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| | 1. |
2009 May 21 |
Phylogenomics of C4 photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence.
Besnard G, Muasya AM, Russier F, Roalson EH, Salamin N, Christin PA
Mol. Biol. Evol. 2009 May 21; [Epub ahead of print]
Abstract
C(4) photosynthesis is an adaptive trait conferring an advantage in warm and open habitats. It originated multiple times and is presently reported in 18 plant families. It has been recently shown that phosphoenolpyruvate carboxylase (PEPC), a key enzyme of the C(4) pathway, evolved through numerous independent but convergent genetic changes in grasses (Poaceae). To compare the genetics of multiple C(4) origins on a broader scale, we reconstructed the evolutionary history of the C(4) pathway in sedges (Cyperaceae), the second most species-rich C(4) family. A sedge phylogeny based on two plastome genes (rbcL and ndhF) has previously identified six fully C(4) clades. A relaxed molecular clock was used to calibrate this tree and showed that the first C(4) acquisition occurred in this family between 19.6 and 10.1 million years ago. According to analyses of PEPC encoding genes (ppc), at least five distinct C(4) origins are present in sedges. Two C(4) Eleocharis species, which were unrelated in the plastid phylogeny, acquired their C(4)-specific PEPC genes from a single source, probably through reticulate evolution or a horizontal transfer event. Acquisitions of C(4) PEPC in sedges have been driven by positive selection on at least 16 codons (3.5% of the studied gene segment). These sites underwent parallel genetic changes across the five sedge C(4) origins. Five of these sites underwent identical changes also in grass and eudicot C(4) lineages, indicating that genetic convergence is most important within families but that identical genetic changes occurred even among distantly related taxa. These lines of evidence give new insights into the constraints that govern molecular evolution, which are discussed here.
[Pubmed: 19461115]
| | 2. |
2009 Apr 10 |
Identifying the most productive breeding sites for malaria mosquitoes in The Gambia
Fillinger, Sombroek, Majambere, van Loon, Takken, Lindsay
Malar J 2009 Apr 10;8:62. published online before print
Abstract
Ideally larval control activities should be targeted at sites that generate the most adult vectors, thereby reducing operational costs. Despite the plethora of potential mosquito breeding sites found in the floodplains of the Gambia River, about 150 km from its mouth, during the rainy season, only a small proportion are colonized by anophelines on any day. This study aimed to determine the characteristics of larval habitats most frequently and most densely populated by anopheline larvae and to estimate the numbers of adults produced in different habitats.
[Pubmed: 19361337]
| | 3. |
2009 Jan 01 |
Necessity of screening water chestnuts for microcystins after cyanobacterial blooms break out.
Xiao FG, Zhao XL, Tang J, Gu XH, Zhang JP, Niu WM
Arch. Environ. Contam. Toxicol. 2009 Aug;57(2):256-63. Epub 2009 Jan 01.
Abstract
Water chestnut is one of the most popular vegetables in Asian countries that grows in shallow water. Eighteen water chestnut samples were collected from Lake Tai and six samples were bought at markets in Wuxi, China, in October 2007. Extraction solution of water chestnut was cleaned up with a solid phase extraction column and immunoaffinity chromatography cartridges, then the microcystin (MC) level was detected by indirect competitive enzyme-linked immunosorbent assay (ELISA) and liquid chromatography-mass spectrometry (LC-MS). The results of ELISA showed that there were six samples collected from Lake Tai which contained MCs; the highest level of total MCs was 7.02 ng/g. The results of LC-MS confirmed that MC-LR and MC-RR were present in five samples. The highest level of MC-LR was 1.02 ng/g and that of MC-RR was 4.44 ng/g. Heavy cyanobacterial blooms had occurred, and MCs were detected in water at the points in Lake Tai where MCs occurred in water chestnuts collected in 2007. MCs were not detected in the six samples bought at Wuxi markets. The results suggest that MCs can accumulate in water chestnuts, which is a potential hazard for human health.
[Pubmed: 19125218]
| | 4. |
2009 Apr |
A junction branch point adjacent to a DNA backbone nick directs substrate cleavage by Saccharomyces cerevisiae Mus81-Mms4
Ehmsen, Heyer
Nucleic Acids Res 2009 Apr;37(6):2026-2036.
Abstract
The DNA structure-selective endonuclease Mus81-Mms4/Eme1 incises a number of nicked joint molecule substrates in vitro. 3′-flaps are an excellent in vitro substrate for Mus81-Mms4/Eme1. Mutants in MUS81 are synthetically lethal with mutations in the 5′-flap endonuclease FEN1/Rad27 in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Considering the possibility for isoenergetic interconversion between 3′- and 5′- flaps, these data are consistent with the hypothesis that Mus81-Mms4/Eme1 acts on 3′-flaps in vivo. FEN1/Rad27 prefers dually flapped substrates and cleaves in a way that allows direct ligation of the resulting nick in the product duplex. Here we test the activity of Mus81-Mms4 on dually flapped substrates and find that in contrast to FEN1/Rad27, Mus81-Mms4 activity is impaired on such substrates, resulting in cleavage products that do not allow direct religation. We conclude that Mus81-Mms4, unlike FEN1/Rad27, does not prefer dually flapped substrates and is unlikely to function as a 3′-flapase counterpart to the 5′-flapase activity of FEN1/Rad27. We further find that joint molecule incision by Mus81-Mms4 occurs in a fashion determined by the branch point, regardless of the position of an upstream duplex end. These findings underscore the significance of a nick adjacent to a branch point for Mus81-Mms4 incision.
[Pubmed: 19211663]
| | 5. |
2009 Mar 15 |
Identification of candidate genes for human pituitary development by EST analysis
Ma, Qi, Du, Song, Feng, Qi, Zhu, Zhang, Xiao, Han, Hao
BMC Genomics 2009 Mar 15;10:109. published online before print
Abstract
The pituitary is a critical neuroendocrine gland that is comprised of five hormone-secreting cell types, which develops in tandem during the embryonic stage. Some essential genes have been identified in the early stage of adenohypophysial development, such as PITX1, FGF8, BMP4 and SF-1. However, it is likely that a large number of signaling molecules and transcription factors essential for determination and terminal differentiation of specific cell types remain unidentified. High-throughput methods such as microarray analysis may facilitate the measurement of gene transcriptional levels, while Expressed sequence tag (EST) sequencing, an efficient method for gene discovery and expression level analysis, may no-redundantly help to understand gene expression patterns during development.
[Pubmed: 19284880]
| | 6. |
2009 Feb 18 |
Description of an early Cretaceous termite (Isoptera: Kalotermitidae) and its associated intestinal protozoa, with comments on their co-evolution.
Poinar GO
Parasit Vectors. 2009;2(1):12. Epub 2009 Feb 18.
