Comparison of selectivity and sensitivity of various ferric selective electrodes prepared using N-((bis(dimethyl amino)methylene)carbamothioyl)benzamide.

N-((Bis(dimethyl amino)methylene)carbamothioyl)benzamide (NBMCB) was synthesized, characterized, and used as an ionophore for producing three novel ion-selective potentiometric sensors for Fe(III) determination. Firstly, using the molecular mechanic-based MMFF94 method, the most stable NBMCB's conformer and its isosteric complexes with various cations were determined. According to the Gibbs free energy results of the reaction, the thermodynamic complexation reactivity of Fe(III) and the ligand was acceptable. These results were obtained using the B3LYP approach and the 6-31G(d,p) basis set that was substituted for heavy metals by the LanL2DZ basis set. We used UV-visible spectrophotometry to confirm the tendency of NBMCB to react with Fe(III). Generally, three diverse liquid membrane ferric selective electrodes were obtained by the use of the specified ligand: classic with a liquid internal electrolyte-ferric selective electrode (LIE-FSE), solid state-FSE (SS-FSE), and coated wire-FSE (CW-FSE). The reactions exhibited Nernstian behavior across all electrodes. The limit of detection was enhanced for the SS-FSE (3 × 10-9 M) and the CW-FSE (3 × 10-7 M) in comparison with that of the LIE-FSE (7 × 10-7 M). The lifetime of the LIE-FSE was 8 weeks, while it was 10 weeks for the SS-FSE and the CW-FSE. Elimination of the internal solution reduced the limit of detection and prolonged the lifespan of the sensors. Also, the three electrodes all had a short response time of around 5-7 s. The sensors were utilized as indicator electrodes during the potentiometric titration of Fe(III) using ethylenediaminetetraacetic acid.

Cellular self-organization: An overdrive in Cambrian diversity?

During the early Cambrian period metazoan life forms diverged at an accelerated rate to occupy multiple ecological niches on earth. A variety of explanations have been proposed to address this major evolutionary phenomenon termed the "Cambrian explosion." While most hypotheses address environmental, developmental, and ecological factors that facilitated evolutionary innovations, the biological basis for accelerated emergence of species diversity in the Cambrian period remains largely conjectural. Herein, we posit that morphogenesis by self-organization enables the uncoupling of genomic mutational landscape from phenotypic diversification. Evidence is provided for a two-tiered interpretation of genomic changes in metazoan animals wherein mutations not only impact upon function of individual cells, but also alter the self-organization outcome during developmental morphogenesis. We provide evidence that the morphological impacts of mutations on self-organization could remain repressed if associated with an unmet negative energetic cost. We posit that accelerated morphological diversification in transition to the Cambrian period has occurred by emergence of dormant (i.e., reserved) morphological novelties whose molecular underpinnings were seeded in the Precambrian period.

A meta-analysis of methane-mitigation potential of feed additives evaluated in vitro.

A systematic literature review of in vitro studies was performed to identify methane (CH4) mitigation interventions with a potential to reduce CH4 emission in vivo. Data from 277 peer-reviewed studies published between 1979 and 2018 were reviewed. Individual CH4 mitigation interventions were classified into 14 categories of feed additives based on their type, chemical composition, and mode of action. Response variables evaluated were absolute CH4 emission (number of treatment means comparisons = 1,325); total volatile fatty acids (n = 1,007), acetate (n = 783), propionate (n = 792), and butyrate (n = 776) concentrations; acetate to propionate ratio (n = 675); digestibility of dry matter (n = 489), organic matter (n = 277), and neutral detergent fiber (n = 177). Total gas production was used as an explanatory variable in the model for CH4 production. Relative mean difference between treatment and control means reported in the studies was calculated and used for statistical analysis. The robust variance estimation method was used to analyze the effects of CH4 mitigation interventions. In vitro CH4 production was decreased by antibodies (-38.9%), chemical inhibitors (-29.2%), electron sinks (-18.9%), essential oils (-18.2%), plant extracts (-14.5%), plant inclusion (-11.7%), saponins (-14.8%), and tannins (-14.5%). Overall effects of direct-fed microbials, enzymes, macroalgae, and organic acids supplementation did not affect CH4 production in the current meta-analysis. When considering the effects of individual mitigation interventions containing a minimum number of 4 degrees of freedom within feed additives categories, Enterococcus spp. (i.e., direct-fed microbial), nitrophenol (i.e., electron sink), and Leucaena spp. (i.e., tannins) decreased CH4 production by 20.3%, 27.1%, and 23.5%, respectively, without extensively, or only slightly, affecting ruminal fermentation and digestibility of nutrients. It should be noted, however, that although the total number of publications (n = 277) and treatment means comparisons (n = 1,325 for CH4 production) in the current analysis were high, data for most mitigation interventions were obtained from less than 5 observations (e.g., maximum number of observations was 4, 7, and 22 for nitrophenol, Enterococcus spp., and Leucaena spp., respectively), because of limited data available in the literature. These should be further evaluated in vitro and in vivo to determine their true potential to decrease enteric CH4 production, yield, and intensity. Some mitigation interventions (e.g., magnesium, Heracleum spp., nitroglycerin, ß-cyclodextrin, Leptospermum pattersoni, Fructulus Ligustri, Salix caprea, and Sesbania grandiflora) decreased in vitro CH4 production by over 50% but did not have enough observations in the database. These should be more extensively investigated in vitro, and the dose effect must be considered before adoption of mitigation interventions in vivo.

