Ruminant Salivary Microbes: Passenger or Player in the Rumen?

Sampling of ruminant saliva has gained interest as a non-invasive proxy for exploring the structure of the rumen microbiome. However, the subsequent data analysis assumes that bacteria originating from the oral cavity are merely passengers in the rumen and play no active role. In this study, it was hypothesised that metabolically active oral bacteria present in the salivary microbiome play a role in the ruminal degradation of plant material. In vitro cultivation-based enumeration confirmed that the ruminant oral cavity harbours a significant number of anaerobic and cellulolytic bacteria that are metabolically active under ruminal conditions. Bacterial 16S rRNA gene profiling of in vitro enrichments also confirmed that oral-derived bacteria were capable of colonising plant material. Preliminary analysis of the colonising bacteria indicated that bacteria belonging to the genus Streptococcus were of particular interest. In conclusion, the findings of the current study clearly indicate that bolus-associated bacteria have the potential to play a metabolically active role in terms of ruminal colonisation and the degradation of plant material. This evidence confirms the merit of the hypothesis that the metabolically active oral bacteria present in the salivary microbiome may play a role in the ruminal degradation of plant material.

Anaerobic fermentation results in loss of viability of Fasciola hepatica metacercariae in grass silage.

The parasitic liver fluke, Fasciola hepatica, has a detrimental impact on food security and poses a welfare concern to ruminant livestock. F. hepatica metacercariae, shed from an intermediate mud snail host, encyst on vegetation and present a source of infection to grazing livestock. Feeding grass silage to ruminants is a common practice, however the role it plays in the transmission of F. hepatica remains largely unknown. Our current understanding relies on historical studies that are not representative of current silage production and did not apply molecular methods to detect F. hepatica DNA persistence within silages. This study determined the impact of specific fermentation factors, including grass dry matter (DM) content (20, 30 & 40 %), length of ensiling period and maintaining an anaerobic environment on F. hepatica metacercariae viability. In vitro excystment assays demonstrated that regardless of grass DM content, metacercariae ensiled under anaerobic conditions were not viable from two weeks post-sealing. Metacercariae recovered from ensiled grass of 20 % DM content subjected to aerobic spoilage, remained viable for up to 10 weeks. DNA of F. hepatica remained detectable for up to 10 weeks in both anaerobic and spoiled silages. This study highlights i) the importance of maintaining an anaerobic ensiling environment to eliminate the risk of F. hepatica transmission from silage and ii) an inverse relationship between grass DM content and duration of metacercariae survival within spoiled silages. Improving our understanding of trematode metacercariae survival rates within silages, especially of highly pathogenic species such as F. hepatica, allows farmers to make informed decisions regarding on-farm parasite control.

The Effect of Ensiling on the Nutritional Composition and Fermentation Characteristics of Brown Seaweeds as a Ruminant Feed Ingredient.

Ensiling could be an effective method to preserve seaweeds for animal feed applications, however, there is limited scientific knowledge in this area. Seaweeds are a promising ruminant feed ingredient, in part due to the content of phenolic compounds, which are receiving considerable interest as alternative antimicrobial agents in feed. The aim of the study was to compare the effect of ensiling on the nutritional composition and fermentation characteristics of two brown seaweed species, Fucus vesiculosus (FV) and Saccharina latissimi (SL) with or without the use of a Lactobacillus plantarum (LAB) inoculant. The effect of ensiling on the stability of phlorotannin was also investigated using nuclear magnetic resonance (NMR). After harvesting, the seaweeds were wilted for 24 h and subsequently ensiled in laboratory-scaled silos for 90 days. SL silage showed a stronger fermentation pattern (pH < 4), dominated by lactic acid (50-60 g/kg Dry Matter (DM)), and a slightly higher acetic acid content compared to FV silages (p < 0.05). The fermentability of FV was limited (pH > 4.8) with low lactic acid production (<5 g/kg DM). The addition of the LAB inoculant showed no effect on the fermentation process but a modest effect on the chemical composition of both species was observed after the 90-day ensiling period. The results showed no losses in the nutrient content of FV after ensiling, however losses in the Crude Protein (CP, -32%), ash (-36%), Neutral Detergent Fibre (NDF, -77%) and Acid Detergent Fibre (ADF, -58%) content of SL were observed. The ensiling process had a limited effect on the in vitro true dry matter digestibility and phenolic content of either species. Therefore, ensilage may be a suitable preservation method for the use of brown seaweeds as a ruminant feed; however, species-specific differences were observed.

