Variation in Coastal Macroinvertebrate Species Diversity on Intertidal Boulders in Trinidad, California.

Coastal environments of Humboldt County provide an optimal habitat for a diversity of macroinvertebrates. This study’s focus is to determine the differences in diversity of coastal macroinvertebrate (CM) species on intertidal boulders. Eleven CM species were visually counted within a one-square-meter quadrat along two height strata of five intertidal boulders. Based upon the Shannon-Wiener diversity index, diversity was measured between the CM species in the lower region (0-1 meter from base of boulder) and the upper region (1-2 meters from base of boulder). The resulting data showed the lower regions of the boulders had a higher average diversity rating, as compared to the upper boulder regions

Thiopurine monotherapy is effective in ulcerative colitis but significantly less so in Crohn’s disease: long-term outcomes for 11 928 patients in the UK inflammatory bowel disease bioresource

Objective: Thiopurines are widely used as maintenance therapy in inflammatory bowel disease (IBD) but the evidence base for their use is sparse and their role increasingly questioned. Using the largest series reported to date, we assessed the long-term effectiveness of thiopurines in ulcerative colitis (UC) and Crohn’s disease (CD), including their impact on need for surgery. Design: Outcomes were assessed in 11 928 patients (4968 UC, 6960 CD) in the UK IBD BioResource initiated on thiopurine monotherapy with the intention of maintaining medically induced remission. Effectiveness was assessed retrospectively using patient-level data and a definition that required avoidance of escalation to biological therapy or surgery while on thiopurines. Analyses included overall effectiveness, time-to-event analysis for treatment escalation and comparison of surgery rates in patients tolerant or intolerant of thiopurines. Results: Using 68 132 patient-years of exposure, thiopurine monotherapy appeared effective for the duration of treatment in 2617/4968 (52.7%) patients with UC compared with 2378/6960 (34.2%) patients with CD (p<0.0001). This difference was corroborated in a multivariable analysis: after adjusting for variables including treatment era, thiopurine monotherapy was less effective in CD than UC (OR 0.47, 95% CI 0.43 to 0.51, p<0.0001). Thiopurine intolerance was associated with increased risk of surgery in UC (HR 2.44, p<0.0001); with a more modest impact on need for surgery in CD (HR=1.23, p=0.0015). Conclusion: Thiopurine monotherapy is an effective long-term treatment for UC but significantly less effective in CD

Multistage and transmission-blocking targeted antimalarials discovered from the open-source MMV Pandemic Response Box

Chemical matter is needed to target the divergent biology associated with the different life cycle stages of Plasmodium. Here, we report the parallel de novo screening of the Medicines for Malaria Venture (MMV) Pandemic Response Box against Plasmodium asexual and liver stage parasites, stage IV/V gametocytes, gametes, oocysts and as endectocides. Unique chemotypes were identified with both multistage activity or stage-specific activity, including structurally diverse gametocyte-targeted compounds with potent transmission-blocking activity, such as the JmjC inhibitor ML324 and the antitubercular clinical candidate SQ109. Mechanistic investigations prove that ML324 prevents histone demethylation, resulting in aberrant gene expression and death in gametocytes. Moreover, the selection of parasites resistant to SQ109 implicates the druggable V-type H+-ATPase for the reduced sensitivity. Our data therefore provides an expansive dataset of compounds that could be redirected for antimalarial development and also point towards proteins that can be targeted in multiple parasite life cycle stages.Supplementary Data 1: Data of the supra-hexagonal plot in Figure 2ASupplementary Data 2: Complete dataset of all MMV PRB compounds’ activity on Plasmodium life cycle stagesSupplementary Data 3: Full SMFA dataset to support Figure 5CSupplementary Data 4: Transcriptome analysis of MMV1580488 (ML324) treated parasites to support Figure 6C.The Medicines for Malaria Venture and South African Technology Innovation Agency (TIA). This project was in part supported by the South African Medical Research Council with funds received from the South African Department of Science and Innovation, in partnership with the Medicines for Malaria Venture; and the DST/NRF South African Research Chairs Initiative Grant; and CSIR Parliamentary Grant funding as well as the Bill and Melinda Gates Foundation and the Australian NHMRC (APP1072217).http://www.nature.com/ncommshj2021BiochemistryGeneticsMicrobiology and Plant PathologyUP Centre for Sustainable Malaria Control (UP CSMC

