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Fulltext Iatrogenic (‘clinician-induced’) damage incurred by human sperm during infertility treatment: postgraduate research and collaborative developments between the universities of Malaya and Oxford

Yelumalai, S., Jones, C., Coward, K.

JUMMEC, 2013;16(2):1-6.
MyJurnal

Assisted Reproductive Technology (ART) is a suite of laboratory techniques designed to rescue infertile phenotypes. While ART has led to the birth of 5 million ART babies worldwide, success rates rarely exceed 40%. One potential factor for this could be iatrogenic (‘clinician-induced’) damage to critical sperm proteins, such as phospholipase C zeta (PLCζ) and protamine, which are fundamental for oocyte activation and sperm DNA integrity, respectively. This report describes how we have begun to investigate the adverse effects of ART techniques upon these key sperm proteins. We also describe the pathway taken by Miss Suseela Yelumalai to acquire a scholarship from the Malaysian Government and her postgraduate experience at the University of Oxford. We introduce the facilities and learning opportunities available at the Institute of Reproductive Sciences (IRS) which houses Dr Kevin Coward’s research laboratory, and finally, highlight the potential for collaborative development between the Universities of Oxford and Malaya.
Determination of plasma concentrations of dapsone, monoacetyl dapsone and pyrimethamine in human subjects dosed with maloprim

Jones CR, Ovenell SM

J. Chromatogr., 1979 Jun 11;163(2):179-85.
PMID: 541369

A high-performance liquid chromatographic method was developed to enable dapsone, monoacetyl dapsone and pyrimethamine to be measured simultaneously in plasma samples from volunteers in England and Malaysia who had been dosed with Maloprim. Mean half-lives of 25 and 80 h were calculated for dapsone and pyrimethamine, respectively, but there was wide individual variation. All subjects were found to be classifiable as "slow acetylators".
Fulltext Detection of aroid leaf rust Pseudocerradoa paullula on Swiss cheese plant Monstera deliciosa in the continental USA

Urbina H, Jones C, Moore M, Gazis R

Plant Dis, 2023 Mar 01.
PMID: 36856652 DOI: 10.1094/PDIS-01-23-0134-PDN

Monstera deliciosa Liebm. (Araceae, Monocots), sometimes referred to as Swiss cheese plant, is one of the most common aroids used as an indoor and landscape ornamental plant (Cedeño et al. 2020). Production of M. deliciosa and other closely related Araceae species represents an important sector of the ornamental nursery business worldwide. Swiss cheese plant is believed to have originated in the tropical forests of southern Mexico, where its fruit is considered a delicacy due to its sweet, exotic flavor (Cedeño et al. 2020). Since 2019, symptomatic Monstera plants from two plant nurseries and residential properties in South Florida were submitted for disease diagnosis to the Florida Department of Agriculture and Consumer Services, Division of Plant Industry (FDACS-DPI) in Gainesville, Florida, and to the University of Florida, Tropical Research and Education Center Plant Clinic in Homestead, Florida. Symptoms included small chlorotic spots on the leaf surface, which expanded and became brown to reddish-brown often with a yellow halo and produced uredinia with abundant urediniospores. The pathogen was identified morphologically as the rust fungus Pseudocerradoa (=Puccinia) paullula (Syd. & P. Syd.) M. Ebinghaus & Dianese (Pucciniaceae, Basidiomycota) (Ebinghaus et al. 2022), characterized by the production of pseudosuprastomatal uredinia. Uredinospores light-brown and globose, echinulate (1 µm height), reddish to light brown, 24 - 31 µm diameter, with thick walls, 1.5 - 2.5 µm height (n=15). Teliospores 2-celled, light-yellow and ellipsoidal, 23 - 28 × 19 - 24 µm (n =15) were observed in sori appearing as dark-brown leaf spots on the adaxial side of the leaves (e-Xtra Fig. 1). Molecular characterization of the fungal pathogen was based on the small subunit (SSU), internal transcribed spacer (ITS), and large subunit (LSU) of the ribosomal RNA genes (Aime 2006) with the addition of a LSU internal primer specific for the rust species Ppaullula_int-forward 5'ATAGTTATTGGCTTTGATTTACA-3' designed in this study to increase the quality and the sequence read length due to a 3'- ~21-Ts-homopolymer (e-Xtra Fig. 2) (GenBank accession number ON887196, ON887197, OQ275200, OQ275201). In addition to morphological identification, the host plant was identified using the Ribulose-1,5-bisphosphate carboxylase-oxygenase (rbcL) and Maturase K (matK) genes (Fazekas et al. 2012) (GenBank accession numbers ON887189, ON887193, respectively). MegaBlast searches confirmed the morphological identification with 100% identity to M. deliciosa vouchers GQ436772 and MK206496, respectively (Chen et al. 2015). Dried specimens were deposited in the Plant Industry Herbarium Gainesville (PIHG 16226, 16227, 17154, 17155). Molecular identification of the rust pathogen P. paullula was carried out through megaBlast (Chen et al. 2015) searches together with a phylogenetic analysis performed in RAxML v8 (Stamatakis 2014) (e-Xtra Fig. 3). Koch's postulates were performed by using urediniospores, collected from an infected sample and were kept for 7 days at 4 C, as an inoculum source. Healthy rooted M. deliciosa plants were inoculated by rubbing the inoculum on both leaf surfaces at >90% RH, room temperature, 12/12 light cycle. After the incubation period (48 h), plants were placed in a climate-controlled greenhouse and watered twice a week, ~30 C, ~65 RH, 12/12 light cycle. After three weeks, all inoculated plants developed symptoms resembling those observed on the samples submitted for disease diagnosis. Controls did not show symptoms. Spores from the pustules of inoculated plants were identified as P. paullula by both morphology and molecular means. The genus Pseudocerradoa comprises P. paullula and its sister species P. rhaphidophorae (Syd.) M. Ebinghaus & Dianese. Both species can be distinguished by size and coloration of urediniospores and their host range within the Araceae. Pseudocerradoa rhaphidophorae produces smaller urediniospores and only occurs on Rhaphidophora species (Shaw 1995). Pseudocerradoa paullula is not considered fully established in Florida, since the host distribution is mainly restricted to indoors and M. deliciosa is rarely used as an outdoor ornamental (Wunderlin et al. 2023). Here we name the disease caused by P. paullula as "aroid leaf rust", due to its ability to infect several species in this plant family. Other closely related hosts reported as susceptible to this pathogen are Monstera standleyana G.S.Bunting (as M.s. cv. variegata), Monstera adansonii var. laniata (Schott) Mayo & I.M. Andrade, Monstera subpinnata (Schott) Engl., Typhonodorum lindleyanum Schott, and Stenospermation sp. (Shaw 1991, 1992, 1995). To date, the aroid leaf rust was only known from Australia, China, Japan, Malaysia, and Philippines (Lee et al. 2012; Shaw 1991). Based on our review, P. paullulla was intercepted once from Malaysia in 2014 at the port of Los Angeles, USA (BPI voucher 893085). This present study reports the establishment of P. paullula in Florida, USA infecting M. deliciosa.
Fulltext Use of Social Media for Cancer Prevention Through Neighborhood Social Cohesion: Protocol for a Feasibility Study

Oakley-Girvan I, Watterson JL, Jones C, Houghton LC, Gibbons MP, Gokal K, et al.

JMIR Res Protoc, 2021 Jul 30;10(7):e28147.
PMID: 34328445 DOI: 10.2196/28147

BACKGROUND: Social cohesion is associated with healthier behaviors and better health outcomes, and therefore may offer a mechanism for promoting better health. Low socioeconomic status (SES) communities face higher rates of chronic disease due to both community- and individual-level factors.
OBJECTIVE: The aim of this study is to leverage social cohesion to promote healthier behaviors and prevent chronic disease in a low SES community. This protocol outlines the methodology for a pilot study to assess the feasibility of an intervention (Free Time For Wellness [FT4W]) using a social networking platform (Nextdoor) with mothers living in an urban, low-income community to improve social cohesion and promote healthy behaviors.
METHODS: The study will involve three phases: (I) co-designing the intervention with mothers in the neighborhoods of interest, (II) implementing the intervention with community leaders through the social networking platform, and (III) evaluating the intervention's feasibility. Phase I of the study will include qualitative data collection and analysis from in-depth, semistructured interviews and a co-design group session with mothers. Phases II and III of the study include a pre- and postintervention survey of participating mothers. Neighborhood-level data on social cohesion will also be collected to enable comparison of outcomes between neighborhoods with higher and lower baseline social cohesion.
RESULTS: As of March 2021, recruitment and data collection for this study are complete. This protocol outlines our original study plan, although the final enrollment numbers and intervention implementation deviated from our initial planned methodology that is outlined in this protocol. These implementation learnings will be shared in subsequent publications of our study results.
CONCLUSIONS: Ultimately, this study aims to: (1) determine the barriers and facilitators to finding free time for wellness among a population of low-income mothers to inform the co-design process, and (2) implement and study the feasibility of an intervention that leverages social cohesion to promote physical activity in a community of low-income mothers. The results of this study will provide preliminary feasibility evidence to inform a larger effectiveness trial, and will further our understanding of how social cohesion might influence well-being.
INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR1-10.2196/28147.
Fulltext Free Time For Wellness: a co-designed intervention utilizing social networks to encourage physical activity for cancer prevention among low resourced mothers

Houghton LC, Gibbons MP, Shekelle J, Oakley-Girvan I, Watterson JL, Magsamen-Conrad K, et al.

