Substructure of inner dynein arms, radial spokes, and the central pair/projection complex of cilia and flagella

The substructure of the components of the axoneme interior--the inner dynein arms, the radial spokes, and the central pair/projection complex--was analyzed for Chlamydomonas. Tetrahymena, Strongelocentrotus, and Mnemiopsis using the quick-freeze, deep-etch technique. The inner arms are shown to resemble the outer arms in overall molecular organization, but they are disposed differently on the microtubule and have two distinct morphologies--dyads with two heads and triads with three. The dyads associate with spokes S3 and S2; the triads associate with S1. The spokes form a three-start right-handed helix with a 288-nm rise; the central pair makes a shallow left-handed twist. The spoke heads are shown to be made up of four major subunits; two bind to the spoke shaft and two bind to a pair of central-sheath projections.     

Measurement of the force produced by an intact bull sperm flagellum in isometric arrest and estimation of the dynein stall force

The force generated by a detergent-extracted reactivated bull sperm flagellum during an isometric stall was measured with a force-calibrated glass microprobe. The average isometric stall force from 48 individual measurements was 2.5 +/- 0.7 x 10(-5) dyne (2.5 +/- 0.7 x 10(-10) N). The force measurements were obtained by positioning a calibrated microprobe in the beat path of sperm cells that were stuck by their heads to a glass microscope slide. The average position of the contact point of the flagellum with the probe was 15 microm from the head-tail junction. This average lever arm length multiplied by the measured force yields an estimate of the active bending moment (torque) of 3.9 x 10(-8) dyne x cm (3.9 x 10(-15) N x m). The force was sustained and was for the most part uniform, despite the fact that the flagellum beyond the point of contact with the probe usually continued beating. It appears that the dynein motors in the basal portion of the flagellum continue to pull in an isometric stall for as long as the motion of the flagellum is blocked. If dynein motors in the flagellum distal to the contact point with the probe were contributing force to the displacement of the probe, then the flagellar segment immediately past the point of contact would have to show a net curvature in the direction of the probe displacement. No such curvature bias was observed in the R-bend arrests, and only a small positive curvature bias was measured in the P-bend arrests. Our analysis of the data suggests that more than 90% of the sustained force component is generated by the part of the flagellum between the probe and the flagellar base. Based on this premise, the isometric stall force per dynein head is estimated to be 5.0 x 10(-7) dyne (5 pN). This equals approximately 1.0 x 10(-6) dyne (10 pN) per intact dynein arm. These values are close to the isometric stall force of isolated dynein. This suggests that all of the dynein heads between the base and the probe, on the active side of the axoneme, are contributing to the force exerted against the probe.     

Comprehensive analysis of the LncRNAs,MiRNAs, and MRNAs acting within the competing endogenous RNA network of LGG

Genetica - Messenger RNA (mRNA) and long noncoding RNA (lncRNA) targets interact via competitive microRNA (miRNA) binding. However, the roles of cancer-specific lncRNAs in the competing endogenous...     

The hemodynamic forces acting on thrombi, from incipient attachment of single cells to maturity and embolization

We consider the steady fluid forces acting on a thrombus from the time of first contact of a single cell with a natural or artificial surface, through the attachment process and growth to embolization. For a hemi-spherical or cylindrical attached cell of height less than 1/100-1/20th of the channel width, shear and tensile stresses are solely dependent on viscosity and on the ratio of average fluid velocity to channel width vt/Dt (shear rate). Large values of this ratio reduce adhesion and increase embolization. The average shear stress on such cells is approximately 1-10 Pa (10-100 dyn cm2), the average tensile stress about three times higher. For other shapes and larger protrusions, stress varies with protrusion height as well. Maturing thrombi composed of cell aggregates embedded in a fibrin mesh do not appear to allow significant fluid flow through their porous structure. The interior forces are then due solely to hydrostatic pressure and initially vary directly with vt/Dt and inversely with thrombus height Hp, thus favouring embolization at an early stage and in arterial systems. Rough surfaces are identified as causing an increase in dwell-time and possibly immobilizing an unattached cell due to 'negative lift'.     