Abstract
ABSTRACT: BACKGROUND: The remarkable mutualistic associations between termites and protists are in large part responsible for the evolutionary success of these eusocial insects. It is unknown when this symbiosis was first established, but the present study shows that fossil termite protists existed in the Mesozoic. RESULTS: A new species of termite (Kalotermes burmensis n. sp.) in Early Cretaceous Burmese amber had part of its abdomen damaged, thus exposing trophic stages and cysts of diverse protists. Some protists were still attached to the gut intima while others were in the amber matrix adjacent to the damaged portion. Ten new fossil flagellate species in the Trichomonada, Hypermastigida and Oxymonadea are described in nine new genera assigned to 6 extant families. Systematic placement and names of the fossil flagellates are based on morphological similarities with extant genera associated with lower termites. The following new flagellate taxa are established: Foainites icelus n. gen. n. sp., Spiromastigites acanthodes n. gen. n. sp., Trichonymphites henis n. gen., n. sp., Teranymphites rhabdotis n. gen. n. sp., Oxymonas protus n. sp., Oxymonites gerus n. gen., n. sp., Microrhopalodites polynucleatis n. gen., n. sp., Sauromonites katatonis n. gen., n. sp., Dinenymphites spiris n. gen., n. sp., Pyrsonymphites cordylinis n. gen., n. sp. A new genus of fossil amoeba is also described as Endamoebites proterus n. gen., n. sp. Fourteen additional trophic and encystid protist stages are figured and briefly characterized. CONCLUSION: This represents the earliest fossil record of mutualism between microorganisms and animals and the first descriptions of protists from a fossil termite. Discovering the same orders, families and possibly genera of protists that occur today in Early Cretaceous kalotermitids shows considerable behaviour and morphological stability of both host and protists. The possible significance of protist cysts associated with the fossil termite is discussed in regards the possibility that coprophagy, as well as proctodeal trophallaxis, was a method by which some termite protozoa were transferred intrastadially and intergenerationally at this time.
[Pubmed: 19226475]
| | 7. |
2009 Feb 24 |
Diagnosis of Human Visceral Pentastomiasis
Tappe, Büttner
PLoS Negl Trop Dis 2009 Feb 24;3(2). published online before print
Abstract
Visceral pentastomiasis in humans is caused by the larval stages (nymphs) of the arthropod-related tongue worms Linguatula serrata, Armillifer armillatus, A. moniliformis, A. grandis, and Porocephalus crotali. The majority of cases has been reported from Africa, Malaysia, and the Middle East, where visceral pentastomiasis may be an incidental finding in autopsies, and less often from China and Latin America. In Europe and North America, the disease is only rarely encountered in immigrants and long-term travelers, and the parasitic lesions may be confused with malignancies, leading to a delay in the correct diagnosis. Since clinical symptoms are variable and serological tests are not readily available, the diagnosis often relies on histopathological examinations. This laboratory symposium focuses on the diagnosis of this unusual parasitic disease and presents its risk factors and epidemiology.
[Pubmed: 19238218]
| | 8. |
2009 Mar 25 |
Complete characterization of wheat-alien metaphase I pairing in interspecific hybrids between durum wheat (Triticum turgidum L.) and jointed goatgrass (Aegilops cylindrica Host).
Cifuentes M, Benavente E
Theor. Appl. Genet. 2009 May;118(8):1609-16. Epub 2009 Mar 25.
Abstract
The pattern of homoeologous metaphase I (MI) pairing has been fully characterized in durum wheat x Aegilops cylindrica hybrids (2n = 4x = 28, ABC(c)D(c)) by an in situ hybridization procedure that has permitted individual discrimination of every wheat and wild constituent genome. One of the three hybrid genotypes examined carried the ph1c mutation. In all cases, MI associations between chromosomes of both species represented around two-third of total. Main results from the analysis are as follows (a) the A genome chromosomes are involved in wheat-wild MI pairing more frequently than the B genome partners, irrespective of the alien genome considered; (b) both durum wheat genomes pair preferentially with the D(c) genome of jointed goatgrass. These findings are discussed in relation to the potential of genetic transference between wheat crops and this weedy relative. It can also be highlighted that inactivation of Ph1 provoked a relatively higher promotion of MI associations involving B genome.
[Pubmed: 19319503]
| | 9. |
2009 Jul |
Clinical and research searching on the wild side: exploring the veterinary literature
Alpi
J Med Libr Assoc 2009 Jul;97(3):169-177.
Abstract
Zoological medicine furthers the health and well-being of captive and free-ranging wild animals. Effective information retrieval of the zoological medicine literature demands searching multiple databases, conference proceedings, and organization websites using a wide variety of keywords and controlled vocabulary. Veterinarians, residents, students, and the librarians who serve them must have patience for multiple search iterations to capture the majority of the available knowledge. The complexities of thorough literature searches are more difficult for nondomestic animal clinical cases and research reviews as demonstrated by three search requests involving poisonous snakes, a gorilla, and spiders. Expanding and better disseminating the knowledgebase of zoological medicine will make veterinary searching easier.
[Pubmed: 19626142]
| | 10. |
2009 Jun 2 |
Convective gas flow development and the maximum depths achieved by helophyte vegetation in lakes.
Sorrell BK, Hawes I
Ann. Bot. 2009 Jun 2; [Epub ahead of print]
Abstract
Background and Aims Convective gas flow in helophytes (emergent aquatic plants) is thought to be an important adaptation for the ability to colonize deep water. In this study, the maximum depths achieved by seven helophytes were compared in 17 lakes differing in nutrient enrichment, light attenuation, shoreline exposure and sediment characteristics to establish the importance of convective flow for their ability to form the deepest helophyte vegetation in different environments. Methods Convective gas flow development was compared amongst the seven species, and species were allocated to 'flow absent', 'low flow' and 'high flow' categories. Regression tree analysis and quantile regression analysis were used to determine the roles of flow category, lake water quality, light attenuation and shoreline exposure on maximum helophyte depths. Key Results Two 'flow absent' species were restricted to very shallow water in all lakes and their depths were not affected by any environmental parameters. Three 'low flow' and two 'high flow' species had wide depth ranges, but 'high flow' species formed the deepest vegetation far more frequently than 'low flow' species. The 'low flow' species formed the deepest vegetation most commonly in oligotrophic lakes where oxygen demands in sediments were low, especially on exposed shorelines. The 'high flow' species were almost always those forming the deepest vegetation in eutrophic lakes, with Eleocharis sphacelata predominant when light attenuation was low, and Typha orientalis when light attenuation was high. Depths achieved by all five species with convective flow were limited by shoreline exposure, but T. orientalis was the least exposure-sensitive species. Conclusions Development of convective flow appears to be essential for dominance of helophyte species in >0.5 m depth, especially under eutrophic conditions. Exposure, sediment characteristics and light attenuation frequently constrain them to a shallower depth than their flow capacity permits.
[Pubmed: 19491087]
| | 11. |
2009 Jun |
Theoretical models of DNA topology simplification by type IIA DNA topoisomerases
Vologodskii
Nucleic Acids Res 2009 Jun;37(10):3125-3133.
Abstract
It was discovered 12 years ago that type IIA topoisomerases can simplify DNA topology—the steady-state fractions of knots and links created by the enzymes are many times lower than the corresponding equilibrium fractions. Though this property of the enzymes made clear biological sense, it was not clear how small enzymes could selectively change the topology of very large DNA molecules, since topology is a global property and cannot be determined by a local DNA–protein interaction. A few models, suggested to explain the phenomenon, are analyzed in this review. We also consider experimental data that both support and contravene these models.
[Pubmed: 19383879]
| | 12. |
2009 Jul 21 |
Processing and phosphorylation of the Fat receptor
Feng, Irvine
Proc Natl Acad Sci U S A 2009 Jul 21;106(29):11989-11994.
Abstract
The Drosophila tumor suppressors fat and discs overgrown (dco) function within an intercellular signaling pathway that controls growth and polarity. fat encodes a transmembrane receptor, but post-translational regulation of Fat has not been described. We show here that Fat is subject to a constitutive proteolytic processing, such that most or all cell surface Fat comprises a heterodimer of stably associated N- and C-terminal fragments. The cytoplasmic domain of Fat is phosphorylated, and this phosphorylation is promoted by the Fat ligand Dachsous. dco encodes a kinase that influences Fat signaling, and Dco is able to promote the phosphorylation of the Fat intracellular domain in cultured cells and in vivo. Evaluation of dco mutants indicates that they affect Fat's influence on growth and gene expression but not its influence on planar cell polarity. Our observations identify processing and phosphorylation as post-translational modifications of Fat, correlate the phosphorylation of Fat with its activation by Dachsous in the Fat-Warts pathway, and enhance our understanding of the requirement for Dco in Fat signaling.
[Pubmed: 19574458]
| | 13. |
2008 Nov 06 |
Action planning with two-handed tools.
Herwig A, Massen C
Psychol Res. 2009 Sep;73(5):727-40. Epub 2008 Nov 06.
Abstract
In tool use, the intended external goals have to be transformed into bodily movements by taking into account the target-to-movement mapping implemented by the tool. In bimanual tool use, this mapping may depend on the part of the tool that is operated and the effector used (e.g. the left and right hand at the handle bar moving in opposite directions in order to generate the same bicycle movement). In our study, we investigated whether participants represent the behaviour of the tool or only the effector-specific mapping when using two-handed tools. In three experiments, participants touched target locations with a two-jointed lever, using either the left or the right hand. In one condition, the joint of the lever was constant and switching between hands was associated with switching the target-to-movement-mapping, whereas in another condition, switching between hands was associated with switching the joint, but the target-to-movement-mapping remained constant. Results indicate pronounced costs of switching hands in the condition with constant joint, whereas they were smaller with constant target-to-movement mapping. These results suggest that participants have tool-independent representations of the effector-specific mappings.
[Pubmed: 18987881]
| | 14. |
2009 Aug 7 |
The position and function of the Notch-mediated eye growth organizer: the roles of JAK/STAT and four-jointed.
Gutierrez-Aviño FJ, Ferres-Marco D, Dominguez M
EMBO Rep. 2009 Aug 7; [Epub ahead of print]
Abstract
In many animal systems, the local activation of patterning signals in spatially confined regions (organizers) is crucial for promoting the growth of developing organs. Nevertheless, how organizers are set up and how their activity influences global organ growth remains poorly understood. In the Drosophila eye, local Notch activation establishes a conserved dorsal-ventral organizer that promotes growth. The dorsal selector Iroquois complex defines the position of the organizer at the mid-first instar, and through its ligand, unpaired, the Janus kinase (JAK)/signal transducers and activator of transcription (STAT) pathway is thought to mediate global growth downstream of the organizer. However, here we show that the unpaired/JAK/STAT pathway is actually a fundamental element in the spatial control of the organizer, upstream from Notch activation. Furthermore, we identify four-jointed, a target of the Fat and Hippo tumour-suppressor pathways, as a mediator of the growth controlled by the organizer. These findings redefine the process of organizer formation and function, and they identify four-jointed as a regulatory node, integrating multiple growth-control pathways.
[Pubmed: 19662079]
| | 15. |
2009 Aug 7 |
Burkholderia heleia sp. nov., a nitrogen-fixing bacterium isolated from an aquatic plant, Eleocharis dulcis, that grows in highly acidic swamps in actual acid sulfate soil areas of Vietnam.
Aizawa T, Ve NB, Nakajima M, Sunairi M
Int. J. Syst. Evol. Microbiol. 2009 Aug 7; [Epub ahead of print]
Abstract
Nitrogen-fixing bacteria, SA41(T), SA42, and SA53, were isolated from an aquatic plant, Eleocharis dulcis, that grows in highly acidic swamps (pH 2-4) in actual acid sulfate soil areas of Vietnam. The isolates were Gram-negative, aerobic, non-spore-forming, and rod-shaped bacteria, having a cellular width of 0.6-0.7 microm and a length of 1.5-1.7 microm. They showed good growth between pH 3.0 and 7.0 and between 17 and 37 degrees C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone, and C(16:0), C(17:0) cyclo, C(18:1)omega7c, summed feature 3 (C(16:1)omega7c and/or iso C(15:0) 2-OH) as major fatty acids. These profiles are similar to the fatty acids reported for other Burkholderia species. The DNA G+C contents of these strains were 64 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Burkholderia. Although their calculated 16S rRNA gene sequence similarity values to B. silvatlantica, B. mimosarum, B. ferrariae, and B. tropica were 98.5 %, 98.2 %, 98.0 %, and 97.0 %, respectively, they formed a group that was distinct in the phylogenetic trees, and the DNA-DNA relatedness values of SA41(T) to these species were 39 %, 41 %, 39 %, and 33 %, respectively. The results of physiological and biochemical tests including whole-cell protein pattern analysis allowed phenotypic differentiation of these strains from the published Burkholderia species. Therefore, strains SA41(T), SA42, and SA53, represent a new species, for which the name Burkholderia heleia sp. nov. is proposed. The type strain is SA41(T) (= NBRC 101817(T) = VTCC-D6-7(T)).
[Pubmed: 19666801]
| | 16. |
2009 Oct |
External fixation as a primary and definitive treatment for tibial diaphyseal fractures
Beltsios, Savvidou, Kovanis, Alexandropoulos, Papagelopoulos
Strategies Trauma Limb Reconstr 2009 Oct;4(2):81-87.
Abstract
The aim of this study was to evaluate the effectiveness of unilateral external fixator as primary and definitive treatment for open tibial fractures, fractures with severe soft tissues injuries, threatened compartment syndrome, and in multiply injured patients. Two hundred and twenty-three tibial shaft fractures (212 patients) were treated. In open fractures, union was achieved in 25 weeks, while in closed in 21. There were 18 nonunions, 21 delayed unions, 4 malunions, 58 pin infections and 3 osteomyelitis. A reoperation was performed in 42 patients. Fat embolism was diagnosed in three patients, pulmonary embolism in five and deep venous thrombosis in 14. The external fixator was definitive treatment in 87.27%. Unilateral external fixators can be used as primary and definitive treatment for complicated tibia shaft fractures. Re-operation or change of the method must be performed only when there is a delay in callus formation.
