bluuebunny/crossref_metadata_2025 huggingface dataset:
ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine
Authors: Matsuta Yoshihiko , Ito Masahiro , Tohsato Yukako
Published: December 2012

Motivation: The enzyme nomenclature system, commonly known as the enzyme commission (EC) number, plays a key role in classifying and predicting enzymatic reactions. However, numerous reactions have been described in various pathways that do not have an official EC number, and the reactions are not expected to have an EC number assigned because of a lack of articles published on enzyme assays. To predict the EC number of a non-classified enzymatic reaction, we focus on the structural similarity of its substrate and product to the substrate and product of reactions that have been classified.

Results: We propose a new method to assign EC numbers using a maximum common substructure algorithm, mutual information and a support vector machine, termed the Enzyme COmmission numbers Handler (ECOH). A jack-knife test shows that the sensitivity, precision and accuracy of the method in predicting the first three digits of the official EC number (i.e. the EC sub-subclass) are 86.1%, 87.4% and 99.8%, respectively. We furthermore demonstrate that, by examining the ranking in the candidate lists of EC sub-subclasses generated by the algorithm, the method can successfully predict the classification of 85 enzymatic reactions that fall into multiple EC sub-subclasses. The better performance of the ECOH as compared with existing methods and its flexibility in predicting EC numbers make it useful for predicting enzyme function.

Availability: ECOH is freely available via the Internet at http://www.bioinfo.sk.ritsumei.ac.jp/apps/ecoh/. This program only works on 32-bit Windows.

Contact:  yukako@sk.ritsumei.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
Fas deficiency in mice with the Balb/c background induces blepharitis with allergic inflammation and hyper-IgE production in conjunction with severe autoimmune disease
Authors: Takahashi Suzuka , Futatsugi-Yumikura Shizue , Fukuoka Ayumi , Yoshimoto Tomohiro , Nakanishi Kenji , Yonehara Shin
Published: December 2012

Fas (CD95) is a cell surface death receptor belonging to the tumor necrosis factor receptor superfamily, which mediates apoptosis-inducing signaling when activated by Fas ligand or its agonistic antibody. lpr mice with a loss of apoptosis-inducing function mutation in the Fas gene develop systemic autoimmune disease and lymphadenopathy but not allergic inflammation. In the case of Fas mutations including lpr and knockout (KO), background genes determine the incidence and severity of lymphadenopathy and histopathological manifestation of systemic autoimmunity: MRL-lpr/lpr mice and C57BL/6-lpr/lpr or C57BL/6 Fas KO mice develop severe and minimum disease, respectively. We generated Fas KO mice with the Balb/c background that show severer autoimmune phenotypes than MRL-lpr/lpr mice, such as critical infiltration of mononuclear cells into lung, liver and spleen, elevated serum levels of auto-antibodies and a decreased life span. To our astonishment, Balb/c Fas KO mice spontaneously develop blepharitis with not only autoimmune inflammation with deposition of auto-antibody but also allergic inflammation with infiltration by eosinophils and mast cells and show the capacity to strongly increase serum level of IgE and IgG1 along with their aging. Thus, Fas expression regulates development of not only autoimmune disease but also allergic inflammation.
Structure and function of cytidine monophosphate kinase from
Yersinia pseudotuberculosis
, essential for virulence but not for survival
Authors: Walker Nicola J. , Clark Elizabeth A. , Ford Donna C. , Bullifent Helen L. , McAlister Erin V. , Duffield Melanie L. , Acharya K. Ravi , Oyston Petra C. F.
Published: December 2012

The need for new antibiotics has become pressing in light of the emergence of antibiotic-resistant strains of human pathogens.
Yersinia pestis
, the causative agent of plague, is a public health threat and also an agent of concern in biodefence. It is a recently emerged clonal derivative of the enteric pathogen
Yersinia pseudotuberculosis.
Previously, we developed a bioinformatic approach to identify proteins that may be suitable targets for antimicrobial therapy and in particular for the treatment of plague. One such target was cytidine monophosphate (CMP) kinase, which is an essential gene in some organisms. Previously, we had thought CMP kinase was essential for
Y. pseudotuberculosis
, but by modification of the mutagenesis approach, we report here the production and characterization of a
Δcmk
mutant. The isogenic mutant had a growth defect relative to the parental strain, and was highly attenuated in mice. We have also elucidated the structure of the CMP kinase to 2.32 Å, and identified three key residues in the active site that are essential for activity of the enzyme. These findings will have implications for the development of novel CMP kinase inhibitors for therapeutic use.
Lactobacillus curieae sp. nov., isolated from stinky tofu brine
Authors: Lei Xiao , Sun Guipeng , Xie Jingli , Wei Dongzhi
Published: December 2012

A lactic acid bacterium, strain CCTCC M 2011381T, isolated from the brine of the traditional Chinese snack, stinky tofu, was studied to determine its taxonomic position. It was a Gram-stain-positive, non-motile, facultatively anaerobic rod-shaped bacterium that did not exhibit catalase activity. The DNA G+C content of the strain was 44.1 % and its peptidoglycan was characterized by the presence of meso-diaminopimelic acid. Levels of 16S rRNA gene sequence similarity between strain CCTCC M 2011381T and the most closely related species

Lactobacillus senioris

JCM 17472T,

Lactobacillus parafarraginis

JCM 14109T and

Lactobacillus diolivorans

JCM 12183T were 96.5, 96.4 and 96.4 %, respectively. Combined with data from high-resolution genomic markers recA, rpoA and pheS, strain CCTCC M 2011381T was classified as representing a novel species. The strain could also be distinguished from other related species of the genus

