Biology Faculty Research, Publications, and Presentations

Permanent URI for this collectionhttps://hdl.handle.net/2097/1715

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Open Access
Inhibition of Staphylococcus aureus biofilm formation by gurmarin, a plant-derived cyclic peptide
(Frontiers Media SA, 2022-10-04) Chang, Adeline W.; Dowd, Scot E.; Brackee, Gordon; Fralick, Joe A.; Vediyappan, Govindsamy
Staphylococcus aureus (Sa) is an opportunistic pathogen capable of causing various infections ranging from superficial skin infections to life-threatening severe diseases including pneumonia and sepsis. Sa produces biofilms readily on biotic and abiotic surfaces. Biofilm cells are embedded in a protective polysaccharide matrix and show an innate resistance to antibiotics, disinfectants, and clearance by host defenses. Additionally, biofilms serve as a source for systemic dissemination. Moreover, infections associated with biofilms may result in longer hospitalizations, a need for surgery, and may even result in death. Agents that inhibit the formation of biofilms and virulence without affecting bacterial growth to avoid the development of drug resistance could be useful for therapeutic purposes. In this regard, we identified and purified a small cyclic peptide, gurmarin, from a plant source that inhibited the formation of Sa biofilm under in vitro growth conditions without affecting the viability of the bacterium. The purified peptide showed a predicted molecular size of ~4.2 kDa on SDS-PAGE. Transcriptomic analysis of Sa biofilm treated with peptide showed 161 differentially affected genes at a 2-fold change, and some of them include upregulation of genes involved in oxidoreductases and downregulation of genes involved in transferases and hydrolases. To determine the inhibitory effect of the peptide against Sa biofilm formation and virulence in vivo, we used a rat-implant biofilm model. Sa infected implants with or without peptide were placed under the neck skin of rats for seven days. Implants treated with peptide showed a reduction of CFU and lack of edema and sepsis when compared to that of control animals without peptide. Taken together, gurmarin peptide blocks Sa biofilm formation in vitro and in vivo and can be further developed for therapeutic use.
Open Access
Specific Changes in Arabidopsis thaliana Rosette Lipids during Freezing Can Be Associated with Freezing Tolerance
(2022-04-23) Sy Vu, Hieu; Shiva, Sunitha; Samarakoon, Thilani; Li, Maoyin; Sarowar, Sujon; Roth, Mary R.; Tamura, Pamela; Honey, Samuel; Lowe, Kaleb; Porras, Hollie; Prakash, Neema; Roach, Charles A.; Stuke, Morgan; Wang, Xuemin; Shah, Jyoti; Gadbury, Gary; Wang, Haiyan; Welti, Ruth
While the roles of a few specific lipids in plant freezing tolerance are understood, the effect of many plant lipids remains to be determined. Acclimation of plants to non-freezing cold before exposure to freezing temperatures improves the outcome of plants, compared to plants exposed to freezing without acclimation. Arabidopsis thaliana plants were subjected to one of three treatments: (1) “control”, i.e., growth at 21 °C, (2) “non-acclimated”, i.e., 3 days at 21 °C, 2 h at −8 °C, and 24 h recovery at 21 °C, and (3) “acclimated”, i.e., 3 days at 4 °C, 2 h at −8 °C, and 24 h recovery at 21 °C. Plants were harvested at seven time points during the treatments, and lipid levels were measured by direct-infusion electrospray ionization tandem mass spectrometry. Ion leakage was measured at the same time points. To examine the function of lipid species in relation to freezing tolerance, the lipid levels in plants immediately following the freezing treatment were correlated with the outcome, i.e., ion leakage 24-h post-freezing. Based on the correlations, hypotheses about the functions of specific lipids were generated. Additionally, analysis of the lipid levels in plants with mutations in genes encoding patatin-like phospholipases, lipoxygenases, and 12-oxophytodienoic acid reductase 3 (opr3), under the same treatments as the wild-type plants, identified only the opr3-2 mutant as having major lipid compositional differences compared to wild-type plants.
