bluuebunny/crossref_metadata_2025 huggingface dataset:
FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots
Authors: Grove Laurie E. , Hall David R. , Beglov Dmitri , Vajda Sandor , Kozakov Dima
Published: March 2013

Computational solvent mapping finds binding hot spots, determines their druggability and provides information for drug design. While mapping of a ligand-bound structure yields more accurate results, usually the apo structure serves as the starting point in design. The FTFlex algorithm, implemented as a server, can modify an apo structure to yield mapping results that are similar to those of the respective bound structure. Thus, FTFlex is an extension of our FTMap server, which only considers rigid structures. FTFlex identifies flexible residues within the binding site and determines alternative conformations using a rotamer library. In cases where the mapping results of the apo structure were in poor agreement with those of the bound structure, FTFlex was able to yield a modified apo structure, which lead to improved FTMap results. In cases where the mapping results of the apo and bound structures were in good agreement, no new structure was predicted.

Availability: FTFlex is freely available as a web-based server at http://ftflex.bu.edu/.

Contact:  vajda@bu.edu or midas@bu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
PLncDB: plant long non-coding RNA database
Authors: Jin Jingjing , Liu Jun , Wang Huan , Wong Limsoon , Chua Nam-Hai
Published: March 2013

Summary: Plant long non-coding RNA database (PLncDB) attempts to provide the following functions related to long non-coding RNAs (lncRNAs): (i) Genomic information for a large number of lncRNAs collected from various resources; (ii) an online genome browser for plant lncRNAs based on a platform similar to that of the UCSC Genome Browser; (iii) Integration of transcriptome datasets derived from various samples including different tissues, developmental stages, mutants and stress treatments; and (iv) A list of epigenetic modification datasets and small RNA datasets. Currently, our PLncDB provides a comprehensive genomic view of Arabidopsis lncRNAs for the plant research community. This database will be regularly updated with new plant genome when available so as to greatly facilitate future investigations on plant lncRNAs.

Availability: PLncDB is freely accessible at http://chualab.rockefeller.edu/gbrowse2/homepage.html and all results can be downloaded for free at the website.

Contact:  chua@rockefeller.edu
Specificity and affinity quantification of protein–protein interactions
Authors: Yan Zhiqiang , Guo Liyong , Hu Liang , Wang Jin
Published: March 2013

Motivation: Most biological processes are mediated by the protein–protein interactions. Determination of the protein–protein structures and insight into their interactions are vital to understand the mechanisms of protein functions. Currently, compared with the isolated protein structures, only a small fraction of protein–protein structures are experimentally solved. Therefore, the computational docking methods play an increasing role in predicting the structures and interactions of protein–protein complexes. The scoring function of protein–protein interactions is the key responsible for the accuracy of the computational docking. Previous scoring functions were mostly developed by optimizing the binding affinity which determines the stability of the protein–protein complex, but they are often lack of the consideration of specificity which determines the discrimination of native protein–protein complex against competitive ones.

Results: We developed a scoring function (named as SPA-PP, specificity and affinity of the protein–protein interactions) by incorporating both the specificity and affinity into the optimization strategy. The testing results and comparisons with other scoring functions show that SPA-PP performs remarkably on both predictions of binding pose and binding affinity. Thus, SPA-PP is a promising quantification of protein–protein interactions, which can be implemented into the protein docking tools and applied for the predictions of protein–protein structure and affinity.

Availability: The algorithm is implemented in C language, and the code can be downloaded from http://dl.dropbox.com/u/1865642/Optimization.cpp.

Contact:  jin.wang.1@stonybrook.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Clinical utility and prognostic value of left atrial volume assessment by cardiovascular magnetic resonance in non‐ischaemic dilated cardiomyopathy
Authors: Gulati Ankur , Ismail Tevfik F. , Jabbour Andrew , Ismail Nizar A. , Morarji Kishen , Ali Aamir , Raza Sadaf , Khwaja Jahanzaib , Brown Tristan D.H. , Liodakis Emmanouil , Baksi Arun J. , Shakur Rameen , Guha Kaushik , Roughton Michael , Wage Ricardo , Cook Stuart A. , Alpendurada Francisco , Assomull Ravi G. , Mohiaddin Raad H. , Cowie Martin R. , Pennell Dudley J. , Prasad Sanjay K.
Published: March 2013

Aims

Echocardiographic studies have shown that left atrial volume (LAV) predicts adverse outcome in small heart failure (HF) cohorts of mixed aetiology. However, the prognostic value of LAV in non‐ischaemic dilated cardiomyopathy (DCM) is unknown. Cardiovascular magnetic resonance (CMR) allows accurate and reproducible measurement of LAV. We sought to determine the long‐term prognostic significance of LAV assessed by CMR in DCM.

Methods and results

We measured LAV indexed to body surface area (LAVi) in 483 consecutive DCM patients referred for CMR. Patients were prospectively followed up for a primary endpoint of all‐cause mortality or cardiac transplantation. During a median follow‐up of 5.3 years, 75 patients died and 9 underwent cardiac transplantation. After adjustment for established risk factors, LAVi was an independent predictor of the primary endpoint [hazard ratio (HR) per 10 mL/m2 1.08; 95% confidence interval (CI) 1.01–1.15; P = 0.022]. LAVi was also independently associated with the secondary composite endpoints of cardiovascular mortality or cardiac transplantation (HR per 10 mL/m2 1.11; 95% CI 1.04–1.19; P = 0.003), and HF death, HF hospitalization, or cardiac transplantation (HR per 10 mL/m2 1.11; 95% CI 1.04–1.18; P = 0.001). The optimal LAVi cut‐off value for predicting the primary endpoint was 72 mL/m2. Patients with LAVi >72 mL/m2 had a three‐fold elevated risk of death or transplantation (HR 3.00; 95% CI 1.92–4.70; P < 0.001). LAVi provided incremental prognostic value for the prediction of transplant‐free survival (net reclassification improvement 0.17; 95% CI 0.05–0.29; P = 0.002).

Conclusions

LAVi is a powerful independent predictor of transplant‐free survival and HF outcomes in DCM. Assessment of LAV improves risk stratification in DCM and should be incorporated into routine CMR examination.
Fluid loss, venous congestion, and worsening renal function in acute decompensated heart failure
Authors: Aronson Doron , Abassi Zaid , Allon Eyal , Burger Andrew J.
Published: March 2013

Aims

To investigate the relationship between decongestion, central venous pressure, and risk of worsening renal function (WRF) in patients with acute decompensated heart failure (ADHF).

Methods and results

We studied 475 patients with ADHF, of whom 238 underwent right heart catheterization. Right atrial pressure (RAP) was measured at baseline and at 24 h. Net fluid loss was recorded in the first 24 h. WRF was defined as a >0.3 mg/dL increase in serum creatinine above baseline. WRF occurred in 84 catheterized patients (35.3%). There was a weak correlation between baseline RAP and baseline estimated glomerular filtration rate (r = –0.17, P = 0.009). The amount of fluid removed during the first 24 h did not correlate with the magnitude of RAP reduction (r = 0.06, P = 0.35). No association was observed between WRF and baseline RAP [odds ratio (OR) 1.06, 95% confidence interval (CI) 0.80–1.41, P = 0.68 per 6.6 mmHg] or the decrease in RAP (adjusted OR 1.13, 95% CI 0.85–1.49, P = 0.40 per 5.3 mmHg reduction in RAP). In contrast, smaller net fluid loss was strongly associated with increased WRF risk. Compared with the first net fluid loss tertile, the adjusted OR was 1.85 (95% CI 0.90–3.80, P = 0.10) and 2.58 (95% CI 1.27–5.25; P = 0.009) for the second and third tertile, respectively (P for trend <0.0001).

Conclusion

Smaller early net fluid loss is associated with increased risk for WRF. RAP is not a reliable surrogate of the magnitude of decongestion and risk of WRF. Future research is necessary to determine if targeting congestion may help prevent WRF.
Physical conditions of the gas in an ALMA [C ii]-identified submillimetre galaxy at z = 4.44
Authors: Huynh M. T. , Norris R. P. , Coppin K. E. K. , Emonts B. H. C. , Ivison R. J. , Seymour N. , Smail Ian , Smolčić V. , Swinbank A. M. , Brandt W. N. , Chapman S. C. , Dannerbauer H. , De Breuck C. , Greve T. R. , Hodge J. A. , Karim A. , Knudsen K. K. , Menten K. M. , van der Werf P. P. , Walter F. , Weiss A.
Published: March 2013

We present 12CO(2–1) observations of the submillimetre galaxy ALESS65.1 performed with the Australia Telescope Compact Array (ATCA) at 42.3 GHz. A previous Atacama Large Millimeter Array study of submillimetre galaxies (SMGs) in the Extended Chandra Deep Field South detected [C ii] 157.74 μm emission from this galaxy at a redshift of z = 4.44. No 12CO(2–1) emission was detected but we derive a firm upper limit to the cold gas mass in ALESS65.1 of $M_{\rm gas} < 1.7 \times 10^{10} {\rm M}_{{\odot }}$. The estimated gas depletion time-scale is <50 Myr, which is similar to other high-redshift SMGs, and consistent with z > 4 SMGs being the likely progenitors of massive red-and-dead galaxies at z > 2. The ratio of the [C ii], 12CO and far-infrared luminosities implies a strong far-ultraviolet field of G0 ≳ 103, as seen in Galactic star-forming regions or local ultraluminous infrared galaxies (ULIRGs). The observed $L_{\rm [C {\small {II}}]}/L_{\rm FIR} = 2.3 \times 10^{-3}$ is high compared to local ULIRGs and, combined with $L_{\rm [C {\small {II}}]}/L_{\rm CO} \gtrsim 2700$, it is consistent with ALESS65.1 either having an extended (several kpc) [C ii] emitting region or lower than solar metallicity.
Supernova 2012ec: identification of the progenitor and early monitoring with PESSTO
Authors: Maund J. R. , Fraser M. , Smartt S. J. , Botticella M. T. , Barbarino C. , Childress M. , Gal-Yam A. , Inserra C. , Pignata G. , Reichart D. , Schmidt B. , Sollerman J. , Taddia F. , Tomasella L. , Valenti S. , Yaron O.
Published: March 2013

We present the identification of the progenitor of the Type IIP SN 2012ec in archival pre-explosion Hubble Space Telescope Wide Field Planetary Camera 2 (WFPC2) and Advanced Camera for Surveys Wide Field Channel F814W images. The properties of the progenitor are further constrained by non-detections in pre-explosion WFPC2 F450W and F606W images. We report a series of early photometric and spectroscopic observations of SN 2012ec. The r′-band light curve shows a plateau with $M_{r^{\prime }}=-17.0$. The early spectrum is similar to the Type IIP SN 1999em, with the expansion velocity measured at Hα absorption minimum of −11 700 km s−1 (at 1 d post-discovery). The photometric and spectroscopic evolution of SN 2012ec shows it to be a Type IIP SN, discovered only a few days post-explosion (<6 d). We derive a luminosity for the progenitor, in comparison with MARCS model spectral energy distributions, of $\log {L/\text{L}}_{\odot } = 5.15\pm 0.19$, from which we infer an initial mass range of 14–22 M⊙. This is the first SN with an identified progenitor to be followed by the Public ESO Spectroscopic Survey of Transient Objects (PESSTO).
Dynamics of gas and dust clouds in active galactic nuclei
Authors: Plewa P. M. , Schartmann M. , Burkert A.
Published: March 2013

We analyse the motion of single optically thick clouds in the potential of a central mass under the influence of an anisotropic radiation field ∼|cos (θ)|, a model applicable to the inner region of active galactic nuclei. Resulting orbits are analytically soluble for constant cloud column densities. All stable orbits are closed, although they have non-trivial shapes. Furthermore, there exists a stability criterion in the form of a critical inclination, which depends on the luminosity of the central source and the column density of the cloud.
Lactobacillus

yonginensis sp. nov., a lactic acid bacterium with ginsenoside converting activity isolated from Kimchi
Authors: Yi Eun-Ji , Yang Jung-Eun , Lee Jung Min , Park YongJin , Park Sang-Yong , Shin Heon-sub , Kook MooChang , Yi Tae-Hoo
Published: March 2013

A Gram-reaction-positive, non-motile, non-spore-forming, catalase-negative, facultatively anaerobic, rod-shaped, β-glucosidase-producing lactic acid bacterium, designated strain THK-V8T, was isolated from the Korean fermented food, Kimchi, and its taxonomic position was investigated by using a polyphasic approach. Strain THK-V8T was able to grow at 4–40 °C (optimum, 30 °C) and pH 4.0–7.0 (optimum, pH 6.0). Strain THK-V8T had the ability to transform ginsenoside Rb1 to Rd. On the basis of 16S rRNA gene sequence similarity data, strain THK-V8T was shown to belong to the genus

Lactobacillus

. Strain THK-V8T was related to

Lactobacillus koreensis

DCY50T (98.8 % sequence similarity),

Lactobacillus parabrevis

LMG 11984T (97.7 %),

Lactobacillus senmaizukei

L13T (97.5 %),

Lactobacillus hammesii

TMW1.1236T (97.3 %) and

Lactobacillus brevis

ATCC 14687T (97.2 %). Subsequently, sequence analysis of the RNA polymerase alpha subunit gene (rpoA) confirmed that strain THK-V8T showed a maximum rpoA gene sequence similarity value of 93 % with

Lactobacillus brevis

LMG 6906T. The G+C content of the genomic DNA was 47.8 mol%. The DNA–DNA hybridization values between strain THK-V8T and

Lactobacillus parabrevis

DCY50T and

Lactobacillus parabrevis

LMG 11984T were 46.1±4.9 % and 10.6±2.9 %, respectively. The major fatty acids were summed feature 7 (comprised of C19 : 0 cyclo ω10c/19ω6), C14 : 0, C16 : 0 and C18 : 1ω9c. The cell wall peptidoglycan was of the A4α l-Lys–d-Asp type. The phenotypic and molecular properties indicated that strain THK-V8T represents a novel species within the genus

Lactobacillus

, for which the name

Lactobacillus

yonginensis sp. nov. is proposed. The type strain is THK-V8T ( = KACC 16236T = JCM 18023T).
Phaeobacter

leonis sp. nov., an alphaproteobacterium from Mediterranean Sea sediments
Authors: Gaboyer Frédéric , Tindall Brian J. , Ciobanu Maria-Cristina , Duthoit Frédérique , Le Romancer Marc , Alain Karine
Published: March 2013

A novel Gram-stain-negative, strictly aerobic, heterotrophic bacterium, designated 306T, was isolated from near-surface (109 cm below the sea floor) sediments of the Gulf of Lions, in the Mediterranean Sea. Strain 306T grew at temperatures between 4 and 32 °C (optimum 17–22 °C), from pH 6.5 to 9.0 (optimum 8.0–9.0) and between 0.5 and 6.0 % (w/v) NaCl (optimum 2.0 %). Its DNA G+C content was 58.8 mol%. On the basis of 16S rRNA gene sequence similarity, the novel isolate belongs to the class

Alphaproteobacteria

and is related to the genus

Phaeobacter

. It shares 98.7 % 16S rRNA sequence identity with

Phaeobacter arcticus

, its closest phylogenetic relative. It contained Q-10 as the only respiratory quinone, C18 : 1ω7c and C16 : 0 as major fatty acids (>5 %) and phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, two unidentified lipids and an aminolipid as polar lipids. The chemotaxonomic data are consistent with the affiliation of strain 306T to the genus

Phaeobacter

. Results of physiological experiments, biochemical tests and DNA–DNA hybridizations (with

P. arcticus

) indicate that strain 306T is genetically and phenotypically distinct from the five species of the genus

Phaeobacter

with validly published names. Strain 306T therefore represents a novel species, for which the name

Phaeobacter

leonis sp. nov. is proposed. The type strain is 306T ( = DSM 25627T = CIP 110369T = UBOCC 3187T).
Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai‘i, and emended description of the genus Flavobacterium
Authors: Kuo Iris , Saw Jimmy , Kapan Durrell D. , Christensen Stephanie , Kaneshiro Kenneth Y. , Donachie Stuart P.
Published: March 2013