Lactobacillus

by its physiological and biochemical characteristics. Based on the phylogenetic, physiological and biochemical data, it is proposed that the new isolate can be classified as representing a novel species of the genus

Lactobacillus

, for which the name Lactobacillus curieae sp. nov. (type strain CCTCC M 2011381T = S1L19T = JCM 18524T) is proposed.
Pleomorphomonas

diazotrophica sp. nov., an endophytic N-fixing bacterium isolated from root tissue of Jatropha curcas L.
Authors: Madhaiyan Munusamy , Jin Tan Yuan , Roy Joseph Jegan , Kim Soo-Jin , Weon Hang-Yeon , Kwon Soon-Wo , Ji Lianghui
Published: December 2012

A novel aerobic, non-motile, pleomorphic, Gram-negative and nitrogen-fixing bacterial strain, designated R5-392T, was isolated from surface-sterilized root tissue of Jatropha curcas. The organism grew optimally at 30 °C in media containing 1 % (w/v) NaCl and at pH 6.0–8.0. The predominant ubiquinone was Q-10 and the major fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0 and C19 : 0 cyclo ω8c. The DNA G+C content was 63.2 mol%. Analysis of the 16S rRNA gene sequence suggested that strain R5-392T is affiliated with the order

Rhizobiales

within the class

Alphaproteobacteria

and is most closely related to

Pleomorphomonas oryzae

F-7T (98.8 % similarity) and

Pleomorphomonas koreensis

Y9T (98.3 % similarity). Analysis of partial nifH gene sequences also revealed a monophyletic lineage within the class

Alphaproteobacteria

, and strain R5-392T was most closely related to

P. oryzae

F-7T (98 %). Highest nitrogenase activity was detected in the presence of low-level organic nitrogen or in the presence of nitrogenase co-factors (Fe/Mo) in N-free media. Phenotypic and chemotaxonomic data suggest that strain R5-392T represents a novel species within the genus

Pleomorphomonas

, for which the name

Pleomorphomonas

diazotrophica sp. nov. is proposed. The type strain is R5-392T ( = KACC 16233T  = DSM 25022T).
Pectobacterium

aroidearum sp. nov., a soft rot pathogen with preference for monocotyledonous plants
Authors: Nabhan Shaza , De Boer Solke H. , Maiss Edgar , Wydra Kerstin
Published: December 2012

Several pectolytic bacterial strains, mainly isolated from monocotyledonous plants and previously identified as

Pectobacterium carotovorum

, were thought to belong to a novel species after several taxonomic analyses including DNA–DNA hybridization. In 16S rRNA gene sequence analyses, these strains had a similarity of >97.9 % to the 16S rRNA gene sequence of strains representing six other pectobacterial species and subspecies. These strains, represented by strain SCRI 109T, also showed some unique chemotaxonomic features and quantitative differences in polar lipids, lipoquinones and fatty acids. A specific feature of strain SCRI 109T was the presence of DMK-8 lipoquinone, while the dominant fatty acids were the summed feature 3 (iso-C15 : 0 2-OH/C16 : 1ω7c), the unsaturated fatty acid C18 : 1ω7c and straight chain fatty acids, mainly C16 : 0. The DNA G+C content of strain SCRI 109T was 50.2 mol%. The taxonomic status of strain SCRI 109T and related strains in 16S rRNA gene sequence, chemotaxonomic, and physiological analyses was corroborated by the distinct clustering of these strains in multi-locus sequence analyses. It is proposed that these strains represent a novel species for which the name

Pectobacterium

aroidearum sp. nov. is proposed; the type strain is SCRI 109T ( = NCPPB 929T = LMG 2417T = ICMP 1522T).
Flavobacterium nitratireducens sp. nov., an amylolytic bacterium of the family Flavobacteriaceae isolated from coastal surface seawater
Authors:   Nupur, Bhumika V. , Srinivas T. N. R. , Kumar P. Anil
Published: December 2012

A novel Gram-negative, rod-shaped, non-motile bacterium, designated strain N1T, was isolated from a marine water sample collected from the sea shore, Bay of Bengal, Visakhapatnam, India. The strain was positive for starch hydrolysis, nitrate reduction and ornithine decarboxylase activities and negative for citrate utilization, urease, oxidase, catalase and DNase activities. The predominant fatty acids were C16 : 03-OH, iso-C15 : 0, iso-C15 : 03-OH, iso-C17 : 03-OH, anteiso-C15 : 0, C16 : 0, C15 : 03-OH, and C16 : 1ω7cand/or iso-C15 : 02-OH (summed feature 3). Strain N1Tcontained menaquinone 6 (MK-6) as the sole respiratory quinone. The only polyamine was homospermidine and the major polar lipids were phosphatidylethanolamine (PE), three unidentified aminolipids (AL1–AL3) and two unidentified lipids (L1, L2). The DNA G+C content of the strain was 36.3 mol%. 16S rRNA gene sequence analysis indicated that strain N1Twas a member of the genusFlavobacteriumand closely related toFlavobacterium resistenswith pairwise sequence similarity of 96.5 %. Phylogenetic analysis showed that strain N1Tclustered withFlavobacterium glycinesandFlavobacterium daejeonensewith a distance of 4.8 and 6.0 % (95.2 and 94.0 % similarity), respectively. Based on the phenotypic characteristics and on phylogenetic inference, strain N1Trepresents a novel species of the genusFlavobacterium, for which the nameFlavobacterium nitratireducenssp. nov. is proposed. The type strain is N1T( = MTCC 11155T = JCM 17678T).
Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments
Authors: Vaishampayan Parag , Moissl-Eichinger Christine , Pukall Rüdiger , Schumann Peter , Spröer Cathrin , Augustus Angela , Roberts Anne Hayden , Namba Greg , Cisneros Jessica , Salmassi Tina , Venkateswaran Kasthuri
Published: December 2012

