Search

Walter Pater's European Imagination, by Lene Ostermark-Johansen; pp. xvii + 396. Oxford: Oxford University Press, 2022, $130.00. Walter Pater is a notoriously difficult writer to place. A classical scholar and [...]

Earlier spring warming and anadromous fish migrations prompted by climate change are linked to shorter freshwater residency. Impacts of phenological change on anadromous fish populations are poorly understood with limited studies focused on iteroparous non-salmonids. We assessed freshwater residence time and reproductive success in an iteroparous clupeid, alewife (Alosa pseudoharengus) using a pedigree analysis and otolith-based spawning dates from captured juveniles. The primary objectives were to (1) estimate adult spawning duration in a freshwater pond (freshwater residence time) and (2) evaluate adult freshwater residence time, arrival date, length, sex, and reproductive success across 2 years in one system. Estimated freshwater residence times varied widely (1-64 days), and longer residence times were associated with earlier arrival dates, higher reproductive success, and more mating events. Longer freshwater residence times may allow alewife to spawn with more mates, produce more gametes, and experience a range of spawning and nursery conditions. Plasticity in alewife freshwater residence time could support earlier and shorter migration periods but may result in lower reproductive output if adults spend less time in freshwater ponds. Key words: phenology, river herring, anadromous fish, iteroparous fish, clupeids, Introduction Global climate change is likely to result in the adaptation or extirpation of many organisms. One frequent adaptation to climate change is altered phenology or changes in the timing [...]

CLOSE ENCOUNTERS OF THE FUNGAL KIND In pursuit of remarkable mushrooms RICHARD FORTEY 336pp. William Collins. 25 [pounds sterling]. Fungi can be found on all continents, thriving even in the [...]

Although human fragmentation of freshwater habitats is ubiquitous, the genetic consequences of isolation and a roadmap to address them are poorly documented for most fishes. This is unfortunate, because translocation for genetic rescue could help mitigate problems. We used genetic data (32 SNPs) from 203 populations of westslope cutthroat trout (Oncorhynchus clarkii lewisi) to (1) document the effect of fragmentation on genetic variation and population structure, (2) identify candidate populations for genetic rescue, and (3) quantify the potential benefits of strategic translocation efforts. Human-isolated populations had substantially lower genetic variation and elevated genetic differentiation, indicating that many populations are strongly influenced by random genetic drift. Based on simple criteria, 23 populations were candidates for genetic rescue, which represented a majority (51%) of suitable populations in one major region (Missouri drainage). Population genetic theory suggests that translocation of a small number of individuals (~5 adults) from nearby populations could dramatically increase heterozygosity by up to 58% (average across populations). This effort provides a clear template for future conservation of westslope cutthroat trout, while simultaneously highlighting the potential need for similar efforts in many freshwater species. Si la fragmentation des habitats d'eau douce causee par l'activite humaine est ubiquiste, les consequences genetiques de l'isolement et une feuille de route pour s'y attaquer demeurent mal documentees pour la plupart des poissons. C'est dommage, puisque le deplacement a des fins de sauvegarde genetique pourrait aider a attenuer certains problemes. Nous avons utilise des donnees genetiques (32 SNP) de 203 populations de truites fardees versant de l'Ouest (Oncorhynchus clarkii lewisi) pour (1) documenter l'effet de la fragmentation sur la variation genetique et la structure des populations, (2) cerner des populations candidates a la sauvegarde genetique et (3) quantifier les avantages potentiels d'efforts de deplacement strategique. Les populations isolees par l'activite humaine presentent une variation genetique considerablement moindre et une differentiation genetique plus grande que les autres populations, ce qui indique qu'une derive genetique aleatoire influence fortement de nombreuses populations. A la lumiere de criteres simples, 23 populations sont de bonnes candidates a la sauvegarde genetique, representant une majorite (51 %) des populations convenables dans une grande region (le bassin versant de la riviere Missouri). La theorie de la genetique des populations indiquerait en outre que le deplacement d'un petit nombre d'individus (~5 adultes) de populations voisines pourrait entrainer une augmentation marquee, de jusqu'a 58 %, de l'heterozygotie (moyenne pour toutes les populations). L'etude constitue manifestement un modele pour les efforts de conservation futurs de la truite fardee versant de l'Ouest, tout en soulignant la possible necessite d'efforts semblables pour de nombreuses autres especes d'eau douce. [Traduit par la Redaction], Introduction Freshwater species are unfortunately positioned as the most-imperiled group of biota on earth (Tickner et al. 2020), and populations of freshwater vertebrates are declining at faster rates than either [...]

Trout and salmon commonly coexist in stream networks. Exploring similarities and differences among species can help explain coexistence and invasive ability. Here, we describe spatial distribution, cohort strengths and size-at-age of three co-occurring species in a small stream network. Spatial distributions varied dramatically among species; native brook trout (Salvellinus fontinalis) occupied all stream reaches, naturalized brown trout (Salmo trutta) were found in the mainstem and lower portions of tributaries and fry-stocked Atlantic salmon (Salmo salar) were limited to the mainstem. Size-at-age also differed among species, Atlantic salmon were consistently the smallest, brook trout were intermediate in size and brown trout were the largest. Despite size differences, mean lengths of brook trout and brown trout were highly correlated among years. Cohort strengths varied considerably across years but were also highly correlated for the two trout species, suggesting strong environmental control on cohort strength and a reduced role for species interactions. At low densities, we observed strong negative effects of density on body sizes and weaker effects otherwise. Overall, these results suggest differences in spatial distribution combined with similarities in response to environmental variation contribute to species coexistence in this small steam network. Des truites et saumons coexistent souvent dans des reseaux hydrographiques. L'examen des similitudes et differences entre especes peut aider a expliquer cette coexistence et la capacite d'envahissement. Nous decrivons la repartition dans l'espace, la force des cohortes et la taille selon l'age de trois especes coexistant dans un petit reseau hydrographique. Les repartitions spatiales presentent des variations considerables entre especes; les ombles de fontaine (Salvellinusfontinalis) indigenes occupent tous les tronqons, les truites brunes (Salmo trutta) naturalisees sont observees dans le cours d'eau principal et les cours inferieurs d'affluents et les saumons atlantiques (Salmo salar) ensemences en tant qu'alevins se limitent au cours d'eau principal. La taille selon l'age varie egalement d'une espece a l'autre, la taille des saumons atlantiques etant uniformement plus petite, les ombles de fontaine etant de taille intermediaire et les truites brunes presentant les plus grandes tailles. Malgre les differences de taille, les longueurs moyennes des ombles de fontaine et des truites brunes sont fortement correlees au sein d'une meme annee. La force des cohortes varie considerablement d'une annee a l'autre, mais est aussi fortement correlee pour les deux especes de truites, ce qui indiquerait que les conditions environnementales exercent un grand controle sur la force des cohortes et que les interactions des especes jouent un role mineur. Nous observons de forts effets negatifs de la densite sur la taille du corps a de faibles densites, mais des effets plus faibles par ailleurs. Globalement, ces resultats indiqueraient que des differences sur le plan de la repartition spatiale combinees a des similitudes des reactions aux variations de conditions environnementales jouent un role dans la coexistence d'especes dans ce petit reseau hydrographique. [Traduit par la Redaction], Introduction Species responses to both extrinsic (environmental) and intrinsic (population dynamics) factors are key to understanding patterns of distribution and abundance. Co-occurring species frequently exhibit differences in habitat use across [...]