[Pubmed: 19714440]
| | 17. |
2009 Oct 5 |
Centralized Modularity of N-Linked Glycosylation Pathways in Mammalian Cells
Kim, Lee, Jeong
PLoS One 2009 Oct 5;4(10). published online before print
Abstract
Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell proliferation and apoptosis, development, immune responses, and pathogenesis. One of the major types of glycans, N-linked glycans, is formed by sequential attachments of monosaccharides to proteins by a limited number of enzymes. Many of these enzymes can accept multiple N-linked glycans as substrates, thereby generating a large number of glycan intermediates and their intermingled pathways. Motivated by the quantitative methods developed in complex network research, we investigated the large-scale organization of such N-linked glycosylation pathways in mammalian cells. The N-linked glycosylation pathways are extremely modular, and are composed of cohesive topological modules that directly branch from a common upstream pathway of glycan synthesis. This unique structural property allows the glycan production between modules to be controlled by the upstream region. Although the enzymes act on multiple glycan substrates, indicating cross-talk between modules, the impact of the cross-talk on the module-specific enhancement of glycan synthesis may be confined within a moderate range by transcription-level control. The findings of the present study provide experimentally-testable predictions for glycosylation processes, and may be applicable to therapeutic glycoprotein engineering.
[Pubmed: 19802388]
| | 18. |
2009 Jun |
The intertarsal joint of the ostrich (Struthio camelus): Anatomical examination and function of passive structures in locomotion.
Schaller NU, Herkner B, Villa R, Aerts P
J. Anat. 2009 Jun;214(6):830-47.
Abstract
The ostrich (Struthio camelus) is the largest extant biped. Being flightless, it exhibits advanced cursorial abilities primarily evident in its characteristic speed and endurance. In addition to the active musculoskeletal complex, its powerful pelvic limbs incorporate passive structures wherein ligaments interact with joint surfaces, cartilage and other connective tissue in their course of motion. This arrangement may enable energy conservation by providing joint stabilisation, optimised limb segment orientation and automated positioning of ground contact elements independently of direct muscle control. The intertarsal joint is of particular interest considering its position near the mid-point of the extended limb and its exposure to high load during stance with significant inertial forces during swing phase. Functional-anatomical analysis of the dissected isolated joint describes the interaction of ligaments with intertarsal joint contours through the full motion cycle. Manual manipulation identified a passive engage-disengage mechanism (EDM) that establishes joint extension, provides bi-directional resistance prior to a transition point located at 115 degrees and contributes to rapid intertarsal flexion at toe off and full extension prior to touch down. This effect was subsequently quantified by measurement of intertarsal joint moments in prepared anatomical specimens in a neutral horizontal position and axially-loaded vertical position. Correlation with kinematic analyses of walking and running ostriches confirms the contribution of the EDM in vivo. We hypothesise that the passive EDM operates in tandem with a stringently coupled multi-jointed muscle-tendon system to conserve the metabolic cost of locomotion in the ostrich, suggesting that a complete understanding of terrestrial locomotion across extinct and extant taxa must include functional consideration of the ligamentous system.
[Pubmed: 19538629]
| | 19. |
2009 Jul 14 |
Hierarchical plasticity from pair distance fluctuations.
Menor SA, de Graff AM, Thorpe MF
Phys Biol. 2009;6(3):36017. Epub 2009 Jul 14.
Abstract
Observations, experiments and simulations often generate large numbers of snapshots of configurations of complex many-body systems. It is important to find methods of extracting useful information from these ensembles of snapshots in order to document the motion as the system evolves in time. Some of the most interesting information is contained in the relative motion of individual constituents, rather than their absolute motion. We present a novel statistical method for identifying hierarchies of plastically connected objects in a system from a series of two or more snapshot configurations. These plastic clusters are distinctive in that although their members tend to remain loosely connected, the clusters may be deformed plastically. This method is demonstrated for a number of systems, including an exactly soluble freely jointed polymer chain model, a two-dimensional simulation of two species of interacting bodies and a protein. These concepts are implemented as TIMME, the Tool for Identifying Mobility in Macromolecular Ensembles.
[Pubmed: 19597264]
| | 20. |
2009 Apr |
Nanoscale Structural and Mechanical Properties of Nontypeable Haemophilus influenzae Biofilmsâ–¿
Arce, Carlson, Monds, Veeh, Hu, Stewart, Lal, Ehrlich, Avci
J Bacteriol 2009 Apr;191(8):2512-2520.
Abstract
Nontypeable Haemophilus influenzae (NTHI) bacteria are commensals in the human nasopharynx, as well as pathogens associated with a spectrum of acute and chronic infections. Two important factors that influence NTHI pathogenicity are their ability to adhere to human tissue and their ability to form biofilms. Extracellular polymeric substances (EPS) and bacterial appendages such as pili critically influence cell adhesion and intercellular cohesion during biofilm formation. Structural components in the outer cell membrane, such as lipopolysaccharides, also play a fundamental role in infection of the host organism. In spite of their importance, these pathogenic factors are not yet well characterized at the nanoscale. Here, atomic force microscopy (AFM) was used in aqueous environments to visualize structural details, including probable Hif-type pili, of live NTHI bacteria at the early stages of biofilm formation. Using single-molecule AFM-based spectroscopy, the molecular elasticities of lipooligosaccharides present on NTHI cell surfaces were analyzed and compared between two strains (PittEE and PittGG) with very different pathogenicity profiles. Furthermore, the stiffness of single cells of both strains was measured and subsequently their turgor pressure was estimated.
[Pubmed: 19218382]
| | 21. |
2009 Oct 14 |
Force-extension formula for the worm-like chain model from a variational principle.
Chan Y, Haverkamp RG, Hill JM
J. Theor. Biol. 2010 Feb 7;262(3):498-504. Epub 2009 Oct 14.
Abstract
Stiff polymers, such as single-stranded DNA, unstructured RNA and cellulose, are all basically extremely long rods with relatively short repeating monomers. The simplest model for describing such stiff polymers is called the freely jointed chain model, which treats a molecule as a chain of perfectly rigid subunits of orientationally independent statistical segments, joined together by perfectly flexible hinges. A more realistic model that incorporates the entropic elasticity of a molecule, called the worm-like chain model, has been proposed by assuming that each monomer resists the bending force. Some force-extension formulae for the worm-like chain model have been previously found in terms of interpolation and numerical solutions resulting from statistical mechanics. In this paper, however, we adopt a variational principle to seek the minimum energy configuration of a stretched molecule by incorporating all the possible orientations of each monomer under thermal equilibrium, i.e., constant temperature. We determine a force-extension formula for the worm-like chain model analytically. We find that our formula suggests new terms such as the free energy and the cut-off force of a molecule, which define a clear transition from the entropic regime to the enthalpic regime and the fracture of the molecule, respectively. In addition, we predict two possible phase changes for a stretched molecule, i.e., from a super-helix to a soliton and then from a soliton to a vertical twisted line. We show theoretically that a molecule must undergo at least one phase change before it is fully stretched into its total contour length. This new formula is used to fit recent experimental data and shows a good agreement with some current literature that uses a statistical approach. Finally, an instability analysis is adopted to investigate the sensitivity of the new formula subject to small changes in temperature.
