MapToGenome: A Comparative Genomic Tool that Aligns Transcript Maps to Sequenced Genomes

Efforts to generate whole genome assemblies and dense genetic maps have provided a wealth of gene positional information for several vertebrate species. Comparing the relative location of orthologous genes among these genomes provides perspective on genome evolution and can aid in translating genetic information between distantly related organisms. However, large-scale comparisons between genetic maps and genome assemblies can prove challenging because genetic markers are commonly derived from transcribed sequences that are incompletely and variably annotated. We developed the program MapToGenome as a tool for comparing transcript maps and genome assemblies. MapToGenome processes sequence alignments between mapped transcripts and whole genome sequence while accounting for the presence of intronic sequences, and assigns orthology based on user-defined parameters. To illustrate the utility of this program, we used MapToGenome to process alignments between vertebrate genetic maps and genome assemblies 1) self/self alignments for maps and assemblies of the rat and zebrafish genome; 2) alignments between vertebrate transcript maps (rat, salamander, zebrafish, and medaka) and the chicken genome; and 3) alignments of the medaka and zebrafish maps to the pufferfish (Tetraodon nigroviridis) genome. Our results show that map-genome alignments can be improved by combining alignments across presumptive intron breaks and ignoring alignments for simple sequence length polymorphism (SSLP) marker sequences. Comparisons between vertebrate maps and genomes reveal broad patterns of conservation among vertebrate genomes and the differential effects of genome rearrangement over time and across lineages

Use of a bacterial hygromycin B resistance gene as a dominant selectable marker in Neurospora crassa transformation

Dominant transformation markers allow maximum flexibility in the choice of transformation recipients

Far-field approximation for hydrodynamic interactions in parallel-wall geometry

A complete analysis is presented for the far-field creeping flow produced by a multipolar force distribution in a fluid confined between two parallel planar walls. We show that at distances larger than several wall separations the flow field assumes the Hele-Shaw form, i.e., it is parallel to the walls and varies quadratically in the transverse direction. The associated pressure field is a two-dimensional harmonic function that is characterized by the same multipolar number m as the original force multipole. Using these results we derive asymptotic expressions for the Green's matrix that represents Stokes flow in the wall-bounded fluid in terms of a multipolar spherical basis. This Green's matrix plays a central role in our recently proposed algorithm [Physica A xx, {\bf xxx} (2005)] for evaluating many-body hydrodynamic interactions in a suspension of spherical particles in the parallel-wall geometry. Implementation of our asymptotic expressions in this algorithm increases its efficiency substantially because the numerically expensive evaluation of the exact matrix elements is needed only for the neighboring particles. Our asymptotic analysis will also be useful in developing hydrodynamic algorithms for wall-bounded periodic systems and implementing acceleration methods by using corresponding results for the two-dimensional scalar potential.Comment: 28 pages 5 figure

ENSO-driven extreme oscillations in mean sea level destabilise critical shoreline mangroves—An emerging threat

Recent ENSO-related, extreme low oscillations in mean sea level, referred to as ‘Taimasa’ in Samoa, have destabilised shoreline mangroves of tropical northern Australia, and possibly elsewhere. In 1982 and 2015, two catastrophic Taimasa each resulted in widespread mass dieback of ~76 km2 of shoreline mangroves along 2,000 km of Australia’s Gulf of Carpentaria. For the 2015 event, we determined that a temporary drop in sea level of ~0.4 metres for up to six months duration caused upper zone shoreline mangroves across the region to die from severe moisture deficit and desiccation. The two dramatic collapse events revealed a previously unrecognised vulnerability of semi-arid tidal wetland habitats to more extreme ENSO influences on sea level. In addition, we also observed a relationship between annual sea level oscillations and mangrove forest productivity where seasonal oscillations in mean sea level were co-incident with regular annual mangrove leaf growth during months of higher sea levels (March-May), and leaf shedding during lower sea levels (September-November). The combination of these periodic fluctuations in sea level defined a mangrove ‘Goldilocks’ zone of seasonal productivity during median-scale oscillations, bracketed by critical threshold events when sea levels became unusually low, or high. On the two occasions reported here when sea levels were extremely low, upper zone mangrove vegetation died en masse in synchrony across northern Australia. Such extreme pulse impacts combined with localised stressors profoundly threaten the longer-term survival of mangrove ecosystems and their benefits, like minimisation of shoreline erosion with rising sea levels. These new insights into such critical influences of climate and sea level on mangrove forests offer further affirmation of the urgency for implementing well-considered mitigation efforts for the protection of shoreline mangroves at risk, especially given predictions of future re-occurrences of extreme events affecting sea levels, combined with on-going pressure of rapidly rising sea levels