Removal of non-native fish populations can be crucial to the conservation of native species, but often presents a complex challenge for managers. The goal of Trojan Y chromosome (TYC) programs is to skew the non-native sex ratio until only males remain, leading to eradication. We present results from a simulation model used to explore effects of alternative management approaches on an in-progress mechanical removal and TYC program to eradicate non-native brook trout (Salvelinus fontinalis). Simulation results indicated that stocking fingerling YY males (~137 mm) was more effective than stocking catchable- sized YY males (~230 mm), although questions about intercohort competition warrant further investigation. Increasing the proportion of mature fingerling YY males reduced treatment time by increasing the number of YY male spawners and increasing density- dependent mortality on young, mature wild brook trout. Maximizing the spatial distribution of YY male releases may be crucial to program success but is also dependent upon immediate dispersal movements. Principles derived from our results can be broadly applied to the management of other aquatic invaded systems using TYC programs to eradicate non-native species. Si le retrait de populations de poissons non indigenes peut s'averer crucial pour la conservation d'especes indigenes, il constitue souvent un defi complexe pour les gestionnaires. L'objectif des programmes bases sur un chromosome Y << cheval de Troie >> (CYCT) est de modifier le rapport de masculinite d'especes non indigenes jusqu'a ce que seuls des males demeurent, menant a leur eradication. Nous presentons les resultats d'un modele de simulation utilise pour explorer les effets de differentes approches de gestion sur un programme en cours de retrait mecanique et base sur les CYCT visant l'eradication d'ombles de fontaine (Salvelinus fontinalis) non indigenes. Les resultats de simulations indiquent que l'ensemencement d'alevins males YY d'un an (~137 mm) est plus efficace que l'ensemencement de males YY de taille exploitable (~230 mm), bien que des questions concernant la concurrence entre cohortes necessitent un examen plus pousse. Une plus grande proportion d'alevins males YY matures reduit la duree du traitement en rehaussant le nombre de geniteurs males YY et la mortalite dependante de la densite des jeunes ombles de fontaine sauvages matures. La maximisation de la repartition spatiale des lachers de males YY pourrait constituer un element cle du succes de tels programmes, mais depend aussi des deplacements de dispersion immediats. Les principes derives de nos resultats peuvent s'appliquer plus largement a la gestion d'autres systemes aquatiques envahis par le recours a des programmes bases sur les CYCT pour eradiquer des especes non indigenes. [Traduit par la Redaction], Introduction The establishment and spread of non-native fish species present substantial challenges for the conservation and management of natural resources (Havel et al. 2015). One approach to the removal of [...]

Climate warming is expected to have substantial impacts on native trout across the Rocky Mountains, but there is little understanding of how these changes affect future distributions of co-occurring native fishes within population strongholds. We used mixed-effects logistic regression to investigate the role of abiotic (e.g., temperature) and biotic factors (bull trout presence, Salvelinus confluentus) on distributions of westslope cutthroat trout (Oncorhynchus clarkii lewisi; WCT) in the North Fork Flathead River, USA and Canada. The probability of WCT presence increased with stream temperature and decreased with channel gradient and bull trout presence, yet the effect of bull trout was reduced with increasing pool densities. Combining this model with spatially explicit stream temperature projections, we predict a 29% increase in suitable habitat under high emissions through 2075, with gains at mid-elevation sites predicted to exceed bull trout thermal tolerances and high-elevation sites expected to become more thermally suitable for WCT. Our study illustrates the importance of considering abiotic and biotic drivers to assess species response to climate change, helping to guide local- scale climate adaptation and management. S'il est prevu que le rechauffement climatique aura des impacts considerables sur les truites et ombles dans toute la region des montagnes Rocheuses, la comprehension de l'incidence de ces changements sur la repartition future de poissons indigenes cooccurrents dans des regions de fortes populations est tres limitee. Nous utilisons la regression logistique a effets mixtes pour examiner le role de facteurs abiotiques (p. ex. la temperature) et biotiques (la presence d'ombles a tete plate, Salvelinus confluentus) sur la repartition de la truite fardee versant de l'ouest (Oncorhynchus clarkii lewisi; TFVO) dans la riviere North Fork Flathead (Etats-Unis et Canada). La probabilite de la presence de TFVO augmente avec la temperature du cours d'eau et diminue avec la pente du chenal et la presence d'ombles a tete plate, une plus grande densite de fosses etant toutefois associee a un effet moindre de la presence d'ombles a tete plate. En combinant ce modele a des projections spatialement explicites de la temperature des cours d'eau, nous predisons une augmentation de cette derniere de 29 % dans les habitats convenables pour des conditions d'emissions fortes jusqu'en 2075, les augmentations dans les sites de moyenne altitude depassant la fourchette de tolerance thermique des ombles a tete plate et les sites de haute altitude devenant plus convenables du point de vue thermique pour la TFVO. L'etude illustre l'importance de tenir compte de facteurs abiotiques et biotiques dans l'evaluation des reactions des especes aux changements climatiques et aide a orienter les mesures d'adaptation climatique et la gestion a l'echelle locale. [Traduit par la Redaction], Introduction Global climate change is causing many species to shift their distributions poleward and towards higher altitudes to track changes in optimal habitat (Parmesan 2006). This is particularly true for [...]

The number of effective breeders ([N.sub.b]) has been touted as a means to monitor freshwater fishes, but the realized application of [N.sub.b] has been limited. Using genetic monitoring data for two Arctic grayling (Thymallus arcticus) populations of conservation concern, we describe temporal trends in genetic variation and [N.sub.b], determine how sampling and variance in reproductive success influence estimates of [N.sub.b], and quantify the relationship among [N.sub.b], effective population size (Ne), and adult abundance ([N.sub.c]). Temporal trends in allelic richness ([A.sub.R]) and [N.sub.b] tracked known or suspected population trajectories. [N.sub.b] increased in one population where there has been extensive conservation action, and both [N.sub.b] and [A.sub.R] tracked a decline in the other population where harsh winter conditions have resulted in overwinter mortality events. After accounting for population demography, [N.sub.e] estimates for each population were 190.7 and 308.8. Overall, this study demonstrates that temporal genetic data effectively resolve demographic and evolutionary status and trend in Arctic grayling, provides insight into the demographic factors that influence genetic variation, and emphasizes the value of temporal genetic data for conservation and management. Il a ete propose que le nombre de geniteurs effectifs ([N.sub.b]) pourrait constituent un moyen de surveillance des poissons d'eau douce, mais les applications qui en ont ete faites sont limitees. En utilisant des donnees de surveillance genetique pour deux populations d'ombres arctiques (Thymallus arcticus) dont la conservation est preoccupante, nous decrivons les tendances temporelles de la variation genetique et de [N.sub.b], determinons l'influence de l'echantillonnage et de la variance du succes de reproduction sur les estimations de [N.sub.b] et quantifions la relation entre [N.sub.b], la taille effective de la population (Ne) et l'abondance des adultes ([N.sub.c]). Les tendances temporelles de la richesse allelique ([A.sub.R]) et de [N.sub.b] coincident avec des trajectoires demographiques connues ou soupqonnees. [N.sub.b] a augmente dans une population qui a fait l'objet de vastes efforts de conservation, et tant [N.sub.b] que Ar temoignent d'un declin dans l'autre population, qui a connu des episodes de mortalite hivernale en raison d'hivers rigoureux. Apres prise en compte de la demographie des populations, les valeurs estimees de [N.sub.e] pour les deux populations etaient de 190,7 et 308,8. Globalement, l'etude demontre que des donnees genetiques temporelles permettent de determiner l'etat et les tendances demographiques et d'evolution chez les ombres arctiques, fournit de l'information sur les facteurs demographiques qui influencent la variation genetique et souligne l'importance des donnees genetiques temporelles pour la conservation et la gestion. [Traduit par la Redaction], Introduction Although population genetic data and theory were integral in forming the field of conservation biology (Soule 1985), systematic monitoring of intraspecific genetic variation remains neglected in the majority of [...]

