New Short Tandem Repeat-Based Molecular Typing Method for Pneumocystis jirovecii Reveals Intrahospital Transmission between Patients from Different Wards

Pneumocystis pneumonia is a severe opportunistic infection in immunocompromised patients caused by the unusual fungus Pneumocystis jirovecii. Transmission is airborne, with both immunocompromised and immunocompetent individuals acting as a reservoir for the fungus. Numerous reports of outbreaks in renal transplant units demonstrate the need for valid genotyping methods to detect transmission of a given genotype. Here, we developed a short tandem repeat (STR)-based molecular typing method for P. jirovecii. We analyzed the P. jirovecii genome and selected six genomic STR markers located on different contigs of the genome. We then tested these markers in 106 P. jirovecii PCR-positive respiratory samples collected between October 2010 and November 2013 from 91 patients with various underlying medical conditions. Unique (one allele per marker) and multiple (more than one allele per marker) genotypes were observed in 34 (32%) and 72 (68%) samples, respectively. A genotype could be assigned to 55 samples (54 patients) and 61 different genotypes were identified in total with a discriminatory power of 0.992. Analysis of the allelic distribution of the six markers and minimum spanning tree analysis of the 61 genotypes identified a specific genotype (Gt21) in our hospital, which may have been transmitted between 10 patients including six renal transplant recipients. Our STR-based molecular typing method is a quick, cheap and reliable approach to genotype Pneumocystis jirovecii in hospital settings and is sensitive enough to detect minor genotypes, thus enabling the study of the transmission and pathophysiology of Pneumocystis pneumonia.     

Individual Consistency and Phenotypic Plasticity in Rockhopper Penguins: Female but Not Male Body Mass Links Environmental Conditions to Reproductive Investment

In marine habitats, increasing ocean temperatures due to global climate change may distinctly reduce nutrient and consequently food availability for seabirds. Food availability is a known driver of body mass and reproductive investment in birds, but these traits may also depend on individual effects. Penguins show extreme intra-annual body mass variation and rely on accumulated body reserves for successful breeding. However, no study so far has tested individual consistency and phenotypic responses in body mass and reproductive investment in this taxon. Using a unique dataset on individually marked female and male southern rockhopper penguins (Eudyptes chrysocome chrysocome) across six years, we investigated 1) the individual consistency in body mass (measured at egg laying), body condition and reproductive investment across years, subsequently 2) identified the best-explanatory temperature-related environmental variables for female and male body mass, and 3) tested the effect of female and male body mass on reproductive investment. Body mass, body condition and reproductive investment were all highly repeatable. As body condition should control for the structural size of the birds, the similarly high repeatability estimates for body mass and body condition suggested that the consistent between-individual body mass differences were independent of structural size. This supported the use of body mass for the subsequent analyses. Body mass was higher under colder environmental conditions (positive Southern Annular Mode), but the overall phenotypic response appeared limited. Reproductive investment increased with female but not male body mass. While environmental effects on body mass in our study period were rather small, one can expect that ongoing global climate change will lead to a deterioration of food availability and we might therefore in the long-term expect a phenotypical decline in body mass and reproductive investment.     

Viral Coat Protein Peptides with Limited Sequence Homology Bind Similar Domains of Alfalfa Mosaic Virus and Tobacco Streak Virus RNAs

An unusual and distinguishing feature of alfalfa mosaic virus (AMV) and ilarviruses such as tobacco streak virus (TSV) is that the viral coat protein is required to activate the early stages of viral RNA replication, a phenomenon known as genome activation. AMV-TSV coat protein homology is limited; however, they are functionally interchangeable in activating virus replication. For example, TSV coat protein will activate AMV RNA replication and vice versa. Although AMV and TSV coat proteins have little obvious amino acid homology, we recently reported that they share an N-terminal RNA binding consensus sequence (Ansel-McKinney et al., EMBO J. 15:5077–5084, 1996). Here, we biochemically compare the binding of chemically synthesized peptides that include the consensus RNA binding sequence and lysine-rich (AMV) or arginine-rich (TSV) environment to 3′-terminal TSV and AMV RNA fragments. The arginine-rich TSV coat protein peptide binds viral RNA with lower affinity than the lysine-rich AMV coat protein peptides; however, the ribose moieties protected from hydroxyl radical attack by the two different peptides are localized in the same area of the predicted RNA structures. When included in an infectious inoculum, both AMV and TSV 3′-terminal RNA fragments inhibited AMV RNA replication, while variant RNAs unable to bind coat protein did not affect replication significantly. The data suggest that RNA binding and genome activation functions may reside in the consensus RNA binding sequence that is apparently unique to AMV and ilarvirus coat proteins.     