Genetic relationships between carcass cut weights predicted from video image analysis and other performance traits in cattle

The objective of this study was to quantify the genetic associations between a range of carcass-related traits including wholesale cut weights predicted from video image analysis (VIA) technology, and a range of pre-slaughter performance traits in commercial Irish cattle. Predicted carcass cut weights comprised of cut weights based on retail value: lower value cuts (LVC), medium value cuts (MVC), high value cuts (HVC) and very high value cuts (VHVC), as well as total meat, fat and bone weights. Four main sources of data were used in the genetic analyses: price data of live animals collected from livestock auctions, live-weight data and linear type collected from both commercial and pedigree farms as well as from livestock auctions and weanling quality recorded on-farm. Heritability of carcass cut weights ranged from 0.21 to 0.39. Genetic correlations between the cut traits and the other performance traits were estimated using a series of bivariate sire linear mixed models where carcass cut weights were phenotypically adjusted to a constant carcass weight. Strongest positive genetic correlations were obtained between predicted carcass cut weights and carcass value (min r_g(MVC) = 0.35; max r_g(VHVC) = 0.69), and animal price at both weaning (min r_g(MVC) = 0.37; max r_g(VHVC) = 0.66) and post weaning (min r_g(MVC) = 0.50; max r_g(VHVC) = 0.67). Moderate genetic correlations were obtained between carcass cut weights and calf price (min r_g(HVC) = 0.34; max r_g(LVC) = 0.45), weanling quality (min r_g(MVC) = 0.12; max r_g(VHVC) = 0.49), linear scores for muscularity at both weaning (hindquarter development: min r_g(MVC) = −0.06; max r_g(VHVC) = 0.46), post weaning (hindquarter development: min r_g(MVC) = 0.23; max r_g(VHVC) = 0.44). The genetic correlations between total meat weight were consistent with those observed with the predicted wholesale cut weights. Total fat and total bone weights were generally negatively correlated with carcass value, auction prices and weanling quality. Total bone weight was, however, positively correlated with skeletal scores at weaning and post weaning. These results indicate that some traits collected early in life are moderate-to-strongly correlated with carcass cut weights predicted from VIA technology. This information can be used to improve the accuracy of selection for carcass cut weights in national genetic evaluations.     

The established and the predicted roles of dynein light chain in the regulation of mitochondrial apoptosis

The mitochondrial pathway of apoptosis is regulated by the interplay between the members of Bcl-2 family. Within this family, BH3-only proteins are the sensors of apoptotic stimuli and can trigger apoptosis either by inhibiting the anti-apoptotic Bcl-2-family proteins or by directly activating the effectors Bax and Bak. An expanding body of research suggests that a number of non-Bcl-2 proteins can also interact with Bcl-2 proteins and contribute to the decision of cell fate. Dynein light chain (LC8, DYNLL or DLC), a hub protein and a dimerizing engine has been proposed to regulate the pro-apoptotic activity of two BH3-only proteins, Bim and Bmf. Our recent work has provided insight into the mechanisms through which DLC1 (DYNLL1) modulates Bim activity. Here we discuss the present day understanding of Bim-DLC interaction and endeavor to evaluate this interaction in the light of information from studies of DLC with other binding partners.     

Phylogenetic relationships within Diadasia, a group of specialist bees

We estimated phylogenetic relationships among species of the bee genus Diadasia, a group of new world, specialist bees. We sequenced approximately 2 kb of the mitochondrial genes cytochrome oxidase subunit I and II and tRNA leucine and approximately 1 kb of the nuclear gene elongation factor 1-alpha for 24 North American Diadasia species, 4 South American species, and five outgroup genera. Parsimony analyses of the two data sets were highly congruent. A combined analysis produced a well-resolved phylogenetic hypothesis that supported the monophyly of Diadasia, but not that of traditional subgenera: Diadasia s. str. was paraphyletic in all analyses. With one exception, the North and South American species formed separate clades, supporting previous hypotheses that two lineages of Diadasia have dispersed from South to North America: a more recent dispersal of D. ochracea and an older dispersal of the ancestor to all other North American species. Different species of Diadasia specialize on pollen from at least five different plant families; the phylogeny presented here, along with known host affinities, indicates that host-switching has been rare.     

Chimaera compacta,a new species from southern Indian Ocean,and an estimate of phylogenetic relationships within the genus Chimaera (Chondrichthyes: Chimaeridae)

Ichthyological Research - Chimaera compacta sp. nov., a new species of shortnose chimaera (Holocephali: Chimaeriformes: Chimaeridae), is described from a single specimen collected at 595–655...     

A quantitative analysis of elastic,entropic, electrostatic,and osmotic forces within relaxed skinned muscle fibers

