Publications by authors named "Alessandra Stella"

99 Publications

Acceleration of the SPADE Method Using a Custom-Tailored FP-Growth Implementation.

Front Neuroinform 2021 16;15:723406. Epub 2021 Sep 16.

Cognitronics and Sensor Systems, CITEC, Bielefeld University, Bielefeld, Germany.

The (spatio-temporal pike ttern etection and valuation) method was developed to find reoccurring spatio-temporal patterns in neuronal spike activity (parallel spike trains). However, depending on the number of spike trains and the length of recording, this method can exhibit long runtimes. Based on a realistic benchmark data set, we identified that the combination of pattern mining (using the algorithm) and the result filtering account for 85-90% of the method's total runtime. Therefore, in this paper, we propose a customized implementation tailored to the requirements of , which significantly accelerates pattern mining and result filtering. Our version allows for parallel and distributed execution, and due to the improvements made, an execution on heterogeneous and low-power embedded devices is now also possible. The implementation has been evaluated using a traditional workstation based on an Intel Broadwell Xeon E5-1650 v4 as a baseline. Furthermore, the heterogeneous microserver platform RECS|Box has been used for evaluating the implementation on two HiSilicon Hi1616 (Kunpeng 916), an Intel Coffee Lake-ER Xeon E-2276ME, an Intel Broadwell Xeon D-D1577, and three NVIDIA Tegra devices (Jetson AGX Xavier, Jetson Xavier NX, and Jetson TX2). Depending on the platform, our implementation is between 27 and 200 times faster than the original implementation. At the same time, the energy consumption was reduced by up to two orders of magnitude.
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http://dx.doi.org/10.3389/fninf.2021.723406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8483730PMC
September 2021

A Combined Flow Cytometric Semen Analysis and miRNA Profiling as a Tool to Discriminate Between High- and Low-Fertility Bulls.

Front Vet Sci 2021 19;8:703101. Epub 2021 Jul 19.

Institute of Agricultural Biology and Biotechnology, National Research Council (IBBA-CNR), Lodi, Italy.

Predicting bull fertility is one of the main challenges for the dairy breeding industry and artificial insemination (AI) centers. Semen evaluation performed in the AI center is not fully reliable to determine the level of bull fertility. Spermatozoa are rich in active miRNA. Specific sperm-borne miRNAs can be linked to fertility. The aim of our study is to propose a combined flow cytometric analysis and miRNA profiling of semen bulls with different fertility to identify markers that can be potentially used for the prediction of field fertility. Sperm functions were analyzed in frozen-thawed semen doses (CG: control group) and high-quality sperm (HQS) fraction collected from bulls with different field fertility levels (estimated relative conception rate or ERCR) by using advanced techniques, such as the computer-assisted semen analysis system, flow cytometry, and small RNA-sequencing. Fertility groups differ for total and progressive motility and in the abnormality degree of the chromatin structure ( < 0.05). A backward, stepwise, multiple regression analysis was applied to define a model with high relation between (e.g., ERCR) and (i.e., semen quality and DE-miRNA) fertility data. The analysis produced two models that accounted for more than 78% of the variation of ERCR (CG: = 0.88; HQS: = 0.78), identifying a suitable combination of parameters useful to predict bull fertility. The predictive equation on CG samples included eight variables: four kinetic parameters and four DNA integrity indicators. For the HQS fraction, the predictive equation included five variables: three kinetic parameters and two DNA integrity indicators. A significant relationship was observed between real and predicted fertility in CG ( = 0.88) and HQS fraction ( = 0.82). We identified 15 differentially expressed miRNAs between high- and low-fertility bulls, nine of which are known (miR-2285n, miR-378, miR-423-3p, miR-191, miR-2904, miR-378c, miR-431, miR-486, miR-2478) while the remaining are novel. The multidimensional preference analysis model partially separates bulls according to their fertility, clustering three semen quality variable groups relative to motility, DNA integrity, and viability. A positive association between field fertility, semen quality parameters, and specific miRNAs was revealed. The integrated approach could provide a model for bull selection in AI centers, increasing the reproductive efficiency of livestock.
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http://dx.doi.org/10.3389/fvets.2021.703101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8329915PMC
July 2021

Methylome Patterns of Cattle Adaptation to Heat Stress.

Front Genet 2021 28;12:633132. Epub 2021 May 28.

Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.

Heat stress has a detrimental impact on cattle health, welfare and productivity by affecting gene expression, metabolism and immune response, but little is known on the epigenetic mechanisms mediating the effect of temperature at the cellular and organism level. In this study, we investigated genome-wide DNA methylation in blood samples collected from 5 bulls of the heat stress resilient Nellore breed and 5 bulls of the Angus that are more heat stress susceptible, exposed to the sun and high temperature-high humidity during the summer season of the Brazilian South-East region. The methylomes were analyzed during and after the exposure by Reduced Representation Bisulfite Sequencing, which provided genome-wide single-base resolution methylation profiles. Significant methylation changes between stressful and recovery periods were observed in 819 genes. Among these, 351 were only seen in Angus, 366 were specific to Nellore, and 102 showed significant changes in methylation patterns in both breeds. KEGG and Gene Ontology (GO) enrichment analyses showed that responses were breed-specific. Interestingly, in Nellore significant genes and pathways were mainly involved in stress responses and cellular defense and were under methylated during heat stress, whereas in Angus the response was less focused. These preliminary results suggest that heat challenge induces changes in methylation patterns in specific loci, which should be further scrutinized to assess their role in heat tolerance.
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http://dx.doi.org/10.3389/fgene.2021.633132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8194315PMC
May 2021

Whole-Genome Sequence Analysis of Italian Honeybees ().