Application of monoclonal antibodies in quantifying fungal growth dynamics during aerobic spoilage of silage.

Proliferation of filamentous fungi following ingress of oxygen to silage is an important cause of dry matter losses, resulting in significant waste. In addition, the production of mycotoxins by some filamentous fungi poses a risk to animal health through mycotoxicosis. Quantitative assessment of fungal growth in silage, through measurement of ergosterol content, colony-forming units or temperature increase is limiting in representing fungal growth dynamics during aerobic spoilage due to being deficient in either representing fungal biomass or being able to identify specific genera. Here, we conducted a controlled environment aerobic exposure experiment to test the efficacy of a monoclonal antibody-based enzyme-linked immunosorbent assay (ELISA) to detect the proliferation of fungal biomass in six silage samples. We compared this to temperature which has been traditionally deployed in such experiments and on-farm to detect aerobic deterioration. In addition, we quantified ergosterol, a second marker of fungal biomass. After 8 days post-aerobic exposure, the ergosterol and ELISA methods indicated an increase in fungal biomass in one of the samples with a temperature increase observed after 16 days. A comparison of the methods with Pearson's correlation coefficient showed a positive association between temperature and ergosterol and both markers of fungal biomass. This work indicates that the technology has potential to be used as an indicator of microbial degradation in preserved forage. Consequently, if it developed as an on-farm technique, this could inform forage management decisions made by farmers, with the goal of decreasing dry matter losses, improving resource and nutrient efficiency and reducing risks to animal health.

Assessing the ability of silage lactic acid bacteria to incorporate and transform inorganic selenium within laboratory scale silos.

Selenium (Se) is a non-metallic trace element essential for normal cellular function, which has been linked with reduced risk of cancer, cardiovascular disease, cognitive decline and thyroid disease in humans. Se deficiency in livestock is associated with white muscle disease, retained placenta, ill-thrift and mastitis. Where Se status or bioavailability from the soil for plants is poor, livestock rely on supplemental Se in their diets predominantly as either sodium selenite (inorganic form) or selenised-yeast (organic form). As lactic acid bacteria (LAB) have been shown to incorporate Se as either organic or elemental (Nano-Se) there may be potential to use silage inoculant bacteria to improve the Se status of feed to provide the Se requirements of livestock. We screened twenty-seven LAB in MRS broth in the presence of sodium selenite for growth and uptake of Se as organic (selenocysteine and selenomethionine), inorganic (selenite and selenate) or/and Nano-Se, with the aim to identify potential candidates for a mini-silo study. Sodium selenite addition into the growth medium of LAB reduced growth rates but also resulted in the conversion of the inorganic sodium selenite into predominately Nano-Se and small quantities of organic-Se. Based on a rank analysis of growth and ability to take up (total Se content) and convert inorganic Se (Nano and organic Se content), three LAB were selected for further investigation as silage inoculants: L. brevis DSMZ (A), L. plantarum LF1 (B), and L. plantarum SSL MC15 (C). Each LAB was used as an inoculant within a grass mini-silo trial, either cultured in the presence of sodium selenite before inoculation or sodium selenite added to the inoculum at inoculation versus controls with no Se. The addition of sodium selenite either into the growth media of LAB or applied at inoculation of grass silage did not interfere with the ability of the LAB to act as a silage inoculant with no difference in silage fermentation characteristic between LAB with no Se added. The addition of sodium selenite either to the LAB growth medium or at inoculation resulted in the conversion of sodium selenite into Nano-Se and organic-Se (Nano-Se, ca. 103 higher than organic), as previously shown in the screening trial. There was no difference between the three LAB for incorporation of Se or in silage quality, indicating the potential to develop silage inoculants to increase the bioavailable form of Se (elemental and organic) to livestock through conversion of inorganic forms during ensiling.

