27 research outputs found
Screening for K-Casein (CSN3) Gene Variation in Carpathian Goat Breed by Isoelectric focusing (IEF) and DNA Sequencing
No full textIn goats, k-casein (CSN3) locus is highly polymorphic with up to 16 allele currently characterized. They produce 13 protein variants (CSN3) that were classified in two groups (AIEF and BIEF), according to their isoelectric point. Isoelectric focusing (IEF) of milk samples allows the detection of these two CSN3 groups, but for correct identification of CSN3 alleles DNA based genotyping methods are needed. Therefore the objective of this study was to identify the types of alleles occurring at the CSN3 locus in Carpathian goat breed by using a combined IEF and DNA sequencing approach. IEF analysis of milk samples collected from two Carpathian goat populations reared in Romania revealed two distinct CSN3 patterns. Amplification and sequencing of CSN3 cDNA obtained from these goats revealed four polymorphic sites located in the exon 4 that are responsible for amino acids substitutions, as compared with the reference sequence of A allele. By comparative analysis of IEF and cDNA sequencing data obtained from the two populations, we shown that AIEF alleles are represented by B allele, while BIEF alleles are represented by D allele. However, the variation of CSN3 locus in Carpathian goat breed could be more complex, therefore further studies are needed to characterize it
Improved algorithms through the lens of continuous optimization
No full textThesis: Ph. D., Massachusetts Institute of Technology, Department of Mathematics, 2017.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 289-302).In this thesis, we build connections between classic methods from convex optimization and the modern toolkit from the fast Laplacian solver literature, in order to make progress on a number of fundamental algorithmic problems: *-- We develop a faster algorithm for the unit capacity minimum cost flow problem, which encompasses the shortest path with negative weights and minimum cost bipartite perfect matching problems. In the case of sparse graphs, this provides the first running time improvement for these problems in over 25 years. *-- We initiate the study of solving linear systems involving directed Laplacian matrices, and devise an almost-linear time algorithm for this task. This primitive enables us to also obtain almost-linear time algorithms for computing an entire host of quantities associated with Markov chains, such as stationary distributions, personalized PageRank vectors, hitting times, or escape probabilities. This significantly improves over the previous state-of-the-art, which was based on simulating random walks, or applying fast matrix multiplication. *-- We develop faster algorithms for scaling and balancing nonnegative matrices, two fundamental problems in scientific computing, significantly improving over the previously known best running times. In particular, if the optimal scalings/balancings have polynomially bounded condition numbers, our algorithms run in nearly-linear time. Beyond that, we leverage and extend tools from convex geometry in order to design an algorithm for online pricing with nearly-optimal regret. We also use convex optimization to shed a new light on the approximate Caratheodory problem, for which we give a deterministic nearly-linear time algorithm, as well as matching lower bounds.by Adrian Valentin Vladu.Ph. D
A genome-wide perspective about the diversity and demographic history of seven Spanish goat breeds
No full textAltres ajuts: Félix Goyache is supported by Grant FICYT GRUPIN14-113. Valentin Balteanu is the recipient of a grant awarded under the frame of the European Social Fund, Human Resources Development Operational Program 2007-2013, Project No. POSDRU/159/1.5/S/132765.Background: The main goal of the current work was to infer the demographic history of seven Spanish goat breeds (Malagueña, Murciano-Granadina, Florida, Palmera, Mallorquina, Bermeya and Blanca de Rasquera) based on genomewide diversity data generated with the Illumina Goat SNP50 BeadChip (population size, N = 176). Five additional populations from Europe (Saanen and Carpathian) and Africa (Tunisian, Djallonké and Sahel) were also included in this analysis (N = 80) for comparative purposes. Results: Our results show that the genetic background of Spanish goats traces back mainly to European breeds although signs of North African admixture were detected in two Andalusian breeds (Malagueña and MurcianoGranadina). In general, observed and expected heterozygosities were quite similar across the seven Spanish goat breeds under analysis irrespective of their population size and conservation status. For the Mallorquina and Blanca de Rasquera breeds, which have suffered strong population declines during the past decades, we observed increased frequencies of large-sized (ROH), a finding that is consistent with recent inbreeding. In contrast, a substantial part of the genome of the Palmera goat breed comprised short ROH, which suggests a strong and ancient founder effect. Conclusions: Admixture with African goats, genetic drift and inbreeding have had different effects across the seven Spanish goat breeds analysed in the current work. This has generated distinct patterns of genome-wide diversity that provide new clues about the demographic history of these populations
