bluuebunny/crossref_metadata_2025 huggingface dataset:
F-actin bundles direct the initiation and orientation of lamellipodia through adhesion-based signaling
Authors: Johnson Heath E. , King Samantha J. , Asokan Sreeja B. , Rotty Jeremy D. , Bear James E. , Haugh Jason M.
Published: February 2015

Mesenchymal cells such as fibroblasts are weakly polarized and reorient directionality by a lamellipodial branching mechanism that is stabilized by phosphoinositide 3-kinase (PI3K) signaling. However, the mechanisms by which new lamellipodia are initiated and directed are unknown. Using total internal reflection fluorescence microscopy to monitor cytoskeletal and signaling dynamics in migrating cells, we show that peripheral F-actin bundles/filopodia containing fascin-1 serve as templates for formation and orientation of lamellipodia. Accordingly, modulation of fascin-1 expression tunes cell shape, quantified as the number of morphological extensions. Ratiometric imaging reveals that F-actin bundles/filopodia play both structural and signaling roles, as they prime the activation of PI3K signaling mediated by integrins and focal adhesion kinase. Depletion of fascin-1 ablated fibroblast haptotaxis on fibronectin but not platelet-derived growth factor chemotaxis. Based on these findings, we conceptualize haptotactic sensing as an exploration, with F-actin bundles directing and lamellipodia propagating the process and with signaling mediated by adhesions playing the role of integrator.
Actin works both sides of the immunological synapse
Authors: Short Ben
Published: February 2015

The cytoskeleton of both T cells and antigen-presenting cells promotes mechanical signaling during T cell activation.
Immature myeloid cells directly contribute to skin tumor development by recruiting IL-17–producing CD4+ T cells
Authors: Ortiz Myrna L. , Kumar Vinit , Martner Anna , Mony Sridevi , Donthireddy Laxminarasimha , Condamine Thomas , Seykora John , Knight Stella C. , Malietzis George , Lee Gui Han , Moorghen Morgan , Lenox Brianna , Luetteke Noreen , Celis Esteban , Gabrilovich Dmitry
Published: February 2015

Evidence links chronic inflammation with cancer, but cellular mechanisms involved in this process remain unclear. We have demonstrated that in humans, inflammatory conditions that predispose to development of skin and colon tumors are associated with accumulation in tissues of CD33+S100A9+ cells, the phenotype typical for myeloid-derived suppressor cells in cancer or immature myeloid cells (IMCs) in tumor-free hosts. To identify the direct role of these cells in tumor development, we used S100A9 transgenic mice to create the conditions for topical accumulation of these cells in the skin in the absence of infection or tissue damage. These mice demonstrated accumulation of granulocytic IMCs in the skin upon topical application of 12-O-tetradecanoylphorbol-13-acetate (TPA), resulting in a dramatic increase in the formation of papillomas during epidermal carcinogenesis. The effect of IMCs on tumorigenesis was not associated with immune suppression, but with CCL4 (chemokine [C-C motif] ligand 4)-mediated recruitment of IL-17–producing CD4+ T cells. This chemokine was released by activated IMCs. Elimination of CD4+ T cells or blockade of CCL4 or IL-17 abrogated the increase in tumor formation caused by myeloid cells. Thus, this study implicates accumulation of IMCs as an initial step in facilitation of tumor formation, followed by the recruitment of CD4+ T cells.
Positions of the cytoplasmic end of BK α S0 helix relative to S1–S6 and of β1 TM1 and TM2 relative to S0–S6
Authors: Liu Guoxia , Zakharov Sergey I. , Yao Yongneng , Marx Steven O. , Karlin Arthur
Published: February 2015

The large-conductance, voltage- and Ca2+-gated K+ (BK) channel consists of four α subunits, which form a voltage- and Ca2+-gated channel, and up to four modulatory β subunits. The β1 subunit is expressed in smooth muscle, where it slows BK channel kinetics and shifts the conductance–voltage (G-V) curve to the left at [Ca2+] > 2 µM. In addition to the six transmembrane (TM) helices, S1–S6, conserved in all voltage-dependent K+ channels, BK α has a unique seventh TM helix, S0, which may contribute to the unusual rightward shift in the G-V curve of BK α in the absence of β1 and to a leftward shift in its presence. Such a role is supported by the close proximity of S0 to S3 and S4 in the voltage-sensing domain. Furthermore, on the extracellular side of the membrane, one of the two TM helices of β1, TM2, is adjacent to S0. We have now analyzed induced disulfide bond formation between substituted Cys residues on the cytoplasmic side of the membrane. There, in contrast, S0 is closest to the S2–S3 loop, from which position it is displaced on the addition of β1. The cytoplasmic ends of β1 TM1 and TM2 are adjacent and are located between the S2–S3 loop of one α subunit and S1 of a neighboring α subunit and are not adjacent to S0; i.e., S0 and TM2 have different trajectories through the membrane. In the absence of β1, 70% of disulfide bonding of W43C (S0) and L175C (S2–S3) has no effect on V50 for activation, implying that the cytoplasmic end of S0 and the S2–S3 loop move in concert, if at all, during activation. Otherwise, linking them together in one state would obstruct the transition to the other state, which would certainly change V50.
Pulmonary Hypertension Associated with Heart Failure with Preserved Ejection Fraction: Acute Hemodynamic Effects of Inhaled Iloprost
Authors: Grossman Nicole L. , Fiack Christopher A. , Weinberg Janice M. , Rybin Denis V. , Farber Harrison W.
Published: February 2015

