The age of chocolate: A diversification history of Theobroma and Malvaceae

Dated molecular phylogenies of broadly distributed lineages can help to compare patterns of diversification in different parts of the world. An explanation for greater Neotropical diversity compared to other parts of the tropics is that it was an accident of the Andean orogeny. Using dated phylogenies, of chloroplast ndhF and nuclear DNA WRKY sequence datasets, generated using BEAST we demonstrate that the diversification of the genera Theobroma and Herrania occurred from 12.7 (11.6-14.9 [95% HPD]) million years ago (Ma) and thus coincided with Andean uplift from the mid-Miocene and that this lineage had a faster diversification rate than other major clades in Malvaceae. We also demonstrate that Theobroma cacao, the source of chocolate, diverged from its most recent common ancestor 9.9 (7.7-12.9 [95% HPD]) Ma, in the mid-to late-Miocene, suggesting that this economically important species has had ample time to generate significant within-species genetic diversity that is useful information for a developing chocolate industry. In addition, we address questions related to the latitudinal gradient in species diversity within Malvaceae. A faster diversification rate is an explanation for the greater species diversity at lower latitudes. Alternatively, tropical conditions may have existed for longer and occupied greater areas than temperate ones meaning that tropical lineages have had more time and space in which to diversify. Our dated molecular phylogeny of Malvaceae demonstrated that at least one temperate lineage within the family diverged from tropical ancestors then diversified at a rate comparable with many tropical lineages in the family. These results are consistent with the hypothesis that Malvaceae are more species rich in the tropics because tropical lineages within the family have existed for longer and occupied more space than temperate ones, and not because of differences in diversification rate. © 2015 Richardson, Whitlock, Meerow and Madriñán

Informing Management of Atlantic Bluefin Tuna Using Telemetry Data

Sustainable management of exploited marine fish and wildlife populations requires knowledge about their productivity. Survival from natural causes of mortality is a key component of population productivity, but is notoriously difficult to estimate. We evaluate the potential for acoustic telemetry as a long-term monitoring tool to estimate rates of natural mortality. We present a Bayesian multistate mark-recapture model for telemetry data collected over a decade from 188 Atlantic bluefin tuna (Thunnus thynnus) and apply it to estimate the rate of natural mortality using only acoustic tag detections for all animals, or using acoustic tag detections for 96 single-tagged tuna plus acoustic tag detections combined with estimated positions from pop-up satellite archival tags for 92 double-tagged animals. We support the model for bluefin tuna with a simulation study to quantify bias in estimates of population dynamics parameters and investigate the effect of auxiliary information from satellite tagging on mortality rate estimates for different acoustic tag detection probability scenarios.We obtained posterior estimates of the instantaneous annual natural mortality (survival) rate across a decade of tagging for Atlantic bluefin tuna of 0.17 yr(-1) (0.84 yr(-1)) both using only acoustic tagging data, and using a combination of acoustic and satellite tagging data. Use of a prior implying a higher rate of fishing mortality yielded an instantaneous annual natural mortality (survival) estimate of 0.10 yr(-1) (0.90 yr(-1)), with combined acoustic and satellite tag data. Results from the simulation study indicate that the use of satellite tags can improve the precision and accuracy of estimates of detection probabilities, area-specific movement probabilities and mortality rates, where the extent of the improvement depends on true underlying acoustic tag detection probabilities. Our work demonstrates that long-term acoustic tagging data sets have strong potential for monitoring of highly migratory marine fish and wildlife populations, providing information on a number of key parameters, including survival and movement rates. However, improved information on tag reporting rates or fishing mortality is needed to better separate natural and fisheries mortality for Atlantic bluefin tuna

Flexible use of a dynamic energy landscape buffers a marine predator against extreme climate variability

Animal migrations track predictable seasonal patterns of resource availability and suitable thermal habitat. As climate change alters this 'energy landscape', some migratory species may struggle to adapt. We examined how climate variability influences movements, thermal habitat selection and energy intake by juvenile Pacific bluefin tuna (Thunnus orientalis) during seasonal foraging migrations in the California Current. We tracked 242 tuna across 15 years (2002-2016) with high-resolution archival tags, estimating their daily energy intake via abdominal warming associated with digestion (the 'heat increment of feeding'). The poleward extent of foraging migrations was flexible in response to climate variability, allowing tuna to track poleward displacements of thermal habitat where their standard metabolic rates were minimized. During a marine heatwave that saw temperature anomalies of up to +2.5 degrees C in the California Current, spatially explicit energy intake by tuna was approximately 15% lower than average. However, by shifting their mean seasonal migration approximately 900 km poleward, tuna remained in waters within their optimal temperature range and increased their energy intake. Our findings illustrate how tradeoffs between physiology and prey availability structure migration in a highly mobile vertebrate, and suggest that flexible migration strategies can buffer animals against energetic costs associated with climate variability and change

