Origin, clonal diversity, and evolution of the parthenogenetic lizard Darevskia unisexualis.

BACKGROUND: The hybridization of female D. raddei and male D. valentini gave rise to the parthenogenetic Caucasian rock lizard Darevskia unisexualis. A previously identified genetic polymorphism in the species consisted of one common and two allozyme clones. Analysis of microsatellites and single nucleotide polymorphisms (SNPs) from the three species yields estimates of clonal diversity and tests the hypothesis of a single origin for D. unisexualis. RESULTS: Genotyping and sequencing of four microsatellite-containing loci for 109 specimens of D. unisexualis, 17 D. valentini, and 45 D. raddei nairensis identified 12 presumptive clones, including one widespread and 11 rare clones. Most individuals in some localities had a rare clone. Clone-specific alleles in D. unisexualis were compared with those of the parental species. The results inferred a single hybridization event. Post-formation mutations best explain the less common clones. CONCLUSIONS: Interspecific analyses identify alleles inherited by D. unisexualis from its bisexual ancestors. SNP analyses fail to reject the hypothesis of a single interspecific origin of D. unisexualis, followed by microsatellite mutations in this initial clone. Microsatellites detect higher clonal diversity in D. unisexualis compared to allozymes and identify the likely origins of clones. Our approach may be applicable to other unisexual species whose origins involve interspecific hybridization.

Preventing Soil Inoculum of Calonectria pseudonaviculata from Splashing onto Healthy Boxwood Foliage by Mulching.

Boxwood blight, caused by Calonectria pseudonaviculata, is an emerging disease of great concern to horticulturists in the United States and other affected countries. The objective of this study was to evaluate the efficacy of mulching as a physical barrier to prevent soil inoculum from splashing onto healthy boxwood foliage. A field trial consisting of two treatments, mulched and nonmulched, was conducted under field conditions in Lowgap, North Carolina, and in a residential landscape setting near Richmond, Virginia, for 2 years at each site. Mulching efficacy was assessed by monitoring and comparing boxwood blight development on detector plants: containerized 'Justin Brouwers' boxwood, which were rotated through mulched and nonmulched plots at 1- and 2-week intervals in the Lowgap and Richmond sites, respectively. Boxwood blight was observed on detector plants in a combined 55 of the 88 monitoring periods during this study at the two sites. Mulching provided complete protection of Justin Brouwers boxwood from infection by C. pseudonaviculata soil inoculum during 33 of the 55 positive monitoring periods (60%) and good to excellent protection during 13 monitoring periods (24%). The potential applications of mulching for boxwood blight mitigation are discussed.

Genomic architecture of haddock (Melanogrammus aeglefinus) shows expansions of innate immune genes and short tandem repeats.

BACKGROUND: Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. RESULTS: Here, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) - a relative of Atlantic cod - using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors (NLRs), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. CONCLUSIONS: The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod - but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates.

Multiple interspecific hybridization and microsatellite mutations provide clonal diversity in the parthenogenetic rock lizard Darevskia armeniaca.

BACKGROUND: The parthenogenetic Caucasian rock lizard Darevskia armeniaca, like most other parthenogenetic vertebrate species, originated through interspecific hybridization between the closely related sexual Darevskia mixta and Darevskia valentini. Darevskia armeniaca was shown to consist of one widespread allozyme clone and a few rare ones, but notwithstanding the origin of clonal diversity remains unclear. We conduct genomic analysis of D. armeniaca and its parental sexual species using microsatellite and SNP markers to identify the origin of parthenogenetic clonal lineages. RESULTS: Four microsatellite-containing loci were genotyped for 111 specimens of D. armeniaca, 17 D. valentini, and four D. mixta. For these species, a total of 47 alleles were isolated and sequenced. Analysis of the data revealed 13 genotypes or presumptive clones in parthenogenetic D. armeniaca, including one widespread clone, two apparently geographically restricted clones, and ten rare clones. Comparisons of genotype-specific markers in D. armeniaca with those of its parental species revealed three founder-events including a common and two rare clones. All other clones appeared to have originated via post-formation microsatellite mutations in the course of evolutionary history of D. armeniaca. CONCLUSION: Our new approach to microsatellite genotyping reveals allele-specific microsatellite and SNP markers for each locus studied. Interspecies comparison of these markers identifies alleles inherited by parthenospecies from parental species, and provides new information on origin and evolution of clonal diversity in D. armeniaca. SNP analyses reveal at least three interspecific origins of D. armeniaca, and microsatellite mutations in these initial clones give rise to new clones. Thus, we first establish multiple origins of D. armeniaca. Our study identifies the most effective molecular markers for elucidating the origins of clonal diversity in other unisexual species that arose via interspecific hybridization.