Assessment Method of Coverage Degree for Pneumatic Sprayers Used in Orchards
No full textAbstractThe use of electronic equipment in plant protection treatments in vineyards and orchards is of great importance both economically and environmentally. In this sense, this paper aims to highlight the importance of spraying equipment in vineyards and orchards. The main goal of this paper was to determine and to evaluate the coverage degree for the Gamberini 500 orchard spraying machine.For the purpose of this paper, the machine Gamberini 500 was used in laboratory conditions to determine and evaluate the coverage degree. This spraying machine is a pneumatic one, with a special boom. In order to evaluate the degree of coverage, a special paper was used, which was placed at different heights (1; 2; 3 m). The paper was scanned, transformed in black and with the MathCad software the degree of coverage was evaluated using the READBMP function. The results obtained showed that the degree of coverage differs with respect to the height. The biggest degree of coverage was obtained at lower heights, due to the small distance to the target. This degree of coverage is mostly influenced by the orientation of the boom, the quantity of water sprayed and the droplets size. In order to achieve a higher degree of coverage it is important to use a fan which has a tower blower, because the distance from boom to target surface is relative equal
Olim multorum patronus et praesidium, nunc ecce cliens: Jono iš Lietuvos kunigaikščių mirtis ir pomirtinis šlovinimas (1538 m. vasaris–gegužė)
No full textWhen Bishop John of the Lithuanian Dukes was translated from Vilnius to Poznań in the spring of 1536 he was already seriously ill with malarial fever. The ceremonies involved with his official ingress to his new see in March 1537 were curtailed and he was active personally in diocesan affairs (the consistory court) only during the spring and summer months. Bishop John died from his illness, quartan fever, on 18 February 1538. This article describes the processes which took place in the three months following the bishop’s demise: the withdrawal of his court and most of his administration from Poznań, his Requiem Mass in his cathedral sung by the suffragan bishop, Adrian Źakowski O.P. and the transportation of his corpse for eventual burial in Vilnius Cathedral, which took place in May 1538. Meanwhile in Leipzig a Mazovian student, Stanisław Czarny Chrościeski composed an epicedion or funerary eulogy in honour of the deceased prelated, dedicated to the Captain General of Greater Poland, Andrzej Górka. This work in Latin prose and verse was published for the first time from a nineteenth-century transcript by the literary historian Ludwik Ćwikliński in 1900 and has gone unremarked by Church historians for more than a century. The sole surviving copy of the 1538 Valentin Schumann imprint is held in the Russian National Library in St Petersburg and is reproduced here with a Lithuanian prose translation. Alongside Chrościeski’s compositions are epigrams by other Leipzig acquaintances of our author, later stars of the Silesian Lutheran Parnassus, Johannes Gigas and Valentin Nitius, master of the local school. Chrościeski’s prose address to Górka is interesting for its conceit that it is not Stanislaw who seeks patronage but Prince John himself. Unfortunately neither this text nor the verse address to the Fates reveals details about the bishop’s life and the circumstances of his death but the references to John as a warrior appear to confirm the reception of the prince-bishop’s own propagated self-image, known from contemporary occasional Latin verse.Po ilgos ligos 1538 m. vasario 18 d. Poznanėje mirė buvęs Vilniaus, tuometinis Poznanės vyskupas Jonas Žygimantaitis iš Lietuvos kunigaikščių. Mirties priežastis – febra diutina quartana, kas ketvirtą dieną atsinaujinantis karščiavimas, maliarijos atmaina. Ta liga pakirto ne vieną XVI a. Europos, įskaitant ir Lenkijos-Lietuvos, dvasininką. Šio straipsnio tikslas – apžvelgti vyskupo Jono mirties pasekmes, jo dvaro ir administracijos gan skubaus atsitraukimo iš Poznanės ir jo įamžinimo priemones, visų pirma Stanislovo Čarnio Epicediją nelaiku mirus Poznanės vyskupui Jonui iš Lietuvos kunigaikščių, 1538 m. spausdintą in 4o formatu Leipcige, Valentino Šumano (Shumann) leidykloje, Didžiosios Lenkijos generalinio seniūno Andriejaus Gurkiečio (Górka) malone. Priede pateikiamas perspausdintas šis veikalas su vertimu į lietuvių kalbą