Iloprost, an inhaled synthetic prostacyclin analogue, improves hemodynamic and clinical status with minimal systemic adversity in patients with pulmonary arterial hypertension. Our single‐site, prospective case series aimed to determine the effects of iloprost in subjects with group 2 pulmonary hypertension and heart failure with preserved ejection fraction. Patients referred to Boston Medical Center for initial evaluation of suspected pulmonary hypertension received a test dose of 2.5 μg inhaled iloprost, followed by two subsequent doses of 5 μg. Hemodynamic measurements were recorded for each inhalation after 15, 30, 60, and 90 minutes. Results were analyzed via paired t test and signed‐rank test. Eight subjects fulfilled criteria and elected to enter the study. There was a reduction of pulmonary arterial pressure (by an average of 7.0 mmHg [P = 0.005] and 4.7 mmHg [P = 0.021] with the first and second 5‐μg inhalations, respectively) and pulmonary vascular resistance (by an average of 161.9 dyn· s/cm5 [P = 0.019] and 95.0 dyn · s/cm5 [P = 0.014] with the first and second 5‐μg inhalations, respectively). There were trends for increased cardiac output and decreased oxygen saturation. There were no changes in other vital or hemodynamic parameters, including pulmonary capillary wedge pressure. All patients completed each cycle of iloprost administration without preestablished termination criteria. In patients with pulmonary hypertension and heart failure with preserved ejection fraction, inhaled iloprost resulted in acute reduction of pulmonary arterial pressure and pulmonary vascular resistance. Further evaluation of iloprost in this subset of patients is warranted.
A multiobjective memetic algorithm for PPI network alignment
Authors: Clark Connor , Kalita Jugal
Published: February 2015

Motivation: There recently has been great interest in aligning protein–protein interaction (PPI) networks to identify potentially orthologous proteins between species. It is thought that the topological information contained in these networks will yield better orthology predictions than sequence similarity alone. Recent work has found that existing aligners have difficulty making use of both topological and sequence similarity when aligning, with either one or the other being better matched. This can be at least partially attributed to the fact that existing aligners try to combine these two potentially conflicting objectives into a single objective.

Results: We present Optnetalign, a multiobjective memetic algorithm for the problem of PPI network alignment that uses extremely efficient swap-based local search, mutation and crossover operations to create a population of alignments. This algorithm optimizes the conflicting goals of topological and sequence similarity using the concept of Pareto dominance, exploring the tradeoff between the two objectives as it runs. This allows us to produce many high-quality candidate alignments in a single run. Our algorithm produces alignments that are much better compromises between topological and biological match quality than previous work, while better characterizing the diversity of possible good alignments between two networks. Our aligner’s results have several interesting implications for future research on alignment evaluation, the design of network alignment objectives and the interpretation of alignment results.

Availability and Implementation: The C++ source code to our program, along with compilation and usage instructions, is available at https://github.com/crclark/optnetaligncpp/

Contact: connor.r.clark@gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.
An Intemperate Map: Orientation and Disorientation in the Old French Fabliau ‘Les Trois Dames de Paris’
Authors: Goyette Stefanie A.
Published: February 2015

This article argues that the early fourteenth-century fabliau ‘Les Trois Dames de Paris’ invites the reader to map its temporal moment and topographical locations in historical space and time, but also that this invitation is frustrated by the events and displacements represented in the story. The subversion of potentially mappable urban topography mirrors the moral straying of the three eponymous women, who set out over the course of the narrative to have a private feast, which descends into an orgy of drunken excess. As the women become increasingly inebriated, their subjective disorientation allows further social and spatial transgression, briefly interrupted by unconsciousness and burial, but finally culminating in their resurgence, seemingly as possessed corpses, into public space. Each of these events represents the women's resistance to social norms, yet in the end their illusory freedom dissolves along with their intoxication, and the fabliau makes their transgression a subject of ridicule.
Commercial fishers' perceptions of jellyfish interference in the Northern California Current
Authors: Conley Keats R. , Sutherland Kelly R.
Published: February 2015

Jellyfish disruption of fisheries has been described in some coastal systems, but few thorough investigations have been conducted. To ascertain the economic impact and trend of jellyfish blooms in the Northern California Current (NCC), we mailed surveys to resident commercial shrimpers, salmon trollers, rockfish (blue, black), and groundfish fishers (n = 872). We asked fishers to estimate the damages caused by jellyfish—including costs of relocating to avoid blooms, lost fishing time, time lost to bycatch sorting, fish depreciation, and gear damage. Of the total respondents (n = 111), 67% reported that jellyfish reduce their seasonal revenue, but the degree of impact ranged considerably by fishery and location. Highest jellyfish nuisance corresponded to regions with the most salmon trolling effort. Using the mean revenue losses provided by respondents, we estimate that the combined economic impact of jellyfish on Oregon's salmon and pink shrimp fishers was over $650 000 in peak jellyfish season (June–September) in 2012. Fishers reported that jellyfish biomass varies annually, but most respondents (51%) reported observing no appreciable change in jellyfish populations in the last 5 years. Since economic impact analyses have been conducted primarily in areas with anomalous, high-density blooms, data from the NCC, which is not known to be experiencing increases in jellyfish abundance, provides baseline information on the socio-economic impact of jellyfish blooms in this region. In addition, the finding that jellyfish impact hook and line fisheries—not solely net fisheries—has implications for many other regions where fishers employ this gear type.
A combination of new screening assays for prioritization of transmission-blocking antimalarials reveals distinct dynamics of marketed and experimental drugs
Authors: Bolscher J. M. , Koolen K. M. J. , van Gemert G. J. , van de Vegte-Bolmer M. G. , Bousema T. , Leroy D. , Sauerwein R. W. , Dechering K. J.
Published: February 2015

Objectives

The development of drugs to reduce malaria transmission is an important part of malaria eradication plans. We set out to develop and validate a combination of new screening assays for prioritization of transmission-blocking molecules.

