Comparison between indicine and taurine cattle DNA methylation reveals epigenetic variation associated to differences in morphological adaptive traits

Indicine and taurine subspecies present distinct morphological traits as a consequence of environmental adaptation and artificial selection. Although the two subspecies have been characterized and compared at genome-wide level and at specific loci, their epigenetic diversity has not yet been explored. In this work, Reduced Representation Bisulphite Sequencing (RRBS) profiling of the taurine Angus (A) and indicine Nellore (N) cattle breeds was applied to identify methylation differences between the two subspecies. Genotyping by sequencing (GBS) of the same animals was performed to detect single nucleotide polymorphisms (SNPs) at cytosines in CpG dinucleotides and remove them from the differential methylation analysis. A total of 660,845 methylated cytosines were identified within the CpG context (CpGs) across the 10 animals sequenced (5 N and 5 A). A total of 25,765 of these were differentially methylated (DMCs). Most DMCs clustered in CpG stretches nearby genes involved in cellular and anatomical structure morphogenesis. Also, sequences flanking DMC were enriched in SNPs compared to all other CpGs, either methylated or unmethylated in the two subspecies. Our data suggest a contribution of epigenetics to the regulation and divergence of anatomical morphogenesis in the two subspecies relevant for cattle evolution and sub-species differentiation and adaptation.

FLT3-targeted therapy restores GATA1 pathway function in NPM1/FLT3-ITD mutated acute myeloid leukaemia

One-third of newly diagnosed adult acute myeloid leukaemia (AML) carry FLT3 mutations, which frequently occur together with nucleophosmin (NPM1) mutations and are associated with worse prognosis. FLT3 inhibitors are widely used in clinics with limitations due to drug resistance. AML cells carrying FLT3 mutations in both mouse models and patients present low expression of GATA1, a gene involved in haematopoietic changes preceding AML. Here, we show that FLT3 inhibition induces cellular responses and restores the GATA1 pathway and functions in NPM1/FLT3-ITD mutated AML, thus providing a new mechanism of action for this drug.

Intermediate dose enoxaparin in hospitalized patients with moderate-severe COVID-19: a pilot phase II single-arm study, INHIXACOVID19

BACKGROUND

Randomized clinical trials in non-critically ill COVID-19 patients showed that therapeutic-dose heparin increased survival with reduced organ support as compared with usual-care thromboprophylaxis, albeit with increased bleeding risk. The purpose of the study is to assess the safety of intermediate dose enoxaparin in hospitalized patients with moderate to severe COVID-19.

METHODS

A phase II single-arm interventional prospective study including patients receiving intermediate dose enoxaparin once daily according to body weight: 60 mg for 45-60 kg, 80 mg for 61-100 kg or 100 mg for > 100 kg for 14 days, with dose adjustment according to anti-factor Xa activity (target range: 0.4-0.6 UI/ml); an observational cohort (OC) included patients receiving enoxaparin 40 mg day for comparison. Follow-up was 90 days. Primary outcome was major bleeding within 30 and 90 days after treatment onset. Secondary outcome was the composite of all-cause 30 and 90-day mortality rates, disease severity at the end of treatment, intensive care unit (ICU) admission and length of ICU stay, length of hospitalization. All outcomes were adjudicated by an independent committee and analyzed before and after propensity score matching (PSm).

RESULTS

Major bleeding was similar in IC (1/98 1.02%) and in the OC (none), with only one event observed in a patient receiving concomitantly anti-platelet therapy. The composite outcome was observed in 53/98 patients (54%) in the IC and 132/203 (65%) patients in the OC (p = 0.07) before PSm, while it was observed in 50/90 patients (55.6%) in the IC and in 56/90 patients (62.2%) in the OC after PSm (p = 0.45). Length of hospitalization was lower in the IC than in OC [median 13 (IQR 8-16) vs 14 (11-21) days, p = 0.001], however it lost statistical significance after PSm (p = 0.08). At 30 days, two patients had venous thrombosis and two pulmonary embolism in the OC. Time to first negative RT-PCR were similar in the two groups.

CONCLUSIONS

Weight adjusted intermediate dose heparin with anti-FXa monitoring is safe with potential positive impact on clinical course in COVID-19 non-critically ill patients.

TRIAL REGISTRATION

The study INHIXACOVID19 was registred on ClinicalTrials.gov with the trial registration number (TRN) NCT04427098 on 11/06/2020.

