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Articles 1 - 20 of 20
Full-Text Articles in Life Sciences
Plant Single-Cell Metabolomics—Challenges And Perspectives, Leonardo Perez De Souza, Monica Borghi, Alisdair R. Fernie
Plant Single-Cell Metabolomics—Challenges And Perspectives, Leonardo Perez De Souza, Monica Borghi, Alisdair R. Fernie
Biology Faculty Publications
Omics approaches for investigating biological systems were introduced in the mid-1990s and quickly consolidated to become a fundamental pillar of modern biology. The idea of measuring the whole complement of genes, transcripts, proteins, and metabolites has since become widespread and routinely adopted in the pursuit of an infinity of scientific questions. Incremental improvements over technical aspects such as sampling, sensitivity, cost, and throughput pushed even further the boundaries of what these techniques can achieve. In this context, single-cell genomics and transcriptomics quickly became a well-established tool to answer fundamental questions challenging to assess at a whole tissue level. Following a …
Stream Dissolved Organic Matter In Permafrost Regions Shows Surprising Compositional Similarities But Negative Priming And Nutrient Effects, Ethan Wologo, Sarah Shakil, Scott Zolkos, Sadie Textor, Stephanie Ewing, Jane Klassen, Robert G. M. Spencer, David C. Podgorski, Suzanne E. Tank, Michelle A. Baker, Jonathan A. O'Donnell, Kimberly P. Wickland, Sydney S. W. Foks, Jay P. Zarnetske, Joseph Lee-Cullin, Futing Liu, Yuanhe Yang, Pirkko Kortelainen, Jaana Kolehmainen, Joshua F. Dean, Jorien E. Vonk, Robert M. Holmes, Gilles Pinay, Michaela M. Powell, Jansen Howe, Rebecca J. Frei, Samuel P. Bratsman, Benjamin W. Abbott
Stream Dissolved Organic Matter In Permafrost Regions Shows Surprising Compositional Similarities But Negative Priming And Nutrient Effects, Ethan Wologo, Sarah Shakil, Scott Zolkos, Sadie Textor, Stephanie Ewing, Jane Klassen, Robert G. M. Spencer, David C. Podgorski, Suzanne E. Tank, Michelle A. Baker, Jonathan A. O'Donnell, Kimberly P. Wickland, Sydney S. W. Foks, Jay P. Zarnetske, Joseph Lee-Cullin, Futing Liu, Yuanhe Yang, Pirkko Kortelainen, Jaana Kolehmainen, Joshua F. Dean, Jorien E. Vonk, Robert M. Holmes, Gilles Pinay, Michaela M. Powell, Jansen Howe, Rebecca J. Frei, Samuel P. Bratsman, Benjamin W. Abbott
Biology Faculty Publications
Permafrost degradation is delivering bioavailable dissolved organic matter (DOM) and inorganic nutrients to surface water networks. While these permafrost subsidies represent a small portion of total fluvial DOM and nutrient fluxes, they could influence food webs and net ecosystem carbon balance via priming or nutrient effects that destabilize background DOM. We investigated how addition of biolabile carbon (acetate) and inorganic nutrients (nitrogen and phosphorus) affected DOM decomposition with 28-day incubations. We incubated late-summer stream water from 23 locations nested in seven northern or high-altitude regions in Asia, Europe, and North America. DOM loss ranged from 3% to 52%, showing a …
Increasing Our Ability To Predict Contemporary Evolution, Patrik Nosil, Samuel M. Flaxman, Jeffrey L. Feder, Zachariah Gompert
Increasing Our Ability To Predict Contemporary Evolution, Patrik Nosil, Samuel M. Flaxman, Jeffrey L. Feder, Zachariah Gompert
Biology Faculty Publications
Classic debates concerning the extent to which scientists can predict evolution have gained new urgency as environmental changes force species to adapt or risk extinction. We highlight how our ability to predict evolution can be constrained by data limitations that cause poor understanding of deterministic natural selection. We then emphasize how such data limits can be reduced with feasible empirical effort involving a combination of approaches.