Animals (Basel) 2021 May 2;11(5). Epub 2021 May 2.

IBBA-CNR, 20133 Milano, Italy.

At the end of the last glaciation, was established in northern Europe. In Italy, adapted to the mild climate and to the rich floristic biodiversity. Today, with the spread of and with the increasing use of pesticides in agriculture, the Ligustica subspecies is increasingly dependent on human action for its survival. In addition, the effects of globalization of bee keeping favored the spread in Italy of other honeybee stocks of , in particular the Buckfast bee. The purpose of this study was to characterize the Italian honeybee's population by sequencing the whole genome of 124 honeybees. Whole genome sequencing was performed by Illumina technology, obtaining a total coverage of 3720.89X, with a mean sample coverage of 29.77X. A total of 4,380,004 SNP variants, mapping on Amel_HAv3.1 chromosomes, were detected. Results of the analysis of the patterns of genetic variation allowed us to identify and subgroup bees according to their type. The investigation revealed the genetic originality of the Sicula, and in limited genetic introgression from the other breeds. Morphometric analysis of 5800 worker bees was in agreement with genomic data.
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http://dx.doi.org/10.3390/ani11051311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8147450PMC
May 2021

The climatic and genetic heritage of Italian goat breeds with genomic SNP data.

Sci Rep 2021 05 26;11(1):10986. Epub 2021 May 26.

Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy.

Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including > 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo-political situation preceding the country unification around two centuries ago. We leveraged the remarkable genetic and geographical diversity of the Italian goat populations and performed landscape genomics analysis to disentangle the relationship between genotype and environment, finding 64 SNPs intercepting genomic regions linked to growth, circadian rhythm, fertility, and inflammatory response. Lastly, we calculated the hypothetical future genotypic frequencies of the most relevant SNPs identified through landscape genomics to evaluate their long-term effect on the genetic structure of the Italian goat populations. Our results provide an insight into the past and the future of the Italian local goat populations, helping the institutions in defining new conservation strategy plans that could preserve their diversity and their link to local realities challenged by climate change.
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http://dx.doi.org/10.1038/s41598-021-89900-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8154919PMC
May 2021

Comparison of the response of mammary gland tissue from two divergent lines of goat with high and low milk somatic cell scores to an experimental Staphylococcus aureus infection.

Vet Immunol Immunopathol 2021 Apr 19;234:110208. Epub 2021 Feb 19.

Università degli Studi di Milano, Dipartimento di Medicina Veterinaria, Via dell'Università, 6, 26900 Lodi, Italy; Cornell University, Animal Heath Diagnostic Center, Quality Milk Production Services, Ithaca, NY, USA.

Mastitis represents one of the major economic and health threats to the livestock sector associated with reduction in milk quality, loss of production and is a major reason for culling. Somatic cell score (SCS) is used as a criterion in breeding programmes to select cows genetically less susceptible to mastitis. The relevance of SCS as a predictor of udder health and susceptibility to mastitis is still untested in goats. In this study, two lines of French Alpine goats selected for extreme breeding values for somatic cell scores, one line with high SCS (HSCS) and the other with low SCS (LSCS), were used to test the hypothesis that the mammary response and function differed between the lines. The aim of the present study was to investigate differences in the early immune response in caprine mammary gland tissues challenged with Staphylococcus aureus, one of the main pathogens responsible for the intra-mammary infection in small ruminants, using transcriptomic and histopathology analyses. The comparison between HSCS and LSCS goat lines, showed differences in the response at the histological level for inflammation, presence of neutrophils and micro-abscess formation, and at the molecular level in the expression of CXCL8, IL-6, NFKBIZ and IL-1β. CXCL8 and CXCL2 genes, which showed a higher level of expression in the experimentally infected HSCS line. The molecular data and histopathology both suggested that following S. aureus infection, mobilization, recruitment, infiltration, and chemotaxis of neutrophil, leads to a more severe inflammation in the HSCS compared to LSCS animals. Our results represent an initial basis for further studies to unravel the genetic basis of early mastitis inflammatory responses and the selection of dairy animals more resistant to bacterial mastitis.
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http://dx.doi.org/10.1016/j.vetimm.2021.110208DOI Listing
April 2021

Employing a systematic approach to biobanking and analyzing clinical and genetic data for advancing COVID-19 research.

Eur J Hum Genet 2021 05 17;29(5):745-759. Epub 2021 Jan 17.

Medical Genetics, University of Siena, Siena, Italy.