CpG DNA methylation changes during epididymal sperm maturation in bulls

BACKGROUND

During epididymal transit spermatozoa acquire specific morphological features which enhance their ability to swim in a progressive manner and interact with the oocytes. At the same time, sperm cells undergo specific molecular rearrangements essential for the fertilizing sperm to drive a correct embryo development. To assess epigenetic sperm changes during epididymal maturation, the caput, corpus and cauda epididymis sperm tracts were isolated from eight bulls and characterized for different sperm quality parameters and for CpG DNA methylation using Reduced Representation Bisulfite Sequencing (RRBS) able to identify differentially methylated regions (DMRs) in higher CpG density regions.

RESULTS

Caput sperm showed significant variation in motility and sperm kinetics variables, whereas spermatozoa collected from the corpus presented morphology variation and significant alterations in variables related to acrosome integrity. A total of 57,583 methylated regions were identified across the eight bulls, showing a significantly diverse distribution for sperm collected in the three epididymal regions. Differential methylation was observed between caput vs corpus (n = 11,434), corpus vs cauda (n = 12,372) and caput vs cauda (n = 2790). During epididymal transit a high proportion of the epigenome was remodeled, showing several regions in which methylation decreases from caput to corpus and increases from corpus to cauda.

CONCLUSIONS

Specific CpG DNA methylation changes in sperm isolated from the caput, corpus, and cauda epididymis tracts are likely to refine the sperm epigenome during sperm maturation, potentially impacting sperm fertilization ability and spatial organization of the genome during early embryo development.

Stable Operation of a Free-Electron Laser Driven by a Plasma Accelerator

The breakthrough provided by plasma-based accelerators enabled unprecedented accelerating fields by boosting electron beams to gigaelectronvolt energies within a few centimeters [1-4]. This, in turn, allows the realization of ultracompact light sources based on free-electron lasers (FELs) [5], as demonstrated by two pioneering experiments that reported the observation of self-amplified spontaneous emission (SASE) driven by plasma-accelerated beams [6,7]. However, the lack of stability and reproducibility due to the intrinsic nature of the SASE process (whose amplification starts from the shot noise of the electron beam) may hinder their effective implementation for user purposes. Here, we report a proof-of-principle experiment using plasma-accelerated beams to generate stable and reproducible FEL light seeded by an external laser. FEL radiation is emitted in the infrared range, showing the typical exponential growth of its energy over six consecutive undulators. Compared to SASE, the seeded FEL pulses have energies 2 orders of magnitude larger and stability that is 3 times higher.

Free-electron lasing with compact beam-driven plasma wakefield accelerator

The possibility to accelerate electron beams to ultra-relativistic velocities over short distances by using plasma-based technology holds the potential for a revolution in the field of particle accelerators^1-4. The compact nature of plasma-based accelerators would allow the realization of table-top machines capable of driving a free-electron laser (FEL)⁵, a formidable tool to investigate matter at the sub-atomic level by generating coherent light pulses with sub-ångström wavelengths and sub-femtosecond durations^6,7. So far, however, the high-energy electron beams required to operate FELs had to be obtained through the use of conventional large-size radio-frequency (RF) accelerators, bound to a sizeable footprint as a result of their limited accelerating fields. Here we report the experimental evidence of FEL lasing by a compact (3-cm) particle-beam-driven plasma accelerator. The accelerated beams are completely characterized in the six-dimensional phase space and have high quality, comparable with state-of-the-art accelerators⁸. This allowed the observation of narrow-band amplified radiation in the infrared range with typical exponential growth of its intensity over six consecutive undulators. This proof-of-principle experiment represents a fundamental milestone in the use of plasma-based accelerators, contributing to the development of next-generation compact facilities for user-oriented applications⁹.

Development of a web platform for COVID-19 integrated care: an experience from an Italian Region

Issue

After the announcement of Public Health Emergency of International Concern about COVID19 by WHO, health authorities need to implement strategies to face the emergency. These responses included early diagnosis, patient isolation, quarantine and symptomatic monitoring of contacts. In this context, integrated care and telemedicine are the best instruments for COVID management.

Description of the problem

The COVID19 epidemic needs a real time integration of epidemiological, clinical and laboratoristic data, in order to better manage patients and to improve public health surveillance. Based on a tool previosly used by GPs for flu vaccination and diabetes integrated care, the Local Health Authority of Pescara, Abruzzo Region, Italy, developed a web-based platform (QuickwebConnect), accessible to public health practitioners (PHP), GPs, infectious diseases physicians and laboratories, in order to integrate information about COVID19 patients. This platform contain individual-level information on patients with laboratory-confirmed COVID19, symptoms, reported onset dates, and basic demographics. Information are in real time accessible to all actors involved in the process. In addition, GPs can use this tool to directly book diagnostic tests for symptomatic or suspected patients.