Environmental drivers of population vital rates, such as temperature and precipitation, often vary at short time scales, and these fluctuations can have important impacts on population dynamics. However, relationships between survival and environmental conditions are typically modeled at coarse temporal scales, ignoring the role of daily environmental variation in survival. Our goal was to determine the importance of fine-scale temporal variation in survival to population dynamics of stream salmonids. We extended the Cormack-Jolly-Seber model to estimate daily survival rates from seasonal samples of individually marked brook trout (Salvelinus fontinalis) in a stream network. Daily variation in temperature and flow were strongly associated with survival, but relationships varied between juvenile and adult trout and among streams. In all streams, juveniles had higher mortality in warm, low-flow conditions, but in the two larger streams, cold, high-flow conditions also reduced juvenile survival. Adult survival decreased during low flows, particularly in the fall spawning period. Differing survival responses among stream network components to short-term environmental events created shifts in optimal location for maximum survival across life stages, seasons, and years. Les facteurs environnementaux qui influencent les indices vitaux dans les populations, comme la temperature et les precipitations, varient souvent a de courtes echelles temporelles, et ces fluctuations peuvent avoir des effets importants sur la dynamique des populations. Cependant, les relations entre la survie et les conditions environnementales sont souvent modelisees a des echelles temporelles grossieres, evacuant du coup le role des variations environnementales journalieres sur la survie. Notre objectif etait de determiner l'importance de variations temporelles de courte duree de la survie pour la dynamique de populations de salmonides de cours d'eau. Nous avons elargi le modele de Cormack-Jolly-Seber pour estimer les taux de survie journaliers a partir d'echantillons saisonniers d'ombles de fontaine (Salvelinus fontinalis) etiquetes individuellement dans un reseau hydrographique. Les variations journalieres de temperature et de debit etaient fortement associees a la survie, mais les relations etaient differentes entre les juveniles et les adultes et d'un cours d'eau a l'autre. Dans tous les cours d'eau, les juveniles presentaient un taux de mortalite plus eleve dans des conditions chaudes et de faible debit, mais dans les deux cours d'eau plus grands, des conditions froides et de debit fort reduisaient egalement la survie des juveniles. La survie des adultes diminuait durant de faibles debits, particulierement durant la saison de frai automnale. Des reactions differentes de la survie dans differentes composantes d'un reseau hydrographique a des episodes environnementaux de courte duree modifiaient l'emplacement optimal pour une survie maximum pour les differentes etapes de cycle de vie et les differentes saisons et annees. [Traduit par la Redaction], Introduction Drivers of population vital rates, such as temperature and stream-flow, often vary at short time scales, and these fluctuations can have important impacts on population dynamics. However, studies of [...]

Environmental conditions can influence biological characteristics, such as phenology and body size, with important consequences for organismal fitness. Examining these fitness consequences under natural conditions through genetic pedigree reconstruction offers a lens into potential population responses to changing environments. Over 3 years (2013-2015), we introduced adult alewife (Alosa pseudoharengus), anadromous, iteroparous clupeids, into one Massachusetts (USA) lake to complete the first detailed examination of this species' mating system and assess relationships among body size, reproductive timing, and seasonal reproductive success. We reconstructed pedigrees using 15 microsatellites and genotypes from all possible parents and samples of naturally produced offspring within 4 months of hatching. In each of the 3 study years, spawning adults had multiple mates and spawned multiple times. Larger females that arrived and were translocated earlier had higher reproductive success. Declining body size and altered migration timing, through an influence on reproductive success, can influence population vital rates and productivity over time. Les conditions ambiantes peuvent influencer des caracteristiques biologiques comme la phenologie et la taille du corps, ce qui peut avoir d'importantes consequences sur l'aptitude des organismes. L'examen de ces consequences sur l'aptitude dans des conditions naturelles par la reconstitution du pedigree genetique jette un eclairage sur les reactions possibles de populations a des milieux changeants. Sur une periode de 3 ans (2013-2015), nous avons introduit des gaspareaux (Alosa pseudoharengus), des clupeides iteropares anadromes, dans un lac du Massachusetts (Etats-Unis) afin de realiser le premier examen detaille du systeme d'accouplement de cette espece et evaluer les relations entre la taille du corps, le moment de la reproduction et le succes de reproduction saisonnier. Nous avons reconstitue les pedigrees en utilisant 15 microsatellites et des genotypes de tous les parents et echantillons possibles de la progeniture produite naturellement, dans les 4 mois suivant l'eclosion. Durant chacune des 3 annees de l'etude, les adultes geniteurs se sont accouples avec plus d'un individu et ont fraye a plusieurs reprises. Les femelles plus grandes arrivees et ayant ete reimplantees plus tot avaient un plus grand succes de reproduction. La diminution de la taille du corps et la modification du moment de la migration au fil du temps, par leur incidence sur le succes de reproduction, peuvent influencer les indices vitaux et la productivite d'une population., Introduction Individual reproductive success provides an important link between phenotypic variation and population dynamics (Kinnison and Hairston 2007; Pelletier et al. 2007; Wright and Trippel 2009; Schoener 2011). Parental characteristics [...]

