Group defence and the predator’s functional response

We derive from first principles the functional response of the predator and the reproduction rate of the prey in the case that the prey form groups as a defence against the predator and the latter captures only single prey. We also give some examples of the resulting predator–prey population dynamics.     

Epistatic Genetic Effects among Alzheimer’s Candidate Genes

Background

Novel risk variants for late-onset Alzheimer’s disease (AD) have been identified and replicated in genome-wide association studies. Recent work has begun to address the relationship between these risk variants and biomarkers of AD, though results have been mixed. The aim of the current study was to characterize single marker and epistatic genetic effects between the top candidate Single Nucleotide Polymorphisms (SNPs) in relation to amyloid deposition.

Methods

We used a combined dataset across ADNI-1 and ADNI-2, and looked within each dataset separately to validate identified genetic effects. Amyloid was quantified using data acquired by Positron Emission Tomography (PET) with ¹⁸F-AV-45.

Results

Two SNP-SNP interactions reached significance when correcting for multiple comparisons, BIN1 (rs7561528, rs744373) x PICALM (rs7851179). Carrying the minor allele in BIN1 was related to higher levels of amyloid deposition, however only in non-carriers of the protective PICALM minor allele.

Conclusions

Our results support previous research suggesting these candidate SNPs do not show single marker associations with amyloid pathology. However, we provide evidence for a novel interaction between PICALM and BIN1 in relation to amyloid deposition. Risk related to the BIN1 minor allele appears to be mitigated in the presence of the PICALM protective variant. In that way, variance in amyloid plaque burden can be better classified within the context of a complex genetic background. Efforts to model cumulative risk for AD should explicitly account for this epistatic effect, and future studies should explicitly test for such effects whenever statistically feasible.     

CWM and Rao’s quadratic diversity: a unified framework for functional ecology

Assessing the effects of environmental constraints on community structure often relies on methods that consider changes in species functional traits in response to environmental processes. Various indices have been proposed to measure relevant aspects of community trait composition from different viewpoints and perspectives. Among these, the ‘community-weighted mean trait value’ (CWM) and the Rao coefficient have been widely used in ecological research for summarizing different facets of functional composition and diversity. Analyzing changes in functional diversity of bee communities along a post-fire successional gradient in southern Switzerland we show that these two measures may be used to describe two complementary aspects of community structure, such as the mean and the dispersion of functional traits within a given species assemblage. While CWM can be adequately used to summarize shifts in mean trait values within communities due to environmental selection for certain functional traits, the Rao coefficient can be effectively applied to analyze patterns of trait convergence or divergence compared to a random expectation.     

Genetic differentiation and limited gene flow among fragmented populations of New Zealand endemic Hector’s and Maui’s dolphins

Gene flow among small fragmented populations is critical for maintaining genetic diversity, and therefore the evolutionary potential of a species. Concern for two New Zealand endemic subspecies, the Hector’s (Cephalorhynchus hectori hectori) and Maui’s (C. h. maui) dolphins, arises from their low abundance, slow rate of reproduction, and susceptibility to fisheries-related mortality. Our work examined genetic differentiation and migration between the subspecies and among regional and local Hector’s dolphin populations using mitochondrial (mt) DNA and microsatellite genotypes from 438 samples. Results confirmed earlier reports of a single unique mtDNA control region haplotype fixed in the Maui’s dolphin, and provided new evidence of reproductive isolation from Hector’s dolphins (9-locus microsatellite F _ST?=?0.167, P?<?0.001). Independent evolutionary trajectories were also supported for Hector’s dolphin populations of the East Coast, West Coast, Te Waewae Bay and Toetoe Bay. Low asymmetrical migration rates were found among several Hector’s dolphin populations and assignment tests identified five Hector’s dolphins likely to have a migrant father from another regional population. There appears to be sufficient step-wise gene flow to maintain genetic diversity within the East and West Coasts; however, the two local South Coast populations exhibited a high degree of differentiation given their close proximity (~100?km). To maintain the evolutionary potential and long-term survival of both subspecies, genetic monitoring and conservation management must focus on maintaining corridors to preserve gene flow and prevent further population fragmentation and loss of genetic diversity, in addition to maintaining local population abundances.     