A review of our current understanding of parasite survival in silage and stored forages, with a focus on Fasciola hepatica metacercariae.

Fasciola hepatica, the parasitic liver fluke, is a re-emerging zoonotic infection and an important cause of morbidity and mortality in ruminant livestock worldwide. A significant animal welfare concern, fasciolosis also has a detrimental impact on food security, with the effects of sub-clinical infection on growth rate and milk yield estimated to cost the UK cattle industry £40.4 million annually. It is understood that up to 50% of infective F. hepatica metacercariae may overwinter on pasture and remain viable to infect grazing livestock the following spring. However, the infection risk posed by feeding grass silage to livestock remains largely unknown as the majority of previous studies are outdated in both experimental design and analysis of ensiled metacercariae viability. Anecdotal reports of fasciolosis outbreaks in housed livestock have reignited interest in F. hepatica metacercariae survival during modern ensiling processes and more importantly if they retain viability within stored forages. Consequently, a comprehensive review of the available literature is required in order to identify knowledge gaps and highlight future research opportunities regarding the role of silage in the transmission of F. hepatica.

Young drivers' perceptions of culpability of sleep-deprived versus drinking drivers.

INTRODUCTION: Sleep-deprived driving can be as dangerous as alcohol-impaired driving, however, little is known about attitudes toward sleep-deprived drivers. This study examined the extent to which young drivers regard sleep-deprived compared to drinking drivers as culpable for a crash, and how their perceptions of driving while in these conditions differ. METHOD: University student participants (N=295; M=20.4years, SD=1.3; 81% women) were randomly assigned to read one of five fatal motor-vehicle crash scenarios, which differed by aspects of the driver's condition. Culpability ratings for the drinking driver were higher than those for the sleep-deprived driver. RESULTS: Qualitative findings revealed that driving while sleep-deprived was viewed as understandable, and driving after drinking was viewed as definitely wrong. The dangers of sleep-deprived driving remain under-recognized.

The structural biology of Toll-like receptors.

The membrane-bound Toll-like receptors (TLRs) trigger innate immune responses after recognition of a wide variety of pathogen-derived compounds. Despite the wide range of ligands recognized by TLRs, the receptors share a common structural framework in their extracellular, ligand-binding domains. These domains all adopt horseshoe-shaped structures built from leucine-rich repeat motifs. Typically, on ligand binding, two extracellular domains form an "m"-shaped dimer sandwiching the ligand molecule bringing the transmembrane and cytoplasmic domains in close proximity and triggering a downstream signaling cascade. Although the ligand-induced dimerization of these receptors has many common features, the nature of the interactions of the TLR extracellular domains with their ligands varies markedly between TLR paralogs.

Dimerization of Toll-like receptor 3 (TLR3) is required for ligand binding.

TLR3 (Toll-like receptor 3) recognizes dsRNA, a potent indicator of viral infection. The extracellular domain of TLR3 dimerizes when it binds dsRNA, and the crystal structure of the dimeric complex reveals three sites of interaction on each extracellular domain, two that bind dsRNA and one that is responsible for dimer formation. The goal of this study was to determine which amino acid residues are essential for forming a stable receptor·ligand complex and whether dimerization of TLR3 is required for dsRNA binding. Using a novel ELISA to analyze dsRNA binding by mutant TLR3 constructs, we identified the essential interacting residues and determined that the simultaneous interaction of all three sites is required for ligand binding. In addition, we show that TLR3 is unable to bind dsRNA when dimerization is prevented by mutating residues in the dimerization site or by immobilizing TLR3 at low density. We conclude that dimerization of TLR3 is essential for ligand binding and that the three TLR3 contact sites individually interact weakly with their binding partners but together form a high affinity receptor·ligand complex.

Spectroscopic and modeling investigations of the gas phase chemistry and composition in microwave plasma activated B2H6/CH4/Ar/H2 mixtures.

A comprehensive study of microwave (MW) activated B2H6/CH4/Ar/H2 plasmas used for the chemical vapor deposition of B-doped diamond is reported. Absolute column densities of ground state B atoms, electronically excited H(n = 2) atoms, and BH, CH, and C2 radicals have been determined by cavity ring down spectroscopy, as functions of height (z) above a molybdenum substrate and of the plasma process conditions (B2H6, CH4, and Ar partial pressures; total pressure, p; and supplied MW power, P). Optical emission spectroscopy has also been used to explore variations in the relative densities of electronically excited H atoms, H2 molecules, and BH, CH, and C2 radicals, as functions of the same process conditions. These experimental data are complemented by extensive 2D(r, z) modeling of the plasma chemistry, which result in substantial refinements to the existing B/C/H/O thermochemistry and chemical kinetics. Comparison with the results of analogous experimental/modeling studies of B2H6/Ar/H2 and CH4/Ar/H2 plasmas in the same MW reactor show that: (i) trace B2H6 additions have negligible effect on a pre-established CH4/Ar/H2 plasma; (ii) the spatial extent of the B and BH concentration profiles in a B2H6/CH4/Ar/H2 plasma is smaller than in a hydrocarbon-free B2H6/Ar/H2 plasma operating at the same p, P, etc.; (iii) B/C coupling reactions (probably supplemented by reactions involving trace O2 present as air impurity in the process gas mixture) play an important role in determining the local BHx (x = 0-3) radical densities; and (iv) gas phase B atoms are the most likely source of the boron that incorporates into the growing B-doped diamond film.

Induced-fit mechanism for prolyl endopeptidase.

Prolyl peptidases cleave proteins at proline residues and are of importance for cancer, neurological function, and type II diabetes. Prolyl endopeptidase (PEP) cleaves neuropeptides and is a drug target for neuropsychiatric diseases such as post-traumatic stress disorder, depression, and schizophrenia. Previous structural analyses showing little differences between native and substrate-bound structures have suggested a lock-and-key catalytic mechanism. We now directly demonstrate from seven structures of Aeromonus punctata PEP that the mechanism is instead induced fit: the native enzyme exists in a conformationally flexible opened state with a large interdomain opening between the beta-propeller and alpha/beta-hydrolase domains; addition of substrate to preformed native crystals induces a large scale conformational change into a closed state with induced-fit adjustments of the active site, and inhibition of this conformational change prevents substrate binding. Absolute sequence conservation among 28 orthologs of residues at the active site and critical residues at the interdomain interface indicates that this mechanism is conserved in all PEPs. This finding has immediate implications for the use of conformationally targeted drug design to improve specificity of inhibition against this family of proline-specific serine proteases.

Solution conformation and dynamics of the HIV-1 integrase core domain.

The human immunodeficiency virus type 1 (HIV-1) integrase (IN) is a critical enzyme involved in infection. It catalyzes two reactions to integrate the viral cDNA into the host genome, 3' processing and strand transfer, but the dynamic behavior of the active site during catalysis of these two processes remains poorly characterized. NMR spectroscopy can reveal important structural details about enzyme mechanisms, but to date the IN catalytic core domain has proven resistant to such an analysis. Here, we present the first NMR studies of a soluble variant of the catalytic core domain. The NMR chemical shifts are found to corroborate structures observed in crystals, and confirm prior studies suggesting that the alpha4 helix extends toward the active site. We also observe a dramatic improvement in NMR spectra with increasing MgCl(2) concentration. This improvement suggests a structural transition not only near the active site residues but also throughout the entire molecule as IN binds Mg(2+). In particular, the stability of the core domain is linked to the conformation of its C-terminal helix, which has implications for relative domain orientation in the full-length enzyme. (15)N relaxation experiments further show that, although conformationally flexible, the catalytic loop of IN is not fully disordered in the absence of DNA. Indeed, automated chemical shift-based modeling of the active site loop reveals several stable clusters that show striking similarity to a recent crystal structure of prototype foamy virus IN bound to DNA.

Spectroscopic and modeling investigations of the gas-phase chemistry and composition in microwave plasma activated B2H6/Ar/H2 mixtures.

