Systems biology in animal sciences

Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes and animal traits are not yet frequently used. This paper aims to explain what systems biology is and which areas of animal sciences could benefit from systems biology approaches. Systems biology aims to understand whole biological systems working as a unit, rather than investigating their individual components. Therefore, systems biology can be considered a holistic approach, as opposed to reductionism. The recently developed ‘omics’ technologies enable biological sciences to characterize the molecular components of life with ever increasing speed, yielding vast amounts of data. However, biological functions do not follow from the simple addition of the properties of system components, but rather arise from the dynamic interactions of these components. Systems biology combines statistics, bioinformatics and mathematical modeling to integrate and analyze large amounts of data in order to extract a better understanding of the biology from these huge data sets and to predict the behavior of biological systems. A ‘system’ approach and mathematical modeling in biological sciences are not new in itself, as they were used in biochemistry, physiology and genetics long before the name systems biology was coined. However, the present combination of mass biological data and of computational and modeling tools is unprecedented and truly represents a major paradigm shift in biology. Significant advances have been made using systems biology approaches, especially in the field of bacterial and eukaryotic cells and in human medicine. Similarly, progress is being made with ‘system approaches’ in animal sciences, providing exciting opportunities to predict and modulate animal traits

Expression profiles of genes regulating dairy cow fertility: recent findings, ongoing activities and future possibilities

Subfertility has negative effects for dairy farm profitability, animal welfare and sustainability of animal production. Increasing herd sizes and economic pressures restrict the amount of time that farmers can spend on counteractive management Genetic improvement will become increasingly important to restore reproductive performance. Complementary to traditional breeding value estimation procedures, genomic selection based on genome-wide information will become more widely applied. Functional genomics, including transcriptomics (gene expression profiling), produces the information to understand the consequences of selection as it helps to unravel physiological mechanisms underlying female fertility traits. Insight into the latter is needed to develop new effective management strategies to combat subfertility. Here, the importance of functional genomics for dairy cow reproduction so far and in the near future is evaluated. Recent gene profiling studies in the field of dairy cow fertility are reviewed and new data are presented on genes that are expressed in the brains of dairy cows and that are involved in dairy cow oestrus (behaviour). Fast-developing new research areas in the field of functional genomics, such as epigenetics, RNA interference, variable copy numbers and nutrigenomics are discussed including their promising future value for dairy cow fertility

Viljelty liha yhteiskuntatieteellisessä tutkimuksessa - haasteiden alustava luokittelu

Non peer reviewe

Inferring the Transcriptional Landscape of Bovine Skeletal Muscle by Integrating Co-Expression Networks

Background: Despite modern technologies and novel computational approaches, decoding causal transcriptional regulation remains challenging. This is particularly true for less well studied organisms and when only gene expression data is available. In muscle a small number of well characterised transcription factors are proposed to regulate development. Therefore, muscle appears to be a tractable system for proposing new computational approaches. Methodology/Principal Findings: Here we report a simple algorithm that asks "which transcriptional regulator has the highest average absolute co-expression correlation to the genes in a co-expression module?" It correctly infers a number of known causal regulators of fundamental biological processes, including cell cycle activity (E2F1), glycolysis (HLF), mitochondrial transcription (TFB2M), adipogenesis (PIAS1), neuronal development (TLX3), immune function (IRF1) and vasculogenesis (SOX17), within a skeletal muscle context. However, none of the canonical pro-myogenic transcription factors (MYOD1, MYOG, MYF5, MYF6 and MEF2C) were linked to muscle structural gene expression modules. Co-expression values were computed using developing bovine muscle from 60 days post conception (early foetal) to 30 months post natal (adulthood) for two breeds of cattle, in addition to a nutritional comparison with a third breed. A number of transcriptional landscapes were constructed and integrated into an always correlated landscape. One notable feature was a 'metabolic axis' formed from glycolysis genes at one end, nuclear-encoded mitochondrial protein genes at the other, and centrally tethered by mitochondrially-encoded mitochondrial protein genes. Conclusions/Significance: The new module-to-regulator algorithm complements our recently described Regulatory Impact Factor analysis. Together with a simple examination of a co-expression module's contents, these three gene expression approaches are starting to illuminate the in vivo transcriptional regulation of skeletal muscle development