Open Access
Iron Dynamics Shape Host-Pathogen Interactions
(2023-01-31) Brooke, Grant M.; Carter, Christopher A.; Dasgupta, Debolina; Gawhale, Snehal G.; Hayes, David T.; Jonak, Carissa M.; Joshi, Prabhu R.; Michel, Kristin; Pandey, Ashmita; Platt, Thomas G.; Tripathi, Aprajita
Hosts and their pathogens often compete for trace metal elements that are essential to each of their survival. Iron is one of these trace metal elements and consequently, iron dynamics are central in host-pathogen interactions. Here we review how competition for iron during infection influences host-pathogen interactions and shapes disease outcomes. Hosts have developed diverse mechanisms to limit nutrient availability to the pathogen, also known as nutritional immunity. In response to infection, vertebrate, invertebrate, and plant hosts generate a hypoferremic environment using a variety of iron-binding proteins and chelators, alongside iron transporters, to limit pathogen replication. To counter nutritional immunity responses, pathogens use TonB-dependent (e.g., siderophores) and TonB-independent mechanisms to scavenge ferric and ferrous iron. Pathogens also compete with the host-associated microbiota to access iron. Competition between microbes for iron can either hinder or facilitate pathogen establishment and proliferation within hosts. Iron dynamics are an exciting new avenue for therapeutic interventions that may be employed against a broad range of pathogens.
Open Access
The Potential Impact of Entomology on Large Animal Veterinary Practice in Texas
(2021-05-11) Hesseltine, Elise B.
On March 23, 2020, I began an internship with Circle T Veterinary Services, which is a mobile veterinary service based in Sandia, Texas. From March to August, I traveled with Dr. Tobin Pennington to farms and ranches across South Texas conducting large animal farm calls. Dr. Pennington is the sole owner and practitioner of Circle T Veterinary Services, which he opened in 2012. It is a 100% mobile service, operating completely out of Dr. Pennington’s truck. Circle T covers a large part of South Texas, with clients residing as north as Oakville, west to Cotulla, east to Rockport, and as south as McAllen. A typical day working at Circle T Veterinary Services starts early in the morning, depending on how far we need to travel to make it to the first call. There is routine work to be completed, such as palpating and deworming cows, castrating calves, vaccinating horses, equine dental floats, and more. I have been able to witness a wide variety of illness and injuries, like broken legs, horses with nasopharyngeal cicatrix syndrome, bovine fetal extractions and fetotomy, and corneal ulcers. Emergencies, such as equine colic or lacerations occur often and must be treated quickly. In one day, we may travel hundreds of miles across South Texas. In this paper, I examine the interconnections between veterinary medicine and another interest of mine, entomology. As a student in the Entomology Minor curriculum at Kansas State University, I have taken great interest in the study of insects and their effects on agriculture, ecosystems, and disease transmission. I wanted to explore the effects of arthropods on veterinary medicine because I plan on pursuing a DVM (Doctor of Veterinary Medicine) degree in the future. Below, I took experiences from my internship and researched them further, creating an in-depth look at the interactions between entomology and veterinary practice. I included a case study that I observed during my internship, which piqued my interest in West Nile Encephalomyelitis. The remainder of this paper then focuses on prevention strategies for several vector-borne diseases and emerging threats to the cattle industry. This analysis demonstrates my passion for entomology and veterinary medicine and my interest in the synergies between these two fields of study. *This manuscript is the product of the undergraduate class BIOL 497: Honors Project, which was taught
Open Access
A New Hypothesis of the Origin of Life ─ Did eukaryotes evolve from the "tamago of life"?
Asano, Katsura; kasano
This article is an English translation of the following original article written in the Japanese language and published in 2008. Its English translation was completed and posted by the same author in March, 2021. Life on Earth is generally classified into bacteria, archaea, and eukaryotes, but how eukaryotes, including humans, were originated is a mystery. Recent achievements in geobiochemistry and genomic biology have overturned previous thoughts that the eukaryotes are relatively new and instead showed that their origin can be as old as those of bacteria and archaea. Therefore, searching for the origin of eukaryotes must be reconciled with searching for the origin of cells, and a certain scenario emerges when this problem is considered along with Earth’s geological history.
Open Access
Host Microbiota Influences Interactions Between Hosts And Pathogens
(2020-12) Eppler, Megan E.; Grimes, Elizabeth A.; Hedden, Emily S.; Hodoameda, Peter; Hughes, Jamie M.; Isle, Kristin C.; Jojola-Mount, Valerie B.; Mason, Lindsay M.; Michel, Kristin; Viteri, Bianca Morejon; Ngwaga, Tshegofatso; Platt; Richie, Tanner G.; Stewart, Savannah C.; Wilson, Elizabeth J.
