Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development.

Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as 'Olfactores conserved non-coding elements'.

Scientific Productions on Precision Livestock Farming: An Overview of the Evolution and Current State of Research Based on a Bibliometric Analysis.

The interest in precision livestock farming (PLF)-a concept discussed for the first time in the early 2000s-has advanced considerably in recent years due to its important role in the development of sustainable livestock production systems. However, a comprehensive bibliometric analysis of the PLF literature is lacking. To address this gap, this study analyzed documents published from 2005 to 2021, aiming to understand the historical influences on technology adoption in livestock farming, identify future global trends, and examine shifts in scientific research on this topic. By using specific search terms in the Web of Science Core Collection, 886 publications were identified and analyzed using the bibliometrix R-package. The analysis revealed that the collection consisted mostly of research articles (74.6%) and reviews (10.4%). The top three core journals were the Journal of Dairy Science, Computers and Electronics in Agriculture, and Animals. Over time, the number of publications has steadily increased, with a higher growth rate in the last five years (29.0%) compared to the initial period (13.7%). Authors and institutions from multiple countries have contributed to the literature, with the USA, the Netherlands, and Italy leading in terms of publication numbers. The analysis also highlighted the growing interest in bovine production systems, emphasizing the importance of behavioral studies in PLF tool development. Automated milking systems were identified as central drivers of innovation in the PLF sector. Emerging themes for the future included "emissions" and "mitigation", indicating a focus on environmental concerns.

TRIM proteins in development.

TRIM proteins play important roles in several patho-physiological processes. Their common activity within the ubiquitylation pathway makes them amenable to a number of diverse biological roles. Many of the TRIM genes are highly and sometimes specifically expressed during embryogenesis, it is therefore not surprising that several of them might be involved in developmental processes. Here, we primarily discuss the developmental implications of two subgroups of TRIM proteins that conserved domain composition and functions from their invertebrate ancestors. The two groups are: the TRIM-NHL proteins implicated in miRNA processing regulation and the TRIM-FN3 proteins involved in ventral midline development.

Unraveling the Relationship between Milk Yield and Quality at the Test Day with Rumination Time Recorded by a PLF Technology.

The study aimed to estimate the components of rumination time (RT) variability recorded by a neck collar sensor and the relationship between RT and milk composition. Milk test day (TD) and RT data were collected from 691 cows in three farms. Daily RT data of each animal were averaged for 3, 7, and 10 days preceding the TD date (RTD). Variance component analysis of RTD, considering the effects of farm, cow, parity, TD date, and lactation phase, showed that a farm, followed by a cow, had major contributions to the total variability. The RT10 variable best performed on TD milk yield and quality records across models by a multi-model inference approach and was adopted to study its relationship with milk traits, by linear mixed models, through a 3-level stratification: low (LRT10 ≤ 8 h/day), medium (8 h/day < MRT10 ≤ 9 h/day), and high (HRT10 > 9 h/day) RT. Cows with HRT10 had greater milk, fat, protein, casein, and lactose daily yield, and lower fat, protein, casein contents, and fat to protein ratio compared to MRT10 and LRT10. Higher percentages of saturated fatty acid and lower unsaturated and monounsaturated fatty acid were found in HRT10, with respect to LRT10 and MRT10 observations.

Effect of a Polyphenol-Based Additive in Pig Diets in the Early Stages of Growth.

The weaning period is a stressful period for the gastrointestinal tract (GIT) of piglets. This work aims to evaluate the effects of the commercial polyphenol-based product GreenFIS® on: (1) GIT health and performance of 60 weaned piglets; (2) digestibility in 18 growing pigs. Three diets were tested: a control diet (C), C plus 2.5 g of GreenFIS®/kg C (T1), and C plus 5 g of GreenFIS®/kg C (T2). After the post-weaning trial three piglets per treatment were sacrificed for the GIT histological analysis. No differences between diets were recorded in terms of growing performance or clinical and biochemical blood parameters. The GIT histological analysis did not show any indicators of inflammation for any of the groups. The feces of the two extreme treatments (C and T2) were analyzed for microbiota, revealing a greater presence of the Ruminococcus bromii group, positively associated with starch degradation, in T2. In the second experiment six pigs per treatment were randomly chosen for the digestibility study. The inclusion of GreenFIS® at both levels led to a higher fecal digestibility of gross energy (86.2%, 89.1%, and 89.5%, for C, T1, and T2, respectively) and crude protein (87.0%, 90.2%, and 90.0%). In conclusion, the additive did not improve, in the excellent experimental hygienic conditions, the gut health, but it did increase nutrient digestibility.

Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements.

BACKGROUND: Ultraconserved elements (UCEs) are highly constrained elements of mammalian genomes, whose functional role has not been completely elucidated yet. Previous studies have shown that some of them act as enhancers in mouse, while some others are expressed in both normal and cancer-derived human tissues. Only one UCE element so far was shown to present these two functions concomitantly, as had been observed in other isolated instances of single, non ultraconserved enhancer elements. RESULTS: We used a custom microarray to assess the levels of UCE transcription during mouse development and integrated these data with published microarray and next-generation sequencing datasets as well as with newly produced PCR validation experiments. We show that a large fraction of non-exonic UCEs is transcribed across all developmental stages examined from only one DNA strand. Although the nature of these transcripts remains a mistery, our meta-analysis of RNA-Seq datasets indicates that they are unlikely to be short RNAs and that some of them might encode nuclear transcripts. In the majority of cases this function overlaps with the already established enhancer function of these elements during mouse development. Utilizing several next-generation sequencing datasets, we were further able to show that the level of expression observed in non-exonic UCEs is significantly higher than in random regions of the genome and that this is also seen in other regions which act as enhancers. CONCLUSION: Our data shows that the concurrent presence of enhancer and transcript function in non-exonic UCE elements is more widespread than previously shown. Moreover through our own experiments as well as the use of next-generation sequencing datasets, we were able to show that the RNAs encoded by non-exonic UCEs are likely to be long RNAs transcribed from only one DNA strand.

A Survey of Italian Dairy Farmers' Propensity for Precision Livestock Farming Tools.

A targeted survey was designed with the aim of describing the diffusion of precision livestock farming (PLF) tools in one of the most intensive dairy farming provinces in Italy. Technicians at the Provincial Breeder Association of Cremona interviewed 490 dairy farmers and obtained data regarding the role and age of the respondents; the land owned by the farmers; their herd sizes (HS, lactating plus dry cows; small HS < 101, medium HS 101-200, large HS > 200 cows/herd); their average 305 day milk yield (low MY < 9501, medium MY 9501-10,500, high MY > 10,500 kg/head); the cow to employed worker ratio (low CW < 33, medium CW 33-47, high CW > 47 cows/worker); the use of PLF tools to monitor production, reproduction, and health; and the criteria and motivations for investing in PLF tools. The use of automated MY recording and estrus detection systems was primarily associated with HS (more present in larger farms), followed by MY (more present in more productive farms), and then CW (more present with a high cow: worker ratio). Concern about the time required to manage data was the most common subjective issue identified as negatively affecting the purchase of these tools. The future of PLF use in this region will depend upon the availability of an effective selection of tools on the market.

Blood parameters in fattening pigs from two genetic types fed diet with three different protein concentrations.

The study aimed to evaluate possible differences between two genetic groups (GG) of pigs, fed diets varying in dietary CP level, in hematological and biochemical plasma profiles. The study was carried out in an experimental farm and involved 36 barrows (average BW 129 ± 11 kg) from two GG: group A (18 Italian Duroc boars × Italian Large White sows) and group D (18 DanBred Duroc), fed three experimental diets: a conventional diet and two low-protein diets (LP1 and LP2). A digestibility/balances trial was carried out on 12 pigs A and 12 pigs D that were housed individually in metabolic cages during four digestibility/balances periods. The experimental design was a factorial design, with 3 diets × 2 GG × 4 periods. The experiment lasted 56 d. Blood was sampled from jugular vein in the morning before feed distribution from all barrows in pens at the start and the end of the experimental period; a supplementary blood sample was collected from the 24 pigs at the end of the four digestibility periods (six pigs per period). Blood was analyzed for hematological and biochemical parameters and serum protein profile using automated analyzers. The GG D showed lower white blood cells (WBC), lymphocyte, and monocyte counts than A group. The GG affected several plasma metabolite concentrations: triglycerides, creatinine, Cl, Fe, alkaline phosphatase, and tartrate-resistant acid phosphatase activities were higher in D groups, while urea, albumin, Ca, Na, total bilirubin, and albumin as percentage of total protein were lower than A group. On the contrary, the dietary protein level neither affects WBC nor their populations; only a trend was reported for erythrocytes (red blood cell) and platelets. The diet affected only plasma urea and total bilirubin concentrations.