Cyclic dinucleotides (CDNs) have central roles in bacterial homeostasis and virulence by acting as nucleotide second messengers. Bacterial CDNs also elicit immune responses during infection when they are detected by pattern-recognition receptors in animal cells. Here we perform a systematic biochemical screen for bacterial signalling nucleotides and discover a large family of cGAS/DncV-like nucleotidyltransferases (CD-NTases) that use both purine and pyrimidine nucleotides to synthesize a diverse range of CDNs. A series of crystal structures establish CD-NTases as a structurally conserved family and reveal key contacts in the enzyme active-site lid that direct purine or pyrimidine selection. CD-NTase products are not restricted to CDNs and also include an unexpected class of cyclic trinucleotide compounds. Biochemical and cellular analyses of CD-NTase signalling nucleotides demonstrate that these cyclic di- and trinucleotides activate distinct host receptors and thus may modulate the interaction of both pathogens and commensal microbiota with their animal and plant hosts. A bacterial family of cGAS/DncV-like nucleotidyltransferases synthesizes a diverse range of cyclic dinucleotide and trinucleotide compounds that are likely to modulate the interaction of both pathogens and commensal microbiota with their animal and plant hosts., Author(s): Aaron T. Whiteley [sup.1] [sup.2] , James B. Eaglesham [sup.1] [sup.2] , Carina C. de Oliveira Mann [sup.1] [sup.2] , Benjamin R. Morehouse [sup.1] [sup.2] , Brianna Lowey [sup.1] [...]

Background Taller adult height is associated with lower risks of ischemic heart disease in mendelian randomization (MR) studies, but little is known about the causal relevance of height for different subtypes of ischemic stroke. The present study examined the causal relevance of height for different subtypes of ischemic stroke. Methods and findings Height-associated genetic variants (up to 2,337) from previous genome-wide association studies (GWASs) were used to construct genetic instruments in different ancestral populations. Two-sample MR approaches were used to examine the associations of genetically determined height with ischemic stroke and its subtypes (cardioembolic stroke, large-artery stroke, and small-vessel stroke) in multiple ancestries (the MEGASTROKE consortium, which included genome-wide studies of stroke and stroke subtypes: 60,341 ischemic stroke cases) supported by additional cases in individuals of white British ancestry (UK Biobank [UKB]: 4,055 cases) and Chinese ancestry (China Kadoorie Biobank [CKB]: 10,297 cases). The associations of genetically determined height with established cardiovascular and other risk factors were examined in 336,750 participants from UKB and 58,277 participants from CKB. In MEGASTROKE, genetically determined height was associated with a 4% lower risk (odds ratio [OR] 0.96; 95% confidence interval [CI] 0.94, 0.99; p = 0.007) of ischemic stroke per 1 standard deviation (SD) taller height, but this masked a much stronger positive association of height with cardioembolic stroke (13% higher risk, OR 1.13 [95% CI 1.07, 1.19], p < 0.001) and stronger inverse associations with large-artery stroke (11% lower risk, OR 0.89 [0.84, 0.95], p < 0.001) and small-vessel stroke (13% lower risk, OR 0.87 [0.83, 0.92], p < 0.001). The findings in both UKB and CKB were directionally concordant with those observed in MEGASTROKE, but did not reach statistical significance: For presumed cardioembolic stroke, the ORs were 1.08 (95% CI 0.86, 1.35; p = 0.53) in UKB and 1.20 (0.77, 1.85; p = 0.43) in CKB; for other subtypes of ischemic stroke in UKB, the OR was 0.97 (95% CI 0.90, 1.05; p = 0.49); and for other nonlacunar stroke and lacunar stroke in CKB, the ORs were 0.89 (0.80, 1.00; p = 0.06) and 0.99 (0.88, 1.12; p = 0.85), respectively. In addition, genetically determined height was also positively associated with atrial fibrillation (available only in UKB), and with lean body mass and lung function, and inversely associated with low-density lipoprotein (LDL) cholesterol in both British and Chinese ancestries. Limitations of this study include potential bias from assortative mating or pleiotropic effects of genetic variants and incomplete generalizability of genetic instruments to different populations. Conclusions The findings provide support for a causal association of taller adult height with higher risk of cardioembolic stroke and lower risk of other ischemic stroke subtypes in diverse ancestries. Further research is needed to understand the shared biological and physical pathways underlying the associations between height and stroke risks, which could identify potential targets for treatments to prevent stroke., Author(s): Andrew B. Linden 1, Robert Clarke 1, Imen Hammami 1, Jemma C. Hopewell 1, Yu Guo 2, William N. Whiteley 1,3, Kuang Lin 1, Iain Turnbull 1, Yiping Chen [...]

Background Thromboses in unusual locations after the Coronavirus Disease 2019 (COVID-19) vaccine ChAdOx1-S have been reported, although their frequency with vaccines of different types is uncertain at a population level. The aim of this study was to estimate the population-level risks of hospitalised thrombocytopenia and major arterial and venous thromboses after COVID-19 vaccination. Methods and findings In this whole-population cohort study, we analysed linked electronic health records from adults living in England, from 8 December 2020 to 18 March 2021. We estimated incidence rates and hazard ratios (HRs) for major arterial, venous, and thrombocytopenic outcomes 1 to 28 and >28 days after first vaccination dose for ChAdOx1-S and BNT162b2 vaccines. Analyses were performed separately for ages Of 46 million adults, 23 million (51%) were women; 39 million (84%) were 28 days post-ChAdOx1-S, 359 (338 to 382), [less than or equal to]28 days post-BNT162b2-S, 241 (229 to 253); >28 days post-BNT162b2-S 277 (263 to 291). The crude incidence rates (per 100,000 person-years) of all arterial events were as follows: prevaccination, 546 (95% CI: 541 to 555); [less than or equal to]28 days post-ChAdOx1-S, 1,211 (1,185 to 1,237); >28 days post-ChAdOx1-S, 1678 (1,630 to 1,726), [less than or equal to]28 days post-BNT162b2-S, 1,242 (1,214 to 1,269); >28 days post-BNT162b2-S, 1,539 (1,507 to 1,572). Adjusted HRs (aHRs) 1 to 28 days after ChAdOx1-S, compared with unvaccinated rates, at ages Rates of intracranial venous thrombosis (ICVT) and of thrombocytopenia in adults aged The main limitations of the study are as follows: (i) it relies on the accuracy of coded healthcare data to identify exposures, covariates, and outcomes; (ii) the use of primary reason for hospital admission to measure outcome, which improves the positive predictive value but may lead to an underestimation of incidence; and (iii) potential unmeasured confounding. Conclusions In this study, we observed increases in rates of ICVT and thrombocytopenia after ChAdOx1-S vaccination in adults aged, Author(s): William N. Whiteley 1,2,*, Samantha Ip 3, Jennifer A. Cooper 4, Thomas Bolton 3,5, Spencer Keene 3, Venexia Walker 4, Rachel Denholm 4, Ashley Akbari 6, Efosa Omigie 7, [...]

In Australia, inspections of food premises are routinely conducted by environmental health officers (EHOs) using a checklist approach; the checklist is either manually written or stored into an electronic device. EHOs primarily assess cleanliness by visual inspection. Microbiological sampling is limited to those occasions requiring statutory evidence collection. The evidence gap between visual inspection and microbial sampling might be assisted by using commercially available rapid adenosine triphosphate (ATP) testing devices. This article presents a pilot study using ATP testing together with a new sampling algorithm in the assessment of surface cleanliness. Surfaces and implements were tested in eight food premises using ATP testing to determine cleanliness on items that passed the visual test of cleanliness. Cleanliness was verified using a cleaning intervention step. Of the 49 of 72 (68%) surfaces and implements assessed as visually clean, they were shown to have inadequate cleanliness (p = .001). The findings support using ATP testing with the new algorithm, as this could provide a reliable approach for surveillance of surface cleanliness by EHOs., Introduction Each year in Australia, it is estimated that there are more than 4 million incidents of food poisoning due to poorly prepared or contaminated food (Food Safety Information Council, [...]

