Faculty of Agricultural and Food Sciences Scholarly Works

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Open Access
17 β-Estradiol mineralization in human waste products and soil in the presence and the absence of antimicrobials
(Taylor Francis, 2016-06) Amarakoon, Inoka; Farenhorst, Annemieke; Rose, Karin; Ascef, B.
Natural steroidal estrogens such as 17 β-estradiol (E2), as well as antimicrobials such as doxycycline and norfloxacin, are excreted by humans and hence detected in sewage sludge and biosolid. The disposal of human waste products on agricultural land results in estrogens and antibiotics being detected as mixtures in soils. The objective of this study was to examine microbial respiration and E2 mineralization in sewage sludge, biosolid and soil in the presence and absence of doxycycline and norfloxacin. The antimicrobials were applied to the media either alone or in combination at total rates of 4 and 40 mg kg-1, with the 4 mg kg-1 rate being an environmentally relevant concentration. The calculated time that half of the applied E2 was mineralized ranged from 294 to 418 d in sewage sludge, from 721 to 869 d in soil and from 2,258 to 14,146 d in biosolid. E2 mineralization followed first-order and the presence of antimicrobials had no significant effect on mineralization half-lives, except for some antimicrobial applications to the human waste products. At 189 d, total E2 mineralization was significantly greater in sewage sludge (38 ±0.7%) > soil (23 ±0.7%) > biosolid (3 ±0.7%), while total respiration was significantly greater in biosolid (1,258 mg CO2) > sewage sludge (253 mg CO2) ≥ soil (131 mg CO2). Strong sorption of E2 to the organic fraction in biosolid may have resulted in reduced E2 mineralization despite the high microbial activity in this media. Total E2 mineralization at 189 d was not significantly influenced by the presence of doxycycline and/or norfloxacin in the media. Antimicrobial additions also did not significantly influence total respiration in media, except that total CO2 respiration at 189 d was significantly greater for biosolid with 40 mg kg-1 doxycycline added, relative to biosolid without antimicrobials. We conclude that it is unlikely for doxycycline and norfloxacin, or their mixtures, to have a significant effect on E2 mineralization in human waste products and soil. However, the potential for E2 to be persistent in biosolids, with and without the presence of antimicrobials, is posing a challenge for biosolid disposal to agricultural lands.
Open Access
17β-Estradiol mineralization under field and laboratory incubations
(2017) Farenhorst, Annemieke; Amarakoon, Inoka; Andronak, Lindsey
Mineralization studies of natural steroid hormones (e.g., 17β-estradiol, E2) are performed in environmental incubators, usually under a constant temperature such as 20°C. In this paper, we present a microcosm protocol that quantified the mineralization of E2 in soils under field temperatures. The nine agricultural soils tested had a wide range of soil organic carbon (1.1 to 5.2%) and clay (9 to 57%) contents. The calculated time over which half of the applied E2 was mineralized (E2-½) ranged from 299 to 910 d, and total E2 mineralization at 48 d (E2-TOT48) ranged from 4 to 13%. In subsequent laboratory incubations, the same soils were incubated under a constant temperature of 20°C, as well as under cyclic temperatures of 14.5°C (14 h) and 11.5°C (10h), which was within the temperature extremes observed in the field microcosms. E2-½ ranged from 157 to 686 d at 20°C and from 103 to 608 d at the cyclic temperatures, with the E2-TOT48 ranging from 6 to 21% at 20°C and from 7 to 30% under cyclic temperatures. Despite the overall 6.75 °C lower mean temperatures under the cyclic versus constant temperatures, E2 mineralization was stimulated by the temperature cycles in three soils. Regardless of the incubation, the same loamy sand soil always showed larger E2 mineralization than the other eight soils and this loamy sand soil also had the smallest E2 sorption. Current modeling approaches do not take into consideration the effects of temperature fluctuations in the field because the input parameters used to describe degradation are derived from laboratory incubations at a constant temperature. Across the eight soils, E2-½ was on average 1.7 times larger and E2-TOT48 was on average 0.8 times smaller under field temperatures than under a constant 20°C. Hence, we conclude that incubations at 20°C give a reasonable representation of E2 mineralization occurring under field conditions to be expected in a typical Prairie summer season.