Ohustatud Euroopa naaritsa (Mustela lutreola) sigimine ja käitumine tehiskeskkonnas

Väitekirja elektrooniline versioon ei sisalda publikatsiooneEuroopa naarits on kriitiliselt ohustatud imetaja, mis on loodusest kadumas. Päästmaks liiki väljasuremisest hakati naaritsaid pidama loomaaedades. Vangistuses on loomade paljundamine keeruline, kuna sealne keskkond erineb looma looduslikust elupaigast. Loomaaias elavatel naaritsatel on täheldatud probleeme sigimisega. Paljud ei saa järglasi, mis võib saada saatuslikuks asurkonna jätkusuutlikkusele. Käesolevas doktoritöös uurisin, miks on naaritsa sigimine loomaaias ebaedukas ja kuidas leida probleemile lahendus. Olukorrast parema ülevaate saamiseks uurisime, mis mõjutab pesakonna suurust ja poegade tõenäosust ellu jääda. Leidsime, et olulised on ema vanus ja kaal, kuid muidu oli emaste sigimisedu sarnane. Lisaks uurisime emase hormonaaltsüklit indlemise ja tiinuse ajal. Tulemused olid ootuspärased, hormonaaltsükkel järgis liigile tüüpilist rada. Me ei leidnud tõendeid, et paaritamiskatsete ebaõnnestumise põhjust tuleks otsida emastest. Leidsime, et ebaedu sigimisel on seotud vangistuses sündinud isastega. Mõni isane on paaritamiskatses emase vastu agressiivne või siis neil puudub indleva emase vastu huvi. Mõistmaks isaste käitumist vaatlesime naaritsate lapsepõlve – uurisime poegade vahelisi suhteid pesakonnas kasvamise ajal. Paljudel imetajatel on tõendatud, et varajane keskkond mõjutab isendi käitumist täiskasvanueas. Me ei leidnud, et naaritsatel oleks pesakonnaperioodil ebanormaalset käitumist. Nagu igati kohane, kulus poegade põhiaeg mängule. Agressiivsust ei olnud palju ja see ei tõusnud ajas. Pesakonnad ei erinenud käitumismustrilt üksteisest, seega ei leidnud me hälbiva poegade käitumisega pesakondi, mis oleksid võinud ebasobiva sigimiskäitumise tekkimist seletada. Töötasime välja metoodika naartisate iseloomutüüpide määramiseks, sest üha enam soovitatakse, et loomadesse tuleks loomaaias suhtuda neist igaühe iseloomu arvestades. Leidsime, et naaritsaid saab eristada julguse, uurivuse ja sotsiaalsuse alusel . Meie töös ilmnes, et probleemid sigimishooajal on seotud eelkõige vangistuses sündinud isastega, nende põhjuseid peaks otsima mujalt kui pesakonnaperioodist, abi võiks olla iga looma iseloomu tundmisest. Saadud tulemused on oluliseks alusteadmisteks töös, mis on suunatud naaritsate tehiskeskkonnas pidamise edukuse tõstmisele.European mink is a critically endangered carnivore which has almost disappeared from nature. To save the species from extinction a captive population was established. Unfortunately, keeping wild animals in captivity always causes problems, just because in a zoo everything is different from the species’ natural habitat. In the case of the European mink, there are problems with breeding in captive conditions. Some animals will fail to produce offspring which may threaten the persistence of the captive population. In this doctorial thesis, I addressed the reasons of breeding failures and how to find solutions to this problem. At first we studied what affects the size and survival of the litter. We found that the weight and age of the mother are most significant. Additionally we studied the hormonal cycle of the females during the mating season and gestation. Results were expectable: the hormonal cycle followed a profile typical of the species. Analysing the diaries kept at Tallinn zoo for 20 years, we did not find that something is wrong on the females’ side. Instead, we found that the breeding problems are caused by males which have been born in captivity. Some males are aggressive toward the female during the mating attempt or remain passive. To understand the reasons for kind of behaviour, we focused on the childhood of the mink: we studied the interactions between the cubs during the litter period. It has often been found that, in mammals, the early environment affects the development of the behaviour of an animal. In our study, however, we did not find abnormalities in cubs’ behaviour during the litter period. As it should be, the most frequent type of behaviour was play. Aggression was low, it did not rise in time and did not differ between the litters. We developed tests to identify personality types in European mink. We found that it is possible to distinguish individual mink in boldness, sociability and exploration. In summary, we found that the main reason why breeding fails in the European mink is in the behaviour of captive born males. The causes of behavioural distortion may not be related to the litter period, an analysis of personality types may help here. The knowledge obtained forms important basis information for the work aimed at improving keeping condition of captive European mink