Seed-Transmitted Wheat Mosaic Virus In Sweet Corn In Utah, Claudia Nischwitz
Seed-Transmitted Wheat Mosaic Virus In Sweet Corn In Utah, Claudia Nischwitz
Biology Faculty Publications
Wheat mosaic virus (WMoV) (syn. High Plains virus) was first observed in corn in 1993 in Colorado, Idaho, Kansas, and Texas (Seifers et al. 1997). The virus causes chlorotic streaks and mosaic on corn foliage, and it stunts ear development. When infected early in the season, plants frequently die. There are anecdotal reports of reduced seed germination rates in infected seed lots. The host range of the virus includes corn, small grains, and yellow and green foxtail. The virus is transmitted by the wheat curl mite (Aceria tosichella Keifer 1969). Seed transmission of WMoV at extremely low rates was …
Brain Micrornas Among Social And Solitary Bees, Karen M. Kapheim, Beryl M. Jones, Eirik Søvik, Eckart Stolle, Robert M. Waterhouse, Guy Bloch, Yehuda Ben-Shahar
Brain Micrornas Among Social And Solitary Bees, Karen M. Kapheim, Beryl M. Jones, Eirik Søvik, Eckart Stolle, Robert M. Waterhouse, Guy Bloch, Yehuda Ben-Shahar
Biology Faculty Publications
Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20–35%) of detected miRNAs had lineage-specific expression in the brain, 24–72% of which did not have homologues in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression …
Morphological Evidence For An Oral Venom System In Caecilian Amphibians, Pedro Luiz Mailho-Fontana, Marta Maria Antoniazzi, Cesar Alexandre, Daniel Carvalho Pimenta, Juliana Mozer Sciani, Edmund D. Brodie Jr., Carlos Jared
Morphological Evidence For An Oral Venom System In Caecilian Amphibians, Pedro Luiz Mailho-Fontana, Marta Maria Antoniazzi, Cesar Alexandre, Daniel Carvalho Pimenta, Juliana Mozer Sciani, Edmund D. Brodie Jr., Carlos Jared
Biology Faculty Publications
Amphibians are known for their skin rich in glands containing toxins employed in passive chemical defense against predators, different from, for example, snakes that have active chemical defense, injecting their venom into the prey. Caecilians (Amphibia, Gymnophiona) are snake-shaped animals with fossorial habits, considered one of the least known vertebrate groups. We show here that amphibian caecilians, including species from the basal groups, besides having cutaneous poisonous glands as other amphibians do, possess specific glands at the base of the teeth that produce enzymes commonly found in venoms. Our analysis of the origin of these glands shows that they originate …
Investigating The Direct And Indirect Effects Of Forest Fragmentation On Plant Functional Diversity, Jenny Zambrano, Norbert J. Cordeiro, Carol Garzon-Lopez, Lauren Yeager, Claire Fortunel, Henry J. Ndangalasi, Noelle G. Beckman
Investigating The Direct And Indirect Effects Of Forest Fragmentation On Plant Functional Diversity, Jenny Zambrano, Norbert J. Cordeiro, Carol Garzon-Lopez, Lauren Yeager, Claire Fortunel, Henry J. Ndangalasi, Noelle G. Beckman
Biology Faculty Publications
Ongoing habitat loss and fragmentation alter the functional diversity of forests. Generalising the magnitude of change in functional diversity of fragmented landscapes and its drivers is challenging because of the multiple scales at which landscape fragmentation takes place. Here we propose a multi-scale approach to determine whether fragmentation processes at the local and landscape scales are reducing functional diversity of trees in the East Usambara Mountains, Tanzania. We employ a structural equation modelling approach using five key plant traits (seed length, dispersal mode, shade tolerance, maximum tree height, and wood density) to better understand the functional responses of trees to …
The Fire And Tree Mortality Database, For Empirical Modeling Of Individual Tree Mortality After Fire, C. Alina Cansler, Sharon M. Hood, J. Morgan Varner, Phillip J. Van Mantgem, Michelle C. Agne, Robert A. Andrus, Matthew P. Ayres, Bruce D. Ayres, Jonathan D. Bakker, Michael A. Battaglia, Barbara J. Bentz, Carolyn R. Breece, James K. Brown, Daniel R. Cluck, Tom W. Coleman, R. Gregory Corace Iii, W. Wallace Covington, Douglas S. Cram, James B. Cronan, Joseph E. Crouse, Adrian J. Das, Ryan S. Davis, Et Al.
The Fire And Tree Mortality Database, For Empirical Modeling Of Individual Tree Mortality After Fire, C. Alina Cansler, Sharon M. Hood, J. Morgan Varner, Phillip J. Van Mantgem, Michelle C. Agne, Robert A. Andrus, Matthew P. Ayres, Bruce D. Ayres, Jonathan D. Bakker, Michael A. Battaglia, Barbara J. Bentz, Carolyn R. Breece, James K. Brown, Daniel R. Cluck, Tom W. Coleman, R. Gregory Corace Iii, W. Wallace Covington, Douglas S. Cram, James B. Cronan, Joseph E. Crouse, Adrian J. Das, Ryan S. Davis, Et Al.
Biology Faculty Publications
Wildland fires have a multitude of ecological effects in forests, woodlands, and savannas across the globe. A major focus of past research has been on tree mortality from fire, as trees provide a vast range of biological services. We assembled a database of individual-tree records from prescribed fires and wildfires in the United States. The Fire and Tree Mortality (FTM) database includes records from 164,293 individual trees with records of fire injury (crown scorch, bole char, etc.), tree diameter, and either mortality or top-kill up to ten years post-fire. Data span 142 species and 62 genera, from 409 fires occurring …
How Many Tree Species Of Birch Are In Alaska? Implications For Wetland Designations, Carol A. Rowe, Robert W. Lichvar, Paul G. Wolf
How Many Tree Species Of Birch Are In Alaska? Implications For Wetland Designations, Carol A. Rowe, Robert W. Lichvar, Paul G. Wolf
Biology Faculty Publications
Wetland areas are critical habitats, especially in northern regions of North America. Wetland classifications are based on several factors, including the presence of certain plant species and assemblages of species, of which trees play a significant role. Here we examined wetland species of birch (Betula) in North America, with a focus on Alaska, and the use of birche tree species in wetland delineation. We sampled over 200 trees from sites, including Alaska, Alberta, Minnesota, and New Hampshire. We used genetic data from over 3000 loci detected by restriction site associated DNA analysis. We used an indirect estimate of …
Solution Blow Spinning Of Polyvinylidene Fluoride Based Fibers For Energy Harvesting Applications: A Review, Rasheed Atif, Jibran Khaliq, Madeleine Combrinck, Ahmed H. Hassanin, Nader Shehata, Eman Elnabawy, Islam Shyha
Solution Blow Spinning Of Polyvinylidene Fluoride Based Fibers For Energy Harvesting Applications: A Review, Rasheed Atif, Jibran Khaliq, Madeleine Combrinck, Ahmed H. Hassanin, Nader Shehata, Eman Elnabawy, Islam Shyha
Biology Faculty Publications
Polyvinylidene fluoride (PVDF)-based piezoelectric materials (PEMs) have found extensive applications in energy harvesting which are being extended consistently to diverse fields requiring strenuous service conditions. Hence, there is a pressing need to mass produce PVDF-based PEMs with the highest possible energy harvesting ability under a given set of conditions. To achieve high yield and efficiency, solution blow spinning (SBS) technique is attracting a lot of interest due to its operational simplicity and high throughput. SBS is arguably still in its infancy when the objective is to mass produce high efficiency PVDF-based PEMs. Therefore, a deeper understanding of the critical parameters …
Acoustic Energy Harvesting And Sensing Via Electrospun Pvdf Nanofiber Membrane, Nader Shehata, Ahmed H. Hassanin, Eman Elnabawy, Remya Nair, Sameer A. Bhat, Ishac Kandas
Acoustic Energy Harvesting And Sensing Via Electrospun Pvdf Nanofiber Membrane, Nader Shehata, Ahmed H. Hassanin, Eman Elnabawy, Remya Nair, Sameer A. Bhat, Ishac Kandas
Biology Faculty Publications
This paper introduces a new usage of piezoelectric poly (vinylidene fluoride) (PVDF) electrospun nanofiber (NF) membrane as a sensing unit for acoustic signals. In this work, an NF mat has been used as a transducer to convert acoustic signals into electric voltage outcomes. The detected voltage has been analyzed as a function of both frequency and amplitude of the excitation acoustic signal. Additionally, the detected AC signal can be retraced as a function of both frequency and amplitude with some wave distortion at relatively higher amplitudes and within a certain acoustic spectrum region. Meanwhile, the NFs have been characterized through …
Developmental Plasticity Shapes Social Traits And Selection In A Facultatively Eusocial Bee, Karen M. Kapheim, Beryl M. Jones, Hailin Pan, Cai Li, Brock A. Harpur, Clement F. Kent, Amro Zayed, Panagiotis Ioannidis, Robert M. Waterhouse, Callum Kingwell, Eckart Stolle, Arián Avalos, Guojie Zhang, W. Owen Mcmillan, William T. Wcislo
Developmental Plasticity Shapes Social Traits And Selection In A Facultatively Eusocial Bee, Karen M. Kapheim, Beryl M. Jones, Hailin Pan, Cai Li, Brock A. Harpur, Clement F. Kent, Amro Zayed, Panagiotis Ioannidis, Robert M. Waterhouse, Callum Kingwell, Eckart Stolle, Arián Avalos, Guojie Zhang, W. Owen Mcmillan, William T. Wcislo
Biology Faculty Publications
Developmental plasticity generates phenotypic variation, but how it contributes to evolutionary change is unclear. Phenotypes of individuals in caste-based (eusocial) societies are particularly sensitive to developmental processes, and the evolutionary origins of eusociality may be rooted in developmental plasticity of ancestral forms. We used an integrative genomics approach to evaluate the relationships among developmental plasticity, molecular evolution, and social behavior in a bee species (Megalopta genalis) that expresses flexible sociality, and thus provides a window into the factors that may have been important at the evolutionary origins of eusociality. We find that differences in social behavior are derived …
Outstanding Questions In Flower Metabolism, Monica Borghi, Alisdair R. Fernie
Outstanding Questions In Flower Metabolism, Monica Borghi, Alisdair R. Fernie
Biology Faculty Publications
The great diversity of flowers, their color, odor, taste, and shape, is mostly a result of the metabolic processes that occur in this reproductive organ when the flower and its tissues develop, grow, and finally die. Some of these metabolites serve to advertise flowers to animal pollinators, other confer protection towards abiotic stresses, and a large proportion of the molecules of the central metabolic pathways have bioenergetic and signaling functions that support growth and the transition to fruits and seeds. Although recent studies have advanced our general understanding of flower metabolism, several questions still await an answer. Here, we have …
Combining Experimental Evolution And Genomics To Understand How Seed Beetles Adapt To A Marginal Host Plant, Alexandre Rêgo, Samridhi Chaturvedi, Amy Springer, Alexandra M. Lish, Caroline L. Barton, Karen M. Kapheim, Frank J. Messina, Zachariah Gompert
Combining Experimental Evolution And Genomics To Understand How Seed Beetles Adapt To A Marginal Host Plant, Alexandre Rêgo, Samridhi Chaturvedi, Amy Springer, Alexandra M. Lish, Caroline L. Barton, Karen M. Kapheim, Frank J. Messina, Zachariah Gompert
Biology Faculty Publications