Two strains of aerobic, non-motile, Gram-reaction-positive cocci were independently isolated from geographically distinct spacecraft assembly clean room facilities (Kennedy Space Center, Florida, USA and Centre Spatial Guyanais, Kourou, French Guiana). A polyphasic study was carried out to delineate the taxonomic identity of these two isolates (1P05MAT and KO_PS43). The 16S rRNA gene sequences exhibited a high similarity when compared to each other (100 %) and lower than 96.7 % relatedness with

Arthrobacter crystallopoietes

ATCC 15481T,

Arthrobacter luteolus

ATCC BAA-272T,

Arthrobacter tumbae

DSM 16406T and

Arthrobacter subterraneus

DSM 17585T. In contrast with previously described

Arthrobacter

species, the novel isolates maintained their coccidal morphology throughout their growth and did not exhibit the rod–coccus life cycle typically observed in nearly all

Arthrobacter

species, except

A. agilis

. The distinct taxonomic identity of the novel isolates was confirmed based on their unique cell-wall peptidoglycan type (A.11.20; Lys-Ser-Ala2) and polar lipid profile (presence of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and two unknown glycolipids). The G+C content of the genomic DNA was 70.6 mol%. The novel strains revealed MK-9(H2) and MK-8(H2) as dominant menaquinones and exhibited fatty acid profiles consisting of major amounts of anteiso-C15 : 0 and anteiso-C17 : 0 and moderate amounts of iso-C15 : 0 discriminating them again from closely related

Arthrobacter

species. Based on these observations, the authors propose that strains 1P05MAT and KO_PS43 be assigned into a separate genus Tersicoccus gen. nov. For this new taxon, comprising strains 1P05MAT and KO_PS43, we propose the name Tersicoccus phoenicis gen. nov., sp. nov. (the type species of Tersicoccus), represented by the type strain Tersicoccus phoenicis 1P05MAT ( = NRRL B-59547T = DSM 30849T).
Taonella mepensis gen. nov., sp. nov., a member of the family

Rhodospirillaceae

isolated from activated sludge
Authors: Xi Xue-dong , Dong Wei-liang , Zhang Jun , Huang Yan , Cui Zhong-li
Published: December 2012

A novel Gram-negative, non-spore-forming, rod-shaped strain, H1T, was isolated from activated sludge by micromanipulation. No close relatives among cultured bacterial isolates were found; phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H1T forms a deep single branch in the family

Rhodospirillaceae

. Cells of strain H1T were slightly curved to straight rods (1.2–1.4×1.5–1.7 µm) and motile by a single polar flagellum. Strain H1T was able to grow in the presence of 0–4 % NaCl and grew optimally at 37 °C and pH 6.0–7.0. Chemotaxonomic analysis revealed that strain H1T possessed Q-10 as the predominant ubiquinone and C18 : 1ω7c, C16 : 0 and C19 : 0 cyclo ω8c as the major fatty acids. The DNA G+C content of strain H1T was 65.1 mol%. Comparative analysis of 16S rRNA gene sequences, and phenotypic and chemotaxonomic data, indicate that strain H1T should represent a novel genus and species of the family

Rhodospirillaceae

. The name Taonella mepensis gen. nov., sp. nov. is proposed. The type strain of Taonella mepensis is H1T ( = CICC 10529T  = CCTCC AB 2012861T  = KACC 16940T).
BAF60 A, B, and Cs of muscle determination and renewal
Authors: Puri Pier Lorenzo , Mercola Mark
Published: December 2012

Developmental biologists have defined many of the diffusible and transcription factors that control muscle differentiation, yet we still have only rudimentary knowledge of the mechanisms that dictate whether a myogenic progenitor cell forms muscle versus alternate lineages, including those that can be pathological in a state of disease or degeneration. Clues about the molecular basis for lineage determination in muscle progenitors are only now emerging from studies of chromatin modifications that avail myogenic genes for transcription, together with analysis of the composition and activities of the chromatin-modifying complexes themselves. Here we review recent progress on muscle determination and explore a unifying theme that environmental cues from the stem or progenitor niche control the selection of specific subunit variants of the switch/sucrose nonfermentable (SWI/SNF) chromatin-modifying complex, creating a combinatorial code that dictates whether cells adopt myogenic versus nonmyogenic cell fates. A key component of the code appears to be the mutually exclusive usage of the a, b, and c variants of the 60-kD structural subunit BAF60 (BRG1/BRM-associated factor 60), of which BAF60c is essential to activate both skeletal and cardiac muscle programs. Since chromatin remodeling governs myogenic fate, the combinatorial assembly of the SWI/SNF complex might be targeted to develop drugs aimed at the therapeutic reduction of compensatory fibrosis and fatty deposition in chronic muscular disorders.
Early Cone Setting in Picea abies acrocona Is Associated with Increased Transcriptional Activity of a MADS Box Transcription Factor
Authors: Uddenberg Daniel , Reimegård Johan , Clapham David , Almqvist Curt , von Arnold Sara , Emanuelsson Olof , Sundström Jens F.
Published: December 2012