Sal-Site: Integrating new and existing ambystomatid salamander research and informational resources

Salamanders of the genus Ambystoma are a unique model organism system because they enable natural history and biomedical research in the laboratory or field. We developed Sal-Site to integrate new and existing ambystomatid salamander research resources in support of this model system. Sal-Site hosts six important resources: 1) Salamander Genome Project: an information-based web-site describing progress in genome resource development, 2) Ambystoma EST Database: a database of manually edited and analyzed contigs assembled from ESTs that were collected from A. tigrinum tigrinum and A. mexicanum, 3) Ambystoma Gene Collection: a database containing full-length protein-coding sequences, 4) Ambystoma Map and Marker Collection: an image and database resource that shows the location of mapped markers on linkage groups, provides information about markers, and provides integrating links to Ambystoma EST Database and Ambystoma Gene Collection databases, 5) Ambystoma Genetic Stock Center: a website and collection of databases that describe an NSF funded salamander rearing facility that generates and distributes biological materials to researchers and educators throughout the world, and 6) Ambystoma Research Coordination Network: a web-site detailing current research projects and activities involving an international group of researchers. Sal-Site is accessible at

Screening by symmetry of long-range hydrodynamic interactions of polymers confined in sheets

Hydrodynamic forces may significantly affect the motion of polymers. In sheet-like cavities, such as the cell's cytoplasm and microfluidic channels, the hydrodynamic forces are long-range. It is therefore expected that that hydrodynamic interactions will dominate the motion of polymers in sheets and will be manifested by Zimm-like scaling. Quite the opposite, we note here that although the hydrodynamic forces are long-range their overall effect on the motion of polymers vanishes due to the symmetry of the two-dimensional flow. As a result, the predicted scaling of experimental observables such as the diffusion coefficient or the rotational diffusion time is Rouse-like, in accord with recent experiments. The effective screening validates the use of the non-interacting blobs picture for polymers confined in a sheet.Comment: http://www.weizmann.ac.il/complex/tlusty/papers/Macromolecules2006.pdf http://pubs.acs.org/doi/abs/10.1021/ma060251

Many-particle hydrodynamic interactions in parallel-wall geometry: Cartesian-representation method

This paper describes the results of our theoretical and numerical studies of hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls, under creeping-flow conditions. We propose a novel algorithm for accurate evaluation of the many-particle friction matrix in this system--no such algorithm has been available so far. Our approach involves expanding the fluid velocity field into spherical and Cartesian fundamental sets of Stokes flows. The interaction of the fluid with the particles is described using the spherical basis fields; the flow scattered with the walls is expressed in terms of the Cartesian fundamental solutions. At the core of our method are transformation relations between the spherical and Cartesian basis sets. These transformations allow us to describe the flow field in a system that involves both the walls and particles. We used our accurate numerical results to test the single-wall superposition approximation for the hydrodynamic friction matrix. The approximation yields fair results for quantities dominated by single particle contributions, but it fails to describe collective phenomena, such as a large transverse resistance coefficient for linear arrays of spheres

Discrete cilia modelling with singularity distributions

We discuss in detail techniques for modelling flows due to finite and infinite arrays of beating cilia. An efficient technique, based on concepts from previous ‘singularity models’ is described, that is accurate in both near and far-fields. Cilia are modelled as curved slender ellipsoidal bodies by distributing Stokeslet and potential source dipole singularities along their centrelines, leading to an integral equation that can be solved using a simple and efficient discretisation. The computed velocity on the cilium surface is found to compare favourably with the boundary condition. We then present results for two topics of current interest in biology. 1) We present the first theoretical results showing the mechanism by which rotating embryonic nodal cilia produce a leftward flow by a ‘posterior tilt,’ and track particle motion in an array of three simulated nodal cilia. We find that, contrary to recent suggestions, there is no continuous layer of negative fluid transport close to the ciliated boundary. The mean leftward particle transport is found to be just over 1 μm/s, within experimentally measured ranges. We also discuss the accuracy of models that represent the action of cilia by steady rotlet arrays, in particular, confirming the importance of image systems in the boundary in establishing the far-field fluid transport. Future modelling may lead to understanding of the mechanisms by which morphogen gradients or mechanosensing cilia convert a directional flow to asymmetric gene expression. 2) We develop a more complex and detailed model of flow patterns in the periciliary layer of the airway surface liquid. Our results confirm that shear flow of the mucous layer drives a significant volume of periciliary liquid in the direction of mucus transport even during the recovery stroke of the cilia. Finally, we discuss the advantages and disadvantages of the singularity technique and outline future theoretical and experimental developments required to apply this technique to various other biological problems, particularly in the reproductive system