Open Access
A descriptive analysis of food pantries in twelve American states: hours of operation, faith-based affiliation, and location
(2022-03-17) Riediger, Natalie D.; Dahl, Lindsey; Biradar, Rajeshwari A.; Mudryj, Adriana N.; Torabi, Mahmoud
Abstract Background Our objectives were to describe both the development, and content, of a charitable food dataset that includes geographic information for food pantries in 12 American states. Methods Food pantries were identified from the foodpantries.org website for 12 states, which were linked to state-, county-, and census-level demographic information. The publicly available 2015 Food Access Research Atlas and the 2010 US Census of Population and Housing were used to obtain demographic information of each study state. We conducted a descriptive analysis and chi-square tests were used to test for differences in patterns of food pantries according to various factors. Results We identified 3777 food pantries in 12 US states, providing an estimated 4.84 food pantries per 100,000 people, but ranged from 2.60 to 7.76 within individual states. The majority of counties (61.2%) had at least one food pantry. In contrast, only 15.7% of all census tracts in the study states had at least one food pantry. A higher proportion of urban census tracts had food pantries compared to rural tracts. We identified 2388 (63.2%) as being faith-based food pantries. More than a third (34.4%) of food pantries did not have information on their days of operation available. Among the food pantries displaying days of operation, 78.1% were open at least once per week. Only 13.6% of food pantries were open ≤1 day per month. Conclusions The dataset developed in this study may be linked to food access and food environment data to further examine associations between food pantries and other aspects of the consumer food system (e.g. food deserts) and population health from a systems perspective. Additional linkage with the U.S. Religion Census Data may be useful to examine associations between church communities and the spatial distribution of food pantries.
Open Access
A double-blind, randomized, crossover trial protocol of whole hemp seed protein and hemp seed protein hydrolysate consumption for hypertension
(2020-04-23) Samsamikor, Maryam; Mackay, Dylan; Mollard, Rebecca C; Aluko, Rotimi E
Abstract Background Primary hypertension accounts for almost 95% of all cases of high blood pressure and is a major modifiable risk factor for cardiovascular diseases. Lifestyle interventions have been shown to prevent hypertension. One of the prominent potential therapeutic lifestyle strategies to prevent or manage hypertension is increasing dietary protein as a macronutrient or as bioactive peptides. An emerging plant-based protein source that may have anti-hypertensive properties is hemp seed. Methods/design A randomized, double-blind, crossover clinical trial will be conducted on 35 hypertensive participants aged 18–75 years, with a BMI between 18.5 and 40 kg/m2, systolic blood pressure (SBP) between 130 and 160 mmHg and diastolic blood pressure (DBP) ≤ 110 mmHg. The trial will be conducted for a period of 22 weeks and will consist of three treatment periods of 6 weeks, separated by 2-week washout periods. The treatments will be consumed twice a day and consist of 25 g casein, hemp seed protein (HSP), or HSP plus HSP hydrolysate (HSP+). The primary outcome of this trial is 24-h SBP, measured on the first day of first phase and the last day of each phase. Office-measured blood pressure, pulse-wave velocity and augmentation index and anthropometrics will be determined at the first and last days of each period. Also, body composition will be assessed by dual x-ray absorptiometry (DXA) scan on the first day of the first phase and within the last 2 days of each treatment period. Blood samples will be collected on the first and last 2 days of each treatment phase whereas urine samples will be collected on the first day of the first phase plus the last day of each phase to be analyzed for specific biomarkers. Discussion This trial protocol is designed to evaluate the hypotensive potential of consuming whole HSP, and HSP+, in comparison to casein protein. This study will be the first trial investigating the potential anti-hypertensive benefit of dietary hemp protein plus bioactive peptide consumption in humans. Trial registration National Clinical Trial (NCT), ID: NCT03508895. Registered on 28 June 2018. Retrospectively registered on the publicly accessible Registry Databank at ClinicalTrials.gov (http://ClinicalTrials.gov).