Results

With the use of this platform, the management of pandemic emergency was improved, allowing direct management of epidemic data both at person and population level. The real time evaluation of clinical and epidemiological data improved patients care, clinical survellance of COVID19 contacts and development of tailored preventive measure in areas with high incidence.

Lessons

COVID19 patients care need to be quick, needing the integrate support of different actors. In addition, public health actions have to be supported by strong data. The use of a cost-effective web platform allow physician and PHP to better manage patiens and develope focused interventions.

Key messages

Integrated care and telemedicine are best instruments for COVID management. The real time evaluation of data aimed to develop tailored preventive measure.

The white coat public art project: using the white coat as a canvas for reflection for women in medicine

OBJECTIVES

Burnout and low job satisfaction have disproportionately impacted female physicians compared with their male counterparts, with gender-specific oppression and bias in the workforce. This project aims to address the relationship of women in medicine to their chosen field through public art.

STUDY DESIGN

A call for using the white coat as a canvas to describe positive attributes and self-reflection was shared with all American Medical Women's Association (AMWA) branches at medical schools.

METHODS

Students in AMWA branches created white coats, designing them to answer the posed question.

RESULTS

White coats were sent to the national conference for display, revealing certain themes, challenges, resilience, and humanization of the training and working experience for women in medicine.

CONCLUSION

This white coat public art project directly and indirectly addresses causes of burnout and serves as a way to create community, address isolation, and empower women in medicine.

55 Peri-conceptional undernourishment perturbs offspring sperm methylome

Whereas an organism’s genotype is relatively static throughout life, the epigenome is highly dynamic and can adapt, or be altered, in response to the external environment such as diet. Intrauterine exposure to nutrient availability can alter the establishment of epigenetic marks, not only in the exposed individuals, but also in their offspring. Inheritance of such an environmentally acquired phenotype by the subsequent generation occurs through epigenetic modifications in the germline. Here, using a genome-wide approach, we evaluate how modification of the maternal diet pre- (14 days) and post- (28 days) conception can affect methylation status of the sperm of male offspring. Specifically, using a sheep model, we focused on the effect of maternal undernutrition on adult sperm methylation and its long-term consequences on sperm physiology and quality. Moreover, we investigated if supplementation of folic acid, to increase the availability of methyl donors, could prevent or ameliorate the adverse uterine environment caused by maternal undernutrition. Male lambs obtained from mothers subjected to different nutritional regimens (UND: undernutrition; FA: undernutrition and folic acid supplementation) appeared normal at birth, with a comparable body weight until Day 30 postpartum. Sperm DNA methylation, obtained by reduced representation bisulfite sequencing, differed in offspring that experienced in utero undernutrition (UND and FA) compared with the control group (CTR). In particular, the number of differentially methylated regions (DMR) was lower when UND and FA groups were compared, whereas a higher number of DMR was observed by comparison of CTR with both experimental groups. In addition, a high percentage of DMR were shared between UND and FA groups when compared with CTR, clearly indicating a influence of maternal nutrition on the offspring sperm DNA methylation rearrangement. Gene ontology (GO) analysis showed variation in functional categories related to sperm functionality such as chondroitin sulfate synthesis, potassium ion import, and others related to metabolism (biotin and glucagon). Furthermore, using computer-assisted semen analysis and flow cytometric measurement, we observed lower a sperm motility index and higher incidence of chromatin structure alterations in spermatozoa collected from UND and FA groups compared with CTR. Finally, to verify the effect of such reported abnormality on lamb fertility, we used the semen for in vitro embryo production. While we obtained good quality blastocysts from all 3 groups, a reduction in the percentage of embryo development, partially compensated in the FA group, was found using spermatozoa from UND rams. Taken together, our results confirm that a nutritional stress during early mammalian development can lead to epigenetic modification in the offspring. This damage can be partially ameliorated with folic acid supplementation; however, some alteration still persists in the germline and could be passed to the next generation, with as yet unknown consequences.

Focusing of High-Brightness Electron Beams with Active-Plasma Lenses

Plasma-based technology promises a tremendous reduction in size of accelerators used for research, medical, and industrial applications, making it possible to develop tabletop machines accessible for a broader scientific community. By overcoming current limits of conventional accelerators and pushing particles to larger and larger energies, the availability of strong and tunable focusing optics is mandatory also because plasma-accelerated beams usually have large angular divergences. In this regard, active-plasma lenses represent a compact and affordable tool to generate radially symmetric magnetic fields several orders of magnitude larger than conventional quadrupoles and solenoids. However, it has been recently proved that the focusing can be highly nonlinear and induce a dramatic emittance growth. Here, we present experimental results showing how these nonlinearities can be minimized and lensing improved. These achievements represent a major breakthrough toward the miniaturization of next-generation focusing devices.