[Pubmed: 19835889]
| | 22. |
2009 Nov 23 |
Cd (II) removal from aqueous solution by Eleocharis acicularis biomass, equilibrium and kinetic studies.
Miretzky P, Muñoz C, Carrillo-Chavez A
Bioresour. Technol. 2009 Nov 23; [Epub ahead of print]
Abstract
Batch experiments were carried out to determine the capacity of Eleocharis acicularis biomass to adsorb Cd(2+) ions from contaminated solutions with respect to pH, initial Cd(2+) concentration, contact time, solution ionic strength and biomass dose. The experimental data were modeled by Langmuir, Freundlich and Dubinin-Radushkevich (D-R) isotherm models. Freundlich and D-R models resulted in the best fit of the adsorption data. The maximum adsorption capacity for Cd(2+) was 0.299mmolg(-1) (33.71mgg(-1)) with efficiency higher than 80% (pH 6.0 and 5gL(-1) biomass dose). The mean adsorption free energy value derived from the D-R model (8.058kJmol(-1)) indicated that adsorption was governed by an ionic exchange process. The pseudo-first order, pseudo-second order, Elovich kinetic models and the intra-particle diffusion models were used to describe the kinetic data and to evaluate rate constants. The best correlation was provided by the second-order kinetic model, implying that chemical sorption was the rate-limiting step, although intra-particle diffusion could not be ignored. The practical implication of this study is the development of an effective and economic technology for Cd(2+) removal from contaminated waters. The macrophyte biomass used in this study did not undergo any chemical or physical pre-treatment, which added to macrophyte abundance and its low cost makes it a good option for Cd(2+) removal from waste water.
[Pubmed: 19932954]
| | 23. |
2009 Oct 23 |
Methanol as the Primary Methanogenic and Acetogenic Precursor in the Cold Zoige Wetland at Tibetan Plateau.
Jiang N, Wang Y, Dong X
Microb. Ecol. 2009 Oct 23; [Epub ahead of print]
Abstract
Previous studies suggested that methanol and acetate were the likely methanogenic precursors in the cold Zoige wetland. In this study, the contribution of the two substances to methanogenesis and the conversion in Zoige wetland were analyzed. It was determined that methanol supported the highest CH(4) formation rate in the enrichments of the soil grown with Eleocharis valleculosa, and even higher at 15 degrees C than at 30 degrees C; while hydrogenotrophic methanogenesis was higher at 30 degrees C. Both methanol- and acetate-using methanogens were counted at the highest (10(7) g(-1)) in the soil, whereas methanol-using acetogens (10(8) g(-1)) were ten times more abundant than either methanol- or acetate-using methanogens. Both methanol and acetate were detected in the methanogenesis-inhibited soil samples, so that both could be the primary methanogenic precursors in E. valleculosa soil. However, the levels of methanol and acetate accumulated in 2-bromoethane-sulfonate (BES)- and CHCl(3)-treated soils were in reverse, i.e., higher methanol in CHCl(3)- and higher acetate in BES-treated soil, so that methanol-derived methanogenesis could be underestimated due to the consumption by acetogens. Analysis of the soil 16S rRNA genes revealed Acetobacterum bakii and Trichococcus pasteurii to be the dominant methanol-using acetogens in the soil, and a strain of T. pasteurii was isolated, which showed the high conversion of methanol to acetate at 15 degrees C.
[Pubmed: 19851805]
| | 24. |
2009 Oct 13 |
Comparative study of two plasticins: specificity, interfacial behavior, and bactericidal activity.
Joanne P, Falord M, Chesneau O, Lacombe C, Castano S, Desbat B, Auvynet C, Nicolas P, Msadek T, El Amri C
Biochemistry. 2009 Oct 13;48(40):9372-83.
Abstract
A comparative study was designed to evaluate the staphylococcidal efficiency of two sequence-related plasticins from the dermaseptin superfamily we screened previously. Their bactericidal activities against Staphylococcus aureus as well as their chemotactic potential were investigated. The impact of the GraS/GraR two-component system involved in regulating resistance to cationic antimicrobial peptides (CAMPs) was evaluated. Membrane disturbing activity was quantified by membrane depolarization assays using the diS-C3 probe and by membrane integrity assays measuring beta-galactosidase activity with recombinant strain ST1065 reflecting compromised membranes and cytoplasmic leakage. Interactions of plasticins with membrane models composed of either zwitterionic lipids mimicking the S. aureus membrane of CAMP-resistant strains or anionic lipids mimicking the negative charge-depleted membrane of CAMP-sensitive strains were analyzed by jointed Brewster angle microscopy (BAM), polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS), and differential scanning calorimetry (DSC) to yield detailed information about the macroscopic interfacial organization, in situ conformation, orientation of the peptides at the lipid-solvent interface, and lipid-phase disturbance. We clearly found evidence of distinct interfacial behaviors of plasticins we linked to the distribution of charges along the peptides and structural interconversion properties at the membrane interface. Our results also suggest that amidation might play a key role in GraS/GraR-mediated CAMP sensing at the bacterial surface.
[Pubmed: 19711984]
| | 25. |
2009 Oct 13 |
The intramandibular joint in Girella: A mechanism for increased force production?
Ferry-Graham LA, Konow N
J. Morphol. 2009 Oct 13; [Epub ahead of print]
Abstract
Intramandibular joints (IMJ) are novel articulations between bony elements of the lower jaw that have evolved independently in multiple fish lineages and are typically associated with biting herbivory. This novel joint is hypothesized to function by augmenting oral jaw expansion during mouth opening, which would increase contact between the tooth-bearing area of the jaws and algal substratum during feeding, resulting in more effective food removal from the substrate. Currently, it is not understood if increased flexibility in a double-jointed mandible also results in increased force generation during herbivorous biting and/or scraping. Therefore, we selected the herbivore Girella laevifrons for a mechanical study of the IMJ lower jaw lever system. For comparative purposes, we selected Graus nigra, a non-IMJ-bearing species, from a putative sister genus. Shortening of the lower jaw, during flexion at the IMJ, resulted in a more strongly force-amplifying closing lever system in the lower jaw, even in the absence of notable changes to the sizes of the muscles that power the lever system. To explain how the IMJ itself functions, we use a four-bar linkage that models the transmission of force and velocity to and through the lower jaw via the IMJ. When combined, the functionally interrelated lever and linkage models predict velocity to be amplified during jaw opening, whereas jaw closing is highly force modified by the presence of the IMJ. Moreover, the function of the IMJ late during jaw closure provides enough velocity to detach sturdy and resilient prey. Thus, this novel jaw system can alternate between amplifying the force or the velocity exerted onto the substrate where food items are attached. This unique mechanical configuration supports the argument that IMJs are functional innovations that have evolved to meet novel mechanical challenges and constraints placed on the feeding apparatus by attached and sturdy food sources. J. Morphol. 2009. (c) 2009 Wiley-Liss, Inc.
