Nest predation and trampling as management risks in grazed coastal meadows

Livestock grazing is an important management tool of agri-environment schemes initiated within the European Union to maintain and restore biodiversity of grassland birds. However, grazing can affect bird populations negatively by depressing reproduction through nest trampling and increasing nest predation. These effects are, however, considered low when using recommended stocking rates. By simulating wader nests, we experimentally quantify and examine the causes of variation in trampling rates on managed Baltic coastal meadows. Secondly, we examine whether livestock presence increases nest predation of one management target, the critically endangered southern dunlin (Calidris alpina schinzii). Trampling rates of experimental nests were high. Only 21% of nests would have survived a three week incubating period early in the grazing season. Trampling rates were most severe at the onset of grazing and decreased with time. Thus, timing of grazing plays a crucial role in determining breeding success on managed meadows. Predation rates of dunlin nests were moderate and did not depend on livestock presence suggesting that incubating dunlin are not disturbed by cattle. While grazing is vital in habitat restoration and in conserving grassland biodiversity, our results suggest that grazing may also threaten the viability of populations if negative effects are underestimated. Therefore, management plans, especially for endangered species, should not only rely on general recommendations on stocking rates but instead planners need to evaluate the significance of negative effects in terms of local conditions (timing of breeding and grazing, space use of cattle and birds, measured trampling rates) and adjust grazing practises accordingly.     

Reddish spring colouring of deciduous leaves: a sign of ecotype?

Several deciduous woody plant species produce anthocyanins during leaf development in spring and again during leaf senescence in autumn. The leaves of Betula pendula Roth (silver birch) commonly exhibit transient reddening in juvenile leaves under northern growing conditions, with the intensity of the red colour varying among individual trees. The objective of our study was to test the hypothesis that the accumulation of foliar anthocyanins during spring in leaves of B. pendula is an ecotypic response. Chlorophyll fluorescence ratio (Fv/Fm), leaf reflectance and anthocyanin concentrations were measured, in relation to phenology in spring, summer and autumn from birches used for landscaping with either red or green-emergent leaves. The results suggest that (1) the trees with green- or red-emergent juvenile leaves represent different populations, and (2) that the red-emergent leaves senesced earlier, indicating that (3) trees with red-emerging leaves belong to a more northern ecotype than the trees with green-emerging leaves. The role of anthocyanin synthesis in a northern radiation environment is discussed.     

Mapping a new spontaneous preterm birth susceptibility gene, IGF1R, using linkage, haplotype sharing, and association analysis

Preterm birth is the major cause of neonatal death and serious morbidity. Most preterm births are due to spontaneous onset of labor without a known cause or effective prevention. Both maternal and fetal genomes influence the predisposition to spontaneous preterm birth (SPTB), but the susceptibility loci remain to be defined. We utilized a combination of unique population structures, family-based linkage analysis, and subsequent case-control association to identify a susceptibility haplotype for SPTB. Clinically well-characterized SPTB families from northern Finland, a subisolate founded by a relatively small founder population that has subsequently experienced a number of bottlenecks, were selected for the initial discovery sample. Genome-wide linkage analysis using a high-density single-nucleotide polymorphism (SNP) array in seven large northern Finnish non-consanginous families identified a locus on 15q26.3 (HLOD 4.68). This region contains the IGF1R gene, which encodes the type 1 insulin-like growth factor receptor IGF-1R. Haplotype segregation analysis revealed that a 55 kb 12-SNP core segment within the IGF1R gene was shared identical-by-state (IBS) in five families. A follow-up case-control study in an independent sample representing the more general Finnish population showed an association of a 6-SNP IGF1R haplotype with SPTB in the fetuses, providing further evidence for IGF1R as a SPTB predisposition gene (frequency in cases versus controls 0.11 versus 0.05, P = 0.001, odds ratio 2.3). This study demonstrates the identification of a predisposing, low-frequency haplotype in a multifactorial trait using a well-characterized population and a combination of family and case-control designs. Our findings support the identification of the novel susceptibility gene IGF1R for predisposition by the fetal genome to being born preterm.     

Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals

Family studies of individual tissues have shown that gene expression traits are genetically heritable. Here, we investigate cis and trans components of heritability both within and across tissues by applying variance-components methods to 722 Icelanders from family cohorts, using identity-by-descent (IBD) estimates from long-range phased genome-wide SNP data and gene expression measurements for approximately 19,000 genes in blood and adipose tissue. We estimate the proportion of gene expression heritability attributable to cis regulation as 37% in blood and 24% in adipose tissue. Our results indicate that the correlation in gene expression measurements across these tissues is primarily due to heritability at cis loci, whereas there is little sharing of trans regulation across tissues. One implication of this finding is that heritability in tissues composed of heterogeneous cell types is expected to be more dominated by cis regulation than in tissues composed of more homogeneous cell types, consistent with our blood versus adipose results as well as results of previous studies in lymphoblastoid cell lines. Finally, we obtained similar estimates of the cis components of heritability using IBD between unrelated individuals, indicating that transgenerational epigenetic inheritance does not contribute substantially to the "missing heritability" of gene expression in these tissue types.     

Beneficial effects of banana (<Emphasis Type="Italic">Musa</Emphasis> sp. var. elakki bale) flower and pseudostem on hyperglycemia and advanced glycation end-products (AGEs) in streptozotocin-induced diabetic rats

Diabetes is a chronic health problem and major cause of death in most of the countries. Diet management plays an important role in controlling diabetes and its complications along with insulin and drugs. We have examined the effect of banana (Musa sp. var. elakki bale) flower and pseudostem on hyperglycemia and advanced glycation end-products (AGEs) in streptozotocin-induced diabetic rats. Our results indicated that banana flower and pseudostem have low glycemic index and have a high content of dietary fiber and antioxidants. Diabetic symptoms like hyperglycemia, polyuria, polyphagia, polydipsia, urine sugar, and body weight were ameliorated in banana flower- and pseudostem-treated rats. Increased glomerular filtration rate in the diabetic group (5.1 ± 0.22 ml/min) was decreased in banana flower-fed (2.5 ± 0.37 ml/min) and pseudostem-fed (3.0 ± 0.45 ml/min) groups and were significant at P < 0.001 and P < 0.01, respectively. Fructosamine and AGEs formed during diabetes were inhibited in treated groups when compared with the diabetic group. The diabetic group showed 11.5 ± 0.64 μg of AGEs/mg protein in kidney, whereas, in banana flower- and pseudostem-fed groups, it was reduced to 9.21 ± 0.32 and 9.29 ± 0.24 μg/mg protein, respectively, and were significant at P < 0.01. These findings suggest that banana flower and pseudostem have anti-diabetic and anti-AGEs properties and are beneficial as food supplements for diabetics.     

Rapid, landscape scale responses in riparian tundra vegetation to exclusion of small and large mammalian herbivores

Productive tundra plant communities composed of a variety of fast growing herbaceous and woody plants are likely to attract mammalian herbivores. Such vegetation is likely to respond to different-sized herbivores more rapidly than currently acknowledged from the tundra. Accentuated by currently changing populations of arctic mammals there is a need to understand impacts of different-sized herbivores on the dynamics of productive tundra plant communities. Here we assess the differential effects of ungulate (reindeer) and small rodent herbivores (voles and lemmings) on high productive tundra vegetation. A spatially extensive exclosure experiment was run for three years on river sediment plains along two river catchments in low-arctic Norway. The river catchments were similar in species pools but differed in species abundance composition of both plants and vertebrate herbivores. Biomass of forbs, deciduous shrubs and silica-poor grasses increased by 40–50% in response to release from herbivory, whereas biomass of silica-rich grasses decreased by 50–75%. Hence both additive and compensatory effects of small rodents and reindeer exclusion caused these significant changes in abundance composition of the plant communities. Changes were also rapid, evident after only one growing season, and are among the fastest and strongest ever documented in Arctic vegetation. The rate of changes indicates a tight link between the dynamics of productive tundra vegetation and both small and large herbivores. Responses were however not spatially consistent, being highly different between the catchments. We conclude that despite similar species pools, variation in plant species abundance and herbivore species dynamics give different prerequisites for change.     