190 Profile of MicroRNAs of Equine Amniotic Mesenchymal Cell-Derived Microvesicles in Different Time-Span of In Vitro Culture

Mesenchymal stromal cells (MSC) were found to secrete many factors with therapeutic relevance for their antioxidants, antiapoptotic, antifibrotic, angiogenic, immunomodulatory, and chemiotactic activities. The culture supernatant of MSC (in our case, of equine amniotic-derived cells) is defined secretome or conditioned medium (CM) and it is composed of soluble and insoluble factors secreted by cells. Soluble factors are represented by cytokines and growth factors, whereas microvesicles (MV), recently demonstrated to be an integral component of cell-to-cell communication during tissue regeneration, represent insoluble factors (Bruno et al. 2009 J. Am. Soc. Nephrol. 20, 1053-1067). Our previous data showed that equine amniotic-derived CM administered in vivo in equine spontaneous tendon lesion is able to regenerate the injured tissue. overlapping the results obtained by using in vivo the cells of origin in the same pathology (Lange-Consiglio et al. 2013 Stem Cells Devel. 22, 3015-3024). We also studied the amniotic-derived MV and found that they are involved in down-regulation of pro-inflammatory genes in in vitro LPS-stressed equine tendon and endometrial cells (Lange-Consiglio et al. 2016 Stem Cells Devel. 25, 610-621; Perrini et al. 2016 Stem Cell Res. Ther. 7, 169). Usually, protocols to produce CM and MV are different: CM is collected after 48 to 96 h of culturing cells without renewal of tissue culture medium, whereas MV are collected after culturing cells overnight. In future comparative studies of regenerative medicine aiming to understand the efficacy of CM and MV, understanding the quality of secretion of cells according to culturing time is crucial. The aim of the present study was to evaluate whether different times of culture can influence the micro-RNA (miRNA) cargo of equine amniotic-derived cells and their MV. Biological triplicates of a pool of amniotic-derived cells from 2 amniotic membranes and their MV, collected after overnight or after 4 days, were used. Following miRNA extraction and library preparation, deep sequencing was carried out on Illumina HisSEqn 2000 (Illumina Inc., San Diego, CA, USA). Mirdeep2 on Illumina high-quality trimmed sequences was used to detect known miRNAs and to support the individuation of novel miRNAs. The analysis identified 335 Equus caballus miRNA, which were quantified in both amniotic cells and MV. Hierarchical clustering of 83 miRNA that were observed in all 12 samples clearly discriminated amniotic cells and MV. The profile of miRNA in AMC and MV was similar between overnight and 4 days of culture. Further functional studies on the predicted target genes and pathways involved in the biological effect of equine amniotic secretome will be performed.

Genomic and transcriptomic comparison between Staphylococcus aureus strains associated with high and low within herd prevalence of intra-mammary infection

Background

Staphylococcus aureus (Staph. aureus) is one of the major pathogens causing mastitis in dairy ruminants worldwide. The chronic nature of Staph. aureus infection enhances the contagiousness risk and diffusion in herds. In order to identify the factors involved in intra-mammary infection (IMI) and diffusion in dairy cows, we investigated the molecular characteristics of two groups of Staph. aureus strains belonging to ST8 and ST398, differing in clinical properties, through comparison of whole genome and whole transcriptome sequencing.

Results

The two groups of strains, one originated from high IMI prevalence herds and the other from low IMI prevalence herds, present a peculiar set of genes and polymorphisms related to phenotypic features, such as bacterial invasion of mammary epithelial cells and host adaptation. Transcriptomic analysis supports the high propensity of ST8 strain to chronicity of infection and to a higher potential cytotoxicity.

Conclusions

Our data are consistent with the invasiveness and host adaptation feature for the strains GTB/ST8 associated to high within-herd prevalence of mastitis. Variation in genes coding for surface exposed proteins and those associated to virulence and defence could constitute good targets for further research.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-017-0931-8) contains supplementary material, which is available to authorized users.

Small RNA sequencing of cryopreserved semen from single bull revealed altered miRNAs and piRNAs expression between High- and Low-motile sperm populations

Background

Small RNAs present in bovine ejaculate can be linked to sperm abnormalities and fertility disorders. At present, quality parameters routinely used in semen evaluation are not fully reliable to predict bull fertility. In order to provide additional quality measurements for cryopreserved semen used for breeding, a method based on deep sequencing of sperm microRNA (miRNA) and Piwi-interacting RNA (piRNA) from individual bulls was developed.

