The Drosophila melanogaster gut microbiota provisions thiamine to its host

The microbiota of Drosophila melanogaster has a substantial impact on host physiology and nutrition. Some effects may involve vitamin provisioning, but the relationships between microbe-derived vitamins, diet, and host health remain to be established systematically. We explored the contribution of microbiota in supplying sufficient dietary thiamine (vitamin B1) to support D. melanogaster at different stages of its life cycle. Using chemically defined diets with different levels of available thiamine, we found that the interaction of thiamine concentration and microbiota did not affect the longevity of adult D. melanogaster Likewise, this interplay did not have an impact on egg production. However, we determined that thiamine availability has a large impact on offspring development, as axenic offspring were unable to develop on a thiamine-free diet. Offspring survived on the diet only when the microbiota was present or added back, demonstrating that the microbiota was able to provide enough thiamine to support host development. Through gnotobiotic studies, we determined that Acetobacter pomorum, a common member of the microbiota, was able to rescue development of larvae raised on the no-thiamine diet. Further, it was the only microbiota member that produced measurable amounts of thiamine when grown on the thiamine-free fly medium. Its close relative Acetobacter pasteurianus also rescued larvae; however, a thiamine auxotrophic mutant strain was unable to support larval growth and development. The results demonstrate that the D. melanogaster microbiota functions to provision thiamine to its host in a low-thiamine environment. Importance: There has been a long-standing assumption that the microbiota of animals provides their hosts with essential B vitamins; however, there is not a wealth of empirical evidence supporting this idea, especially for vitamin B1 (thiamine). To determine whether this assumption is true, we used Drosophila melanogaster and chemically defined diets with different thiamine concentrations as a model. We found that the microbiota does provide thiamine to its host, enough to allow the development of flies on a thiamine-free diet. The power of the Drosophila-microbiota system allowed us to determine that one microbiota member in particular, Acetobacter pomorum, is responsible for the thiamine provisioning. Thereby, our study verifies this long-standing hypothesis. Finally, the methods used in this work are applicable for interrogating the underpinnings of other aspects of the tripartite interaction between diet, host, and microbiota

The evolution of plasticity at geographic range edges

Acknowledgments This article is the product of a working group funded by a grant from the Quebec Centre for Biodiversity Sciences to J-P.L. and K.E.M. J-P.L. is funded by a Concordia University Research Chair and an NSERC Discovery Grant (RGPIN-2015-06081). D.L. is supported by the Sustainability and Energy Research Initiative PhD grant. K.E.M. is supported by an NSERC Discovery Grant (RGPIN-2019-04239). C.J.G., A.L.A., and C.S. are funded by NSERC Discovery Grants. T.U. is supported by the UBC International Doctoral Fellowship.Peer reviewedPostprin

Interannual variations in continental-scale net carbon exchange and sensitivity to observing networks estimated from atmospheric CO2 inversions for the period 1980 to 2005

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 22 (2008): GB3025, doi:10.1029/2007GB003082.Interannually varying net carbon exchange fluxes from the TransCom 3 Level 2 Atmospheric Inversion Intercomparison Experiment are presented for the 1980 to 2005 time period. The fluxes represent the model mean, net carbon exchange for 11 land and 11 ocean regions after subtraction of fossil fuel CO2 emissions. Both aggregated regional totals and the individual regional estimates are accompanied by a model uncertainty and model spread. We find that interannual variability is larger on the land than the ocean, with total land exchange correlated to the timing of both El Niño/Southern Oscillation (ENSO) as well as the eruption of Mt. Pinatubo. The post-Pinatubo negative flux anomaly is evident across much of the tropical and northern extratropical land regions. In the oceans, the tropics tend to exhibit the greatest level of interannual variability, while on land, the interannual variability is slightly greater in the tropics and northern extratropics. The interannual variation in carbon flux estimates aggregated by land and ocean across latitudinal bands remains consistent across eight different CO2 observing networks. The interannual variation in carbon flux estimates for individual flux regions remains mostly consistent across the individual observing networks. At all scales, there is considerable consistency in the interannual variations among the 13 participating model groups. Finally, consistent with other studies using different techniques, we find a considerable positive net carbon flux anomaly in the tropical land during the period of the large ENSO in 1997/1998 which is evident in the Tropical Asia, Temperate Asia, Northern African, and Southern Africa land regions. Negative anomalies are estimated for the East Pacific Ocean and South Pacific Ocean regions. Earlier ENSO events of the 1980s are most evident in southern land positive flux anomalies

Long-term ecological research on Colorado Shortgrass Steppe

The SGS-LTER research site was established in 1980 by researchers at Colorado State University as part of a network of long-term research sites within the US LTER Network, supported by the National Science Foundation. Scientists within the Natural Resource Ecology Lab, Department of Forest and Rangeland Stewardship, Department of Soil and Crop Sciences, and Biology Department at CSU, California State Fullerton, USDA Agricultural Research Service, University of Northern Colorado, and the University of Wyoming, among others, have contributed to our understanding of the structure and functions of the shortgrass steppe and other diverse ecosystems across the network while maintaining a common mission and sharing expertise, data and infrastructure.Poster presented at the LTER All Scientists Meeting held in Estes Park, CO on September 10-13, 2012

Evaluating triple oxygen isotope estimates of gross primary production at the Hawaii Ocean Time-series and Bermuda Atlantic Time-series Study sites

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 117 (2012): C05012, doi:10.1029/2010JC006856.The triple oxygen isotopic composition of dissolved oxygen (17Δ) is a promising tracer of gross oxygen productivity (P) in the ocean. Recent studies have inferred a high and variable ratio of P to 14C net primary productivity (12–24 h incubations) (e.g., P:NPP(14C) of 5–10) using the 17Δ tracer method, which implies a very low efficiency of phytoplankton growth rates relative to gross photosynthetic rates. We added oxygen isotopes to a one-dimensional mixed layer model to assess the role of physical dynamics in potentially biasing estimates of P using the 17Δ tracer method at the Bermuda Atlantic Time-series Study (BATS) and Hawaii Ocean Time-series (HOT). Model results were compared to multiyear observations at each site. Entrainment of high 17Δ thermocline water into the mixed layer was the largest source of error in estimating P from mixed layer 17Δ. At both BATS and HOT, entrainment bias was significant throughout the year and resulted in an annually averaged overestimate of mixed layer P of 60 to 80%. When the entrainment bias is corrected for, P calculated from observed 17Δ and 14C productivity incubations results in a gross:net productivity ratio of 2.6 (+0.9 −0.8) at BATS. At HOT a gross:net ratio decreasing linearly from 3.0 (+1.0 −0.8) at the surface to 1.4 (+0.6 −0.6) at depth best reproduced observations. In the seasonal thermocline at BATS, however, a significantly higher gross:net ratio or large lateral fluxes of 17Δ must be invoked to explain 17Δ field observations.We acknowledge support from Center for Microbial Oceanography Research and Education (CMORE) (NSF EF-0424599) and NOAA Global Carbon Program (NA 100AR4310093). BL thanks the USA-Israel Binational Science Foundation for supporting his project at BATS.2012-11-0

Assessing the congruence of thermal niche estimations derived from distribution and physiological data. A test using diving beetles.

A basic aim of ecology is to understand the determinants of organismal distribution, the niche concept and species distribution models providing key frameworks to approach the problem. As temperature is one of the most important factors affecting species distribution, the estimation of thermal limits is crucially important for inferring range constraints. It is expectable that thermal physiology data derived from laboratory experiments and species' occurrences may express different aspects of the species' niche. However, there is no study systematically testing this prediction in a given taxonomic group while controlling by potential phylogenetic inertia. We estimate the thermal niches of twelve Palaearctic diving beetles species using physiological data derived from experimental analyses in order to examine the extent to which these coincided with those estimated from distribution models based on observed occurrences. We found that thermal niche estimates derived from both approaches lack general congruence, and these results were similar before and after controlling by phylogeny. The congruence between potential distributions obtained from the two different procedures was also explored, and we found again that the percentage of agreement were not very high (~60%). We confirm that both thermal niche estimates derived from geographical and physiological data are likely to misrepresent the true range of climatic variation that these diving beetles are able to tolerate, and so these procedures could be considered as incomplete but complementary estimations of an inaccessible reality

The case for the continued use of the genus name Mimulus for all monkeyflowers

The genus Mimulus is a well-studied group of plant species, which has for decades allowed researchers to address a wide array of fundamental questions in biology (Wu & al. 2008; Twyford & al. 2015). Linnaeus named the type species of Mimulus (ringens L.), while Darwin (1876) used Mimulus (luteus L.) to answer key research questions. The incredible phenotypic diversity of this group has made it the focus of ecological and evolutionary study since the mid-20th century, initiated by the influential work of Clausen, Keck, and Hiesey as well as their students and collaborators (Clausen & Hiesey 1958; Hiesey & al. 1971, Vickery 1952, 1978). Research has continued on this group of diverse taxa throughout the 20th and into the 21st century (Bradshaw & al. 1995; Schemske & Bradshaw 1999; Wu & al. 2008; Twyford & al. 2015; Yuan 2019), and Mimulus guttatus was one of the first non-model plants to be selected for full genome sequencing (Hellsten & al. 2013). Mimulus has played a key role in advancing our general understanding of the evolution of pollinator shifts (Bradshaw & Schemske 2003; Cooley & al. 2011; Byers & al. 2014), adaptation (Lowry & Willis 2010; Kooyers & al. 2015; Peterson & al. 2016; Ferris & Willis 2018; Troth & al. 2018), speciation (Ramsey & al. 2003; Wright & al. 2013; Sobel & Streisfeld 2015; Zuellig & Sweigart 2018), meiotic drive (Fishman & Saunders 2008), polyploidy (Vallejo-Marín 2012; Vallejo-Marín & al. 2015), range limits (Angert 2009; Sexton et al. 2011; Grossenbacher & al. 2014; Sheth & Angert 2014), circadian rhythms (Greenham & al. 2017), genetic recombination (Hellsten & al. 2013), mating systems (Fenster & Ritland 1994; Dudash & Carr 1998; Brandvain & al. 2014) and developmental biology (Moody & al. 1999; Baker & al. 2011, 2012; Yuan 2019). This combination of a rich history of study coupled with sustained modern research activity is unparalleled among angiosperms. Across many interested parties, the name Mimulus therefore takes on tremendous biological significance and is recognizable not only by botanists, but also by zoologists, horticulturalists, naturalists, and members of the biomedical community. Names associated with a taxonomic group of this prominence should have substantial inertia, and disruptive name changes should be avoided. As members of the Mimulus community, we advocate retaining the genus name Mimulus to describe all monkeyflowers. This is despite recent nomenclature changes that have led to a renaming of most monkeyflower species to other genera.Additional co-authors: Jannice Friedman, Dena L Grossenbacher, Liza M Holeski, Christopher T Ivey, Kathleen M Kay, Vanessa A Koelling, Nicholas J Kooyers, Courtney J Murren, Christopher D Muir, Thomas C Nelson, Megan L Peterson, Joshua R Puzey, Michael C Rotter, Jeffrey R Seemann, Jason P Sexton, Seema N Sheth, Matthew A Streisfeld, Andrea L Sweigart, Alex D Twyford, John H Willis, Kevin M Wright, Carrie A Wu, Yao-Wu Yua

Process-evaluation of tropospheric humidity simulated by general circulation models using water vapor isotopic observations: 2. Using isotopic diagnostics to understand the mid and upper tropospheric moist bias in the tropics and subtropics

Evaluating the representation of processes controlling tropical and subtropical tropospheric relative humidity (RH) in atmospheric general circulation models (GCMs) is crucial to assess the credibility of predicted climate changes. GCMs have long exhibited a moist bias in the tropical and subtropical mid and upper troposphere, which could be due to the mis-representation of cloud processes or of the large-scale circulation, or to excessive diffusion during water vapor transport. The goal of this study is to use observations of the water vapor isotopic ratio to understand the cause of this bias. We compare the three-dimensional distribution of the water vapor isotopic ratio measured from space and ground to that simulated by several versions of the isotopic GCM LMDZ. We show that the combined evaluation of RH and of the water vapor isotopic composition makes it possible to discriminate the most likely cause of RH biases. Models characterized either by an excessive vertical diffusion, an excessive convective detrainment or an underestimated in situ cloud condensation will all produce a moist bias in the free troposphere. However, only an excessive vertical diffusion can lead to a reversed seasonality of the free tropospheric isotopic composition in the subtropics compared to observations. Comparing seven isotopic GCMs suggests that the moist bias found in many GCMs in the mid and upper troposphere most frequently results from an excessive diffusion during vertical water vapor transport. This study demonstrates the added value of water vapor isotopic measurements for interpreting shortcomings in the simulation of RH by climate models

Metagenomics for Bacteriology

The study of bacteria, or bacteriology, has gone through transformative waves since its inception in the 1600s. It all started by the visualization of bacteria using light microscopy by Antonie van Leeuwenhoek, when he first described “animalcules.” Direct cellular observation then evolved into utilizing different wavelengths on novel platforms such as electron, fluorescence, and even near-infrared microscopy. Understanding the link between microbes and disease (pathogenicity) began with the ability to isolate and cultivate organisms through aseptic methodologies starting in the 1700s. These techniques became more prevalent in the following centuries with the work of famous scientists such as Louis Pasteur and Robert Koch, and many others since then. The relationship between bacteria and the host’s immune system was first inferred in the 1800s, and to date is continuing to unveil its mysteries. During the last century, researchers initiated the era of molecular genetics. The discovery of the first-generation sequencing technology, the Sanger method, and, later, the polymerase chain reaction technology propelled the molecular genetics field by exponentially expanding the knowledge of relationship between gene structure and function. The rise of commercially available next-generation sequencing methodologies, in the beginning of this century, is drastically allowing larger amount of information to be acquired, in a manner open to the democratization of the approach

Repair of the injured adult heart involves resident cardiac stem cell derived new myocytes

The ability of the adult heart to generate new myocytes after injury is not established. Our purpose was to determine if the adult heart has the capacity to generate new myocytes after injury, and to gain insight into their source. Cardiac injury was induced in the adult feline heart by infusing Isoproterenol (ISO) for 10 days with minipumps and then animals were allowed to recover for 7 or 28 days. Cardiac function was measured with echocardiography and proliferative cells were identified by nuclear incorporation of 5-bromodeoxyuridine (BrdU; 7 day minipump infusion). BrdU was infused for 7 days before euthanasia at Day 10 (injury), Day 17 (early recovery), and Day 38 (late recovery) and, with a separate group of animals, was infused during injury and removed at Day 10, with animals euthanized at Day 38 for a pulse-chase experiment. Isoproterenol caused a reduction in cardiac function with evidence of myocyte loss from necrosis. During the injury phase there was a significant increase in the number of proliferative cells in the atria and ventricle, including an increase in cKit+/BrdU+ proliferative cardiac precursor cells, but there was no increase in the number of BrdU+ new myocytes (Day 10). During the first seven days of recovery (Day 17) there was a significant reduction in cellular proliferation (total BrdU+ nuclei, including cKit+/BrdU+ proliferative cardiac precursor cells) but a significant increase in BrdU+ myocytes. There was modest improvement in cardiac structure and function during recovery. At Day 38 (late recovery), overall cell proliferation (BrdU+ cells) was not different than control (BrdU infused from Days 31-38); however, increased numbers of (“bright”) BrdU+ myocytes were found at Day 38 in the pulse-chase experiment, when BrdU was infused during injury (and removed at Day 10). Some of the newly formed myocytes (from the pulse-chase group; Day 38), derived from BrdU+ cardiac precursors appear to be transiently proliferative (between Days 10-38) producing a population of “dimly” BrdU+ myocytes in our pulse-chase protocol (BrdU infused during injury, Days 3-10, and removed at Day 10, with heart explant at Day 38). No significant numbers of “dimly” BrdU+ nuclei were found in any of the hearts in which BrdU was infused for 7 days prior to the animal being euthanized (Control, Day 10, Day 17, Day 38). These observations are most consistent with the conclusions stated. Our results also suggest that myocyte regeneration, as defined by BrdU+ myocytes, was more robust in the atria than the ventricle. The reasons for these differences are not clear and deserve additional study. If true, our findings suggest that cardiac precursors isolated and expanded from atrial tissue might be a better source of cells for autologous cardiac cell therapy. In summary, our data shows that the adult heart has the ability to generate new myocytes after injury, suggests that ISO injury activates cardiac precursor cells that can differentiate into new myocytes during cardiac repair, but that the environment of the ISO injured heart blunts the differentiation of cardiac precursors into functional new myocytes. The contribution of new myocytes to improved function of the ventricle would appear to be small, unless we have underestimated the number of these cells. This is quite possible, and further study is warranted to incorporate the number of “dimly” BrdU+ myocytes that may have undergone a proliferative phase as a progenitor cell and/or as an immature cardiac myocyte. Further understanding the factors that limit endogenous new myocyte formation could significantly contribute to new therapeutic applications and improve the quality of life, and potentially the lifespan, of patients in heart failure