Methods

We developed high-throughput assays for screening compounds against gametocytes, the parasite stages responsible for onward transmission to mosquitoes. An existing gametocyte parasitic lactate dehydrogenase (pLDH) assay was adapted for use in 384-well plates, and a novel homogeneous immunoassay to monitor the functional transition of female gametocytes into gametes was developed. A collection of 48 marketed and experimental antimalarials was screened and subsequently tested for impact on sporogony in Anopheles mosquitoes, to directly quantify the transmission-blocking properties of antimalarials in relation to their effects on gametocyte pLDH activity or gametogenesis.

Results and Conclusions

The novel screening assays revealed distinct stage-specific kinetics and dynamics of drug effects. Peroxides showed the most potent transmission-blocking effects, with an intermediate speed of action and IC50 values that were 20–40-fold higher than the IC50s against the asexual stages causing clinical malaria. Finally, the novel synthetic peroxide OZ439 appeared to be a promising drug candidate as it exerted gametocytocidal and transmission-blocking effects at clinically relevant concentrations.
ICD-10-CM Crosswalks in the primary care setting: assessing reliability of the GEMs and reimbursement mappings
Authors: Turer Robert W. , Zuckowsky Theresa D. , Causey H. Jennifer , Rosenbloom S. Trent
Published: February 2015

Objective The general equivalence mappings (GEMs) and reimbursement mappings (RMs) facilitate translation between ICD-9-CM and ICD-10-CM. This study compared prospectively dual-encoded diagnoses assigned by professional coders with the GEMs/RMs in a clinical setting.

Materials and Methods Professional coders manually encoded diagnoses from 100 primary care notes into both ICD-9-CM and ICD-10-CM. The investigators evaluated whether manual mappings were reproducible using the GEMs/RMs. Reproducible mappings with one ICD-9-CM and one ICD-10-CM code (“one-to-one”) were classified as exact or approximate using GEMs flags. Mismatches were characterized manually.

Results Manual encodings were reproducible from the forward GEMs, backward GEMs, and RMs in 85.2%, 90.4%, and 88.1% of diagnoses, respectively. For one-to-one, reproducible mappings, 61% (forward) and 63% (backward) were approximate mappings compared to 85% and 95% in the GEMs as a whole. Mismatches between manual and GEMs encodings were due to differences in coder interpretation (11%–13%), subtle hierarchical differences (52%–55%), or unknown reasons (32%–35%).

Discussion This study highlights inconsistencies between manual encoding and using the GEMs/RMs. The number of approximate mappings in our population compared to all one-to-one GEMs entries supports the notion that statistics describing the GEMs as a whole might not represent the most important mappings for each organization. The mismatch characteristics highlight the subtle differences between manual encoding and using the GEMs/RMs.

Conclusion These results support the need for organizations to assess the GEMs and RMs in their own environment to avoid changes in reimbursement and longitudinal statistics.
Evaluation of an electronic health record-supported obesity management protocol implemented in a community health center: a cautionary note
Authors: Steglitz Jeremy , Edberg Deborah , Sommers Mary , Talen Mary R , Thornton Louise K , Spring Bonnie
Published: February 2015

Objective

Primary care clinicians are well-positioned to intervene in the obesity epidemic. We studied whether implementation of an obesity intake protocol and electronic health record (EHR) form to guide behavior modification would facilitate identification and management of adult obesity in a Federally Qualified Health Center serving low-income, Hispanic patients.

Materials and Methods

In three studies, we examined clinician and patient outcomes before and after the addition of the weight management protocol and form. In the Clinician Study, 12 clinicians self-reported obesity management practices. In the Population Study, BMI and order data from 5000 patients and all 40 clinicians in the practice were extracted from the EHR preintervention and postintervention. In the Exposure Study, EHR-documented outcomes for a sub-sample of 46 patients actually exposed to the obesity management form were compared to matched controls.

Results

Clinicians reported that the intake protocol and form increased their performance of obesity-related assessments and their confidence in managing obesity. However, no improvement in obesity management practices or patient weight-loss was evident in EHR records for the overall clinic population. Further analysis revealed that only 55 patients were exposed to the form. Exposed patients were twice as likely to receive weight-loss counseling following the intervention, as compared to before, and more likely than matched controls. However, their obesity outcomes did not differ.