Within the GEN-COVID Multicenter Study, biospecimens from more than 1000 SARS-CoV-2 positive individuals have thus far been collected in the GEN-COVID Biobank (GCB). Sample types include whole blood, plasma, serum, leukocytes, and DNA. The GCB links samples to detailed clinical data available in the GEN-COVID Patient Registry (GCPR). It includes hospitalized patients (74.25%), broken down into intubated, treated by CPAP-biPAP, treated with O supplementation, and without respiratory support (9.5%, 18.4%, 31.55% and 14.8, respectively); and non-hospitalized subjects (25.75%), either pauci- or asymptomatic. More than 150 clinical patient-level data fields have been collected and binarized for further statistics according to the organs/systems primarily affected by COVID-19: heart, liver, pancreas, kidney, chemosensors, innate or adaptive immunity, and clotting system. Hierarchical clustering analysis identified five main clinical categories: (1) severe multisystemic failure with either thromboembolic or pancreatic variant; (2) cytokine storm type, either severe with liver involvement or moderate; (3) moderate heart type, either with or without liver damage; (4) moderate multisystemic involvement, either with or without liver damage; (5) mild, either with or without hyposmia. GCB and GCPR are further linked to the GCGDR, which includes data from whole-exome sequencing and high-density SNP genotyping. The data are available for sharing through the Network for Italian Genomes, found within the COVID-19 dedicated section. The study objective is to systematize this comprehensive data collection and begin identifying multi-organ involvement in COVID-19, defining genetic parameters for infection susceptibility within the population, and mapping genetically COVID-19 severity and clinical complexity among patients.
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http://dx.doi.org/10.1038/s41431-020-00793-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7811682PMC
May 2021

Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed.

PLoS One 2021 15;16(1):e0232436. Epub 2021 Jan 15.

Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Firenze, Italy.

The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (~25 goats/breed), whose genotypes were available from the AdaptMap project [Argentata (ARG), Bionda dell'Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of breed traceability via discriminant analysis on principal components (DAPC) based on cross-validation. ROH analyses was used to assess the genetic diversity of GRF, while admixture and DAPC to evaluate its relationship to the other breeds. For GRF, common ROH (more than 45% in GRF samples) was detected on CHR 12 at, roughly 50.25-50.94Mbp (ARS1 assembly), which spans the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area of common ROH was also present in DIT, while a broader region (~49.25-51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis revealed a small region of common ancestry from GRF shared by BIO, VSS, ARG and CCG breeds. The DAPC model yielded 100% assignment success for GRF. Overall, our results support the identification of GRF as a distinct native Italian goat breed. This work can contribute to planning conservation programmes to save GRF from extinction and will improve the understanding of the socio-agro-economic factors related with the farming of GRF.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232436PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7810337PMC
April 2021

A Randomized Controlled Trial of Teat-Sealant and Antibiotic Dry-Cow Treatments for Mastitis Prevention Shows Similar Effect on the Healthy Milk Microbiome.

Front Vet Sci 2020 2;7:581. Epub 2020 Sep 2.

Università degli Studi di Milano, Dipartimento di Medicina Veterinaria, via dell'Università 6, Lodi, Italy.

Lactating cows are routinely treated at dry-off with antibiotic infusions in each quarter for the cure and prevention of pathogenic intramammary infection, which remains the most common disease in dairy herds. This approach is known as blanket dry-cow therapy, usually effective for the prevention and cure of infections, but has been shown to potentially contribute to the emergence and spreading of antibiotic resistant bacterial strains. Exploring the use of non-antibiotic treatments coupled with selective dry-cow therapy is necessary to reduce the risk of antibiotic resistance and potential interference with milk microbiome balance. The impact of selective dry-cow therapy on the physiological milk microbiome needs to be carefully evaluated. In this small-scale trial, five healthy (no mastits, SCC <200,000 cells mL) second-parity cows from dry-off to 5 days after calving were sampled. For every cow, each quarter received a different treatment: (i) bismuth salnitrate (internal teat sealant, OrbSeal®, Zoetis, Italy), front right quarter; (ii) cephalonium dihydrate (Cepravin®, MSD, Italy), rear right quarter; (iii) benzathine cloxacillin (Cloxalene dry, Ati, Italy), rear left quarter. No treatment was applied to the remaining quarter (front left) which served as experimental control. For 16S rRNA gene sequencing, bacterial DNA was extracted from 5 ml of milk samples, amplified using the primers for the V3-V4 hypervariable regions and sequenced in one MiSeq (Illumina) run with 2 × 250-base paired-end reads. Bacteriological results confirmed that the quarters were all healthy. The phyla , and were the most abundant for all treatments and controls at all three timepoints, accounting for over 80% of the entire milk microbiota composition. No significant differences were found between treatments and controls in terms of the major alpha and beta diversity indexes, revealing that antibiotic, and non-antibiotic treatments for selective dry-cow therapy did not alter significantly the milk microbiome of dairy cows. The milk microbiota composition showed a clear evolution over the lactation cycle, and the overall changes in the milk microbiota diversity over the lactation cycle were mainly independent of treatments.
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http://dx.doi.org/10.3389/fvets.2020.00581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7492605PMC
September 2020

Seasonal effects on miRNA and transcriptomic profile of oocytes and follicular cells in buffalo (Bubalus bubalis).

Sci Rep 2020 08 11;10(1):13557. Epub 2020 Aug 11.