The elastic behavior of mechanically skinned skeletal muscle fibers in relaxing solution is modelled using equations developed by Flory (1953) for the elasticity of non-biological polymers. Mechanically, the relaxed skinned fiber is considered to be a semi-crystalline network of inextensible polymer chains, which are periodically cross-linked and which are bathed in an aqueous medium. We consider (1) configurational elastic forces in the network, (2) entropic forces due to mixing of polymer and water, (3) electrostatic forces due to fixed charges on the muscle proteins and mobile charges in the bathing solution, and (4) compressive forces due to large colloids in the bathing solution. Van der Waals forces are not considered since calculations show that they are probably negligible under our conditions. We derive an expression which relates known quantities (ionic strength, osmotic compressive pressure, and fiber width), experimentally estimated quantities (fixed charge density and volume fraction of muscle proteins), and derived quantities (concentration of cross-links and a parameter reflecting the interaction energy between protein and water).The model was tested by comparison with observed changes in skinned fiber width under a variety of experimental conditions which included changes in osmotic compressive pressure, pH, sarcomere length, and ionic strength. Over a wide range of compressive pressure (0–36 atm) the theory predicted the nonlinear relation between fiber width and logarithm of pressure. The direction and magnitude of the decrease in width when pH was decreased to 4 could be modelled asssuming the fixed charge density on the protein network was 0.34 moles of electrons per liter protein, a value in accordance with the estimates of others. The relation between width and sarcomere length over the complete range of compressive pressures could be modelled with the assumption that the number of cross-links increases somewhat with sarcomere length. Changes of width with ionic strength were modelled assuming that increasing salt concentration both increased the electrostatic shielding of fixed charges and decreased the number of cross-links. The decrease of fiber width in 1% glutaraldehyde was modelled by assuming that the concentration of crosslinks increased by some 10%. The theory predicted the order of magnitude but not the detailed shape of the passive tension-length relation which may indicate that, as with non-biological polymers, the theory does not adequately describe the behavior of semi-crystalline networks at high degrees of deformation.In summary, the theory provides a semiquantitative approach to an understanding of the nature and relative magnitudes of the forces underlying the mechanical behavior of relaxed skinned fibers. It indicates, for instance, that when fibers are returned to near their in vivo size with 3% PVP, the forces in order of their importance are: ¦ elastic forces ¦ ¦ entropic forces > ¦ electrostatic forces ¦ ¦ osmotic compressive forces ¦.     

Axonal projections within the brain-retrocerebral complex of the cricket,Teleogryllus commodus

Summary The cerebral origins and axonal trajectories of neurons projecting to the retrocerebral complex of the cricket, Teleogryllus commodus, were examined in silver-intensified nickel preparations. Spatially separate groups of somata in the pars intercerebralis (PI) and in the pars lateralis (PL), commonly accepted as neurosecretory loci, were found to give rise to axons which terminate in the nervus corporis allati 2, the corpus allatum, or the corpus cardiacum. Additional findings demonstrated a distinct group of somata from the PI whose axons run in the esophageal nerve (stomatogastric nervous system), nine somata in the subesophageal ganglion with axons projecting into the nervus corporis allati 2, and also a small cluster of tritocerebral perikarya with axons terminating in the corpus cardiacum. Somata residing in the PI and PL were found to be compartmentally organized based upon the retrocerebral destinations of their axons. Possible functional consequences of these results with respect to the insect neurosecretory system are discussed.     

Kinetic analysis of axoneme and dynein ATPase from sea urchin sperm

The behavior of the ATPase of axoneme (detergent-treated flagellum) and dynein from sea urchin sperm was investigated. The activation of the ATPase by divalent cations was attributed to formation of a complex of ATP and the divalent cation; the metal-ATP complex is an effective substrate. However, free ATP is a modifier of the ATPase. Free ATP markedly changes the affinity of the metal-ATP complex to the enzymes. Calcium-activated ATPase activity of axoneme decreased at high concentration of CaCl₂, but that of dynein did not decrease.     

Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons

Since operons are unstable across Prokaryotes, it has been suggested that perhaps they re-combine in a conservative manner. Thus, genes belonging to a given operon in one genome might re-associate in other genomes revealing functional relationships among gene products. We developed a system to build networks of functional relationships of gene products based on their organization into operons in any available genome. The operon predictions are based on inter-genic distances. Our system can use different kinds of thresholds to accept a functional relationship, either related to the prediction of operons, or to the number of non-redundant genomes that support the associations. We also work by shells, meaning that we decide on the number of linking iterations to allow for the complementation of related gene sets. The method shows high reliability benchmarked against knowledge-bases of functional interactions. We also illustrate the use of Nebulon in finding new members of regulons, and of other functional groups of genes. Operon rearrangements produce thousands of high-quality new interactions per prokaryotic genome, and thousands of confirmations per genome to other predictions, making it another important tool for the inference of functional interactions from genomic context.     

Structural conformation of ciliary dynein arms and the generation of sliding forces in Tetrahymena cilia

The sliding tubule model of ciliary motion requires that active sliding of microtubules occur by cyclic cross-bridging of the dynein arms. When isolated, demembranated Tetrahymena cilia are allowed to spontaneously disintegrate in the presence of ATP, the structural conformation of the dynein arms can be clearly resolved by negative contrast electron microscopy. The arms consist of three structural subunits that occur in two basic conformations with respect to the adjacent B subfiber. The inactive conformation occurs in the absence of ATP and is characterized by a uniform, 32 degrees base-directed polarity of the arms. Inactive arms are not attached to the B subfiber of adjacent doublets. The bridged conformation occurs strictly in the presence of ATP and is characterized by arms having the same polarity as inactive arms, but the terminal subunit of the arms has become attached to the B subfiber. In most instances the bridged conformation is accompanied by substantial tip-directed sliding displacement of the bridged doublets. Because the base-directed polarity of the bridged arms is opposite to the direction required for force generation in these cilia and because the bridges occur in the presence of ATP, it is suggested that the bridged conformation may represent the initial attachment phase of the dynein cross-bridge cycle. The force-generating phase of the cycle would then require a tip-directed deflection of the arm subunit attached to the B subfiber.     