Bacterial microbiota have significant effects on host interactions with pathogens in both vertebrate and invertebrate organisms. Here we discuss the direct and indirect impacts of microbiota on defense against pathogens. We found that microbiota have direct effects on host defense against pathogens through interference and niche competition, and by influencing host immune system development and function. The host microbiota also impacts host-pathogen interactions beyond immunity, by influencing physical barriers and physiological responses. In addition, it can influence the establishment of tumorigenic microbes thereby increasing cancer risk. Thus, the relationship between the host and its microbiota has short- and long-term impacts on overall health. Research that aims to identify and characterize the mechanisms that underlie these direct and indirect effects on host health will inform future medical treatments.
Open Access
Autophagy–lysosome pathway alterations and alpha-synuclein up-regulation in the subtype of neuronal ceroid lipofuscinosis, CLN5 disease
(2019) Adams, Jessie; Feuerborn, Melissa; Molina, Joshua A.; Wilden, Alexa R.; Adhikari, Babita; Budden, Theodore; Lee, Stella Y.
Neuronal ceroid lipofuscinoses (NCLs) are a group of inherited neurodegenerative lysosomal storage disorders. CLN5 deficiency causes a subtype of NCL, referred to as CLN5 disease. CLN5 is a soluble lysosomal protein with an unclear function in the cell. Increased levels of the autophagy marker protein LC3-II have been reported in several subtypes of NCLs. In this report, we examine whether autophagy is altered in CLN5 disease. We found that the basal level of LC3-II was elevated in both CLN5 disease patient fibroblasts and CLN5-deficient HeLa cells. Further analysis using tandem fluorescent mRFP-GFP-LC3 showed the autophagy flux was increased. We found the alpha-synuclein (α-syn) gene SNCA was highly up-regulated in CLN5 disease patient fibroblasts. The aggregated form of α-syn is well known for its role in the pathogenicity of Parkinson’s disease. Higher α-syn protein levels confirmed the SNCA up-regulation in both patient cells and CLN5 knockdown HeLa cells. Furthermore, α-syn was localized to the vicinity of lysosomes in CLN5 deficient cells, indicating it may have a lysosome-related function. Intriguingly, knocking down SNCA reversed lysosomal perinuclear clustering caused by CLN5 deficiency. These results suggest α-syn may affect lysosomal clustering in non-neuronal cells, similar to its role in presynaptic vesicles in neurons.
Open Access
Bioorthogonal click chemistry for fluorescence imaging of choline phospholipids in plants
(2018-04-18) Paper, Janet M.; Mukherjee, Thiya; Schrick, Kathrin
Background: Phospholipids are important structural and signaling molecules in plant membranes. Some fluorescent dyes can stain general lipids of membranes, but labeling and visualization of specific lipid classes have yet to be developed for most components of the membrane. New techniques for visualizing membrane lipids are needed to further delineate their dynamic structural and signaling roles in plant cells. In this study we examined whether propargylcholine, a bioortholog of choline, can be used to label the major membrane lipid, phosphatidylcholine, and other choline phospholipids in plants. We established that propargylcholine is readily taken up by roots, and that its incorporation is not detrimental to plant growth. After plant tissue is harvested and fixed, a click-chemistry reaction covalently links the alkyne group of propargylcholine to a fluorescently-tagged azide, resulting in specific labeling of choline phospholipids. Results: Uptake of propargylcholine, followed by click chemistry with fluorescein or Alexa Fluor 594 azide was used to visualize choline phospholipids in cells of root, leaf, stem, silique and seed tissues from Arabidopsis thaliana. Colocalization with various subcellular markers indicated coinciding fluorescent signals in cell membranes, such as the tonoplast and the ER. Among different cell types in the leaf epidermis, guard cells displayed strong labeling. Mass spectrometry-based lipidomic analysis of the various plant tissues revealed that incorporation of propargylcholine was strongest in roots with approximately 50% of total choline phospholipids being labeled, but it was also incorporated in the other tissues including seeds. Phospholipid profiling confirmed that, in each tissue analyzed, incorporation of the bioortholog had little impact on the pool of choline plus choline-like phospholipids or other lipid species. Conclusion: We developed and validated a click-chemistry based method for fluorescence imaging of choline phospholipids using a bioortholog of choline, propargylcholine, in various cell-types and tissues from Arabidopsis. This click-chemistry method provides a direct way to metabolically tag and visualize specific lipid molecules in plant cells. This work paves the way for future studies addressing in situ localization of specific lipids in plants.