Open Access
A major quantitative trait locus conferring adult plant partial resistance to crown rust in oat
(2014-09-27) Lin, Yang; Gnanesh, Belaghihalli N; Chong, James; Chen, Gang; Beattie, Aaron D; Mitchell Fetch, Jennifer W; Kutcher, H R; Eckstein, Peter E; Menzies, Jim G; Jackson, Eric W; McCartney, Curt A
Abstract Background Crown rust, caused by Puccinia coronata f. sp. avenae, is the most important disease of oat worldwide. Adult plant resistance (APR), based upon partial resistance, has proven to be a durable rust management strategy in other cereal rust pathosystems. The crown rust APR in the oat line MN841801 has been effective for more than 30 years. The genetic basis of this APR was studied under field conditions in three recombinant inbred line (RIL) populations: 1) AC Assiniboia/MN841801, 2) AC Medallion/MN841801, and 3) Makuru/MN841801. The populations were evaluated for crown rust resistance with the crown rust isolate CR251 (race BRBB) in multiple environments. The 6 K oat and 90 K wheat Illumina Infinium single nucleotide polymorphism (SNP) arrays were used for genotyping the AC Assiniboia/MN841801 population. KASP assays were designed for selected SNPs and genotyped on the other two populations. Results This study reports a high density genetic linkage map constructed with oat and wheat SNP markers in the AC Assiniboia/MN841801 RIL population. Most wheat SNPs were monomorphic in the oat population. However the polymorphic wheat SNPs could be scored accurately and integrated well into the linkage map. A major quantitative trait locus (QTL) on oat chromosome 14D, designated QPc.crc-14D, explained up to 76% of the APR phenotypic variance. This QTL is flanked by two SNP markers, GMI_GBS_90753 and GMI_ES14_c1439_83. QPc.crc-14D was validated in the populations AC Medallion/MN841801 and Makuru/MN841801. Conclusions We report the first APR QTL in oat with a large and consistent effect. QPc.crc-14D was statistically significant in all environments tested in each of the three oat populations. QPc.crc-14D is a suitable candidate for use in marker-assisted breeding and also an excellent target for map-based cloning. This is also the first study to use the 90 K wheat Infinium SNP array on oat for marker development and comparative mapping. The Infinium SNP array is a useful tool for saturating oat maps with markers. Synteny with wheat suggests that QPc.crc-14D is orthologous with the stripe rust APR gene Yr16 in wheat.
Open Access
A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]
(2020-05-24) Hu, Shunkai; Zhang, Mi; Yang, Yiqing; Xuan, Wei; Zou, Zhongwei; Arkorful, Emmanuel; Chen, Yi; Ma, Qingping; Jeyaraj, Anburaj; Chen, Xuan; Li, Xinghui
Abstract Background Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverages worldwide. In tea, lateral roots (LRs) are the main organ responsible for the absorption of moisture and mineral nutrients from the soil. Lateral roots formation and development are regulated by the nitrogen and auxin signaling pathways. In order to understand the role of auxin and nitrogen signaling in LRs formation and development, transcriptome analysis was employed to investigate the differentially expressed genes involved in lateral roots of tea plants treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high concentrations of nitrogen. Results A total of 296 common differentially expressed genes were identified and annotated to four signaling pathways, including nitrogen metabolism, plant hormone signal transduction, glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of transcripts, thereby, regulating lateral roots formation. Furthermore, metabolism of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration increased with the decreased nitrogen level in lateral roots. Thus, tea plant lateral roots formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. Conclusion This study provided insights into the mechanisms associated with nitrogen and auxin signaling pathways in LRs formation and provides information on the efficient utilization of nitrogen in tea plant at the genetic level.
Open Access
A qualitative analysis of the perceived socio-cultural contexts and health concerns of sugar-sweetened beverages among adults studying or working at a post-secondary institution in Dharwad, India
(2021-05-29) Riediger, Natalie; Dhalla, Anika; Cooper, Maureen; Bombak, Andrea; Sreeramaiah, Hemalatha
Abstract Background We sought to explore the perceptions of the socio-cultural contexts and health concerns of consuming sugar-sweetened beverages (SSB) among Indian adults working or studying at a post-secondary institution in Karnataka, India. Methods We completed a qualitative study, including 24 semi-structured interviews between 2017 and 2018 at the University of Agricultural Sciences, Dharwad, Karnataka, India. Data were analyzed using thematic content analysis. Results One over-arching theme emerged, westernization and changing perceptions of food, sugar, and health. Participants discussed SSB and associated health concerns in the broad context of westernization and overall economic development in India. Three sub-themes regarding the health perceptions of consuming SSB were: healthy drinks are clean and natural; hydration and energy; and moderation and body weight. Hygienically-prepared beverages were a consistent concern among participants. Juices and beverages, such as tea or coffee, sweetened with jaggery were viewed positively due to their naturalness and lack of processed sugar. Participants perceived SSB as providing hydration and energy, particularly in hot weather. Lastly, if consumed in moderation, SSB were thought to have no direct adverse health consequences. Though some participants noted excessive, ‘addictive’ consumption would contribute to weight gain and diabetes. Conclusion Perceived health concerns of SSB reflect dominant health issues in India, namely, food insecurity, food safety, and increasingly, diabetes. Policymakers tend to prioritize acute challenges over long-term concerns. As such, the capacity of any policy to address chronic nutritional concerns related to SSB are likely to be muted in the absence of improvements to food safety and security.