Temperature-Mediated Changes in Rates of Predator Forgetting in Woodfrog Tadpoles

Hundreds of studies have investigated the sources and nature of information that prey gather about their predators and the ways in which prey use this information to mediate their risk of predation. However, relatively little theoretical or empirical work has considered the question of how long information should be maintained and used by prey animals in making behavioural decisions. Here, we tested whether the size of the memory window associated with predator recognition could be affected by an intrinsic factor, such as size and growth rate of the prey. We maintained groups of predator-naive woodfrog, Lithobates sylvaticus, tadpoles at different temperatures for 8 days to induce differences in tadpole size. We then conditioned small and large tadpoles to recognize the odour of a predatory tiger salamander, Ambystoma tigrinum. Tadpoles were then maintained either on a high or low growth trajectory for another 8 days, after which they were tested for their response to the predator. Our results suggest that the memory window related to predator recognition of tadpoles is determined by both their size and/or growth rate at the time of learning and their subsequent growth rate post-learning.     

The influence of day-length on imaginal diapause in the Red Locust, Nomadacris septemfasciata (Serv.)

The main permanent habitats of the Red Locust (Nomadacris septemfasciata (Serv.)) in tropical Africa lie between latitudes 7° and 9° S and between 10° and 16° N. Breeding is confined to the rainy season, which occurs during the longest days of the year in these areas. Both north and south of the equator, the adults emerge as day-length is diminishing and undergo a prolonged imaginal diapause until the next rainy season.When reared in the laboratory in London, adults which emerge in spring or early summer become sexually mature within two months; those which emerge in late summer and autumn, although kept at the same temperature and humidity, enter diapause and do not copulate or oviposit until the following spring. By controlling the length of the daily photoperiod, it has been shown that the seasonal differences in day-length are responsible for the onset of diapause. Constant short photoperiods usually induce a rather shorter diapause than photoperiods diminishing so as to simulate autumn day-length at this latitude (51.5° N). The critical constant photoperiod for the establishment of diapause lies between 12 and 13 hours which corresponds approximately to maximum and minimum day-lengths at 7° N or S. It is therefore possible that day-length is responsible for the establishment of the natural diapause.