Gene expression patterns in four brain areas associate with quantitative measure of estrous behavior in dairy cows

<p>Abstract</p> <p>Background</p> <p>The decline noticed in several fertility traits of dairy cattle over the past few decades is of major concern. Understanding of the genomic factors underlying fertility, which could have potential applications to improve fertility, is very limited. Here, we aimed to identify and study those genes that associated with a key fertility trait namely estrous behavior, among genes expressed in four bovine brain areas (hippocampus, amygdala, dorsal hypothalamus and ventral hypothalamus), either at the start of estrous cycle, or at mid cycle, or regardless of the phase of cycle.</p> <p>Results</p> <p>An average heat score was calculated for each of 28 primiparous cows in which estrous behavior was recorded for at least two consecutive estrous cycles starting from 30 days post-partum. Gene expression was then measured in brain tissue samples collected from these cows, 14 of which were sacrificed at the start of estrus and 14 around mid cycle. For each brain area, gene expression was modeled as a function of the orthogonally transformed average heat score values using a Bayesian hierarchical mixed model. Genes whose expression patterns showed significant linear or quadratic relationships with heat scores were identified. These included genes expected to be related to estrous behavior as they influence states like socio-sexual behavior, anxiety, stress and feeding motivation (<it>OXT, AVP, POMC, MCHR1</it>), but also genes whose association with estrous behavior is novel and warrants further investigation.</p> <p>Conclusions</p> <p>Several genes were identified whose expression levels in the bovine brain associated with the level of expression of estrous behavior. The genes <it>OXT </it>and <it>AVP </it>play major roles in regulating estrous behavior in dairy cows. Genes related to neurotransmission and neuronal plasticity are also involved in estrous regulation, with several genes and processes expressed in mid-cycle probably contributing to proper expression of estrous behavior in the next estrus. Studying these genes and the processes they control improves our understanding of the genomic regulation of estrous behavior expression.</p

13th Annual Research in the Capitol [Program], April 3, 2018

Program of research presentations given at the Capitol by students from the University of Northern Iowa, Iowa State University, and the University of Iowa.https://scholarworks.uni.edu/programs_rcapitol/1002/thumbnail.jp

Evolution of host support for two ancient bacterial symbionts with differentially degraded genomes in a leafhopper host.