The fate of notch-1 transcript is linked to cell cycle dynamics by activity of a natural antisense transcript.

A core imprint of metazoan life is that perturbations of cell cycle are offset by compensatory changes in successive cellular generations. This trait enhances robustness of multicellular growth and requires transmission of signaling cues within a cell lineage. Notably, the identity and mode of activity of transgenerational signals remain largely unknown. Here we report the discovery of a natural antisense transcript encoded in exon 25 of notch-1 locus (nAS25) by which mother cells control the fate of notch-1 transcript in daughter cells to buffer against perturbations of cell cycle. The antisense transcript is transcribed at G1 phase of cell cycle from a bi-directional E2F1-dependent promoter in the mother cell where the titer of nAS25 is calibrated to the length of G1. Transmission of the antisense transcript from mother to daughter cells stabilizes notch-1 sense transcript in G0 phase of daughter cells by masking it from RNA editing and resultant nonsense-mediated degradation. In consequence, nAS25-mediated amplification of notch-1 signaling reprograms G1 phase in daughter cells to compensate for the altered dynamics of the mother cell. The function of nAS25/notch-1 in integrating G1 phase history of the mother cell into that of daughter cells is compatible with the predicted activity of a molecular oscillator, slower than cyclins, that coordinates cell cycle within cell lineage.

Effects of replacement of barley with oats on milk fatty acid composition in dairy cows fed grass silage-based diets.

This study consists of milk fatty acid (FA) data collected during 2 in vivo experiments. For this study, 8 cows from each experiment were included in a replicated 4 × 4 Latin square design. At the start of experiment 1 (Exp1) cows were at (mean ± standard deviation) 87 ± 34.6 d in milk, 625 ± 85.0 kg of body weight, and 32.1 ± 4.17 kg/d milk yield and at the start of experiment 2 (Exp2) cows were at 74 ± 18.2 d in milk, 629 ± 87.0 kg of body weight, and 37.0 ± 3.2 kg/d milk yield. In Exp1, we examined the effects of gradual replacement of barley with hulled oats (oats with hulls) on milk FA composition. The basal diet was grass silage and rapeseed meal (58 and 10% of diet DM, respectively), and the 4 grain supplements were formulated so that barley was gradually replaced by hulled oats at levels of 0, 33, 67, and 100% on dry matter basis. In Exp2, we examined (1) the effects of replacing barley with both hulled and dehulled oats (oats without hulls) and (2) the effects of gradual replacement of hulled oats with dehulled oats on milk FA composition. The basal diet was grass silage and rapeseed meal (60 and 10% of diet DM, respectively), and the 4 pelleted experimental concentrates were barley, hulled oats, a 50:50 mixture of hulled and dehulled oats, and dehulled oats on dry matter basis. In Exp1, gradual replacement of barley with hulled oats decreased relative proportions of 14:0, 16:0, and total saturated FA (SFA) in milk fat linearly, whereas proportions of 18:0, 18:1, total monounsaturated FA, and total cis unsaturated FA increased linearly. Transfer efficiency of total C18 decreased linearly when barley was replaced by hulled oats in Exp1. In Exp2, relative proportions of 14:0, 16:0, and total SFA were lower, whereas proportions of 18:0, 18:1, monounsaturated FA, and cis unsaturated FA were higher in milk from cows fed the oat diets than in milk from cows fed the barley diet. Moreover, in Exp2, gradual replacement of hulled oats with dehulled oats slightly decreased the relative proportion of 14:0 in milk fat but did not affect the proportions of 16:0, 18:0, 18:1, total SFA, monounsaturated FA, trans FA, or polyunsaturated FA. In Exp2, transfer efficiency of total C18 was lower when cows were fed the oat diets than when fed the barley diet and decreased linearly when hulled oats were replaced with dehulled oats. Predictions of daily CH4 emissions (g/d) using the on-farm available variables energy-corrected milk yield and body weight were not markedly improved by including milk concentrations of individual milk FA in prediction equations. In conclusion, replacement of barley with oats as a concentrate supplement for dairy cows fed a grass silage-based diet could offer a practical strategy to change the FA composition of milk to be more in accordance with international dietary guidelines regarding consumption of SFA.