The phylogenetic relationships within the Chamaeleonidae, with comments on some aspects of cladistic analysis

The phylogenetic relationships of the African mainland species of the genus Rhampholeon (formerly referred to the genus Brookesia ) with respect to Brookesia superciliaris, Bradypodion pumilus , and the genus Chamaeleo are analysed. Rhampholeon constitutes a genus well separated from Brookesia and may itself be subdivided in two subgroups on the basis of characters derived from the nasal and parietal complexes. A final section investigates problems of cladistic analysis, viz. the relationship of parsimony to character weighting, and pattern versus process as complementary perspectives of character analysis and coding.     

Protein targeting of an unusual, evolutionarily conserved adenylate kinase to a eukaryotic flagellum

The eukaryotic flagellum is a large structure into which specific constituent proteins must be targeted, transported and assembled after their synthesis in the cytoplasm. Using Trypanosoma brucei and a proteomic approach, we have identified and characterized a novel set of adenylate kinase proteins that are localized to the flagellum. These proteins represent unique isoforms that are targeted to the flagellum by an N-terminal extension to the protein and are incorporated into an extraaxonemal structure (the paraflagellar rod). We show that the N-terminal extension is both necessary for isoform location in the flagellum and sufficient for targeting of a green fluorescent protein reporter protein to the flagellum. Moreover, these N-terminal extension sequences are conserved in evolution and we find that they allow the identification of novel adenylate kinases in the genomes of humans and worms. Given the existence of specific isoforms of certain central metabolic enzymes, and targeting sequences for these isoforms, we suggest that these isoforms form part of a complex, "solid-phase" metabolic capability that is built into the eukaryotic flagellum.     

Independent analysis of the flagellum surface and matrix proteomes provides insight into flagellum signaling in mammalian-infectious Trypanosoma brucei

The flagellum of African trypanosomes is an essential and multifunctional organelle that functions in motility, cell morphogenesis, and host-parasite interaction. Previous studies of the trypanosome flagellum have been limited by the inability to purify flagella without first removing the flagellar membrane. This limitation is particularly relevant in the context of studying flagellum signaling, as signaling requires surface-exposed proteins in the flagellar membrane and soluble signaling proteins in the flagellar matrix. Here we employ a combination of genetic and mechanical approaches to purify intact flagella from the African trypanosome, Trypanosoma brucei, in its mammalian-infectious stage. We combined flagellum purification with affinity-purification of surface-exposed proteins to conduct independent proteomic analyses of the flagellum surface and matrix fractions. The proteins identified encompass a broad range of molecular functionalities, including many predicted to function in signaling. Immunofluorescence and RNA interference studies demonstrate flagellum localization and function for proteins identified and provide insight into mechanisms of flagellum attachment and motility. The flagellum surface proteome includes many T. brucei-specific proteins and is enriched for proteins up-regulated in the mammalian-infectious stage of the parasite life-cycle. The combined results indicate that the flagellum surface presents a diverse and dynamic host-parasite interface that is well-suited for host-parasite signaling.     

Phylogenetic relationships within the Retiolitidae (Graptolithina) and a new genus, Cometograptus

A new retiolitid genus Cometograptus, restricted to the lundgreni Biozone (Late Wenlock), is characterized by a combination of primitive features such as strong transverse rods and ancora sleeve lists with seams facing out, with advanced features such as a long sicula, central, free nema and pustulose bandages. Cometograptus links two Subfamilies of the Family Retiolitidae. The Subfamily Retiolitinae is divided into redefined lineages: Pseudoretiolites, Retiolites, Paraplectograptus, whereas the Subfamily Plectograptinae is divisible into the Sokolovograptus (questionable), Gothograptus, Spinograptus, Plectograptus lineages, and Cometograptus. The Sokolovograptus group, the first retiolitids bearing ancora sleeve lists with seams facing out, did not survive the lundgreni crisis. The only survivors were Upper Wenlock retiolitids of the Gothograptus lineage. The new genus Cometograptus includes Cometograptus koreni n.gen. and n.sp., Cometograptus tomczyki n.gen. and n.sp., as well as the previously described Cometograptus nevadensis, Cometograptus marsupium and Cometograptus apoxys.