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Mite communities within Protea infructescences in South Africa

Thesis (MScConEcol)--University of Stellenbosch, 2011.ENGLISH ABSTRACT: The role of mites as primary vectors of various fungi within Protea infructescences was recently confirmed and raised questions about their general diversity and their role within this unique niche. Although mites evidently form an integral part of Fynbos ecosystems and probably play a significant role in Protea population dynamics, there is a general void in our knowledge of mite diversity within the Cape Floristic Region. These organisms do not only affect ecological processes within the CFR, but also the economic value of Protea exports. This study sets out to describe mite communities within the infructescences of a variety Protea species. In the process, the role of various environmental variables and differences in host characteristics affecting these communities are also explored. A total of 24281 mite individuals, comprising of 36 morphospecies in 23 families, were collected from 16 surveyed Protea spp. Mite community structure and composition were significantly influenced by plant taxonomy, phenology and infructescence architecture in different Protea spp. At a temporal scale, infructescence age and season were influential factors on mite community structure. Collection locality significantly influenced mite communities within the infructescences of a single Protea sp. Host architecture had no influence on mite communities within a single host species. Geographic distance had no significant influence on mite community structure within Protea infructescences. This implies that factors particular to particular host species determine mite communities. These include factors such as the mode of pollination of the host plant, level of serotiny and plant life form. Numerous newly recorded mite species collected from Protea infructescences are also described in this study. An identification key to the Tydeidoidae of South Africa is provided here for the first time. This study forms a baseline dataset for future studies on the biodiversity of mites in this extremely diverse eco-region.AFRIKAANSE OPSOMMING: Die rol van myte as primêre vektore van verskeie funguses binne Protea vrugtekoppe is onlangs bevestig, en het vrae laat ontstaan oor hulle algemene diversiteit en rol binne hierdie unieke nis. Alhoewel myte duidelik ‘n integrale deel vorm van Fynbos ekosisteme en waarskynlik ‘n belangrike rol speel in Protea populasie-dinamika, is daar ‘n algemene leemte in ons kennis van mytdiversiteit binne die Kaapse Floristiese Ryk (KFR). Hierdie organismes affekteer nie slegs ekologiese prosesse binne die KFR nie, maar ook die ekonomiese waarde van Protea-uitvoere. Hierdie studie mik as vertrekpunt om die verkillende myt-gemeenskappe binne die vrugtekoppe van verskeie Protea spesies te beskryf. In die proses is die rol van verskillende omgewingsveranderlikes en verskille in gasheer kenmerke wat hierdie gemeenskappe affekteer, ook ondersoek. ‘n Totaal van 24281 myt individue, saamgestel uit 36 morfspesies in 23 families, mytgemeenskappe is beduidende beinvloed deur die taksonomie van die plant, die fenologie en die vrugtekop-argitektuur van verskillende Protea spesies. Op ‘n temporale skaal is gevind dat vrugtekop-ouderdom en seisoen beduidende faktore is in die samestelling van mytgemeenskapstruktuur. Versamel-lokaliteit het verder mytgemeenskappe binne die vrugtekoppe mytgemeenskappe binne ‘n enkele gasheerspesie getoon nie. Geografiese afstand het geen beduidende invloed op mytgemeenskapstruktuur binne Protea vrugtekoppe getoon nie. Dit faktore in soos die metode van bestuiwing van die gasheer plant, die vlak van saadhoudendheid van die Protea koppe en plant-lewensvorm. Verskeie nuwe myt spesies wat uit Protea vrugtekoppe versamel is, word ook in hierdie studie beskryf. ‘n Identifikasie-sleutel vir die Tydeidoidae van Suid-Afrika word verder vir die eerste keer hier verskaf. Hierdie studie vorm die basis datastel vir toekomstige studies van die biodiversiteit van myte in hierdie besonder diverse eko-omgewing

Mite (acari) ecology within protea communities in the Cape Floristic Region, South Africa

Thesis (PhD)--Stellenbosch University, 2018.ENGLISH ABSTRACT: Protea is a key component in the Fynbos Biome of the globally recognised Cape Floristic Region biodiversity hotspot, not only because of its own diversity, but also for its role in the maintenance of numerous other organisms such as birds, insects, fungi and mites. Protea is also internationally widely cultivated for its very showy inflorescences and, therefore, has great monetary value. Some of the organisms associated with these plants are destructive, leading to reduced horticultural and floricultural value. However, they are also involved in intricate associations with Protea species in natural ecosystems, which we still understand very poorly. Mites, for example, have an international reputation to negatively impact crops, but some taxa may be good indicators of sound management practices within cultivated systems. Their role in natural systems is even less well-understood. In this dissertation I explore the role of mites within Protea populations in both natural and cultivated systems, focussing on assemblages from inflorescences, infructescences and soil. Protea inflorescences and infructescences provide a niche for a unique assemblage of mites that have associations with a group of arthropod-associated fungi, the ophiostomatoid fungi. The mites feed on the fungi and carry their spores to new inflorescences as phoretic partners of Protea-pollinating beetles. As it was shown that some of the fungi have a panmictic population genetic structure over as much as 1000 km, it was assumed that organisms other than beetles must be responsible for this extremely long-range dispersal. Here I present the first concrete evidence of the ability of birds to vector spore-carrying mites to new Protea trees. I also provide evidence for a newly discovered mite-fungus mutualism within ornithophilous Protea neriifolia inflorescences between a Glycyphagus sp. mite and various species within the ophiostomatoid genus Sporothrix. New mite-mite commensalisms between the Proctolaelaps vandenbergi flower mite and the Glycyphagus sp. mite was also discovered and documented. In this intriguing system the Glycyphagus sp. mites have a mutualistic association with species in the fungal genus Sporothrix. These small mites are phoretic on the larger P. vandenbergi mites that, in turn, are phoretic on Protea pollinating birds, explaining genetic evidence for the long distance dispersal of the fungi. It is well-known that flower-associated mites such as Proctolaelaps kirmsei are nectar and pollen thieves of hummingbird pollinated plants in America. These mites reduce nectar and pollen rewards for pollinators, which influences pollinator visitation patterns and decreases available pollen for dispersal, thereby negatively influencing seed-set and plant population dynamics. This phenomenon has, however, not been investigated in similar systems in other parts of the world. I, therefore, set out to determine the possible role of P. vandenbergi flower mites, the most abundant flower mite within Protea inflorescences, as pollen and nectar thieves and as secondary pollinators of P. neriifolia. I provide the first evidence that P. vandenbergi feeds on nectar and pollen and that its reproduction is strongly linked to pollen availability. Nectar consumption rates of P. vandenbergi likely have little effect on total nectar availability for pollinators, but they can significantly reduce available pollen in inflorescences and may ultimately negatively influence seed set. This is exacerbated by the fact that I could show that they do not contribute to Protea pollination. There is rising global concern about the negative impact of land transformation on natural ecosystems. With the increase in land transformation for agriculture, natural flora is replaced by intensively managed exotic crops. This has devastating effects on biodiversity and ecosystem services. Ecologically more friendly management systems are thus urgently required. One proposed such system is the production of native plants as crops, as these can provide known niche space for native organisms including beneficial ones, which may reduce required management inputs. Protea is of high ecological significance and economic value as it is harvested for export within both natural and cultivated systems in South Africa. Although mites associated with these plants can be beneficial, they are usually regarded as pests and/or organisms that pose significant phytosanitary risks. I, therefore, investigated the impact of Protea repens cultivation on the mite assemblages associated with inflorescences, infructescences (the crop products where the presence of mites pose agricultural risks) and the rhizosphere (where most of the agriculturally beneficial mite species would reside). I show that this indigenous crop may well be able to maintain a large native mite biodiversity component in all three of these niches. However, essential environmental services such as the maintenance of sound soil ecology may be hindered even with very low management intensity. Results also indicated that current intensive pest management strategies do not effectively control mites associated with inflorescences. Continued improvement of post-harvest pest management practices, as difficult as these are for sensitive and fresh produce, are urgently needed. Less reliance on intensive management systems during the production phases of Protea inflorescences would also help preserve some natural ecological processes, such as the ones discovered