The population biology of the living coelacanth studied over 21 years

Between 1986 and 2009 nine submersible and remote-operated vehicle expeditions were carried out to study the population biology of the coelacanth Latimeria chalumnae in the Comoro Islands, located in the western Indian Ocean. Latimeria live in large overlapping home ranges that can be occupied for as long as 21 years. Most individuals are confined to relatively small home ranges, resting in the same caves during the day. One hundred and forty five coelacanths are individually known, and we estimate the total population size of Grande Comore as approximately 300–400 adult individuals. The local population inhabiting a census area along an 8-km section of coastline remained stable for at least 18 years. Using LASER-assisted observations, we recorded length frequencies between 100 and 200 cm total length and did not encounter smaller-bodied individuals (\100 cm total length). It appears that coelacanth recruitment in the observation areas occur mainly by immigrating adults. We estimate that the mean numbers of deaths and newcomers are 3–4 individuals per year, suggesting that longevity may exceed 100 years. The domestic fishery represents a threat to the long-term survival of coelacanths in the study area. Recent changes in the local fishery include a decrease in the abundance of the un-motorized canoes associated with exploitation of coelacanths and an increase in motorized canoes. Exploitation rates have fallen in recent years, and by 2000, had fallen to lowest ever reported. Finally, future fishery developments are discussed

Transfer RNA-derived small RNAs in the cancer transcriptome

The cellular lifetime includes stages such as differentiation, proliferation, division, senescence and apoptosis.These stages are driven by a strictly ordered process of transcription dynamics. Molecular disruption to RNA polymerase assembly, chromatin remodelling and transcription factor binding through to RNA editing, splicing, post-transcriptional regulation and ribosome scanning can result in significant costs arising from genome instability. Cancer development is one example of when such disruption takes place. RNA silencing is a term used to describe the effects of post-transcriptional gene silencing mediated by a diverse set of small RNA molecules. Small RNAs are crucial for regulating gene expression and microguarding genome integrity.RNA silencing studies predominantly focus on small RNAs such as microRNAs, short-interfering RNAs and piwi-interacting RNAs. We describe an emerging renewal of inter-est in a‘larger’small RNA, the transfer RNA (tRNA).Precisely generated tRNA-derived small RNAs, named tRNA halves (tiRNAs) and tRNA fragments (tRFs), have been reported to be abundant with dysregulation associated with cancer. Transfection of tiRNAs inhibits protein translation by displacing eukaryotic initiation factors from messenger RNA (mRNA) and inaugurating stress granule formation.Knockdown of an overexpressed tRF inhibits cancer cell proliferation. Recovery of lacking tRFs prevents cancer metastasis. The dual oncogenic and tumour-suppressive role is typical of functional small RNAs. We review recent reports on tiRNA and tRF discovery and biogenesis, identification and analysis from next-generation sequencing data and a mechanistic animal study to demonstrate their physiological role in cancer biology. We propose tRNA-derived small RNA-mediated RNA silencing is an innate defence mechanism to prevent oncogenic translation. We expect that cancer cells are percipient to their ablated control of transcription and attempt to prevent loss of genome control through RNA silencing

A hybrid radiation detector for simultaneous spatial and temporal dosimetry

In this feasibility study an organic plastic scintillator is calibrated against ionisation chamber measurements and then embedded in a polymer gel dosimeter to obtain a quasi-4D experimental measurement of a radiation field. This hybrid dosimeter was irradiated with a linear accelerator, with temporal measurements of the dose rate being acquired by the scintillator and spatial measurements acquired with the gel dosimeter. The detectors employed in this work are radiologically equivalent; and we show that neither detector perturbs the intensity of the radiation field of the other. By employing these detectors in concert, spatial and temporal variations in the radiation intensity can now be detected and gel dosimeters can be calibrated for absolute dose from a single irradiation

Evaluation of two dairy herd reproductive performance indicators that are adjusted for voluntary waiting period