Conifers normally go through a long juvenile period, for Norway spruce (Picea abies) around 20 to 25 years, before developing male and female cones. We have grown plants from inbred crosses of a naturally occurring spruce mutant (acrocona). One-fourth of the segregating acrocona plants initiate cones already in their second growth cycle, suggesting control by a single locus. The early cone-setting properties of the acrocona mutant were utilized to identify candidate genes involved in vegetative-to-reproductive phase change in Norway spruce. Poly(A+) RNA samples from apical and basal shoots of cone-setting and non-cone-setting plants were subjected to high-throughput sequencing (RNA-seq). We assembled and investigated 33,383 expressed putative protein-coding acrocona transcripts. Eight transcripts were differentially expressed between selected sample pairs. One of these (Acr42124_1) was significantly up-regulated in apical shoot samples from cone-setting acrocona plants, and the encoded protein belongs to the MADS box gene family of transcription factors. Using quantitative real-time polymerase chain reaction with independently derived plant material, we confirmed that the MADS box gene is up-regulated in both needles and buds of cone-inducing shoots when reproductive identity is determined. Our results constitute important steps for the development of a rapid cycling model system that can be used to study gene function in conifers. In addition, our data suggest the involvement of a MADS box transcription factor in the vegetative-to-reproductive phase change in Norway spruce.
Pipecolic Acid, an Endogenous Mediator of Defense Amplification and Priming, Is a Critical Regulator of Inducible Plant Immunity
Authors: Návarová Hana , Bernsdorff Friederike , Döring Anne-Christin , Zeier Jürgen
Published: December 2012

Metabolic signals orchestrate plant defenses against microbial pathogen invasion. Here, we report the identification of the non-protein amino acid pipecolic acid (Pip), a common Lys catabolite in plants and animals, as a critical regulator of inducible plant immunity. Following pathogen recognition, Pip accumulates in inoculated Arabidopsis thaliana leaves, in leaves distal from the site of inoculation, and, most specifically, in petiole exudates from inoculated leaves. Defects of mutants in AGD2-LIKE DEFENSE RESPONSE PROTEIN1 (ALD1) in systemic acquired resistance (SAR) and in basal, specific, and β-aminobutyric acid–induced resistance to bacterial infection are associated with a lack of Pip production. Exogenous Pip complements these resistance defects and increases pathogen resistance of wild-type plants. We conclude that Pip accumulation is critical for SAR and local resistance to bacterial pathogens. Our data indicate that biologically induced SAR conditions plants to more effectively synthesize the phytoalexin camalexin, Pip, and salicylic acid and primes plants for early defense gene expression. Biological priming is absent in the pipecolate-deficient ald1 mutants. Exogenous pipecolate induces SAR-related defense priming and partly restores priming responses in ald1. We conclude that Pip orchestrates defense amplification, positive regulation of salicylic acid biosynthesis, and priming to guarantee effective local resistance induction and the establishment of SAR.
LSM Proteins Provide Accurate Splicing and Decay of Selected Transcripts to Ensure NormalArabidopsisDevelopment
Authors: Perea-Resa Carlos , Hernández-Verdeja Tamara , López-Cobollo Rosa , Castellano María del Mar , Salinas Julio
Published: December 2012

In yeast and animals, SM-like (LSM) proteins typically exist as heptameric complexes and are involved in different aspects of RNA metabolism. Eight LSM proteins, LSM1 to 8, are highly conserved and form two distinct heteroheptameric complexes, LSM1-7 and LSM2-8,that function in mRNA decay and splicing, respectively. A search of the Arabidopsis thaliana genome identifies 11 genes encoding proteins related to the eight conserved LSMs, the genes encoding the putative LSM1, LSM3, and LSM6 proteins being duplicated. Here, we report the molecular and functional characterization of the Arabidopsis  LSM gene family. Our results show that the 11 LSM genes are active and encode proteins that are also organized in two different heptameric complexes. The LSM1-7 complex is cytoplasmic and is involved in P-body formation and mRNA decay by promoting decapping. The LSM2-8 complex is nuclear and is required for precursor mRNA splicing through U6 small nuclear RNA stabilization. More importantly, our results also reveal that these complexes are essential for the correct turnover and splicing of selected development-related mRNAs and for the normal development of Arabidopsis. We propose that LSMs play a critical role in Arabidopsis development by ensuring the appropriate development-related gene expression through the regulation of mRNA splicing and decay.
PSBP-DOMAIN PROTEIN1, a Nuclear-Encoded Thylakoid Lumenal Protein, Is Essential for Photosystem I Assembly in Arabidopsis
Authors: Liu Jun , Yang Huixia , Lu Qingtao , Wen Xiaogang , Chen Fan , Peng Lianwei , Zhang Lixin , Lu Congming
Published: December 2012