A standard photomap of the ovarian nurse cell chromosomes for the dominant malaria vector in Europe and Middle East Anopheles sacharovi.

BACKGROUND: Anopheles sacharovi is a dominant malaria vector species in South Europe and the Middle East which has a highly plastic behaviour at both adult and larval stages. Such plasticity has prevented this species from eradication by several anti-vector campaigns. The development of new genome-based strategies for vector control will benefit from genome sequencing and physical chromosome mapping of this mosquito. Although a cytogenetic photomap for chromosomes from salivary glands of An. sacharovi has been developed, no cytogenetic map suitable for physical genome mapping is available. METHODS: Mosquitoes for this study were collected at adult stage in animal shelters in Armenia. Polytene chromosome preparations were prepared from ovarian nurse cells. Fluorescent in situ hybridization (FISH) was performed using PCR amplified probes. RESULTS: This study constructed a high-quality standard photomap for polytene chromosomes from ovarian nurse cells of An. sacharovi. Following the previous nomenclature, chromosomes were sub-divided into 39 numbered and 119 lettered sub-divisions. Chromosomal landmarks for the chromosome recognition were described. Using FISH, 4 PCR-amplified genic probes were mapped to the chromosomes. The positions of the probes demonstrated gene order reshuffling between An. sacharovi and Anopheles atroparvus which has not been seen cytologically. In addition, this study described specific chromosomal landmarks that can be used for the cytotaxonomic diagnostics of An. sacharovi based on the banding pattern of its polytene chromosomes. CONCLUSIONS: This study constructed a high-quality standard photomap for ovarian nurse cell chromosomes of An. sacharovi and validated its utility for physical genome mapping. Based on the map, cytotaxonomic features for identification of An. sacharovi have been described. The cytogenetic map constructed in this study will assist in creating a chromosome-based genome assembly for this mosquito and in developing cytotaxonomic tools for identification of other species from the Maculipennis group.

Dietary fats and F2-isoprostanes: A review of the clinical evidence.

Evidence supports that a high dietary fat intake increases oxidative stress and the risk of diet-induced metabolic disorders such as obesity, diabetes and cardiovascular diseases. F2-isoprostanes (F2-isoP) are formed by the non-enzymatic oxidation of arachidonic acid and are widely used as reliable biomarkers of oxidative stress in clinical studies. Dietary fats may influence F2-isoP levels, as they (1) are metabolic substrates for their formation, (2) modify the lipid composition of tissues, and (3) affect the plasma lipoprotein concentrations which are involved in F2-isoP transport. This review examined the latest clinical evidence on how dietary fats can affect blood circulation and excretion of F2-isoP in individuals with healthy or deteriorated metabolic profiles. Clinical studies reported that saturated or monounsaturated fat-rich diets did not affect F2-isoP levels in adults with healthy or deteriorated metabolic profiles. Though, ω-3 polyunsaturated fatty acids decreased F2-isoP levels in numerous studies, whereas trans-fatty acids raised F2-isoP excretion. Yet, the reported heterogeneous results reveal important considerations, such as the health status of the participants, the biological fluids used to determine F2-isoP, the analytical methods employed and the specific F2-isoP isomers detected. Therefore, future clinical studies should be designed in order to consider these issues in the studies of the effects of fat intake on oxidative stress.

Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha).

Anadromous Chinook salmon populations vary in the period of river entry at the initiation of adult freshwater migration, facilitating optimal arrival at natal spawning. Run timing is a polygenic trait that shows evidence of rapid parallel evolution in some lineages, signifying a key role for this phenotype in the ecological divergence between populations. Studying the genetic basis of local adaptation in quantitative traits is often impractical in wild populations. Therefore, we used a novel approach, Random Forest, to detect markers linked to run timing across 14 populations from contrasting environments in the Columbia River and Puget Sound, USA. The approach permits detection of loci of small effect on the phenotype. Divergence between populations at these loci was then examined using both principle component analysis and FST outlier analyses, to determine whether shared genetic changes resulted in similar phenotypes across different lineages. Sequencing of 9107 RAD markers in 414 individuals identified 33 predictor loci explaining 79.2% of trait variance. Discriminant analysis of principal components of the predictors revealed both shared and unique evolutionary pathways in the trait across different lineages, characterized by minor allele frequency changes. However, genome mapping of predictor loci also identified positional overlap with two genomic outlier regions, consistent with selection on loci of large effect. Therefore, the results suggest selective sweeps on few loci and minor changes in loci that were detected by this study. Use of a polygenic framework has provided initial insight into how divergence in a trait has occurred in the wild.

