The Dynamics of Networks of Identical Theta Neurons.

We consider finite and infinite all-to-all coupled networks of identical theta neurons. Two types of synaptic interactions are investigated: instantaneous and delayed (via first-order synaptic processing). Extensive use is made of the Watanabe/Strogatz (WS) ansatz for reducing the dimension of networks of identical sinusoidally-coupled oscillators.

Relative orientation of collagen molecules within a fibril: a homology model for homo sapiens type I collagen.

Type I collagen is an essential extracellular protein that plays an important structural role in tissues that require high tensile strength. However, owing to the molecule's size, to date no experimental structural data are available for the Homo sapiens species. Therefore, there is a real need to develop a reliable homology model and a method to study the packing of the collagen molecules within the fibril.

Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software.

Much is still not understood about how gene regulatory interactions control cell fate decisions in single cells, in part due to the difficulty of directly observing gene regulatory processes in vivo. We introduce here a novel integrated setup consisting of a microfluidic chip and accompanying analysis software that enable long-term quantitative tracking of growth and gene expression in single cells. The dual-input Mother Machine (DIMM) chip enables controlled and continuous variation of external conditions, allowing direct observation of gene regulatory responses to changing conditions in single cells.

Effect on the mechanical properties of type I collagen of intra-molecular lysine-arginine derived advanced glycation end-product cross-linking.

Non-enzymatic advanced glycation end product (AGE) cross-linking of collagen molecules has been hypothesised to result in significant changes to the mechanical properties of the connective tissues within the body, potentially resulting in a number of age related diseases. We have investigated the effect of two of these cross-links, glucosepane and DOGDIC, on the tensile and lateral moduli of the collagen molecule through the use of a steered molecular dynamics approach, using previously identified preferential formation sites for intra-molecular cross-links. Our results show that the presence of intra-molecular AGE cross-links increases the tensile and lateral Young's moduli in the low strain domain by between 3.

ForceGen: atomic covalent bond value derivation for Gromacs.

A large number of crystallographic protein structures include ligands, small molecules and post-translational modifications. Atomic bond force values for computational atomistic models of post-translational or non-standard amino acids, metal binding active sites, small molecules and drug molecules are not readily available in most simulation software packages. We present ForceGen, a Java tool that extracts the bond stretch and bond angle force values and equilibrium values from the Hessian of a Gaussian vibrational frequency analysis.

Short and fast vs long and slow: age changes courtship in male orb-web spiders (Argiope keyserlingi).

Male reproductive performance can vary with condition, age and future reproductive opportunities. Web-building spiders are ideal models to examine the effects of senescence on fitness-related behaviours due to strong selection on male courtship to reduce pre-copulatory sexual cannibalism. Argiope keyserlingi spiders generate courtship vibrations, or 'shudders', that reduce female aggression.

Maternal serum IGF-1, IGFBP-1 and 3, and placental growth hormone at 20weeks' gestation in pregnancies complicated by preeclampsia.

Objective: To investigate whether maternal serum concentrations of placental growth hormone (GH-V), insulin-like growth factor (IGF) 1 and 2, and IGF binding proteins (IGFBP) 1 and 3 were altered in pregnancies complicated by later preeclampsia (PE).

Study Design: In a nested case-control study, PE cases (n=71) and matched controls (n=71) were selected from the Screening for Pregnancy Endpoints (SCOPE) biobank in Auckland, New Zealand. Maternal serum hormone concentrations at 20weeks of gestation were determined by ELISA.

The incidence of bent dorsal fins in free-ranging cetaceans.

Laterally bent dorsal fins are rarely observed in free-ranging populations of cetaceans, contrary to captivity, where most killer whale Orcinus orca adult males have laterally collapsed fins. This topic has been poorly explored, and data/information on its occurrence and possible causes are limited. The present study: (i) undertakes a review of the available information on bent dorsal fins in free-ranging cetaceans, and updates it with new records, (ii) reports on the proportion of bent fins in different study populations, and (iii) discusses possible causes.

Examining object recognition and object-in-Place memory in plateau zokors, Eospalax baileyi.

Recognition memory is important for the survival and fitness of subterranean rodents due to the barren underground conditions that require avoiding the burden of higher energy costs or possible conflict with conspecifics. Our study aims to examine the object and object/place recognition memories in plateau zokors (Eospalax baileyi) and test whether their underground life exerts sex-specific differences in memory functions using Novel Object Recognition (NOR) and Object-in-Place (OiP) paradigms. Animals were tested in the NOR with short (10min) and long-term (24h) inter-trial intervals (ITI) and in the OiP for a 30-min ITI between the familiarization and testing sessions.

Chasing the agostic interaction in ligand assisted cyclometallation reactions of palladium(ii).

A 500 MHz NMR study of the reaction between 1-tetralone oxime and PdCl in CDOD shows resonances attributable to a potential agostic intermediate prior to the formation of the insoluble cyclopalladated product which itself was characterised by X-ray crystallography. Calculated structural, spectroscopic, QTAIM, NBO and NCI analysis results obtained from density functional theory (DFT) calculations give a full description of the putative agostic intermediate [PdCl(1-tetralone oxime)] (1) which is shown to include a previously unrecognised π-electron density donation from the aromatic ring to the metal in close proximity to the agostic carbon atom. Changing the (N)-OH donor to (N)-OMe does not effect the magnitude of these interactions.