Open Access
Age of introduction of first complementary feeding for infants: a systematic review
(2015-09-02) Qasem, Wafaa; Fenton, Tanis; Friel, James
Abstract Background Despite a World Health Organization recommendation for exclusive breastfeeding of all full-term infants to 6 months of age, it is not clear what the health implications may be. Breast milk alone may not meet the nutrition needs for all growing infants, leaving them at risk for deficiencies. The objective of this study was to investigate the relationship between moderate (4 months) versus late (6 months) introduction of complementary foods to the full-term breastfed infant on iron status and growth. Methods An electronic search of peer-reviewed and gray-literature was conducted for randomized control trials (RCTs) and observational studies related to the timing of introduction of complementary foods. Iron status and growth data from the relevant RCTs were analyzed using RevMan 5.2.11. Results Three RCTs and one observational study met the inclusion criteria. Meta-analysis showed significantly higher hemoglobin levels in infants fed solids at 4 months versus those fed solids at 6 months in developing countries [mean difference [MD]: 5.0 g/L; 95 % CI: 1.5, 8.5 g/L; P = 0.005]. Meta-anaysis also showed higher serum ferritin levels in the 4-month group in both developed and developing countries [MD: 26.0 μg/L; 95 % CI: -0.1, 52.1 μg/L, P = 0.050], [MD: 18.9 μg/L; 95 % CI: 0.7, 37.1 μg/L, P = 0.040]. Short follow-up periods and small sample sizes of the included studies were the major limitations. Conclusions RCT evidence suggests the rate of iron deficiency anemia in breastfed infants could be positively altered by introduction of solids at 4 months.
Open Access
Age-related Changes in p56lck Protein Levels and Phenotypic Distribution of T Lymphocytes in Young Rats
(2005-03) Hosea, Heather J.; Rector, Edward S.; Taylor, Carla G.
p56lck is involved in the maturation of T-cells from double negative (DN) into double positive (DP) T-cells. The objective of this experiment was to determine changes in the levels of thymic and splenic T-cell p56lck using Western immunoblotting, along with the proportion and number of T-cell subsets in thymus, spleen and blood using flow cytometry in growing Sprague-Dawley rats. Thymic p56lck levels were negatively correlated with age (r=-0.42, p=0.04) and positively correlated with age in the spleen (r=0.50, p=0.01). Nine-week-old rats had a higher percentage of thymic DN and CD8 cells with fewer DP cells compared to younger rats. There were minor differences in the proportions of T-cell subsets in the spleen and blood. T-cell numbers remained proportional to body weight in the lymphoid organs; however, the lower absolute number of T-cells in the younger rats might indicate that they are less able to respond to antigens.
Open Access
Are we really “eating well with Canada’s food guide”?
(2018-05-22) Slater, Joyce J; Mudryj, Adriana N
Abstract Background Canada’s Food Guide (CFG) has been an important health promotion tool for over seventy years. The most recent version was released in 2007. This study examined Canadians’ exposure to, knowledge, and use of CFG. Methods Data came from the Canadian Community Health Survey’s Rapid Response on the Awareness and Usage of Canada’s Food Guide, which included 10,098 Canadians ≥12 y in all ten provinces. Questions were asked on familiarity, awareness and usage of CFG and Canada’s Food Guide for First Nations, Inuit and Métis, as well as healthy eating principles and behaviours. Descriptive statistics and logistic regression were used to observe counts and differences among key demographic variables. Results More than 80% of Canadians have heard of CFG however significantly more women than men were aware of the Guide. Most knew that ‘Vegetables and Fruit’ had the most recommended servings and that dark green vegetables should be consumed daily; however fewer than half knew this of orange vegetables. Just under one third had a copy in their homes, and the most common sources for obtaining CFG were child’s school and health professional/trainer. Those who consulted CFG recently were more likely to consume the recommended servings of vegetables and fruits, and to state that their eating habits were ‘much better’ than one year previously. Conclusions CFG has “brand recognition” among Canadians however there are gaps between awareness and eating behaviours. The new Food Guide could consider additional dissemination tools including social media, videos and workbooks tailored to various age groups, demographic groups and settings.