Open Access
Convergent evolution of reduced energy demands in extremophile fish
(2017-10-27) Passrow, Courtney N.; Arias-Rodriguez, Lenin; Tobler, Michael; Rutherford, Suzannah
Convergent evolution in organismal function can arise from nonconvergent changes in traits that contribute to that function. Theory predicts that low resource availability and high maintenance costs in extreme environments select for reductions in organismal energy demands, which could be attained through modifications of body size or metabolic rate. We tested for convergence in energy demands and underlying traits by investigating livebearing fish (genus Poecilia) that have repeatedly colonized toxic, hydrogen sulphide-rich springs. We quantified variation in body size and routine metabolism across replicated sulphidic and non-sulphidic populations in nature, modelled total organismal energy demands, and conducted a common-garden experiment to test whether population differences had a genetic basis. Sulphidic populations generally exhibited smaller body sizes and lower routine metabolic rates compared to non-sulphidic populations, which together caused significant reductions in total organismal energy demands in extremophile populations. Although both mechanisms contributed to variation in organismal energy demands, variance partitioning indicated reductions of body size overall had a greater effect than reductions of routine metabolism. Finally, population differences in routine metabolism documented in natural populations were maintained in common-garden reared individuals, indicating evolved differences. In combination with other studies, these results suggest that reductions in energy demands may represent a common theme in adaptation to physiochemical stressors. Selection for reduced energy demand may particularly affect body size, which has implications for life history evolution in extreme environments.
Open Access
Dynamics of epizootic hemorrhagic disease virus infection within the vector, Culicoides sonorensis (Diptera: Ceratopogonidae)
(2017-11-27) Mills, Mary K.; Ruder, Mark G.; Nayduch, Dana; Michel, Kristin; Drolet, Barbara S.; Mans, Ben J.
Culicoides sonorensis biting midges are confirmed vectors of epizootic hemorrhagic disease virus (EHDV), which causes mortality in white-tailed deer and ruminant populations. Currently, of the seven EHDV serotypes, only 1, 2, and 6 are detected in the USA, and very few studies have focused on the infection time course of these serotypes within the midge. The objective of this current research was to characterize EHDV-2 infection within the midge by measuring infection prevalence, virus dissemination, and viral load over the course of infection. Midges were fed a blood meal containing 106.9 PFU/ml EHDV-2, collected every 12 h from 0–2 days post feeding (dpf) and daily from 3–10 dpf, and cohorts of 20 C. sonorensis were processed using techniques that assessed EHDV infection and dissemination. Cytopathic effect assays and quantitative (q)PCR were used to determine infection prevalence, revealing a 50% infection rate by 10 dpf using both methods. Using immunohistochemistry, EHDV-2 infection was detectable at 5 dpf, and shown to disseminate from the midgut to other tissues, including fat body, eyes, and salivary glands by 5 dpf. Stain intensity increased from 5–8 dpf, indicating replication of EHDV-2 in secondary infection sites after dissemination. This finding is also supported by trends in viral load over time as determined by plaque assays and qPCR. An increase in titer between 4–5 dpf correlated with viral replication in the midgut as seen with staining at day 5, while the subsequent gradual increase in viral load from 8–10 dpf suggested viral replication in midges with disseminated infection. Overall, the data presented herein suggest that EHDV-2 disseminates via the hemolymph to secondary infection sites throughout the midge and demonstrate a high potential for transmission at five days at 25°C after an infective blood-meal.