A meta-analysis of methane mitigation potential of feed additives evaluated in vitro.

A systematic literature review of in vitro studies was performed to identify methane (CH4) mitigation interventions with a potential to reduce CH4 emission in vivo. Data from 277 peer-reviewed studies published between 1979 and 2018 were reviewed. Individual CH4 mitigation interventions were classified into 14 categories of feed additives based on their type, chemical composition, and mode of action. Response variables evaluated were absolute CH4 emission (number of treatment means comparisons = 1,325); total volatile fatty acids (VFA; n = 1,007), acetate (n = 783), propionate (n = 792), and butyrate (n = 776) concentrations; acetate to propionate ratio (A:P; n = 675); digestibility of dry matter (DM; n = 489), organic matter (OM; n = 277), and neutral detergent fiber (NDF; n = 177). Total gas production was used as an explanatory variable in the model for CH4 production. Relative mean difference between treatment and control means reported in the studies were calculated and used for statistical analysis. Robust variance estimation method was used to analyze the effects of CH4 mitigation interventions. In vitro CH4 production was decreased by antibodies (-38.9%), chemical inhibitors (-29.2%), electron sinks (-18.9%), essential oils (-18.2%), plant extracts (-14.5%), plants inclusion (-11.7%), saponins (-14.8%), and tannins (-14.5%). Overall effects of direct fed microbials, enzymes, macroalgae, and organic acids supplementation did not affect CH4 production in the current meta-analysis. When considering the effects of individual mitigation interventions containing a minimum number of 4 degrees of freedom within feed additives categories, Enterococcus spp. (i.e., direct fed microbial), nitrophenol (i.e., electron sink), and Leucaena spp. (i.e., tannins) decreased CH4 production by 20.3, 27.1, and 23.5%, respectively, without extensively, or only slightly, affecting ruminal fermentation and digestibility of nutrients. It should be noted, however, that although the total number of publications (n = 277) and treatment means comparisons (n = 1,325 for CH4 production) in the current analysis were high, data for most mitigation interventions were obtained from less than 5 observations (e.g., maximum number of observations was 4, 7, and 22 for nitrophenol, Enterococcus spp., and Leucaena spp., respectively), because of limited data available in the literature. These should be further evaluated in vitro and in vivo to determine their true potential to decrease enteric CH4 production, yield, and intensity. Some mitigation interventions (e.g., magnesium, Heracleum spp., nitroglycerin, ß-cyclodextrin, Leptospermum pattersoni, Fructulus Ligustri, Salix caprea, and Sesbania grandiflora) decreased in vitro CH4 production by over 50% but did not have enough observations in the database. These should be more extensively investigated in vitro, and the dose effect must be considered before adoption of mitigation interventions in vivo.

Notch ankyrin domain: evolutionary rise of a thermodynamic sensor.

Notch signalling pathway plays a key role in metazoan biology by contributing to resolution of binary decisions in the life cycle of cells during development. Outcomes such as proliferation/differentiation dichotomy are resolved by transcriptional remodelling that follows a switch from Notchon to Notchoff state, characterised by dissociation of Notch intracellular domain (NICD) from DNA-bound RBPJ. Here we provide evidence that transitioning to the Notchoff state is regulated by heat flux, a phenomenon that aligns resolution of fate dichotomies to mitochondrial activity. A combination of phylogenetic analysis and computational biochemistry was utilised to disclose structural adaptations of Notch1 ankyrin domain that enabled function as a sensor of heat flux. We then employed DNA-based micro-thermography to measure heat flux during brain development, followed by analysis in vitro of the temperature-dependent behaviour of Notch1 in mouse neural progenitor cells. The structural capacity of NICD to operate as a thermodynamic sensor in metazoans stems from characteristic enrichment of charged acidic amino acids in ß-hairpins of the ankyrin domain that amplify destabilising inter-residue electrostatic interactions and render the domain thermolabile. The instability emerges upon mitochondrial activity which raises the perinuclear and nuclear temperatures to 50 °C and 39 °C, respectively, leading to destabilization of Notch1 transcriptional complex and transitioning to the Notchoff state. Notch1 functions a metazoan thermodynamic sensor that is switched on by intercellular contacts, inputs heat flux as a proxy for mitochondrial activity in the Notchon state via the ankyrin domain and is eventually switched off in a temperature-dependent manner. Video abstract.

