Miracle-dz/UniFAR-FTUs huggingface dataset:
A bioluminescence sensor of NLRP3 inflammasome activation

The innate immune system is many organisms first line of defense against pathogenic insult or tissue damage [1]. This defense strategy is intent on restoring homeostasis upon perturbation. Upon activation of the innate immune system in humans, an oligomeric protein complex termed the “Inflammasome” forms in myeloid cells [2]. The canonical output of activation of any subset of inflammasome is Caspase-1-mediated secretion of pro-inflammatory cytokines IL1β and IL18 [3, 4]. Chronic or uncontrolled inflammasome activation is at the core of myriad economically burdening diseases [5-8]. In many of these diseases, endogenous factors chronically engage the innate immune system. To study these diseases in in vivo, over time as they progress, in a transgenic organism will segue into the development of next generation therapeutics. In this study we sought to utilize a modified Firefly Luciferase (pGLO) construct to measure Caspase1, and thus, inflammasome activity. pGLO has been engineered to be catalytically activated in response to targeted cleavage by a protease [9]. We report that insertion of a short peptide sequence targeted by Caspase-1 into the linker region of a circularly permuted Firefly Luciferase (pGLO) has allowed us to quantitatively assess the level of inflammasome activation in live cells. A successful in vitro experiment demonstrating sensitive and specific quantification of Caspase-1 activity should lead to an in vivo mouse model for the study of inflammatory disease.
Nutrient utilisation and energy balance associated with two contrasting winter milk production systems for high genetic merit autumn calving dairy cows

Autumn calving dairy cows were managed on two contrasting grassland-based systems of milk production for a full lactation, either high forage (HF) or high concentrate (HC). During the winter, animals on system HF (n = 19) were offered grass silage with high feed-value characteristics, supplemented with 5.5 kg/day of concentrate (crude protein concentration 280 g/kg dry matter (DM)) through an out-of-parlour feeding system. Animals on system HC (n = 20) were offered grass silage of medium feed-value characteristics, mixed with approximately 14.0 kg/day of concentrate (crude protein 202 g/kg DM in the form of a 'complete diet'). Animals remained on these winter management systems for a mean of 132 days, with total milk outputs over this period of 3926 (HF) and 4475 (HC) kg. Studies were conducted during this period to examine nutrient utilisation and energy balance associated with each of the two systems. Ammonia nitrogen concentration in rumen liquor was higher with system HF compared to system HC (P < 0.01). Urinary energy and nitrogen losses, as a proportion of gross energy and nitrogen intakes, were significantly higher for HF than HC (P < 0.001). Minimum energy balance values were -50 (HF) and -33 (HC) MJ/day, while animals reached positive energy balance at 132 (HF) and 84 (HC) days post calving. Diet had a significant effect (P < 0.05) on plasma urea, beta-hydroxybutyrate and non-esterified fatty acid concentrations. Fertility for both systems was poor, with proportionally only 0.38 of animals showing commencement of luteal activity within 28 days of calving, while proportion conceiving to first service was 0.26 and 0.21 for systems HF and HC, respectively. Neither blood metabolite concentrations nor energy balance were found to be directly correlated with fertility.
Pedigree analysis of Cashmere goat breed of South Khorasan

Abstract The genealogical data of Cashmere goat breed of South Khorasan province of Iran was analysed in this study. Records from a total of 10,635 animals collected during 1988–2014 from 20 registered flocks were analysed for evaluating pedigree parameters. The reference population was defined as the living reproductive animals born from 2010 till 2014. The average inbreeding coefficient in the studied breed was about 0.07% (ranging from 0 to 25%). In addition, the average inbreeding coefficient for the reference population was about 0.85%. The main reason for the low inbreeding level obtained in Cashmere goat population was related to the extensive production system and lack of sire registration in a large number of animals (about 78% missing sire information). A total of 200 animals were inbred. The inbred animals were all related to the breeding station flock which was acting as a closed nucleus flock and was under the control of Animal Breeding and Milk Improvement Centre of Iran. The result of analysis for gene origin parameters indicated the lack of pedigree depth, which could leads to management problems for conservation of the studied breed.
Use of PCR-based molecular markers to identify weedy Amaranthus species