This Review highlights how we can build upon the relatively new and rapidly developing field of research into bacterial quorum sensing (QS). We now have a depth of knowledge about how bacteria use QS signals to communicate with each other and to coordinate their activities. In recent years there have been extraordinary advances in our understanding of the genetics, genomics, biochemistry, and signal diversity of QS. We are beginning to understand the connections between QS and bacterial sociality. This foundation places us at the beginning of a new era in which researchers will be able to work towards new medicines to treat devastating infectious diseases, and use bacteria to understand the biology of sociality., Author(s): Marvin Whiteley [1]; Stephen P. Diggle [1]; E. Peter Greenberg (corresponding author) [2, 3] Humans have provided descriptions of the natural history of animals for millennia. Apart from basic [...]

Often in applications such as rare events estimation or optimal control it is required that one calculates the principal eigenfunction and eigenvalue of a nonnegative integral kernel. Except in the finite-dimensional case, usually neither the principal eigenfunction nor the eigenvalue can be computed exactly. In this paper, we develop numerical approximations for these quantities. We show how a generic interacting particle algorithm can be used to deliver numerical approximations of the eigenquantities and the associated so-called 'twisted' Markov kernel as well as how these approximations are relevant to the aforementioned applications. In addition, we study a collection of random integral operators underlying the algorithm, address some of their mean and pathwise properties, and obtain error estimates. Finally, numerical examples are provided in the context of importance sampling for computing tail probabilities of Markov chains and computing value functions for a class of stochastic optimal control problems. Keywords: interacting particle methods * eigenfunctions * rare events estimation * optimal control * diffusion Monte Carlo, 1. Introduction On a state space X consider a bounded function G: X -[much greater than] [R.sub.+], a Markov probability kernel M. The central object of interest in this paper [...]

ZUNI -TIWA AND -TSA Zuni names show a substantial minority with male -tiwa endings and a plurality with -tsa female endings. Parsons (1923b:176) infers that Zuni probably borrowed -tiwa names [...]

INTRODUCTION The Pueblo Indians of the United States Southwest and their ascendants, the 'Ancestral Pueblos' (formerly 'Anasazi,' 'Mogollon,' etc.), offer a rich field for the investigation of sociocultural evolution. Following [...]

Intracellular pathogens are responsible for much of the world-wide morbidity and mortality due to infectious diseases. To colonize their hosts successfully, pathogens must sense their environment and regulate virulence gene expression appropriately. Accordingly, on entry into mammalian cells, the facultative intracellular bacterial pathogen Listeria monocytogenes remodels its transcriptional program by activating the master virulence regulator PrfA. Here we show that bacterial and host-derived glutathione are required to activate PrfA. In this study a genetic selection led to the identification of a bacterial mutant in glutathione synthase that exhibited reduced virulence gene expression and was attenuated 150-fold in mice. Genome sequencing of suppressor mutants that arose spontaneously in vivo revealed a single nucleotide change in prfA that locks the protein in the active conformation (PrfA*) and completely bypassed the requirement for glutathione during infection. Biochemical and genetic studies support a model in which glutathionedependent PrfA activation is mediated by allosteric binding of glutathione to PrfA. Whereas glutathione and other low-molecular-weight thiols have important roles in redox homeostasis in all forms of life, here we demonstrate that glutathione represents a critical signalling molecule that activates the virulence of an intracellular pathogen., Listeria monocytogenes is a Gram-positive pathogen of animals and humans that cycles between a saprophytic lifestyle and an intracellular pathogen that escapes from a vacuole and grows in the cytosol [...]

We develop and test a new analytic approach, termed 'sib-split', to detect fish passage through road crossings. This new approach is based on the genetic analysis of full-siblings on opposite sides of potential barriers. We used simulations and data from two empirical case studies involving brook trout (Salvelinusfontinalis) movement with respect to barriers that varied in strength of effect on fish passage. Simulations revealed that both sib-split and the population assignment-based method (STRUCTURE) were highly accurate (mean accuracy > 99%) under easy-to-detect conditions (moderate to strong genetic differentiation and no movement). However, under difficult-to-detect simulated conditions (no genetic differentiation, 10% movement each generation), sib-split had higher accuracy (mean accuracy = 98%) than STRUCTURE (mean accuracy = 84%). Sib-split also outperformed STRUCTURE (mean accuracy 98% versus 89%) under a more difficult-to-detect simulated management scenario (simulated construction of a new complete barrier to movement). Sib-split provided more reliable and easily interpretable movement detection in both easy- and difficult-to-detect empirical case studies. With the empirical case studies, sensitivity to the prior on migration rate precluded use of STRUCTURE by itself, but a two-step approach where sib-split results were used to provide an informed migration prior for STRUCTURE provided additional information for both case studies. Nous avons mis au point et valide une nouvelle approche analytique designee' sib-split' pour deceler le passage de poissons par des franchissements de route. Cette approche repose sur l'analyse genetique de groupes de fratrie de part et d'autre de barrieres potentielles. Nous avons utilise des simulations et les donnees de deux etudes empiriques de cas portant sur les deplacements des ombles de fontaine (Salvelinusfontinalis) par rapport a des barrieres presentant differentes intensites d'effet sur le passage des poissons. Les simulations ont demontre que tant l'approche sib-split que la methode d'affectation a des populations (STRUCTURE) etaient tres exactes (exactitude moyenne > 99 %) pour des conditions de detection facile (differentiation genetique moderee a forte et aucun deplacement). Cependant, dans des conditions simulees de detection difficile (pas de differentiation genetique, 10 % de deplacements pour chaque generation), l'approche sib-split etait plus exacte (exactitude moyenne = 98 %) que STRUCTURE (exactitude moyenne = 84 %). La methode sib-split a egalement donne de meilleurs resultats que STRUCTURE (exactitude moyenne de 98 % contre 89 %) pour un scenario de gestion simule avec detection plus difficile (construction simulee d'une nouvelle barriere completement etanche aux deplacements). L'approche sib-split permettait une detection des deplacements plus fiable et facile a interpreter pour les etudes de cas empiriques de detection facile et difficile. En ce qui concerne les etudes de cas empiriques, la sensibilite aux informations a priori sur le taux de migration n'a pas permis la seule utilisation de STRUCTURE, mais une approche en deux etapes dans laquelle les resultats de l'approche sib-split etaient utilises pour fournir de l'information a priori sur la migration pour la methode STRUCTURE a fourni des renseignements supplementaires pour les deux etudes de cas. [Traduit par la Redaction], Introduction Complete or partial barriers to aquatic organism passage fragment populations and increase risk of local extirpation (Dunham et al. 1997; Letcher et al. 2007; Olden et al. 2010). There [...]

We tested the relative influence of habitat patch size and connectivity on genetic structure and effective population size in eight brook trout (Salvelinus fontinalis) habitat patches in a watershed in Virginia, USA. Variation at eight microsatellite loci in 2229 young-of-the-year brook trout for two successive cohorts (2010 and 2011) was examined. Genetic differentiation across all populations was pronounced. Overall [F'.sub.ST] was 0.397 (95% CI: 0.322-0.525) and overall [F.sub.ST] was 0.124 (95% CI: 0.096-0.159). Above-barrier patch size had a strong positive relationship with genetic diversity, [[??].sub.b], and genetic differentiation. Our analysis is consistent with greater extinction risk in smaller above-barrier patches. Larger above-barrier patches contained greater genetic diversity but reduced [[??\].sub.b] relative to adjacent below-barrier patches. The primary effect of barriers may be to reduce available above-barrier spawning habitat, even for larger above-barrier patches. Below-barrier patches also showed evidence of reduced genetic diversity and lack of connectivity. Genetic monitoring focused at gaining a broader understanding of the relationships here will be necessary to fully evaluate local extinction risks. Nous avons teste l'influence relative de la taille et de la connectivity des parcelles d'habitat sur la structure genetique et la taille effective de la population dans huit parcelles d'habitat de l'omble de fontaine (Salvelinus fontinalis) dans un bassin versant en Virginie (Etats-Unis). Les variations en huit loci de microsatellites chez 2229 jeunes de l'annee pour deux cohortes successives (2010 et 2011) d'ombles de fontaine ont ete examinees. La differentiation genetique entre les differentes populations etait marquee. Le [F'.sub.ST] global etait de 0,397 (IC a 95 %: 0,322-0,525) et le [F.sub.ST] global, de 0,124 (IC a 95 %: 0,096-0,159). La taille des parcelles en amont de barrieres presentait une forte relation positive avec la diversite genetique, et la differentiation genetique. Notre analyse concorde avec un risque de disparition accru dans les parcelles de tailles plus petites en amont de barrieres. Les parcelles de plus grandes tailles en amont de barrieres presentaient une plus grande diversite genetique, mais des [[??].sub.b] plus faibles comparativement aux parcelles attenantes en aval de barrieres. Le principal effet des barrieres pourrait etre une moins grande disponibilite d'habitats de frai en amont de barrieres et ce, meme pour les plus grandes parcelles en amont de barrieres. Les parcelles en aval de barrieres presentaient egalement des signes de diversite genetique reduite et d'absence de connectivite. Une surveillance genetique visant a etablir une comprehension plus large de ces relations sera necessaire a une evaluation exhaustive des risques de disparition locale. [Traduit par la Redaction], Introduction Landscape changes (deforestation, dams, road systems, impassable culverts, invasive species) have greatly reduced available habitat and connectivity among populations of headwater stream fishes (Dunham et al. 1997; Morita and [...]

The Internet is a major source of health-related information for parents of sick children despite concerns surrounding quality. For neurodevelopmental disorders, the websites of advocacy groups are a largely unexamined source of information. We evaluated treatment information posted on nine highly-trafficked advocacy websites for autism, cerebral palsy, and fetal alcohol spectrum disorder. We found that the majority of claims about treatment safety and efficacy were unsubstantiated. Instead, a range of rhetorical strategies were used to imply scientific support. When peer-reviewed publications were cited, 20 % were incorrect or irrelevant. We call for new partnerships between advocacy and experts in developmental disorders to ensure better accuracy and higher transparency about how treatment information is selected and evidenced on advocacy websites. Keywords Autism cerebral palsy * Foetal alcohol spectrum disorder * Advocacy * Internet * Treatment information * Science communication * Ethics * Content analysis, Introduction One of the greatest challenges faced by parents of children with neurodevelopmental disorders is making treatment decisions. This challenge is compounded by the vast landscape of information available to [...]

Purpose Nicotine replacement therapy (NRT) has been used to ameliorate nicotine withdrawal in the intensive care unit (ICU). Previous cohort studies have suggested an increased mortality with NRT use: methodological problems may call into question the validity of these findings. We undertook a retrospective cohort study to determine if NRT use was associated with adverse outcomes. Methods This retrospective cohort study was conducted in a 30-bed, university affiliated, teaching hospital ICU. Results We identified 423 smokers admitted over 2 years, of whom 73 received transdermal NRT. Cox proportional hazard regression models, with NRT modelled as a time-varying covariate, were used to test the hypothesis that NRT was associated with an altered ICU or hospital mortality. A second analysis utilized propensity scores. The unadjusted ICU and hospital mortalities were lower for the NRT group; although both differences were non-significant. The Cox models showed that, after adjustment for APACHE risk, age, sex and alcohol use, risk associated with NRT administration was not statistically different than non-administration for both ICU (hazard ratio 0.50, [95 % CI 0.20-1.24], p = 0.14) and hospital (hazard ratio 0.95, [95 % CI 0.52-1.75], p = 0.88) mortality. Similar findings occurred with the propensity matched analysis. Conclusion We were unable to demonstrate any harm associated with NRT, with the ICU model actually trending towards benefit. We conclude that a randomised, blinded, placebo controlled trial is required to assess adequately the safety and efficacy of NRT as a treatment in critically ill smokers., Author(s): Michael A. Gillies [sup.1], C. A. McKenzie [sup.1], C. Whiteley [sup.1], R. J. Beale [sup.1] [sup.2], S. M. Tibby [sup.1] Author Affiliations: (1) grid.420545.2, Department of Critical Care, First [...]

She's So Fine: Reflections on Whiteness, Femininity, Adolescence and Class in 1960s Music. Edited by Laurie Stras. Farnham, UK, and Burlington, VT: Ashgate, 2010. 266 pp. IT'S ALWAYS EXCITING TO [...]

Aggregatibacter actinomycetemcomitans is an opportunistic pathogen that resides primarily in the mammalian oral cavity. In this environment, A. actinomycetemcomitans faces numerous host. and microbederived stresses, including intense competition for nutrients and exposure to the host immune system. While it is clear that A. actinomycetemcomitans responds to precise cues that allow it to adapt and proliferate in the presence of these stresses, little is currently known about the regulatory mechanisms that underlie these responses. Many bacteria use noncoding regulatory RNAs (ncRNAs) to rapidly alter gene expression in response to environmental stresses. Although no ncRNAs have been reported in A. actinomycetemcomitans, we propose that they are likely important for colonization and persistence in the oral cavity. Using a bioinformatic and experimental approach, we identified three putative metabolite-sensing riboswitches and nine small regulatory RNAs (sRNAs) in A. actinomycetemcomitans during planktonic and biofilm growth. Molecular characterization of one of the riboswitches revealed that it is a lysine riboswitch and that its target gene, lysT, encodes a novel lysine-specific transporter. Finally, we demonstrated that lysT and the lysT lysine riboswitch are conserved in over 40 bacterial species, including the phylogenetically related pathogen Haemophilus influenzae. doi: 10.1128/JB.00935-10

Summary There is now, for the first time, an integrated approach to complaints so that, where issues cross health and social care, the authorities must work together to produce one [...]