Strain IK-1Twas isolated from decaying tissues of the shrubWikstroemia oahuensiscollected on O‘ahu, Hawai‘i. Cells were rods that stained Gram-negative. Gliding motility was not observed. The strain was oxidase-negative and catalase-positive. Zeaxanthin was the major carotenoid. Flexirubin-type pigments were not detected. The most abundant fatty acids in whole cells of IK-1Tgrown on R2A were iso-C15 : 0and one or both of C16 : 1ω7cand C16 : 1ω6c. Based on comparisons of the nucleotide sequence of the 16S rRNA gene, the closest neighbouring type strains wereFlavobacterium rivuliWB 3.3-2TandFlavobacterium subsaxonicumWB 4.1-42T, with which IK-1Tshares 93.84 and 93.67 % identity, respectively. The G+C content of the genomic DNA was 44.2 mol%. On the basis of distance from its nearest phylogenetic neighbours and phenotypic differences, the speciesFlavobacteriumakiainvivenssp. nov. is proposed to accommodate strain IK-1T( = ATCC BAA-2412T = CIP 110358T) as the type strain. The description of the genusFlavobacteriumis emended to reflect the DNA G+C contents ofFlavobacteriumakiainvivensIK-1Tand other species of the genusFlavobacteriumdescribed since the original description of the genus.
Methylobacterium haplocladii sp. nov. and Methylobacterium brachythecii sp. nov., isolated from bryophytes
Authors: Tani Akio , Sahin Nurettin
Published: March 2013

Pink-pigmented, facultatively methylotrophic bacteria, strains 87eTand 99bT, were isolated from the bryophytesHaplocladium microphyllumandBrachythecium plumosum, respectively. The cells of both strains were Gram-reaction-negative, motile, non-spore-forming rods. On the basis of 16S rRNA gene sequence similarity, strains 87eTand 99bTwere found to be related toMethylobacterium organophilumATCC 27886T(97.1 % and 97.7 %, respectively). Strains 87eTand 99bTshowed highest 16S rRNA gene similarity toMethylobacterium gnaphalii23eT(98.3 and 99.0 %, respectively). The phylogenetic similarities to all other species of the genusMethylobacteriumwith validly published names were less than 97 %. Major cellular fatty acids of both strains were C18 : 1ω7cand C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA andcpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted, laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains 87eTand 99bTfrom their phylogenetically closest relatives. We propose that strains 87eTand 99bTrepresent novel species within the genusMethylobacterium, for which the namesMethylobacteriumhaplocladiisp. nov. (type strain 87eT = DSM 24195T = NBRC 107714T) andMethylobacteriumbrachytheciisp. nov. (type strain 99bT = DSM 24105T = NBRC 107710T) are proposed.
Chiayiivirga flava gen. nov., sp. nov., a novel bacterium of the family

Xanthomonadaceae

isolated from an agricultural soil, and emended description of the genus

Dokdonella
Authors: Hsu Yi-Han , Lai Wei-An , Lin Shih-Yao , Hameed Asif , Shahina Mariyam , Shen Fo-Ting , Zhu Zhi-Long , Young Li-Sen , Young Chiu-Chung
Published: March 2013

A novel Gram-reaction-negative, yellow-pigmented, aerobic, non-motile and rod-shaped bacterium designated strain CC-YHH031T was isolated from an agricultural soil collected at Chiayi County, Taiwan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CC-YHH031T formed a discrete monophyletic lineage in the family

Xanthomonadaceae

, sharing high pairwise sequence similarity of 93.5–95.2 and 94.8 % with species of the genus

Dokdonella

(94.9 % similarity to the type strain of the type species) and

Aquimonas voraii

GPTSA 20T, respectively. The genomic DNA G+C content of strain CC-YHH031T was 68.6±0.7 mol% and the predominant respiratory quinone was ubiquinone Q-8. Spermidine was the principal polyamine, with minor amounts of putrescine. Major fatty acids (>5 % of total fatty acids) were iso-C16 : 0, iso-C15 : 0, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3), iso-C17 : 1ω9c, iso-C14 : 0, iso-C11 : 0 and iso-C11 : 0 3-OH. The polar lipid profile of strain CC-YHH031T included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminophospholipids (APL1–2) and four unidentified phospholipids (PL1–4). Strain CC-YHH031T was distinguished particularly from the type species of the genus

Dokdonella

(

Dokdonella koreensis

) by the presence of major amounts of iso-C14 : 0 and summed feature 3 and minor amounts of iso-C17 : 0 and by the complete absence of anteiso-C17 : 0, the presence of PL1–3 and APL1–2, the absence of APL3 and the presence of putrescine in the former. On the basis of distinguishing genotypic and phenotypic evidence, strain CC-YHH031T is proposed to represent a novel genus and species within the family

Xanthomonadaceae

, for which the name Chiayiivirga flava gen. nov., sp. nov. is proposed. The type strain of Chiayiivirga flava is CC-YHH031T ( = BCRC 80273T = DSM 24163T).
Blastococcus

endophyticus sp. nov., an actinobacterium isolated from Camptotheca acuminata
Authors: Zhu Wen-Yong , Zhang Jin-Li , Qin Yu-Li , Xiong Zi-Jun , Zhang Dao-Feng , Klenk Hans-Peter , Zhao Li-Xing , Xu Li-Hua , Li Wen-Jun
Published: March 2013

A novel endophytic actinobacterium, designated strain YIM 68236T, was isolated from healthy leaves of Camptotheca acuminata. and characterized by using a polyphasic approach. Cells of this strain occurred singly, in pairs or in tetrads. It grew at 10–45 °C, at pH 5.0–8.0 (optimum pH 7.0) and in the presence of 0–3 % (w/v) NaCl. The DNA G+C content was 71.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 68236T belongs to the genus

Blastococcus

. However, it differed from its closest relatives,

Blastococcus aggregatus

DSM 4725T,

Blastococcus saxobsidens

DSM 44509T and

Blastococcus jejuensis

DSM 19597T in many phenotypic characteristics. Moreover, the DNA–DNA relatedness values between the novel isolate and the three above-mentioned type strains were 49.0±1.6 %, 46.1±3.2 % and 39.8±1.5 %, respectively. Based on comparative analysis of physiological and chemotaxonomic data, strain YIM 68236T represents a novel species of the genus