Comparison of Molly and Karoline models to predict methane production in growing and dairy cattle.

Numerous empirical and mechanistic models predicting methane (CH4) production are available. The aim of this work was to evaluate the Molly cow model and the Nordic cow model Karoline in predicting CH4 production in cattle using a data set consisting of 267 treatment means from 55 respiration chamber studies. The dietary and animal characteristics used for the model evaluation represent the range of diets fed to dairy and growing cattle. Feedlot diets and diets containing additives mitigating CH4 production were not included in the data set. The relationships between observed and predicted CH4 (pCH4) were assessed by regression analysis using fixed and mixed model analysis. Residual analysis was conducted to evaluate which dietary factors were related to prediction errors. The fixed model analysis showed that the Molly predictions were related to the observed data (± standard error) as CH4 (g/d) = 0.94 (±0.022) × pCH4 (g/d) + 31 (±6.9) [root mean squared prediction error (RMSPE) = 45.0 g/d (14.9% of observed mean), concordance correlation coefficient (CCC) = 0.925]. The corresponding equation for the Karoline model was CH4 (g/d) = CH4 (g/d) = 0.98 (±0.019) × pCH4 (g/d) + 7.0 (±6.0) [RMSPE = 35.0 g/d (11.6%), CCC = 0.953]. Proportions of mean squared prediction error attributable to mean and linear bias and random error were 10.6, 2.2, and 87.2% for the Molly model, and 1.3, 0.3, and 98.6% for the Karoline model, respectively. Mean and linear bias were significant for the Molly model but not for the Karoline model. With the mixed model regression analysis RMSPE adjusted for random study effects were 10.9 and 7.9% for the Molly model and the Karoline model, respectively. The residuals of CH4 predictions were more strongly related to factors associated with CH4 production (feeding level, digestibility, fat concentrations) with the Molly model compared with the Karoline model. Especially large mean (underprediction) and linear bias (overprediction of low digestibility diets relative to high digestibility diets) contributed to the prediction error of CH4 yield with the Molly model. It was concluded that both models could be used for prediction of CH4 production in cattle, but Karoline was more accurate and precise based on smaller RMSPE, mean bias, and slope bias, and greater CCC. The importance of accurate input data of key variables affecting diet digestibility is emphasized.

A Microfluidic Platform to Monitor Real-Time Effects of Extracellular Vesicle Exchange between Co-Cultured Cells across Selectively Permeable Barriers.

Exosomes and other extracellular vesicles (EVs) play a significant yet poorly understood role in cell-cell communication during homeostasis and various pathological conditions. Conventional in vitro and in vivo approaches for studying exosome/EV function depend on time-consuming and expensive vesicle purification methods to obtain sufficient vesicle populations. Moreover, the existence of various EV subtypes with distinct functional characteristics and submicron size makes their analysis challenging. To help address these challenges, we present here a unique chip-based approach for real-time monitoring of cellular EV exchange between physically separated cell populations. The extracellular matrix (ECM)-mimicking Matrigel is used to physically separate cell populations confined within microchannels, and mimics tissue environments to enable direct study of exosome/EV function. The submicron effective pore size of the Matrigel allows for the selective diffusion of only exosomes and other smaller EVs, in addition to soluble factors, between co-cultured cell populations. Furthermore, the use of PEGDA hydrogel with a very small pore size of 1.2 nm in lieu of Matrigel allows us to block EV migration and, therefore, differentiate EV effects from effects that may be mediated by soluble factors. This versatile platform bridges purely in vitro and in vivo assays by enabling studies of EV-mediated cellular crosstalk under physiologically relevant conditions, enabling future exosome/EV investigations across multiple disciplines through real-time monitoring of vesicle exchange.

Replacement of barley with oats and dehulled oats: Effects on milk production, enteric methane emissions, and energy utilization in dairy cows fed a grass silage-based diet.