Genetic distances among the diabetic “Punjabis” and comparative populations from North India

Non-insulin dependent diabetes mellitus (NIDDM) is emerging as a major non-communicable disease in developing countries. Using principal component and Mahalanobis' generalized distance analyses, we examined gene frequency data at 3 polymorphic loci in sedentee urban controls, urban diabetics of the “Punjabi” population along with other comparative populations from North India. Mahalanobis generalized distance analysis suggests relative dissimilarity in the “Punjabi” disease subgroups indicating possible genetic heterogeneity. The genetic distance analysis also identified clinal variation along a north-west to south-east axis in North India.     

Purification and functional characterization of the first stilbene glucoside-specific β-glucosidase isolated from Lactobacillus kimchi

This study aimed to develop viable enzymes for bioconversion of resveratrol-glucoside into resveratrol. Out of 13 bacterial strains tested, Lactobacillus kimchi JB301 could completely convert polydatin into resveratrol. The purified enzyme had an optimum temperature of 30–40 °C and optimum pH of pH 5.0 against polydatin. This enzyme showed high substrate specificities towards different substrates in the following order: isorhaponticin >> polydatin >> mulberroside A > oxyresveratrol-3-O-glucoside. Additionally, it rarely hydrolyzed astringin and desoxyrhaponticin. Based on these catalytic specificities, we suggest this enzyme be named stilbene glucoside-specific β-glucosidase. Furthermore, polydatin extracts from Polygonum cuspidatum were successfully converted to resveratrol with a high yield (of over 99%). Stilbene glucoside-specific β-glucosidase is the first enzyme isolated from lactic acid bacteria capable of bio-converting various stilbene glucosides into stilbene.     

Genetic diversity of Horvath’s Rock Lizard meets current environmental restrictions

Conservation Genetics - The Horvath’s rock lizard Iberolacerta horvathi (Méhely, 1904) is an understudied lacertid species, which is geographically isolated from its congeners and...     

Genetic diversity analysis of North Africa’s barley using SSR markers

It was demonstrated that some North Africa barley accessions have diverse tolerance sources for abiotic stresses and a good nutritional quality, but the studies done were incomplete since they were realized separately in each country apart.To implement a more complete analysis, 31 barley accessions originated from North Africa (Algeria, Tunisia and Egypt) were analyzed using 11 SSR markers selected from the seven barley linkage groups for studying the genetic diversity among these chosen barley accessions.Over the 11 SSR markers, a total of 478 reproducible bands were scored with an average of 2.13 alleles/primer and the average polymorphism information content of 0.5.Genetic distance analysis of the 31 accessions showed a large genetic diversity and high number of different groups. The most accessions are clustered according to their eco-geographical origin, according to their pedigree and agronomic characters or according to the caryopsis character (hulled or naked caryopsis). This high number of obtained groups is an invaluable aid in crop improvement strategies and confirms the opinion suggesting that North Africa could be a secondary center of origin of barley. The various growing conditions and the multiple uses of barley in each country may be the cause of the large variability of the barley germplasm in each region.     

Genetic diversity and population structure of North America’s rarest heron, the reddish egret (Egretta rufescens)

The global distribution of the reddish egret is characterized by disjunct colonies occurring from the Pacific side of Northwest Mexico to the Caribbean. We examined distantly isolated colonies of reddish egret to determine global population genetic structure. We used seven polymorphic microsatellites to accomplish five goals: (1) to assess range wide population differentiation among reddish egret (Egretta rufescens) populations, (2) identify extent of gene flow, (3) determine any historical occurrence of bottlenecks, (4) assess genetic differentiation between color morphs, (5) clarify subspecies status of E. r. dickeyi, a completely dark morph population located in and around the Baja California peninsula, Mexico. Genetic differentiation was dramatic (global Fst = 0.161) throughout the reddish egrets range extending from Baja California, Mexico to Great Inagua, Bahamas. Differentiation occurred among three distinct regions (Fst = 0.238) but not among colonies/islands within regions suggesting regional philopatry. Genetic diversity (alleles per locus, and heterozygosity) in Baja California Sur, Mexico and Great Inagua, Bahamas populations is lower than in the Texas/Mexico population due to minimal dispersal between regions and smaller population sizes. Dark and white color morphs when present within the same region showed no differentiation. Patterns of recent population bottlenecks are not evident in each of the three regional populations. With evidence of limited gene flow in addition to low genetic diversity and prospects of habitat loss we recommend that reddish egrets be managed as three distinct or evolutionary significant units.     