Blastococcus

, for which the name

Blastococcus

endophyticus sp. nov. is proposed. The type strain is YIM 68236T ( = CCTCC AA 209045T = DSM 45413T = KCTC 19998T).
Mucilaginibacter

gynuensis sp. nov., isolated from rotten wood
Authors: Khan Haji , Chung Eu Jin , Jeon Che Ok , Chung Young Ryun
Published: March 2013

A Gram-staining-negative, rod-shaped, aerobic bacterial strain designated YC7003T, was isolated from a piece of rotten wood collected at Jinju, Korea. The taxonomic position of the strain was investigated using a polyphasic approach. The strain was catalase- and oxidase-positive, grew at 4–35 °C (optimum, 30 °C) and at pH 5.0–10.0 (optimum, pH 6.5–7.0). The major cellular fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3), iso-C15 : 0 and C16 : 1ω5c and the major respiratory quinone was MK-7. The total genomic DNA G+C content was 49.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YC7003T belonged to the genus

Mucilaginibacter

in the family

Sphingobacteriaceae

with 94.4–97.2 % sequence similarities with type strains of species of the genus

Mucilaginibacter

. The most closely related species was

Mucilaginibacter mallensis

MP1X4T (97.2 %). The DNA–DNA relatedness value between strain YC7003T and

M. mallensis

MP1X4T was 21.7±3.3 %. Based on these data, strain YC7003T represents a novel species of the genus

Mucilaginibacter

, for which the name

Mucilaginibacter

gynuensis sp. nov. is proposed. The type strain is YC7003T ( = KACC 15532T = JCM 17705T).
Lysobacter

oligotrophicus sp. nov., isolated from an Antarctic freshwater lake in Antarctica
Authors: Fukuda Wakao , Kimura Tomomi , Araki Shigeo , Miyoshi Yuki , Atomi Haruyuki , Imanaka Tadayuki
Published: March 2013

A Gram-stain-negative, non-spore-forming, rod-shaped, aerobic bacterium (strain 107-E2T) was isolated from freshwater samples containing microbial mats collected at a lake in Skarvsnes, Antarctica (temporary lake name, Lake Tanago Ike). Strain 107-E2T grew between 5 and 25 °C, with an optimum of 23 °C. Moreover, colony formation was observed on agar media even at −5 °C. The pH range for growth was between 6.0 and 9.0, with an optimum of pH 7.0–8.0. The range of NaCl concentration for growth was between 0.0 and 0.5 % (w/v), with an optimum of 0.0 %. No growth was observed in media containing organic compounds at high concentrations, which indicated that strain 107-E2T was an oligotroph. In the late stationary phase, strain 107-E2T produced a dark brown water-soluble pigment. Esterase, amylase and protease production was observed. Antimicrobial-lytic activities for Gram-negative bacteria and yeast were observed. Ubiquinone-8 was the major respiratory quinone. The major fatty acids were iso-C15 : 0, iso-C17 : 1ω9c and iso-C15 : 1 at 5. The G+C content of genomic DNA was 66.1 mol%. Analysis of the 16S rRNA gene sequences revealed that strain 107-E2T belonged to the genus

Lysobacter

, and low DNA–DNA relatedness values with closely related species distinguished strain 107-E2T from recognized species of the genus

Lysobacter

. The phylogenetic situation and physiological characteristics indicated that strain 107-E2T should be classified as a representative of a novel species of the genus

Lysobacter

, for which the name

Lysobacter

oligotrophicus sp. nov. is proposed. The type strain is 107-E2T ( = JCM 18257T = ATCC BAA-2438T).
Enteroaggregative Escherichia coli strain in a novel weaned mouse model: exacerbation by malnutrition, biofilm as a virulence factor and treatment by nitazoxanide
Authors: Bolick David T. , Roche James K. , Hontecillas Raquel , Bassaganya-Riera Josep , Nataro James P. , Guerrant Richard L.
Published: March 2013

Enteroaggregative Escherichia coli (EAEC) is increasingly recognized as a common cause of diarrhoea in healthy, malnourished and immune-deficient adults and children. There is no reproducible non-neonatal animal model for longitudinal studies of disease mechanism or therapy. Using two strains of human-derived EAEC to challenge weaned C57BL/6 mice, we explored an in vivo model of EAEC infection in mice, in which disease was monitored quantitatively as the growth rate, stool shedding and tissue burden of organisms; nutritional status was varied, and a new class of therapeutics was assessed. A single oral challenge of EAEC strain 042 resulted in significant growth shortfalls (5–8 % of body weight in 12 days), persistent shedding of micro-organisms in stools [>103.2 c.f.u. (10 mg stool)−1 for at least 14 days] and intestinal tissue burden [~103 c.f.u. (10 mg tissue)−1 detectable up to 14 days post-challenge]. Moderate malnourishment of mice using a ‘regional basic diet’ containing 7 % protein and reduced fat and micronutrients heightened all parameters of infection. Nitazoxanide in subMIC doses, administered for 3 days at the time of EAEC challenge, lessened growth shortfalls (by >10 % of body weight), stool shedding [by 2–3 logs (10 mg stool)−1] and tissue burden of organisms (by >75 % in the jejunum and colon). Thus, weaned C57BL/6 mice challenged with EAEC is a convenient, readily inducible model of EAEC infection with three highly quantifiable outcomes in which disease severity is dependent on the nutritional status of the host, and which is modifiable in the presence of inhibitors of pyruvate ferredoxin oxidoreductase such as nitazoxanide.
Catheter-related bloodstream infection by Lindnera fabianii in a neutropenic patient
Authors: Yun Jae Won , Park Kyung Sun , Ki Chang-Seok , Lee Nam Yong
Published: March 2013