[Pubmed: 19827158]
| | 26. |
2009 Oct 9 |
Burkholderia acidipaludis sp. nov., aluminum-tolerant bacteria isolated from the Chinese water chestnut, Eleocharis dulcis, that grows in highly acidic swamps in Southeast Asia.
Aizawa T, Ve NB, Vijarnsorn P, Nakajima M, Sunairi M
Int. J. Syst. Evol. Microbiol. 2009 Oct 9; [Epub ahead of print]
Abstract
Two strains of aluminum-tolerant bacteria, SA33(T) and 7A078(BCC 36999), were isolated from the Chinese water chestnut (Eleocharis dulcis) that grows in highly acidic swamps (pH 2 - 4) in actual acid sulfate soil areas of Vietnam and Thailand, SA33(T) from Vietnam and 7A078 from Thailand. The strains were Gram-negative, aerobic, non-spore-forming, and rod-shaped bacteria, having a cellular width of 0.6 - 0.7 mum and a length of 1.3 - 1.7 mum. These strains showed good growth between pH 3.0 and 8.0 and between 17 and 37 degrees C. The organisms contained ubiquinone Q-8 as the predominant isoprenoid quinone and C(16 : 0), C(18 : 1)omega7c, and C(17 : 0) cyclo as their major fatty acids. Their fatty acid profiles are similar to those reported for other Burkholderia species. The DNA G+C content of these strains was 64 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Burkholderia. Although the calculated 16S rRNA gene sequence similarity values of SA33(T) to 7A078, B. kururiensis, B. sacchari, and B. tuberum were 100 %, 97.3 %, 97.1%, and 97.0 %, respectively, SA33(T) and 7A078 formed a group that was distinct in the phylogenetic trees, and the DNA-DNA relatedness values of SA33(T) to 7A078 and these other species were 90 %, 47 %, 46 %, and 45 %, respectively. The results of physiological and biochemical tests including whole-cell protein pattern analysis allowed phenotypic differentiation of these strains from the published Burkholderia species. Therefore, strains SA33(T) and 7A078 represent a new species, for which the name Burkholderia acidipaludis sp. nov. is proposed. The type strain is SA33(T) (= NBRC 101816(T) = VTCC-D6-6(T)).
[Pubmed: 19819996]
| | 27. |
2009 Sep 02 |
Topological origins of chromosomal territories.
Dorier J, Stasiak A
Nucleic Acids Res. 2009 Oct;37(19):6316-22. Epub 2009 Sep 02.
Abstract
Using freely jointed polymer model we compare equilibrium properties of crowded polymer chains whose segments are either permeable or not permeable for other segments to pass through. In particular, we addressed the question whether non-permeability of long chain molecules, in the absence of excluded volume effect, is sufficient to compartmentalize highly crowded polymer chains, similarly to what happens during formation of chromosomal territories in interphase nuclei. Our results indicate that even polymers without excluded volume compartmentalize and show strongly reduced intermingling when they are mutually non-permeable. Judging from the known fact that chromatin fibres originating from different chromosomes show very limited intermingling in interphase nuclei, we propose that regular chromatin fibres during chromosome decondensation can hardly serve as a substrate of cellular type II DNA topoisomerases.
[Pubmed: 19726582]
| | 28. |
2009 Apr 07 |
Cell division orientation and planar cell polarity pathways.
Segalen M, Bellaïche Y
Semin. Cell Dev. Biol. 2009 Oct;20(8):972-7. Epub 2009 Apr 07.
Abstract
The orientation of cell division has a crucial role in early embryo body plan specification, axis determination and cell fate diversity generation, as well as in the morphogenesis of tissues and organs. In many instances, cell division orientation is regulated by the planar cell polarity (PCP) pathways: the Wnt/Frizzled non-canonical pathway or the Fat/Dachsous/Four-jointed pathway. Firstly, using asymmetric cell division in both Drosophila and C. elegans, we describe the central role of the Wnt/Frizzled pathway in the regulation of asymmetric cell division orientation, focusing on its cooperation with either the Src kinase pathway or the heterotrimeric G protein pathway. Secondly, we describe our present understanding of the mechanisms by which the planar cell polarity pathways drive tissue morphogenesis by regulating the orientation of symmetric cell division within a field of cells. Finally, we will discuss the important avenues that need to be explored in the future to better understand how planar cell polarity pathways control embryo body plan determination, cell fate specification or tissue morphogenesis by mitotic spindle orientation.
[Pubmed: 19447051]
| | 29. |
2009 Aug 07 |
Biologically-inspired humanoid postural control.
Tahboub KA
J. Physiol. Paris.;103(3-5):195-210. Epub 2009 Aug 07.
Abstract
This article presents a biologically-inspired framework for humanoid postural control. It complies with the main features of human postural control that are extracted from recent studies. In this article, the human body is abstracted as a single-inverted pendulum jointed with a foot that rests freely on a supporting surface. In particular, disturbances affecting posture are addressed and accommodated within the proposed framework. Among these are external forces and motion of support surface on which the body stands. The main components of this framework are: 1. A state-feedback mechanism for stabilizing the unstable dynamics of the body. 2. A tracking loop for robustly achieving desired voluntary orientations. 3. A feed-forward control primarily for improving the response to voluntary motions. 4. A stand-alone vestibular sensory fusion algorithm for estimating body orientation. 5. An external-disturbance estimator and a corresponding compensation for minimizing the effect of external disturbances. These components are interconnected in a way that qualifies this framework to modularly address the multi-segment body postural control problem. Although no postural stability measure is explicitly incorporated, experiments run on a special-purpose humanoid demonstrate the stability and the performance merits of the presented framework.
[Pubmed: 19665559]
| | 30. |
2009 Sep 1 |
Full view of single-molecule force spectroscopy of polyaniline in oxidized, reduced, and doped states.
Yu Y, Zhang Y, Jiang Z, Zhang X, Zhang H, Wang X
Langmuir. 2009 Sep 1;25(17):10002-6.
Abstract
The macroscopic mechanical properties of polyaniline (PANI) lie mainly on two factors, the structure of molecular aggregations of polymers and the mechanical properties of a single polymer chain. The former factor is well revealed; however, the latter is rarely studied. In this article, we have employed atomic force microscopy-based single-molecule force spectroscopy to investigate the mechanical properties of a kind of water-soluble PANI at a single-molecular level. We have carried out the study comparatively on single-chain-stretching experiments of oxidized, reduced, and doped PANI and obtained a full view of the single-chain elasticity of PANI in all these states. It is found that oxidized and reduced PANI chains are rigid, and the oxidized PANI is more rigid than the reduced PANI. Such a difference in single-chain elasticity can be rationalized by the molecular structures that are composed of benzenoid diamine and quinoid diimine in different proportions. The doped PANI has been found to be more flexible than the oxidized and reduced PANI, and the modified freely jointed chain parameters of doped PANI are similar with those of a common flexible-chain polymer. The results have explained the molecular-level origin of the outstanding flexibilities of materials made of doped PANI.