Host immunity in the protective response to vaccination with heat-killed Burkholderia mallei

<p>Abstract</p> <p>Background</p> <p>We performed initial cell, cytokine and complement depletion studies to investigate the possible role of these effectors in response to vaccination with heat-killed <it>Burkholderia mallei </it>in a susceptible BALB/c mouse model of infection.</p> <p>Results</p> <p>While protection with heat-killed bacilli did not result in sterilizing immunity, limited protection was afforded against an otherwise lethal infection and provided insight into potential host protective mechanisms. Our results demonstrated that mice depleted of either B cells, TNF-α or IFN-γ exhibited decreased survival rates, indicating a role for these effectors in obtaining partial protection from a lethal challenge by the intraperitoneal route. Additionally, complement depletion had no effect on immunoglobulin production when compared to non-complement depleted controls infected intranasally.</p> <p>Conclusion</p> <p>The data provide a basis for future studies of protection via vaccination using either subunit or whole-organism vaccine preparations from lethal infection in the experimental BALB/c mouse model. The results of this study demonstrate participation of B220⁺cells and pro-inflammatory cytokines IFN-γ and TNF-α in protection following HK vaccination.</p

Phylogenetic Relationships of Malvatheca (Bombacoideae and Malvoideae; Malvaceae sensu lato) as Inferred from Plastid DNA Sequences

Previous molecular phylogenetic analyses have revealed that elements of the former families Malvaceae sensu stricto and Bombacaceae together form a well-supported clade that has been named Malvatheca. Within Malvatheca, two major lineages have been observed; one, Bombacoideae, corresponds approximately to the palmate-leaved Bombacaceae, and the other, Malvoideae, includes the traditional Malvaceae (the mallows or Eumalvoideae). However, the composition of these two groups and their relationships to other elements of Malvatheca remain a source of uncertainty. Sequence data from two plastid regions, ndhF and trnK/matK, from 34 exemplars of Malvatheca and six outgroups were analyzed. Parsimony, likelihood, and Bayesian analyses of the sequence data provided a well-resolved phylogeny except that relationships among five lineages at the base of Malvatheca are poorly resolved. Nonetheless, a 6-bp insertion in matK suggests that Fremontodendreae is sister to the remainder of Malvatheca. Our results suggest that the Malvoideae originated in the Neotropics and that a mangrove taxon dispersed across the Pacific from South America to Australasia and later radiated out of Australasia to give rise to the ca. 1,700 living species of Eumalvoideae. Local clock analyses imply that the plastid genome underwent accelerated molecular evolution coincident with the dispersal out of the Americas and again with the radiation into the three major clades of Eumalvoideae

Effect of Kisspeptin on Regulation of Growth Hormone

Kisspeptin ( KP ), a neuroendocrine regulator of reproduction, is hypothesized to be an integrator of metabolism and hormones critical to the regulation of reproduction. Lactation is associated with enhanced growth hormone (GH) responsiveness and reduced fertility. Our study was designed to determine the effects of lactation on KP-stimulated GH and luteinizing hormone (LH) secretion. Five non-lactating and five lactating dairy cows were used in the study. Experiments were conducted with lactating cows at weeks 1, 5 and 11 after parturition. The experimental treatments ( saline and KP [100 and 400 pmol / kg body weight]) were given intravenously and blood was collected and plasma was stored until later assay to determine concentrations of GH, LH, progesterone and non-esterified fatty acids. We found that neither dose of KP stimulated an increase in GH secretion. The low dose of KP increased (P \u3c0. 05) LH concentrations only in lactating cows. The higher dose of KP elicited an increase in circulating LH concentrations in both lactating and non-lactating cows. The lower dose of KP increased (P \u3c 0. 05) the area under the curve for LH only in cows during week 5 of lactation, and the area under the curve of LH following the highest dose of KP was greater (P \u3c 0. 05) in cows during week 5 of lactation than that for the other groups of cows. In summary, lactation status and stage of lactation did not change the sensitivity of the GH system to KP. However, an effect of stage of lactation on KP-stimulated LH secretion was detected in the dairy cows. Study of the KP system during lactation in dairy cows may provide critical insights into the mechanisms for lactation associated changes in the reproductive axis

Protective Antigens Against Glanders Identified by Expression Library Immunization