To gain insights into the molecular details of photosystem I (PSI) biogenesis, we characterized the PsbP-domain protein1 (ppd1) mutant of Arabidopsis thaliana that specifically lacks PSI activity. Deletion of PPD1 results in an inability of the mutant to grow photoautotrophically and a specific loss of the stable PSI complex. Unaltered transcription and translation of plastid-encoded PSI genes indicate that PPD1 acts at the posttranslational level. In vivo protein labeling experiments reveal that the rate of synthesis of PSI reaction center proteins PsaA/B in ppd1 is comparable to that of wild-type plants, whereas the rate of turnover of PsaA/B proteins is higher in ppd1 than in wild-type plants. With increasing leaf age, PPD1 content decreases considerably, while PSI content remains constant. PPD1 is a nuclear-encoded thylakoid lumenal protein and is associated with PSI but is not an integral subunit of PSI. Biochemical and molecular analyses reveal that PPD1 interacts directly and specifically with PsaB and PsaA. Yeast two-hybrid experiments show that PPD1 interacts with some lumenal loops of PsaB and PsaA. Our results suggest that PPD1 is a PSI assembly factor that assists the proper folding and integration of PsaB and PsaA into the thylakoid membrane.
Challenges in Designing Mechatronic Systems
Authors: Mørkeberg Torry-Smith Jonas , Qamar Ahsan , Achiche Sofiane , Wikander Jan , Henrik Mortensen Niels , During Carl
Published: December 2012

Development of mechatronic products is traditionally carried out by several design experts from different design domains. Performing development of mechatronic products is thus greatly challenging. In order to tackle this, the critical challenges in mechatronics have to be well understood and well supported through applicable methods and tools. This paper aims at identifying the major challenges, by conducting a systematic and thorough survey of the most relevant research work in mechatronic design. Solutions proposed in literature are assessed and illustrated through a case study in order to investigate if the challenges can be handled appropriately by the methods, tools, and mindsets suggested by the mechatronic community. Using a real-world mechatronics case, the paper identifies the areas where further research is required, by showing a clear connection between the actual problems faced during the design task and the nature of the solutions currently available. From the results obtained from this research, one can conclude that although various attempts have been developed to support conceptual design of mechatronics, these attempts are still not sufficient to help in assessing the consequences of selecting between alternative conceptual solutions across multiple domains. We believe that a common language is essential in developing mechatronics, and should be evaluated based on: its capability to represent the desired views effectively, its potential to be understood by engineers from the various domains, and its effect on the efficiency of the development process.
Tendon Fascicles Exhibit a Linear Correlation Between Poisson's Ratio and Force During Uniaxial Stress Relaxation
Authors: Reese Shawn P. , Weiss Jeffrey A.
Published: December 2012

The underlying mechanisms for the viscoelastic behavior of tendon and ligament tissue are poorly understood. It has been suggested that both a flow-dependent and flow-independent mechanism may contribute at different structural levels. We hypothesized that the stress relaxation response of a single tendon fascicle is consistent with the flow-dependent mechanism described by the biphasic theory (Armstrong et al., 1984, “An Analysis of the Unconfined Compression of Articular Cartilage,” ASME J. Biomech. Eng., 106, pp. 165–173). To test this hypothesis, force, lateral strain, and Poisson's ratio were measured as a function of time during stress relaxation testing of six rat tail tendon fascicles from a Sprague Dawley rat. As predicted by biphasic theory, the lateral strain and Poisson's ratio were time dependent, a large estimated volume loss was seen at equilibrium and there was a linear correlation between the force and Poisson's ratio during stress relaxation. These results suggest that the fluid dependent mechanism described by biphasic theory may explain some or all of the apparent viscoelastic behavior of single tendon fascicles.
Optimized Design of an Instrumented Spatial Linkage that Minimizes Errors in Locating the Rotational Axes of the Tibiofemoral Joint: A Computational Analysis
Authors: Bonny Daniel P. , Hull M. L. , Howell S. M.
Published: December 2012

An accurate method to locate of the flexion-extension (F-E) axis and longitudinal rotation (LR) axis of the tibiofemoral joint is required to accurately characterize tibiofemoral kinematics. A method was recently developed to locate these axes using an instrumented spatial linkage (ISL) (2012, “On the Estimate of the Two Dominant Axes of the Knee Using an Instrumented Spatial Linkage,” J. Appl. Biomech., 28(2), pp. 200–209). However, a more comprehensive error analysis is needed to optimize the design and characterize the limitations of the device before using it experimentally. To better understand the errors in the use of an ISL in finding the F-E and LR axes, our objectives were to (1) develop a method to computationally determine the orientation and position errors in locating the F-E and LR axes due to transducer nonlinearity and hysteresis, ISL size and attachment position, and the pattern of applied tibiofemoral motion, (2) determine the optimal size and attachment position of an ISL to minimize these errors, (3) determine the best pattern of pattern of applied motion to minimize these errors, and (4) examine the sensitivity of the errors to range of flexion and internal-external (I-E) rotation. A mathematical model was created that consisted of a virtual “elbow-type” ISL that measured motion across a virtual tibiofemoral joint. Two orientation and two position errors were computed for each axis by simulating the axis-finding method for 200 iterations while adding transducer errors to the revolute joints of the virtual ISL. The ISL size and position that minimized these errors were determined from 1080 different combinations. The errors in locating the axes using the optimal ISL were calculated for each of three patterns of motion applied to the tibiofemoral joint, consisting of a sequential pattern of discrete tibiofemoral positions, a random pattern of discrete tibiofemoral positions, and a sequential pattern of continuous tibiofemoral positions. Finally, errors as a function of range of flexion and I-E rotation were determined using the optimal pattern of applied motion. An ISL that was attached to the anterior aspect of the knee with 300-mm link lengths had the lowest maximum error without colliding with the anatomy of the joint. A sequential pattern of discrete tibiofemoral positions limited the largest orientation or position error without displaying large bias error. Finally, the minimum range of applied motion that ensured all errors were below 1 deg or 1 mm was 30 deg flexion with ±15 deg I-E rotation. Thus a method for comprehensive analysis of error when using this axis-finding method has been established, and was used to determine the optimal ISL and range of applied motion; this method of analysis could be used to determine the errors for any ISL size and position, any applied motion, and potentially any anatomical joint.
Molecular beam epitaxial growth of ultralow absorption GaN high electron mobility transistor material on sapphire substrates for infrared transparent conductors
Authors: Hoke William E. , Kirchner Amanda J. , Mosca John J. , Resler Daniel P. , Kennedy Theodore D. , Holz Michael , Kerr Amanda J. , Collins Steven R.
Published: December 2012