[Pubmed: 19463011]
| | 31. |
2009 Aug 7 |
Diffusion of linear polymer melts in shear and extensional flows.
Hunt TA, Todd BD
J Chem Phys. 2009 Aug 7;131(5):054904.
Abstract
We present results from molecular dynamics simulations for the anisotropic self-diffusion tensor and the velocity autocorrelation functions of monodisperse systems of dense linear chain molecules under flow. Two molecular models are used in these simulations: The finitely extensible nonlinear elastic chain and the freely jointed tangent sphere chain. Nonequilibrium molecular dynamics is used to simulate these systems under planar Couette flow and planar extensional flow. Under planar extensional flow, results presented here are the first, from simulation, for diffusion and velocity autocorrelation functions of molecules, while for planar Couette flow, we compare the broadest range of conditions. An explicit derivation is provided of the Green-Kubo expression for the diffusion tensor. This expression is then used to derive the relation involving the mean-squared displacement-an often used alternative method to calculate diffusion coefficients. Velocity autocorrelation functions have been used, in combination with results on the alignment of molecules from a previous paper, to provide some details of the molecular scale dynamics that influence diffusive transport under flow.
[Pubmed: 19673585]
| | 32. |
2009 Jul 28 |
The Omega Connector - A Module for Jointed Coupling of Titanium Total Prostheses in the Middle Ear.
Schmid G, Steinhardt U, Heckmann W
Laryngorhinootologie. 2009 Jul 28; [Epub ahead of print]
Abstract
THE Omega CONNECTOR - A MODULE FOR JOINTED COUPLING OF TITANIUM TOTAL PROSTHESES IN THE MIDDLE EARBACKGROUND: Hearing improvement after reconstruction of a defect ossicular chain depends on material, design and - crucially - coupling of the prosthesis. Coupling a total ossicular replacement prosthesis to the stapes footplate can be problematic and lead to prosthesis instability. In order to solve this problem, the Omega Connector was developed, a module allowing the middle ear surgeon to couple a titanium total prosthesis to the stapes footplate in a flexible, angle-variable manner. MATERIAL AND METHOD: The Omega Connector is made of pure titanium and consists of three compenents: head, neck and base plate. The head allows a jointed coupling to the stem of a titanium total prosthesis. Positioned between the remnants of the stapes crura, the bas plate proves for a stable connection with the stapes footplate. RESULTS: The Omega Connector was implanted during 14 revisions surgeries. In 10 of these surgeries a total ossicular replacement prosthesis was removed which was implanted at an earlier date and which was fixed and no longer functioning. In all 14 cases it was possible intraoperatively to position the Omega Connector correctly and to couple it to a titanium total prosthesis. The post-operative hearing gain was between 10 to 25 dB, with an average of 18 dB. CONCLUSION: For the first time, the Omega Connector offers to the surgeon the option to couple a titanium total prosthesis via a micro ball joint. Hearing results achieved so far are satisfying. The results confirm the advantages of the Omega Connector during implantation of a titanium total prosthesis. For a final evalua-tion, long-term studies have yet to be made.
[Pubmed: 19639531]
| | 33. |
2009 Apr 28 |
Toxic tubular injury in kidneys from Pkd1-deletion mice accelerates cystogenesis accompanied by dysregulated planar cell polarity and canonical Wnt signaling pathways.
Happé H, Leonhard WN, van der Wal A, van de Water B, Lantinga-van Leeuwen IS, Breuning MH, de Heer E, Peters DJ
Hum. Mol. Genet. 2009 Jul 15;18(14):2532-42. Epub 2009 Apr 28.
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is characterized by large fluid-filled cysts and progressive deterioration of renal function necessitating renal replacement therapy. Previously, we generated a tamoxifen-inducible, kidney epithelium-specific Pkd1-deletion mouse model and showed that inactivation of the Pkd1 gene induces rapid cyst formation in developing kidneys and a slow onset of disease in adult mice. Therefore, we hypothesized that injury-induced tubular epithelial cell proliferation may accelerate cyst formation in the kidneys of adult Pkd1-deletion mice. Mice were treated with the nephrotoxicant 1,2-dichlorovinyl-cysteine (DCVC) after Pkd1-gene inactivation, which indeed accelerated cyst formation significantly. After the increased proliferation during tissue regeneration, proliferation decreased to basal levels in Pkd1-deletion mice just as in DCVC-treated controls. However, in severe cystic kidneys, 10-14 weeks after injury, proliferation increased again. This biphasic response suggests that unrestricted cell proliferation after injury is not the underlying mechanism for cyst formation. Aberrant planar cell polarity (PCP) signaling and increased canonical Wnt signaling are suggested to be involved in cyst formation. Indeed, we show here that in Pkd1 conditional deletion mice expression of the PCP component Four-jointed (Fjx1) is decreased while its expression is required during tissue regeneration. In addition, we show that altered centrosome position and the activation of canonical Wnt signaling are early effects of Pkd1-gene disruption. This suggests that additional stimuli or events are required to trigger the process of cyst formation. We propose that during tissue repair, the integrity of the newly formed Pkd1-deficient cells is modified rendering them susceptible to subsequent cyst formation.
[Pubmed: 19401297]
| | 34. |
2009 Feb 03 |
Mechanics of forced unfolding of proteins.
Su T, Purohit PK
Acta Biomater. 2009 Jul;5(6):1855-63. Epub 2009 Feb 03.
Abstract
We describe and solve a two-state kinetic model for the forced unfolding of proteins. The protein oligomer is modeled as a heterogeneous, freely jointed chain with two possible values of Kuhn length and contour length representing its folded and unfolded configurations. We obtain analytical solutions for the force-extension response of the protein oligomer for different types of loading conditions. We fit the analytical solutions for constant-velocity pulling to the force-extension data for ubiquitin and fibrinogen and obtain model parameters, such as Kuhn lengths and kinetic coefficients, for both proteins. We then predict their response under a linearly increasing force and find that our solutions for ubiquitin are consistent with a different set of experiments. Our calculations suggest that the refolding rate of proteins at low forces is several orders larger than the unfolding rate, and neglecting it can lead to lower predictions for the unfolding force, especially at high stretching velocities. By accounting for the refolding of proteins we obtain a critical force below which equilibrium is biased in favor of the folded state. Our calculations also suggest new methods to determine the distance of the transition state from the energy wells representing the folded and unfolded states of a protein.
[Pubmed: 19251493]
| | 35. |
2009 Jul |
The phyllolepid placoderm Cowralepis mclachlani: insights into the evolution of feeding mechanisms in jawed vertebrates.
