Biology Commons^™

Lianas And Soil Nutrients Predict Fine‐Scale Distribution Of Above‐Ground Biomass In A Tropical Moist Forest, Alicia Ledo, Janine B. Illian, Stefan A. Schnitzer, S. Joseph Wright, James W. Dalling, David F.R.P. Burslem

Biological Sciences Faculty Research and Publications

Summary

1. Prediction of carbon dynamics in response to global climate change requires an understanding of the processes that govern the distribution of carbon stocks. Above‐ground biomass (AGB) in tropical forests is regulated by variation in soil fertility, climate, species composition and topography at regional scales, but the drivers of fine‐scale variation in tropical forest AGB are poorly understood. The factors that control the growth and mortality of individual trees may be obscured by the low resolution of studies at regional scales.
2. In this paper, we evaluated the effects of soil nutrients, topography and liana abundance on the fine‐scale spatial distribution …

Supercomplex-Associated Cox26 Protein Binds To Cytochrome C Oxidase, Valentina Strecker, Zibirnisa Kadeer, Juliana Heidler, Cristina-Maria Cruciat, Heike Angerer, Heiko Giese, Kathy Pfeiffer, Rosemary A. Stuart, Ilka Wittig

Biological Sciences Faculty Research and Publications

Here we identified a hydrophobic 6.4 kDa protein, Cox26, as a novel component of yeast mitochondrial supercomplex comprising respiratory complexes III and IV. Multi-dimensional native and denaturing electrophoretic techniques were used to identify proteins interacting with Cox26. The majority of the Cox26 protein was found non-covalently bound to the complex IV moiety of the III–IV supercomplexes. A population of Cox26 was observed to exist in a disulfide bond partnership with the Cox2 subunit of complex IV. No pronounced growth phenotype for Cox26 deficiency was observed, indicating that Cox26 may not play a critical role in the COX enzymology, and we …

Using Rad‐Seq To Recognize Sex‐Specific Markers And Sex Chromosome Systems, Tony Gamble

Biological Sciences Faculty Research and Publications

Next‐generation sequencing methods have initiated a revolution in molecular ecology and evolution (Tautz et al. 2010). Among the most impressive of these sequencing innovations is restriction site‐associated DNA sequencing or RAD‐seq (Baird et al. 2008; Andrews et al. 2016). RAD‐seq uses the Illumina sequencing platform to sequence fragments of DNA cut by a specific restriction enzyme and can generate tens of thousands of molecular genetic markers for analysis. One of the many uses of RAD‐seq data has been to identify sex‐specific genetic markers, markers found in one sex but not the other (Baxter et …

Spa47 Is An Oligomerization-Activated Type Three Secretion System (T3ss) Atpase From Shigella Flexneri, Jamie L. Burgess, Heather B. Jones, Prashant Kumar, Ronald T. Toth Iv, C. Russell Middaugh, Edwin Antony, Nicholas E. Dickenson

Biological Sciences Faculty Research and Publications

Gram-negative pathogens often use conserved type three secretion systems (T3SS) for virulence. The Shigella type three secretion apparatus (T3SA) penetrates the host cell membrane and provides a unidirectional conduit for injection of effectors into host cells. The protein Spa47 localizes to the base of the apparatus and is speculated to be an ATPase that provides the energy for T3SA formation and secretion. Here, we developed an expression and purification protocol, producing active Spa47 and providing the first direct evidence that Spa47 is a bona fide ATPase. Additionally, size exclusion chromatography and analytical ultracentrifugation identified multiple oligomeric species of Spa47 with …

Application Of Alternative Nucleic Acid Extraction Protocols To Progastro Sscs Assay For Detection Of Bacterial Enteric Pathogens, Erik Munson, Maureen Napierala, Kimber L. Munson, Dorothy Bilbo, Michael A. Schulte

Clinical Lab Sciences Faculty Research and Publications

As an alternative to automated extraction, fecal specimens were processed by investigational lysis/heating (i.e., manual) and by chromatography/centrifugation (i.e., column) methods. ProGastro SSC and Shiga toxin-producing Escherichia coli (i.e., STEC) indeterminate rates for 101 specimens were 1.0% to 3.0% for automated, 11.9% for manual, and 24.8% to 37.6% for column methods. Following freeze-thaw of 247 specimens, indeterminate rates were 1.6% to 2.4% for manual and 0.8 to 5.3% for column methods. Mean processing times for manual and column methods were 30.5 and 69.2 min, respectively. Concordance of investigational methods with automated extraction was ≥98.8%.

