Transcriptional profiling of bovine milk using RNA sequencing

<p>Abstract</p> <p>Background</p> <p>Cow milk is a complex bioactive fluid consumed by humans beyond infancy. Even though the chemical and physical properties of cow milk are well characterized, very limited research has been done on characterizing the milk transcriptome. This study performs a comprehensive expression profiling of genes expressed in milk somatic cells of transition (day 15), peak (day 90) and late (day 250) lactation Holstein cows by RNA sequencing. Milk samples were collected from Holstein cows at 15, 90 and 250 days of lactation, and RNA was extracted from the pelleted milk cells. Gene expression analysis was conducted by Illumina RNA sequencing. Sequence reads were assembled and analyzed in CLC Genomics Workbench. Gene Ontology (GO) and pathway analysis were performed using the Blast2GO program and GeneGo application of MetaCore program.</p> <p>Results</p> <p>A total of 16,892 genes were expressed in transition lactation, 19,094 genes were expressed in peak lactation and 18,070 genes were expressed in late lactation. Regardless of the lactation stage approximately 9,000 genes showed ubiquitous expression. Genes encoding caseins, whey proteins and enzymes in lactose synthesis pathway showed higher expression in early lactation. The majority of genes in the fat metabolism pathway had high expression in transition and peak lactation milk. Most of the genes encoding for endogenous proteases and enzymes in ubiquitin-proteasome pathway showed higher expression along the course of lactation.</p> <p>Conclusions</p> <p>This is the first study to describe the comprehensive bovine milk transcriptome in Holstein cows. The results revealed that 69% of NCBI Btau 4.0 annotated genes are expressed in bovine milk somatic cells. Most of the genes were ubiquitously expressed in all three stages of lactation. However, a fraction of the milk transcriptome has genes devoted to specific functions unique to the lactation stage. This indicates the ability of milk somatic cells to adapt to different molecular functions according to the biological need of the animal. This study provides a valuable insight into the biology of lactation in the cow, as well as many avenues for future research on the bovine lactome.</p

Manipulation of the Spatial Grazing Behaviour of Livestock in Extensive Grassland Systems

Spatial behaviour of livestock is a critical factor in grassland management. Recent and ongoing research suggests that new approaches can be used to manipulate where cattle graze. The combination of strategic supplement placement and low-stress herding can be used to target cattle grazing and potentially may be useful for managing fine fuels. A phenotype to genotype association study of cattle spatial behavior suggests that use of rugged terrain and areas far from water is inherited. Although more research is needed, selection for animals specifically adapted for mountainous terrain or extensive paddocks may be an alternative for managing grasslands in the near future

RNA-seq analysis of single bovine blastocysts

Background: Use of RNA-Seq presents unique benefits in terms of gene expression analysis because of its wide dynamic range and ability to identify functional sequence variants. This technology provides the opportunity to assay the developing embryo, but the paucity of biological material available from individual embryos has made this a challenging prospect. Results: We report here the first application of RNA-Seq for the analysis of individual blastocyst gene expression, SNP detection, and characterization of allele specific expression (ASE). RNA was extracted from single bovine blastocysts (n = 5), amplified, and analyzed using high-throughput sequencing. Approximately 38 million sequencing reads were generated per embryo and 9,489 known bovine genes were found to be expressed, with a high correlation of expression levels between samples (r > 0.97). Transcriptomic data was analyzed to identify SNP in expressed genes, and individual SNP were examined to characterize allele specific expression. Expressed biallelic SNP variants with allelic imbalances were observed in 473 SNP, where one allele represented between 65-95% of a variant’s transcripts. Conclusions: This study represents the first application of RNA-seq technology in single bovine embryos allowing a representation of the embryonic transcriptome and the analysis of transcript sequence variation to describe specific allele expression.EEA BalcarceFil: Chitwood, James L. University of California Davis. Department of Animal Science; Estados UnidosFil: Rincon, Gonzalo. University of California Davis. Department of Animal Science; Estados UnidosFil: Kaiser, German Gustavo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Medrano, Juan F. University of California Davis. Department of Animal Science; Estados UnidosFil: Ross, Pablo J. University of California Davis. Department of Animal Science; Estados Unido

A clone-free, single molecule map of the domestic cow (Bos taurus) genome.

BackgroundThe cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1&nbsp;and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation.ResultsThe optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30&nbsp;Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91&nbsp;Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts).ConclusionAlignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI's current designation of UMD3.1 sequence assembly as the "reference assembly" and the Btau4.6 as the "alternate assembly." The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds

Design and construction of a solar tracking system for Linear Fresnel Concentrator

An open circuit solar tracking system has been designed, manufactured, simulated and implemented for a handcrafted prototype of a small scale linear Fresnel reflector with a single axis of motion. The electronic control system is governed by an Arduino UNO R3 board and two main auxiliary systems; a Microstep Driver TB6600 and an RTC DS1302 module. Further, a mechanism was implemented that joins the reflectors to a stepper motor that executes a single movement per sequence, to move the set of reflector mirrors that make up the reflection system of the device. The positioning angles of the reflectors determined by the control algorithm models for solar tracking, allowed to feed the TONATIUH software to evaluate the path of the solar rays through the 3D modeling of the Linear Fresnel reflector on a real scale. The software was designed to follow the path of the sun by means of astronomical equations. In this way, the mirrors of the Linear Fresnel reflector can follow the solar path on a single axis from 7 am to 5 pm, making changes in the position of each element in 15-minute intervals. The percentage of position deviation of the reflectors does not exceed 1% between the location of the full-scale system mirrors and the position angles provided by the control algorithm. The efficiency of the implemented automatic solar tracking system increased by more than 50% compared to the manual tracking system