Genetic variation underlying resistance to infectious hematopoietic necrosis virus in a steelhead trout (Oncorhynchus mykiss) population.

Understanding the mechanisms of host resistance to pathogens will allow insights into the response of wild populations to the emergence of new pathogens. Infectious hematopoietic necrosis virus (IHNV) is endemic to the Pacific Northwest and infectious to Pacific salmon and trout (Oncorhynchus spp.). Emergence of the M genogroup of IHNV in steelhead trout O. mykiss in the coastal streams of Washington State, between 2007 and 2011, was geographically heterogeneous. Differences in host resistance due to genetic change were hypothesized to be a factor influencing the IHNV emergence patterns. For example, juvenile steelhead trout losses at the Quinault National Fish Hatchery (QNFH) were much lower than those at a nearby facility that cultures a stock originally derived from the same source population. Using a classical quantitative genetic approach, we determined the potential for the QNFH steelhead trout population to respond to selection caused by the pathogen, by estimating the heritability for 2 traits indicative of IHNV resistance, mortality (h² = 0.377 (0.226 - 0.550)) and days to death (h² = 0.093 (0.018 - 0.203)). These results confirm that there is a genetic basis for resistance and that this population has the potential to adapt to IHNV. Additionally, genetic correlation between days to death and fish length suggests a correlated response in these traits to selection. Reduction of genetic variation, as well as the presence or absence of resistant alleles, could affect the ability of populations to adapt to the pathogen. Identification of the genetic basis for IHNV resistance could allow the assessment of the susceptibility of other steelhead populations.

First Report of Reduced Sensitivity to a QoI Fungicide in Apple Scab (Venturia inaequalis) in Virginia and Maryland.

Apple scab caused by Venturia inaequalis (Cooke) Winter continues to be a significant concern for apple growers in Virginia and Maryland. Management of scab has relied on foliar fungicides including strobilurins (QoIs) such as trifloxystrobin (TFX). In recent years, populations of V. inaequalis with reduced sensitivity to the QoIs have been reported in other apple-growing regions of the United States (1,2). Although QoIs generally remain effective in the mid-Atlantic, concerns about the development of resistance in some Virginia and Maryland orchards prompted this study. Twenty-five isolates of V. inaequalis were obtained from scabby leaves from commercial and experimental orchards in Virginia in 2010 (n = 6) and 2011 (n = 14) and from a commercial orchard in Maryland (n = 5) in 2011. Orchards had previously been treated with QoI or sterol-inhibiting (SI) fungicides. Isolates of V. inaequalis were grown on potato dextrose agar (PDA) amended with 0, 0.1, or 1.0 µg ml-1 TFX with 100 µg ml-1 salicylhydroxamic acid (SHAM) and incubated at 19°C. Colony growth was measured weekly for 4 weeks. To account for the SI use at some orchards, isolates of V. inaequalis were also evaluated on PDA amended with 0, 0.5, or 1.0 µg ml-1 myclobutanil. Fungicide sensitivities were expressed as a percentage of the difference in colony growth using a discriminatory dose of 1.0 µg ml-1 TFX with SHAM or 1.0 µg ml-1 myclobutanil at 28 days. Isolates with <25% growth suppression (GS) were classified as fully resistant, whereas those with >70% GS were classified as sensitive. Isolates with 25 to 70% GS were classified as partially resistant. Effective concentration (EC50) values (TFX concentration inhibiting colony growth by 50%) were also calculated for a subset of fully resistant and sensitive isolates. Of the 25 isolates tested, six were fully resistant to TFX (mean EC50 value greater than 10.0 µg ml-1) and 10 were sensitive (mean EC50 value of 0.04 µg ml-1 ± 0.05 µg ml-1). Nine isolates were classified as partially resistant. Some isolates showed more than a 200-fold increase in resistance to TFX, and one isolate grew almost as well on 10.0 µg ml-1 TFX as on the unamended control (GS of 3%). Current-season use of QoIs on isolate source trees was significantly associated with a lack of sensitivity Ç2 (1) = 3.72 (P < 0.06). All six fully resistant isolates originated from QoI-treated commercial orchards, which had shown control failures. Seven of 10 isolates sensitive to QoIs originated from trees that had been treated with SIs during the isolation year. Resistance to myclobutanil was not significantly associated with resistance to TFX Ç2 (1) = 1.220 (P < 0.5), and only one isolate was resistant (i.e. >25% GS) to both. Despite the long history of QoI use at the experimental orchards, no isolates fully resistant to TFX were identified there. To our knowledge, this is the first report of V. inaequalis isolates with resistance to TFX in Virginia and Maryland. Since SI resistance has been documented in Virginia (3) and resistance to both the SI and QoI chemical classes is a concern in the mid-Atlantic region (4), tank-mixing or alternating QoIs with broad-spectrum fungicides with different modes of action is recommended. References: (1). K. M. Cox et al. Phythopathology 99:S25, 2009. (2). K. E. Lesniak et al. Plant Dis. 95:927, 2011. (3) S. C. Marine et al. Plant Health Progress. doi:10.1094/PHP-2007-1113-01-RS, 2007. (4) E. E. Pfeufer and H. K. Ngugi. Phytopathology 102:272, 2012.

The mixed liver and kidney transcriptome dataset of Darevskia valentini rock lizard.

OBJECTIVES: This study is performed in the frame of a bigger study dedicated to genomics and transcriptomics of parthenogenesis in vertebrates. Among vertebrates, obligate parthenogenesis was first described in the lizards of the genus Darevskia. In this genus, all found parthenogenetic species originated via interspecific hybridization. It remains unknown which genetic or genomic factors play a key role in the generation of parthenogenetic organisms. Comparative genomic and transcriptomic analysis of parthenogens and their parental species may elucidate this problem. Darevskia valentini is a paternal species for four (of seven) parthenogens of this genus, which we promote as a particularly important species for the generation of parthenogenetic forms. DATA DESCRIPTION: Total cellular RNA was isolated from kidney and liver tissues using the standard Trizol Tissue RNA Extraction protocol. Sequencing of transcriptome libraries prepared by random fragmentation of cDNA samples was performed on an Illumina HiSeq2500. Obtained raw sequences contained 117,6 million reads with the GC content of 47%. After preprocessing, raw data was assembled by Trinity and produced 491,482 contigs.

De novo transcriptome assembly and annotation of parthenogenetic lizard Darevskia unisexualis and its parental ancestors Darevskia valentini and Darevskia raddei nairensis.

Darevskia rock lizards include 29 sexual and seven parthenogenetic species of hybrid origin distributed in the Caucasus. All seven parthenogenetic species of the genus Darevskia were formed as a result of interspecific hybridization of only four sexual species. It remains unknown what are the main advantages of interspecific hybridization along with switching on parthenogenetic reproduction in evolution of reptiles. Data on whole transcriptome sequencing of parthenogens and their parental ancestors can provide value impact in solving this problem. Here we have sequenced ovary tissue transcriptomes from unisexual parthenogenetic lizard D. unisexualis and its parental bisexual ancestors to facilitate the subsequent annotation and to obtain the collinear characteristics for comparison with other lizard species. Here we report generated RNAseq data from total mRNA of ovary tissues of D. unisexualis, D. valentini and D. raddei with 58932755, 51634041 and 62788216 reads. Obtained RNA reads were assembled by Trinity assembler and 95141, 62123, 61836 contigs were identified with N50 values of 2409, 2801 and 2827 respectively. For further analysis top Gene Ontology terms were annotated for all species and transcript number was calculated. The raw data were deposited in the NCBI SRA database (BioProject PRJNA773939). The assemblies are available in Mendeley Data and can be accessed via doi:10.17632/rtd8cx7zc3.1.

Single-Cell Transcriptome Profiling of Immune Cell Repertoire of the Atlantic Cod Which Naturally Lacks the Major Histocompatibility Class II System.

The Atlantic cod's unusual immune system, entirely lacking the Major Histocompatibility class II pathway, has prompted intriguing questions about what mechanisms are used to combat bacterial infections and how immunological memory is generated. By single-cell RNA sequencing we here report an in-depth characterisation of cell types found in immune tissues, the spleen and peripheral blood leukocytes of Atlantic cod. Unbiased transcriptional clustering revealed eleven distinct immune cell signatures. Resolution at the single cell level enabled characterisation of the major cell subsets including the cytotoxic T cells, B cells, erythrocytes, thrombocytes, neutrophils, and macrophages. Additionally, to our knowledge we are the first to uncover cell subsets in Atlantic cod which may represent dendritic cells, natural killer-like cells, and a population of cytotoxic cells expressing GATA-3, a master transcription factor of T helper 2 cells. We further identify putative gene markers for each cluster and describe the relative proportions of each cell type in the spleen and peripheral blood leukocytes. Of the major haematopoietic cell populations, the lymphocytes make up 55 and 68% of the spleen and peripheral blood leukocytes respectively, while the myeloid cells make up 45 and 32%. By single-cell analysis, this study provides the most detailed molecular and cellular characterisation of the immune system of the Atlantic cod so far.

New records and geographic distribution of the sympatric zones of unisexual and bisexual rock lizards of the genus Darevskia in Armenia and adjacent territories.

BACKGROUND: Caucasian rock lizards of the genus Darevskia are unique taxa, including both bisexual and parthenogenetic species. The parthenogenetic species have originated as a result of natural hybridisation between females and males of different bisexual species. The species involved in interspecific hybridisation are called parental. However, sympatric zones (SZ) of unisexual and bisexual rock lizards of the Caucasus are still poorly studied, although they are very important for understanding the role of hybrid individuals of different origin in reticulate evolution. This paper presents the location of the SZs of parthenogenetic and their parental bisexual rock lizards of the genus Darevskia in Armenia and adjacent territories of Georgia and Nagorno-Karabakh. We summarised the locations of the SZs identified from 1957 to the present, based on our field survey data gathered in 2018-2019 and records from publications and museum collections. This dataset includes 39 SZs of three types: SZ of parental bisexual species, SZ of parental species with unisexual species and SZ of the parthenogenetic species. For each zone, species composition, geographical and altitudinal distribution are presented. New records expand our knowledge of the geographical and altitudinal distribution of SZs in these species and provide additional data for understanding the mechanisms of reticulate evolution and hybridogeneous speciation in the past, present and future. NEW INFORMATION: The new records, including geographical and altitudinal distributions of three types of SZs, are presented, which expand the previously-known list to 39 locations of contact zones for parthenogenetic and its bisexual parental species of rock lizards of the genus Darevskia in Armenia and the adjacent territories of Georgia and Nagorno-Karabakh.

Publisher Correction: Sex-dependent dominance maintains migration supergene in rainbow trout.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Sex-dependent dominance maintains migration supergene in rainbow trout.

Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.

A practical introduction to Random Forest for genetic association studies in ecology and evolution.

Large genomic studies are becoming increasingly common with advances in sequencing technology, and our ability to understand how genomic variation influences phenotypic variation between individuals has never been greater. The exploration of such relationships first requires the identification of associations between molecular markers and phenotypes. Here, we explore the use of Random Forest (RF), a powerful machine-learning algorithm, in genomic studies to discern loci underlying both discrete and quantitative traits, particularly when studying wild or nonmodel organisms. RF is becoming increasingly used in ecological and population genetics because, unlike traditional methods, it can efficiently analyse thousands of loci simultaneously and account for nonadditive interactions. However, understanding both the power and limitations of Random Forest is important for its proper implementation and the interpretation of results. We therefore provide a practical introduction to the algorithm and its use for identifying associations between molecular markers and phenotypes, discussing such topics as data limitations, algorithm initiation and optimization, as well as interpretation. We also provide short R tutorials as examples, with the aim of providing a guide to the implementation of the algorithm. Topics discussed here are intended to serve as an entry point for molecular ecologists interested in employing Random Forest to identify trait associations in genomic data sets.

Genomewide association analyses of fitness traits in captive-reared Chinook salmon: Applications in evaluating conservation strategies.