Sexual Differentiation Of Circadian Clock Function In The Adrenal Gland, Ian Kloehn, Savin B. Pillai, Laurel Officer, Claire Klement, Paul J. Gasser, Jennifer A. Evans

Biological Sciences Faculty Research and Publications

Sex differences in glucocorticoid production are associated with increased responsiveness of the adrenal gland in females. However, the adrenal-intrinsic mechanisms that establish sexual dimorphic function remain ill defined. Glucocorticoid production is gated at the molecular level by the circadian clock, which may contribute to sexual dimorphic adrenal function. Here we examine sex differences in the adrenal gland using an optical reporter of circadian clock function. Adrenal glands were cultured from male and female Period2::Luciferase (PER2::LUC) mice to assess clock function in vitro in real time. We confirm that there is a pronounced sex difference in the intrinsic capacity to …

Relating Anaerobic Digestion Microbial Community And Process Function, Kaushik Venkiteshwaran, Benjamin T.W. Bocher, James Maki, Daniel Zitomer

Biological Sciences Faculty Research and Publications

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production …

Liana Canopy Cover Mapped Throughout A Tropical Forest With High-Fidelity Imaging Spectroscopy, David C. Marvin, Gregory P. Asner, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Increasing size and abundance of lianas relative to trees are pervasive changes in Neotropical forests that may lead to reduced forest carbon stocks. Yet the liana growth form is chronically understudied in large-scale tropical forest censuses, resulting in few data on the scale, cause, and impact of increasing lianas. Satellite and airborne remote sensing provide potential tools to map and monitor lianas at much larger spatial and rapid temporal scales than are possible with plot-based forest censuses. We combined high-resolution airborne imaging spectroscopy and a ground-based tree canopy census to investigate whether tree canopies supporting lianas could be discriminated from …

Using Alien Resources: Caribbean Dwarf Geckos Nesting Communally In Invasive Flora, Justin M. Bernstein, Aaron H. Griffing, Juan D. Daza, Tony Gamble, Aaron M. Bauer

Biological Sciences Faculty Research and Publications

No abstract provided.

Mcra Gene Abundance Correlates With Hydrogenotrophic Methane Production Rates In Full-Scale Anaerobic Waste Treatment Systems, R. L. Morris, Vaibhav Panjabrao Tale, P. P. Mathai, Daniel Zitomer, James Maki

Biological Sciences Faculty Research and Publications

Anaerobic treatment is a sustainable and economical technology for waste stabilization and production of methane as a renewable energy. However, the process is under-utilized due to operational challenges. Organic overload or toxicants can stress the microbial community that performs waste degradation, resulting in system failure. In addition, not all methanogenic microbial communities are equally capable of consistent, maximum biogas production. Opinion varies as to which parameters should be used to monitor the fitness of digester biomass. No standard molecular tools are currently in use to monitor and compare full-scale operations. It was hypothesized that determining the number of gene copies …

Would Ecology Fail The Repeatability Test?, Stefan A. Schnitzer, Walter P. Carson

Biological Sciences Faculty Research and Publications

No abstract provided.

Lianas Suppress Seedling Growth And Survival Of 14 Tree Species In A Panamanian Tropical Forest, Laura Martinez Izquierdo, Maria M. Garcia, Jennifer S. Powers, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Lianas are a common plant growth form in tropical forests, where they compete intensely with trees, decreasing tree recruitment, growth, and survival. If the detrimental effects of lianas vary significantly with tree species identity, as is often assumed, then lianas may influence tree species diversity and community composition. Furthermore, recent studies have shown that liana abundance and biomass are increasing relative to trees in neotropical forests, which will likely magnify the detrimental effects of lianas and may ultimately alter tree species diversity, relative abundances, and community composition. Few studies, however, have tested the responses of multiple tree species to the …