On the basis of the connectionist model of leadership, we examined perceptions of leadership as a function of the contextual factors of race (Asian American, Caucasian American) and occupation (engineering, sales) in 3 experiments (1 student sample and 2 industry samples). Race and occupation exhibited differential effects for within- and between-race comparisons. With regard to within-race comparisons, leadership perceptions of Asian Americans were higher when race--occupation was a good fit (engineer position) than when race--occupation was a poor fit (sales position) for the two industry samples. With regard to between-race comparisons, leadership perceptions of Asian Americans were low relative to those of Caucasian Americans. Additionally, when race--occupation was a good fit for Asian Americans, such individuals were evaluated higher on perceptions of technical competence than were Caucasian Americans, whereas they were evaluated lower when race--occupation was a poor fit. Furthermore, our results demonstrated that race affects leadership perceptions through the activation of prototypic leadership attributes (i.e., implicit leadership theories). Implications for the findings are discussed in terms of the connectionist model of leadership and leadership opportunities for Asian Americans. Keywords: implicit leadership theory, perceptions, prototypes, leadership, Asian American DOI: 10.1037/a0019501

Objective: To examine the relationship between psychiatric disorders and sexual behaviors among adolescents receiving mental health treatment. Adolescents in mental health treatment have been found to have higher rates of HIV risk behavior than their peers, but data concerning the relationship between psychopathology and risk are inconsistent and limited. Method: Eight hundred and forty adolescents (56% female, 58% African American, mean age = 14.9 years) and their parents completed computerized assessments of psychiatric symptoms via the Computerized Diagnostic Interview Schedule for Children (Shaffer, 2000a, 2000b). Adolescents also reported on sexual risk behaviors (vaginal/anal sex, condom use at last sex) and completed urine screens for a sexually transmitted infection (STI). Results: Adolescents meeting criteria for mania, externalizing disorders (oppositional defiant, conduct, and attention-deficit/hyperactivity disorders), or comorbid for externalizing and internalizing disorders (major depressive, generalized anxiety, and posttraumatic stress disorders) were significantly more likely to report a lifetime history of vaginal or anal sex than those who did not meet criteria for any psychiatric disorder (odds ratio [OR] = 2.0, 2.3, and 1.9, respectively). Adolescents meeting criteria for mania were significantly more likely to have 2 or more partners in the past 90 days (OR = 3.2) and to test positive for a STI (OR = 4.3) relative to adolescents who did not meet criteria for a psychiatric disorder. Conclusions: The presence of internalizing and externalizing disorders, especially mania, suggests the need for careful screening and targeting of adolescent sexual behavior during psychiatric treatment. Keywords: adolescents, mental health, sexual risk DOI: 10.1037/a0019632

This study presents experimental results on the flow of magnetorheological grease (MRG) through microchannels. MR materials flowing through microchannels create microvalves. The flow is controlled by injecting the MRG through microchannels with controlled adjustable rates. To study the effect of different channel diameters and surface roughnesses, microchannels made of stainless steel, PEEK, and fused silica materials with nominal internal diameters ranging from 1 mm to 0.075 mm (75 [micro]m) are tested. A magnetic field is applied perpendicular to the microchannel flow and is controlled by an input electric current. The pressure drop of the flow is measured across the length of the microchannels. The dynamic pressure drop range and surface roughness effects are also discussed. The Herschel--Bulkley model for non-Newtonian fluid flow is employed to the experimental results with good agreement. The results show a significant pressure drop for different magnetic field strengths. [DOI: 10.1115/1.4000922]

Rising atmospheric C[O.sub.2] levels are predicted to have major consequences on carbon cycling and the functioning of terrestrial ecosystems. Increased photosynthetic activity is expected, especially for C-3 plants, thereby influencing vegetation dynamics; however, little is known about the path of fixed carbon into soil-borne communities and resulting feedbacks on ecosystem function. Here, we examine how arbuscular mycorrhizal fungi (AMF) act as a major conduit in the transfer of carbon between plants and soil and how elevated atmospheric C[O.sub.2] modulates the belowground translocation pathway of plant-fixed carbon. Shifts in active AMF species under elevated atmospheric C[O.sub.2] conditions are coupled to changes within active rhizosphere bacterial and fungal communities. Thus, as opposed to simply increasing the activity of soil-borne microbes through enhanced rhizodeposition, elevated atmospheric C[O.sub.2] clearly evokes the emergence of distinct opportunistic plant-associated microbial communities. Analyses involving RNA-based stable isotope probing, neutral/phosphate lipid fatty acids stable isotope probing, community fingerprinting, and real-time PCR allowed us to trace plant-fixed carbon to the affected soil-borne microorganisms. Based on our data, we present a conceptual model in which plant-assimilated carbon is rapidly transferred to AMF, followed by a slower release from AMF to the bacterial and fungal populations well-adapted to the prevailing (myco-)rhizosphere conditions. This model provides a general framework for reappraising carbon-flow paths in soils, facilitating predictions of future interactions between rising atmospheric C[O.sub.2] concentrations and terrestrial ecosystems. [sup.13]c | arbuscular mycorrhizal | climate change | RNA-based stable isotope probing | rhizosphere doi/ 10.1073/pnas.0912421107

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen often associated with chronic infections in the lungs of individuals with the heritable disease cystic fibrosis (CF). Previous work from our laboratory demonstrated that aromatic amino acids within CF lung secretions (sputum) not only serve as carbon and energy sources but also enhance synthesis of the cell signaling molecule Pseudomonas quinolone signal (PQS). The present study investigates the role of the aromatic amino acid-responsive regulator PhhR in mediating these phenotypes. Transcriptome analysis revealed that PhhR controls four putative transcriptional units (phhA, hpd, hmgA, and dhcA) involved in aromatic amino acid catabolism; however, genes involved in PQS biosynthesis were unaffected. The phhA, hpd, hmgA, and dhcA promoters were mapped by primer extension, and purified [His.sub.6]-PhhR was shown to bind the phhA, hpd, and dhcA promoters in vitro by use of electrophoretic mobility shift assays. Our work characterizes a transcriptional regulator of catabolic genes induced during P. aeruginosa growth in CF sputum. doi: 10.1128/JB.00112-10

A three phase model for the growth of a tissue construct within a perfusion bioreactor is examined. The cell population (and attendant extracellular matrix), culture medium, and porous scaffold are treated as distinct phases. The bioreactor system is represented by a two-dimensional channel containing a cell-seeded rigid porous scaffold (tissue construct), which is perfused with a culture medium. Through the prescription of appropriate functional forms for cell proliferation and extracellular matrix deposition rates, the model is used to compare the influence of cell density-, pressure-, and culture medium shear stress-regulated growth on the composition of the engineered tissue. The governing equations are derived in O'Dea et al. 'A Three Phase Model for Tissue Construct Growth in a Perfusion Bioreactor,' Math. Med. Biol., in which the long-wavelength limit was exploited to aid analysis; here, finite element methods are used to construct two-dimensional solutions to the governing equations and to investigate thoroughly their behavior. Comparison of the total tissue yield and averaged pressures, velocities, and shear stress demonstrates that quantitative agreement between the two-dimensional and long-wavelength approximation solutions is obtained for channel aspect ratios of order [10.sup.-2] and that much of the qualitative behavior of the model is captured in the long-wavelength limit, even for relatively large channel aspect ratios. However, we demonstrate that in order to capture accurately the effect of mechanotransduction mechanisms on tissue construct growth, spatial effects in at least two dimensions must be included due to the inherent spatial variation of mechanical stimuli relevant to perfusion bioreactors, most notably, fluid shear stress, a feature not captured in the long-wavelength limit. [DOI: 10.1115/1.4001160]