Cannabidiol and cannabis-inspired terpene blends have acute prosocial effects in the BTBR mouse model of autism spectrum disorder

IntroductionCannabidiol (CBD) is a non-intoxicating phytocannabinoid with increasing popularity due to its purported therapeutic efficacy for numerous off-label conditions including anxiety and autism spectrum disorder (ASD). Those with ASD are commonly deficient in endogenous cannabinoid signaling and GABAergic tone. CBD has a complex pharmacodynamic profile that includes enhancing GABA and endocannabinoid signaling. Thus, there is mechanistic justification for investigating CBD’s potential to improve social interaction and related symptoms in ASD. Recent clinical trials in children with ASD support CBD’s beneficial effects in numerous comorbid symptoms, but its impact on social behavior is understudied.MethodsHere, we tested the prosocial and general anxiolytic efficacy of a commercially available CBD-rich broad spectrum hemp oil delivered by repeated puff vaporization and consumed via passive inhalation in the female cohort of the BTBR strain, a common inbred mouse line for preclinical assessment of ASD-like behaviors.ResultsWe observed that CBD enhanced prosocial behaviors using the 3-Chamber Test with a different vapor dose-response relationship between prosocial behavior and anxiety-related behavior on the elevated plus maze. We also identified that inhalation of a vaporized terpene blend from the popular OG Kush cannabis strain increased prosocial behavior independently of CBD and acted together with CBD to promote a robust prosocial effect. We observed similar prosocial effects with two additional cannabis terpene blends from the Do-Si-Dos and Blue Dream strains, and further reveal that these prosocial benefits rely on the combination of multiple terpenes that comprise the blends.DiscussionOur results illustrate the added benefit of cannabis terpene blends for CBD-based treatment of ASD

Sex in the PAC: A hidden affair in dark septate endophytes?

<p>Abstract</p> <p>Background</p> <p>Fungi are asexually and sexually reproducing organisms that can combine the evolutionary advantages of the two reproductive modes. However, for many fungi the sexual cycle has never been observed in the field or <it>in vitro </it>and it remains unclear whether sexual reproduction is absent or cryptic. Nevertheless, there are indirect approaches to assess the occurrence of sex in a species, such as population studies, expression analysis of genes involved in mating processes and analysis of their selective constraints. The members of the <it>Phialocephala fortinii </it>s. l. - <it>Acephala applanata </it>species complex (PAC) are ascomycetes and the predominant dark septate endophytes that colonize woody plant roots. Despite their abundance in many ecosystems of the northern hemisphere, no sexual state has been identified to date and little is known about their reproductive biology, and how it shaped their evolutionary history and contributes to their ecological role in forest ecosystems. We therefore aimed at assessing the importance of sexual reproduction by indirect approaches that included molecular analyses of the mating type (<it>MAT</it>) genes involved in reproductive processes.</p> <p>Results</p> <p>The study included 19 PAC species and > 3, 000 strains that represented populations from different hosts, continents and ecosystems. Whereas <it>A. applanata </it>had a homothallic (self-fertile) <it>MAT </it>locus structure, all other species were structurally heterothallic (self-sterile). Compatible mating types were observed to co-occur more frequently than expected by chance. Moreover, in > 80% of the populations a 1:1 mating type ratio and gametic equilibrium were found. <it>MAT </it>genes were shown to evolve under strong purifying selection.</p> <p>Conclusions</p> <p>The signature of sex was found in worldwide populations of PAC species and functionality of <it>MAT </it>genes is likely preserved by purifying selection. We hypothesize that cryptic sex regularely occurs in the PAC and that further field studies and <it>in vitro </it>crosses will lead to the discovery of the sexual state. Although structurally heterothallic species prevail, it cannot be excluded that homothallism represents the ancestral breeding system in the PAC.</p