A novel application of genomewide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus tshawytscha) and then determined how two alternative management approaches for captive rearing affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return timing), length and weight at return, age at maturity, spawn timing, and daily growth coefficient were identified using 9108 restriction site-associated markers and random forest, an approach suitable for polygenic traits. Mapping of trait-associated loci, gene annotations, and integration of results across multiple studies revealed candidate regions involved in several fitness-related traits. Genotypes at trait-associated loci were then compared between two hatchery populations that were derived from the same source but are now managed as separate lines, one integrated with and one segregated from the wild population. While no broad-scale change was detected across four generations, there were numerous regions where trait-associated loci overlapped with signatures of adaptive divergence previously identified in the two lines. Many regions, primarily with loci linked to return and spawn timing, were either unique to or more divergent in the segregated line, suggesting that these traits may be responding to domestication selection. This study is one of the first to utilize genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait-associated-and potentially adaptive-loci. The results will promote the development of trait-specific tools to better monitor genetic change in captive and wild populations.

Whey protein hydrolysate and branched-chain amino acids downregulate inflammation-related genes in vascular endothelial cells.

A recent review of clinical studies reports that dairy products may improve inflammation, a key etiologic cardiovascular disease risk factor. Yet the impact of dairy proteins on inflammatory markers is controversial and could be mediated by a differential impact of whey proteins and caseins. In this study, we hypothesized that whey proteins may have a greater anti-inflammatory effect than caseins. A model of human umbilical vein endothelial cells, with or without TNF-α stimulation, was used to investigate the effect of several dairy protein compounds on inflammation. Specifically, the impact of whey proteins either isolate or hydrolysate, caseins, and their amino acids on expression of TNF, VCAM-1, SOD2, and eNOS was examined. After a 24-hour incubation period, whey protein hydrolysate, leucine, isoleucine, and valine attenuated the TNF-α-induced endothelial inflammation by normalizing TNF and eNOS gene expression. This effect was not observed in unstimulated cells. Oppositely, caseins, a whey protein/casein mixture (1:4 w/w), and glutamine aggravated the TNF-α-induced TNF and SOD2 gene expression. Yet caseins and whey protein/casein mixture decreased VCAM-1 expression in both unstimulated and stimulated human umbilical vein endothelial cells. Measurement of TNF-α in cell supernatants by immunoassay substantiates gene expression data without reaching statistical significance. Taken together, this study showed that whey proteins and their major amino acids normalize TNF-α-induced proinflammatory gene expression in endothelial cells.

Influence of Amino Acids in Dairy Products on Glucose Homeostasis: The Clinical Evidence.

Dairy products have been hypothesized to protect against type 2 diabetes because of their high content of whey proteins, rich in branched-chain amino acids (BCAAs) - leucine, isoleucine and valine - and lysine, which may decrease postprandial glucose responses and stimulate insulin secretion. Paradoxically, epidemiologic studies also show that higher levels of plasma BCAAs have been linked to insulin resistance and type 2 diabetes. Therefore, the objective was to review the recent clinical evidence concerning the intake of amino acids found in dairy proteins so as to determine their impact on glucose homeostasis in healthy persons and in those with prediabetes and type 2 diabetes. Clinical studies have reported that the major dairy amino acids, namely, leucine, isoleucine, glutamine, phenylalanine, proline and lysine, have beneficial effects on glucose homeostasis. Yet the reported doses of amino acids investigated are too elevated to be reached through adequate dairy product intake. The minor dairy amino acids, arginine and glycine, may improve glucose homeostasis by improving other risk factors for type 2 diabetes. Further, the combination of amino acids may also improve glucose-related outcomes, suggesting additive or synergistic effects. Nevertheless, additional long-term studies in individuals with prediabetes and type 2 diabetes are needed to ascertain the benefits for glucose homeostasis of amino acids found in dairy foods.

Intrinsic paleointensity bias and the long-term history of the geodynamo.

Many geodynamo models predict an inverse relationship between geomagnetic reversal frequency and field strength. However, most of the absolute paleointensity data, obtained predominantly by the Thellier method from bulk volcanic rocks, fail to confirm this relationship. Although low paleointensities are commonly observed during periods of high reversal rate (notably, in the late Jurassic), higher than present-day intensity values are rare during periods of no or few reversals (superchrons). We have identified a fundamental mechanism that results in a pervasive and previously unrecognized low-field bias that affects most paleointensity data in the global database. Our results provide an explanation for the discordance between the experimental data and numerical models, and lend additional support to an inverse relationship between the reversal rate and field strength as a fundamental property of the geodynamo. We demonstrate that the accuracy of future paleointensity analyses can be improved by integration of the Thellier protocol with low-temperature demagnetizations.