Carr RK, Johanson Z, Ritchie A
J. Morphol. 2009 Jul;270(7):775-804.
Abstract
Remarkably preserved specimens of Cowralepis mclachlani Ritchie, 2005 (Proc Linn Soc NSW 126:215-259) (Phyllolepida, Placodermi) represent a unique ontogenetic sequence adding to our understanding of anatomy, function, and phylogeny among basal jawed vertebrates (gnathostomes). A systematic review demonstrates that the Phyllolepida are a subgroup of the Arthrodira. Consideration of visceral and neurocranial characters supports the hypothesis that placoderms are the sister group to remaining gnathostomes. Placoderms possess, as adult plesiomorphic features, a number of characters that are only seen in the development of extant gnathostomes-a peramorphic shift relative to placoderms. Developmental evidence in vertebrates leads to a revised polarity of character transitions. These include 1) hyomandibula-neurocranium and ventral parachordal-palatoquadrate articulations (vertebrate synapomorphies); 2) jointed pharynx, paired basibranchials, anterior ethmoidal-palatoquadrate articulation, short trabeculae cranii, and anterior and posterior neurocranial fissures (gnathostome synapomorphies); and 3) fused basibranchials, dorsal palatoquadrate-neurocranium articulation, loss of the anterior neurocranial fissure, elongated trabeculae cranii, and transfer of the ventral parachordal-palatoquadrate articulation to the trabeculae (crown group gnathostomes). The level of preservation in C. mclachlani provides the basis for a reinterpretation of phyllolepid anatomy and function. Cowralepis mclachlani possesses paired basibranchials allowing the reinterpretation of the visceral skeleton in other placoderms. Mandible depression in C. mclachlani follows an osteichthyan pattern and the ventral visceral skeleton acts as a functional unit. Evidence for hypobranchial musculature demonstrates the neural crest origin of the basibranchials and that Cowralepis was a suction feeder. Finally, the position of the visceral skeleton relative to the neurocranium in placoderms parallels the condition in selachians and osteichthyans, but differs in the elongation of the occiput. The cucullaris fossa of placoderms (interpreted as a site of muscle attachment) is shown to represent, in part, the parabranchial chamber.
[Pubmed: 19215000]
| | 36. |
2009 Jul 20 |
Contact network in nearly jammed disordered packings of hard-sphere chains.
Karayiannis NCh, Foteinopoulou K, Laso M
Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jul;80(1 Pt 1):011307. Epub 2009 Jul 20.
Abstract
We present salient results of the analysis of the geometrical structure of a large fully equilibrated ensemble of nearly jammed packings of linear freely jointed chains of tangent hard spheres generated via extensive Monte Carlo simulations. In spite the expected differences due to chain connectivity, both the pair-correlation function and the contact network for chain packings are found to strongly resemble those in packings of monomeric hard spheres at the maximally random jammed (MRJ) state. A remarkable finding of the present work is the tendency of chains to form closed loops at the MRJ state as a consequence of chain collapse. Our simulations on disordered nearly jammed chain packings yield an average coordination number of 6, which fulfills the isostaticity condition and is in excellent agreement with the corresponding simulation [A. Donev, S. Torquato, and F. H. Stillinger, Phys. Rev. E 71, 011105 (2005)] and experimental [T. Aste, M. Saadatfar, and T. J. Senden, Phys. Rev. E 71, 061302 (2005)] findings for jammed packings of monatomic hard spheres. An exact correspondence between the statistical-mechanical ensembles of monomeric spheres and of hard-sphere chains offers insights regarding the structure and topology of the contact network of hard-sphere systems at the MRJ state.
[Pubmed: 19658698]
| | 37. |
2009 Jun 26 |
FAM20B is a kinase that phosphorylates xylose in the glycosaminoglycan-protein linkage region.
Koike T, Izumikawa T, Tamura J, Kitagawa H
Biochem. J. 2009 Jul 15;421(2):157-62. Epub 2009 Jun 26.
Abstract
2-O-phosphorylation of xylose has been detected in the glycosaminoglycan-protein linkage region, GlcAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser, of proteoglycans. Recent mutant analyses in zebrafish suggest that xylosyltransferase I and FAM20B, a protein of unknown function that shows weak similarity to a Golgi kinase encoded by four-jointed, operate in a linear pathway for proteoglycan production. In the present study, we identified FAM20B as a kinase that phosphorylates the xylose residue in the linkage region. Overexpression of FAM20B increased the amount of both chondroitin sulfate and heparan sulfate in HeLa cells, whereas the RNA interference of FAM20B resulted in a reduction of their amount in the cells. Gel-filtration analysis of the glycosaminoglycan chains synthesized in the overexpressing cells revealed that the glycosaminoglycan chains had a similar length to those in mock-transfected cells. These results suggest that FAM20B regulates the number of glycosaminoglycan chains by phosphorylating the xylose residue in the glycosaminoglycan-protein linkage region of proteoglycans.
[Pubmed: 19473117]
| | 38. |
2009 Apr 28 |
Effect of knotting on polymer shapes and their enveloping ellipsoids.
Millett KC, Plunkett P, Piatek M, Rawdon EJ, Stasiak A
J Chem Phys. 2009 Apr 28;130(16):165104.
Abstract
We simulate freely jointed chains to investigate how knotting affects the overall shapes of freely fluctuating circular polymeric chains. To characterize the shapes of knotted polygons, we construct enveloping ellipsoids that minimize volume while containing the entire polygon. The lengths of the three principal axes of the enveloping ellipsoids are used to define universal size and shape descriptors analogous to the squared radius of gyration and the inertial asphericity and prolateness. We observe that polymeric chains forming more complex knots are more spherical and also more prolate than chains forming less complex knots with the same number of edges. We compare the shape measures, determined by the enveloping ellipsoids, with those based on constructing inertial ellipsoids and explain the differences between these two measures of polymer shape.
[Pubmed: 19405636]
| | 39. |
2009 Apr 28 |
The structure of random packings of freely jointed chains of tangent hard spheres.
Karayiannis NCh, Foteinopoulou K, Laso M
J Chem Phys. 2009 Apr 28;130(16):164908.
Abstract
We analyze the structure of dense random packings of freely jointed chains of tangent hard spheres as a function of concentration (packing density) with particular emphasis placed on the behavior in the vicinity of their maximally random jammed (MRJ) state. Representative configurations over the whole density range are generated through extensive off-lattice Monte Carlo simulations on systems of average chain lengths ranging from N=12 to 1000 hard spheres. Several measures of order are used to quantitatively describe either local structure (sphere arrangements and bonded geometry) or global behavior (chain conformations and statistics). In addition, the employed measures are used to elucidate the effect of connectivity on structure, by comparing monatomic and chain assemblies of hard spheres at the MRJ state.
[Pubmed: 19405631]
| | 40. |
2009 Apr 9 |
Density functional approach to adsorption and retention of spherical molecules on surfaces modified with end-grafted polymers.
Borówko M, Rzysko W, Sokołowski S, Staszewski T
J Phys Chem B. 2009 Apr 9;113(14):4763-70.
Abstract
A density functional approach to describe adsorption of Lennard-Jones fluids on a surface modified with grafted chains is proposed. The theory is extended to the solute retention in chromatography with chemically bonded phases. The chain molecules are modeled as freely jointed tangent spheres with end segments linked to the surface. The segments interact via Lennard-Jones potential. The effects of grafting density and molecular interactions are discussed. The results are compared with the Monte Carlo simulation data. The theory predicts the most important features of the retention process.
[Pubmed: 19296624]
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