Dipartimento di Medicina Veterinaria e Produzioni Animali (DMVPA), Università Degli Studi di Napoli Federico II, Via F. Delpino 1, 80137, Naples, Italy.

Season clearly influences oocyte competence in buffalo (Bubalus bubalis); however, changes in the oocyte molecular status in relation to season are poorly understood. This study characterizes the microRNA (miRNA) and transcriptomic profiles of oocytes (OOs) and corresponding follicular cells (FCs) from buffalo ovaries collected in the breeding (BS) and non-breeding (NBS) seasons. In the BS, cleavage and blastocyst rates are significantly higher compared to NBS. Thirteen miRNAs and two mRNAs showed differential expression (DE) in FCs between BS and NBS. DE-miRNAs target gene analysis uncovered pathways associated with transforming growth factor β (TGFβ) and circadian clock photoperiod. Oocytes cluster in function of season for their miRNA content, showing 13 DE-miRNAs between BS and NBS. Between the two seasons, 22 differentially expressed genes were also observed. Gene Ontology (GO) analysis of miRNA target genes and differentially expressed genes (DEGs) in OOs highlights pathways related to triglyceride and sterol biosynthesis and storage. Co-expression analysis of miRNAs and mRNAs revealed a positive correlation between miR-296-3p and genes related to metabolism and hormone regulation. In conclusion, season significantly affects female fertility in buffalo and impacts on oocyte transcriptomic of genes related to folliculogenesis and acquisition of oocyte competence.
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http://dx.doi.org/10.1038/s41598-020-70546-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7419291PMC
August 2020

Genetic parameters of weeping teats in Italian Saanen and Alpine dairy goats and their relationship with milk production and somatic cell score.

J Dairy Sci 2020 Oct 23;103(10):9167-9176. Epub 2020 Jul 23.

Department of Veterinary Medicine, University of Milan, 20133 Milan, Italy.

This paper reports a quantitative genetics analysis of weeping teats (WT), an abnormality of the mammary gland in goats. Weeping teats are characterized by milk oozing out of the teat or by the presence of multiple cysts near its base. This abnormality has been routinely recorded in Italian Alpine and Saanen goats since 2000 using a score of 0 or 1 (0 = defect not present, 1 = defect present). No information is available on the genetic background of WT or its relationship with production or other udder-related traits. Data obtained by the Italian National Sheep and Goat Breeders Association (Rome, Italy) were used to estimate both heritability of WT and its genetic correlation with milk yield, somatic cell score, and udder traits. The final data set used in the analysis included 2,178 Saanen and 2,309 Alpine primiparous goats kidding from 2009 to 2014. The pedigree data included 7,333 Saanen and 7,421 Alpines, respectively. A threshold-linear multivariate animal model was used to estimate variance and covariance components. A genealogical data analysis was also implemented, including genealogical data completeness, inbreeding, and identification of possible most recent common ancestors. On average, around 4 and 13% of primiparous Saanen and Alpine females kidding from 2009 to 2014 showed mammary gland abnormality, respectively. Weeping teats heritability was 0.27 and 0.26 for Saanen and Alpine, respectively. Genetic correlations between milk production or somatic cell score ranged from -0.16 in Saanen to 0.43 in Alpine, but the standard error of the estimates was very large. Positive genetic correlations were observed among WT and teat characteristics in both Saanen and Alpine. The average inbreeding of abnormality carriers was 2.4 and 5.1 for Saanen and Alpine, respectively. The genealogical data analysis identified 4 common ancestors of affected does in Saanen and 2 in Alpine. These results indicate that WT have a possible genetic background. A genome-wide association study might help in understanding the polygenic or monogenic determination of this abnormality.
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http://dx.doi.org/10.3168/jds.2020-18175DOI Listing
October 2020

Maternal peri-conceptional undernourishment perturbs offspring sperm methylome.

Reproduction 2020 05;159(5):513-523

Laboratory of Experimental Embryology, Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy.

The genotype of an organism is stable throughout its life; however, its epigenome is dynamic and can be altered in response to environmental factors, such as diet. Inheritance of acquired epigenetic modifications by the next generation occurs through the germline, although the precise mechanisms remain to be elucidated. Here, we used a sheep model to evaluate if modification of the maternal diet (CTR; control, UND: undernutrition; FA: undernutrition and folic acid supplementation) during the peri-conceptional period affects the genome-wide methylation status of the gametes of male offspring. Sperm DNA methylation, measured by Reduced Representation Bisulfite Sequencing (RRBS), identified Differentially Methylated Regions (DMR) in offspring that experienced in utero undernutrition, both in UND (244) and FA (240), compared with CTR. Gene ontology (GO) analysis identified DMRs in categories related to sperm function, therefore we investigated whether the fertilizing capacity of the semen from the three groups differed in an in vitro fertilization assay. Spermatozoa from the undernourished groups showed lower motility and sperm chromatin structure abnormalities, represented by a higher percentage of DNA fragmentation and an increased number of immature cells, compared with CTR. While good quality blastocysts were obtained from all three groups, the proportion of embryos reaching the blastocyst stage was reduced in the UND vs CTR, an effect partially rescued by the FA treatment. The data reported here show that nutritional stress during early pregnancy leads to epigenetic modifications in the semen of the resulting offspring, the effects of which in next generation remain to be elucidated.
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http://dx.doi.org/10.1530/REP-19-0549DOI Listing
May 2020

Mutations in orthologous PETALOSA TOE-type genes cause a dominant double-flower phenotype in phylogenetically distant eudicots.