Mutations In Mtr4 Structural Domains Reveal Their Important Role In Regulating TrnaI Met Turnover In Saccharomyces Cerevisiae And Mtr4p Enzymatic Activities In Vitro, Yan Li, Joseph Burclaff, James T. Anderson

Biological Sciences Faculty Research and Publications

RNA processing and turnover play important roles in the maturation, metabolism and quality control of a large variety of RNAs thereby contributing to gene expression and cellular health. The TRAMP complex, composed of Air2p, Trf4p and Mtr4p, stimulates nuclear exosome-dependent RNA processing and degradation in Saccharomyces cerevisiae. The Mtr4 protein structure is composed of a helicase core and a novel so-called arch domain, which protrudes from the core. The helicase core contains highly conserved helicase domains RecA-1 and 2, and two structural domains of unclear functions, winged helix domain (WH) and ratchet domain. How the structural domains (arch, WH …

Copper Oxide Nanoparticles Inhibit The Metabolic Activity Of Saccharomyces Cerevisiae , Michael Joseph Mashock, Anthony D. Kappell, Nadia Hallaj, Krassimira R. Hristova

Biological Sciences Faculty Research and Publications

Copper oxide nanoparticles (CuO NPs) are used increasingly in industrial applications and consumer products and thus may pose risk to human and environmental health. The interaction of CuO NPs with complex media and the impact on cell metabolism when exposed to sublethal concentrations are largely unknown. In the present study, the short-term effects of 2 different sized manufactured CuO NPs on metabolic activity of Saccharomyces cerevisiae were studied. The role of released Cu²⁺ during dissolution of NPs in the growth media and the CuO nanostructure were considered. Characterization showed that the 28 nm and 64 nm CuO NPs used …

Single-Particle Imaging Reveals Intraflagellar Transport–Independent Transport And Accumulation Of Eb1 In Chlamydomonas Flagella, J. Aaron Harris, Yi Liu, Pinfen Yang, Peter Kner, Karl F. Lechtreck

Biological Sciences Faculty Research and Publications

The microtubule (MT) plus-end tracking protein EB1 is present at the tips of cilia and flagella; end-binding protein 1 (EB1) remains at the tip during flagellar shortening and in the absence of intraflagellar transport (IFT), the predominant protein transport system in flagella. To investigate how EB1 accumulates at the flagellar tip, we used in vivo imaging of fluorescent protein–tagged EB1 (EB1-FP) in Chlamydomonas reinhardtii. After photobleaching, the EB1 signal at the flagellar tip recovered within minutes, indicating an exchange with unbleached EB1 entering the flagella from the cell body. EB1 moved independent of IFT trains, and EB1-FP recovery did …

A Reply To Verbeeck And Kearsley: Addressing The Challenges Of Including Lianas In Global Vegetation Models, Stefan A. Schnitzer, Geertje M. F. Van Der Heijden, Jennifer S. Powers

Biological Sciences Faculty Research and Publications

Verbeeck and Kearsley (1) rightfully point out that global vegetation models would greatly benefit from implicitly including the effects of lianas. Recent experimental evidence that lianas substantially reduce the capacity of tropical forests to uptake and store carbon is compelling (2, 3). Furthermore, lianas are increasing relative to trees rapidly in many neotropical forests (4), which will further change the way that forests uptake, cycle, and store carbon.

Myc-Binding Protein Orthologue Interacts With Akap240 In The Central Pair Apparatus Of The Chlamydomonas Flagella, Venkatramanan G. Rao, Ruhi B. Sarafdar, Twinkle S. Chowdhury, Priyanka Sivadas, Pinfen Yang, Prabhakar M. Dongre, Jacinta S. D'Souza

Biological Sciences Faculty Research and Publications

Background

Flagella and cilia are fine thread-like organelles protruding from cells that harbour them. The typical ‘9 + 2’ cilia confer motility on these cells. Although the mechanistic details of motility remain elusive, the dynein-driven motility is regulated by various kinases and phosphatases. A-kinase anchoring proteins (AKAPs) are scaffolds that bind to a variety of such proteins. Usually, they are known to possess a dedicated domain that in vitro interacts with the regulatory subunits (RI and RII) present in the cAMP-dependent protein kinase (PKA) holoenzyme. These subunits conventionally harbour contiguous stretches of a.a. residues that reveal the presence of the …