Sixteen Nordic Red dairy cows, at 80 ± 4.6 d in milk and with an average body weight of 624 ± 91.8 kg, were used in a replicated 4 × 4 Latin square design to investigate the effects of different concentrate supplements on milk production, enteric CH4 emissions, ruminal fermentation, digestibility, and energy utilization. The cows were blocked into 4 groups based on parity and milk yield and randomly assigned to 1 of 4 experimental concentrates: (1) barley, (2) hulled oats, (3) an oat mixture consisting of hulled and dehulled oats, 50:50 on dry matter basis, and (4) dehulled oats; canola meal was a protein supplement in all 4 concentrates. The cows were fed grass silage and experimental concentrate (forage-to-concentrate ratio 60:40 on dry matter basis) ad libitum. To compare the effects of barley and oats, the barley diet was compared with the overall mean of the hulled oat, oat mixture, and dehulled oat diets. To investigate the effects of gradual replacement of hulled oats with dehulled oats, linear and quadratic contrasts were specified. Milk and energy-corrected milk (ECM) yield were higher on the oat diets compared with the barley diet but were not affected by the type of oats. Concentrations of milk constituents were not affected by grain species or type of oats, except for protein concentration, which was lower on the oat diets than on the barley diet. Feeding the oat diets led to higher milk protein yield and higher milk urea N concentrations. Feed efficiency tended to be higher on the oat diets, and linearly increased with increased inclusion of dehulled oats. Methane emissions (g/d) and CH4 yield (g/kg of dry matter intake) were unaffected by grain species but increased linearly with increasing inclusion of dehulled oats in the diet. Because of higher ECM yield, CH4 intensity (g/kg of ECM) was on average 5.7% lower from cows on the oat diets than on the barley diet. Ruminal fermentation was not affected by dietary treatment. Total-tract apparent digestibility of organic matter, crude protein, and neutral detergent fiber was unaffected by grain species but linearly increased with increasing inclusion of dehulled oats. Gross energy content was higher on the oat diets and linearly increased with increasing inclusion of dehulled oats. Feeding the oat diets led to a lower ratio of CH4 energy to gross energy intake, greater milk energy and heat production but no change in energy balance. Gradual replacement of hulled oats with dehulled oats linearly increased gross energy digestibility, CH4 energy, metabolizable energy intake, heat production, and energy balance. We observed no effect of dietary treatment on efficiency of metabolizable energy use for lactation. In conclusion, replacing barley with any type of oats increased milk and ECM yield, which led to a 5.7% decrease in CH4 intensity. In addition, dehulling of oats before feeding is unnecessary because it did not significantly improve production performance of dairy cows in positive energy balance.

The effects of gradual replacement of barley with oats on enteric methane emissions, rumen fermentation, milk production, and energy utilization in dairy cows.

This study evaluated the effects of gradual replacement of barley with oats on enteric CH4 emissions, rumen fermentation, diet digestibility, milk production, and energy utilization in dairy cows fed a grass silage-based diet. Sixteen lactating Nordic Red dairy cows received a total mixed ration [58:42 forage:concentrate on dry matter (DM) basis]. Grass silage (Phleum pratense) was the sole forage with canola meal (10% of diet DM) as a protein supplement. The effects of gradual replacement of barley with oats on DM basis were evaluated using a replicated 4 × 4 Latin square design with 21 d periods. The grain supplements (30% of diet DM) consisted of 100% barley, 67% barley and 33% oats, 33% barley and 67% oats, and 100% oats. In addition to intake, milk production, and digestibility measurements, CH4 emissions were measured by the GreenFeed system (C-Lock Inc.). The energy metabolism was estimated from the gas exchange measurements recorded by the GreenFeed unit. The last 10 d of each period were used for recordings of gas exchanges, feed intake and milk production. Dry matter intake, body weight, milk yield, and energy-corrected milk yield were not affected by gradual replacement of barley with oats in the diet. Increased inclusion of oats linearly decreased CH4 emissions from 467 to 445 g/d, and CH4 intensity from 14.7 to 14.0 g/kg energy-corrected milk. In addition, the ratio of CH4 to CO2 decreased with increasing inclusion of oats in the diet. Digestibility of organic matter, neutral detergent fiber, and potentially digestible neutral detergent fiber decreased linearly with increasing inclusion of oats. Increased inclusion of oats linearly increased fecal energy from 121 to 133 MJ/d, whereas urinary energy and heat production were not affected by dietary treatment. This resulted in a linear decrease in metabolizable energy intake. However, increased levels of oat in the diet did not significantly affect energy balance or efficiency of metabolizable energy utilization for lactation. This study concludes that barley could be replaced with oats in the diet of dairy cows fed a grass silage-based diet to mitigate CH4 emissions without having any adverse effects on productivity or energy balance. However, the effect of replacing barley with oats on CH4 emissions is dependent on the differences between barley and oats in the concentrations of indigestible neutral detergent fiber and fat.

Effects of different barley and oat varieties on methane production, digestibility, and fermentation pattern in vitro.