Lindnera (Pichia) fabianii (Candida fabianii teleomorph) is a yeast species that is an uncommon cause of invasive human infections. This report describes what we believe to be the first human case of a catheter-related L. fabianii bloodstream infection in a neutropenic patient. The Clinical and Laboratory Standards Institute guidelines do not offer antifungal breakpoints in this neutropenic case and empirical chemotherapy was considered. Sharing our experience, we will discuss the choice of an effective antifungal agent in this uncommon clinical situation.
Prevalence of tetracycline resistance genes and identification of tet(M) in clinical isolates of Escherichia coli from sick ducks in China
Authors: Hu Gong-Zheng , Pan Yu-Shan , Wu Hua , Hu Han , Xu Rui , Yuan Li , Liu Jian-Hua , Feng Jian-Kun
Published: March 2013

Tetracycline resistance is one of the most frequently encountered resistance properties in bacteria of animal origin. The aim of the present study was to investigate the prevalence and diversity of tetracycline resistance (tet) genes among Escherichia coli clinical isolates from diseased ducks in China and to report the identification and sequencing of the tet(M) gene. The susceptibility of 85 Escherichia coli strains to tetracyclines was determined by broth microdilution, and the presence of tet genes was investigated by multiplex PCR. All of the 85 isolates were fully resistant to both oxytetracycline and tetracycline, and 76.5 % were resistant to doxycycline. Seventy-seven of the isolates (90.6 %) encoded multiple tet genes, with 17.6, 38.8 and 34.1 % encoding two, three and four tet genes, respectively, and only 7.1 % encoded a single tet(A) gene. The MICs of oxytetracycline and tetracycline for all isolates ranged from 16 to ≥128 µg ml−1 with a MIC90 of >128 µg ml−1, regardless of the type or number of tet genes encoded. Isolates containing tet(M) commonly had more than one tet gene per strain. The doxycycline resistance rate in the tet(M)-positive isolates was significantly higher than in the tet(M)-negative isolates (P<0.05). A full-length tet(M) gene, including the promoter region, was obtained by PCR in seven of the 41 tet(M)-positive isolates and was sequenced and cloned. The cloned tet(M) gene conferred resistance to tetracyclines in the recombinant Escherichia coli host strain. These results revealed that, in these isolates, the prevalence of multiple tet genes was strikingly high and that tet(M) played a role in doxycycline resistance.
Demodex mite infestation of unknown significance in a patient with rhinocerebral mucormycosis due to Apophysomyces elegans species complex
Authors: Hallur Vinaykumar , Singh Gagandeep , Rudramurthy Shivaprakash M. , Kapoor Rakesh , Chakrabarti Arunaloke
Published: March 2013

Demodex mites have been reported in the past as a cause of facial rash in immunosuppressed patients. Here, we report an interesting case of possible demodicosis associated with rhinocerebral mucormycosis. The association of mites with a fungus was detected on direct microscopic examination of the scrapings of a nasal ulcer. The mite and the fungus were identified as Demodex folliculorum and Apophysomyces elegans species complex, respectively.
Late acyltransferase genes lpxX and lpxL jointly contribute to the biological activities of Moraxella catarrhalis
Authors: Gao Song , Ren Dabin , Peng Daxin , Zhang Wenhong , Muszyński Artur , Carlson Russell W. , Gu Xin-Xing
Published: March 2013

Lipo-oligosaccharide (LOS) is a major surface component and virulence factor of the human respiratory pathogen Moraxella catarrhalis. Two late acyltransferase genes, lpxX and lpxL, have been identified involved in the incorporation of acyloxyacyl-linked secondary acyl chains into lipid A during M. catarrhalis LOS biosynthesis. In this study, a double mutant with a deletion of both the lpxX and lpxL genes in M. catarrhalis strain O35E was constructed and named O35ElpxXL. Structural analysis of lipid A showed that the O35ElpxXL mutant lacked two decanoic acids (10 : 0) and one dodecanoic (lauric) acid (12 : 0). In comparison with the O35E parental strain and the single mutants O35ElpxX and O35ElpxL, the double mutant O35ElpxXL displayed prominently decreased endotoxin content, reduced resistance to normal human serum and accelerated bacterial clearance at 0, 3 and 6 h after an aerosol challenge in a mouse model of bacterial pulmonary clearance. These results indicate that these two genes encoding late acyltransferases responsible for lipid A biosynthesis jointly contribute to the biological activities and pathogenicity of M. catarrhalis. The double mutant O35ElpxXL with dramatically reduced toxicity is proposed as a potential vaccine candidate against M. catarrhalis infections for further investigation.
Aetiology and antibiotic resistance patterns of urinary tract infections in the elderly: a 6-month study
Authors: De Vecchi Elena , Sitia Simona , Romanò Carlo Luca , Ricci Cristian , Mattina Roberto , Drago Lorenzo
Published: March 2013