To validate our method, two populations of spermatozoa isolated from high and low motile fractions separated by Percoll were sequenced, and their small RNAs content characterized.

Results

Sperm cells from frozen thawed semen samples of 4 bulls were successfully separated in two fractions. We identified 83 miRNAs and 79 putative piRNAs clusters that were differentially expressed in both fractions. Gene pathways targeted by 40 known differentially expressed miRNAs were related to apoptosis. Dysregulation of miR-17-5p, miR-26a-5p, miR-486-5p, miR-122-5p, miR-184 and miR-20a-5p was found to target three pathways (PTEN, PI3K/AKT and STAT).

Conclusions

Small RNAs sequencing data obtained from single bulls are consistent with previous findings. Specific miRNAs are differentially represented in low versus high motile sperm, suggesting an alteration of cell functions and increased germ cell apoptosis in the low motile fraction.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3394-7) contains supplementary material, which is available to authorized users.

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine: Brussels, Belgium. 15-18 March 2016

[This corrects the article DOI: 10.1186/s13054-016-1208-6.].

Endovascular Repair as First-Choice Treatment for Anastomotic and True Iliac Aneurysms

Purpose:

To report our experience with the endovascular repair of iliac aneurysms secondary to aortoiliac bypass grafting.

Methods:

Thirteen patients (12 men; age range 62–86 years) with histories of aortoiliac reconstructions were treated with endovascular stent-grafts for 11 false and 2 true iliac aneurysms that averaged 5.2 cm in diameter (range 3.0–7.0). Via a percutaneous access and 9-F or 12-F sheaths, Passager or Wallgraft stent-grafts were delivered to exclude the aneurysms.

Results:

Twelve (92%) of 13 interventions were completed satisfactorily; 1 procedure for a true iliac aneurysm was converted to traditional bypass grafting. Two patients underwent additional surgical procedures. The average hospital stay for the patients with endovascular repairs only was 3 days (range 2–5). After a mean follow-up of 28 months (range 17–40), no complication or endoleak has been detected in any patient, and all endografts are patent.

Conclusions:

Endovascular repair is an effective treatment for secondary aneurysms arising after aortoiliac surgery. It is less invasive and involves a shorter hospital stay. Endovascular repair should be the first choice treatment for iliac aneurysms.

Genome-wide association scan suggests basis for microtia in Awassi sheep

Hereditary underdevelopment of the ear, a condition also known as microtia, has been observed in several sheep breeds as well as in humans and other species. Its genetic basis in sheep is unknown. The Awassi sheep, a breed native to southwest Asia, carries this phenotype and was targeted for molecular characterization via a genome-wide association study. DNA samples were collected from sheep in Jordan. Eight affected and 12 normal individuals were genotyped with the Illumina OvineSNP50(®) chip. Multilocus analyses failed to identify any genotypic association. In contrast, a single-locus analysis revealed a statistically significant association (P = 0.012, genome-wide) with a SNP at basepair 34 647 499 on OAR23. This marker is adjacent to the gene encoding transcription factor GATA-6, which has been shown to play a role in many developmental processes, including chondrogenesis. The lack of extended homozygosity in this region suggests a fairly ancient mutation, and the time of occurrence was estimated to be approximately 3000 years ago. Many of the earless sheep breeds may thus share the causative mutation, especially within the subgroup of fat-tailed, wool sheep.

A method for single nucleotide polymorphism selection for parentage assessment in goats

Accurate pedigrees are essential to optimize genetic improvement and conservation of animal genetic resources. In goats, the use of mating groups and kidding management procedures hamper the identification of parentage. Small panels of single nucleotide polymorphisms (SNP) have been proposed in other species to substitute microsatellites for parentage assessment. Using data from the current GoatSNP50 chip, we developed a new 3-step procedure to identify a low-density SNP panel for highly accurate parentage assessment. Methodologies for SNP selection used in other species are less suitable in the goat because of uncertainties in the genome assembly. The procedure developed in this study is based on parent-offspring identification and on estimation of Mendelian errors, followed by canonical discriminant analysis identification and stepwise regression reduction. Starting from a reference sample of 109 Alpine goats with known pedigree relationships, we first identified a panel of 200 SNP that was further reduced to 2 final panels of 130 and 114 SNP with random coincidental match inclusion of 1.51×10(-57) and 2.94×10(-34), respectively. In our reference data set, all panels correctly identified all parent-offspring combinations, revealing a 40% pedigree error rate in the information provided by breeders. All reference trios were confirmed by official tests based on microsatellites. Panels were also tested on Saanen and Teramana breeds. Although the testing on a larger set of breeds in the reference population is still needed to validate these results, our findings suggest that our procedure could identify SNP panels for accurate parentage assessment in goats or in other species with unreliable marker positioning.