The objective of this in vitro study was to determine the effects of different barley and oat varieties on CH4 production, digestibility, and rumen fermentation patterns in dairy cows. Our hypothesis was that oat-based diets would decrease CH4 production compared with barley-based diets, and that CH4 production would differ between varieties within grain species. To evaluate this hypothesis, we conducted an in vitro experiment using a fully automated gas production technique, in which the total gas volume was automatically recorded by the system. The experiment consisted of triplicate 48-h incubations with 16 treatments, including 8 different varieties of each grain. The grain varieties were investigated as a mix with an early-cut grass silage (1:1 ratio of grain to silage on a dry matter basis) and mixed with buffered rumen fluid. We estimated predicted in vivo total gas production and CH4 production by applying a set of models to the gas production data obtained by the in vitro system. We also evaluated in vitro digestibility and fermentation characteristics. The variety of grain species did not affect total gas production, CH4 production, or fermentation patterns in vitro. However, in vitro-determined digestibility and pH were affected by variety of grain species. Grain species affected total gas and CH4 production: compared with barley-based diets, oat-based diets decreased total gas production and CH4 production by 8.2 and 8.9%, respectively, relative to dry matter intake. Grain species did not affect CH4 production relative to in vitro true dry matter digestibility. Oat-based diets decreased digestibility and total volatile fatty acid production, and maintained a higher pH at 48 h of incubation compared with barley-based diets. Grain species did not affect fermentation patterns, except for decreased molar proportions of valerate with oat-based diets. These results suggest that replacing barley with oats in dairy cow diets could decrease enteric CH4 production.

Notch pathway: a bistable inducer of biological noise?

Notch signalling pathway is central to development of metazoans. The pathway codes a binary fate switch. Upon activation, downstream signals contribute to resolution of fate dichotomies such as proliferation/differentiation or sub-lineage differentiation outcome. There is, however, an interesting paradox in the Notch signalling pathway. Despite remarkable predictability of fate outcomes instructed by the Notch pathway, the associated transcriptome is versatile and plastic. This inconsistency suggests the presence of an interface that compiles input from the plastic transcriptome of the Notch pathway but communicates only a binary output in biological decisions. Herein, we address the interface that determines fate outcomes. We provide an alternative hypothesis for the Notch pathway as a biological master switch that operates by induction of genetic noise and bistability in order to facilitate resolution of dichotomous fate outcomes in development.

Characterization of inter-crystallite peptides in human enamel rods reveals contribution by the Y allele of amelogenin.

Proteins of the inter-rod sheath and peptides within the narrow inter-crystallite space of the rod structure are considered largely responsible for visco-elastic and visco-plastic properties of enamel. The present study was designed to investigate putative peptides of the inter-crystallite space. Entities of 1-6 kDa extracted from enamel rods of erupted permanent teeth were analysed by mass spectrometry (MS) and shown to comprise N-terminal amelogenin (AMEL) peptides either containing or not containing exon 4 product. Other dominant entities consisted of an N-terminal peptide from ameloblastin (AMBN) and a series of the most hydrophobic peptides from serum albumin (ALBN). Amelogenin peptides encoded by the Y-chromosome allele were strongly detected in Enamel from male teeth. Location of N-terminal AMEL peptides as well as AMBN and ALBN, between apatite crystallites, was disclosed by immunogold scanning electron microscopy (SEM). Density plots confirmed the relative abundance of these products including exon 4+ AMEL peptides that have greater capacity for binding to hydroxyapatite. Hydrophilic X and Y peptides encoded in exon 4 differ only in substitution of non-polar isoleucine in Y for polar threonine in X with reduced disruption of the hydrophobic N-terminal structure in the Y form. Despite similarity of X and Y alleles of AMEL the non-coding region upstream from exon 4 shows significant variation with implications for segregation of processing of transcripts from exon 4. Detection of fragments from multiple additional proteins including keratins (KER), fetuin A (FETUA), proteinases and proteinase inhibitors, likely reflect biochemical events during enamel formation.

Discovery of Novel Small-Molecule Inhibitors of LIM Domain Kinase for Inhibiting HIV-1.

A dynamic actin cytoskeleton is necessary for viral entry, intracellular migration, and virion release. For HIV-1 infection, during entry, the virus triggers early actin activity by hijacking chemokine coreceptor signaling, which activates a host dependency factor, cofilin, and its kinase, the LIM domain kinase (LIMK). Although knockdown of human LIM domain kinase 1 (LIMK1) with short hairpin RNA (shRNA) inhibits HIV infection, no specific small-molecule inhibitor of LIMK has been available. Here, we describe the design and discovery of novel classes of small-molecule inhibitors of LIMK for inhibiting HIV infection. We identified R10015 as a lead compound that blocks LIMK activity by binding to the ATP-binding pocket. R10015 specifically blocks viral DNA synthesis, nuclear migration, and virion release. In addition, R10015 inhibits multiple viruses, including Zaire ebolavirus (EBOV), Rift Valley fever virus (RVFV), Venezuelan equine encephalitis virus (VEEV), and herpes simplex virus 1 (HSV-1), suggesting that LIMK inhibitors could be developed as a new class of broad-spectrum antiviral drugs.IMPORTANCE The actin cytoskeleton is a structure that gives the cell shape and the ability to migrate. Viruses frequently rely on actin dynamics for entry and intracellular migration. In cells, actin dynamics are regulated by kinases, such as the LIM domain kinase (LIMK), which regulates actin activity through phosphorylation of cofilin, an actin-depolymerizing factor. Recent studies have found that LIMK/cofilin are targeted by viruses such as HIV-1 for propelling viral intracellular migration. Although inhibiting LIMK1 expression blocks HIV-1 infection, no highly specific LIMK inhibitor is available. This study describes the design, medicinal synthesis, and discovery of small-molecule LIMK inhibitors for blocking HIV-1 and several other viruses and emphasizes the feasibility of developing LIMK inhibitors as broad-spectrum antiviral drugs.

