Flightin Is Necessary for Length Determination, Structural Integrity, and Large Bending Stiffness of Insect Flight Muscle Thick Filaments

Despite the fundamental role of thick filaments in muscle contraction, little is known about the mechanical behavior of these filaments and how myosin-associated proteins dictate differences between muscle types. In this study, we used atomic force microscopy to study the morphological and mechanical properties of fully hydrated native thick filaments isolated from indirect flight muscle (IFM) of normal and mutant Drosophila lacking flightin (fln⁰). IFM thick filaments from newly eclosed (0-1 h old) wild-type flies have a mean length of 3.04 ± 0.05 μm. In contrast, IFM thick filaments from newly eclosed fln⁰ flies are more variable in length and, on average, are significantly longer (3.90 ± 1.33 μm) than wild-type filaments from flies of the same age. In the absence of flightin, thick filaments can attain lengths > 300% of wild-type filaments, indicating that flightin is required for setting the proper filament length in vivo. Filaments lacking flightin are structurally compromised, and filament preparations from fully matured 3- to 5-day-old adult fln⁰ IFM yielded fragments of variable length much shorter than 3.20 ± 0.04 μm, the length obtained from wild-type flies of similar age. The persistence length, an index of bending stiffness, was calculated from measurements of filament end-to-end length and contour length. We show that the presence of flightin increases persistence length by more than 40% and that wild-type filaments increase in stiffness with age. These results indicate that flightin fulfills an essential role in defining the structural and mechanical properties of IFM thick filaments.     

The population genetics of phenotypic deterioration in experimental populations of Bacillus subtilis

Although many examples of trait loss exist in nature, the underlying population genetic mechanism responsible for the loss is usually unknown. Selective or neutral processes can result in the deterioration of a trait, and often one of these is inferred based on indirect evidence. Furthermore, selective pressures that are unique to particular environments and the effect these might have on the population genetic cause of trait loss are not well understood. Here we describe an experimental evolution system where two different environments were used for addressing the population genetic cause of trait loss throughout evolutionary time. We found that growth in minimal medium (i.e., prototrophy) was lost in all populations regardless of the experimental environment and that the pattern of trait loss in one environment was due to selection, whereas in the other environment the cause remains inconclusive.     

Acute tryptophan depletion does not improve endurance cycling capacity in a warm environment

Newsholme’s theory of central fatigue suggests that acute tryptophan depletion should improve endurance exercise capacity in a warm environment by reducing serotonergic activity in the brain. Eight males cycled to volitional exhaustion at 55 % $ \dot{V}{\rm O}_{2} $ peak in 30.1 ± 0.5 °C and 30 ± 7 % relative humidity on two separate occasions, after consuming either an amino acid load to deplete their circulating tryptophan concentration (TD), or a control amino acid load (CON). Blood samples were taken before ingesting the amino acids, before the start of exercise, every 15 min during exercise and at the point of exhaustion. Heart rate (HR), core (Tc) and skin (Tsk) temperatures and ratings of perceived exertion (RPE) and thermal comfort (TC) were also monitored every 10 min during exercise. Plasma tryptophan (P = 0.003) and free tryptophan (P < 0.001) concentrations, and the free tryptophan to branched-chain amino acid ratio (P = 0.004) were all lower on the TD trial than on the CON trial. There was no difference in endurance exercise capacity (TD 99.2 ± 24.4 min as compared to CON 108.4 ± 21.6 min; P = 0.088). There was a tendency for HR (P = 0.053) and Tc (P = 0.069) to be higher on the TD trials. There were no differences for any of the other parameters. Endurance cycling capacity in a warm environment is not improved by acute tryptophan depletion, suggesting tryptophan availability is not a significant factor in the development of fatigue in such situations.     

Analysis of the Cystic Fibrosis Lung Microbiota via Serial Illumina Sequencing of Bacterial 16S rRNA Hypervariable Regions

The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq): a method for deep sequencing of the bacterial 16S rRNA gene using next-generation sequencing technology. SI-Seq serially sequences portions of the V5, V6 and V7 hypervariable regions from barcoded 16S rRNA amplicons using an Illumina short-read genome analyzer. SI-Seq obtains taxonomic resolution similar to 454 pyrosequencing for a fraction of the cost, and can produce hundreds of thousands of reads per sample even with very high multiplexing. We validated SI-Seq using single species and mock community controls, and via a comparison to cystic fibrosis lung microbiota sequenced using 454 FLX Titanium. Our control runs show that SI-Seq has a dynamic range of at least five orders of magnitude, can classify >96% of sequences to the genus level, and performs just as well as 454 and paired-end Illumina methods in estimation of standard microbial ecology diversity measurements. We illustrate the utility of SI-Seq in a pilot sample of central airway secretion samples from cystic fibrosis patients.     