Radial Spokes-A Snapshot Of The Motility Regulation, Assembly, And Evolution Of Cilia And Flagella, Xiaoyan Zhu, Yi Liu, Pinfen Yang

Biological Sciences Faculty Research and Publications

Propulsive forces generated by cilia and flagella are used in events that are critical for the thriving of diverse eukaryotic organisms in their environments. Despite distinctive strokes and regulations, the majority of them adopt the 9+2 axoneme that is believed to exist in the last eukaryotic common ancestor. Only a few outliers have opted for a simpler format that forsakes the signature radial spokes and the central pair apparatus, although both are unnecessary for force generation or rhythmicity. Extensive evidence has shown that they operate as an integral system for motility control. Recent studies have made remarkable progress on the …

Cryptic Lineages And Diversification Of An Endemic Anole Lizard (Squamata, Dactyloidae) Of The Cerrado Hotspot, Carlos E. Guarnizo, Fernanda P. Werneck, Lilian G. Giugliano, Marcella G. Santos, Jéssica Fenker, Lucas Sousa, Annelise B. D;Angiolella, Adriana R. Dos Santos, Christine Strussmann, Miguel T. Rodrigues, Tainá F. Dorado-Rodrigues, Tony Gamble, Guarino R. Colli

Biological Sciences Faculty Research and Publications

The Cerrado is a wide Neotropical savanna with tremendously high endemic diversity. Yet, it is not clear what the prevalent processes leading to such diversification are. We used the Cerrado-endemic lizard Norops meridionalis to investigate the main abiotic factors that promoted genetic divergence, the timings of these divergence events, and how these relate to cryptic diversity in the group. We sequenced mitochondrial and nuclear genes from 21 sites of N. meridionalis to generate species tree, divergence time estimations, and estimate species limits. We also performed population-level analysis and estimated distribution models to test the roles of niche conservatism and divergence …

Triclocarban Influences Antibiotic Resistance And Alters Anaerobic Digester Microbial Community Structure, Daniel Elliott Carey, Daniel Zitomer, Krassimira R. Hristova, Anthony D. Kappell, Patrick J. Mcnamara

Civil and Environmental Engineering Faculty Research and Publications

Triclocarban (TCC) is one of the most abundant organic micropollutants detected in biosolids. Lab-scale anaerobic digesters were amended with TCC at concentrations ranging from the background concentration of seed biosolids (30 mg/kg) to toxic concentrations of 850 mg/kg to determine the effect on methane production, relative abundance of antibiotic resistance genes, and microbial community structure. Additionally, the TCC addition rate was varied to determine the impacts of acclimation time. At environmentally relevant TCC concentrations (max detect = 440 mg/kg), digesters maintained function. Digesters receiving 450 mg/kg of TCC maintained function under gradual TCC addition, but volatile fatty acid concentrations increased, …

Impact Of Sleep And Circadian Disruption On Energy Balance And Diabetes: A Summary Of Workshop Discussions, Deanna M. Arble, Joseph Bass, Cecilia Diniz Behn, Matthew P. Butler, Etienne Challet, Charles Czeisler, Christopher M. Depner, Joel Elmquist, Paul Franken, Michael A. Grandner, Erin C. Hanlon, Alex C. Keene, Michael J. Joyner, Ilia Karatsoreos, Philip A. Kern, Samuel Klein, Christopher J. Morris, Allan I. Pack, Satchidananda Panda, Louis J. Ptacek, Naresh M. Punjabi, Paolo Sessone-Corsi, Frank A. Scheer, Richa Saxena, Elizabeth R. Seaquest, Matthew S. Thimgan, Eve Van Cauter, Kenneth P. Wright

Biological Sciences Faculty Research and Publications

A workshop was held at the National Institute for Diabetes and Digestive and Kidney Diseases with a focus on the impact of sleep and circadian disruption on energy balance and diabetes. The workshop identified a number of key principles for research in this area and a number of specific opportunities. Studies in this area would be facilitated by active collaboration between investigators in sleep/circadian research and investigators in metabolism/diabetes. There is a need to translate the elegant findings from basic research into improving the metabolic health of the American public. There is also a need for investigators studying the impact …

