Silage review: Factors affecting dry matter and quality losses in silages.

An overview was made of dry matter (DM) and quality losses that occur during the ensiling process from the field through the feeding phase. The aim was to review the relevant published literature of the last 15 yr focusing on developments achieved after the publication of the book Silage Science and Technology. This review discusses the factors affecting DM and quality losses in terms of field and pre-ensiling conditions, respiration and temperature at ensiling, fermentation patterns, methods of covering and weighting the silage cover, and management of aerobic deterioration. The possibility of reducing DM and quality losses during the ensiling process requires knowledge of how to measure losses on farm and establish the status of the silage during the feed-out phase, implementing the most effective management practices to avoid air exposure during conservation and reduce silage aerobic deterioration during feeding. The paper concludes with future perspectives and recommended management practices to reduce losses and increase efficiency over the whole ensiling process in view of increasing sustainability of the livestock production chain.

mTORC2/AKT/HSF1/HuR constitute a feed-forward loop regulating Rictor expression and tumor growth in glioblastoma.

Overexpression of Rictor has been demonstrated to result in increased mechanistic target of rapamycin C2 (mTORC2) nucleation and activity leading to tumor growth and increased invasive characteristics in glioblastoma multiforme (GBM). However, the mechanisms regulating Rictor expression in these tumors is not clearly understood. In this report, we demonstrate that Rictor is regulated at the level of mRNA translation via heat-shock transcription factor 1 (HSF1)-induced HuR activity. HuR is shown to directly bind the 3' untranslated region of the Rictor transcript and enhance translational efficiency. Moreover, we demonstrate that mTORC2/AKT signaling activates HSF1 resulting in a feed-forward cascade in which continued mTORC2 activity is able to drive Rictor expression. RNAi-mediated blockade of AKT, HSF1 or HuR is sufficient to downregulate Rictor and inhibit GBM growth and invasive characteristics in vitro and suppress xenograft growth in mice. Modulation of AKT or HSF1 activity via the ectopic expression of mutant alleles support the ability of AKT to activate HSF1 and demonstrate continued HSF1/HuR/Rictor signaling in the context of AKT knockdown. We further show that constitutive overexpression of HuR is able to maintain Rictor expression under conditions of AKT or HSF1 loss. The expression of these components is also examined in patient GBM samples and correlative associations between the relative expression of these factors support the presence of these signaling relationships in GBM. These data support a role for a feed-forward loop mechanism by which mTORC2 activity stimulates Rictor translational efficiency via an AKT/HSF1/HuR signaling cascade resulting in enhanced mTORC2 activity in these tumors.

Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material.

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

Therapeutic potential of targeting IRES-dependent c-myc translation in multiple myeloma cells during ER stress.

Protein translation is inhibited by the unfolded protein response (UPR)-induced eIF-2α phosphorylation to protect against endoplasmic reticulum (ER) stress. In addition, we found additional inhibition of protein translation owing to diminished mTORC1 (mammalian target of rapamycin complex1) activity in ER-stressed multiple myeloma (MM) cells. However, c-myc protein levels and myc translation was maintained. To ascertain how c-myc was maintained, we studied myc IRES (internal ribosome entry site) function, which does not require mTORC1 activity. Myc IRES activity was upregulated in MM cells during ER stress induced by thapsigargin, tunicamycin or the myeloma therapeutic bortezomib. IRES activity was dependent on upstream MAPK (mitogen-activated protein kinase) and MNK1 (MAPK-interacting serine/threonine kinase 1) signaling. A screen identified hnRNP A1 (A1) and RPS25 as IRES-binding trans-acting factors required for ER stress-activated activity. A1 associated with RPS25 during ER stress and this was prevented by an MNK inhibitor. In a proof of principle, we identified a compound that prevented binding of A1 to the myc IRES and specifically inhibited myc IRES activity in MM cells. This compound, when used alone, was not cytotoxic nor did it inhibit myc translation or protein expression. However, when combined with ER stress inducers, especially bortezomib, a remarkable synergistic cytotoxicity ensued with associated inhibition of myc translation and expression. These results underscore the potential for targeting A1-mediated myc IRES activity in MM cells during ER stress.