This paper describes a three-pronged study of microwave (MW) activated B(2)H(6)/Ar/H(2) plasmas as a precursor to diagnosis of the B(2)H(6)/CH(4)/Ar/H(2) plasmas used for the chemical vapor deposition of B-doped diamond. Absolute column densities of B atoms and BH radicals have been determined by cavity ring-down spectroscopy as a function of height (z) above a molybdenum substrate and of the plasma process conditions (B(2)H(6) and Ar partial pressures, total pressure, and supplied MW power). Optical emission spectroscopy has been used to explore variations in the relative densities of electronically excited BH, H, and H(2) species as a function of the same process conditions and of time after introducing B(2)H(6) into a pre-existing Ar/H(2) plasma. The experimental measurements are complemented by extensive 2-D(r, z) modeling of the plasma chemistry, which results in refinements to the existing B/H chemistry and thermochemistry and demonstrates the potentially substantial loss of gas-phase BH(x) species through reaction with trace quantities of air/O(2) in the process gas mixture and heterogeneous processes occurring at the reactor wall.

The toll-like receptor 3:dsRNA signaling complex.

Toll-like receptors (TLRs) recognize conserved molecular patterns in invading pathogens and trigger innate immune responses. TLR3 recognizes dsRNA, a molecular signature of most viruses via its ectodomain (ECD). The TLR3-ECD structure consists of a 23 turn coil bent into the shape of a horseshoe with specialized domains capping the N and C-terminal ends of the coil. TLR3-ECDs bind as dimeric units to dsRNA oligonucleotides of at least 45 bp in length, the minimal length required for signal transduction. X-ray analysis has shown that each TLR3-ECD of a dimer binds dsRNA at two sites located at opposite ends of the TLR3 "horseshoe" on the one lateral face that lacks N-linked glycans. Intermolecular contacts between the C-terminal domains of two TLR3-ECDs stabilize the dimer and position the C-terminal residues within 20-25 A of each other, which is thought to be essential for transducing a signal across the plasma membrane in intact TLR3 molecules. Interestingly, in TLRs 1, 2 and 4, which bind lipid ligands using very different interactions from TLR3, the ligands nevertheless promote the formation of a dimer in which the same two lateral surfaces as in the TLR3-ECD:dsRNA complex face each other, bringing their C-termini in close proximity. Thus, a pattern is emerging in which pathogen-derived substances bind to TLR-ECDs, thereby promoting the formation of a dimer in which the glycan-free ligand binding surfaces face each other and the two C-termini are brought in close proximity for signal transduction.

Structural basis of toll-like receptor 3 signaling with double-stranded RNA.

Toll-like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA), a molecular signature of most viruses, and triggers inflammatory responses that prevent viral spread. TLR3 ectodomains (ECDs) dimerize on oligonucleotides of at least 40 to 50 base pairs in length, the minimal length required for signal transduction. To establish the molecular basis for ligand binding and signaling, we determined the crystal structure of a complex between two mouse TLR3-ECDs and dsRNA at 3.4 angstrom resolution. Each TLR3-ECD binds dsRNA at two sites located at opposite ends of the TLR3 horseshoe, and an intermolecular contact between the two TLR3-ECD C-terminal domains coordinates and stabilizes the dimer. This juxtaposition could mediate downstream signaling by dimerizing the cytoplasmic Toll interleukin-1 receptor (TIR) domains. The overall shape of the TLR3-ECD does not change upon binding to dsRNA.

The TLR3 signaling complex forms by cooperative receptor dimerization.