Genetic Determinants of Pelvic Organ Prolapse among African American and Hispanic Women in the Women’s Health Initiative

Current evidence suggests a multifactorial etiology to pelvic organ prolapse (POP), including genetic predisposition. We conducted a genome-wide association study of POP in African American (AA) and Hispanic (HP) women from the Women’s Health Initiative Hormone Therapy study. Cases were defined as any POP (grades 1–3) or moderate/severe POP (grades 2–3), while controls had grade 0 POP. We performed race-specific multiple logistic regression analyses between SNPs imputed to 1000 genomes in relation to POP (grade 0 vs 1–3; grade 0 vs 2–3) adjusting for age at diagnosis, body mass index, parity, and genetic ancestry. There were 1274 controls and 1427 cases of any POP and 317 cases of moderate/severe POP. Although none of the analyses reached genome-wide significance (p<5x10^-8), we noted variants in several loci that met p<10⁻⁶. In race-specific analysis of grade 0 vs 2–3, intronic SNPs in the CPE gene (rs28573326, OR:2.14; 95% CI 1.62–2.83; p = 1.0x10^-7) were associated with POP in AAs, and SNPs in the gene AL132709.5 (rs1950626, OR:2.96; 95% CI 1.96–4.48, p = 2.6x10^-7) were associated with POP in HPs. Inverse variance fixed-effect meta-analysis of the race-specific results showed suggestive signals for SNPs in the DPP6 gene (rs11243354, OR:1.36; p = 4.2x10^-7) in the grade 0 vs 1–3 analyses and for SNPs around PGBD5 (rs740494, OR:2.17; p = 8.6x10^-7) and SHC3 (rs2209875, OR:0.60; p = 9.3x10^-7) in the grade 0 vs 2–3 analyses. While we did not identify genome-wide significant findings, we document several SNPs reaching suggestive statistical significance. Further interrogation of POP in larger minority samples is warranted.     

Mesophilic and psychrotrophic aerobe sporulating microorganisms in raw cow’s milk

We studied the occurrence of mesophilic and psychrotrophic aerobic sporulating microorganisms (MPAS) in raw cow’s milk and their relations to microflora in milk. We took 294 samples of raw cow’s milk from 14 farms during one year. Briefly the method for MPAS assessment is to inactivate the milk sample by heating it to 80-82°C for 30 minutes. Mesophilic aerobic sporulates are incubated at 30°C for 3 days-, and psychrotrophic aerobic sporulates at 7°C for 10 days. Results of studied microbiological parameters characterize the sampled milk as complying with requirements of the EU regulation 92/46 and standard STN 57 0529. MPAS count was within the span 2.5–340 CFU/ml. The average value ofMPAS was 59.4 CFU/ml, with variation coefficient 93.1%. Counts up to 50 CFU/ml were in 55.4% samples, the value was not higher than 100 in 85%, and in 3.1% of the samples the MPAS count was higher than 200. MPAS do not show correlation with any of the studied microbiological parameters; marked influences of season were not observed either. On the basis of obtained results, it is possible to support the proposal of an initial limit of maximum 200 CFU/ml for the introduction of a MPAS parameter. MPAS count found in the same dishes at incubation for mesophilic and subsequently strictly psychrophilic microorganisms was 56.9 CFU/ml on average. This represents 95.8% of total CFU sums of individual dishes at two temperatures. The correlation coefficient of these two types of results, r = 0.99,gives evidence of close dependence expressed by the linear regression equation. Use of two incubation temperatures, one after another with an identical set of dishes, enables us to exclude overestimation of results due to sporulates able to grow at both incubation temperatures.     