Conclusion

Results suggest that an obesity intake protocol and EHR-based weight management form may facilitate clinician weight-loss counseling among those exposed to the form. Significant implementation barriers can limit exposure, however, and need to be addressed.
Aggregate Demand, Idle Time, and Unemployment *
Authors: Michaillat Pascal , Saez Emmanuel
Published: February 2015

This article develops a model of unemployment fluctuations. The model keeps the architecture of the general-disequilibrium model of Barro and Grossman (1971) but takes a matching approach to the labor and product markets instead of a disequilibrium approach. On the product and labor markets, both price and tightness adjust to equalize supply and demand. Since there are two equilibrium variables but only one equilibrium condition on each market, a price mechanism is needed to select an equilibrium. We focus on two polar mechanisms: fixed prices and competitive prices. When prices are fixed, aggregate demand affects unemployment as follows. An increase in aggregate demand leads firms to find more customers. This reduces the idle time of their employees and thus increases their labor demand. This in turn reduces unemployment. We combine the predictions of the model and empirical measures of product market tightness, labor market tightness, output, and employment to assess the sources of labor market fluctuations in the United States. First, we find that product market tightness and labor market tightness fluctuate a lot, which implies that the fixed-price equilibrium describes the data better than the competitive-price equilibrium. Next, we find that labor market tightness and employment are positively correlated, which suggests that the labor market fluctuations are mostly due to labor demand shocks and not to labor supply or mismatch shocks. Last, we find that product market tightness and output are positively correlated, which suggests that the labor demand shocks mostly reflect aggregate demand shocks and not technology shocks.
Could tyrosine and tryptophan serve multiple roles in biological redox processes?
Authors: Winkler Jay R. , Gray Harry B.
Published: February 2015

Single-step electron tunnelling reactions can transport charges over distances of 15–20 Åin proteins. Longer-range transfer requires multi-step tunnelling processes along redox chains, often referred to as hopping. Long-range hopping via oxidized radicals of tryptophan and tyrosine, which has been identified in several natural enzymes, has been demonstrated in artificial constructs of the blue copper protein azurin. Tryptophan and tyrosine serve as hopping way stations in high-potential charge transport processes. It may be no coincidence that these two residues occur with greater-than-average frequency in O
2
- and H
2
O
2
-reactive enzymes. We suggest that appropriately placed tyrosine and/or tryptophan residues prevent damage from high-potential reactive intermediates by reduction followed by transfer of the oxidizing equivalent to less harmful sites or out of the protein altogether.
The elements of life and medicines
Authors: Chellan Prinessa , Sadler Peter J
Published: February 2015

Which elements are essential for human life? Here we make an element-by-element journey through the periodic table and attempt to assess whether elements are essential or not, and if they are, whether there is a relevant code for them in the human genome. There are many difficulties such as the human biochemistry of several so-called essential elements is not well understood, and it is not clear how we should classify elements that are involved in the destruction of invading microorganisms, or elements which are essential for microorganisms with which we live in symbiosis. In general, genes do not code for the elements themselves, but for specific chemical species, i.e. for the element, its oxidation state, type and number of coordinated ligands, and the coordination geometry. Today, the biological periodic table is in a position somewhat similar to Mendeleev's chemical periodic table of 1869: there are gaps and we need to do more research to fill them. The periodic table also offers potential for novel therapeutic and diagnostic agents, based on not only essential elements, but also non-essential elements, and on radionuclides. Although the potential for inorganic chemistry in medicine was realized more than 2000 years ago, this area of research is still in its infancy. Future advances in the design of inorganic drugs require more knowledge of their mechanism of action, including target sites and metabolism. Temporal speciation of elements in their biological environments at the atomic level is a major challenge, for which new methods are urgently needed.
Metal–ligand cooperation by aromatization–dearomatization as a tool in single bond activation
Authors: Milstein David
Published: February 2015

Metal–ligand cooperation (MLC) plays an important role in bond activation processes, enabling many chemical and biological catalytic reactions. A recent new mode of activation of chemical bonds involves ligand aromatization–dearomatization processes in pyridine-based pincer complexes in which chemical bonds are broken reversibly across the metal centre and the pincer-ligand arm, leading to new bond-making and -breaking processes, and new catalysis. In this short review, such processes are briefly exemplified in the activation of C–H, H–H, O–H, N–H and B–H bonds, and mechanistic insight is provided. This new bond activation mode has led to the development of various catalytic reactions, mainly based on alcohols and amines, and to a stepwise approach to thermal H
2
and light-induced O
2
liberation from water.
Superconductivity in room-temperature stable electride and high-pressure phases of alkali metals
Authors: Hosono Hideo , Kim Sung-Wng , Matsuishi Satoru , Tanaka Shigeki , Miyake Atsushi , Kagayama Tomoko , Shimizu Katsuya
Published: February 2015

S-band metals such as alkali and alkaline earth metals do not undergo a superconducting transition (SCT) at ambient pressure, but their high-pressure phases do. By contrast, room-temperature stable electride [Ca
24
Al
28
O
64
]
4+
⋅4e
−
(C12A7:e
−
) in which anionic electrons in the crystallographic sub-nanometer-size cages have high s-character exhibits SCT at 0.2–0.4 K at ambient pressure. In this paper, we report that crystal and electronic structures of C12A7:e
−
are close to those of the high-pressure superconducting phase of alkali and alkaline earth metals and the SCT of both materials is induced when electron nature at Fermi energy (
E
F
) switches from s- to sd-hybridized state.
Bacillus oleivorans sp. nov., a diesel oil-degrading and solvent-tolerant bacterium
Authors: Azmatunnisa M. , Rahul K. , Subhash Y. , Sasikala Ch. , Ramana Ch. V.
Published: February 2015

Two Gram-stain-positive, diesel oil-degrading, solvent-tolerant, aerobic, endospore-forming, rod-shaped bacteria were isolated from a contaminated laboratory plate. Based on 16S rRNA gene sequence analysis, strains JC228T and JC279 were identified as belonging to the genus

Bacillus

within the family

Bacillaceae

of the phylum

Firmicutes

and were found to be most closely related to

Bacillus carboniphilus

JCM 9731T (98.1 % 16S rRNA gene sequence similarity) and shared <96.0 % 16S rRNA gene sequence similarity with other members of the genus

Bacillus

. The DNA–DNA hybridization value between the two strains was 88±2 %. Strain JC228T showed 23.4±1 % reassociation (based on DNA–DNA hybridization) with

B. carboniphilus

LMG 18001T. The DNA G+C content of strains JC228T and JC279 was 39 and 38.4 mol%, respectively. Both strains were positive for catalase and oxidase activities, and negative for hydrolysis of starch and Tween 80. Strains JC228T and JC279 grew chemoorganoheterotrophically with optimum growth at pH 7 (range pH 7–9.5) and 35 °C (range 25–40 °C). Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid (PL2) were the major polar lipids. Major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 and C16 : 0. Whole-cell hydrolysates contained l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. Both strains utilized diesel oil as sole carbon and energy source. The results of physiological, biochemical, chemotaxonomic and molecular analyses allowed clear differentiation of strains JC228T and JC279 from their closest phylogenetic neighbours. Therefore strains JC228T and JC279 represent a novel species of the genus

Bacillus

, for which the name Bacillus oleivorans sp. nov. is proposed. The type strain is JC228T ( = LMG 28084T = CCTCC AB 2013353T).
Myceligenerans cantabricum sp. nov., a barotolerant actinobacterium isolated from a deep cold-water coral
Authors: Sarmiento-Vizcaíno Aida , González Verónica , Braña Alfredo F. , Molina Axayacatl , Acuña José L. , García Luis A. , Blanco Gloria
Published: February 2015

An actinobacterium strain (M-201T) was isolated from a deep-sea scleractinian coral (Fam. Caryophillidae) collected at 1500 m depth in the Avilés Canyon in the Cantabrian Sea, Asturias, Spain. Strain M-201T grew at pH 6.0–9.0 (optimum pH 7.0), between 4 and 37 °C (optimum 28 °C) and at salinities of 0.5–10.5 % (w/v) NaCl (optimum 0.5–3.0 %). The peptidoglycan contained the amino acids Lys, Ala, Thr, Glu and one unknown amino acid component, and belonged to type A4α, and the cell-wall sugars are glucose, mannose and galactose. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unknown phosphoglycolipid and seven unknown glycolipids. The predominant menaquinones were MK-9(H4) and MK-9(H6). Major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 72.4 mol%. The chemotaxonomic properties supported the affiliation of strain M-201T to the genus

Myceligenerans

. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism was most closely related to

Myceligenerans crystallogenes

CD12E2-27T (98.2 % 16S rRNA gene sequence similarity). However, it had a relatively low DNA–DNA relatedness value with the above strain (48 %). The isolate showed antibiotic activity against

Escherichia coli

,

Micrococcus luteus

ATCC 14452 and Saccharomyces cerevisiae var. carlsbergensis. To the best of our knowledge, this is the first report of antibiotic production in the genus

Myceligenerans

. The differences in phenotypic, metabolic, ecological and phylogenetic characteristics justify the proposal of a novel species of the genus

Myceligenerans

, Myceligenerans cantabricum sp. nov., with M-201T ( = CECT 8512T = DSM 28392T) as the type strain.
Flavirhabdus iliipiscaria gen. nov., sp. nov., isolated from intestine of flounder (Paralichthys olivaceus) and emended descriptions of the genera Flavivirga, Algibacter, Bizionia and Formosa
Authors: Shakeela Qismat , Shehzad Ahmed , Zhang Yunhui , Tang Kaihao , Zhang Xiao-Hua
Published: February 2015

A Gram-stain-negative, orange-coloured, rod-shaped bacterium, designated strain Th68T, was isolated from the intestine of flounder (Paralichthys olivaceus). The isolate required sea salts for growth. Gliding motility was not observed. Flexirubin-type pigments were present. 16S rRNA gene sequence analysis indicated that strain Th68T represented a distinct phyletic line within the family

Flavobacteriaceae

with less than 96.1 % similarity to members of the recognized genera of the family. The DNA G+C content was 33.0 mol%. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. Menaquinone 6 (MK-6) was the only respiratory quinone. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain Th68T represents a novel species of a new genus in the family

Flavobacteriaceae

, for which the name Flavirhabdus iliipiscaria gen. nov., sp. nov. is proposed. The type strain of Flavirhabdus iliipiscaria is Th68T ( = JCM 18637T = KCTC 32141T).
N
ovosphingobium fluoreni sp. nov., isolated from rice seeds
Authors: Gao Shumei , Zhang Yingjun , Jiang Na , Luo Laixin , Li Qing X. , Li Jianqiang
Published: February 2015

A yellow-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterium designated strain HLJ-RS18T, which could degrade fluorene, was isolated from rice seeds collected from Heilongjiang Province, China. Similarities of full-length of 16S rRNA gene sequences between strain HJL-RS18T and the type strains of the genus

Novosphingobium

with validly published names ranged from 93.8 to 97.1 %. Phylogenetic analysis with maximum-likelihood and neighbour-joining methods revealed that strain HLJ-RS18T belonged to genus

Novosphingobium

and strain HLJ-RS18T formed a distinct clade to

Novosphingobium chloroacetimidivorans

BUT-14T (96.9 % similarity based on 16S rRNA gene). DNA–DNA hybridization of HLJ-RS18T and BUT-14T showed a low relatedness value of 22.4±0.9 %, which indicated that strain HLJ-RS18T represents a novel species of the genus

Novosphingobium

. The genomic DNA G+C content of strain HLJ-RS18T was 62 mol%. Ubiquinone Q-10 was the major respiratory quinone. Spermidine was the predominant polyamine. Polar lipids consisted mainly of aminophospholipid, phosphatidylglycerol, phosphatidylethanolamine, phospholipid and sphingoglycolipid. The predominant fatty acid composition of HLJ-RS18T were summed 8 (C18 : 1ω7c and/or C18 : 1ω6c, 61.5 %), C16 : 0 (14.2 %), summed 3 (C16 : 1ω7c and/or C16 : 1ω6c, 13.5 %) and C14 : 0 2-OH (6.8 %). Phylogenetic analysis, DNA–DNA hybridization, chemotaxonomic data and phenotypic characteristics support the conclusion that HLJ-RS18T represents a novel species within the genus

Novosphingobium

. Therefore, we propose the species Novosphingobium fluoreni sp. nov. with HLJ-RS18T ( = DSM 27568T = ACCC19180T) as the type strain.
Permissivity of primary hepatocytes and hepatoma cell lines to support hepatitis C virus infection
Authors: Wilson Garrick K. , Farquhar Michelle J. , Meredith Luke , Dhawan Anil , Mitry Ragai , Balfe Peter , McKeating Jane A.
Published: February 2015

The major cell type supporting hepatitis C virus (HCV) infection is the hepatocyte; however, most reports studying viral entry and replication utilize transformed hepatoma cell lines. We demonstrate that HCV pseudoparticles (HCVpp) infect primary hepatocytes with comparable rates to hepatoma cells, demonstrating the limited variability in donor hepatocytes to support HCV receptor-glycoprotein-dependent entry. In contrast, we observed a 2-log range in viral replication between the same donor hepatocytes. We noted that cell proliferation augments pseudoparticle reporter activity and arresting hepatoma cells yields comparable levels of infection to hepatocytes. This study demonstrates comparable rates of HCVpp entry into primary hepatocytes and hepatoma cells, validating the use of transformed cells as a model system to study HCV entry.
Integrated Metabolomics and Transcriptomics Reveal Enhanced Specialized Metabolism in Medicago truncatula Root Border Cells
Authors: Watson Bonnie S. , Bedair Mohamed F. , Urbanczyk-Wochniak Ewa , Huhman David V. , Yang Dong Sik , Allen Stacy N. , Li Wensheng , Tang Yuhong , Sumner Lloyd W.
Published: February 2015

Integrated metabolomics and transcriptomics of Medicago truncatula seedling border cells and root tips revealed substantial metabolic differences between these distinct and spatially segregated root regions. Large differential increases in oxylipin-pathway lipoxygenases and auxin-responsive transcript levels in border cells corresponded to differences in phytohormone and volatile levels compared with adjacent root tips. Morphological examinations of border cells revealed the presence of significant starch deposits that serve as critical energy and carbon reserves, as documented through increased β-amylase transcript levels and associated starch hydrolysis metabolites. A substantial proportion of primary metabolism transcripts were decreased in border cells, while many flavonoid- and triterpenoid-related metabolite and transcript levels were increased dramatically. The cumulative data provide compounding evidence that primary and secondary metabolism are differentially programmed in border cells relative to root tips. Metabolic resources normally destined for growth and development are redirected toward elevated accumulation of specialized metabolites in border cells, resulting in constitutively elevated defense and signaling compounds needed to protect the delicate root cap and signal motile rhizobia required for symbiotic nitrogen fixation. Elevated levels of 7,4′-dihydroxyflavone were further increased in border cells of roots exposed to cotton root rot (Phymatotrichopsis omnivora), and the value of 7,4′-dihydroxyflavone as an antimicrobial compound was demonstrated using in vitro growth inhibition assays. The cumulative and pathway-specific data provide key insights into the metabolic programming of border cells that strongly implicate a more prominent mechanistic role for border cells in plant-microbe signaling, defense, and interactions than envisioned previously.
A Small Phospholipase A2-α from Castor Catalyzes the Removal of Hydroxy Fatty Acids from Phosphatidylcholine in Transgenic Arabidopsis Seeds
Authors: Bayon Shen , Chen Guanqun , Weselake Randall J. , Browse John
Published: February 2015

Ricinoleic acid, an industrially useful hydroxy fatty acid (HFA), only accumulates to high levels in the triacylglycerol fraction of castor (Ricinus communis) endosperm, even though it is synthesized on the membrane lipid phosphatidylcholine (PC) from an oleoyl ester. The acyl chains of PC undergo intense remodeling through the process of acyl editing. The identities of the proteins involved in this process, however, are unknown. A phospholipase A2 (PLA2) is thought to be involved in the acyl-editing process. We show here a role for RcsPLA2α in the acyl editing of HFA esterified to PC. RcsPLA2α was identified by its high relative expression in the castor endosperm transcriptome. Coexpression in Arabidopsis (Arabidopsis thaliana) seeds of RcsPLA2α with the castor fatty acid hydroxylase RcFAH12 led to a dramatic decrease in seed HFA content when compared with RcFAH12 expression alone in both PC and the neutral lipid fraction. The low-HFA trait was heritable and gene dosage dependent, with hemizygous lines showing intermediate HFA levels. The low seed HFA levels suggested that RcsPLA2α functions in vivo as a PLA2 with HFA specificity. Activity assays with yeast (Saccharomyces cerevisiae) microsomes showed a high specificity of RcsPLA2α for ricinoleic acid, superior to that of the endogenous Arabidopsis PLA2α. These results point to RcsPLA2α as a phospholipase involved in acyl editing, adapted to specifically removing HFA from membrane lipids in seeds.
Tricin, a Flavonoid Monomer in Monocot Lignification
Authors: Lan Wu , Lu Fachuang , Regner Matthew , Zhu Yimin , Rencoret Jorge , Ralph Sally A. , Zakai Uzma I. , Morreel Kris , Boerjan Wout , Ralph John
Published: February 2015