Burkholderia are highly evolved Gram-negative bacteria that primarily infect solipeds but are transmitted to humans by ingestion and cutaneous or aerosol exposures. Heightened concern over human infections of Burkholderia mallei and the very closely related species B. pseudomallei is due to the pathogens’ proven effectiveness as bioweapons, and to the increased potential for natural opportunistic infections in the growing diabetic and immuno-compromised populations. These Burkholderia species are nearly impervious to antibiotic treatments and no vaccine exists. In this study, the genome of the highly virulent B. mallei ATCC23344 strain was examined by expression library immunization for gene-encoded protective antigens. This protocol for genomic-scale functional screening was customized to accommodate the unusually large complexity of Burkholderia, and yielded 12 new putative vaccine candidates. Five of the candidates were individually tested as protein immunogens and three were found to confer significant partial protection against a lethal pulmonary infection in a murine model of disease. Determinations of peripheral blood cytokine and chemokine profiles following individual protein immunizations show that interleukin-2 (IL-2) and IL-4 are elicited by the three confirmed candidates, but unexpectedly interferon-γ and tumor necrosis factor-α are not. We suggest that these pathogen components, discovered using genetic immunization and confirmed in a conventional protein format, will be useful toward the development of a safe and effective glanders vaccine

Intraspecific Inversions Pose a Challenge for the trnH-psbA Plant DNA Barcode

BACKGROUND: The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species. METHODOLOGY/PRINCIPAL FINDINGS: Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships. CONCLUSIONS/SIGNIFICANCE: Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding

Quality of life utility values for hereditary haemochromatosis in Australia

Background: Hereditary hemochromatosis (HH) is a common autosomal recessive disorder amongst persons of northern European heritage. If untreated, iron accumulates in parenchymal tissues causing morbidity and mortality. As diagnosis often follows irreversible organ damage, screening programs have been suggested to increase early diagnosis. A lack of economic evidence has been cited as a barrier to establishing such a program. Previous analyses used poorly estimated utility values. This study sought to measure utilities directly from people with HH in Australia. Methods: Volunteers with HH were recruited to complete a web-based survey. Utility was assessed using the Assessment of Quality of Life 4D (AQOL-4D) instrument. Severity of HH was graded into four categories. Multivariable regression analysis was performed to identify parameters associated with HSUV. Results: Between November 2013 and November 2014, 221 people completed the survey. Increasing severity of HH was negatively associated with utility. Mean (standard deviation) utilities were 0.76 (0.21), 0.81 (0.18), 0.60 (0.27), and 0.50 (0.27) for categories 1-4 HH respectively. Lower mean utility was found for symptomatic participants (categories 3 and 4) compared with asymptomatic participants (0.583 v. 0.796). Self-reported HH-related symptoms were negatively associated with HSUV (r = -0.685). Conclusions: Symptomatic stages of HH and presence of multiple self-reported symptoms were associated with decreasing utility. Previous economic analyses have used higher utilities which likely resulted in underestimates of the cost effectiveness of HH interventions. The utilities reported in this paper are the most robust available, and will contribute to improving the validity of future economic models for HH

Effects of Screening and Brief Intervention Training on Resident and Faculty Alcohol Intervention Behaviours: A Pre- Post-Intervention Assessment

Background: Many hazardous and harmful drinkers do not receive clinician advice to reduce their drinking. Previous studies suggest under-detection and clinician reluctance to intervene despite awareness of problem drinking (PD). The Healthy Habits Project previously reported chart review data documenting increased screening and intervention with hazardous and harmful drinkers after training clinicians and implementing routine screening. This report describes the impact of the Healthy Habits training program on clinicians\u27 rates of identification of PD, level of certainty in identifying PD and the proportion of patients given advice to reduce alcohol use, based on self-report data using clinician exit questionnaires. Methods: 28 residents and 10 faculty in a family medicine residency clinic completed four cycles of clinician exit interview questionnaires before and after screening and intervention training. Rates of identifying PD, level of diagnostic certainty, and frequency of advice to reduce drinking were compared across intervention status (pre vs. post). Findings were compared with rates of PD and advice to reduce drinking documented on chart review. Results: 1,052 clinician exit questionnaires were collected. There were no significant differences in rates of PD identified before and after intervention (9.8% vs. 7.4%, p = .308). Faculty demonstrated greater certainty in PD diagnoses than residents (p = .028) and gave more advice to reduce drinking (p = .042) throughout the program. Faculty and residents reported higher levels of diagnostic certainty after training (p = .039 and .030, respectively). After training, residents showed greater increases than faculty in the percentage of patients given advice to reduce drinking (p = .038), and patients felt to be problem drinkers were significantly more likely to receive advice to reduce drinking by all clinicians (50% vs. 75%, p = .047). The number of patients receiving advice to reduce drinking after program implementation exceeded the number of patients felt to be problem drinkers. Recognition rates of PD were four to eight times higher than rates documented on chart review (p = .028). Conclusion: This program resulted in greater clinician certainty in diagnosing PD and increases in the number of patients with PD who received advice to reduce drinking. Future programs should include booster training sessions and emphasize documentation of PD and brief intervention