Genomic population structure of Grass Pickerel (Esox americanus vermiculatus) in Canada: management guidance for an at-risk fish at its northern range limit

Eighty nine (42%) of Canada’s 215 freshwater fish species have been assessed as at risk by the Committee on the Status of Endangered Wildlife in Canada. This study examines genomic population structure of the at-risk Grass Pickerel (Esox americanus vermiculatus), a small (≤?33 cm) predatory fish that in Canada has a range spanning approximately 114,000 km² of southern Ontario. Within this range it occupies approximately ten sites that are mostly shallow, weedy, and slow-flowing. Its populations and habitat are declining. This study defines population clusters and quantifies genomic diversity within and between populations based on?>?5500 loci and?>?950 SNPs from genomes of 66 individuals representing the subspecies’ entire Canadian range. Ordination and STRUCTURE analyses revealed four major geographic/genomic clusters centered in the Georgian Bay-Severn River, southeastern shore of Lake Huron, Niagara Peninsula, and upper St. Lawrence River. Major clusters were distinguished by relatively high Hudson Fst values (0.205–0.480), with Georgian Bay-Severn River being consistently most distinct. The Niagara Peninsula major cluster contained an additional three discernable sub-clusters differentiated by Fst values as great or greater than major clusters, despite spanning only ca. 200 km². Genomically distinct Niagara sub-clusters occurred in Abino Drain, Big Forks Creek, and Tea Creek. Samples from sites between both major and minor clusters exhibited admixture from adjacent clusters. Despite current management of Grass Pickerel under a single designatable unit throughout its Canadian range, we map considerable geographic population structure that should help guide the designation of additional conservation units.

     

Axial Length Measurement Failure Rates with the IOLMaster and Lenstar LS 900 in Eyes with Cataract

Purpose

To evaluate axial length (AL) measurement failure rate with the IOLMaster (Carl Zeiss AG, Germany) and Lenstar LS 900 (Haag-Streit AG, Switzerland) in eyes with cataract.

Methods

Two hundred and ninety-six eyes of 170 patients with cataract were enrolled. Cataract type and severity were graded using the Lens Opacities Classification System III (LOCS III) and AL measurements were attempted with IOLMaster (version 5.4) and Lenstar LS 900 (version 1.1). Chi-squared analysis was used to assess if the difference in AL measurement acquisition rate was statistically significant between the two devices. The association of the different cataract types and severity with the AL measurement acquisition rate was evaluated with logistic regression analysis.

Results

AL measurements were obtained in 184 eyes (62.16%) using the IOLMaster and 191 eyes (64.53%) using the Lenstar, which corresponds to a failure rate of 37.84% and 35.47% respectively. Chi-square analysis indicated no significant difference between the Lenstar and IOLMaster for AL measurement failure rate (x² = 0.356, P = 0.550). Logistic regression analysis indicated no association between acquisition rates and cortical or nuclear cataracts with either device. There was a statistically significant association between acquisition rates and increasing severity of posterior subcapsular cataracts with the IOLMaster (β = -1.491, P<0.001) and Lenstar LS 900 (β = -1.507, P<0.001).

Conclusion

The IOLMaster and Lenstar LS 900 have similar AL measurement failure rates (35–38%) for Chinese public hospital cataract patients. Increasing severity of posterior subcapsular cataracts was problematic for both devices.     

Lack of a relationship between Lewis antigen expression and cagA, CagA, vacA and VacA status of Irish Helicobacter pylori isolates

The cagA gene, vacA gene, CagA (cytotoxin-associated gene A product) and VacA (vacuolating cytotoxin) status of a collection of Helicobacter pylori isolates from the geographically distinct Irish population was determined, the potential association of these traits with Lewis (Le) antigen expression was assessed, and the relationship between these bacterial properties and the pathology associated with H. pylori infection was evaluated. Of the 57 isolates, a higher proportion from ulcer than from non-ulcer patients expressed VacA (71% vs. 53%). H. pylori isolates which were cagA-positive were no more significantly associated with peptic ulcers than non-ulcer disease (71% vs. 67%, P = 0.775), nor were CagA-positive isolates (57% vs. 50%, P = 0.783), but 80% of the isolates from duodenal ulcer patients were cagA-positive. Thirty-seven of the 57 isolates were tested for Le antigen expression. No statistically significant relationship (P > 0.05) was found between the occurrence and level of expression of Le(x) or Le(y) and cagA, vacA, or VacA status. This lack of an association in the Irish H. pylori isolates contrasts with that previously reported for predominantly North American isolates, and may be attributable to the adaptation of H. pylori strains with differing attributes to different human populations.     

Malawi’s Energy Needs and Agroforestry: Adoption Potential of Woodlots

Rapid urbanization and population growth have resulted in increasing demand for fuelwood and higher rates of deforestation in Malawi. Agroforestry fuelwood technology (AFT) offers a sustainable approach to addressing this problem. Adoption levels, however, remain low due to several factors. This study explores the influence and interactions among these factors based on analyses of data collected from a large-scale extension effort using binary regression and interaction tests. The results show AFT adoption throughout the country is influenced positively by factors such as farming groups and education; further, labor availability and landholdings are important in the relatively less fertile South. While increased levels of individual income were found to mediate positive influences on adoption, environmental governance was found to moderate negative influences. Based on our results, we suggest closer monitoring of lead farmers, targeted training, promotion of environmental governance, and increased emphasis on due diligence during extension planning.     

Reduced levels of two modifiers of epigenetic gene silencing,Dnmt3a and Trim28, cause increased phenotypic noise

Background  

Inbred individuals reared in controlled environments display considerable variance in many complex traits but the underlying cause of this intangible variation has been an enigma. Here we show that two modifiers of epigenetic gene silencing play a critical role in the process.     

Colonization of broilers by <Emphasis Type="Italic">Campylobacter jejuni</Emphasis> internalized within <Emphasis Type="Italic">Acanthamoeba castellanii</Emphasis>

Although Campylobacter survives within amoeba in-vitro, it is unknown if intra-amoeba Campylobacter jejuni can colonize broilers. Five groups of 28 day-of-hatch chicks were placed into separate isolators. Groups (1) and (2) were challenged with page’s amoeba saline (PAS), and disinfected planktonic C. jejuni NCTC 11168, respectively. Groups (3), (4) and (5) were challenged with a C. jejuni positive control, C. jejuni in PAS, and intra-amoeba C. jejuni, respectively. After 1, 3, 7 and 14 days post challenge, seven birds from each unit were examined for C. jejuni colonization. For the first time we report that intra-amoeba C. jejuni colonized broilers.     

Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques

The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cost-effective methods for the enrichment of 5hmC marked DNA for downstream analysis. We tested three commonly used affinity-based enrichment techniques; (i) antibody, (ii) chemical capture and (iii) protein affinity enrichment and assessed their ability to accurately and reproducibly report 5hmC profiles in mouse tissues containing high (brain) and lower (liver) levels of 5hmC. The protein-affinity technique is a poor reporter of 5hmC profiles, delivering 5hmC patterns that are incompatible with other methods. Both antibody and chemical capture-based techniques generate highly similar genome-wide patterns for 5hmC, which are independently validated by standard quantitative PCR (qPCR) and glucosyl-sensitive restriction enzyme digestion (gRES-qPCR). Both antibody and chemical capture generated profiles reproducibly link to unique chromatin modification profiles associated with 5hmC. However, there appears to be a slight bias of the antibody to bind to regions of DNA rich in simple repeats. Ultimately, the increased specificity observed with chemical capture-based approaches makes this an attractive method for the analysis of locus-specific or genome-wide patterns of 5hmC.