<p>Abstract</p> <p>Background</p> <p>Overall reproductive performance of dairy herds is monitored by various indicators. Most of them do not consider all eligible animals and do not consider different management strategies at farm level. This problem can be alleviated by measuring the proportion of pregnant cows by specific intervals after their calving date or after a fixed time period, such as the voluntary waiting period. The aim of this study was to evaluate two reproductive performance indicators that consider the voluntary waiting period at the herd. The two indicators were: percentage of pregnant cows in the herd after the voluntary waiting period plus 30 days (PV30) and percentage of inseminated cows in the herd after the voluntary waiting period plus 30 days (IV30). We wanted to assess how PV30 and IV30 perform in a simulation of herds with different reproductive management and physiology and to compare them to indicators of reproductive performance that do not consider the herd voluntary waiting period.</p> <p>Methods</p> <p>To evaluate the reproductive indicators we used the SimHerd-program, a stochastic simulation model, and 18 scenarios were simulated. The scenarios were designed by altering the reproductive management efficiency and the status of reproductive physiology of the herd. Logistic regression models, together with receiver operating characteristics (ROC), were used to examine how well the reproductive performance indicators could discriminate between herds of different levels of reproductive management efficiency or reproductive physiology.</p> <p>Results</p> <p>The logistic regression models with the ROC analysis showed that IV30 was the indicator that best discriminated between different levels of management efficiency followed by PV30, calving interval, 200-days not-in calf-rate (NotIC200), in calf rate at100-days (IC100) and a fertility index. For reproductive physiology the ROC analysis showed that the fertility index was the indicator that best discriminated between different levels, followed by PV30, NotIC200, IC100 and the calving interval. IV30 could not discriminate between the two levels.</p> <p>Conclusion</p> <p>PV30 is the single best performance indicator for estimating the level of both herd management efficiency and reproductive physiology followed by NotIC200 and IC100. This indicates that PV30 could be a potential candidate for inclusion in dairy herd improvement schemes.</p

Plasmonically Enhanced Reflectance of Heat Radiation from Low-Bandgap Semiconductor Microinclusions

Increased reflectance from the inclusion of highly scattering particles at low volume fractions in an insulating dielectric offers a promising way to reduce radiative thermal losses at high temperatures. Here, we investigate plasmonic resonance driven enhanced scattering from microinclusions of low-bandgap semiconductors (InP, Si, Ge, PbS, InAs and Te) in an insulating composite to tailor its infrared reflectance for minimizing thermal losses from radiative transfer. To this end, we compute the spectral properties of the microcomposites using Monte Carlo modeling and compare them with results from Fresnel equations. The role of particle size-dependent Mie scattering and absorption efficiencies, and, scattering anisotropy are studied to identify the optimal microinclusion size and material parameters for maximizing the reflectance of the thermal radiation. For composites with Si and Ge microinclusions we obtain reflectance efficiencies of 57 - 65% for the incident blackbody radiation from sources at temperatures in the range 400 - 1600 {\deg}C. Furthermore, we observe a broadbanding of the reflectance spectra from the plasmonic resonances due to charge carriers generated from defect states within the semiconductor bandgap. Our results thus open up the possibility of developing efficient high-temperature thermal insulators through use of the low-bandgap semiconductor microinclusions in insulating dielectrics.Comment: Main article (8 Figures and 2 Tables) + Supporting Information (8 Figures

Microguards and micromessengers of the genome

The regulation of gene expression is of fundamental importance to maintain organismal function and integrity and requires a multifaceted and highly ordered sequence of events. The cyclic nature of gene expression is known as ‘transcription dynamics’. Disruption or perturbation of these dynamics can result in significant fitness costs arising from genome instability, accelerated ageing and disease. We review recent research that supports the idea that an important new role for small RNAs, particularly microRNAs (miRNAs), is in protecting the genome against short-term transcriptional fluctuations, in a process we term ‘microguarding’. An additional emerging role for miRNAs is as ‘micromessengers’—through alteration of gene expression in target cells to which they are trafficked within microvesicles. We describe the scant but emerging evidence that miRNAs can be moved between different cells, individuals and even species, to exert biologically significant responses. With these two new roles, miRNAs have the potential to protect against deleterious gene expression variation from perturbation and to themselves perturb the expression of genes in target cells. These interactions between cells will frequently be subject to conflicts of interest when they occur between unrelated cells that lack a coincidence of fitness interests. Hence, there is the potential for miRNAs to represent both a means to resolve conflicts of interest, as well as instigate them. We conclude by exploring this conflict hypothesis, by describing some of the initial evidence consistent with it and proposing new ideas for future research into this exciting topic