J Exp Bot 2020 05;71(9):2585-2595

Università degli Studi di Milano - DiSAA, Milano, Italy.

The double-flower phenotype has been selected by humans for its attractiveness in various plant species and it is of great commercial value for the ornamental market. In this study we investigated the genetic determinant of the dominant double-flower trait in carnation, petunia, and Rosa rugosa, and identified mutant alleles of TARGET OF EAT (TOE)-type genes characterized by a disruption of the miR172 target sequence and of the C-terminal portion of the encoded protein. Despite the phylogenetic distance between these eudicots, which diverged in the early Cretaceous, the orthologous genes carrying these mutations all belong to a single TOE-type subgroup, which we name as PETALOSA (PET). Homology searches allowed us to identify PET sequences in various other species. To confirm the results from naturally occurring mutations, we used CrispR-Cas9 to induce lesions within the miR172 target site of Nicotiana tabacum PET genes, and this resulted in the development of supernumerary petaloid structures. This study describes pet alleles in economically important ornamental species and provides evidence about the possibility of identifying and engineering PET genes to obtain the desirable double-flower trait in different plants.
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http://dx.doi.org/10.1093/jxb/eraa032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7210751PMC
May 2020

Epigenetic analysis of high and low motile sperm populations reveals methylation variation in satellite regions within the pericentromeric position and in genes functionally related to sperm DNA organization and maintenance in Bos taurus.

BMC Genomics 2019 Dec 6;20(1):940. Epub 2019 Dec 6.

Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Einstein, 26900, Lodi, Italy.

Background: Sperm epigenetics is an emerging area of study supported by observations reporting that abnormal sperm DNA methylation patterns are associated with infertility. Here, we explore cytosine-guanine dinucleotides (CpGs) methylation in high (HM) and low motile (LM) Bos taurus sperm populations separated by Percoll gradient. HM and LM methylation patterns were investigated by bisulfite sequencing.

Results: Comparison between HM and LM sperm populations revealed that methylation variation affects genes involved in chromatin organization. CpG Islands (CGIs), were highly remodelled. A high proportion of CGIs was found to be methylated at low/intermediate level (20-60%) and associated to the repetitive element BTSAT4 satellite. The low/intermediate level of methylation in BTSAT4 was stably maintained in pericentric regions of chromosomes. BTSAT4 was hypomethylated in HM sperm populations.

Conclusions: The characterization of the epigenome in HM and LM Bos taurus sperm populations provides a first step towards the understanding of the effect of methylation on sperm fertility. Methylation variation observed in HM and LM populations in genes associated to DNA structure remodelling as well as in a repetitive element in pericentric regions suggests that maintenance of chromosome structure through epigenetic regulation is probably crucial for correct sperm functionality.
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http://dx.doi.org/10.1186/s12864-019-6317-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6898967PMC
December 2019

3d-SPADE: Significance evaluation of spatio-temporal patterns of various temporal extents.

Biosystems 2019 Nov 23;185:104022. Epub 2019 Aug 23.

Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6), JARA Brain Inst I (INM-10), Jülich Research Centre, Jülich, Germany; Theoretical Systems Neurobiology, RWTH Aachen University, Aachen, Germany.

The Spike Pattern Detection and Evaluation (SPADE) analysis is a method to find reoccurring spike patterns in parallel spike train data, and to determine their statistical significance. Here we introduce an extension of the original statistical testing procedure which explicitly accounts for the temporal duration of the patterns. The extension improves the performance in the presence of patterns with different durations, as here demonstrated by application to various synthetic data. We further introduce an implementation of SPADE in form of a sub-module of the Python library Elephant (ELEctroPHysiological ANalysis Toolkit). The code is made publicly available on GitHub, together with detailed documentation, tutorials, and the results presented here.
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http://dx.doi.org/10.1016/j.biosystems.2019.104022DOI Listing
November 2019

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.

Mol Ecol Resour 2019 Nov 9;19(6):1497-1515. Epub 2019 Sep 9.

University of Grenoble-Alpes, University of Savoy Mont Blanc, CNRS, LECA, Grenoble, France.

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.
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http://dx.doi.org/10.1111/1755-0998.13070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7115901PMC
November 2019

Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array.

PLoS One 2019 31;14(5):e0217687. Epub 2019 May 31.

Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, South Australia, Australia.