Predicting omasal flow of nonammonia N and milk protein yield from in vitro-determined utilizable crude protein at the duodenum.

This study evaluated the relationship between utilizable crude protein (uCP) at the duodenum estimated in vitro and omasal flow of crude protein (CP; omasal flow of nonammonia N × 6.25) measured in lactating dairy cows. In vivo data were obtained from previous studies estimating omasal digesta flow using a triple-marker method and 15N as microbial marker. A total of 34 different diets based on grass and red clover silages were incubated with buffered rumen fluid previously preincubated with carbohydrates for 3 h. The buffer solution was modified to contain 38 g of NaHCO3 and 1 g of (NH4)HCO3 in 1,000 mL of distilled water. Continuous sampling of the liquid phase for determination of ammonia-N was performed at 0.5, 4, 8, 12, 24, and 30 h after the start of incubation. The ammonia N concentrations after incubation were used to calculate uCP. The natural logarithm of uCP [g/kg of dry matter (DM)] at time points 0.5, 4, 8, 12, 24, and 30 h of incubation was plotted against time to estimate the concentration of uCP (g/kg of DM) at time points 16, 20, and 24 h using an exponential function. Fixed model regression analysis and mixed model regression analysis with random study effect were used to evaluate the relationships between predicted uCP (supply and concentration) and observed omasal CP flow and milk protein yield. Residual analysis was also conducted to evaluate whether any dietary factors influenced the relationships. The in vitro uCP method ranked the diets accurately in terms of total omasal CP flow (kg/d) or omasal CP flow per kilogram of DM intake. We also noted a close relationship between estimated uCP supply and adjusted omasal CP flow, as demonstrated by a coefficient of determination of 0.87, although the slope of 0.77 indicated that estimated uCP supply (kg/d) was greater than the value determined in vivo. The linear bias with mixed model analysis indicated that uCP supply overestimated the difference in omasal CP flow between the diets within a study, an error most likely related to study differences in feed intake, animals, and methodology. Predicting milk protein yield from uCP supply showed a positive relationship using a mixed model (coefficient of determination = 0.79), and we observed no difference in model fit between the time points of incubation (16, 20, or 24 h). The results of this study indicate that the in vitro method can be a useful tool in evaluating protein value of ruminant diets.

Exosomes from HIV-1-infected Cells Stimulate Production of Pro-inflammatory Cytokines through Trans-activating Response (TAR) RNA.

HIV-1 infection results in a chronic illness because long-term highly active antiretroviral therapy can lower viral titers to an undetectable level. However, discontinuation of therapy rapidly increases virus burden. Moreover, patients under highly active antiretroviral therapy frequently develop various metabolic disorders, neurocognitive abnormalities, and cardiovascular diseases. We have previously shown that exosomes containing trans-activating response (TAR) element RNA enhance susceptibility of undifferentiated naive cells to HIV-1 infection. This study indicates that exosomes from HIV-1-infected primary cells are highly abundant with TAR RNA as detected by RT-real time PCR. Interestingly, up to a million copies of TAR RNA/µl were also detected in the serum from HIV-1-infected humanized mice suggesting that TAR RNA may be stable in vivo. Incubation of exosomes from HIV-1-infected cells with primary macrophages resulted in a dramatic increase of proinflammatory cytokines, IL-6 and TNF-ß, indicating that exosomes containing TAR RNA could play a direct role in control of cytokine gene expression. The intact TAR molecule was able to bind to PKR and TLR3 effectively, whereas the 5' and 3' stems (TAR microRNAs) bound best to TLR7 and -8 and none to PKR. Binding of TAR to PKR did not result in its phosphorylation, and therefore, TAR may be a dominant negative decoy molecule in cells. The TLR binding through either TAR RNA or TAR microRNA potentially can activate the NF-κB pathway and regulate cytokine expression. Collectively, these results imply that exosomes containing TAR RNA could directly affect the proinflammatory cytokine gene expression and may explain a possible mechanism of inflammation observed in HIV-1-infected patients under cART.

