Discovery and development of exome‐based,co‐dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.)

Globally, wheat is the most widely grown crop and one of the three most important crops for human and livestock feed. However, the complex nature of the wheat genome has, until recently, resulted in a lack of single nucleotide polymorphism (SNP)‐based molecular markers of practical use to wheat breeders. Recently, large numbers of SNP‐based wheat markers have been made available via the use of next‐generation sequencing combined with a variety of genotyping platforms. However, many of these markers and platforms have difficulty distinguishing between heterozygote and homozygote individuals and are therefore of limited use to wheat breeders carrying out commercial‐scale breeding programmes. To identify exome‐based co‐dominant SNP‐based assays, which are capable of distinguishing between heterozygotes and homozygotes, we have used targeted re‐sequencing of the wheat exome to generate large amounts of genomic sequences from eight varieties. Using a bioinformatics approach, these sequences have been used to identify 95 266 putative single nucleotide polymorphisms, of which 10 251 were classified as being putatively co‐dominant. Validation of a subset of these putative co‐dominant markers confirmed that 96% were true polymorphisms and 65% were co‐dominant SNP assays. The new co‐dominant markers described here are capable of genotypic classification of a segregating locus in polyploid wheat and can be used on a variety of genotyping platforms; as such, they represent a powerful tool for wheat breeders. These markers and related information have been made publically available on an interactive web‐based database to facilitate their use on genotyping programmes worldwide.     

Patterns of bee diversity in mosaic agricultural landscapes of central Uganda: implication of pollination services conservation for food security

Little is known about bee communities and pollination services conservation strategies in sub-Sahara Africa. A study was conducted at 26 different sites with varying local landscape characteristics in farmlands of central Uganda in 2006. Bees were sampled using coloured pantraps, handnet and line transect counts. Overall 80,883 bee individuals from 6 families and 652 species were encountered. The bee fauna was characterized by a lower diversity of Melittidae and Andrenidae and a high diversity of Apidae, Megachilidae and Halictidae. Megachile and Lasioglossum were the two most species-rich genera. The most abundant species was Apis mellifera adansonii Linnaeus (23 % of total individuals) followed by Hypotrigona gribodoi Magretti (19 %), Meliponula ferruginea Lepeletier (13 %), Lasioglossum ugandicum Cockerell (7 %), Apis mellifera scutellata Latreille (6 %), Allodapula acutigera Cockerell (6 %), Ceratina rufigastra Cockerell (5 %), Ceratina tanganyicensis Strand (5 %), Braunsapis angolensis Cockerell (5 %), Megachile rufipes Fabricius (5 %), Meliponula bocandei Spinola (5 %) and Seladonia jucundus Smith (5 %). The mean number of species recorded per study site per day ranged between 14 and 49, whereas the abundance ranged between 188 and 1,859 individuals. Study sites in areas with intense land-use had species-poor bee communities compared to sites with medium to low land-use intensities. Study sites with riparian forest fragments and wetlands, or with forest fallows in their vicinity had significantly (P < 0.05) higher species richness and diversity than sites dominated by small-scale monoculture/polyculture fields or sites dominated by either simple or complex traditional agroforestry systems. An ordination analysis also revealed that bee communities were significantly (P < 0.01) influenced by the presence of semi-natural habitats (woodlands, fallows) and forest fragments in the surrounding of fields. Thus, natural and semi-natural habitats are of great value for afrotropical farmland bee communities. There is a need to put in place strategies and policies for semi-natural and forest fragments preservation for spatio-temporal stability of pollination services in rural landscapes. Farmers are recommended to increase on-farm trees cover to safeguard and enhance pollination function and services in fields. Mimicking natural vegetation through promoting establishment of forest plantations and village community forestry in rural landscapes is also critical for conserving pollination services.     

Association between Depressive Symptoms and Bone Stiffness Index in Young Adults: The Kangwha Study

Objective

Young adulthood is an important period for both bone and mental health. This study investigated the association between depressive symptoms and bone density in apparently healthy Korean men and women aged 29−32 years.

Methods

This study is a cross-sectional analysis of data from 123 men and 133 women who completed follow-up examinations of the Kangwha study in 2010−2011. Bone stiffness index (SI) was measured at the os calcis using a quantitative ultrasound device. Depressive symptoms were evaluated using the Korean version of the Beck Depression Inventory (K-BDI) and classified as normal (K-BDI <10), mild (K-BDI 10–15), and moderate to severe (K-BDI ≥16).

Results

Moderate to severe depressive symptoms were prevalent among 11.4% of men and 19.6% of women. Higher K-BDI scores were significantly correlated to SI in men, before (ρ = –0.286, p = 0.001) and after (ρ = –0.228, p = 0.013) adjustment for covariates. Men with depressive symptoms tended to have a lower SI; multivariate-adjusted mean SI in men with normal, mild, and moderate to severe depressive symptoms was 104.1±3.1, 100.9±5.9, and 94.1±7.8, respectively (p for trend = 0.021). In contrast, no significant correlations were identified in women.