Open Access
Association of bovine major histocompatibility complex (BoLA) gene polymorphism with colostrum and milk microbiota of dairy cows during the first week of lactation
(2018-11-12) Derakhshani, Hooman; Plaizier, Jan C; De Buck, Jeroen; Barkema, Herman W; Khafipour, Ehsan
Abstract Background The interplay between host genotype and commensal microbiota at different body sites can have important implications for health and disease. In dairy cows, polymorphism of bovine major histocompatibility complex (BoLA) gene has been associated with susceptibility to several infectious diseases, most importantly mastitis. However, mechanisms underlying this association are yet poorly understood. In the present study, we sought to explore the association of BoLA gene polymorphism with the dynamics of mammary microbiota during the first week of lactation. Results Colostrum and milk samples were collected from multiparous Holstein dairy cows at the day of calving and days 1 and 6 after calving. Microbiota profiling was performed using high-throughput sequencing of the V1-V2 regions of the bacterial 16S rRNA genes and ITS2 region of the fungal ribosomal DNA. Polymorphism of BoLA genes was determined using PCR-RFLP of exon 2 of the BoLA-DRB3. In general, transition from colostrum to milk resulted in increased species richness and diversity of both bacterial and fungal communities. The most dominant members of intramammary microbiota included Staphylococcus, Ruminococcaceae, and Clostridiales within the bacterial community and Alternaria, Aspergillus, Candida, and Cryptococcus within the fungal community. Comparing the composition of intramammary microbiota between identified BoLA-DRB3.2 variants (n = 2) revealed distinct clustering pattern on day 0, whereas this effect was not significant on the microbiota of milk samples collected on subsequent days. On day 0, proportions of several non-aureus Staphylococcus (NAS) OTUs, including those aligned to Staphylococcus equorum, Staphylococcus gallinarum, Staphylococcus sciuri, and Staphylococcus haemolyticus, were enriched within the microbiota of one of the BoLA-DRB3.2 variants, whereas lactic acid bacteria (LAB) including Lactobacillus and Enterococcus were enriched within the colostrum microbiota of the other variant. Conclusion Our results suggest a potential role for BoLA-gene polymorphism in modulating the composition of colostrum microbiota in dairy cows. Determining whether BoLA-mediated shifts in the composition of colostrum microbiota are regulated directly by immune system or indirectly by microbiota-derived colonization resistant can have important implications for future development of preventive/therapeutic strategies for controlling mastitis.
Open Access
Associations between digital dermatitis lesion grades in dairy cattle and the quantities of four Treponema species
(2018-10-29) Beninger, Caroline; Naqvi, Syed A; Naushad, Sohail; Orsel, Karin; Luby, Chris; Derakhshani, Hooman; Khafipour, Ehsan; De Buck, Jeroen
Abstract Digital dermatitis (DD) presents as painful, ulcerative or proliferative lesions that lead to bovine lameness affecting economic efficiency and animal welfare. Although DD etiological agent(s) have not been established, it is widely accepted that DD is a polymicrobial disease significantly associated with species of Treponema and the non-linear disease progression may be attributed to interactions among infecting bacteria. We postulated the morphological changes associated with DD lesion grades are related to interactions among infecting species of Treponema. We developed a novel species-specific qPCR that can identify the absolute abundance of the four of the most common species of Treponema in DD, T. phagedenis, T. medium, T. pedis and T. denticola, in a single reaction. We found species abundance and the number of distinct Treponema species present is higher in active, ulcerative lesions than in healing lesions, chronic lesions, and DD-free skin. Treponema spp. were present in both DD-free skin and M3 lesions following treatment with oxytetracycline. We have also found positive correlations among T. phagedenis, T. medium and T. pedis indicating they are significantly more likely to be found together than apart and their absolute quantities tend to increase together, a relationship which is not present with T. denticola. Further, we found Treponema, particularly viable T. denticola, in lesions 5 days post treatment with oxytetracycline (M3). Our findings suggest that pathogenicity may be closely associated with Treponema abundance, particularly T. phagedenis, T. medium and T. pedis, and interactions among them, independent of T. denticola. Our results provide a novel, consistent method to identify species of Treponema within DD lesions and associate Treponema spp. and abundance with morphological changes related to host pathogenicity.
Open Access
Avian influenza virus circulation and immunity in a wild urban duck population prior to and during a highly pathogenic H5N1 outbreak
(BMC, 2024-11-22) Wight, Jordan; Rahman, Ishraq; Wallace, Hannah L.; Cunningham, Joshua T.; Roul, Sheena; Robertson, Gregory J.; Russell, Rodney S.; Xu, Wanhong; Zhmendak, Dmytro; Alkie, Tamiru N.; Berhane, Yohannes; Hargan, Kathryn E.; Lang, Andrew S.