Weedy species of the genus Amaranthus, commonly referred to as pigweeds, have increased in frequency and severity over the past few years. Identification of these weeds is difficult because of similar morphological characteristics among species and variation within species. Studies were initiated to develop a molecular marker identification system utilizing restriction enzyme analysis of amplified ribosomal DNA (rDNA). A set of polymerase chain reaction (PCR) markers was developed to distinguish 10 weedy species of pigweeds. Restriction-site variation, utilizing five endonucleases, within the internal transcribed spacers (ITS) of the rDNA allowed for the positive identification of eight species and one pair of species. These markers will be useful for biological and ecological studies on the genus.
Feeding Bacillus subtilis C-3102 to sows and suckling piglets and to weaned piglets improves parameters of gut health and feed:gain ratio in weaners

The effect of feeding Bacillus subtilis C-3102 (Calsporin) to sows and piglets on performance and gut health of weaned piglets was studied. The experiment contained 4 treatments. First, 8 of 16 sows were supplemented with 3 x 10(5) cfu B. subtilis C-3102/g feed during gestation and lactation whereas the other 8 sows were not supplemented. The probiotic was also included in the creep feed of the suckling offspring of the supplemented sows at an equal dose. Furthermore, at weaning (19-20 d of age), each of the 2 experimental groups were split up into 2 subgroups to yield 4 treatments. Therefore, 5 piglets of each sow were fed a control diet voided of probiotics and 5 littermates were offered the control diet supplemented with 3 x 10(5) cfu B. subtilis C-3102/g feed until 42 d after weaning (8 pen replicates with 5 piglets each). Piglets were sampled at d 0, 5, 13, and 42 after weaning. Supplementation of the probiotic to sows and suckling piglets resulted in higher short-chain fatty acid production in the distal small intestine and mid colon at weaning but not at d 5 and 13 after weaning, whereas villus atrophy in the small intestine and crypt deepening in the proximal small intestine was lower. Postweaning supplementation improved the feed:gain ratio for the total period (1.39 vs. 1.45; P = 0.031) and resulted in a trend for lower mRNA of IL-1 alpha (P = 0.091), higher lactobacillus counts (P = 0.074), and a significantly lower number of crypt goblet cells in distal small intestine mucosa in the early postweaning period. In addition, B. subtilis C-3102 was detected only in colonic contents or feces of piglets from the supplemented groups. Only 1 significant interaction between pre- and postweaning supplementation was found throughout the study. To conclude, preweaning supplementation positively affected some gut health parameters and postweaning supplementation improved the feed:gain ratio.
A simple, economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine

A simplified method is presented for using 3H-leucine (3H-leu) incorporation to measure bacterial protein synthesis rates in seawater. This method uses small volumes (< 2.0 ml) of seawater and centrifugation instead of filtration. Using high specific activity 3H-leu (5 TBq mmol-1), this method is sensitive enough for measurements in open ocean and mesopelagic samples. The centrifugation method provides substantial savings in cost per sample as well as a reduction in the amount of radioactive waste generated. This method is preferable to the filtration method especially for large scale oceanographic programs involving extensive measurements of bacterial carbon production. This centrifugation method should also allow the investigation of small scale patchiness of bacterial carbon production.
EFFECT OF HETEROTROPHIC BACTERIAL COMMUNITIES ON PYTHIUM SPP. IN RECYCLED IRRIGATION WATER