Short And Long-Term Soil Moisture Effects Of Liana Removal In A Seasonally Moist Tropical Forest, Joseph P. Reid, Stefan A. Schnitzer, Jennifer S. Powers

Biological Sciences Faculty Research and Publications

Lianas (woody vines) are particularly abundant in tropical forests, and their abundance is increasing in the neotropics. Lianas can compete intensely with trees for above- and belowground resources, including water. As tropical forests experience longer and more intense dry seasons, competition for water is likely to intensify. However, we lack an understanding of how liana abundance affects soil moisture and hence competition with trees for water in tropical forests. To address this critical knowledge gap, we conducted a large-scale liana removal experiment in a seasonal tropical moist forest in central Panama. We monitored shallow and deep soil moisture over the …

Huntington’S Disease Cerebrospinal Fluid Seeds Aggregation Of Mutant Huntingtin, Z. Tan, W. Dai, Theo G.M. Van Erp, J. Overman, A. Demuro, M. A. Digman, A. Hatami, R. Albay, Emily M. Sontag, K. T. Potkin, S. Ling, F. Macciardi, W. E. Bunney, J. D. Long, J. S. Paulsen, J. M. Ringman, I. Parker, Charles G. Glabe, L. M. Thompson, W. Chiu, Steven G. Potkin

Biological Sciences Faculty Research and Publications

Huntington’s disease (HD), a progressive neurodegenerative disease, is caused by an expanded CAG triplet repeat producing a mutant huntingtin protein (mHTT) with a polyglutamine-repeat expansion. Onset of symptoms in mutant huntingtin gene-carrying individuals remains unpredictable. We report that synthetic polyglutamine oligomers and cerebrospinal fluid (CSF) from BACHD transgenic rats and from human HD subjects can seed mutant huntingtin aggregation in a cell model and its cell lysate. Our studies demonstrate that seeding requires the mutant huntingtin template and may reflect an underlying prion-like protein propagation mechanism. Light and cryo-electron microscopy show that synthetic seeds nucleate and enhance mutant huntingtin aggregation. …

The Reverse Transcription Signature Of N-1-Methyladenosine In Rna-Seq Is Sequence Dependent, Ralf Hauenschild, Lyudmil Tserovski, Katharina Schmid, Kathrin Thuring, Marie-Luise Winz, Sunny Sharma, Karl-Dieter Entian, Ludvine Wacheul, Denis L.J. Lafontaine, James T. Anderson, Juan Alfonzo, Andreas Hildebrandt, Andres Jaschke, Yuri Motorin, Mark Helm

Biological Sciences Faculty Research and Publications

The combination of Reverse Transcription (RT) and high-throughput sequencing has emerged as a powerful combination to detect modified nucleotides in RNA via analysis of either abortive RT-products or of the incorporation of mismatched dNTPs into cDNA. Here we simultaneously analyze both parameters in detail with respect to the occurrence of N-1-methyladenosine (m¹A) in the template RNA. This naturally occurring modification is associated with structural effects, but it is also known as a mediator of antibiotic resistance in ribosomal RNA. In structural probing experiments with dimethylsulfate, m¹A is routinely detected by RT-arrest. A specifically developed RNA-Seq protocol …

A Cytotoxic, Co-Operative Interaction Between Energy Deprivation And Glutamate Release From System XC− Mediates Aglycemic Neuronal Cell Death, Trista L. Thorn, Yan He, Nicole A. Jackman, Doug Lobner, James A. Hewett, Sandra J. Hewett

Biological Sciences Faculty Research and Publications

The astrocyte cystine/glutamate antiporter (system x_c⁻) contributes substantially to the excitotoxic neuronal cell death facilitated by glucose deprivation. The purpose of this study was to determine the mechanism by which this occurred. Using pure astrocyte cultures, as well as, mixed cortical cell cultures containing both neurons and astrocytes, we found that neither an enhancement in system x_c⁻ expression nor activity underlies the excitotoxic effects of aglycemia. In addition, using three separate bioassays, we demonstrate no change in the ability of glucose-deprived astrocytes—either cultured alone or with neurons—to remove glutamate from the extracellular space. Instead, we …