Open Access
Competition between translation initiation factor eIF5 and its mimic protein 5MP determines non-AUG initiation rate genome-wide
(2017-11-16) Tang, Leiming; Morris, Jacob; Wan, Ji; Moore, Chelsea; Fujita, Yoshihiko; Gillaspie, Sarah; Aube, Eric; Nanda, Jagpreet; Marques, Maud; Jangal, Maika; Anderson, Abbey; Cox, Christian; Hiraishi, Hiroyuki; Dong, Leiming; Saito, Hirohide; Singh, Chingakham Ranjit; Witcher, Michael; Topisirovic, Ivan; Qian, Shu-Bing; Asano, Katsura
In the human genome, translation initiation from nonAUG codons plays an important role in various gene regulation programs. However, mechanisms regulating the non-AUG initiation rate remain poorly understood. Here, we show that the non-AUG initiation rate is nearly consistent under a ﬁxed nucleotide context in various human and insect cells. Yet, it ranges from <1% to nearly 100% compared to AUG translation, depending on surrounding sequences, including Kozak, and possibly additional nucleotide contexts. Mechanistically, this range of non-AUG initiation is controlled in part, by the eIF5-mimic protein (5MP). 5MP represses non-AUG translation by competing with eIF5 for the Met-tRNAi-binding factor eIF2. Consistently, eIF5 increases, whereas 5MP decreases translation of NAT1/EIF4G2/DAP5, whose sole start codon is GUG. By modulating eIF5 and 5MP1 expression in combination with ribosome proﬁling we identiﬁed a handful of previously unknown non-AUG initiation sites, some of which serve as the exclusive start codons. If the initiation rate for these codons is low, then an AUG-initiated downstream ORF prevents the generation of shorter, AUGinitiated isoforms. We propose that the homeostasis of the non-AUG translatome is maintained through balanced expression of eIF5 and 5MP.
Open Access
Genomic abundance and transcriptional activity of diverse gypsy and copia long terminal repeat retrotransposons in three wild sunflower species
(2018-01-05) Qiu, Fan; Ungerer, Mark C.
Background: Long terminal repeat (LTR) retrotransposons are highly abundant in plant genomes and require transcriptional activity for their proliferative mode of replication. These sequences exist in plant genomes as diverse sublineages within the main element superfamilies (i.e., gypsy and copia). While transcriptional activity of these elements is increasingly recognized as a regular attribute of plant transcriptomes, it is currently unknown the extent to which different sublineages of these elements are transcriptionally active both within and across species. In the current report, we utilize next generation sequencing methods to examine genomic copy number abundance of diverse LTR retrotransposon sublineages and their corresponding levels of transcriptional activity in three diploid wild sunflower species, Helianthus agrestis, H. carnosus and H. porteri. Results: The diploid sunflower species under investigation differ in genome size 2.75-fold, with 2C values of 22.93 for H. agrestis, 12.31 for H. carnosus and 8.33 for H. porteri. The same diverse gypsy and copia sublineages of LTR retrotransposons were identified across species, but with gypsy sequences consistently more abundant than copia and with global gypsy sequence abundance positively correlated with nuclear genome size. Transcriptional activity was detected for multiple copia and gypsy sequences, with significantly higher activity levels detected for copia versus gypsy. Interestingly, of 11 elements identified as transcriptionally active, 5 exhibited detectable expression in all three species and 3 exhibited detectable expression in two species. Conclusions: Combined analyses of LTR retrotransposon genomic abundance and transcriptional activity across three sunflower species provides novel insights into genome size evolution and transposable element dynamics in this group. Despite considerable variation in nuclear genome size among species, relatively conserved patterns of LTR retrotransposon transcriptional activity were observed, with a highly overlapping set of copia and gypsy sequences observed to be transcriptionally active across species. A higher proportion of copia versus gypsy elements were found to be transcriptionally active and these sequences also were expressed at higher levels.
Open Access
Towards a mechanistic understanding of fish species niche divergence along a river continuum
(2014-04-01) Troia, Matthew J.; Gido, Keith B.
Environmental niche modeling is a valuable tool but it often fails to identify causal links between environmental gradients and individual- or population-level performance that drive species' distributions. Correlation between the abundances of stream fish species and longitudinal position in stream networks is well documented and is hypothesized to occur through differential environmental filtering of trophic traits. Still, trophically similar congeners often exhibit complementary distributions along stream size gradients, suggesting that other mechanisms are important. We present niche models to test the hypothesis that four congeneric pairs (Teleostei: Cyprinidae) exhibit complementary distributions along a gradient of stream size in the central Great Plains of Kansas, USA. Stream size was the strongest predictor of abundance compared to five other environmental variables tested and three of the four species pairs exhibited complementary distributions along a stream size gradient. We carried out field experiments to quantify potentially causal environmental gradients (food resources, temperature, and turbidity) and four measures of individual performance (adult spawning success and juvenile survival, condition, and growth) along a stream size gradient for one congeneric pair: Pimephales notatus, a tributary species and P. vigilax, a river mainstem species. These experiments revealed an increase in temperature and food resources with stream size, along with a corresponding increase in adult spawning success, juvenile condition, and juvenile growth for both species. We conclude that these congeners respond similarly to abiotic gradients associated with the river continuum and that complementary distributions are a consequence of biotic interactions, differential environmental filtering evident in an unmeasured performance metric, or differential environmental filtering by a direct environmental gradient operating at longer timescales.
Open Access
Prey type and foraging ecology of Sanderlings Calidris alba in different climate zones: are tropical areas more favourable than temperate sites?
(2015-08-11) Grond, Kirsten; Ntiamoa-Baidu, Yaa; Piersma, Theunis; Reneerkens, Jeroen
Sanderlings (Calidris alba) are long-distance migratory shorebirds with a non-breeding range that spans temperate and tropical coastal habitats. Breeding in the High Arctic combined with non-breeding seasons in the tropics necessitate long migrations, which are energetically demanding. On an annual basis, the higher energy expenditures during migration might pay off if food availability in the tropics is higher than at temperate latitudes. We compared foraging behaviour of birds at a north temperate and a tropical non-breeding site in the Netherlands and Ghana, respectively. In both cases the birds used similar habitats (open beaches), and experienced similar periods of daylight, which enabled us to compare food abundance and availability, and behavioural time budgets and food intake. During the non-breeding season, Sanderlings in the Netherlands spent 79% of their day foraging; in Ghana birds spent only 38% of the daytime period foraging and the largest proportion of their time resting (58%). The main prey item in the Netherlands was the soft-bodied polychaete Scolelepis squamata, while Sanderlings in Ghana fed almost exclusively on the bivalve Donax pulchellus, which they swallowed whole and crushed internally. Average availability of polychaete worms in the Netherlands was 7.4 g ash free dry mass (AFDM) m−2, which was one tenth of the 77.1 g AFDM m−2 estimated for the beach in Ghana. In the tropical environment of Ghana the Sanderlings combined relatively low energy requirements with high prey intake rates (1.64 mg opposed to 0.13 mg AFDM s−1 for Ghana and the Netherlands respectively). Although this may suggest that the Ghana beaches are the most favourable environment, processing the hard-shelled bivalve (D. pulchellus) which is the staple food could be costly. The large amount of daytime spent resting in Ghana may be indicative of the time needed to process the shell fragments, rather than indicate rest.
Open Access
Essential role of eIF5-mimic protein in animal development is linked to control of ATF4 expression
(2014-09-15) Hiraishi, Hiroyuki; Oatman, Jamie; Haller, Sherry L.; Blunk, Logan; McGivern, Benton; Morris, Jacob; Papadopoulos, Evangelos; Gutierrez, Wade; Gordon, Michelle; Bokhari, Wahaj; Ikeda, Yuka; Miles, David; Fellers, John; Asano, Masayo; Wagner, Gerhard; Tazi, Loubna; Rothenburg, Stefan; Brown, Susan J.; Asano, Katsura
Translational control of transcription factor ATF4 through paired upstream ORFs (uORFs) plays an important role in eukaryotic gene regulation. While it is typically induced by phosphorylation of eIF2␣, ATF4 translation can be also induced by expression of a translational inhibitor protein, eIF5-mimic protein 1 (5MP1, also known as BZW2) in mammals. Here we show that the 5MP gene is maintained in eukaryotes under strong purifying selection, but is uniquely missing in two major phyla, nematoda and ascomycota. The common function of 5MP from protozoa, plants, fungi and insects is to control translation by inhibiting eIF2. The afﬁnity of human 5MP1 to eIF2␤ was measured as being equivalent to the published value of human eIF5 to eIF2␤, in agreement with effective competition of 5MP with eIF5 for the main substrate, eIF2. In the red ﬂour beetle, Tribolium castaneum, RNA interference studies indicate that 5MP facilitates expression of GADD34, a downstream target of ATF4. Furthermore, both 5MP and ATF4 are essential for larval development. Finally, 5MP and the paired uORFs allowing ATF4 control are conserved in the entire metazoa except nematoda. Based on these ﬁndings, we discuss the phylogenetic and functional linkage between ATF4 regulation and 5MP expression in this group of eukaryotes.
Open Access
Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5
Obayashi, E.; Luna, R. E.; Nagata, T.; Martin-Marcos, P.; Hiraishi, H.; Singh, Chingakham Ranjit; Erzberger, J. P.; Zhang, F.; Arthanari, H.; Morris, J.; Pellarin, R.; Moore, C.; Harmon, I.; Papadopoulos, E.; Yoshida, H.; Nasr, M. L.; Unzai, S.; Thompson, B.; Aube, E.; Hustak, S.; Stengel, F.; Dagraca, E.; Ananbandam, A.; Gao, P.; Urano, T.; Hinnebusch, A. G.; Wagner, G.; Asano, Katsura; csingh; kasano; Singh, Chingakham Ranjit; Asano, Katsura
During eukaryotic translation initiation, eIF3 binds the solvent-accessible side of the 40S ribosome and recruits the gate-keeper protein eIF1 and eIF5 to the decoding center. This is largely mediated by the N-terminal domain (NTD) of eIF3c, which can be divided into three parts: 3c0, 3c1, and 3c2. The N-terminal part, 3c0, binds eIF5 strongly but only weakly to the ribosome-binding surface of eIF1, whereas 3c1 and 3c2 form a stoichiometric complex with eIF1. 3c1 contacts eIF1 through Arg-53 and Leu-96, while 3c2 faces 40S protein uS15/S13, to anchor eIF1 to the scanning pre-initiation complex (PIC). We propose that the 3c0:eIF1 interaction diminishes eIF1 binding to the 40S, whereas 3c0:eIF5 interaction stabilizes the scanning PIC by precluding this inhibitory interaction. Upon start codon recognition, interactions involving eIF5, and ultimately 3c0:eIF1 association, facilitate eIF1 release. Our results reveal intricate molecular interactions within the PIC, programmed for rapid scanning-arrest at the start codon.
Open Access
Effect of tcdR Mutation on Sporulation in the Epidemic Clostridium difficile Strain R20291
Girinathan, B. P.; Monot, M.; Boyle, Daniel L.; McAllister, K. N.; Sorg, J. A.; Dupuy, B.; Govind, Revathi; dboyle; rgovind; Boyle, Daniel L.; Govind, Revathi
Clostridium difficile is an important nosocomial pathogen and the leading cause of hospital-acquired diarrhea. Antibiotic use is the primary risk factor for the development of C. difficile-associated disease because it disrupts normally protective gut flora and enables C. difficile to colonize the colon. C. difficile damages host tissue by secreting toxins and disseminates by forming spores. The toxin-encoding genes, tcdA and tcdB, are part of a pathogenicity locus, which also includes the tcdR gene that codes for TcdR, an alternate sigma factor that initiates transcription of tcdA and tcdB genes. We created a tcdR mutant in epidemic-type C. difficile strain R20291 in an attempt to identify the global role of tcdR. A site-directed mutation in tcdR affected both toxin production and sporulation in C. difficile R20291. Spores of the tcdR mutant were more heat sensitive than the wild type (WT). Nearly 3-fold more taurocholate was needed to germinate spores from the tcdR mutant than to germinate the spores prepared from the WT strain. Transmission electron microscopic analysis of the spores also revealed a weakly assembled exosporium on the tcdR mutant spores. Accordingly, comparative transcriptome analysis showed many differentially expressed sporulation genes in the tcdR mutant compared to the WT strain. These data suggest that regulatory networks of toxin production and sporulation in C. difficile strain R20291 are linked with each other. IMPORTANCE C. difficile infects thousands of hospitalized patients every year, causing significant morbidity and mortality. C. difficile spores play a pivotal role in the transmission of the pathogen in the hospital environment. During infection, the spores germinate, and the vegetative bacterial cells produce toxins that damage host tissue. Thus, sporulation and toxin production are two important traits of C. difficile. In this study, we showed that a mutation in tcdR, the toxin gene regulator, affects both toxin production and sporulation in epidemic-type C. difficile strain R20291.
Open Access
Drosophila Condensin II subunit Chromosome-associated protein D3 regulates cell fate determination through non-cell-autonomous signaling
Klebanow, L. R.; Peshel, E. C.; Schuster, A. T.; De, K.; Sarvepalli, K.; Lemieux, M. E.; Lenoir, J. J.; Moore, A. W.; McDonald, Jocelyn A.; Longworth, M. S.; jmcdona; McDonald, Jocelyn A.