Urinary tract infections (UTIs) are a common cause of bacteraemia in the elderly and are associated with a high probability of hospitalization. Despite the impact of UTIs on health status and quality of life, a limited number of studies have evaluated their aetiology in this population. This study aimed to evaluate the microbial aetiology and pattern of susceptibility of bacteria causing UTIs in the elderly. For this purpose, a retrospective cohort study of elderly residents (n = 472, aged >65 years) in 14 nursing homes in Milan (Italy) and its province was performed. Globally, 393 micro-organisms from 328 samples were isolated: Escherichia coli was the most prevalent (44.8 %), followed by Proteus mirabilis (20.4 %), Providencia spp. (8.9 %), Klebsiella spp. (6.4 %) and Pseudomonas aeruginosa (4.6 %). Enterococci were the most frequently isolated Gram-positive organisms (7.4 %). Almost all Enterobacteriaceae were susceptible to nitrofurantoin, carbapenems and amikacin. Extended-spectrum β-lactamases were detected in 42.1 % of isolates. The most active antibiotics against P. aeruginosa were colistin, amikacin and piperacillin/tazobactam. All Gram-positive organisms were susceptible to glycopeptides and linezolid, and 90 % were susceptible to nitrofurantoin. Fluoroquinolones showed a limited activity against all the tested micro-organisms. Escherichia coli remains the major micro-organism responsible for UTIs in older people, although to a lesser extent than in a younger population. The high rates of resistance observed in this study make careful use of antibiotics advisable to limit further development of resistance.
Expression and display of Clostridium difficile protein FliD on the surface of Bacillus subtilis spores
Authors: Negri Alessandro , Potocki Wojciech , Iwanicki Adam , Obuchowski Michał , Hinc Krzysztof
Published: March 2013

The endospores of Bacillus subtilis can serve as a tool for surface presentation of heterologous proteins. The unique properties of the spore protective layers make them perfect vehicles for orally administered vaccines. In this study, we successfully displayed a fragment of Clostridium difficile FliD protein on the surface of B. subtilis spores using the CotB, CotC, CotG and CotZ spore coat proteins. The presence of the fusion proteins in the spore coat was verified by Western blotting and immunofluorescence microscopy. The amount of recombinant proteins was assessed by a dot-blot technique. C. difficile is one of the most common infectious agents in nosocomial infections and is especially associated with antibiotic therapies. FliD is a flagellar cap protein of C. difficile and is known to be one of the immunogenic surface antigens of this bacterium. Therefore, its use in vaccine formulations gives a good perspective for successful immunization with a FliD-based vaccine. The recombinant spores presented here may be good candidates for C. difficile oral vaccines.
Chronotropic and pressor effects of water ingestion at rest and in response to incremental dynamic exercise
Authors: Mendonca Goncalo V. , Teixeira Micael S. , Heffernan Kevin S. , Fernhall Bo
Published: March 2013

New Findings

What is the central question of this study?

The effects of water ingestion on the chronotropic response to dynamic exercise, performed below and above the ventilatory threshold, have not been previously explored.

What is the main finding and its importance?

Drinking 500 ml of water before exercise reduces the chronotropic response to submaximal exercise performed below and above the ventilatory threshold, but not at maximal exercise intensities.

Ingestion of water attenuates the chronotropic response to submaximal exercise. However, it is not known whether this effect is equally manifested during dynamic exercise below and above the ventilatory threshold (VT). We explored the effects of water ingestion on the heart rate response to an incremental cycle‐ergometer protocol. In a randomized fashion, 19 healthy adults (10 men and nine women, age 20.9 ± 1.8 years) ingested 50 and 500 ml of water before completing a cycle‐ergometer protocol on two separate days. The heart rate and oxygen uptake () responses to water ingestion were analysed both at rest and during exercise performed below and above the VT. The effects of water intake on brachial blood pressure were measured only at rest. Resting mean arterial pressure increased and resting heart rate decreased, but only after 500 ml of water (P < 0.05). Compared with that seen after 50 ml of water, the 500 ml volume elicited an overall decrease in submaximal heart rate (P < 0.05). In contrast, drinking 500 ml of water did not affect submaximal . The participants’ maximal heart rate, maximal and VT were similar between conditions. Our results therefore indicate that, owing to its effects on submaximal heart rate over a broad spectrum of intensities, the drinking of water should be recognized as a potential confounder in cardiovascular exercise studies. However, by showing no differences between conditions for submaximal , they also suggest that the magnitude of heart rate reduction after drinking 500 ml of water may be of minimal physiological significance for exercise cardiorespiratory capacity.
More than Skew: Asymmetric Wave Propagation in a Reaction-Diffusion-Convection System
Authors: Flach Edward H. , Norbury John , Schnell Santiago
Published: March 2013

Convection-induced instability in reaction-diffusion systems produces complicated patterns of oscillations behind propagating wavefronts. We transform the system twice: into lambda-omega form, then into polar variables. We find analytical estimates for the wavefront speed which we confirm numerically.Our previous work examined a simpler system [E. H. Flach, S. Schnell, and J. Norbury, Phys. Rev. E 76, 036216 (2007)]; the onset of instability is qualitatively different В in numerical solutions of this system. We modify our estimates and connect the two different behaviours. Our estimate explains how the Turing instability fits with pattern found in reaction-diffusion-convection systems. Our results can have important applications to the pattern formation analysis of biological systems.
Community Microrespirometry and Molecular Analyses Reveal a Diverse Energy Economy in Great Boiling Spring and Sandy's Spring West in the U.S. Great Basin
Authors: Murphy Caitlin N. , Dodsworth Jeremy A. , Babbitt Aaron B. , Hedlund Brian P.
Published: March 2013

Microrespirometry showed that several organic and inorganic electron donors stimulated oxygen consumption in two ∼80°C springs. Sediment and planktonic communities were structurally and functionally distinct, and quantitative PCR revealed catabolically distinct subpopulations of
Thermocrinis
. This study suggests that a variety of chemolithotrophic metabolisms operate simultaneously in these springs.
Improving Escherichia coli FucO for Furfural Tolerance by Saturation Mutagenesis of Individual Amino Acid Positions
Authors: Zheng Huabao , Wang Xuan , Yomano Lorraine P. , Geddes Ryan D. , Shanmugam Keelnatham T. , Ingram Lonnie O.
Published: March 2013