Abstract Highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b viruses were first detected in St. John’s, Canada in late 2021. To investigate the patterns of avian influenza virus (AIV) infection and immune responses subsequent to the arrival of H5N1, we sampled the wild urban duck population in this area for a period of 16 months after the start of the outbreak and compared these findings to those from archived samples. Antibody seroprevalence was relatively stable before the outbreak (2011–2014) at 27.6% and 3.9% for anti-AIV (i.e., NP) and H5-specific antibodies, respectively. During the winter of 2022, AIV-NP and H5-specific antibody seroprevalence both reached 100%, signifying a population-wide infection event, which was observed again in late February 2023 following a second H5N1 incursion from Eurasia. As expected, population-level immunity waned over time, with ducks seropositive for anti-AIV-NP antibodies for approximately twice as long as for H5-specific antibodies, with the population seronegative to the latter after approximately six months. We observed a clear relationship of increasing antibody levels with decreasing viral RNA loads that allowed for interpretation of the course of infection and immune response in infected individuals and applied these findings to two cases of resampled ducks to infer infection history. Our study highlights the value of applying both AIV surveillance and seroprevalence monitoring to provide a better understanding of AIV dynamics in wild populations, which may be crucial following the global dissemination of clade 2.3.4.4b H5Nx subtypes to assess the threats they pose to both wild and domestic animals, and to humans.
Open Access
Bacteria in drinking water sources of a First Nation reserve in Canada
(Elsevier, 2016-09-29) Farenhorst, Annemieke; Li, Ru; Musarrat, Jahan; Tun, Hein Min; Mi, Ruidong; Amarakoon, Inoka; Kumar, Ayush; Khafipour, Ehsan
Approximately 20% of the 600 First Nations reserves across Canada are under a drinking water advisory, often due to unacceptable levels of bacteria. In this study, we detected fecal bacteria at an alarmingly high frequency in drinking water sources in a fly-in First Nations community, most notably in buckets/drums of homes without running water where Escherichia coli levels ranged from 20 to 62,000 CFU/100mL. The water leaving the water treatment plant was free of E. coli and its free residual chlorine concentration (0.67 mg/L) was within the range typically observed for treated water in Canada. Water samples from taps in homes served by cisterns, and those sampled from the water truck and community standpipe, always showed unacceptable levels of E. coli (1 to 2,100 CFU/100mL) and free residual chlorine concentrations below the 0.2 mg/L required to prevent bacterial regrowth. Samples from taps in homes served by piped water had lower levels of E. coli (0 to 2 CFU/100mL). DNA- and RNA-based 16S rRNA Illumina sequencing demonstrated that piped and cisterns water distribution systems showed an abundance of viable cells of Alphaproteobacteria indicative of biofilm formation in pipes and cisterns. The alpha diversity, based on observed OTUs and three other indices, was lowest in water truck samples that supplied water to the cistern and the low free residual chlorine concentration (0.07 mg/L) and predominance of Betaproteobacteria (63% of viable cells) that were immediately detected after the truck had filled up at the water treatment plant was indicative of contamination by particulate matter. Given these findings, First Nation residents living without running water and relying on inadequate water distribution systems are at higher risk of contracting water-born illnesses. We urge all governments in Canada to expand their investments in supporting and sustaining water as a human right in Canada’s First Nations communities.
Open Access
BioLegato: a programmable, object-oriented graphic user interface
(BMC, 2023-08-21) Alvare, Graham; Roche-Lima, Abiel; Fristensky, Brian
Background Biologists are faced with an ever-changing array of complex software tools with steep learning curves, often run on High Performance Computing platforms. To resolve the tradeoff between analytical sophistication and usability, we have designed BioLegato, a programmable graphical user interface (GUI) for running external programs. Results BioLegato can run any program or pipeline that can be launched as a command. BioLegato reads specifications for each tool from files written in PCD, a simple language for specifying GUI components that set parameters for calling external programs. Thus, adding new tools to BioLegato can be done without changing the BioLegato Java code itself. The process is as simple as copying an existing PCD file and modifying it for the new program, which is more like filling in a form than writing code. PCD thus facilitates rapid development of new applications using existing programs as building blocks, and getting them to work together seamlessly. Conclusion BioLegato applies Object-Oriented concepts to the user experience by organizing applications based on discrete data types and the methods relevant to that data. PCD makes it easier for BioLegato applications to evolve with the succession of analytical tools for bioinformatics. BioLegato is applicable not only in biology, but in almost any field in which disparate software tools need to work as an integrated system.