GaN HEMT structures have been grown on sapphire substrates that exhibit very low absorption loss at 1 μm and low sheet resistance, which are attractive properties for infrared transparent conductors. Initial GaN HEMT/sapphire films showed highly variable absorptions, which were determined to be caused by oxygen outdiffusion from the sapphire substrate into the AlN buffer layer. Growth conditions were modified enabling reproducible growth of low absorption and low sheet resistance material. Absorption losses as low as 0.1% with concomitant film conductivities of 350 Ω/sq or less were demonstrated. Consequently, free carriers in the GaN HEMT channel do not cause significant infrared absorption. The concomitant properties of low absorption and low sheet resistance exceed the properties of transparent conducting oxides. These properties of the GaN HEMT/sapphire structure are also more thermally stable compared to transparent conducting oxides. The low absorption characteristic of the GaN HEMT/sapphire structure is expected to extend into the visible spectrum enabling visible transparent conductor applications as well.
Model generation of coronary artery bifurcations from CTA and single plane angiography
Authors: Cárdenes Rubén , Díez José L. , Duchateau Nicolas , Pashaei Ali , Frangi Alejandro F.
Published: December 2012

Purpose:

To generate accurate and realistic models of coronary artery bifurcations before and after percutaneous coronary intervention (PCI), using information from two image modalities. Because bifurcations are regions where atherosclerotic plaque appears frequently and intervention is more challenging, generation of such realistic models could be of high value to predict the risk of restenosis or thrombosis after stent implantation, and to study geometrical and hemodynamical changes.

Methods:

Two image modalities have been employed to generate the bifurcation models: computer tomography angiography (CTA) to obtain the 3D trajectory of vessels, and 2D conventional coronary angiography (CCA) to obtain radius information of the vessel lumen, due to its better contrast and image resolution. In addition, CCA can be acquired right before and after the intervention in the operation room; therefore, the combination of CTA and CCA allows the generation of realistic preprocedure and postprocedure models of coronary bifurcations. The method proposed is semiautomatic, based on landmarks manually placed on both image modalities.

Results:

A comparative study of the models obtained with the proposed method with models manually obtained using only CTA, shows more reliable results when both modalities are used together. The authors show that using preprocedure CTA and postprocedure CCA, realistic postprocedure models can be obtained. Analysis carried out of the Murray's law in all patient bifurcations shows the geometric improvement of PCI in our models, better than using manual models from CTA alone. An experiment using a cardiac phantom also shows the feasibility of the proposed method.

Conclusions:

The authors have shown that fusion of CTA and CCA is feasible for realistic generation of coronary bifurcation models before and after PCI. The method proposed is efficient, and relies on minimal user interaction, and therefore is of high value to study geometric and hemodynamic changes of treated patients.
Rapid additive manufacturing of MR compatible multipinhole collimators with selective laser melting of tungsten powder
Authors: Deprez Karel , Vandenberghe Stefaan , Van Audenhaege Karen , Van Vaerenbergh Jonas , Van Holen Roel
Published: December 2012

Purpose:

The construction of complex collimators with a high number of oblique pinholes is very labor intensive, expensive or is sometimes impossible with the current available techniques (drilling, milling or electric discharge machining). All these techniques are subtractive: one starts from solid plates and the material at the position of the pinholes is removed. The authors used a novel technique for collimator construction, called metal additive manufacturing. This process starts with a solid piece of tungsten on which a first layer of tungsten powder is melted. Each subsequent layer is then melted on the previous layer. This melting is done by selective laser melting at the locations where the CAD design file defines solid material.

Methods:

A complex collimator with 20 loftholes with 500 μm diameter pinhole opening was designed and produced (16 mm thick and 70 × 52 mm2 transverse size). The density was determined, the production accuracy was measured (GOM ATOS II Triple Scan, Nikon AZ100M microscope, Olympus IMT200 microscope). Point source measurements were done by mounting the collimator on a SPECT detector. Because there is increasing interest in dual‐modality SPECT‐MR imaging, the collimator was also positioned in a 7T MRI scanner (Bruker Pharmascan). A uniform phantom was acquired using T1, T2, and T2* sequences to check for artifacts or distortion of the phantom images due to the collimator presence. Additionally, three tungsten sample pieces (250, 500, and 750 μm thick) were produced. The density, attenuation (140 keV beam), and uniformity (GE eXplore Locus SP micro‐CT) of these samples were measured.

Results:

The density of the collimator was equal to 17.31 ± 0.10 g/cm3 (89.92% of pure tungsten). The production accuracy ranges from −260 to +650 μm. The aperture positions have a mean deviation of 5 μm, the maximum deviation was 174 μm and the minimum deviation was −122 μm. The mean aperture diameter is 464 ± 19 μm. The calculated and measured sensitivity and resolution of point sources at different positions in the field‐of‐view agree well. The measured and expected attenuation of the three sample pieces are in a good agreement. There was no influence of the 7T magnetic field on the collimator (which is paramagnetic) and minimal distortion was noticed on the MR scan of the uniform phantom.