A Rapid Extraction Method for mammalian cell cultures, suitable for quantitative immunoblotting analysis of proteins, including phosphorylated GCN2 and eIF2α.

Many studies require the detection and relative quantitation of proteins from cell culture samples using immunoblotting. Limiting factors are the cost of protease inhibitors, the time required to break cells and generate samples, as well as the high risk of protein loss during cell breakage procedures. In addition, a common problem is the viscosity of lysed samples due to the released genomic DNA.

So much for the city: Urban-rural song variation in a widespread Asiatic songbird.

Song plays a fundamental role in intraspecific communication in songbirds. The temporal and structural components of songs can vary in different habitats. These include urban habitats where anthropogenic sounds and alteration of habitat structure can significantly affect songbird vocal behavior.

Complete Genome Sequences of Cluster A Mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih.

Seven mycobacteriophages from distinct geographical locations were isolated, using mc155 as the host, and then purified and sequenced. All of the genomes are related to cluster A mycobacteriophages, BobSwaget and Lokk in subcluster A2; Fred313, KADY, Stagni, and StepMih in subcluster A3; and MyraDee in subcluster A18, the first phage to be assigned to that subcluster.

Genome-wide profiling of transcribed enhancers during macrophage activation.

Background: Macrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression.

Species identity and depth predict bleaching severity in reef-building corals: shall the deep inherit the reef?

Mass bleaching associated with unusually high sea temperatures represents one of the greatest threats to corals and coral reef ecosystems. Deeper reef areas are hypothesized as potential refugia, but the susceptibility of Scleractinian species over depth has not been quantified. During the most severe bleaching event on record, we found up to 83% of coral cover severely affected on Maldivian reefs at a depth of 3-5 m, but significantly reduced effects at 24-30 m.

Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri.

Transposon mutagenesis is a method that allows gene disruption via the random genomic insertion of a piece of DNA called a transposon. The protocol below outlines a method for high efficiency transfer between bacterial strains of a plasmid harboring a transposon containing a kanamycin resistance marker. The plasmid-borne transposase is encoded by a variant tnp gene that inserts the transposon into the genome of the recipient strain with very low insertional bias.

Male cooperation for breeding opportunities contributes to the evolution of multilevel societies.

A small number of primate species including snub-nosed monkeys (colobines), geladas (papionins) and humans live in multilevel societies (MLSs), in which multiple one-male polygamous units (OMUs) coexist to form a band, and non-breeding males associate in bachelor groups. Phylogenetic reconstructions indicate that the papionin MLS appears to have evolved through internal fissioning of large mixed-sex groups, whereas the colobine MLS evolved through the aggregation of small, isolated OMUs. However, how agonistic males maintain tolerance under intensive competition over limited breeding opportunities remains unclear.

A New First Break Picking for Three-Component VSP Data Using Gesture Sensor and Polarization Analysis.

A new first break picking for three-component (3C) vertical seismic profiling (VSP) data is proposed to improve the estimation accuracy of first arrivals, which adopts gesture detection calibration and polarization analysis based on the eigenvalue of the covariance matrix. This study aims at addressing the problem that calibration is required for VSP data using the azimuth and dip angle of geophones, due to the direction of geophones being random when applied in a borehole, which will further lead to the first break picking possibly being unreliable. Initially, a gesture-measuring module is integrated in the seismometer to rapidly obtain high-precision gesture data (including azimuth and dip angle information).

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer.

Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding.

On the Calculation of Acyl Chain Order Parameters from Lipid Simulations.

For molecular dynamics simulations of biological membrane systems to live up to the potential of providing accurate atomic level detail into membrane properties and functions, it is essential that the force fields used to model such systems are as accurate as possible. One membrane property that is often used to assess force field accuracy is the carbon-hydrogen (or carbon-deuterium) order parameters of the lipid tails, which can be accurately measured using experimental NMR techniques. There are a variety of analysis tools available to calculate these order parameters from simulations and it is essential that these computational tools work correctly to ensure the accurate assessment of the simulation force fields.

Residency and movement patterns of an apex predatory shark (Galeocerdo cuvier) at the Galapagos Marine Reserve.

The potential effectiveness of marine protected areas (MPAs) as a conservation tool for large sharks has been questioned due to the limited spatial extent of most MPAs in contrast to the complex life history and high mobility of many sharks. Here we evaluated the movement dynamics of a highly migratory apex predatory shark (tiger shark Galeocerdo cuvier) at the Galapagos Marine Reserve (GMR). Using data from satellite tracking passive acoustic telemetry, and stereo baited remote underwater video, we estimated residency, activity spaces, site fidelity, distributional abundances and migration patterns from the GMR and in relation to nesting beaches of green sea turtles (Chelonia mydas), a seasonally abundant and predictable prey source for large tiger sharks.

Nematode grazing promotes bacterial community dynamics in soil at the aggregate level.

Nematode predation has important roles in determining bacterial community composition and dynamics, but the extent of the effects remains largely rudimentary, particularly in natural environment settings. Here, we investigated the complex microbial-microfaunal interactions in the rhizosphere of maize grown in red soils, which were derived from four long-term fertilization regimes. Root-free rhizosphere soil samples were separated into three aggregate fractions whereby the abundance and community composition were examined for nematode and total bacterial communities.