A main concern in commercial greenhouses is the harboring of Pythium species in recycled irrigation water and their spread into susceptible crops. Pythium species are among the most damaging pathogens of horticultural crops causing damping-off of seedlings as well as root and stem rots in ornamental plants. Despite frequent attempts to recover Pythium from recycled water, success in isolation is sporadic. This raises the question of possible microbial suppression of Pythium present in recycled irrigation water. The present study focused on the deleterious effect of microbial communities in recycled irrigation water on the development of Pythium aphanidermatum, P. irregulare, and P. cryptoirregulare. Microscopic observations of the interaction between microorganisms in recycled irrigation water and Pythium species indicated a deleterious effect on Pythium development. The amount of sporangia produced in the presence of the microbial community was negatively affected when compared to water samples with no microorganisms. In addition, research was conducted to evaluate heterotrophic bacteria isolated from recycled irrigation water that reduced the growth in vitro of the three highly pathogenic Pythium species. We isolated a variety of bacteria some of which inhibited the three Pythium spp. growth, others bound to their hyphae, and still others seemed to enhance the growth of the Pythium species. Known biocontrol agents against Pythium (Pseudomonas and Bacillus) and some potentially new biocontrol agents (Acidovorax, Microbacterium, and Chryseobacterium) were identified as isolates inhibiting the growth of P. aphanidermatum, P. irregulare, and P. cryptoirregulare in vitro. The use of biological control agents to control Pythium spp. is not new. However, in most cases, commercially available beneficial organisms are from other environments. Utilization of naturally occurring suppressive bacterial communities in recycled irrigation water may provide an environmentally friendly ecologically sound biological control strategy. We observed that Pythium grew slower when bacterial isolates bound to their hyphae. This phenomenon was previously observed but is not fully understood. These isolates were identified as Acinetobacter, Enterobacter, Pantoea, and Pseudomonas species. Surprisingly, we also isolated
Efficiency of Pseudomonas fluorescens and Bacillus subtilis against Phytophthora spp. in citrus.

Phytophthora was recorded in all the soil samples collected from citrus orchards and nurseries. Out of 25 soil samples Isolates of Pseudomonas fluorescens and Bacillus subtilis recorded from 11 and 5 soil samples, respectively. In vitro, four isolates of Pseudomonas fluorescens and two isolates of Bacillus subtilis were found effective against Phytophthora parasitica and other fungal pathogens of citrus viz., Pythium sp. , Fusarium sp. and Colletotrichum gloeosporioides. Efficacy tested under sick soil method, only Bs-K 1 (a) isolate of Bacillus subtilis was found most effective giving maximum disease control (81.34%), while other isolates of Pseudomonas fluorescens and Bacillus subtilis were not found much efficient. How to view point the article : Shinde, S.B. and Sadgir, M.D. (2016). Efficiency of Pseudomonas fluorescens and Bacillus subtilis against Phytophthora spp. in citrus. Internat. J. Plant Protec. , 9(1) : 15-20.
Effects of chlorination on the inactivation and reactivation of Escherichia coli K12 and its ampicillin resistance gene

Antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) are an emerging threat to public health and are identified as contaminants in aquatic environments. This study investigated the effect of chlorine on the inactivation and reactivation of Escherichia coli K12 and its ampicillin resistance gene. Inactivation of K12 was achieved with exposure to chlorine for 10 minutes, which were then allowed to reactivate in the dark for 24 hours. Bacterial populations were enumerated using heterotrophic plate counts containing concentrations of ampicillin, which caused further inactivation. The results showed that nearly 100% of the bacterial population was inactivated by ampicillin regardless of chlorination. Upon reactivation, a sharp decrease in bacterial concentration is observed between the control (0 mg/L Ampicillin) and any ampicillin concentration in unchlorinated samples. However, after chlorination, there is a much less decrease, suggesting that bacteria that survived chlorination were more resistant to ampicillin. Both inhibitory concentrations (MIC50 and MIC90) were greater than 16 mg/L Amp for at 1 mg/L Cl2. At higher chlorine concentrations, the MIC90 shifted from 0-4 mg/L to 4-8 mg/L ampicillin.
Cytologic and cytometric analysis of oral mucosa in Alzheimer's disease.

OBJECTIVE To analyze cytomorphologically the buccal mucosa of patients with Alzheimer's disease (AD). STUDY DESIGN Brush biopsies were obtained from 10 patients with AD and 9 age-matched controls without neurologic symptoms from 3 distinct oral sites. RESULTS A significant reduction in partially keratinized intermediate (red) cells was observed in the buccal mucosa of the AD group. In the AD group, parabasal cells from the floor of the mouth (p = 0.017) and buccal mucosa (p = 0.058) and red cells,from the tongue dorsum (p = 0.013) and buccal mucosa (p = 0.002), exhibited significantly greater nuclear areas. With regard to the nuclear to cytoplasmic (N:C) ratio, intermediate (red) cells from the buccal mucosa and tongue dorsum of AD individuals showed a decrease in this parameter (p <0.0001), while superficial (yellow) cells (from buccal mucosa) (p= 0.042) and parabasal (blue) cells (from the tongue dorsum) (p = 0.003) exhibited an increased N:C ratio. No significant differences were detected in the cells from the floor of the mouth. CONCLUSIONS Our findings indicate that cytologic and cytometric changes were detectable in the exfoliative cytology of the buccal mucosa and tongue in the AD group.
Bonding beyond the pair in a monogamous bird: impact on social structure in adult rooks (Corvus frugilegus)