Conclusions:

Additive manufacturing is a very promising technique for the production of complex multipinhole collimators and may also be used for producing other complex collimators. The cost of this technique is only related to the amount of powder needed and the time it takes to have the collimator built. The timeframe from design to collimator production is significantly reduced.
Why Orange Guaymas Basin Beggiatoa spp. Are Orange: Single-Filament-Genome-Enabled Identification of an Abundant Octaheme Cytochrome with Hydroxylamine Oxidase, Hydrazine Oxidase, and Nitrite Reductase Activities
Authors: MacGregor Barbara J. , Biddle Jennifer F. , Siebert Jason R. , Staunton Eric , Hegg Eric L. , Matthysse Ann G. , Teske Andreas
Published: December 2012

Orange, white, and yellow vacuolated
Beggiatoaceae
filaments are visually dominant members of microbial mats found near sea floor hydrothermal vents and cold seeps, with orange filaments typically concentrated toward the mat centers. No marine vacuolate
Beggiatoaceae
are yet in pure culture, but evidence to date suggests they are nitrate-reducing, sulfide-oxidizing bacteria. The nearly complete genome sequence of a single orange
Beggiatoa
(“
Candidatus
Maribeggiatoa”) filament from a microbial mat sample collected in 2008 at a hydrothermal site in Guaymas Basin (Gulf of California, Mexico) was recently obtained. From this sequence, the gene encoding an abundant soluble orange-pigmented protein in Guaymas Basin mat samples (collected in 2009) was identified by microcapillary reverse-phase high-performance liquid chromatography (HPLC) nano-electrospray tandem mass spectrometry (μLC–MS-MS) of a pigmented band excised from a denaturing polyacrylamide gel. The predicted protein sequence is related to a large group of octaheme cytochromes whose few characterized representatives are hydroxylamine or hydrazine oxidases. The protein was partially purified and shown by
in vitro
assays to have hydroxylamine oxidase, hydrazine oxidase, and nitrite reductase activities. From what is known of
Beggiatoaceae
physiology, nitrite reduction is the most likely
in vivo
role of the octaheme protein, but future experiments are required to confirm this tentative conclusion. Thus, while present-day genomic and proteomic techniques have allowed precise identification of an abundant mat protein, and its potential activities could be assayed, proof of its physiological role remains elusive in the absence of a pure culture that can be genetically manipulated.
Efficient Bioconversion of Echinocandin B to Its Nucleus by Overexpression of Deacylase Genes in Different Host Strains
Authors: Shao Lei , Li Jian , Liu Aijuan , Chang Qing , Lin Huimin , Chen Daijie
Published: December 2012

Anidulafungin, which noncompetitively inhibits β-(1,3)-
d
-glucan synthase in fungal cell wall biosynthesis, is the newest antifungal drug to be developed. Echinocandin B deacylase from
Actinoplanes utahensis
NRRL 12052 catalyzes the cleavage of the linoleoyl group of echinocandin B, a key step in the process of manufacturing anidulafungin. Unfortunately, the natural yield of echinocandin B nucleus is low. In our study, the echinocandin B deacylase gene was systematically overexpressed by genetic engineering in its original producer,
A. utahensis
, and in the heterologous hosts
Streptomyces lividans
TK24 and
Streptomyces albus
. The introduction of additional copies of the gene, under the control of
PermE
* or its native promoter, into hosts showed significant increases in its transcription level and in the efficiency of the bioconversion of echinocandin B to its nucleus. The conditions for the cultivation and bioconversion of
A. utahensis
have been optimized further to improve production. As a result, while the wild-type strain initially produced 0.36 g/liter, a concentration of 4.21 g/liter was obtained after the generation of a strain with additional copies of the gene and further optimization of the reaction conditions. These results are useful for enhancing echinocandin B nucleus production in
A. utahensis
. Our study could enable the engineering of commercially useful echinocandin B nucleus-overproducing stains.
Extensive Reduction of Cell Viability and Enhanced Matrix Production in Pseudomonas aeruginosa PAO1 Flow Biofilms Treated with a
d
-Amino Acid Mixture
Authors: Sanchez Zoe , Tani Akio , Kimbara Kazuhide
Published: December 2012

Treatment of
Pseudomonas aeruginosa
PAO1 flow biofilms with a
d
-amino acid mixture caused significant reductions in cell biomass by 75% and cell viability by 71%. No biofilm disassembly occurred, and matrix production increased by 30%, thereby providing a thick protective cover for remaining viable or persister cells.
Microbial Gutta-Percha Degradation Shares Common Steps with Rubber Degradation by Nocardia nova SH22a
Authors: Luo Quan , Hiessl Sebastian , Poehlein Anja , Steinbüchel Alexander
Published: December 2012