71 CIRCULATING microRNAs AS POTENTIAL BIOMARKERS OF EARLY PREGNANCY IN HIGH-PRODUCING DAIRY COWS

Lactation induces changes in the metabolic status of postpartum dairy cows that negatively affects the likelihood of pregnancy establishment. At present, pregnancy diagnosis with confidence is only possible after the third week of gestation. Earlier diagnosis could facilitate earlier re-breeding, reduce calving intervals, and improve profits for the industry. MicroRNAs (miRNAs) released in body fluids have been identified as minimally invasive biomarkers of several diseases. In addition, distinct miRNA profiles have been directly related to specific stages of human pregnancy. The aim of this study was to profile circulating miRNAs in the blood of high-producing dairy cows in order to identify biomarkers of early pregnancy. In-calf primiparous Holstein-Friesian cows (n = 22) with a similar economic breeding index were used. At calving, cows were randomly assigned to one of two groups: (1) lactating (n = 11; milked twice per day) or (2) non-lactating (n = 11; dried off immediately). Around 65 to 75 days postpartum (dpp), oestrous cycles were synchronized and a single embryo from a superovulated Holstein-Friesian donor was transferred at Day 7 post-oestrus. Plasma samples were analysed at Day 13 (initiation of conceptus elongation) and at Day 19 (initiation of implantation). Pregnancy rate, established by the presence of conceptus at Day 19, was 5/11 (45%) for lactating and 8/11 (73%) for non-lactating cows, respectively. Circulating miRNA levels were profiled in 4 animals per group in non-lactating pregnant, and lactating pregnant and nonpregnant cows at selected timepoints using Illumina HiSEqn 2000 (Illumina Inc., San Diego, CA, USA) for smallRNA sequencing. Annotation and discovery of miRNAs were done using MirDeep2, and read counts were analysed using edgeR to identify differentially expressed miRNAs. Target genes analysis was run with miRWalk and pathways interactions were built using Cytoscape (P ≤ 0.05). Differentially abundant miRNAs between lactating and non-lactating cows were found at both time points (FDR ≤ 0.05). At Day 13, non-lactating cows had a distinct miRNA profile compared with lactating cows showing 8 differentially expressed miRNA (6 v. pregnant and 2 v. nonpregnant cows). At Day 19, no significant differences were found within pregnant cows, but 5 differentially expressed miRNAs were identified between pregnant and nonpregnant cows, regardless of metabolic status. Interestingly, one miRNA, bta-mir140, was up-regulated in non-lactating pregnant cows from Day 13 onwards compared with nonpregnant cows. Furthermore, the same miRNA was up-regulated in lactating pregnant v. nonpregnant at Day 19. Among bta-mir140 target genes, CD274, SLC44A4, CXCL12, and SIRPA were strictly associated with immune tolerance. In conclusion, the maternal plasma miRNome may represent an early indicator of pregnancy status. In particular, the up-regulation of bta-mir140 in pregnant cows suggests that this miRNA may be a good candidate as an early biomarker of fertility. Furthermore, the positive correlation between this miRNA and pathways involved in T-cell response may indicate a role of immune tolerance in preventing rejection at the initiation of implantation.

Software solutions for the livestock genomics SNP array revolution

Since the beginning of the genomic era, the number of available single nucleotide polymorphism (SNP) arrays has grown considerably. In the bovine species alone, 11 SNP chips not completely covered by intellectual property are currently available, and the number is growing. Genomic/genotype data are not standardized, and this hampers its exchange and integration. In addition, software used for the analyses of these data usually requires not standard (i.e. case specific) input files which, considering the large amount of data to be handled, require at least some programming skills in their production. In this work, we describe a software toolkit for SNP array data management, imputation, genome-wide association studies, population genetics and genomic selection. However, this toolkit does not solve the critical need for standardization of the genotypic data and software input files. It only highlights the chaotic situation each researcher has to face on a daily basis and gives some helpful advice on the currently available tools in order to navigate the SNP array data complexity.

Imputation accuracy is robust to cattle reference genome updates

Genotype imputation is routinely applied in a large number of cattle breeds. Imputation has become a need due to the large number of SNP arrays with variable density (currently, from 2900 to 777,962 SNPs). Although many authors have studied the effect of different statistical methods on imputation accuracy, the impact of a (likely) change in the reference genome assembly on imputation from lower to higher density has not been determined so far. In this work, 1021 Italian Simmental SNP genotypes were remapped on the three most recent reference genome assemblies. Four imputation methods were used to assess the impact of an update in the reference genome. As expected, the four methods behaved differently, with large differences in terms of accuracy. Updating SNP coordinates on the three tested cattle reference genome assemblies determined only a slight variation on imputation results within method.