Genes that affect adaptive traits have been identified, but our knowledge of the genetic basis of adaptation in a more general sense (across multiple traits) remains limited. We combined population-genomic analyses of evolve-and-resequence experiments, genome-wide association mapping of performance traits, and analyses of gene expression to fill this knowledge gap and shed light on the genomics of adaptation to a marginal host (lentil) by the seed beetle Callosobruchus maculatus. Using population-genomic approaches, we detected modest parallelism in allele frequency change across replicate lines during adaptation to lentil. Mapping populations derived from each lentil-adapted line revealed a polygenic basis for …
Microbial Lag Phase Can Be Indicative Of, Or Independent From, Cellular Stress, Philip G. Hamill, Andrew Stevenson, Phillip E. Mcmullan, James P. Williams, Abiann D. R. Lewis, Sudharsan S., Kath E. Stevenson, Keith D. Farnsworth, Galina Khroustalyova, Jon Y. Takemoto, John P. Quinn, Alexander Rapoport, John E. Hallsworth
Microbial Lag Phase Can Be Indicative Of, Or Independent From, Cellular Stress, Philip G. Hamill, Andrew Stevenson, Phillip E. Mcmullan, James P. Williams, Abiann D. R. Lewis, Sudharsan S., Kath E. Stevenson, Keith D. Farnsworth, Galina Khroustalyova, Jon Y. Takemoto, John P. Quinn, Alexander Rapoport, John E. Hallsworth
Biology Faculty Publications
Measures of microbial growth, used as indicators of cellular stress, are sometimes quantified at a single time-point. In reality, these measurements are compound representations of length of lag, exponential growth-rate, and other factors. Here, we investigate whether length of lag phase can act as a proxy for stress, using a number of model systems (Aspergillus penicillioides; Bacillus subtilis; Escherichia coli; Eurotium amstelodami, E. echinulatum, E. halophilicum, and E. repens; Mrakia frigida; Saccharomyces cerevisiae; Xerochrysium xerophilum; Xeromyces bisporus) exposed to mechanistically distinct types of cellular stress including low water activity, …
Introduction To The Special Issue: The Role Of Seed Dispersal In Plant Populations: Perspectives And Advances In A Changing World, Noelle G. Beckman, Clare E. Aslan, Haldre S. Rogers
Introduction To The Special Issue: The Role Of Seed Dispersal In Plant Populations: Perspectives And Advances In A Changing World, Noelle G. Beckman, Clare E. Aslan, Haldre S. Rogers
Biology Faculty Publications
Despite the importance of seed dispersal as a driving process behind plant community assembly, our understanding of the role of seed dispersal in plant population persistence and spread remains incomplete. As a result, our ability to predict the effects of global change on plant populations is hampered. We need to better understand the fundamental link between seed dispersal and population dynamics in order to make predictive generalizations across species and systems, to better understand plant community structure and function, and to make appropriate conservation and management responses related to seed dispersal. To tackle these important knowledge gaps, we established the …
Dramatic Dietary Shift Maintains Sequestered Toxins In Chemically Defended Snakes, Tatsuya Yoshida, Rinako Ujiie, Alan H. Savitzky, Teppei Jono, Takato Inoue, Naoko Yoshinaga, Shunsuke Aburaya, Wataru Aoki, Hirohiko Takeuchi, Li Ding, Qin Chen, Chengquan Cao, Tein-Shun Tsai, Anslem De Silva, Dharshani Mahaulpatha, Et Al.
Dramatic Dietary Shift Maintains Sequestered Toxins In Chemically Defended Snakes, Tatsuya Yoshida, Rinako Ujiie, Alan H. Savitzky, Teppei Jono, Takato Inoue, Naoko Yoshinaga, Shunsuke Aburaya, Wataru Aoki, Hirohiko Takeuchi, Li Ding, Qin Chen, Chengquan Cao, Tein-Shun Tsai, Anslem De Silva, Dharshani Mahaulpatha, Et Al.
Biology Faculty Publications
Unlike other snakes, most species of Rhabdophis possess glands in their dorsal skin, sometimes limited to the neck, known as nucho-dorsal and nuchal glands, respectively. Those glands contain powerful cardiotonic steroids known as bufadienolides, which can be deployed as a defense against predators. Bufadienolides otherwise occur only in toads (Bufonidae) and some fireflies (Lampyrinae), which are known or believed to synthesize the toxins. The ancestral diet of Rhabdophis consists of anuran amphibians, and we have shown previously that the bufadienolide toxins of frog-eating species are sequestered from toads consumed as prey. However, one derived clade, the Rhabdophis nuchalis Group, has …
Invasive Vegetation Affects Amphibian Skin Microbiota And Body Condition, Obed HernáNdez-GóMez, Allison Q. Byrne, Alex R. Gunderson, Thomas S. Jenkinson, Clay F. Noss, Andrew P. Rothstein, Molly C. Womack, Erica B. Rosenblum
Invasive Vegetation Affects Amphibian Skin Microbiota And Body Condition, Obed HernáNdez-GóMez, Allison Q. Byrne, Alex R. Gunderson, Thomas S. Jenkinson, Clay F. Noss, Andrew P. Rothstein, Molly C. Womack, Erica B. Rosenblum
Biology Faculty Publications
Invasive plants are major drivers of habitat modification and the scale of their impact is increasing globally as anthropogenic activities facilitate their spread. In California, an invasive plant genus of great concern is Eucalyptus. Eucalyptus leaves can alter soil chemistry and negatively affect underground macro- and microbial communities. Amphibians serve as excellent models to evaluate the effect of Eucalyptus invasion on ground-dwelling species as they predate on soil arthropods and incorporate soil microbes into their microbiotas. The skin microbiota is particularly important to amphibian health, suggesting that invasive plant species could ultimately affect amphibian populations. To investigate the potential for …
In-Situ Gold–Ceria Nanoparticles: Superior Optical Fluorescence Quenching Sensor For Dissolved Oxygen, Nader Shehata, Ishac Kandas, Effat Samir
In-Situ Gold–Ceria Nanoparticles: Superior Optical Fluorescence Quenching Sensor For Dissolved Oxygen, Nader Shehata, Ishac Kandas, Effat Samir
Biology Faculty Publications
Cerium oxide (ceria) nanoparticles (NPs) have been proved to be an efficient optical fluorescent material through generating visible emission (~530 nm) under violet excitation. This feature allowed ceria NPs to be used as an optical sensor via the fluorescence quenching Technique. In this paper, the impact of in-situ embedded gold nanoparticles (Au NPs) inside ceria nanoparticles was studied. Then, gold–ceria NPs were used for sensing dissolved oxygen (DO) in aqueous media. It was observed that both fluorescence intensity and lifetime were changed due to increased concentration of DO. Added gold was found to enhance the sensitivity of ceria to DO …
Investigating The Relationship Between Corticosterone And Glucose In A Reptile, Lorin A. Neuman-Lee, Spencer B. Hudson, Alison C. Webb, Susannah S. French
Investigating The Relationship Between Corticosterone And Glucose In A Reptile, Lorin A. Neuman-Lee, Spencer B. Hudson, Alison C. Webb, Susannah S. French
Biology Faculty Publications
The glucocorticoid hormone corticosterone (CORT) has classically been used in ecophysiological studies as a proxy for stress and energy mobilization, but rarely are CORT and the energy metabolites themselves concurrently measured. To examine CORT's role in mobilizing glucose in a wild reptile, we conducted two studies. The first study measured natural baseline and stress-induced blood-borne CORT and glucose levels in snakes during spring emergence and again when snakes return to the denning sites in autumn. The second study manipulated the hypothalamic–pituitary–adrenal (HPA) axis in male snakes in the autumn by taking a baseline blood sample, then subjecting individuals to one …