Nocardia novaSH22a, a bacterium capable of degrading gutta-percha (GP) and natural rubber (NR), was used to investigate the GP degradation mechanism and the relations between the GP and NR degradation pathways. For this strain, a protocol of electroporation was systematically optimized, and an efficiency of up to 4.3 × 107CFU per μg of plasmid DNA was achieved. By applying this optimized protocol toN. novaSH22a, a Tn5096-based transposon mutagenesis library of this bacterium was constructed. Among about 12,000 apramycin-resistant transformants, we identified 76 stable mutants defective in GP or NR utilization. Whereas 10 mutants were specifically defective in GP utilization, the growth of the other 66 mutants was affected on both GP and NR. This indicated that the two degradation pathways are quite similar and share many common steps. The larger number of GP-degrading defective mutants could be explained in one of two ways: either (i) the GP pathway is more complex and harbors more specific steps or (ii) the steps for both pathways are almost identical, but in the case of GP degradation there are fewer enzymes involved in each step. The analysis of transposition loci and genetic studies on interesting genes confirmed the crucial role of an α-methylacyl-coenzyme A racemase in the degradation of both GP and NR. We also demonstrated the probable involvement of enzymes participating in oxidoreduction reactions, β-oxidation, and the synthesis of complex cell envelope lipids in the degradation of GP.
Patterned Hydrophobic Domains in the Exopolymer Matrix of Shewanella oneidensis MR-1 Biofilms
Authors: Aldeek Fadi , Schneider Raphaël , Fontaine-Aupart Marie-Pierre , Mustin Christian , Lécart Sandrine , Merlin Christophe , Block Jean-Claude
Published: December 2012

Water-dispersible amphiphilic surface-engineered quantum dots (QDs) were found to be strongly accumulated within discrete zones of the exopolymer network of
Shewanella oneidensis
MR-1 biofilms, but not on the cell surfaces. These microdomains showed a patterned distribution in the exopolymer matrix, which led to a restricted diffusion of the amphiphilic nanoparticles.
Microbial Mechanisms Mediating Increased Soil C Storage under Elevated Atmospheric N Deposition
Authors: Eisenlord Sarah D. , Freedman Zachary , Zak Donald R. , Xue Kai , He Zhili , Zhou Jizhong
Published: December 2012

Future rates of anthropogenic N deposition can slow the cycling and enhance the storage of C in forest ecosystems. In a northern hardwood forest ecosystem, experimental N deposition has decreased the extent of forest floor decay, leading to increased soil C storage. To better understand the microbial mechanisms mediating this response, we examined the functional genes derived from communities of actinobacteria and fungi present in the forest floor using GeoChip 4.0, a high-throughput functional-gene microarray. The compositions of functional genes derived from actinobacterial and fungal communities was significantly altered by experimental nitrogen deposition, with more heterogeneity detected in both groups. Experimental N deposition significantly decreased the richness and diversity of genes involved in the depolymerization of starch (∼12%), hemicellulose (∼16%), cellulose (∼16%), chitin (∼15%), and lignin (∼16%). The decrease in richness occurred across all taxonomic groupings detected by the microarray. The compositions of genes encoding oxidoreductases, which plausibly mediate lignin decay, were responsible for much of the observed dissimilarity between actinobacterial communities under ambient and experimental N deposition. This shift in composition and decrease in richness and diversity of genes encoding enzymes that mediate the decay process has occurred in parallel with a reduction in the extent of decay and accumulation of soil organic matter. Our observations indicate that compositional changes in actinobacterial and fungal communities elicited by experimental N deposition have functional implications for the cycling and storage of carbon in forest ecosystems.
The Rare
ospC
Allele L of Borrelia burgdorferi Sensu Stricto, Commonly Found among Samples Collected in a Coastal Plain Area of the Southeastern United States, Is Associated with Ixodes affinis Ticks and Local Rodent Hosts Peromyscus gossypinus and Sigmodon hispidus
Authors: Rudenko Nataliia , Golovchenko Maryna , Grubhoffer Libor , Oliver James H.
Published: December 2012

The rare
ospC
allele L was detected in 30% of
Borrelia burgdorferi
sensu stricto strains cultured from a tick species,
Ixodes affinis
, and two rodent host species,
Peromyscus gossypinus
and
Sigmodon hispidus
, collected in a coastal plain area of Georgia and South Carolina, in the southeastern United States.
A
uvs-5
Strain Is Deficient for a Mitofusin Gene Homologue,
fzo1
, Involved in Maintenance of Long Life Span in Neurospora crassa
Authors: Kurashima Kiminori , Chae Michael , Inoue Hirokazu , Hatakeyama Shin , Tanaka Shuuitsu
Published: December 2012

Mitochondria are highly dynamic organelles that continuously fuse and divide. To maintain mitochondria, cells establish an equilibrium of fusion and fission events, which are mediated by dynamin-like GTPases. We previously showed that an
mus-10
strain, a mutagen-sensitive strain of the filamentous fungus
Neurospora crassa
, is defective in an F-box protein that is essential for the maintenance of mitochondrial DNA (mtDNA), long life span, and mitochondrial morphology. Similarly, a
uvs-5
mutant accumulates deletions within its mtDNA, has a shortened life span, and harbors fragmented mitochondria, the latter of which is indicative of an imbalance between mitochondrial fission and fusion. Since the
uvs-5
mutation maps very close to the locus of
fzo1
, encoding a mitofusin homologue thought to mediate mitochondrial outer membrane fusion, we determined the sequence of the
fzo1
gene in the
uvs-5
mutant. A single amino acid substitution (Q368R) was found in the GTPase domain of the FZO1 protein. Expression of wild-type FZO1 in the
uvs-5
strain rescued the mutant phenotypes, while expression of a mutant FZO1 protein did not. Moreover, when knock-in of the Q368R mutation was performed on a wild-type strain, the resulting mutant displayed phenotypes identical to those of the
uvs-5
mutant. Therefore, we concluded that the previously unidentified
uvs-5
gene is
fzo1
. Furthermore, we used immunoprecipitation analysis to show that the FZO1 protein interacts with MUS-10, which suggests that these two proteins may function together to maintain mitochondrial morphology.