Age and growth of the tiger shark Galeocerdo cuvier off the east coast of Australia.

Total lengths (L(T)) at age and growth rates for south-west Pacific Galeocerdo cuvier were estimated from vertebral growth-band counts of 202 sagitally sectioned centra from 112 females (71-430 cm L(T)), 79 males (72-351 cm L(T)) and 11 of unknown sex. Captive growth data were also examined to complement vertebral age estimations. The sexes combined modelled growth coefficient (k = 0.08) was smaller than previously reported for G. cuvier populations elsewhere. Split-band and narrow banding patterns were identified as potential sources of age underestimation in this species.

Evidence-informed healthcare through integration of health research.

A foundational element of modern healthcare is an evidence-based practice. However, the conduct of research to generate evidence and the subsequent application of research findings are viewed by many Canadian healthcare organizations as separate from healthcare delivery. This mindset impedes effective translation of knowledge into practice. In this article, underlying issues that enable this disintegrated model to persist are described, and strategies to help healthcare organizations achieve integration of research are summarized.

Microbial water quality communication: public and practitioner insights from British Columbia, Canada.

This work examines the communication interactions of water suppliers and health authorities with the general public regarding microbial source water quality for recreational and drinking water. We compare current approaches to risk communication observable in British Columbia (BC), Canada, with best practices derived from the communications literature, finding significant gaps between theory and practice. By considering public views and government practices together, we identify key disconnects, leading to the conclusion that at present, neither the public's needs nor public health officials' goals are being met. We find: (1) there is a general lack of awareness and poor understanding by the public of microbial threats to water and the associated health implications; (2) the public often does not know where to find water quality information; (3) public information needs are not identified or met; (4) information sharing by authorities is predominantly one-way and reactive (crisis-oriented); and (5) the effectiveness of communications is not evaluated. There is a need for both improved public understanding of water quality-related risks, and new approaches to ensure information related to water quality reaches audiences. Overall, greater attention should be given to planning and goal setting related to microbial water risk communication.

High-visibility two-photon interference of frequency-time entangled photons generated in a quasi-phase-matched AlGaAs waveguide.

We demonstrate experimentally the frequency-time entanglement of photon pairs produced in a CW-pumped quasi-phased-matched AlGaAs superlattice waveguide. A visibility of 96.0±0.7% without background subtraction has been achieved, which corresponds to the violation of the Bell inequality by 52 standard deviations.

Niche differentiation of ammonia-oxidising archaea (AOA) and bacteria (AOB) in response to paper and pulp mill effluent.

Sediment organic loading has been shown to affect estuarine nitrification and denitrification, resulting in changes to sediment biogeochemistry and nutrient fluxes detrimental to estuarine health. This study examined the effects of organic loading on nutrient fluxes and microbial communities in sediments receiving effluent from a paper and pulp mill (PPM) by applying microcosm studies and molecular microbial ecology techniques. Three sites near the PPM outfall were compared to three control sites, one upstream and two downstream of the outfall. The control sites showed coupled nitrification-denitrification with minimal ammonia release from the sediment. In contrast, the impacted sites were characterised by nitrate uptake and substantial ammonia efflux from the sediments, consistent with a decoupling of nitrification and denitrification. Analysis of gene diversity demonstrated that the composition of nitrifier communities was not significantly different at the impacted sites compared to the control sites; however, analysis of gene abundance indicated that whilst there was no difference in total bacteria, total archaea or ammonia-oxidising archaea (AOA) abundance between the control and impacted sites, there was a significant reduction in ammonia-oxidising bacteria (AOB) at the impacted sites. The results of this study demonstrate an effect of organic loading on estuarine sediment biogeochemistry and highlight an apparent niche differentiation between AOA and AOB.

Active polarisation control of a quantum cascade laser using tuneable birefringence in waveguides.