Plant sap-feeding insects (Hemiptera) rely on bacterial symbionts for nutrition absent in their diets. These bacteria experience extreme genome reduction and require genetic resources from their hosts, particularly for basic cellular processes other than nutrition synthesis. The host-derived mechanisms that complete these processes have remained poorly understood. It is also unclear how hosts meet the distinct needs of multiple bacterial partners with differentially degraded genomes. To address these questions, we investigated the cell-specific gene-expression patterns in the symbiotic organs of the aster leafhopper (ALF), Macrosteles quadrilineatus (Cicadellidae). ALF harbors two intracellular symbionts that have two of the smallest known bacterial genomes: Nasuia (112 kb) and Sulcia (190 kb). Symbionts are segregated into distinct host cell types (bacteriocytes) and vary widely in their basic cellular capabilities. ALF differentially expresses thousands of genes between the bacteriocyte types to meet the functional needs of each symbiont, including the provisioning of metabolites and support of cellular processes. For example, the host highly expresses genes in the bacteriocytes that likely complement gene losses in nucleic acid synthesis, DNA repair mechanisms, transcription, and translation. Such genes are required to function in the bacterial cytosol. Many host genes comprising these support mechanisms are derived from the evolution of novel functional traits via horizontally transferred genes, reassigned mitochondrial support genes, and gene duplications with bacteriocyte-specific expression. Comparison across other hemipteran lineages reveals that hosts generally support the incomplete symbiont cellular processes, but the origins of these support mechanisms are generally specific to the host-symbiont system

Examination Of The Effects Breed And Nutrition Have On The Milk Protein Profile Produced By Lactating Dairy Cattle

Milk is a highly nutritious natural product and research over the last 10 years has proven that these milk proteins not only provide a rich source of amino acids to the consumer but also contains many bioactive proteins and peptides known to exert biological activity benefitting human health. In this research, proteomic methods were first used to characterize the low abundance proteome within the skim milk fraction produced by Holstein and Jersey dairy cows maintained under the same diet, management and environmental conditions. Milk samples were collected over a seven day period from six Holstein and six Jersey dairy cows. Samples were depleted of casein (CN) by acidification and ultracentrifugation followed by ProteoMiner treatment. Extracts were subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) separation followed by liquid chromatography mass spectrometry (LC-MS). Over 930 low abundance proteins were identified and label-free proteomic analysis allowed for semi-quantification of proteins. Gene ontology (GO) classified proteins into various cellular localization and function categories. Forty-three low abundance proteins were differentially expressed between the two dairy breeds. Some bioactive proteins with immunomodulatory activities were present at significantly different abundance between breeds such as lactotransferrin (P \u3c0.01) and Complement C2 (P \u3c0.01), whereas others like osteopontin (P = 0.17) and lactoperoxidase (P = 0.29) were present at similar levels. This work has identified the highest number of low abundance proteins within the whey fraction in bovine skim milk, providing a foundation for future research exploring the bovine milk proteome. Nutrition is a significant animal factor that has potential to alter milk protein composition. Therefore in the second phase of this work, nutritional perturbances were used to alter the bovine milk proteome by feeding Holstein dairy cows different proportions of rumen degradable (RDP) and rumen undegradable protein (RUP) to alter whole-body nitrogen (N) metabolism. Six multiparous Holstein cows in mid-lactation were randomly assigned to one of two treatment groups. The experiment was conducted as a double-crossover design consisting of three 21-day periods. Within each period, treatment groups received diets with either 1) a high RDP:RUP ratio (control: 62.4:37.6 % of CP) or 2) a low RDP:RUP ratio (RUP: 51.3:48.7 % of CP). Both diets were isonitrogenous (CP = 18.5%) and isoenergetic (NEL = 0.8 Mcal lbs-1). Feeding a diet high in RUP decreased β-casein (P = 0.06), κ-casein (P =0.04) and total milk casein concentrations in milk (P \u3c0.001). Milk urea nitrogen (MUN) and plasma urea nitrogen (PUN) were significantly higher in the RDP group (P = 0.04; P \u3c 0.01, respectively). Over 590 low abundance proteins were identified and only three proteins were found to be differentially expressed between the two dietary groups. The high dietary crude protein (CP) inclusion may explain the lack of treatment effect since protein synthesis within the mammary gland (MG) may not be responsive to dietary changes when total CP levels is offered in excess. Additional feeding trials are needed to alter N utilization patterns within a dairy cow while maintaining isonitrogenous and isoenergetic diets and offering normal CP levels. Nutritional perturbances offer opportunities to selectively alter the bovine proteome, providing a tool to enhance the healthfulness of milk