Accuracy of genome-wide association studies, and the successful implementation of genomic selection depends on the level of linkage disequilibrium (LD) across the genome and also the persistence of LD phase between populations. In the present study LD between adjacent SNPs and LD decay between SNPs was calculated in three Iranian water buffalo populations. Persistence of LD phase was evaluated across these populations and effective population size (Ne) was estimated from corrected r2 information. A set of 404 individuals from three Iranian buffalo populations were genotyped with the Axiom Buffalo Genotyping 90K Array. Average r2 and |D'| between adjacent SNP pairs across all chromosomes was 0.27 and 0.66 for AZI, 0.29 and 0.68 for KHU, and 0.32 and 0.72 for MAZ. The LD between the SNPs decreased with increasing physical distance from 100Kb to 1Mb between markers, from 0.234 to 0.018 for AZI, 0.254 to 0.034 for KHU, and 0.297 to 0.119 for MAZ, respectively. These results indicate that a density of 90K SNP is sufficient for genomic analyses relying on long range LD (e.g. GWAS and genomic selection). The persistence of LD phase decreased with increasing marker distances across all the populations, but remained above 0.8 for AZI and KHU for marker distances up to 100Kb. For multi-breed genomic evaluation, the 90K SNP panel is suitable for AZI and KHU buffalo breeds. Estimated effective population sizes for AZI, KHU and MAZ were 477, 212 and 32, respectively, for recent generations. The estimated effective population sizes indicate that the MAZ is at risk and requires careful management.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217687PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6544294PMC
January 2020

Durum wheat genome highlights past domestication signatures and future improvement targets.

Nat Genet 2019 05 8;51(5):885-895. Epub 2019 Apr 8.

CREA-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy.

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.
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http://dx.doi.org/10.1038/s41588-019-0381-3DOI Listing
May 2019

A validation study of loci associated with mastitis resistance in two French dairy sheep breeds.

Genet Sel Evol 2019 Feb 13;51(1). Epub 2019 Feb 13.

GenPhySE, Université de Toulouse, INRA, ENVT, Castanet-Tolosan, France.

Background: The identification of loci associated with resistance to mastitis or of the causative mutations may be helpful in breeding programs for dairy sheep as it is for cattle worldwide. Seven genomic regions that control milk somatic cell counts, an indirect indicator of udder infection, have already been identified in sheep (Spanish Churra, French Lacaune and Italian Sardinian-Lacaune backcross populations). In this study, we used a 960 custom-designed ovine single nucleotide polymorphism (SNP) chip in Lacaune and Manech Tête Rousse dairy sheep to validate these seven genomic regions associated with mastitis.

Results: The most significant SNP (rs868996547) on Ovis aries chromosome (OAR) 3 was a previously described mutation in the suppressor of cytokine signalling 2 (SOCS2) gene. An antagonist effect of this causal candidate between health and growth in Lacaune sheep was confirmed. Effects of the mutation on the infectious status of the udder, i.e. increases in milk somatic cell counts and bacteria shedding, were also identified. This SNP was not present in the data available on Manech Tête Rousse. Three other regions associated with mastitis were also confirmed on OAR16 (Manech Tête Rousse), 19 (Lacaune) and 2 (both breeds). For the OAR2 region, we validated previously detected SNPs in several other breeds (Sarda, Churra, and Chios). For significant SNPs in the four mastitis regions, the effect varied from 0.24 to 0.67 phenotypic standard deviation of the traits. Two of the mastitis quantitative trait loci (QTL) regions (OAR2 and 16) that we validated here were also associated in opposite ways with milk production traits in both populations.

Conclusions: These results indicate, at least in part, a genomic basis for the trade-off between milk production and mastitis resistance. Four of the seven mastitis QTL regions that were previously identified in independent populations, were confirmed in this study, which demonstrates partial sharing of mastitis-related genetic mechanisms between different distant dairy sheep populations.
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http://dx.doi.org/10.1186/s12711-019-0448-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375205PMC
February 2019

AdaptMap: exploring goat diversity and adaptation.

Genet Sel Evol 2018 Nov 19;50(1):61. Epub 2018 Nov 19.

Laboratory of Geographic Information Systems, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1186/s12711-018-0427-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240945PMC
November 2018

Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes.

Genet Sel Evol 2018 Nov 19;50(1):58. Epub 2018 Nov 19.

Fondazione Parco Tecnologico Padano, Lodi, Italy.

Background: Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats.

Results: A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows.

Conclusions: After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.
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http://dx.doi.org/10.1186/s12711-018-0422-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240949PMC
November 2018

Functional SNP panel for parentage assessment and assignment in worldwide goat breeds.

Genet Sel Evol 2018 Nov 19;50(1):55. Epub 2018 Nov 19.

GenPhySE, INRA, Université de Toulouse, INPT, ENVT, 31326, Castanet Tolosan, France.

Background: International standard panels of single nucleotide polymorphisms (SNPs) have replaced microsatellites in several species for parentage assessment and assignment (PA) purposes. However, such a resource is still lacking in goats. The application of a cheap tool for PA would help the management of goat populations by improving the reliability of pedigree registration and, consequently, allow a better implementation of breeding schemes or conservation programs.

Results: Using data from the current GoatSNP50 chip, starting from a worldwide dataset of more than 4000 animals belonging to more than 140 breeds and populations from the AdaptMap initiative, we selected a panel of 195 SNPs. The assignment rate of this panel was up to 100% on an additional dataset that included 2000 Alpine and Saanen animals and highly related candidate sires.