Modeling spatial and dynamic variation in growth,yield, and yield stability of the bioenergy crops Miscanthus × giganteus and Panicum virgatum across the conterminous United States

C₄ perennial grasses are being considered as environmentally and economically sustainable high yielding bioenergy feedstocks. Temporal and spatial variation in yield across the conterminious United States is uncertain due to the limited number of field trials. Here, we use a semi‐mechanistic dynamic crop growth and production model to explore the potential of Miscanthus × giganteus (Greef et. Deu.) and Panicum virgatum L. across the conterminous United States. By running the model for 32 years (1979–2010), we were able to estimate dry biomass production and stability. The maximum rainfed simulated end‐of‐growth‐season harvestable biomass for M. × giganteus was ca. 40 Mg ha^?1 and ca. 20 Mg ha^?1 for P. virgatum. In addition, regions of the southeastern United States were identified as promising due to their high potential production and stability and their relative advantage when compared with county‐level maize biomass production. Regional and temporal variation was most strongly influenced by precipitation and soil water holding capacity. Miscanthus × giganteus was on average 2.2 times more productive than P. virgatum for locations where yields were ≥10 Mg ha^?1. The predictive ability of the model for P. virgatum was tested with 30 previously published studies covering the eastern half of the United States and resulted in an index of agreement of 0.71 and a mean bias of only ?0.62 Mg ha^?1 showing that, on average, the model tended to only slightly overestimate productivity. This study provides with potential production and variability which can be used for regional assessment of the suitability of dedicated bioenergy crops.     

Intact p53-Dependent Responses in miR-34-Deficient Mice

MicroRNAs belonging to the miR-34 family have been proposed as critical modulators of the p53 pathway and potential tumor suppressors in human cancers. To formally test these hypotheses, we have generated mice carrying targeted deletion of all three members of this microRNA family. We show that complete inactivation of miR-34 function is compatible with normal development in mice. Surprisingly, p53 function appears to be intact in miR-34-deficient cells and tissues. Although loss of miR-34 expression leads to a slight increase in cellular proliferation in vitro, it does not impair p53-induced cell cycle arrest or apoptosis. Furthermore, in contrast to p53-deficient mice, miR-34-deficient animals do not display increased susceptibility to spontaneous, irradiation-induced, or c-Myc-initiated tumorigenesis. We also show that expression of members of the miR-34 family is particularly high in the testes, lungs, and brains of mice and that it is largely p53-independent in these tissues. These findings indicate that miR-34 plays a redundant function in the p53 pathway and suggest additional p53-independent functions for this family of miRNAs.     

Phosphotyrosine recognition domains: the typical, the atypical and the versatile

Infertility affects one in seven couples globally and has recently been classified as a disease by the World Health Organisation (WHO). While in-vitro fertilisation (IVF) offers effective treatment for many infertile couples, cases exhibiting severe male infertility (19?C57%) often remain difficult, if not impossible to treat. In such cases, intracytoplasmic sperm injection (ICSI), a technique in which a single sperm is microinjected into the oocyte, is implemented. However, 1?C5% of ICSI cycles still fail to fertilise, affecting over 1000 couples per year in the UK alone. Pregnancy and delivery rates for IVF and ICSI rarely exceed 30% and 23% respectively. It is therefore imperative that Assisted Reproductive Technology (ART) protocols are constantly modified by associated research programmes, in order to provide patients with the best chances of conception. Prior to fertilisation, mature oocytes are arrested in the metaphase stage of the second meiotic division (MII), which must be alleviated to allow the cell cycle, and subsequent embryogenesis, to proceed. Alleviation occurs through a series of concurrent events, collectively termed ??oocyte activation??. In mammals, oocytes are activated by a series of intracellular calcium (Ca²⁺) oscillations following gamete fusion. Recent evidence implicates a sperm-specific phospholipase C, PLCzeta (PLC??), introduced into the oocyte following membrane fusion as the factor responsible. This review summarises our current understanding of oocyte activation failure in human males, and describes recent advances in our knowledge linking certain cases of male infertility with defects in PLC?? expression and activity. Systematic literature searches were performed using PubMed and the ISI-Web of Knowledge. Databases compiled by the United Nations and World Health Organisation databases (UNWHO), and the Human Fertilization and Embryology Authority (HFEA) were also scrutinised. It is clear that PLC?? plays a fundamental role in the activation of mammalian oocytes, and that genetic, molecular, or biochemical perturbation of this key enzyme is strongly linked to human infertility where oocyte activation is deficient. Consequently, there is significant scope for our understanding of PLC?? to be translated to the ART clinic, both as a novel therapeutic agent with which to rescue oocyte activation deficiency (OAD), or as a prognostic/diagnostic biomarker of oocyte activation ability in target sperm samples.     

Evolution of the NANOG pseudogene family in the human and chimpanzee genomes

Background  

The NANOG gene is expressed in mammalian embryonic stem cells where it maintains cellular pluripotency. An unusually large family of pseudogenes arose from it with one unprocessed and ten processed pseudogenes in the human genome. This article compares the NANOG gene and its pseudogenes in the human and chimpanzee genomes and derives an evolutionary history of this pseudogene family.