Department of Biological Science

: Venom Complexity in a Pitviper Produced by Facultative Parthenogenesis.; Facultative parthenogenesis (FP) is asexual reproduction in plant and animal species that would otherwise reproduce sexually. This process in vertebrates typically results from automictic development (likely terminal fusion) and is phylogenetically widespread. In squamate reptiles and chondrichthyan fishes, FP has been reported to occur in nature and can result in the production of reproductively viable offspring; suggesting that it is of ecological and evolutionary significance. However, terminal fusion automixis is believed to result in near genome-wide reductions in heterozygosity; thus, FP seems likely to affect key phenotypic characters, yet this remains almost completely unstudied. Snake venom is a complex phenotypic character primarily used to subjugate prey and is thus tightly linked to individual fitness. Surprisingly, the composition and function of venom produced by a parthenogenetic pitviper exhibits a high degree of similarity to that of its mother and conspecifics from the same population. Therefore, the apparent loss of allelic diversity caused by FP appears unlikely to have a significant impact on the prey-capturing ability of this snake. Accordingly, the pitviper offspring produced by FP retained complex phenotypic characteristics associated with fitness. This result reinforces the potential ecological and evolutionary importance of FP and questions our understanding of the inheritance of venom-associated genes., Grant Number: , 200517/Z/16/Z, 200517/Z/16/Z, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6070573.

: Vertical organization of the division of labor within nests of the Florida harvester ant, Pogonomyrmex badius.; In the Florida harvester ant, Pogonomyrmex badius, foragers occur only in the top 15 cm of the nest, whereas brood and brood-care workers reside mostly in the deepest regions, yet the food and seeds foragers collect must be transported downward 30 to 80 cm to seed chambers and up to 2 m to brood chambers. Using mark-recapture techniques with fluorescent printer's ink, we identified a class of workers that ranges widely within the vertical structure of the nest, rapidly moving materials dropped by foragers in the upper regions downward, and excavated soil from deeper upward. Within the nest, only 5% of foragers were recovered below 20 cm depth, but about 30% of transfer workers and 82% of unmarked workers were found there. Below 70 cm depth, 90% of workers were unmarked, and were probably involved mostly in brood care. During the summer, the transfer workers comprise about a quarter of the nest population, while foragers make up about 40%. Workers marked as transfer workers later appear as foragers, while those marked as foragers die and disappear from the foraging population, suggesting that transfer workers are younger, and age into foraging. The importance of these findings for laboratory studies of division of labor are discussed. The efficient allocation of labor is a key component of superorganismal fitness., Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5705139.

: Viral recombination blurs taxonomic lines; Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the complex collection of many viral families that infect a broad range of hosts. To examine this collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops (Circoviridae and Geminiviridae), and model organisms for genetics and evolution studies (Microviridae). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as Circoviridae, Geminiviridae, and Microviridae, many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group., Keywords: amplification, Circoviridae, diversity, Evolution, feces, Geminiviridae, genomics, High-throughput sequencing, metagenomic analysis, Metagenomics, Microviridae, patterns, sludge, Viral diversity, Publication Note: The publisher’s version of record is available at https://doi.org/10.7717/peerj.2585

: Viral recombination blurs taxonomic lines; Understanding the structure and dynamics of microbial communities, especially those of economic concern, is of paramount importance to maintaining healthy and efficient microbial communities at agricultural sites and large industrial cultures, including bioprocessors. Wastewater treatment plants are large bioprocessors which receive water from multiple sources, becoming reservoirs for the collection of many viral families that infect a broad range of hosts. To examine this complex collection of viruses, full-length genomes of circular ssDNA viruses were isolated from a wastewater treatment facility using a combination of sucrose-gradient size selection and rolling-circle amplification and sequenced on an Illumina MiSeq. Single-stranded DNA viruses are among the least understood groups of microbial pathogens due to genomic biases and culturing difficulties, particularly compared to the larger, more often studied dsDNA viruses. However, the group contains several notable well-studied examples, including agricultural pathogens which infect both livestock and crops ( and ), and model organisms for genetics and evolution studies (). Examination of the collected viral DNA provided evidence for 83 unique genotypic groupings, which were genetically dissimilar to known viral types and exhibited broad diversity within the community. Furthermore, although these genomes express similarities to known viral families, such as , , and , many are so divergent that they may represent new taxonomic groups. This study demonstrated the efficacy of the protocol for separating bacteria and large viruses from the sought after ssDNA viruses and the ability to use this protocol to obtain an in-depth analysis of the diversity within this group., Keywords: Circoviridae, Geminiviridae, High-throughput sequencing, Metagenomics, Microviridae, Viral diversity, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5075696.