Conclusions: In this study, we defined a highly informative SNP panel, which will be publicly available to worldwide breeders and laboratories. Its development on such a large number of breeds and populations, together with validation on a second set of cosmopolitan breeds, makes it a promising and important genomic tool for the goat species.
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http://dx.doi.org/10.1186/s12711-018-0423-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240953PMC
November 2018

Signatures of selection and environmental adaptation across the goat genome post-domestication.

Genet Sel Evol 2018 Nov 19;50(1):57. Epub 2018 Nov 19.

Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133, Milan, Italy.

Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds.

Results: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments.

Conclusions: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.
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http://dx.doi.org/10.1186/s12711-018-0421-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240954PMC
November 2018

Diversity of copy number variation in the worldwide goat population.

Heredity (Edinb) 2019 05 6;122(5):636-646. Epub 2018 Nov 6.

Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.

Goats (Capra hircus) are an important farm animal species. Copy number variation (CNV) represents a major source of genomic structural variation. We investigated the diversity of CNV distribution in goats using CaprineSNP50 genotyping data generated by the ADAPTmap Project. We identified 6286 putative CNVs in 1023 samples from 50 goat breeds using PennCNV. These CNVs were merged into 978 CNV regions, spanning ~262 Mb of total length and corresponding to ~8.96% of the goat genome. We then divided the samples into six subgroups per geographic distribution and constructed a comparative CNV map. Our results revealed a population differentiation in CNV across different geographical areas, including Western Asia, Eastern Mediterranean, Alpine & Northern Europe, Madagascar, Northwestern Africa, and Southeastern Africa groups. The results of a cluster heatmap analysis based on the CNV count per individual across different groups was generally consistent with the one generated from the SNP data, likely reflecting the population history of different goat breeds. We sought to determine the gene content of these CNV events and found several important CNV-overlapping genes (e.g. EDNRA, ADAMTS20, ASIP, KDM5B, ADAM8, DGAT1, CHRNB1, CLCN7, and EXOSC4), which are involved in local adaptations such as coat color, muscle development, metabolic processes, osteopetrosis, and embryonic development. Therefore, this research generated an extensive CNV map in the worldwide population of goat, which offers novel insight into the goat genome and its functional annotation.
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http://dx.doi.org/10.1038/s41437-018-0150-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6462038PMC
May 2019

Different Culture Times Affect MicroRNA Cargo in Equine Amniotic Mesenchymal Cells and Their Microvesicles.

Tissue Eng Part C Methods 2018 10;24(10):596-604

3 Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, via Einstein , Lodi, Italy .

Conditioned medium (CM) and microvesicles (MVs) are produced using different protocols: CM is collected following 12-96 h of cell culture without renewal of tissue culture medium, while MVs are collected after overnight cell culture. For future comparative studies in regenerative medicine looking at the efficacy of CM and MVs, it is important to understand how the quality of cell secretions is affected by culture. The aim of this study was to evaluate whether the duration of culturing influences the micro-RNAs (miRNAs) cargo of equine amniotic mesenchymal cells (AMCs) and their MVs. The analysis identified 990 miRNAs. After one night, there were 347 differently expressed (DE)-miRNAs between MVs and cells, whereas after four nights there were 359. About 58.3% of the DE-miRNAs were shared between samples produced under the two conditions. The comparison between miRNA content in AMC cells cultured for one night versus four nights showed eight DE-Equus caballus (eca)-miRNAs, which target genes were involved in immune response to external stimulus, inflammatory response, and production of reactive oxygen species. Comparing MVs isolated from one or four nights, four DE-miRNAs that target genes regulating cell cycle progression and production of reactive oxygen species were found, but only eca-miR-214 was enriched in the MVs after four nights. In conclusion, after 4 days of cell culture, the profile of AMC miRNAs was altered, indicating a probable phenotypic transition versus a new cell culture environment and aging. After this time, MVs accumulated eca-miR-214, which may help cells survive or adapt to new culture conditions.
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http://dx.doi.org/10.1089/ten.TEC.2018.0205DOI Listing
October 2018

A genome-wide scan for signatures of selection in Azeri and Khuzestani buffalo breeds.

BMC Genomics 2018 Jun 11;19(1):449. Epub 2018 Jun 11.

Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.

Background: Identification of genomic regions that have been targets of selection may shed light on the genetic history of livestock populations and help to identify variation controlling commercially important phenotypes. The Azeri and Kuzestani buffalos are the most common indigenous Iranian breeds which have been subjected to divergent selection and are well adapted to completely different regions. Examining the genetic structure of these populations may identify genomic regions associated with adaptation to the different environments and production goals.

Results: A set of 385 water buffalo samples from Azeri (N = 262) and Khuzestani (N = 123) breeds were genotyped using the Axiom® Buffalo Genotyping 90 K Array. The unbiased fixation index method (F) was used to detect signatures of selection. In total, 13 regions with outlier F values (0.1%) were identified. Annotation of these regions using the UMD3.1 Bos taurus Genome Assembly was performed to find putative candidate genes and QTLs within the selected regions. Putative candidate genes identified include FBXO9, NDFIP1, ACTR3, ARHGAP26, SERPINF2, BOLA-DRB3, BOLA-DQB, CLN8, and MYOM2.