"Olim multorum patronus et praesidium, nunc ecce cliens": the death and posthumous eulogy of Prince John of the Lithuanian Dukes, Spring 1538
No full textPo ilgos ligos 1538 m. vasario 18 d. Poznanėje mirė buvęs Vilniaus, tuometinis Poznanės vyskupas Jonas Žygimantaitis iš Lietuvos kunigaikščių. Mirties priežastis – febra diutina quartana, kas ketvirtą dieną atsinaujinantis karščiavimas, maliarijos atmaina. Ta liga pakirto ne vieną XVI a. Europos, įskaitant ir Lenkijos-Lietuvos, dvasininką. Šio straipsnio tikslas – apžvelgti vyskupo Jono mirties pasekmes, jo dvaro ir administracijos gan skubaus atsitraukimo iš Poznanės ir jo įamžinimo priemones, visų pirma Stanislovo Čarnio "Epicediją" nelaiku mirus Poznanės vyskupui Jonui iš Lietuvos kunigaikščių, 1538 m. spausdintą in 4° formatu Leipcige, Valentino Šumano (Shumann) leidykloje, Didžiosios Lenkijos generalinio seniūno Andriejaus Gurkiečio (Górka) malone. Priede pateikiamas perspausdintas šis veikalas su vertimu į lietuvių kalbą.When Bishop John of the Lithuanian Dukes was translated from Vilnius to Poznań in the spring of 1536 he was already seriously ill with malarial fever. The ceremonies involved with his official ingress to his new see in March 1537 were curtailed and he was active personally in diocesan affairs (the consistory court) only during the spring and summer months. Bishop John died from his illness, quartan fever, on 18 February 1538. This article describes the processes which took place in the three months following the bishop’s demise: the withdrawal of his court and most of his administration from Poznań, his Requiem Mass in his cathedral sung by the suffragan bishop, Adrian Źakowski O.P. and the transportation of his corpse for eventual burial in Vilnius Cathedral, which took place in May 1538. Meanwhile in Leipzig a Mazovian student, Stanisław Czarny Chrościeski composed an epicedion or funerary eulogy in honour of the deceased prelated, dedicated to the Captain General of Greater Poland, Andrzej Górka. This work in Latin prose and verse was published for the first time from a nineteenth-century transcript by the literary historian Ludwik Ćwikliński in 1900 and has gone unremarked by Church historians for more than a century. The sole surviving copy of the 1538 Valentin Schumann imprint is held in the Russian National Library in St Petersburg and is reproduced here with a Lithuanian prose translation. Alongside Chrościeski’s compositions are epigrams by other Leipzig acquaintances of our author, later stars of the Silesian Lutheran Parnassus, Johannes Gigas and Valentin Nitius, master of the local school. Chrościeski’s prose address to Górka is interesting for its conceit that it is not Stanislaw who seeks patronage but Prince John himself. Unfortunately neither this text nor the verse address to the Fates reveals details about the bishop’s life and the circumstances of his death but the references to John as a warrior appear to confirm the reception of the prince-bishop’s own propagated self-image, known from contemporary occasional Latin verse
A high throughput genotyping approach reveals distinctive autosomal genetic signatures for European and Near Eastern wild boar
No full textThe lack of a Near Eastern genetic signature in modern European porcine breeds indicates that, although domestic pigs from the Fertile Crescent entered Europe during the Neolithic, they were completely replaced by their European counterparts in a short window of time. Whilst the absence of such genetic signature has been convincingly demonstrated at the mitochondrial level, variation at the autosomal genomes of European and Near Eastern Sus scrofa has not been compared yet. Herewith, we have explored the genetic relationships among 43 wild boar from Europe (N = 21), Near East (N = 19) and Korea (N = 3), and 40 Iberian (N = 16), Canarian (N = 4) and Mangalitza (N = 20) pigs by using a high throughput SNP genotyping platform. After data filtering, 37,167 autosomal SNPs were used to perform population genetics analyses. A multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK showed that Near Eastern and European wild boar populations are genetically differentiated. Maximum likelihood trees built with TreeMix supported this conclusion i.e. an early population split between Near Eastern and European Sus scrofa was observed. Moreover, analysis of the data with Structure evidenced that the sampled Iberian, Canarian and Mangalitza pigs did not carry any autosomal signature compatible with a Near Eastern ancestry, a finding that agrees well with previous mitochondrial studies