Tricin was recently discovered in lignin preparations from wheat (Triticum aestivum) straw and subsequently in all monocot samples examined. To provide proof that tricin is involved in lignification and establish the mechanism by which it incorporates into the lignin polymer, the 4′-O-β-coupling products of tricin with the monolignols (p-coumaryl, coniferyl, and sinapyl alcohols) were synthesized along with the trimer that would result from its 4′-O-β-coupling with sinapyl alcohol and then coniferyl alcohol. Tricin was also found to cross couple with monolignols to form tricin-(4′-O-β)-linked dimers in biomimetic oxidations using peroxidase/hydrogen peroxide or silver (I) oxide. Nuclear magnetic resonance characterization of gel permeation chromatography-fractionated acetylated maize (Zea mays) lignin revealed that the tricin moieties are found in even the highest molecular weight fractions, ether linked to lignin units, demonstrating that tricin is indeed incorporated into the lignin polymer. These findings suggest that tricin is fully compatible with lignification reactions, is an authentic lignin monomer, and, because it can only start a lignin chain, functions as a nucleation site for lignification in monocots. This initiation role helps resolve a long-standing dilemma that monocot lignin chains do not appear to be initiated by monolignol homodehydrodimerization as they are in dicots that have similar syringyl-guaiacyl compositions. The term flavonolignin is recommended for the racemic oligomers and polymers of monolignols that start from tricin (or incorporate other flavonoids) in the cell wall, in analogy with the existing term flavonolignan that is used for the low-molecular mass compounds composed of flavonoid and lignan moieties.
FlowerNet: A Gene Expression Correlation Network for Anther and Pollen Development
Authors: Pearce Simon , Ferguson Alison , King John , Wilson Zoe A.
Published: February 2015

Floral formation, in particular anther and pollen development, is a complex biological process with critical importance for seed set and for targeted plant breeding. Many key transcription factors regulating this process have been identified; however, their direct role remains largely unknown. Using publicly available gene expression data from Arabidopsis (Arabidopsis thaliana), focusing on those studies that analyze stamen-, pollen-, or flower-specific expression, we generated a network model of the global transcriptional interactions (FlowerNet). FlowerNet highlights clusters of genes that are transcriptionally coregulated and therefore likely to have interacting roles. Focusing on four clusters, and using a number of data sets not included in the generation of FlowerNet, we show that there is a close correlation in how the genes are expressed across a variety of conditions, including male-sterile mutants. This highlights the important role that FlowerNet can play in identifying new players in anther and pollen development. However, due to the use of general floral expression data in FlowerNet, it also has broad application in the characterization of genes associated with all aspects of floral development and reproduction. To aid the dissection of genes of interest, we have made FlowerNet available as a community resource (http://www.cpib.ac.uk/anther). For this resource, we also have generated plots showing anther/flower expression from a variety of experiments: These are normalized together where possible to allow further dissection of the resource.
2-Cysteine Peroxiredoxins and Thylakoid Ascorbate Peroxidase Create a Water-Water Cycle That Is Essential to Protect the Photosynthetic Apparatus under High Light Stress Conditions
Authors: Awad Jasmin , Stotz Henrik U. , Fekete Agnes , Krischke Markus , Engert Cornelia , Havaux Michel , Berger Susanne , Mueller Martin J.
Published: February 2015

Different peroxidases, including 2-cysteine (2-Cys) peroxiredoxins (PRXs) and thylakoid ascorbate peroxidase (tAPX), have been proposed to be involved in the water-water cycle (WWC) and hydrogen peroxide (H2O2)-mediated signaling in plastids. We generated an Arabidopsis (Arabidopsis thaliana) double-mutant line deficient in the two plastid 2-Cys PRXs (2-Cys PRX A and B, 2cpa 2cpb) and a triple mutant deficient in 2-Cys PRXs and tAPX (2cpa 2cpb tapx). In contrast to wild-type and tapx single-knockout plants, 2cpa 2cpb double-knockout plants showed an impairment of photosynthetic efficiency and became photobleached under high light (HL) growth conditions. In addition, double-mutant plants also generated elevated levels of superoxide anion radicals, H2O2, and carbonylated proteins but lacked anthocyanin accumulation under HL stress conditions. Under HL conditions, 2-Cys PRXs seem to be essential in maintaining the WWC, whereas tAPX is dispensable. By comparison, this HL-sensitive phenotype was more severe in 2cpa 2cpb tapx triple-mutant plants, indicating that tAPX partially compensates for the loss of functional 2-Cys PRXs by mutation or inactivation by overoxidation. In response to HL, H2O2- and photooxidative stress-responsive marker genes were found to be dramatically up-regulated in 2cpa 2cpb tapx but not 2cpa 2cpb mutant plants, suggesting that HL-induced plastid to nucleus retrograde photooxidative stress signaling takes place after loss or inactivation of the WWC enzymes 2-Cys PRX A, 2-Cys PRX B, and tAPX.
Crystal structure of [1,3-bis(diphenylphosphanyl)propane-κ2P,P′](N,N′-dimethylthiourea-κS)(thiocyanato-κN)copper(I)
Authors: Wattanakanjana Yupa , Nimthong-Roldán Arunpatcha , Ratthiwan Janejira
Published: February 2015