Conclusions

Depressive symptoms were significantly associated with lower SI in men, but not in women. Further studies are necessary to evaluate the impact of depression on developing osteoporosis or osteoporotic fractures later in life.     

Prevalence estimates of chronic kidney disease in Canada: results of a nationally representative survey

Background:

Chronic kidney disease is an important risk factor for death and cardiovascular-related morbidity, but estimates to date of its prevalence in Canada have generally been extrapolated from the prevalence of end-stage renal disease. We used direct measures of kidney function collected from a nationally representative survey population to estimate the prevalence of chronic kidney disease among Canadian adults.

Methods:

We examined data for 3689 adult participants of cycle 1 of the Canadian Health Measures Survey (2007–2009) for the presence of chronic kidney disease. We also calculated the age-standardized prevalence of cardiovascular risk factors by chronic kidney disease group. We cross-tabulated the estimated glomerular filtration rate (eGFR) with albuminuria status.

Results:

The prevalence of chronic kidney disease during the period 2007–2009 was 12.5%, representing about 3 million Canadian adults. The estimated prevalence of stage 3–5 disease was 3.1% (0.73 million adults) and albuminuria 10.3% (2.4 million adults). The prevalence of diabetes, hypertension and hypertriglyceridemia were all significantly higher among adults with chronic kidney disease than among those without it. The prevalence of albuminuria was high, even among those whose eGFR was 90 mL/min per 1.73 m² or greater (10.1%) and those without diabetes or hypertension (9.3%). Awareness of kidney dysfunction among adults with stage 3–5 chronic kidney disease was low (12.0%).

Interpretation:

The prevalence of kidney dysfunction was substantial in the survey population, including individuals without hypertension or diabetes, conditions most likely to prompt screening for kidney dysfunction. These findings highlight the potential for missed opportunities for early intervention and secondary prevention of chronic kidney disease.Chronic kidney disease is defined as the presence of kidney damage or reduced kidney function for more than 3 months and requires either a measured or estimated glomerular filtration rate (eGFR) of less than 60 mL/min per 1.73 m², or the presence of abnormalities in urine sediment, renal imaging or biopsy results.¹ Between 1.3 million and 2.9 million Canadians are estimated to have chronic kidney disease, based on an extrapolation of the prevalence of end-stage renal disease.² In the United States, the 1999–2004 National Health and Nutrition Examination Survey reported a prevalence of 5.0% for stage 1 and 2 disease and 8.1% for stage 3 and 4 disease.^3,4Chronic kidney disease has been identified as a risk factor for death and cardiovascular-related morbidity and is a substantial burden on the health care system.^1,5 Hemodialysis costs the Canadian health care system about $60 000 per patient per year of treatment.¹ The increasing prevalence of chronic kidney disease can be attributed in part to the growing elderly population and to increasing rates of diabetes and hypertension.^1,6,7Albuminuria, which can result from abnormal vascular permeability, atherosclerosis or renal disease, has gained recognition as an independent risk factor for progressive renal dysfunction and adverse cardiovascular outcomes.^8–10 In earlier stages of chronic kidney disease, albuminuria has been shown to be more predictive of renal and cardiovascular events than eGFR.^4,9 This has prompted the call for a new risk stratification for cardiovascular outcomes based on both eGFR and albuminuria.¹¹A recent review advocated screening people for chronic kidney disease if they have hypertension, diabetes, clinically evident cardiovascular disease or a family history of kidney failure or are more than 60 years old.⁴ The Canadian Society of Nephrology published guidelines on the management of chronic kidney disease but did not offer guidance on screening.¹ The Canadian Diabetes Association recommends annual screening with the use of an albumin:creatinine ratio,¹² and the Canadian Hypertension Education Program guideline recommends urinalysis as part of the initial assessment of hypertension.¹³ Screening for chronic kidney disease on the basis of eGFR and albuminuria is not considered to be cost-effective in the general population, among older people or among people with hypertension.¹⁴The objective of our study was to use direct measures (biomarkers) of kidney function to generate nationally representative, population-based prevalence estimates of chronic kidney disease among Canadian adults overall and in clinically relevant groups.     