A novel fixative improves opportunities of nucleic acids and proteomic analysis in human archive's tissues.

All tissues from biopsy or surgery origin are fixed and paraffin embedded as a routine procedure in the hospital departments of pathology. The traditional method of tissue preservation is the fixation in formalin, followed by paraffin embedding. In this way tissue's integrity is ensured also for future analyses, because there is no further chemical degradation of nucleic acids and proteins in tissues embedded in paraffin. After few sections for the histopathological examination the tissues are stored for decades in the hospital archives. Even if formalin fixation compromises the quality and integrity of nucleic acids, it has already been demonstrated that it is possible to recover and analyze DNA and RNA from these archive's tissues, even of autopsy origin. Protein analysis is on the contrary completely blocked, due to the fact that formalin fixation creates covalent links between proteins and the only way to study protein expression is immunohistochemistry. In this study we present our results concerning the use of a new formalin free fixative, the FineFIX. After extraction of nucleic acids, PCR and RT-PCR analyses were performed in DNA and RNA respectively. For DNA analysis it was possible to obtain amplicons of 2400 bps, while in formalin-fixed samples the maximum length achieved was less than 400 bps. RT-PCR analysis show that it was possible to study RNA fragments of 600 bps from FineFIX fixed tissues, against a maximum length of about 150 bps achieved by formalin-fixed tissues. These tissues were analyzed also by Western Blot analysis, showing that the proteins obtained from FineFIX treated samples are amenable and comparable in quality with those obtained from fresh frozen tissues. Protein extracts from FineFix treated tissues were also compared with fresh tissues'ones by two dimensional electrophoresis, demonstrating that the protein pattern were well comparable for number and distribution of the spots.

Hydrogen and oxygen stable isotope fractionation in body fluid compartments of dairy cattle according to season, farm, breed, and reproductive stage.

Environmental temperature affects water turnover and isotope fractionation by causing water evaporation from the body in mammals. This may lead to rearrangement of the water stable isotope equilibrium in body fluids. We propose an approach to detect possible variations in the isotope ratio in different body fluids on the basis of different homoeothermic adaptations in varying reproductive stages. Three different reproductive stages (pregnant heifer, primiparous lactating cow, and pluriparous lactating cow) of two dairy cattle breeds (Italian Friesian and Modenese) were studied in winter and summer. Blood plasma, urine, faecal water, and milk were sampled and the isotope ratios of H (2H/1H) and O (18O/16O) were determined. Deuterium excess and isotope-fractionation factors were calculated for each passage from plasma to faeces, urine and milk. The effects of the season, reproductive stages and breed on δ2H and δ18O were significant in all the fluids, with few exceptions. Deuterium excess was affected by season in all the analysed fluids. The correlations between water isotope measurements in bovine body fluids ranged between 0.6936 (urine-milk) and 0.7848 (urine-plasma) for δ2H, and between 0.8705 (urine-milk) and 0.9602 (plasma-milk) for δ18O. The increase in both isotopic δ values in all body fluids during summer is representative of a condition in which fractionation took place as a consequence of a different ratio between ingested and excreted water, which leads to an increased presence of the heavy isotopes. The different body water turnover between adult lactating cattle and non-lactating heifers was confirmed by the higher isotopic δ for the latter, with a shift in the isotopic equilibrium towards values more distant from those of drinking water.

Intranasal administration of recombinant TRAIL down-regulates CXCL-1/KC in an ovalbumin-induced airway inflammation murine model.