Edificios nZEB, análisis de la tendencia de investigación

In this paper, the research trend in relation to the NZEB buildings is explored, through the analysis of selected scientific articles published in 11 journals collected in chronological order from 2014 to 2020. The analysis is carried out on the basis and terms of annual investigative publications of the documents in relation to the NZEB, such as contributions made by countries, institutions, authors, and research topics covered. The study carried out uses a document review methodology. The analysis reveals a growing interest in energy efficiency research in recent times, implying that the importance that the construction industry attaches to NZEB in consequences of global warming and accelerating environmental problems. The findings also indicate that, during the period studied, researchers in developed economy areas such as the US and Italy contributed higher rates to promoting research on NZEB. Developing countries like China also went to great lengths to promote research. Research topics covered tend to focus on studies completed with NZEB project delivery and development, building rehabilitation, energy performance, and advanced technologies applied for energy improvement in buildings. This research provides a valuable platform for industry professionals and researchers to understand NZEB construction research trends and developments, including their applicability and their future research and contributions to the topic.En el presente trabajo se exploran la tendencia de investigación con relación a los edificios NZEB, mediante el análisis de artículos científicos seleccionados publicados en 11 revistas recopilados en orden cronológico desde el año 2014 hasta el 2020. El análisis se realiza en base y términos de publicaciones investigativas anuales de los documentos con relación a los NZEB, como contribuciones realizadas por países, instituciones, autores, y temas de investigación cubiertos. El estudio realizado utiliza una metodología de revisión documental. El análisis revela un creciente interés de investigación de rendimiento energético en los últimos tiempos, lo que implica la importancia que la industria de la construcción atribuye a NZEB en consecuencias al calentamiento global y problemática ambiental se está acelerando. Los hallazgos también indican que, durante el período estudiado, los investigadores de las zonas con economías desarrolladas como los EE. UU., e Italia contribuye-ron con índices más altos a promover la investigación sobre NZEB. Los países en desarrollo como China también hicieron grandes esfuerzos para promover la investigación. Los temas de investigación cubiertos tienden a centrarse en los estudios finalizados con la entrega y el desarrollo de proyectos de NZEB, rehabilitación de edificios, rendimiento energético y tecnologías avanzadas que se aplican para el mejoramiento energético en las edificaciones. Esta investigación proporciona una plataforma valiosa para que los profesionales e investigadores de la industria comprendan las tendencias y los desarrollos de investigación de la construcción NZEB, incluida su aplicabilidad, sus futuras investigaciones y contribuciones al tema

Edificios nZEB, análisis de la tendencia de investigación

In this paper, the research trend in relation to the NZEB buildings is explored, through the analysis of selected scientific articles published in 11 journals collected in chronological order from 2014 to 2020. The analysis is carried out on the basis and terms of annual investigative publications of the documents in relation to the NZEB, such as contributions made by countries, institutions, authors, and research topics covered. The study carried out uses a document review methodology. The analysis reveals a growing interest in energy efficiency research in recent times, implying that the importance that the construction industry attaches to NZEB in consequences of global warming and accelerating environmental problems. The findings also indicate that, during the period studied, researchers in developed economy areas such as the US and Italy contributed higher rates to promoting research on NZEB. Developing countries like China also went to great lengths to promote research. Research topics covered tend to focus on studies completed with NZEB project delivery and development, building rehabilitation, energy performance, and advanced technologies applied for energy improvement in buildings. This research provides a valuable platform for industry professionals and researchers to understand NZEB construction research trends and developments, including their applicability and their future research and contributions to the topic.En el presente trabajo se exploran la tendencia de investigación con relación a los edificios NZEB, mediante el análisis de artículos científicos seleccionados publicados en 11 revistas recopilados en orden cronológico desde el año 2014 hasta el 2020. El análisis se realiza en base y términos de publicaciones investigativas anuales de los documentos con relación a los NZEB, como contribuciones realizadas por países, instituciones, autores, y temas de investigación cubiertos. El estudio realizado utiliza una metodología de revisión documental. El análisis revela un creciente interés de investigación de rendimiento energético en los últimos tiempos, lo que implica la importancia que la industria de la construcción atribuye a NZEB en consecuencias al calentamiento global y problemática ambiental se está acelerando. Los hallazgos también indican que, durante el período estudiado, los investigadores de las zonas con economías desarrolladas como los EE. UU., e Italia contribuye-ron con índices más altos a promover la investigación sobre NZEB. Los países en desarrollo como China también hicieron grandes esfuerzos para promover la investigación. Los temas de investigación cubiertos tienden a centrarse en los estudios finalizados con la entrega y el desarrollo de proyectos de NZEB, rehabilitación de edificios, rendimiento energético y tecnologías avanzadas que se aplican para el mejoramiento energético en las edificaciones. Esta investigación proporciona una plataforma valiosa para que los profesionales e investigadores de la industria comprendan las tendencias y los desarrollos de investigación de la construcción NZEB, incluida su aplicabilidad, sus futuras investigaciones y contribuciones al tema