Rapid Liana Colonization Along A Secondary Forest Chronosequence, Kathryn E. Barry, Stefan A. Schnitzer, Michiel Van Breugel, Jefferson S. Hall

Biological Sciences Faculty Research and Publications

Lianas (woody vines) can have profound effects on tree recruitment, growth, survival, and diversity in tropical forests. However, the dynamics of liana colonization soon after land abandonment are poorly understood, and thus it is unknown whether lianas alter tree regeneration early in succession. We examined the liana community in 43 forests that ranged from 1 to 31 yr old in central Panama to determine how fast lianas colonize young forests and how the liana community changes with forest succession. We found that lianas reached high densities early in succession, commonly exceeding 1000 stems/ha within the first 5 yr of forest …

The Evolution Of Digit Form In Gonatodes (Gekkota: Sphaerodactylidae) And Its Bearing On The Transition From Frictional To Adhesive Contact In Gekkotans, Anthony P. Russell, Joelle Baskerville, Tony Gamble, Timothy E. Higham

Biological Sciences Faculty Research and Publications

Although the phenomenon of adhesion in geckos has been intensively studied for over 200 years, our understanding of how the morphological apparatus associated with this arose is less clear. Indeed, whether or not all of the intricate morphological hierarchy that is implicated in the attachment and removal of the adhesive setae originated at the same time is unknown. To explore whether setae may have arisen prior to the other parts of this structural hierarchy, we undertook morphological observations of Gonatodes, an ancestrally padless, sphaerodatyline genus known to exhibit the expression of incipient subdigital pads in some species. Focusing on …

Viral Vector-Based Improvement Of Optic Nerve Regeneration: Characterization Of Individual Axons' Growth Patterns And Synaptogenesis In A Visual Target, Benjamin J. Yungher, Xueting Luo, Yadira Salgueiro, Murray G. Blackmore

Biological Sciences Faculty Research and Publications

Lack of axon growth ability in the central nervous system poses a major barrier to achieving functional connectivity after injury. Thus, a non-transgenic regenerative approach to reinnervating targets has important implications in clinical and research settings. Previous studies using knockout (KO) mice have demonstrated long distance axon regeneration. Using an optic nerve injury model, here we evaluate the efficacy of viral, RNAi and pharmacological approaches that target the PTEN and STAT3 pathways to improve long distance axon regeneration in wild type (WT) mice. Our data show that adeno-associated virus (AAV) expressing short hairpin RNA (shRNA) against PTEN (shPTEN) enhances retinal …

Lianas Reduce Carbon Accumulation And Storage In Tropical Forests, Geertje M. F. Van Der Heijden, Jennifer S. Powers, Stefan A. Schnitzer

Biological Sciences Faculty Research and Publications

Tropical forests store vast quantities of carbon, account for one-third of the carbon fixed by photosynthesis, and are a major sink in the global carbon cycle. Recent evidence suggests that competition between lianas (woody vines) and trees may reduce forest-wide carbon uptake; however, estimates of the impact of lianas on carbon dynamics of tropical forests are crucially lacking. Here we used a large-scale liana removal experiment and found that, at 3 y after liana removal, lianas reduced net above-ground carbon uptake (growth and recruitment minus mortality) by ∼76% per year, mostly by reducing tree growth. The loss of carbon uptake …

GabaB Receptors Couple To GαQ To Mediate Increases In Voltage-Dependent Calcium Current During Development, Andrew S. Karls, Michelle Mynlieff

Biological Sciences Faculty Research and Publications

Metabotropic GABA_B receptors are known to modulate the activity of voltage-dependent calcium channels. Previously, we have shown that GABA_B receptors couple to a non-G_i/o G-protein to enhance calcium influx through L-type calcium channels by activating protein kinase C in neonatal rat hippocampal neurons. In this study, the components of this signaling pathway were investigated further. Gα_q was knocked down using morpholino oligonucleotides prior to examining GABA_B-mediated enhancement of calcium influx. When Gα_q G-proteins were eliminated using morpholino-mediated knockdown, the enhancing effects of the GABA_B receptor agonist baclofen (10 μM) on calcium current …