and described in this dissertation.AFRIKAANSE OPSOMMING: Protea is ʼn sleutelkomponent in die Fynbos Bioom van die wêreldwyd erkende Kaapse Floristiese Streek biodiversiteit sentrum, nie net as gevolg van die genus se eie diversiteit nie, maar ook vir sy rol in die behoud van verskeie organismes soos voëls, insekte, fungi en myte. Protea word ook internasionaal wyd gekweek vir hul baie aanskoulike bloeiwyses en is daarom van groot monetêre belang. Sommige van die organismes wat met hierdie plante geassosieer word, is destruktief, wat lei tot verminderde hortologiese en snyblom waarde. Hulle is egter ook betrokke in komplekse assosiasies met Protea spesies in hul natuurlike ekosisteme, wat ons steeds baie swak verstaan. Myte, byvoorbeeld, het ʼn internasionale reputasie daarvoor dat hulle gewasse negatief beïnvloed, maar sommige taksa mag goeie aanduiders wees van gesonde bestuurspraktyke binne gekultiveerde sisteme. Hulle rol in natuurlike sisteme word nog swakker verstaan. In hierdie dissertasie verken ek die rol van myte binne Protea populasies in beide natuurlike en gekultiveerde sisteme, en fokus op groeperings vanuit bloeiwyses, saadkeëls en die grond. Protea bloeiwyses en saadkeëls bied ʼn nis vir ʼn unieke versameling myte wat assosiasies het met ʼn groep fungi wat weer met geleedpotiges geassosieer word, naamlik die ophiostomatoide fungi. Die myte voed op die fungi en dra hul spore na nuwe bloeiwyses as foretiese maats van Protea-bestuiwende kewers. Aangesien dit getoon is dat sommige fungi ʼn panmiktiese populasie genetiese struktuur oor meer as 1000 km het, is dit aangeneem dat ander organismes as kewers verantwoordelik moes wees vir hierdie geweldige langafstand verspreiding. Hier bied ek die eerste konkrete bewyse van die vermoë van voëls om as vektore van spoordraende myte na nuwe Protea bome op te tree. Ek verskaf ook bewyse vir ʼn nuut ontdekte myt-fungus mutualisme binne voëlbestuifde Protea neriifolia bloeiwyses tussen ‘n Glycyphagus sp. myt en verskeie Sporothrix spp. fungi. Nuwe myt-myt kommensialismes tussen die Proctolaelaps vandenbergi blommyte en die Glycyphagus sp. myte is ook ontdek en gedokumenteer. In hierdie interessante sisteem het die Glycyphagus sp. myte ʼn mutualistiese assosiasie met die Sporothrix spp. fungi. Hierdie klein myte is foreties op die groter P. vandenbergi myte wat op hulle beurt weer foreties is op Protea-bestuiwende voëls, wat die genetiese bewyse van langafstand vervoer van die fungi verduidelik. Dis is goed bekend dat blomgeassosieerde myte soos Proctolaelaps kirmsei nektar en stuifmeel diewe van kolibrie bestuifde plante in Amerika is. Hierdie myte verminder nektar en stuifmeel belonings vir bestuiwers, wat bestuiwer besoekpatrone beïnvloed en die hoeveelheid beskikbare stuifmeel en nektar verminder. Dit beïnvloed saad-vorming en plant populasiedinamika negatief. Hierdie fenomeen is egter nog nooit in eenderse sisteme in ander dele van die wêreld ondersoek nie. Ek het daarom ten doel gehad om die moontlike rol van P. vandenbergi blommyte, die mees volop blommyt binne Protea bloeiwyses, as stuifmeel en nektardiewe en as sekondêre bestuiwers van P. neriifolia te ondersoek. Ek verskaf die eerste bewyse dat P. vandenbergi op nektar en stuifmeel voed en dat sy reproduksie sterk gekoppel is aan die beskikbaarheid van stuifmeel. Tempo van nektarinname het waarskynlik min effek op die totale beskikbaarheid vir bestuiwers, maar hulle kan die hoeveelheid beskikbare stuifmeel in die bloeiwyse beduidend verminder, en mag so uiteindelik saadvorming negatief beïnvloed. Dit word vererger deur die feit dat ek kon wys dat hulle nie bydra tot Protea bestuiwing nie. Daar is toenemende globale kommer oor die negatiewe impak van landtransformasie op natuurlike ekosisteme. Met die toename in landtransformasie vir landbou, word natuurlike flora verplaas deur intensief beheerde uitheemse gewasse. Dit het verwoestende effekte op biodiversiteit en ekosisteem dienste. Ekologies vriendeliker bestuursisteme word dus dringend benodig. Een voorgestelde sodanige sisteem is die produksie van natuurlike plante as gewasse, aangesien hulle natuurlike nisspasies vir inheemse organinsmes, insluitend voordeliges, kan bied, wat die bestuursinsette wat benodig word mag verminder. Protea is van groot ekologiese en ekonomiese belang aangesien dit geoes word vir uitvoere in beide natuurlike en aangeplante sisteme in Suid Afrika. Alhoewel myte wat met hierdie plante geassosieer word voordelig kan wees, word hulle gewoonlik as peste en/of organisme wat ʼn fitosanitêre risiko dra beskou. Ek het daarom die impak van Protea repens aanplanting op myt samestellings wat met bloeiwyses, saadkeëls (die gewasprodukte waar die aanwesigheid van myte landboukundige gevare inhou) en die risosfeer (waar meeste van die landboukundig voordelige myte aangetref word) geassosieer word ondersoek. Ek wys dat hierdie inheemse gewas wel in staat mag wees om ʼn groot natuurlike myt biodiversiteit in al drie hierdie nisse te onderhou. Essensiële omgewingsdienste soos die voorsiening van gesonde grond-ekologie mag egter verhinder word deur self lae bestuursintensiteit. Resultate het ook aangetoon dat die huidige intensiewe pesbestrydings strategieë nie myte wat met bloeiwyses geassosieer word doeltreffend bestry nie. Volgehoue verbetering van na-oes pesbeheer praktyke word dringend benodig, ongeag hoe moeilik hulle toepassing is vir sensitiewe en vars produkte. ʼn Verminderde afhanklikheid van hierdie intensiewe bestuursisteme tydens die produksie fases van Protea bloeiwyses sal ook help om sommige natuurlike ekosisteem prosesse te bewaar, soos dié wat in hierdie dissertasie ontdek en beskryf is