Conclusions: Candidate genes identified in regions potentially under selection were associated with physiological pathways including milk production, cytoskeleton organization, growth, metabolic function, apoptosis and domestication-related changes include immune and nervous system development. The QTL identified are involved in economically important traits in buffalo related to milk composition, udder structure, somatic cell count, meat quality, and carcass and body weight.
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http://dx.doi.org/10.1186/s12864-018-4759-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5996463PMC
June 2018

Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus.

BMC Genomics 2018 May 30;19(1):417. Epub 2018 May 30.

Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy.

Background: Molecular regulation of the hypothalamic-pituitary-gonadal (HPG) axis plays an essential role in the fine tuning of seasonal estrus in Capra hircus. Noncoding RNAs (ncRNAs) are emerging as key regulators in sexual development and mammalian reproduction. In order to identify ncRNAs and to assess their expression patterns, along the HPG axis, we sequenced ncRNA libraries from hypothalamus, pituitary and ovary of three goats.

Results: Among the medium length noncoding RNAs (mncRNAs) identified, small nucleolar RNAs (snoRNAs) and transfer RNAs (tRNAs) were found to be more abundant in ovary and hypothalamus, respectively. The observed GC content was representative for different classes of ncRNAs, allowing the identification of a tRNA-derived RNA fragments (tRFs) subclass, which had a peak distribution around 32-38% GC content in the hypothalamus. Differences observed among organs confirmed the specificity of microRNA (miRNA) profiles for each organ system.

Conclusions: Data on ncRNAs in organs constituting the HPG axis will contribute to understanding their role in the physiological regulation of reproduction in goats.
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http://dx.doi.org/10.1186/s12864-018-4767-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977473PMC
May 2018

MicroRNAs of Equine Amniotic Mesenchymal Cell-derived Microvesicles and Their Involvement in Anti-inflammatory Processes.

Cell Transplant 2018 01;27(1):45-54

3 Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche IBBA CNR, Lodi, Italy.

Cell-derived microvesicles (MVs) are a recently discovered mechanism of cell-to-cell communication. Our previous data show that MVs secreted by equine amniotic mesenchymal-derived cells (AMCs) are involved in downregulation of proinflammatory genes in lipopolysaccharide-stressed equine tendon and endometrial cells. The aim of the present study was to evaluate whether AMC-MVs contain selected microRNAs (miRNAs) involved in inflammation. Two pools of cells, derived from 3 amniotic membranes each, and their respective MVs were collected. Small RNAs were extracted and deep sequenced, followed by miRNA in silico detection. The analysis identified 1,285 miRNAs, which were quantified both in AMCs and MVs. Among these miRNAs, 401 were classified as Equus caballus miRNAs, 257 were predicted by homology with other species (cow, sheep, and goat), and 627 were novel candidate miRNAs. Moreover, 146 miRNAs differentially expressed (DE) in AMCs and MVs were identified, 36 of which were known and the remaining were novel. Among the known DE miRNAs, 17 showed higher expression in MVs. Three of these were validated by real time polymerase chain reaction: eca-miR-26, eca-miR-146a, and eca-miR-223. Gene ontology analysis of validated targets showed that the DE miRNAs in cells and MVs could be involved both in immune system regulation by modulating interleukin signaling and in the inflammatory process. In conclusion, this study suggests a significant role of AMCs in modulating immune response through cell-cell communication via MV-shuttling miRNAs.
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http://dx.doi.org/10.1177/0963689717724796DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6434479PMC
January 2018

New Insights on Water Buffalo Genomic Diversity and Post-Domestication Migration Routes From Medium Density SNP Chip Data.

Front Genet 2018 2;9:53. Epub 2018 Mar 2.

Department of Animal Science, Faculty of Agriculture, Namik Kemal University, Tekirdag, Turkey.

The domestic water buffalo is native to the Asian continent but through historical migrations and recent importations, nowadays has a worldwide distribution. The two types of water buffalo, i.e., river and swamp, display distinct morphological and behavioral traits, different karyotypes and also have different purposes and geographical distributions. River buffaloes from Pakistan, Iran, Turkey, Egypt, Romania, Bulgaria, Italy, Mozambique, Brazil and Colombia, and swamp buffaloes from China, Thailand, Philippines, Indonesia and Brazil were genotyped with a species-specific medium-density 90K SNP panel. We estimated the levels of molecular diversity and described population structure, which revealed historical relationships between populations and migration events. Three distinct gene pools were identified in pure river as well as in pure swamp buffalo populations. Genomic admixture was seen in the Philippines and in Brazil, resulting from importations of animals for breed improvement. Our results were largely consistent with previous archeological, historical and molecular-based evidence for two independent domestication events for river- and swamp-type buffaloes, which occurred in the Indo-Pakistani region and close to the China/Indochina border, respectively. Based on a geographical analysis of the distribution of diversity, our evidence also indicated that the water buffalo spread out of the domestication centers followed two major divergent migration directions: river buffaloes migrated west from the Indian sub-continent while swamp buffaloes migrated from northern Indochina via an east-south-eastern route. These data suggest that the current distribution of water buffalo diversity has been shaped by the combined effects of multiple migration events occurred at different stages of the post-domestication history of the species.
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http://dx.doi.org/10.3389/fgene.2018.00053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841121PMC
March 2018
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