Toll-like receptors (TLRs) initiate immune responses by recognizing pathogen-associated molecules, but the molecular basis for recognition is poorly understood. In particular, it is unclear how receptor-ligand interactions lead to the initiation of downstream signaling. Here, we describe the mechanism by which TLR3 recognizes its ligand, double-stranded RNA (dsRNA), and forms an active signaling complex. We show that dsRNA binds saturably, specifically, and reversibly to a defined ligand-binding site (or sites) on the TLR3 ectodomain (TLR3ecd). Binding affinities increase with both buffer acidity and ligand size. Purified TLR3ecd protein is exclusively monomeric in solution, but through a highly cooperative process, it forms dimers when bound to dsRNA, and multiple TLR3ecd dimers bind to long dsRNA strands. The smallest dsRNA oligonucleotides that form stable complexes with TLR3ecd (40-50 bp) each bind one TLR3ecd dimer, and these are also the smallest oligonucleotides that efficiently activate TLR3 in cells. We conclude that TLR3 assembles on dsRNA as stable dimers and that the minimal signaling unit is one TLR3 dimer.

The type 1 insulin-like growth factor receptor is over-expressed in bladder cancer.

OBJECTIVE: To analyse bladder cancer biopsies and investigate the pattern of expression of the type 1 insulin-like growth factor receptor (IGF1R), a receptor tyrosine kinase that mediates tumour cell proliferation, motility and protection from apoptosis. MATERIALS AND METHODS: Formalin-fixed specimens of bladder cancer (40 whole-mount, 80 cores on a tumour microarray) and normal bladder (15 samples) were stained immunohistochemically for the IGF1R. The IGF1R expression was also measured by quantitative reverse transcription-polymerase chain reaction (Q-RT-PCR) on RNA extracted from fresh frozen bladder cancers (61) and benign bladder (12). RESULTS: Of the 15 samples of normal bladder, 14 showed negligible (1+) or light (2+) IGF1R immunostaining. By contrast moderate (3+) or heavy (4+) staining for IGF1R was detected in 89 (74%) of the 120 samples of malignant urothelium. Q-RT-PCR showed significantly higher levels of steady-state IGF1R mRNA in tumours (all cases, Ta-T4) than in normal bladder (P < 0.05), indicating up-regulation at the transcriptional level. This difference was particularly evident when comparing normal urothelium with superficial (Ta-T1) or invasive (T2-4) tumours; only the latter showed significant IGF1R over-expression at the RNA level (P < 0.05 vs normal bladder). CONCLUSION: The IGF1R is up-regulated in bladder cancer compared with non-malignant bladder, and might contribute to a propensity for invasion.

Reconstructing the early evolution of Fungi using a six-gene phylogeny.

The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.

The dsRNA binding site of human Toll-like receptor 3.

Pathogen recognition by Toll-like receptors (TLRs) initiates innate immune responses that are essential for inhibiting pathogen dissemination and for the development of acquired immunity. The TLRs recognize pathogens with their N-terminal ectodomains (ECD), but the molecular basis for this recognition is not known. Recently we reported the x-ray structure for unliganded TLR3-ECD; however, it has proven difficult to obtain a crystal structure of TLR3 with its ligand, dsRNA. We have now located the TLR3 ligand binding site by mutational analysis. More than 50 single-residue mutations have been generated throughout the TLR3-ECD, but only two, H539E and N541A, resulted in the loss of TLR3 activation and ligand binding functions. These mutations locate the dsRNA binding site on the glycan-free, lateral surface of TLR3 toward the C terminus and suggest a model for dsRNA binding and TLR3 activation.

Sub-microsecond protein folding.

We have investigated the structure, equilibria, and folding kinetics of an engineered 35-residue subdomain of the chicken villin headpiece, an ultrafast-folding protein. Substitution of two buried lysine residues by norleucine residues stabilizes the protein by 1 kcal/mol and increases the folding rate sixfold, as measured by nanosecond laser T-jump. The folding rate at 300 K is (0.7 micros)(-1) with little or no temperature dependence, making this protein the first sub-microsecond folder, with a rate only twofold slower than the theoretically predicted speed limit. Using the 70 ns process to obtain the effective diffusion coefficient, the free energy barrier height is estimated from Kramers theory to be less than approximately 1 kcal/mol. X-ray crystallographic determination at 1A resolution shows no significant change in structure compared to the single-norleucine-substituted molecule and suggests that the increased stability is electrostatic in origin. The ultrafast folding rate, very accurate X-ray structure, and small size make this engineered villin subdomain an ideal system for simulation by atomistic molecular dynamics with explicit solvent.