Open Access
BULK DEPOSITION OF PESTICIDES IN A CANADIAN CITY: PART 1 GLYPHOSATE AND OTHER AGRICULTURAL PESTICIDES
(2015-03) Farenhorst, Annemieke; Andronak, Lyndsey; McQueen, Ross
Winnipeg is a city in the Canadian Prairies with a population of about 600,000. Like many other cities and towns in this region of Canada, the city is surrounded by agriculture. Weekly bulk deposition samples were collected from May to September in 2010 and 2011 and analyzed for forty-three pesticides used in Prairie agriculture. Fourteen herbicides, five herbicide metabolites, two insecticides and two fungicides were detected with 98.5% of the samples containing chemical mixtures. Glyphosate is the most widely used pesticide in Prairie agriculture and accounted for 65% of the total pesticide deposition over the two years. Seasonal glyphosate deposition was more than five times larger in 2011 (182 mm rain) than 2010 (487 mm rain), suggesting increased glyphosate particulate transport in the atmosphere during the drier year. The seasonal deposition of ten other frequently herbicides was significantly positively correlated with the amount of herbicides applied both in and around Winnipeg (r=0.90, P<0.001) and with agricultural herbicide use around Winnipeg (r=0.63, P=0.05), but not with agricultural herbicide use province wide (p=0.23). Herbicides 2,4-D, dicamba, and mecoprop had known urban applications and were more consistently detected in samples relative to bromoxynil and MCPA whose frequency of detections decreased throughout August and September. The Canadian Water Quality Guidelines for irrigation water were frequently exceeded for both dicamba (75%) and MCPA (49%) concentrations in rain. None of glyphosate concentrations in rain exceeded any of the Canadian Water Quality Guidelines established for this herbicide.
Open Access
BULK DEPOSITION OF PESTICIDES IN A CANADIAN CITY: PART 2. IMPACT OF MALATHION USE WITHIN CITY-LIMITS
(2015-03) Farenhorst, Annemieke; Andronak, Lyndsey; McQueen, Ross
Malathion is an organophosphate insecticide registered for use in cities throughout North America to control adult mosquitoes. The objective of this study was to determine the impact of urban malathion applications on the levels of malathion detected in bulk deposition. In 2010, malathion was applied by the City of Winnipeg’s Insect Control Branch for a total amount of 6,632 kg in the city, as well as by the general public in relatively small amounts. In 2011, no malathion was applied by the city. Malathion was detected in 41% of the samples in 2010 with deposition rates ranging from 0.5 to 107.7 μg/m2/week. Only 9% of the samples contained malathion in 2011 with deposition rates always being < 0.4 μg/m2/week. Between 6 to 25% of the samples in 2010 exceeded the toxicological threshold levels of malathion to a range of freshwater amphipods, water fleas and stoneflies, including Daphnia magna which is a bioindicator of good environmental health. The weekly maximum malathion concentration detected in this study (5.2 μg/L for a week in June 2010) was at least 26 times greater than the maximum concentration of malathion reported in other atmospheric deposition studies. For the two insect management areas (7.4 and 37.6 km2) where the bulk deposition samplers had been placed, calculations suggested that between 1.2 to 5.1% of the malathion applied by the city became bulk deposition. Percutaneous absorption by humans of malathion in rainfall is unknown.
Open Access
Calcium-sensing Receptor is not Expressed in the Absorptive Enterocytes of Weaned Piglets
(2022-03-16) Zhao, Xiaoya; Hui, Qianqu; Azevedo, Paula A; Nyachoti, Charles M.; O, Karmin; Yang, Chengbo
The calcium-sensing receptor (CaSR) is a kokumi receptor that plays an essential role in nutrient sensing and animal physiology, growth, and development. Pig CaSR (pCaSR) was identified and characterized in the intestine. However, further research is still needed to confirm the expression of CaSR in the epithelial cells isolated from weaned piglets. In this study, primary enterocytes were isolated and characterized from the ileum of weaned piglets by the Weiser distended intestinal sac technique and fluorescence-activated cell sorting (FACS) based on sucrase-isomaltase as an enterocyte-specific marker. The expression of CaSR was investigated in both primary enterocytes and the intestinal porcine enterocyte cell line (IPEC-J2) by droplet digital PCR (ddPCR), immunofluorescence staining, and western blotting. Results demonstrated that porcine enterocytes could be obtained using FACS with the sucrase-isomaltase as the enterocyte-specific marker and that pCaSR is not expressed in both porcine ileal enterocytes and IPEC-J2 cells, which specifically identified the expression of pCaSR in ileal enterocytes with sensitive and specific approaches.