We discuss the design, modelling, fabrication and characterisation of an integrated tuneable birefringent waveguide for quantum cascade lasers. We have fabricated quantum cascade lasers operating at wavelengths around 4450 nm that include polarisation mode converters and a differential phase shift section. We employed below laser threshold electroluminescence to investigate the single pass operation of the integrated device. We use a theory based on the electro-optic properties of birefringence in quantum cascade laser waveguides combined with a Jones matrix based description to gain an understanding of the electroluminescence results. With the quantum cascade lasers operating above threshold we demonstrated polarisation control of the output.

DNA-DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIe, IIh and IIi, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov.

The taxonomic classification of 182 phenotypically similar isolates was evaluated using DNA-DNA hybridization and 16S rRNA gene sequence analysis. These bacterial isolates were mainly derived from clinical sources; all were Gram-negative non-fermenters and most were indole-producing. Phenotypically, they resembled species from the genera Chryseobacterium, Elizabethkingia or Empedobacter or belonged to CDC groups IIc, IIe, IIh and IIi. Based on these analyses, four novel species are described: Chryseobacterium bernardetii sp. nov. (type strain NCTC 13530(T) = CCUG 60564(T) = CDC G229(T)), Chryseobacterium carnis sp. nov. (type strain NCTC 13525(T) = CCUG 60559(T) = CDC G81(T)), Chryseobacterium lactis sp. nov. (type strain NCTC 11390(T) = CCUG 60566(T) = CDC KC1864(T)) and Chryseobacterium nakagawai sp. nov. (type strain NCTC 13529(T) = CCUG 60563(T) = CDC G41(T)). The new combination Chryseobacterium taklimakanense comb. nov. (type strain NCTC 13490(T) = X-65(T) = CCTCC AB 208154(T) = NRRL B-51322(T)) is also proposed to accommodate the reclassified Planobacterium taklimakanense.

Quantum cascade lasers with an integrated polarization mode converter.

We discuss the design, fabrication and characterization of waveguide polarization mode converters for quantum cascade lasers operating at 4.6 µm. We have fabricated a quantum cascade laser with integrated polarization mode converter that emits light of 69% Transverse Electrical (TE) polarization from one facet and 100% Transverse Magnetic (TM) polarization from the other facet.

A semiconductor laser with monolithically integrated dynamic polarization control.

We report the first demonstration of a semiconductor laser monolithically integrated with an active polarization controller, which consists of a polarization mode converter followed by an active, differential phase shifter. High speed modulation of the device output polarization is demonstrated via current injection to the phase shifter section.

Exploring the effect of different plant lignin content and composition on ionic liquid pretreatment efficiency and enzymatic saccharification of Eucalyptus globulus L. mutants.

There are several approaches being investigated to improve the efficiency of biomass conversion into fermentable sugars, including those that engineer the feedstocks to enhance digestibility. In this study it was evaluated the impact of genotype modifications of three mutants of Eucalyptus globulus L., and of the corresponding wild type on cellulose hydrolyzability before and after ionic liquid (IL) pretreatment. Both untreated and IL-treated samples were chemically characterized and tested for cellulose hydrolizability. Results obtained indicate that genetic modifications altered wood lignin-S/G ratio. This alteration resulted in a different hydrolyzability of cellulose for untreated samples, i.e. high lignin-S/G ratio produced low glucose yield (r=-0.97; P<0.03; n=4), but did not affect glucose yield after IL pretreatment. IL pretreated samples had increased glucose yields compared to that of untreated samples due to the modification of microcrystalline cellulose I to mixtures of more hydrolysable cellulose II and amorphous cellulose, and to the partial removal of the steric impediment, or removal of the lignin "sheath" protecting cellulose, to enzymes. The efficiency of the IL pretreatment used in this study does not appear to be affected by the S/G content of the E. globulus.

A review of the application of molecular genetics for fisheries management and conservation of sharks and rays.

Since the first investigation 25 years ago, the application of genetic tools to address ecological and evolutionary questions in elasmobranch studies has greatly expanded. Major developments in genetic theory as well as in the availability, cost effectiveness and resolution of genetic markers were instrumental for particularly rapid progress over the last 10 years. Genetic studies of elasmobranchs are of direct importance and have application to fisheries management and conservation issues such as the definition of management units and identification of species from fins. In the future, increased application of the most recent and emerging technologies will enable accelerated genetic data production and the development of new markers at reduced costs, paving the way for a paradigm shift from gene to genome-scale research, and more focus on adaptive rather than just neutral variation. Current literature is reviewed in six fields of elasmobranch molecular genetics relevant to fisheries and conservation management (species identification, phylogeography, philopatry, genetic effective population size, molecular evolutionary rate and emerging methods). Where possible, examples from the Indo-Pacific region, which has been underrepresented in previous reviews, are emphasized within a global perspective.