BMC Public Health, 2021 10 07;21(1):1805.
PMID: 34620141 DOI: 10.1186/s12889-021-11775-9

BACKGROUND: Physical activity is central to chronic disease prevention. Low resource mothers face structural barriers preventing them from increasing their physical activity to reduce their chronic disease risk. We co-designed an intervention, with the ultimate goal of building social cohesion through social media to increase physical activity for low resourced mothers in urban settings.
METHODS: In 2019, we interviewed 10 mothers of children (
"Mother's Health and Well-Being Matters: Is a Mediated Social Cohesion Public Health Intervention Feasible?"

Jones C, Gibbons M, Magsamen-Conrad K, Ulanday KT, Watterson J, Oakley-Girvan I, et al.

Am J Health Promot, 2022 Mar;36(3):410-420.
PMID: 34907785 DOI: 10.1177/08901171211055317

PURPOSE: To test the feasibility of introducing 'Free Time for Wellness' (FT4W) an intervention to increase healthy behaviours and reduce the risk of cancer.
DESIGN: Feasibility study; Setting: Washington Heights, New York, USA is a low socioeconomic status area.
SUBJECTS: Mothers aged 18 and above with children under 12 years of age and living in Washington Heights were recruited.
INTERVENTION: FT4W, a community-based intervention delivered through a neighbourhood-based app, offering weekly dance and yoga classes, food pantry visits and group playdates. Childcare professionals cared for participants' children during wellness activities.
MEASURES: A bespoke before and after survey was designed and tested for its ability to collect relevant data to assess the impact of FT4W. Outcomes included recruitment rates, participation, attrition, acceptability, and success of the community champion.
ANALYSIS: Comparisons of proportions and means.
RESULTS: Twenty-one mothers participated in the study of which 90% attended ≥ 1 FT4W activity; 65% ≥ 2; 52% ≥ 3. The survey was completed by a 100% of participants indicating it was easy to understand and not too burdensome. All measures detected change in constructs from baseline to follow-up. Availability of childcare was the most commonly (66%) reported reason participants were able to engage in the offered wellness activities.
CONCLUSION: Conducting a larger-scale trial to assess the impact of FT4W is feasible considering 4 major lessons. (1) Recruitment, retention, and acceptability rates were high; however, moms need additional support to increase participation in wellness activities and improve tech literacy. (2) Research measures were sensitive enough to detect change, but the timing of assessments needs to be considered. (3) Participants greatly valued access to professional childcare. (4) The Community Champion is a necessary, but difficult role to fill that requires careful consideration by the Institutional Review Board (IRB).
Fulltext Structural dissection of two redox proteins from the shipworm symbiont Teredinibacter turnerae

Rajagopal BS, Yates N, Smith J, Paradisi A, Tétard-Jones C, Willats WGT, et al.

IUCrJ, 2024 Mar 01;11(Pt 2):260-274.
PMID: 38446458 DOI: 10.1107/S2052252524001386

The discovery of lytic polysaccharide monooxygenases (LPMOs), a family of copper-dependent enzymes that play a major role in polysaccharide degradation, has revealed the importance of oxidoreductases in the biological utilization of biomass. In fungi, a range of redox proteins have been implicated as working in harness with LPMOs to bring about polysaccharide oxidation. In bacteria, less is known about the interplay between redox proteins and LPMOs, or how the interaction between the two contributes to polysaccharide degradation. We therefore set out to characterize two previously unstudied proteins from the shipworm symbiont Teredinibacter turnerae that were initially identified by the presence of carbohydrate binding domains appended to uncharacterized domains with probable redox functions. Here, X-ray crystal structures of several domains from these proteins are presented together with initial efforts to characterize their functions. The analysis suggests that the target proteins are unlikely to function as LPMO electron donors, raising new questions as to the potential redox functions that these large extracellular multi-haem-containing c-type cytochromes may perform in these bacteria.
Evaluation of e-Lung automated quantitative computed tomography biomarkers in idiopathic pulmonary fibrosis

George PM, Rennison-Jones C, Benvenuti G, Sifostratoudaki A, Ottink FA, Bou-Zeid W, et al.