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Resume On a déjà constaté que, quand on élève le criquet rouge, Nomadacris septemfasciata (Serv.), au laboratoire à Londres, les adultes, malgré le fait qu'on les retient dans une ambiance très constante, montrent de grandes différences saisonnières dans la durie du développement qui conduit à la maturité sexuelle. Les adultes qui émergent à partir du mois d'avril jusque'au mois de juillet deviennent matures sexuellement sans diapause en 11/2 à 2 mois; tandis que ceux qui émergent au début de l'automne, à partir de la mi-août approximativement jusqu'à la fin de septembre, ont une diapause prolongée de 7 à 8 mois; et ceux qui émergent encore plus tard dans l'année, du mois d'octobre jusqu'à mi-décembre, ont une diapause plus courte de 41/2 à 51/2 mois. Les périodes de maturation des adultes qui émergent à partir de janvier et plus tard, diminuent progressivement, en se fondant dans les groupes des non-diapause, qui commencent à émerger au début d'avril. Les expériences exposées dans cette thèse indiquent que les différences saisonnières de la longueur des jours, sont responsables des temps de maturation.Certains groupes de criquets, émergeant comme adultes vers la fin de l'été ou en automne, ont été soumis à des journées de longueur artificielle qui correspondait à la durée des jours de printems qui n'exerce son influence que sur la vie adulte, suffit à produire ce dans les délais semblables à ceux des groupes qui émergent au printemps. La longueur des jours de printemps qui n'excerce son influence que sur la vie adulte, suffit à produire ce résultat.Quelques larves étaient élevées simultanément dans les conditions d'une durée artificielle des jours du printemps, d'une durée artificielle des jours d'automne, et d'une lumière naturelle des jours d'été à Londres. Les adultes qui avaient émergé au mois de juin étaient ou maintenus dans le même régime de longueur de journée que les larves, ou transférés dans une des autres conditions. Tous les temps de maturation étaient appropriés aux saisons qui correspondaient au régime de durée du jour auquel les adultes étaient retenus, et il n'y avait nulle évidence qu'ils étaient influencés par la durée des jours pendant leur vie larvaire.Les groupes diapause, quand ils étaient soumis à la lumière normale du laboratoire, sont devenus matures, au printemps, au moment où les jours s'allongeaient. Pourtant la maturation n'est pas due à la stimulation causée par un accroissement de la longueur du jour, car on à observé qu'elle arrive en même temps si les criquets ne la subissent pas. Ceci est vrai également à l'égard des deux groupes, celui de longue diapause (qui émerge au début de l'automne) et celui de courte diapause (qui émerge vers la fin de l'automne); il s'ensuit que la diapause plus courte du dernier groupe n'est pas attribuable, comme il semblait probable, au fait qu'on l'avait exposé à la longueur des jours du printemps plus tôt dans la vie adulte. On a trouvé que ces groupes de la dernière partie de l'automne étaient devenus matures dans le même temps s'ils étaient retenus aux courtes photo-périodes constantes de 8 ou 11 heures, ou à la durée changeante des jours d'hiver. On a conclu qu'ils répondent comme à la durée de constants jours courts.Les groupes intermédaires (qui émergent à partir de janvier jusqu'a mars) d'autre part, sont exposés aux jours plus longs du printemps et de l'été encore plus tôt dans la vie adulte, et dans leur cas la diapause est empêchée, ou au moins abrégée, par les jours plus longs. Quand ces groupes sont retenus aux constantes photo-périodes courtes, ils deviennent matures plus lentement que s'ils étaient maintenus à la lumière du jour, et ils ont une diapause de la même longueur que les groupes de courte-diapause.On a conclu de ces résultats que, quand les groupes sont retenus dans conditions de jours-courts, les processus de maturation (manifestés par un accroissement du poids du corps, et par le développement de l'ovaire) sont repris à un certain stade indépendamment de la longueur du jour et sous l'action de stimuli internes. L'exposition aux conditions de jours longs n'est effective que pour accélérer la maturation si elle a lieu avant que ce stade soit atteint.L'observation que les adultes émergeant au début de l'automne ont une diapause plus longue que ceux qui émergent vers la fin de l'automne, reste sans explication. Ceux-là sont exposés à la durée de jours qui décroissent rapidement pendant la vie larvaire et du commencement de la vie adulte, et il semble probable que le changement propre des jours longs aux jours courts puisse amener une diapause plus longue que ne le feraient des jours courts dès le début. A présent, on étudie les effets de la variation de durée des jours.Les adultes retenus dans l'obscurité constante sont devenus matures sans diapause.La grande fluctuation de la longueur des jours, caractéristique de la latitude de Londres, n'est pas nécessaire pour induire les deux types de maturation diapause ou non-diapause. Les plus grandes différences de réponse aux photo-périodes constantes ont eu lieu entre les moyennes correspondant à peu près avec les minimum et maximum de longueurs de jour (y compris les périodes de crépuscule) dans les habitats tropicaux du criquet.Il est discuté ici de la probabilité que le cours de la diapause dans l'habitat tropical naturel soit influencé par la faible fluctuation des longueurs de jour de cet habitat.

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The author is Mrs O. W. Richards     

From gametogenesis to spawning: How climate-driven warming affects teleost reproductive biology

Ambient temperature modulates reproductive processes, especially in poikilotherms such as teleosts. Consequently, global warming is expected to impact the reproductive function of fish, which has implications for wild population dynamics, fisheries and aquaculture. In this extensive review spanning tropical and cold-water environments, we examine the impact of higher-than-optimal temperatures on teleost reproductive development and physiology across reproductive stages, species, generations and sexes. In doing so, we demonstrate that warmer-than-optimal temperatures can affect every stage of reproductive development from puberty through to the act of spawning, and these responses are mediated by age at spawning and are associated with changes in physiology at multiple levels of the brain–pituitary–gonad axis. Response to temperature is often species-specific and changes with environmental history/transgenerational conditioning, and the amplitude, timing and duration of thermal exposure within a generation. Thermally driven changes to physiology, gamete development and maturation typically culminate in poor sperm and oocyte quality, and/or advancement/delay/inhibition of ovulation/spermiation and spawning. Although the field of teleost reproduction and temperature is advanced in many respects, we identify areas where research is lacking, especially for males and egg quality from “omics” perspectives. Climate-driven warming will continue to disturb teleost reproductive performance and therefore guide future research, especially in the emerging areas of transgenerational acclimation and epigenetic studies, which will help to understand and project climate change impacts on wild populations and could also have implications for aquaculture.     

Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana)

Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here, we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional data set containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two data sets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations.