov., comb. nov. is proposed.