ERJ Open Res, 2024 Nov;10(6).
PMID: 39624378 DOI: 10.1183/23120541.00570-2024

BACKGROUND: In patients with idiopathic pulmonary fibrosis (IPF) there is a need to identify biomarkers that 1) are associated with increased risk of adverse outcome and 2) can be used to monitor treatment response or identify disease progression over time.
METHODS: Two consecutive cohorts of patients with IPF were accessed from the Open Source Imaging Consortium database. Automated computed tomography (CT) biomarkers of disease severity incorporating fibrotic and pulmonary vascular features (the reticulovascular score and weighted reticulovascular score (WRVS)) were studied. Relationships between imaging biomarkers, lung function and survival were analysed.
RESULTS: In separate test and validation cohorts, 168 and 176 patients with IPF respectively (median survival 2.6 years) were studied. A threshold of WRVS ≥15% at baseline CT was most strongly associated with transplant-free survival (HR 3.00, 95% CI 1.47-6.10, p=0.002) when adjusted for baseline forced vital capacity (FVC) and age. In patients with 12-month follow-up CT and lung function tests (n=89) an increase in 3% of WRVS (the minimal clinically important difference) was also significantly associated with reduced survival independent of FVC, and outperformed visual evaluation of progressive fibrosis.
CONCLUSIONS: WRVS is an automated CT biomarker which can identify patients with IPF at increased risk of progression and is able to reliably capture disease progression over time.
Fulltext The atmospheric chemistry of trace gases and particulate matter emitted by different land uses in Borneo

MacKenzie AR, Langford B, Pugh TA, Robinson N, Misztal PK, Heard DE, et al.

Philos Trans R Soc Lond B Biol Sci, 2011 Nov 27;366(1582):3177-95.
PMID: 22006961 DOI: 10.1098/rstb.2011.0053

We report measurements of atmospheric composition over a tropical rainforest and over a nearby oil palm plantation in Sabah, Borneo. The primary vegetation in each of the two landscapes emits very different amounts and kinds of volatile organic compounds (VOCs), resulting in distinctive VOC fingerprints in the atmospheric boundary layer for both landscapes. VOCs over the Borneo rainforest are dominated by isoprene and its oxidation products, with a significant additional contribution from monoterpenes. Rather than consuming the main atmospheric oxidant, OH, these high concentrations of VOCs appear to maintain OH, as has been observed previously over Amazonia. The boundary-layer characteristics and mixing ratios of VOCs observed over the Borneo rainforest are different to those measured previously over Amazonia. Compared with the Bornean rainforest, air over the oil palm plantation contains much more isoprene, monoterpenes are relatively less important, and the flower scent, estragole, is prominent. Concentrations of nitrogen oxides are greater above the agro-industrial oil palm landscape than over the rainforest, and this leads to changes in some secondary pollutant mixing ratios (but not, currently, differences in ozone). Secondary organic aerosol over both landscapes shows a significant contribution from isoprene. Primary biological aerosol dominates the super-micrometre aerosol over the rainforest and is likely to be sensitive to land-use change, since the fungal source of the bioaerosol is closely linked to above-ground biodiversity.
Fulltext Nitrogen management is essential to prevent tropical oil palm plantations from causing ground-level ozone pollution

Hewitt CN, MacKenzie AR, Di Carlo P, Di Marco CF, Dorsey JR, Evans M, et al.

Proc Natl Acad Sci U S A, 2009 Nov 3;106(44):18447-51.
PMID: 19841269 DOI: 10.1073/pnas.0907541106

More than half the world's rainforest has been lost to agriculture since the Industrial Revolution. Among the most widespread tropical crops is oil palm (Elaeis guineensis): global production now exceeds 35 million tonnes per year. In Malaysia, for example, 13% of land area is now oil palm plantation, compared with 1% in 1974. There are enormous pressures to increase palm oil production for food, domestic products, and, especially, biofuels. Greater use of palm oil for biofuel production is predicated on the assumption that palm oil is an "environmentally friendly" fuel feedstock. Here we show, using measurements and models, that oil palm plantations in Malaysia directly emit more oxides of nitrogen and volatile organic compounds than rainforest. These compounds lead to the production of ground-level ozone (O(3)), an air pollutant that damages human health, plants, and materials, reduces crop productivity, and has effects on the Earth's climate. Our measurements show that, at present, O(3) concentrations do not differ significantly over rainforest and adjacent oil palm plantation landscapes. However, our model calculations predict that if concentrations of oxides of nitrogen in Borneo are allowed to reach those currently seen over rural North America and Europe, ground-level O(3) concentrations will reach 100 parts per billion (10(9)) volume (ppbv) and exceed levels known to be harmful to human health. Our study provides an early warning of the urgent need to develop policies that manage nitrogen emissions if the detrimental effects of palm oil production on air quality and climate are to be avoided.
Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, et al.

Autophagy, 2016;12(1):1-222.
PMID: 26799652 DOI: 10.1080/15548627.2015.1100356

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