Indoor pollution and burning practices in wood stove management

This study evaluates effects of good burning practice and correct installation and management of wood heaters on indoor air pollution in an Italian rural area. The same study attests the role of education in mitigating wood smoke pollution. In August 2007 and winters of 2007 and 2008, in a little mountain village of Liguria Apennines (Italy), indoor and outdoor benzene, toluene, ethylbenzene, and xylene (BTEX) concentrations were measured in nine wood-heated houses. During the first sampling, several mistakes in heating plant installations and management were found in all houses. Indoor BTEX concentrations increased during use of wood burning. Low toluene/benzene ratios were in agreement with wood smoke as main indoor and outdoor pollution source. Other BTEX sources were identified as the indoor use ofsolvents andpaints and incense burning. Results obtained during 2007 were presented and discussed with homeowners. Following this preventive intervention, in the second winter sampling all indoor BTEX concentrations decreased, in spite of the colder outdoor air temperatures. Information provided to families has induced the adoption of effective good practices in stoves and fire management. These results highlight the importance ofeducation, supported by reliable data on air pollution, as an effective method to reduce wood smoke exposures.

Proximal aortic neck angle does not affect early and late EVAR outcomes: an AnacondaTM Italian Registry analysis

AIM

The aim of this paper was to evaluate early and 3-year results of the endovascular repair (EVAR) for abdominal aortic aneurysm (AAA) using the AnacondaTM endograft in patients with severe proximal aortic neck angle.

METHODS

A retrospective analysis of the AnacondaTM Italian Registry was carried out. Two groups of patients were identified according to the presence of a severe (Group A, GA: ≥ 60°) or an absent (Group B, GB: <45°) proximal aortic neck angle. Preoperative, procedural and follow-up data were evaluated. Mortality, proximal type I endoleak, freedom from iliac leg thrombosis and conversion to open repair were analyzed at 30-day and 3-year follow-up. The results of GA and GB were compared.

RESULTS

From 2005 to 2012, 1030 patients were enrolled in the Registry. Sixty-five patients (6.3%) were included in GA and 737 (71.5%) in GB. The mean age and AAA diameter were respectively 76.8 years and 62.7 mm in GA and 77.2 years and 56.5 mm in GB (P=NS). The ASA ≥ 3 was reported in the 95.3% of GA vs. 81% of GB (P=0.005). The endograft main-body was repositioned in 35% of cases in GA and 20.7% in GB (P=0.008); there were no differences in the main-body ballooning and proximal aortic cuff placement. There were no statistical differences in 30-day mortality (GA 1.5% vs. GB 1.3%), proximal type I endoleaks (GA 1.5% vs. GB 0.8%), iliac leg thrombosis (GA 1.5% vs. GB 1.4%) and conversion to open repair (GA 3% vs. GB 0.6%). The 3-year survival was 95.4% in GA and 94.7% in GB (P=NS). Freedom from proximal type I endoleak, iliac leg thrombosis and conversion to open repair were respectively 98.5%, 95.4%, and 95.4% in GA and 97.8%, 96.9%, and 98.5% in GB (P=NS).

CONCLUSION

The AnacondaTM Italian Registry reports good results in terms of clinical success at 3-year follow-up. AAA with severe proximal aortic neck can be treated with similar outcomes to AAA with favorable neck anatomy. The endograft repositionability is a benefit in cases with severe neck angle.

Bypass to the ankle and foot in the era of endovascular therapy of tibial disease. Results and factors influencing the outcome

AIM

Endovascular therapy (ET) is the treatment of choice for critical limb ischemia (CLI) and tibial arteries disease (TAD) in focal lesions with restorable run-off; ankle and foot bypass (BPG) is indicated in patients unfit for ET with foot or ankle arteries suitable for surgery. The aim of this study was to evaluate limb salvage (LS), primary patency (PP) and survival (S) of patients underwent BPG in the era of ET for TAD and to define the correlated prognostic factors.

METHODS

Between February 2000 and November 2008, patients with CLI and TAD were collected prospectively in a data-base (demographics, Fontaine's stage, Texas University Wound Classification [TUC]of ulcers, risk-factors, TAD, techniques of foot revascularization and surgical factors). BPG was performed in tibial arteries occlusion longer than 4 cm or focal occlusion without line-flow to pedal arteries. Clinical and Duplex-ultrasound follow-up was performed at discharge, 1, 3, 6 months and every 6 months. LS, PP, and S rates were assessed with Kaplan-Meier method; factors influencing outcomes were sought by multivariate Cox proportional hazards model analysis.