Genetic Ancestry and Asthma and Rhinitis Occurrence in Hispanic Children: Findings from the Southern California Children’s Health Study

BackgroundAsthma and rhinitis are common childhood health conditions. Being an understudied and rapidly growing population in the US, Hispanic children have a varying risk for these conditions that may result from sociocultural (including acculturative factors), exposure and genetic diversities. Hispanic populations have varying contributions from European, Amerindian and African ancestries. While previous literature separately reported associations between genetic ancestry and acculturation factors with asthma, whether Amerindian ancestry and acculturative factors have independent associations with development of early-life asthma and rhinitis in Hispanic children remains unknown. We hypothesized that genetic ancestry is an important determinant of early-life asthma and rhinitis occurrence in Hispanic children independent of sociodemographic, acculturation and environmental factors.MethodsSubjects were Hispanic children (5–7 years) who participated in the southern California Children’s Health Study. Data from birth certificates and questionnaire provided information on acculturation, sociodemographic and environmental factors. Genetic ancestries (Amerindian, European, African and Asian) were estimated based on 233 ancestry informative markers. Asthma was defined by parental report of doctor-diagnosed asthma. Rhinitis was defined by parental report of a history of chronic sneezing or runny or blocked nose without a cold or flu. Sample sizes were 1,719 and 1,788 for investigating the role of genetic ancestry on asthma and rhinitis, respectively.ResultsChildren had major contributions from Amerindian and European ancestries. After accounting for potential confounders, per 25% increase in Amerindian ancestry was associated with 17.6% (95% confidence interval [CI]: 0.74–0.99) and 13.6% (95% CI: 0.79–0.98) lower odds of asthma and rhinitis, respectively. Acculturation was not associated with either outcome.ConclusionsEarlier work documented that Hispanic children with significant contribution from African ancestry are at increased asthma risk; however, in Hispanic children who have little contribution from African ancestry, Amerindian ancestry was independently associated with lower odds for development of early-childhood asthma and rhinitis.     

Structure and functional analyses of the 26S proteasome subunits from plants – Plant 26S proteasome

As initial steps to define how the 26S proteasome degrades ubiquitinated proteins in plants, we have characterized many of the subunits that comprise the proteolytic complex from Arabidopsis thaliana. A set of 23 Arabidopsis genes encoding the full complement of core particle (CP) subunits and a collection encoding 12 out of 18 known eukaryotic regulatory particle (RP) subunits, including six AAA-ATPase subunits, were identified. Several of these 26S proteasome genes could complement yeast strains missing the corresponding orthologs. Using this ability of plant subunits to functionally replace yeast counterparts, a parallel structure/function analysis was performed with the RP subunit RPN10/MCB1, a putative receptor for ubiquitin conjugates. RPN10 is not essential for yeast viability but is required for amino acid analog tolerance and degradation of proteins via the ubiquitin-fusion degradation pathway, a subpathway within the ubiquitin system. Surprisingly, we found that the C-terminal motif required for conjugate recognition by RPN10 is not essential for in vivo functions. Instead, a domain near the N-terminus is required. We have begun to exploit the moss Physcomitrella patens as a model to characterize the plant 26S proteasome using reverse genetics. By homologous recombination, we have successfully disrupted the RPN10 gene. Unlike yeast rpn10 strains which grow normally, Physcomitrella rpn10 strains are developmentally arrested, being unable to initiate gametophorogenesis. Further analysis of these mutants revealed that RPN10 is likely required for a developmental program triggered by plant hormones.     

Experimental history and Herman Boerhaave’s chemistry of plants

In the early eighteenth century, chemistry became the main academic locus where, in Francis Bacon’s words, Experimenta lucifera were performed alongside Experimenta fructifera and where natural philosophy was coupled with natural history and ‘experimental history’ in the Baconian and Boyleian sense of an inventory and exploration of the extant operations of the arts and crafts. The Dutch social and political system and the institutional setting of the university of Leiden endorsed this empiricist, utilitarian orientation toward the sciences, which was forcefully propagated by one of the university’s most famous representatives in the first half of the eighteenth century, the professor of medicine, botany and chemistry Herman Boerhaave. Recent historical investigations on Boerhaave’s chemistry have provided important insights into Boerhaave’s religious background, his theoretical and philosophical goals, and his pedagogical agenda. But comparatively little attention has been paid to the chemical experiments presented in Boerhaave’s famous chemical textbook, the Elementa chemiae, and to the question of how these experiments relate not only to experimental philosophy but also to experimental history and natural history, and to contemporary utilitarianism. I argue in this essay that Boerhaave shared a strong commitment to Baconian utilitarianism and empiricism with many other European chemists around the middle of the eighteenth century, in particular to what Bacon designated ‘experimental history’ and I will provide evidence for this claim through a careful analysis of Boerhaave’s plant-chemical experiments presented in the Elementa chemiae.