S-nitrosylation of peroxiredoxin 1 contributes to viability of lung epithelial cells during Bacillus anthracis infection.

BACKGROUND: Using Bacillus anthracis as a model gram-positive bacterium, we investigated the effects of host protein S-nitrosylation during bacterial infection. B. anthracis possesses a bacterial nitric oxide synthase (bNOS) that is important for its virulence and survival. However, the role of S-nitrosylation of host cell proteins during B. anthracis infection has not been determined. METHODS: Nitrosoproteomic analysis of human small airway epithelial cells (HSAECs) infected with toxigenic B. anthracis Sterne was performed, identifying peroxiredoxin 1 (Prx1) as one predominant target. Peroxidase activity of Prx during infection was measured using 2-Cys-Peroxiredoxin activity assay. Chaperone activity of S-nitrosylated Prx1 was measured by insulin aggregation assay, and analysis of formation of multimeric species using Native PAGE. Griess assay and DAF-2DA fluorescence assay were used to measure NO production. Cell viability was measured using the Alamar Blue assay and the ATPlite assay (Perkin Elmer). RESULTS: S-nitrosylation of Prx1 in Sterne-infected HSAECs leads to a decrease in its peroxidase activity while enhancing its chaperone function. Treatment with bNOS inhibitor, or infection with bNOS deletion strain, reduces S-nitrosylation of Prx1 and decreases host cell survival. Consistent with this, siRNA knockdown of Prx1 lowers bNOS-dependent protection of HSAEC viability. CONCLUSIONS: Anthrax infection results in S-nitrosylation of multiple host proteins, including Prx1. The nitrosylation-dependent decrease in peroxidase activity of Prx1 and increase in its chaperone activity is one factor contributing to enhancing infected cell viability. GENERAL SIGNIFICANCE: These results provide a new venue of mechanistic investigation for inhalational anthrax that could lead to novel and potentially effective countermeasures.

A dual role for SOX10 in the maintenance of the postnatal melanocyte lineage and the differentiation of melanocyte stem cell progenitors.

During embryogenesis, the transcription factor, Sox10, drives the survival and differentiation of the melanocyte lineage. However, the role that Sox10 plays in postnatal melanocytes is not established. We show in vivo that melanocyte stem cells (McSCs) and more differentiated melanocytes express SOX10 but that McSCs remain undifferentiated. Sox10 knockout (Sox10(fl); Tg(Tyr::CreER)) results in loss of both McSCs and differentiated melanocytes, while overexpression of Sox10 (Tg(DctSox10)) causes premature differentiation and loss of McSCs, leading to hair graying. This suggests that levels of SOX10 are key to normal McSC function and Sox10 must be downregulated for McSC establishment and maintenance. We examined whether the mechanism of Tg(DctSox10) hair graying is through increased expression of Mitf, a target of SOX10, by asking if haploinsufficiency for Mitf (Mitf(vga9) ) can rescue hair graying in Tg(DctSox10) animals. Surprisingly, Mitf(vga9) does not mitigate but exacerbates Tg(DctSox10) hair graying suggesting that MITF participates in the negative regulation of Sox10 in McSCs. These observations demonstrate that while SOX10 is necessary to maintain the postnatal melanocyte lineage it is simultaneously prevented from driving differentiation in the McSCs. This data illustrates how tissue-specific stem cells can arise from lineage-specified precursors through the regulation of the very transcription factors important in defining that lineage.

Exosomes and their role in CNS viral infections.

Exosomes are small membrane-bound vesicles that carry biological macromolecules from the site of production to target sites either in the microenvironment or at distant sites away from the origin. Exosomal content of cells varies with the cell type that produces them as well as environmental factors that alter the normal state of the cell such as viral infection. Human DNA and RNA viruses alter the composition of host proteins as well as incorporate their own viral proteins and other cargo into the secreted exosomes. While numerous viruses can infect various cell types of the CNS and elicit damaging neuropathologies, few have been studied for their exosomal composition, content, and function on recipient cells. Therefore, there is a pressing need to understand how DNA and RNA viral infections in CNS control exosomal release. Some of the more recent studies including HIV-1, HTLV-1, and EBV-infected B cells indicate that exosomes from these infections contain viral miRNAs, viral transactivators, and a host of cytokines that can control the course of infection. Finally, because exosomes can serve as vehicles for the cellular delivery of proteins and RNA and given that the blood-brain barrier is a formidable challenge in delivering therapeutics to the brain, exosomes may be able to serve as ideal vehicles to deliver protein or RNA-based therapeutics to the brain.