The asymmetric unit of the title compound, [Cu(NCS)(C3H8N2S)(C27H26P2)], contains two independent mononuclear complex molecules. In each, the CuIion exhibits a distorted tetrahedral geometry by coordination with two P atoms from one 1,3-bis(diphenylphosphino)propane (dppm) ligand, one terminal S atom of oneN,N′-dimethylthiourea (dmtu) ligand and one terminal N atom of the thiocyanato ligand. The dppp ligand is involved in a bidentate coordination mode with the CuIion, forming a six-membered CuP2C3ring. In both molecules, the coordination of the dmtu ligand is further stabilized by an intramolecular N—H...N hydrogen bond with anS(6) graph-set motif. In the crystal, molecules are linked by N—H...S hydrogen bonds forming a zigzag chain along thea-axis direction. In one independent molecule, one of the phenyl rings of the dppp ligand is disordered over two sites with refined occupancies 0.639 (11):0.361 (11) and this corresponds with a mutual disorder of the dmtu ligand in the other independent molecule giving the same ratio of refined occupancies. The structure was refined as a two-component inversion twin.
Crystal structure of pseudoguainolide
Authors: Beghidja Noureddine , Benayache Samir , Benayache Fadila , Knight David W. , Kariuki Benson M.
Published: February 2015

The lactone ring in the title molecule, C15H22O3(systematic name: 3,4a,8-trimethyldodecahydroazuleno[6,5-b]furan-2,5-dione), assumes an envelope conformation with the methine C atom adjacent to the the methine C atom carrying the methyl substituent being the flap atom. The other five-membered ring adopts a twisted conformation with the twist being about the methine–methylene C—C bond. The seven-membered ring is based on a twisted boat conformation. No specific interactions are noted in the the crystal packing.
Filleting sharp edges of multi-partitioned volume finite element meshes
Authors: Lou Ruding , Pernot Jean-Philippe , Giannini Franca , Veron Philippe , Falcidieno Bianca
Published: February 2015

Purpose

– The purpose of this paper is to set up a new framework to enable direct modifications of volume meshes enriched with semantic information associated to multiple partitions. An instance of filleting operator is prototyped under this framework and presented in the paper.

Design/methodology/approach

– In this paper, a generic mesh modification operator has been designed and a new instance of this operator for filleting finite element (FE) sharp edges of tetrahedral multi-partitioned meshes is also pro-posed. The filleting operator works in two main steps. The outer skin of the tetrahedral mesh is first deformed to round user-specified sharp edges while satisfying constraints relative to the shape of the so-called Virtual Group Boundaries. Then, in the filleting area, the positions of the inner nodes are relaxed to improve the aspect ratio of the mesh elements.

Findings

– The classical mainstream methodology for product behaviour optimization involves the repetition of four steps: CAD modelling, meshing of CAD models, enrichment of models with FE simulation semantics and FEA. This paper highlights how this methodology could be simplified by two steps: simulation model modification and FEA. The authors set up a new framework to enable direct modifications of volume meshes enriched with semantic information associated to multiple partitions and the corresponding fillet operator is devised.

Research limitations/implications

– The proposed framework shows only a paradigm of direct modifications of semantic enriched meshes. It could be further more improved by adding or changing the modules inside. The fillet operator does not take into account the exact radius imposed by user. With this proposed fillet operator the mesh element density may not be enough high to obtain wished smoothness.

Originality/value

– This paper fulfils an identified industry need to speed up the product behaviour analysis process by directly modifying the simulation semantic enriched meshes.
Virtual prototyping in the design process of optimized mould gating system for high pressure die casting
Authors: Raffaeli Roberto , Favi Claudio , Mandorli Ferruccio
Published: February 2015

Purpose

– High pressure die casting is a widely used industrial process to manufacture complex-shaped products in light alloys. Virtual prototyping techniques, especially numeric-based simulations of the casting process, allow the die filling process to be evaluated and help faster optimization of the gating system, which is the most critical element of the mould. The purpose of this paper is to present a four step approach to design optimal moulds taking advantage of the simulation tools.

Design/methodology/approach

– No formalized method to design an optimal gating system is available yet and the majority of the studies aim to optimize existing geometries or to choose from alternative solutions. Rather than optimizing the geometries of predefined designs by running attempt trials, the proposed approach defines a procedure to position cavities, gating systems and, finally, to determine the whole mould geometry.

Findings

– The approach is demonstrated through three different industrial applications. The design of a six-cavity mould for gas cooking burners is reported at first. Then, two test cases, a cup and a radiator, are reported for showing different arrangements of the gating system. The reached quality of the mould design has been assessed using metallographic analyses of the casts.

Originality/value

– The design of a mould is strictly correlated to its product and mainly based on a trial-and-error approach. Numerical simulations offer a powerful and not expensive way to study the effectiveness of different die designs and filling processes. The paper proposes a structured approach for the definition of the gating system. It ultimately leads to improvements in both product quality and process productivity, including more effective control of the die filling and die thermal performance.