A comprehensive analysis of the genetic diversity and environmental adaptability in worldwide Merino and Merino-derived sheep breeds
No full textBackground: To enhance and extend the knowledge about the global historical and phylogenetic relationships between Merino and Merino-derived breeds, 19 populations were genotyped with the OvineSNP50 BeadChip specifically for this study, while an additional 23 populations from the publicly available genotypes were retrieved. Three complementary statistical tests, Rsb (extended haplotype homozygosity between-populations), XP-EHH (cross-population extended haplotype homozygosity), and runs of homozygosity (ROH) islands were applied to identify genomic variants with potential impact on the adaptability of Merino genetic type in two contrasting climate zones. Results: The results indicate that a large part of the Merino's genetic relatedness and admixture patterns are explained by their genetic background and/or geographic origin, followed by local admixture. Multi-dimensional scaling, Neighbor-Net, Admixture, and TREEMIX analyses consistently provided evidence of the role of Australian, Rambouillet and German strains in the extensive gene introgression into the other Merino and Merino-derived breeds. The close relationship between Iberian Merinos and other South-western European breeds is consistent with the Iberian origin of the Merino genetic type, with traces from previous contributions of other Mediterranean stocks. Using Rsb and XP-EHH approaches, signatures of selection were detected spanning four genomic regions located on Ovis aries chromosomes (OAR) 1, 6 and 16, whereas two genomic regions on OAR6, that partially overlapped with the previous ones, were highlighted by ROH islands. Overall, the three approaches identified 106 candidate genes putatively under selection. Among them, genes related to immune response were identified via the gene interaction network. In addition, several candidate genes were found, such as LEKR1, LCORL, GHR, RBPJ, BMPR1B, PPARGC1A, and PRKAA1, related to morphological, growth and reproductive traits, adaptive thermogenesis, and hypoxia responses. Conclusions: To the best of our knowledge, this is the first comprehensive dataset that includes most of the Merino and Merino-derived sheep breeds raised in different regions of the world. The results provide an in-depth picture of the genetic makeup of the current Merino and Merino-derived breeds, highlighting the possible selection pressures associated with the combined effect of anthropic and environmental factors. The study underlines the importance of Merino genetic types as invaluable resources of possible adaptive diversity in the context of the occurring climate changes
Differential distribution of Y-chromosome haplotypes in Swiss and Southern European goat breeds.
No full textThe analysis of Y-chromosome variation has provided valuable clues about the paternal history of domestic animal populations. The main goal of the current work was to characterize Y-chromosome diversity in 31 goat populations from Central Eastern (Switzerland and Romania) and Southern Europe (Spain and Italy) as well as in reference populations from Africa and the Near East. Towards this end, we have genotyped seven single nucleotide polymorphisms (SNPs), mapping to the SRY, ZFY, AMELY and DDX3Y Y-linked loci, in 275 bucks from 31 populations. We have observed a low level of variability in the goat Y-chromosome, with just five haplotypes segregating in the whole set of populations. We have also found that Swiss bucks carry exclusively Y1 haplotypes (Y1A: 24%, Y1B1: 15%, Y1B2: 43% and Y1C: 18%), while in Italian and Spanish bucks Y2A is the most abundant haplotype (77%). Interestingly, in Carpathian goats from Romania the Y2A haplotype is also frequent (42%). The high Y-chromosome differentiation between Swiss and Italian/Spanish breeds might be due to the post-domestication spread of two different Near Eastern genetic stocks through the Danubian and Mediterranean corridors. Historical gene flow between Southern European and Northern African goats might have also contributed to generate such pattern of genetic differentiation
Multidimensional scaling plot based on genome-wide identity-by-state pairwise distances inferred with PLINK.
No full text<p>This graph displays the genetic relationships between Near Eastern, Korean and European wild boar and Iberian, Canarian and Mangalitza pigs.</p