The TDR Tuberculosis Strain Bank: a resource for basic science, tool development and diagnostic services.

BACKGROUND: The Special Programme for Research and Training in Tropical Diseases recently launched a Mycobacterium tuberculosis strain bank (TDR-TB Strain Bank). OBJECTIVE: To describe the TDR-TB Strain Bank, the characterisation of strains, bank management and the procedure for releasing materials. RESULTS: The TDR-TB Strain Bank consists of 229 clinical M. tuberculosis isolates (single-colony derived cultures) plus five mycobacterial reference strains for purposes of identification. These are available as freeze-dried, viable strains or as heat-inactivated bacterial suspensions, quality controlled for purity, viability and authenticity. Isolates originated from diverse geographical settings and were selected for their resistance profiles against first- and second-line drugs. Low and high levels of resistance were determined by the minimum inhibitory concentrations of isoniazid, rifampicin, ethambutol, streptomycin, ofloxacin, kanamycin, capreomycin, ethionamide and para-aminosalicylic acid. Sequencing for drug resistance mutations was performed on the relevant sections of the rpoB, katG, inhA, embB, rpsL, rrs, gyrA and gyrB genes. Typing using lineage-defining loci of mycobacterial interspersed repetitive unit-variable number tandem repeats indicated that the most important genetic lineages were represented. CONCLUSIONS: The TDR-TB Strain Bank is a high quality bioresource for basic science, supporting the development of new diagnostics and drug-resistant detection tools and providing reference materials for laboratory quality management programmes.

Identification and genomovar assignation of clinical strains of Pseudomonas stutzeri.

The identification of Pseudomonas stutzeri clinical isolates through conventional phenotypic methods was compared with identification through partial rpoD gene sequencing. We observed that commercial phenotypic systems easily confuse P. stutzeri with other Pseudomonas species. We also demonstrated that most of the clinical strains of P. stutzeri herein studied (79%) belonged to genomovar 1 of the species. We propose the use of partial rpoD gene sequence analysis as a complementary molecular tool for the precise routine identification and genomovar assignation of P. stutzeri clinical isolates, as well as for typing and epidemiological studies.

The contribution of breakfast cereals to the nutritional intake of the materially deprived UK population.

BACKGROUND/OBJECTIVES: Breakfast is an important source of micronutrients in the diet and its consumption has been linked to positive health outcomes. The present analysis investigated the contribution that breakfast cereals make to the nutrient intakes of the materially deprived (low income) UK population. SUBJECTS/METHODS: Data for 3728 respondents aged 2 years and over from the UK Low Income Diet and Nutrition Survey (2003-2005) were analysed. Nutrient intakes of consumers and non-consumers of breakfast cereal were compared. RESULTS: Breakfast cereals were consumed by 49% of men, 58% of women, 80% of boys and 80% of girls, and median intakes were: 35, 25, 29 and 21 g/d, respectively. Consumers of breakfast cereals had higher intakes of thiamin, riboflavin, niacin, biotin, folate, vitamin B(6), vitamin B(12), iron and zinc than non-consumers. Breakfast cereal consumption was also related to higher intakes of calcium, attributable to higher milk consumption. The intake of wholegrain and high-fibre breakfast cereals was associated with a higher intake of non-starch polysaccharides. Intakes of niacin, biotin, calcium and zinc were higher but that of vitamin B(6) was lower among consumers of exclusively wholegrain and high-fibre breakfast cereals compared with consumers of other breakfast cereals. There were no significant differences observed in intakes of non-milk extrinsic sugars according to type of breakfast cereal consumed. CONCLUSIONS: Breakfast cereals make a significant contribution to the micronutrient intake of the low-income UK population.