Biotic and abiotic constraints that facilitate host exclusivity of Gondwanamyces and Ophiostoma on Protea

Estimations of global fungal diversity are hampered by a limited understanding of the forces that dictate host exclusivity in saprobic microfungi. To consider this problem for Gondwanamyces and Ophiostoma found in the flower heads of Protea in South Africa, we determined the role of various factors thought to influence their host exclusivity. Results showed that various biotic and abiotic factors influence the growth and survival of these fungi in vitro. Monitoring temperature and relative humidity (RH) fluctuations within infructescences in vivo revealed considerable microclimatic differences between different Protea spp. Fungal growth and survival at different RH levels experienced in the field suggested that this factor does not play a major role in host exclusivity of these fungi. Maximum temperatures within infructescences and host preferences of the vectors of Gondwanamyces and Ophiostoma appear to play a substantial part in determining colonisation of Protea in general. However, these factors did not explain host exclusivity of specific fungal species towards particular Protea hosts. In contrast, differential growth of fungal species on media containing macerated tissue of Protea showed that Gondwanamyces and Ophiostoma grow best on tissue from their natural hosts. Thus, host chemistry plays a role in host exclusivity of these fungi, although some species grew vigorously on tissue of Protea spp. with which they are not naturally associated. A combination of host chemistry and temperature partially explains host exclusivity, but the relationship for these factors on the tested saprobic microfungi and their hosts is clearly complex and most likely includes combinations of various biotic and abiotic factors including those emerging from this study.National Research Foundation (NRF) and the NRF/ DST Centre of Excellence in Tree Health Biotechnology (CTHB).http://www.elsevier.com/locate/funbionf201

Birds mediate a fungus-mite mutualism

Mutualisms between ophiostomatoid fungi and arthropods have been well documented. These fungi commonly aid arthropod nutrition and, in turn, are transported to new niches by these arthropods. The inflorescences of Protea trees provide a niche for a unique assemblage of ophiostomatoid fungi. Here, mites feed on Sporothrix fungi and vector the spores to new niches. Protea-pollinating beetles transport the spore-carrying mites between Protea trees. However, many Protea species are primarily pollinated by birds that potentially play a central role in the Protea-Sporothrix-mite system. To investigate the role of birds in the movement of mites and/or fungal spores, mites were collected from Protea inflorescences and cape sugarbirds, screened for Sporothrix fungal spores and tested for their ability to feed and reproduce on the fungal associates. Two mite species where abundant in both Protea inflorescences and on cape sugarbirds and regularly carried Sporothrix fungal spores. One of these mite species readily fed and reproduced on its transported fungal partner. For dispersal, this mite (a Glycyphagus sp.) attached to a larger mite species (Proctolaelaps vandenbergi) which, in turn, were carried by the birds to new inflorescences. The results of this study provide compelling evidence for a new mite-fungus mutualism, new mite-mite commensalisms and the first evidence of birds transporting mites with Sporothrix fungal spores to colonise new Protea trees.The Department of Science and Technology/National Research Foundation Centre of Excellence in Tree Health Biotechnology and the Harry Crossley Foundation.http://link.springer.com/journal/2482019-05-01hj2018Forestry and Agricultural Biotechnology Institute (FABI

Frequent Suboptimal Thermocycler Ramp Rate Usage Negatively Impacts GenoType MTBDRsl VER 2.0 Performance for Second-Line Drug-Resistant Tuberculosis Diagnosis

Strengthening second-line drug-resistant tuberculosis (TB) detection is a priority. GenoType MTBDRplus VER 2.0 performance is reduced with non-recommended ramp rate usage (temperature change speed between PCR cycles); however, ramp rate's effect on GenoType MTBDRsl VER 2.0 (MTBDRsl) performance, is unknown. Fifty-two Xpert MTB/RIF Ultra-positive rifampicin-resistant smear-negative sputa and a Mycobacterium tuberculosis dilution series were tested at a manufacturer-recommended (2.2°C/second) or suboptimal (4.0°C/second) ramp rate. M. tuberculosis-complex-DNA positivity, indeterminates, fluoroquinolone- and second-line injectable-resistance accuracy, banding differences, and, separately, inter-reader variability were assessed. Five (39%) of 13 re-surveyed laboratories did not use the manufacturer-recommended ramp rate. On sputum, 2.2°C/second improved indeterminates versus 4.0°C/second (0 of 52 versus 7 of 51; P = 0.006), incorrect drug-class diagnostic calls (0 of 104 versus 6 of 102; P = 0.013), and incorrect banding calls (0 of 1300 versus 54 of 1275; P &lt; 0.001). Similarly, 2.2°C/second improved valid results [(52 of 52 versus 41 of 51; +21% (P = 0.001)] and banding call inter-reader variability [34 of 1300 (3%) versus 52 of 1300 (4%); P = 0.030]. At the suboptimal ramp rate, false-resistance and false-susceptible calls resulted from wild-type band absence rather than mutant band appearance, resulting in misclassification of moxifloxacin resistance level from high-to-low. Suboptimal ramp rate contributes to poor MTBDRsl performance. Laboratories must ensure that the manufacturer-recommended ramp rate is used