The generalized minimal residual (GMRES) method is a common choice for solving the large nonsymmetric linear systems that arise when numerically computing solutions of incompressible nonlinear elasticity problems using the finite element method. Analytic results on the performance of GMRES are available on linear problems such as linear elasticity or Stokes' flow (where the matrices in the corresponding linear systems are symmetric), or on the nonlinear problem of the Navier--Stokes flow (where the matrix is block-symmetric/block-skew-symmetric); however, there has been very little investigation into the GMRES performance in incompressible nonlinear elasticity problems, where the nonlinearity of the incompressibility constraint means the matrix is not block-symmetric/block-skew-symmetric. In this short paper, we identify one feature of the problem formulation, which has a huge impact on unpreconditioned GMRES convergence. We explain that it is important to ensure that the matrices are perturbations of a block-skew-symmetric matrix rather than a perturbation of a block-symmetric matrix. This relates to the choice of sign before the incompressibility constraint integral in the weak formulation (with both choices being mathematically equivalent). The incorrect choice is shown to have a hugely detrimental effect on the total computation time. [DOI: 10.1115/1.4000414]

The opportunistic pathogen Pseudomonas aeruginosa causes a variety of infections in immunocompromised individuals, including individuals with the heritable disease cystic fibrosis. Like the carbon sources metabolized by many disease-causing bacteria, the carbon sources metabolized by P. aeruginosa at the host infection site are unknown. We recently reported that L-alanine is a preferred carbon source for P. aeruginosa and that two genes potentially involved in alanine catabolism (dadA and dadX) are induced during in vivo growth in the rat peritoneum and during in vitro growth in sputum (mucus) collected from the lungs of individuals with cystic fibrosis. The goals of this study were to characterize factors required for alanine catabolism in P. aeruginosa and to assess the importance of these factors for in vivo growth. Our results reveal that dadA and dadX are arranged in an operon and are required for catabolism of L-alanine. The dad operon is inducible by L-alanine, D-alanine, and L-valine, and induction is dependent on the transcriptional regulator Lrp. Finally, we show that a mutant unable to catabolize DL-alanine displays decreased competitiveness in a rat lung model of infection. doi: 10.1128/JB.00817-09

Pyritization of soft tissues is extremely rare. Pyritized fossils have been discovered at six new localities spanning 54 km of outcrop of the Ordovician Lorraine Group of New York State, suggesting that soft-tissue pyritization is widespread in the Taconic basin. Notable new taxa with soft-tissue preservation include ostracods and other arthropods. Such fossils are rare and occur within 4-9-cm-thick mudstones representing single rapid depositional events. High ratios of reactive iron to total iron and high values of [[delta].sup.34]S, together with a near-absence of disarticulated and fragmented skeletal material, suggest that organisms in these pyritic horizons were buried rapidly and underwent bacterial sulfate reduction in porewaters rich in highly reactive iron and low in organic carbon. These conditions facilitated iron sulfide precipitation within and on decaying carcasses. Such conditions occur repeatedly in some finegrained distal turbiditic facies of the Taconic foreland basin. Pyritized soft-bodied fossils await discovery elsewhere in the Lorraine Group.

Previous work has demonstrated that genomic incompatibilities work together with ecologically divergent selection to promote and maintain reproductive isolation between incipient species (dwarf and normal) of lake whitefish (Coregonus clupeaformis (Mitchill, 1818)). Whitefish spawn in groups with external fertilization, which creates conditions for strong sperm competition. In this study, we asked whether reduced sperm performance in hybrids from whitefish species-pair matings might contribute to postzygotic isolating mechanisms between these taxa. We examined two sperm traits, sperm swimming speed and flagellum length, in pure dwarf and normal whitefish and in their F1 and backcross hybrids. We observed significantly reduced sperm swimming speed in backcross but not in F1 hybrids. Sperm flagellum length was not significantly correlated with sperm swimming speed. These results demonstrate that F1 hybrids formed in nature should be capable of the same fertilization success as the parental species during sperm competition, everything else being equal. However, reduced sperm performance in the backcross generation is consistent with other evidence suggesting that genomic incompatibilities create a range of negative fitness effects in post-F1 whitefish hybrids and provides evidence for an additional postzygotic isolation mechanism involved in the incipient speciation of sympatric dwarf and normal whitefish. Des travaux anterieurs ont demontre que les incompatibilites genetiques agissent de concert avec la selection divergente en fonction de l'ecologie pour favoriser et maintenir l'isolement genetique entre les especes en emergence (naines et normales) chez les grands coregones (Coregonus clupeaformis (Mitchill, 1818)). Les coregones fraient en groupes et ont une fecondation externe, ce qui cree des conditions de forte competition spermatique. Dans notre etude, nous cherchons a savoir si la performance reduite des spermatozoides des hybrides provenant de l'accouplement de paires d'especes de coregones peut contribuer aux mecanismes d'isolement post-zygotique entre ces taxons. Nous examinons deux caracteristiques des spermatozoides, la vitesse de nage et la longueur du flagelle des spermatozoides, chez des coregones nains et normaux purs et leurs hybrides de F1 et de retrocroisement. Il y a une reduction significative de la vitesse de nage des spermatozoides chez les hybrides de retrocroisement, mais non ceux de F1. Il n'existe pas de correlation significative entre la longueur du flagelle et la vitesse de nage des spermatozoides. Ces resultats demontrent que les hybrides de F1 formes en nature devraient pouvoir obtenir le meme succes de fecondation que les especes parentales durant la competition spermatique, toutes autres choses etant egales. Cependant, la performance reduite des spermatozoides de la generation de retrocroisement est compatible avec d'autres indications qui laissent croire que les incompatibilites genetiques creent une gamme d'effets negatifs de fitness chez les hybrides post F1 de coregones; elle fournit aussi des preuves de l'implication d'un mecanisme additionnel d'isolement post-zygotique dans la speciation en emergence des coregones sympatriques nains et normaux. [Traduit par la Redaction], Introduction Our understanding of the process of speciation has increased dramatically in recent decades (Schluter 2000; Coyne and Orr 2004). Many studies have focused on the ecological processes of speciation, [...]

Pseudomonas aeruginosa produces the quorum signal 2-heptyl-3-hydroxy-4-quinolone (Pseudomonas quinolone signal), which is important for stimulating outer membrane vesicle (MV) formation. Here we describe the importance of the 3-hydroxyl and 2-alkyl chain for MV production and the length of the 2-alkyl chain for association with MVs.