Disruption of mouse Slx4, a regulator of structure-specific nucleases, phenocopies Fanconi anemia

International audienc

An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection

peer-reviewedBackground Obtaining chloroplast genome sequences is important to increase the knowledge about the fundamental biology of plastids, to understand evolutionary and ecological processes in the evolution of plants, to develop biotechnological applications (e.g. plastid engineering) and to improve the efficiency of breeding schemes. Extraction of pure chloroplast DNA is required for efficient sequencing of chloroplast genomes. Unfortunately, most protocols for extracting chloroplast DNA were developed for eudicots and do not produce sufficiently pure yields for a shotgun sequencing approach of whole plastid genomes from the monocot grasses. Methodology/Principal Findings We have developed a simple and inexpensive method to obtain chloroplast DNA from grass species by modifying and extending protocols optimized for the use in eudicots. Many protocols for extracting chloroplast DNA require an ultracentrifugation step to efficiently separate chloroplast DNA from nuclear DNA. The developed method uses two more centrifugation steps than previously reported protocols and does not require an ultracentrifuge. Conclusions/Significance The described method delivered chloroplast DNA of very high quality from two grass species belonging to highly different taxonomic subfamilies within the grass family (Lolium perenne, Pooideae; Miscanthus×giganteus, Panicoideae). The DNA from Lolium perenne was used for whole chloroplast genome sequencing and detection of SNPs. The sequence is publicly available on EMBL/GenBank

Towards a quantum representation of the ampere using single electron pumps

Electron pumps generate a macroscopic electric current by controlled manipulation of single electrons. Despite intensive research towards a quantum current standard over the last 25 years, making a fast and accurate quantised electron pump has proved extremely difficult. Here we demonstrate that the accuracy of a semiconductor quantum dot pump can be dramatically improved by using specially designed gate drive waveforms. Our pump can generate a current of up to 150 pA, corresponding to almost a billion electrons per second, with an experimentally demonstrated current accuracy better than 1.2 parts per million (ppm) and strong evidence, based on fitting data to a model, that the true accuracy is approaching 0.01 ppm. This type of pump is a promising candidate for further development as a realisation of the SI base unit ampere, following a re-definition of the ampere in terms of a fixed value of the elementary charge.Comment: 8 pages, 7 figure

Smc5/6 coordinates formation and resolution of joint molecules with chromosome morphology to ensure meiotic divisions

During meiosis, Structural Maintenance of Chromosome (SMC) complexes underpin two fundamental features of meiosis: homologous recombination and chromosome segregation. While meiotic functions of the cohesin and condensin complexes have been delineated, the role of the third SMC complex, Smc5/6, remains enigmatic. Here we identify specific, essential meiotic functions for the Smc5/6 complex in homologous recombination and the regulation of cohesin. We show that Smc5/6 is enriched at centromeres and cohesin-association sites where it regulates sister-chromatid cohesion and the timely removal of cohesin from chromosomal arms, respectively. Smc5/6 also localizes to recombination hotspots, where it promotes normal formation and resolution of a subset of joint-molecule intermediates. In this regard, Smc5/6 functions independently of the major crossover pathway defined by the MutLγ complex. Furthermore, we show that Smc5/6 is required for stable chromosomal localization of the XPF-family endonuclease, Mus81-Mms4Eme1. Our data suggest that the Smc5/6 complex is required for specific recombination and chromosomal processes throughout meiosis and that in its absence, attempts at cell division with unresolved joint molecules and residual cohesin lead to severe recombination-induced meiotic catastroph