The formation of social bonds outside the mated pair is not frequently reported in monogamous birds, although it may be expected in some species like rooks, living in groups all year round. Here we explore the social structure of captive adult rooks over three breeding seasons. We recorded proximities and affiliations (i.e., allofeeding, allopreening, contact-sit) to classify relationships according to their strength. Three categories of relationships emerged: primary (i.e., pairs), secondary and weak relationships. Affiliations and sexual behaviours were not restricted to pairs, and secondary relationships were clearly recognizable. Mixed-sex secondary relationships were qualitatively equivalent to pairs (i.e., same behaviours in the same proportions), although they were quantitatively less intense. Same sex pairs occurred, and were qualitatively equivalent to mixed-sex pairs. Overall we found that rooks social structure is more than just an aggregation of pairs, which highlights the importance of considering extra-pair relationships in socially monogamous birds.
Endomicrobia in termite guts: symbionts within a symbiont (Phylogeny, cospeciation with host flagellates, and preliminary genome analysis)

"Endomicrobia", a distinct and diverse group of uncultivated bacteria in the candidate phylum Termite Group I (TG-1), have been found exclusively in the gut of lower termites and wood-feeding cockroaches. In a previous study, we had demonstrated that the "Endomicrobia" clones retrieved from Reticulitermes santonensis represent intracellular symbionts of the two major gut flagellates of this termite. Here, we document that "Endomicrobia" are present also in many other gut flagellates of lower termites. Phylogeny and host specificity of "Endomicrobia" were investigated by cloning and sequencing of the small subunit ribosomal RNA genes of the host flagellate and the symbionts, which originated from suspensions of individual flagellates isolated by micropipette. Each flagellate harbored a distinct phylogenetic lineage of "Endomicrobia". The results of fluorescent in situ hybridization with "Endomicrobia"-specific oligonucleotide probes corroborated that "Endomicrobia" are intracellular symbionts specifically affiliated with their flagellate host. Interestingly, the "Endomicrobia" sequences obtained from flagellates belonging to the genus Trichonympha formed a monophyletic group, suggesting cospeciation between symbiont and host.
Ecosystem carbon pools, fluxes, and balances within mature tallgrass prairie restorations

Tallgrass prairie restorations can quickly accrue organic C in soil and biomass, but the rate of C accumulation diminishes through time and is highly variable among more mature prairies. Long‐term soil organic carbon (SOC) accumulation in prairies has been linked to edaphic factors such as soil texture, soil moisture, and SOC content, but it is unclear how these factors affect the ecosystem processes that are responsible for observed differences in C accumulation rates in older prairies. We measured belowground plant and SOC pools and fluxes within 27–36‐year‐old restored tallgrass prairies in order to quantify total C storage, determine the net ecosystem production of C (NEP‐C), and explore which edaphic factors influence the ecosystem processes responsible for divergent NEP‐C. We found that 11% of organic C was stored in biomass, and we estimate that one‐third of post‐restoration C sequestration has occurred in biomass, thereby highlighting biomass as a large but often overlooked C pool. Belowground biomass and soil C pools were notably smaller than those reported for remnant prairie, suggesting that future belowground C accumulation could still occur. During this study, the prairies appeared to be a net source of C, although the range of NEP‐C values encompassed zero. Sand content positively affected NEP‐C via increased belowground biomass production‐C inputs, and SOC negatively affected NEP‐C due to increased soil respiration C outputs. However, soil moisture had a smaller negative effect on soil respiration, indicating that both SOC and soil moisture play important roles in determining prairie C balance.
The pleomorphic role of stromal cells in the formation and maintenance of tertiary lymphoid organs