RESULTS

A total of 410 revascularizations were performed in patients with CLI and TAD; BPG in 153 patients (mean age: 69.3±10.6, male/female=117/36, diabetes mellitus=75.2% hyperlypidemia=54.9%, hypertension=87.6%, renal disease=32.7%, coronary arteries disease=51.6%, Fontaine stage IV=96.1%, TUC grade-III=65.4%, TUC stage-D=51%). All autologous grafts in 96.7% (non-reversed saphenous vein=74.5%, reversed=7.2%, composite vein graft=12.4%, arm's veins=2.6%). LS and S after 1 month were 88.2% and 97.1%, respectively. Mean follow-up was 23 months. At 12 and 36 months: LS 76.7% and 70.9%, PP 62.3% and 52.9%, S 91.5% and 74.6%. LS was negatively associated with age (HR=1.041 [95%CI=1.005-1.079]), infected ulcers (HR=3.377 [95%CI=1.571-7.258]), run-off arteries diameter <1.8 mm (HR=5.854[95% CI=2.274-15.070]). PP was negatively associated with hyperlipidemia (HR=2.555 [95% CI=1.418-4.603]), female gender (HR=2.125[95% CI=1.182-3.823]), run-off arteries diameter <1.8 mm (HR=6.165 [95% CI=2.774-13.699]), reversed saphenous graft (HR=3.105 [95% CI=1.166-8.272]), composite vein graft (HR=2.930 [95% CI=1.406-6.107]) and homograft (HR=2.762 [95% CI=1.040-7.333]); instead it is positively related with hypertension (HR=4.229 [95% CI=2.089-8.563]). S was negatively correlated with renal disease (HR=3.035 [95% CI=1.363-6.756]).

CONCLUSION

BPG may be a reasonable first treatment for CLI patients with TAD unfit for ET; female gender, hyperlipidemia, use of reversed saphenous, composite vein or alternative grafts, foot infection and renal disease are associated with worse outcome.

Kinetic modelling of haemodialysis removal of myoglobin in rhabdomyolysis patients

An extended two compartment model is proposed to describe the dynamics of myoglobin in rhabdomyolysis patients undergoing dialysis. Before using clinical data to estimate the model's unknown parameters, structural identifiability analysis was performed to determine the parameters uniqueness given certain clinical observations. A Taylor series expansion method was implemented which found that the model was structurally globally/uniquely identifiable for both on- and off-dialysis phases. The fitted model was then used in a predictive capacity showing that the use of Theralite high cut-off (HCO) or HCO 1100 dialyser gave a significant reduction in myoglobin renal exposure compared to standard haemodialysis (HD).

Urinary exosomes and diabetic nephropathy: a proteomic approach

Urinary exosomes (UE) are nanovesicles released by every epithelial cell facing the urinary space and they are considered a promising source of molecular markers for renal dysfunction and structural injury. Exosomal proteomics has emerged as a powerful tool for understanding the molecular composition of exosomes and has potential to accelerate biomarker discovery. We employed this strategy in the study of diabetic nephropathy (DN) and the consequent end stage renal disease, which represent the dramatic evolution of diabetes, often leading the patients to dialysis or kidney transplantation. The identification of DN biomarkers is likely to help monitoring the disease onset and progression. A label free LC-MS/MS approach was applied to investigate the alteration of the proteome of urinary exosomes isolated from the Zucker diabetic fatty rats (ZDF), as a model of type 2 DN. We collected 24 hour urine samples from 7 ZDF and from 7 control rats at different ages (6, 12 and 20 weeks old) to monitor the development of DN. Exosomes were isolated by ultracentrifugation and their purity assessed by immunoblotting for known exosomal markers. Exosomal proteins from urine samples of 20 week old rats were pooled and analyzed by nLC-ESI-UHR-QToF-MS/MS after pre-filtration and tryptic digestion, leading to the identification and label free quantification of 286 proteins. Subcellular localization and molecular functions were assigned to each protein by UniprotKB, showing that the majority of identified proteins were membrane-associated or cytoplasmic and involved in transport, signalling and cellular adhesion, typical functions of exosomal proteins. We further validated label free mass spectrometry results by immunoblotting, as exemplified by: Xaa-Pro dipeptidase, Major Urinary Protein 1 and Neprilysin, which resulted increased, decreased and not different, respectively, in exosomes isolated from diabetic urine samples compared to controls, by both techniques. In conclusion we show the potential of exosome proteomics for DN biomarker discovery.