Ovalbumin (OVA)-sensitized BALB/c mice were i.n. instilled with recombinant TNF-related apoptosis inducing ligand (TRAIL) 24 hours before OVA challenge. The total number of leukocytes and the levels of the chemokine CXCL-1/KC significantly increased in the bronchoalveolar lavage (BAL) fluids of allergic animals with respect to control littermates, but not in the BAL of mice i.n. pretreated with recombinant TRAIL before OVA challenge. In particular, TRAIL pretreatment significantly reduced the BAL percentage of both eosinophils and neutrophils. On the other hand, when TRAIL was administrated simultaneously to OVA challenge its effect on BAL infiltration was attenuated. Overall, the results show that the i.n. pretreatment with TRAIL down-modulated allergic airway inflammation.

Plasma estrone sulfate, clinical biochemistry, and milk yield of dairy cows carrying a fetus from a bull or its clone.

The aim of this article was to compare plasma estrone sulfate (E1SO4), clinical biochemistry, and milk yield of dairy cows carrying a female fetus from a bull (BULL) or from its clone (CLONE), evaluating also the relationship between the former variables and the birth weight of the newborn. Sixteen recipient dairy Friesian heifers (10 BULL and 7 CLONE) received a female embryo, obtained by in vitro embryo production and sexing by polymerase chain reaction with the semen of the BULL or the CLONE. Blood samples on all cows were obtained before feed distribution in the morning from jugular vein from 4 weeks before to 4 weeks after calving, to be analyzed for metabolic profile. The samples from late gestation were also analyzed for E1SO4 concentration. To separately assess the effect of calf birth weight (CBW), data were categorized as follows: low (<39 kg; BWT-A), mid (39-46 kg; BWT-B), and high (>46 kg; BWT-C). The plasma concentrations of ß-hydroxybutyric acid (BHB, P=0.019), Na (P=0.002), Cl (P=0.026), strong cation-anion balance (P=0.020), total bilirubin (P=0.054), and α1-globulin (P=0.044) were higher in prepartum BULL recipients than those in CLONE, whereas BHB (P=0.021) and Mg (P=0.090) were higher in postpartum BULL recipients, while no differences were recorded in the remaining postpartum parameters. The CBW class had significant interaction with week of gestation on antepartum plasma estrone sulfate (P=0.021), whereas CBW per se affected antepartum plasma BHB (P=0.021), and nonesterified fatty acids (NEFA; P=0.011) being higher in BWT-C which also had the lower NEFA concentration during postpartum. Milk yield was unaffected by the sire used, both for quantitative and qualitative aspects. Cows carrying heavier fetus (BWT-C) had a different lactation affected by month compared with the other 2 CBW groups. From these results, there were no differences between BULL and CLONE recipients. Estrone sulfate, BHB, and NEFA may be used to predict CBW and provide different nutritional management during gestation.

Human discs large and scrib are localized at the same regions in colon mucosa and changes in their expression patterns are correlated with loss of tissue architecture during malignant progression.

Loss of cell polarity is one of the hallmarks of malignant carcinomas. Most of the understanding about the link between cell polarity and proliferation control comes from studies on the Drosophila tumor suppressors discs large (Dlg), scribble (Scrib) and lethal giant larvae (lgl). Mammalian homologues of these proteins have been described and are conserved in sequence and function. Human Dlg (hDlg) and Scrib were independently shown to be down-regulated during malignant progression. This, and other lines of evidence, points toward the participation of both hDlg and hScrib in a common pathway involved in polarity control and tumor suppression. We investigated the correlation between the expression of both proteins in tissues and their relative contributions to the maintenance of tissue architecture during colon cancer development. We analyzed the levels and distribution of hDlg and hScrib by immunohistochemistry, using serial sections of the same sample. We used normal and neoplastic colon mucosa, since it offers a good model for analyzing these features in progressive dysplastic stages. The results demonstrate that both proteins localize at the same regions in polarized colon epithelia, and that in normal samples the proteins' distribution varies as cells differentiate at the surface mucosa. In neoplasia, alterations in the expression pattern of hDlg and of hScrib increase during tumor progression; down-regulation of both proteins being associated with lack of epithelial cell polarity and disorganized tissue architecture. The results, therefore, demonstrate that there is an inverse relationship between the levels of hDlg and hScrib expression and the loss of cell polarity and tissue architecture in the colon.