A large body of evidence supports the role of activated stromal cells in the persistence of inflammation. The switch from resting to pathogenic stroma appears to be associated with the development of tertiary lymphoid organs (TLOs) within sites of chronic inflammation. However little is known about the immunological function of the stromal component. We utilised a murine model of inducible TLO formation in inflamed salivary glands to investigate the role of activated stromal cells characterised by the expression of gp38 and FAP during TLO development. We demonstrated that during inflammation, stroma-derived ICOSL engages ICOS on T cells, necessary for the release of lymphotoxin α and consequent TLO formation. Whilst dissecting the role of stromal cells in this context, we demonstrate that gp38 expression is required for the upregulation of adhesion molecules involved in cell clustering. Depletion of gp38+FAP+ stromal cells led to a significant reduction in lymphoid chemokine production, a decreased number of infiltrating lymphocytes and severely compromised TLO formation. Collectively, we provide evidence that activated stromal cells express FAP, provide co-stimulatory signals, and are necessary for the establishment of viral-induced TLOs, highlighting a potential novel therapeutic target in TLO-associated autoimmune diseases.
Relative Passage Rates of Lipid and Aqueous Digesta in the Formation of Stomach Oils

Utilisation de glycerol triether marque au tritium comme marqueur de la phase lipide non-absorbable et de polyethylene glycol marque au carbone 14 comme marqueur de la phase aqueuse non-absorbable pour l'etude du transit gastrointestinal d'un repas de poisson homogeneise chez des pingouins
Blood profile of broiler chickens fed supplemented garlic-based diets

Conventional supplements have been criticised for their potential negative impact on the food chain. Poultry researchers and nutritionists have been searching for viable alternative feed additives. Poultry production is still facing challenges of diseases and a lot of research are still on going. This study was carried out to investigate the effects of garlic (Allium sativum) supplementation on the blood profile of broiler chicken. One hundred and fifty-day old Marshal strains of broiler chicken were assigned to five dietary treatments with thirty birds in a Completely Randomized Design. The thirty chicks were subdivided into three replicates of 10 birds each. Feed and water were offered ad libitum and mortality was recorded as it occurred. Blood were collected from two birds per replicate to determine haematological and serum biochemical responses. No significant (p>0.05) difference was observed in the haematological response and serum biochemistry profile of broilers fed experimental diets, with the exception of the Cholesterol level which significantly (p<0.05) decreased as the level of inclusion of the garlic increased, with the control diet having the highest value (135.38mg/dL) while the least value (129.80mg/dL) was obtained from diets containing 0.8% inclusion of garlic. Therefore, the inclusion of garlic (Allium sativum) in the diets of broiler chicken had no deleterious effects on the blood profile of the experimental birds but improved the cholesterol level of the birds at the inclusion level of 0.4g/ton of feed.
Investigation of tunnel junctions on proximitized topological insulator nanoribbons

Since A. Yu. Kitaev predicted in 2001 that quasi-one-dimensional p-wave superconductors are a possible platform for Majorana bound states (MBSs), numerous experiments have been conducted to find signatures and prove the existence of these MBSs. The majority of these experiments focused on tunnel spectroscopy on proximitized III-V semiconductor nanowires. Another possible platform to realize this exotic superconductivity are 3D topological insulators (3D-TIs) proximitized by s-wave superconductors. A major challenge to perform such tunnel spectroscopy experiments on 3D-TIs is the prevention of deterioration of the sensitive 3D-TI surface and the additional need to fabricate a suitable tunnel barrier. In this thesis selective area epitaxy of BiSbTe is conducted to obtain nanoribbons of this 3D-TI. Moreover, a multi-stage in situ fabrication technique for the assembly of tunnel junctions at the ends of niobium-proximitized BiSbTe nanoribbons is demonstrated. The process presented here allows to grow and deposit nanostructures of four different materials completely under UHV (ultra-high vacuum) conditions, i.e. in situ. First measurements at ultra-low temperatures were performed on tunnel junctions fabricated with this method. Two different models are derived and discussed to provide a physical explanation of the features shown in these measurements. Additionally, I present quantum transport simulations of such proximitized 3D-TI tunnel junctions.