Open Access
Cardiovascular disease protective properties of blueberry polyphenols (Vaccinium corymbosum): a concise review
(BioMed Central (BMC), 2023-03-21) Onuh, John O.; Dawkins, Norma L.; Aluko, Rotimi E.
Abstract Increasing epidemiological evidence suggests inverse association between consumption of diets rich in fruits and vegetables and the incidence of cardiovascular diseases (CVD), metabolic syndrome disorders, certain types of cancer, neurodegenerative disorders, and other forms of human chronic diseases. This may be due to the contents of some bioactive phytochemicals, especially polyphenols, which are abundant in fruits and vegetables and have antioxidant effects. Berry fruits are reported to have the highest total antioxidant capacity (TAC) among fruits. They may protect against CVD and hypertension either directly or in tandem with other cellular mechanisms. Blueberry anthocyanins have been reported to exhibit cardiovascular protective health effects by preventing cholesterol-induced atherosclerosis, and reduction of oxidative and inflammatory damages to the endothelium through several mechanisms. Such mechanisms may involve suppressing the release of inflammatory mediators, protection against ischemic damage of the heart as well as cardiomyocyte survival, lower systolic and mean arterial pressures and renal nitrite content in addition to multiple other beneficial effects. However, several limitations in existing studies make it difficult to draw conclusions regarding the preventive effects of blueberries and other polyphenols-rich foods, especially as data supporting a causal relationship between direct antioxidant capacity and CVD are insufficient or limited. It is also unclear, which molecules exert this effect since few studies with isolated polyphenols have been conducted in addition to a lack of proper understanding of other mechanisms that may be involved. This review is, therefore aimed at discussing some of the current literature information on the cardiovascular protective effects of blueberries with suggestions for future research directions. Graphical Abstract Graphical abstract demonstrating the overall mechanisms of CVD protection by blueberry and blueberry polyphenols and anthocyanins. Blueberry consumption leads to reduced CVD complications due to the modulation of several mechanisms associated with CVD.
Open Access
Combining deep sequencing and conventional molecular approaches reveals broad diversity and distribution of fleas and Bartonella in rodents and shrews from Arctic and Subarctic ecosystems
(2022-10-13) Buhler, Kayla J.; Fernando, Champika; Hill, Janet E.; Galloway, Terry; Carriere, Suzanne; Fenton, Heather; Fauteux, Dominique; Jenkins, Emily J.
Abstract Background Bartonella are intracellular bacteria that are transmitted via animal scratches, bites and hematophagous arthropods. Rodents and their associated fleas play a key role in the maintenance of Bartonella worldwide, with > 22 species identified in rodent hosts. No studies have addressed the occurrence and diversity of Bartonella species and vectors for small mammals in Arctic and Subarctic ecosystems, which are increasingly impacted by invasive species and climate change. Methods In this study, we characterized the diversity of rodent fleas using conventional PCR targeting the mitochondrial cytochrome c oxidase II gene (COII) and Bartonella species in rodents and shrews (n = 505) from northern Canada using conventional PCR targeting the ITS (intergenic transcribed spacer) region and gltA (citrate synthase) gene. Metagenomic sequencing of a portion of the gltA gene was completed on a subset of 42 rodents and four rodent flea pools. Results Year, total summer precipitation the year prior to sampling, average minimum spring temperature and small mammal species were significant factors in predicting Bartonella positivity. Occurrence based on the ITS region was more than double that of the gltA gene and was 34% (n = 349) in northern red-backed voles, 35% (n = 20) in meadow voles, 37% (n = 68) in deer mice and 31% (n = 59) in shrews. Six species of Bartonella were identified with the ITS region, including B. grahamii, B. elizabethae, B. washoensis, Candidatus B. rudakovii, B. doshiae, B. vinsonii subsp. berkhoffii and subsp. arupensis. In addition, 47% (n = 49/105) of ITS amplicons had < 97% identity to sequences in GenBank, possibly due to a limited reference library or previously unreported species. An additional Bartonella species (B. heixiaziensis) was detected during metagenomic sequencing of the gltA gene in 6/11 rodents that had ITS sequences with < 97% identity in GenBank, highlighting that a limited reference library for the ITS marker likely accounted for low sequence similarity in our specimens. In addition, one flea pool from a northern red-backed vole contained multiple species (B. grahamii and B. heixiaziensis). Conclusion Our study calls attention to the usefulness of a combined approach to determine the occurrence and diversity of Bartonella communities in hosts and vectors. Graphical Abstract