Phylogeography of the ant Myrmica rubra and its inquiline social parasite

Widely distributed Palearctic insects are ideal to study phylogeographic patterns owing to their high potential to survive in many Pleistocene refugia and-after the glaciation-to recolonize vast, continuous areas. Nevertheless, such species have received little phylogeographic attention. Here, we investigated the Pleistocene refugia and subsequent postglacial colonization of the common, abundant, and widely distributed ant Myrmica rubra over most of its Palearctic area, using mitochondrial DNA (mtDNA). The western and eastern populations of M. rubra belonged predominantly to separate haplogroups, which formed a broad secondary contact zone in Central Europe. The distribution of genetic diversity and haplogroups implied that M. rubra survived the last glaciation in multiple refugia located over an extensive area from Iberia in the west to Siberia in the east, and colonized its present areas of distribution along several routes. The matrilineal genetic structure of M. rubra was probably formed during the last glaciation and subsequent postglacial expansion. Additionally, because M. rubra has two queen morphs, the obligately socially parasitic microgyne and its macrogyne host, we tested the suggested speciation of the parasite. Locally, the parasite and host usually belonged to the same haplogroup but differed in haplotype frequencies. This indicates that genetic differentiation between the morphs is a universal pattern and thus incipient, sympatric speciation of the parasite from its host is possible. If speciation is taking place, however, it is not yet visible as lineage sorting of the mtDNA between the morphs.     

The etiology of multiple sclerosis: genetic evidence for the involvement of the human endogenous retrovirus HERV-Fc1

We have investigated the role of human endogenous retroviruses in multiple sclerosis by analyzing the DNA of patients and controls in 4 cohorts for associations between multiple sclerosis and polymorphisms near viral restriction genes or near endogenous retroviral loci with one or more intact or almost-intact genes. We found that SNPs in the gene TRIM5 were inversely correlated with disease. Conversely, SNPs around one retroviral locus, HERV-Fc1, showed a highly significant association with disease. The latter association was limited to a narrow region that contains no other known genes. We conclude that HERV-Fc1 and TRIM5 play a role in the etiology of multiple sclerosis. If these results are confirmed, they point to new modes of treatment for multiple sclerosis.     

Alginate Hydrogels for Three-Dimensional Organ Culture of Ovaries and Oviducts

Ovarian cancer is the fifth leading cause of cancer deaths in women and has a 63% mortality rate in the United States¹. The cell type of origin for ovarian cancers is still in question and might be either the ovarian surface epithelium (OSE) or the distal epithelium of the fallopian tube fimbriae^2,3. Culturing the normal cells as a primary culture in vitro will enable scientists to model specific changes that might lead to ovarian cancer in the distinct epithelium, thereby definitively determining the cell type of origin. This will allow development of more accurate biomarkers, animal models with tissue-specific gene changes, and better prevention strategies targeted to this disease.Maintaining normal cells in alginate hydrogels promotes short term in vitro culture of cells in their three-dimensional context and permits introduction of plasmid DNA, siRNA, and small molecules. By culturing organs in pieces that are derived from strategic cuts using a scalpel, several cultures from a single organ can be generated, increasing the number of experiments from a single animal. These cuts model aspects of ovulation leading to proliferation of the OSE, which is associated with ovarian cancer formation. Cell types such as the OSE that do not grow well on plastic surfaces can be cultured using this method and facilitate investigation into normal cellular processes or the earliest events in cancer formation⁴.Alginate hydrogels can be used to support the growth of many types of tissues⁵. Alginate is a linear polysaccharide composed of repeating units of β-D-mannuronic acid and α-L-guluronic acid that can be crosslinked with calcium ions, resulting in a gentle gelling action that does not damage tissues^6,7. Like other three-dimensional cell culture matrices such as Matrigel, alginate provides mechanical support for tissues; however, proteins are not reactive with the alginate matrix, and therefore alginate functions as a synthetic extracellular matrix that does not initiate cell signaling⁵. The alginate hydrogel floats in standard cell culture medium and supports the architecture of the tissue growth in vitro.A method is presented for the preparation, separation, and embedding of ovarian and oviductal organ pieces into alginate hydrogels, which can be maintained in culture for up to two weeks. The enzymatic release of cells for analysis of proteins and RNA samples from the organ culture is also described. Finally, the growth of primary cell types is possible without genetic immortalization from mice and permits investigators to use knockout and transgenic mice.Download video file.^{(42M, mov)}