The pattern of the Drosophila melanogaster adult wing is heavily influenced by the expression of proteins that dictate cell fate decisions between intervein and vein during development. dSRF (Blistered) expression in specific regions of the larval wing disc promotes intervein cell fate, whereas EGFR activity promotes vein cell fate. Here, we report that the chromatin-organizing protein CAP-D3 acts to dampen dSRF levels at the anterior/posterior boundary in the larval wing disc, promoting differentiation of cells into the anterior crossvein. CAP-D3 represses KNOT expression in cells immediately adjacent to the anterior/posterior boundary, thus blocking KNOT-mediated repression of EGFR activity and preventing cell death. Maintenance of EGFR activity in these cells depresses dSRF levels in the neighboring anterior crossvein progenitor cells, allowing them to differentiate into vein cells. These findings uncover a novel transcriptional regulatory network influencing Drosophila wing vein development, and are the first to identify a Condensin II subunit as an important regulator of EGFR activity and cell fate determination in vivo.
Open Access
An Agent-Based Model of a Hepatic Inflammatory Response to Salmonella: A Computational Study under a Large Set of Experimental Data
Shi, Z. Z.; Chapes, Stephen K.; Ben-Arieh, David; Wu, Chih-Hang J.; skcbiol; davidbe; chw; Chapes, Stephen; Ben-Arieh, David; Wu, Chih-Hang J.
We present an agent-based model (ABM) to simulate a hepatic inflammatory response (HIR) in a mouse infected by Salmonella that sometimes progressed to problematic proportions, known as "sepsis". Based on over 200 published studies, this ABM describes interactions among 21 cells or cytokines and incorporates 226 experimental data sets and/or data estimates from those reports to simulate a mouse HIR in silico. Our simulated results reproduced dynamic patterns of HIR reported in the literature. As shown in vivo, our model also demonstrated that sepsis was highly related to the initial Salmonella dose and the presence of components of the adaptive immune system. We determined that high mobility group box-1, C-reactive protein, and the interleukin-10: tumor necrosis factor-a ratio, and CD4+ T cell: CD8+ T cell ratio, all recognized as biomarkers during HIR, significantly correlated with outcomes of HIR. During therapy-directed silico simulations, our results demonstrated that anti-agent intervention impacted the survival rates of septic individuals in a time-dependent manner. By specifying the infected species, source of infection, and site of infection, this ABM enabled us to reproduce the kinetics of several essential indicators during a HIR, observe distinct dynamic patterns that are manifested during HIR, and allowed us to test proposed therapy-directed treatments. Although limitation still exists, this ABM is a step forward because it links underlying biological processes to computational simulation and was validated through a series of comparisons between the simulated results and experimental studies.
Open Access
Temporal variability in large grazer space use in an experimental landscape
Raynor, E. J.; Joern, Anthony; Skibbe, A.; Sowers, M.; Briggs, John M.; Laws, A. N.; Goodin, Douglas G.; ajoern; Joern, Anthony
Land use, climate change, and their interaction each have great potential to affect grazing systems. With anticipated more frequent and extensive future drought, a more complete understanding of the mechanisms that determine large grazer landscape-level distribution under varying climatic conditions is integral to ecosystem management. Using an experimental setting with contrasting fire treatments, we describe the inter-annual variability of the effect of landscape topography and disturbance from prescribed spring fire on large grazer space use in years of variable resource availability. Using GPS telemetry, we investigated space use of plains bison (Bison bison bison) as they moved among watersheds managed with variable experimental burn treatments (1-, 2-, 4-, and 20-year burn intervals) during a seven-year period spanning years of average-to-above average forage production and severe drought. At the landscape scale, bison more strongly favored high-elevation and recently burned watersheds with watersheds burned for the first time in 2 or 4 yr consistently showing higher use relative to annually burned watersheds. In particular, watersheds burned for the first time in 4 yr were avoided to lesser extent than other more frequently burned watersheds during the dormant season. This management type also maintained coupling between bison space use and post-fire regrowth across post-drought growing season months, whereas watersheds with more frequent fire-return intervals attracted bison in only the first month post-fire. Hence, fire frequency played a role in maintaining the coupling of grazer and post-fire regrowth, the fire-grazer interaction, in response to drought-induced reduction in fuel loads. Moreover, bison avoided upland habitat in poor forage production years, when forage regrowth is less likely to occur in upland than in lowland habitats. Such quantified responses of bison to landscape features can aid future conservation management efforts and planning to sustain fire-grazer interactions and resulting spatial heterogeneity in grassland ecosystems.