Furfural is an inhibitory side product formed during the depolymerization of hemicellulose with mineral acids. In
Escherichia coli
, furfural tolerance can be increased by expressing the native
fucO
gene (encoding lactaldehyde oxidoreductase). This enzyme also catalyzes the NADH-dependent reduction of furfural to the less toxic alcohol. Saturation mutagenesis was combined with growth-based selection to isolate a mutated form of
fucO
that confers increased furfural tolerance. The mutation responsible, L7F, is located within the interfacial region of FucO homodimers, replacing the most abundant codon for leucine with the most abundant codon for phenylalanine. Plasmid expression of the mutant gene increased FucO activity by more than 10-fold compared to the wild-type
fucO
gene and doubled the rate of furfural metabolism during fermentation. No inclusion bodies were evident with either the native or the mutated gene. mRNA abundance for the wild-type and mutant
fucO
genes differed by less than 2-fold. The

K
m

(furfural) for the mutant enzyme was 3-fold lower than that for the native enzyme, increasing efficiency at low substrate concentrations. The L7F mutation is located near the FucO N terminus, within the ribosomal binding region associated with translational initiation. Free-energy calculations for mRNA folding in this region (nucleotides −7 to +37) were weak for the native gene (−4.1 kcal mol
−1
) but weaker still for the
fucO
mutant (−1.0 to −0.1 kcal mol
−1
). The beneficial L7F mutation in FucO is proposed to increase furfural tolerance by improving gene expression and increasing enzyme effectiveness at low substrate levels.
Microbe-Dependent and Nonspecific Effects of Procedures To Eliminate the Resident Microbiota from Drosophila melanogaster
Authors: Ridley Emma V. , Wong Adam C. N. , Douglas Angela E.
Published: March 2013

Comparisons of animals bearing and lacking microorganisms can offer valuable insight into the interactions between animal hosts and their resident microbiota. Most hosts are naturally infected, and therefore, these comparisons require specific procedures (e.g., antibiotic treatment or physical exclusion of microorganisms) to disrupt the microbiota, but the potential for confounding nonspecific effects of the procedure on the traits of the host exists. Microbe-dependent and nonspecific effects can be discriminated by using multiple procedures: microbe-dependent effects are evident in hosts made microbe free by different procedures, but nonspecific effects are unique to individual procedures. As a demonstration, two procedures, oral administration of chlortetracycline (50 μg ml−1diet) and microbiota removal by egg dechorionation, were applied toDrosophila melanogasterin a 2-by-2 factorial design. Microorganisms were undetectable in flies from dechorionated eggs and reduced by >99% in chlortetracycline-treated flies.Drosophilaflies subjected to both protocols displayed an extended preadult development time, suggesting that the microbiota promotes the development rate. Female chlortetracycline-treated flies, whether from untreated or dechorionated eggs, displayed reduced protein content and egg fecundity, which could be attributed to the nonspecific effect of the antibiotic. We recommend that procedures used to disrupt the microbiota of animals should be selected, following systematic analysis of alternative mechanistically distinct procedures, on the basis of two criteria: those that achieve the greatest reduction (ideally, elimination) of the microbiota and those that achieve minimal nonspecific effects.
High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology
Authors: Ercolini Danilo
Published: March 2013

Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.
Persistence of Vibrio parahaemolyticus in the Pacific Oyster, Crassostrea gigas, Is a Multifactorial Process Involving Pili and Flagella but Not Type III Secretion Systems or Phase Variation
Authors: Aagesen Alisha M. , Phuvasate Sureerat , Su Yi-Cheng , Häse Claudia C.
Published: March 2013

Vibrio parahaemolyticus
can resist oyster depuration, suggesting that it possesses specific factors for persistence. We show that type I pili, type IV pili, and both flagellar systems contribute to
V. parahaemolyticus
persistence in Pacific oysters whereas type III secretion systems and phase variation do not.
Deletion of
FPS1
, Encoding Aquaglyceroporin Fps1p, Improves Xylose Fermentation by Engineered Saccharomyces cerevisiae
Authors: Wei Na , Xu Haiqing , Kim Soo Rin , Jin Yong-Su
Published: March 2013

Accumulation of xylitol in xylose fermentation with engineered
Saccharomyces cerevisiae
presents a major problem that hampers economically feasible production of biofuels from cellulosic plant biomass. In particular, substantial production of xylitol due to unbalanced redox cofactor usage by xylose reductase (XR) and xylitol dehydrogenase (XDH) leads to low yields of ethanol. While previous research focused on manipulating intracellular enzymatic reactions to improve xylose metabolism, this study demonstrated a new strategy to reduce xylitol formation and increase carbon flux toward target products by controlling the process of xylitol secretion. Using xylitol-producing
S. cerevisiae
strains expressing XR only, we determined the role of aquaglyceroporin Fps1p in xylitol export by characterizing extracellular and intracellular xylitol. In addition, when
FPS1
was deleted in a poorly xylose-fermenting strain with unbalanced XR and XDH activities, the xylitol yield was decreased by 71% and the ethanol yield was substantially increased by nearly four times. Experiments with our optimized xylose-fermenting strain also showed that
FPS1
deletion reduced xylitol production by 21% to 30% and increased ethanol yields by 3% to 10% under various fermentation conditions. Deletion of
FPS1
decreased the xylose consumption rate under anaerobic conditions, but the effect was not significant in fermentation at high cell density. Deletion of
FPS1
resulted in higher intracellular xylitol concentrations but did not significantly change the intracellular NAD
+
/NADH ratio in xylose-fermenting strains. The results demonstrate that Fps1p is involved in xylitol export in
S. cerevisiae
and present a new gene deletion target,
FPS1
, and a mechanism different from those previously reported to engineer yeast for improved xylose fermentation.