Voices of the past: a review of Paleozoic and Mesozoic animal sounds

Here, I present a review and synthesis of fossil and neontological evidence to find major trends in the pre-Cenozoic evolution of animal acoustic behaviour. Anatomical, ecological and phylogenetic data support the following scenario. Stridulating insects, including crickets, performed the first terrestrial twilight choruses during the Triassic. The twilight chorus was joined by water boatmen in the Lower Jurassic, anurans in the Upper Jurassic, geckoes and birds in the Lower Cretaceous, and cicadas and crocodilians in the Upper Cretaceous. Parallel evolution of defensive stridulation took place multiple times within Malacostraca, Arachnida and Coleoptera. Parallel evolution of defensive and courtship-related sound production took place in Actinopterygii, possibly as early as the Devonian. Defensive vocalisations by tetrapods probably did not appear until their predators acquired tympanic ears in the Permian. Tympanic ears appeared independently in Diadectomorpha, Seymouriamorpha, Parareptilia, Diapsida and derived Synapsida. Crocodilians and birds acquired vocal organs independently, and there is no anatomical evidence for vocal ability in bird-line archosaurs basal to the avian clade Ornithothoraces. Acoustic displays by non-avian dinosaurs were therefore probably non-vocal. Other aspects of the evolution of acoustic behaviour in these and other lineages are also discussed.     

Green Rust Formation from the Bioreduction of γ –FeOOH (Lepidocrocite): Comparison of Several Shewanella Species

Green rusts are mixed ferrous/ferric hydroxides that typically form under weakly acidic to alkaline conditions in suboxic environments. The recent identification of green rusts as products of the reduction of Fe(III) oxides and oxyhydroxides by Shewanella putrefaciens, a dissimilatory iron-reducing bacterium (DIRB), suggests that green rusts may play a role in the redox cycling of Fe in many aquatic and terrestrial environments. We examined the potential for green rust formation resulting from the bioreduction of lepidocrocite(γ -FeOOH) by a series of Shewanella species (S. alga BrY, S. amazonensis SB2B, S. baltica OS155, S. denitrificans OS217T, S. loihica PV-4, S. oneidensis MR-1, S. putrefaciens ATCC 8071, S. putrefaciens CN32, S. saccharophilia, and Shewanella sp. ANA-3). All Shewanella species, with the exception of S. denitrificans OS217T, were able to couple the oxidation of formate to the reduction of Fe(III) in lepidocrocite; however there were significant differences among species with respect to the rate and extent of Fe(II) production. Despite these differences, green rust was the only Fe(II)-bearing solid phase formed under our experimental conditions, as indicated by X-ray diffraction, Mössbauer spectroscopy, and scanning electron microscopy. The formation of green rust by Shewanella species isolated from a wide range of habitats and possessing varied metabolic capabilities suggests that under favorable conditions biogenic green rusts may be formed by a diverse array of DIRB.     

An estuarine species of the alga Vaucheria (Xanthophyceae) displays an increased capacity for turgor regulation when compared to a freshwater species

Turgor regulation is the process by which walled organisms alter their internal osmotic potential to adapt to osmotic changes in the environment. Apart from a few studies on freshwater oomycetes, the ability of stramenopiles to turgor regulate has not been investigated. In this study, turgor regulation and growth were compared in two species of the stramenopile alga Vaucheria, Vaucheria erythrospora isolated from an estuarine habitat, and Vaucheria repens isolated from a freshwater habitat. Species were identified using their rbcL sequences and respective morphologies. Using a single cell pressure probe to directly measure turgor in Vaucheria after hyperosmotic shock, V. erythrospora was found to recover turgor after a larger shock than V. repens. Threshold shock values for this ability were >0.5 MPa for V. erythrospora and <0.5 MPa for V. repens. Recovery was more rapid in V. erythrospora than V. repens after comparable shocks. Turgor recovery in V. erythrospora was inhibited by Gd³⁺ and TEA, suggesting a role for mechanosensitive channels, nonselective cation channels, and K⁺ channels in the process. Growth studies showed that V. erythrospora was able to grow over a wider range of NaCl concentrations. These responses may underlie the ability of V. erythrospora to survive in an estuarine habitat and restrict V. repens to freshwater. The fact that both species can turgor regulate may indicate a fundamental difference between members of the Stramenopila, as research to date on oomycetes suggests they are unable to turgor regulate.     

Candidate target genes for the Saccharomyces cerevisiae transcription factor, Yap2

In Saccharomyces cerevisiae, the Yap family of basic leucine zipper (bZip) proteins contains eight members. The Yap family proteins are implicated in a variety of stress responses; among these proteins, Yap1 acts as a major regulator of oxidative stress responses. However, the functional roles of the remaining Yap family members are poorly understood. To elucidate the function of Yap2, we mined candidate target genes of Yap2 by proteomic analysis. Among the identified genes, FRM2 was previously identified as a target gene of Yap2, which confirmed the validity of our screening method. YNL134C and YDL124W were also identified as candidate Yap2 target genes. These genes were upregulated in strains overexpressing Yap2 and possess Yap2 target sequences in their promoter regions. Furthermore, chromatin immunoprecipitation assays showed that YNL134C and YDL124W have Yap2 binding motif. These data will help to elucidate the functional role of Yap2.