: Where Is Natural History In Ecological, Evolutionary, And Behavioral Science?; Natural history is the careful observation of nature, wherever nature is. Ultimately, it is what ecological, evolutionary, and behavioral science are supposed to explain. It is difficult to use natural history alone to test hypotheses in these fields because of the complex paths between process and pattern. Few patterns are predicted by one and only one hypothesis, so experiments are almost always necessary. However, the robustness of experimental results depends on how well experimental conditions reflect the integration of natural history. Natural history also plays a vital role in how well we can apply Krogh's principle to our work. Krogh's principle is that scientists begin with an important hypothesis and find a system(organism, habitat, species interaction) with which to test it. However, natural history is essential for knowing whether the question applies to the system or whether we are forcing the question on the system. There is value in beginning one's research not by identifying an interesting question and searching for the right system but by identifying an interesting systemin which to ask the right question. This approach carries the danger of parochialism, which can be avoided only by having a command of theory as well as natural history. A command of both areas allows nature to tell us which question to ask instead of demanding that nature answer the question we find most interesting., models, size, selection, calibrating experiments, character displacement, coastal-plain, competition, experimental realism, hypothesis principle, invasion success, manipulations, natural history, observational data, predation, species-abundance, The publisher's version of record is availible at https://doi.org/10.1086/708765

: Where Is Natural History In Ecological, Evolutionary, And Behavioral Science?; Natural history is the careful observation of nature, wherever nature is. Ultimately, it is what ecological, evolutionary, and behavioral science are supposed to explain. It is difficult to use natural history alone to test hypotheses in these fields because of the complex paths between process and pattern. Few patterns are predicted by one and only one hypothesis, so experiments are almost always necessary. However, the robustness of experimental results depends on how well experimental conditions reflect the integration of natural history. Natural history also plays a vital role in how well we can apply Krogh's principle to our work. Krogh's principle is that scientists begin with an important hypothesis and find a system (organism, habitat, species interaction) with which to test it. However, natural history is essential for knowing whether the question applies to the system or whether we are forcing the question on the system. There is value in beginning one's research not by identifying an interesting question and searching for the right system but by identifying an interesting system in which to ask the right question. This approach carries the danger of parochialism, which can be avoided only by having a command of theory as well as natural history. A command of both areas allows nature to tell us which question to ask instead of demanding that nature answer the question we find most interesting., models, size, selection, calibrating experiments, character displacement, coastal-plain, competition, experimental realism, invasion success, manipulations, natural history, observational data, predation, species-abundance, hypothesis testing, Krogh's principle, The publisher's version of record is availible at https://doi.org/10.1086/708765

: Why Does The Magnitude Of Genotype-by-environment Interaction Vary?; Genotype-by-environment interaction (GxE), that is, genetic variation in phenotypic plasticity, is a central concept in ecology and evolutionary biology. GxE has wide-ranging implications for trait development and for understanding how organisms will respond to environmental change. Although GxE has been extensively documented, its presence and magnitude vary dramatically across populations and traits. Despite this, we still know little about why GxE is so evident in some traits and populations, but minimal or absent in others. To encourage synthetic research in this area, we review diverse hypotheses for the underlying biological causes of variation in GxE. We extract common themes from these hypotheses to develop a more synthetic understanding of variation in GxE and suggest some important next steps., Keywords: individual-differences, genetic-variation, drosophila-melanogaster, quantitative genetics, phenotypic plasticity, niche construction, reaction norms, aggressive-behavior, behavioral plasticity, ecological consequences, genetic variation, genotype-by-environment interaction, phenotypic plasticity, Publication Note: The publisher’s version of record is available at https://doi.org/10.1002/ece3.4128

: Why does the magnitude of genotype-by-environment interaction vary?; Genotype-by-environment interaction (G × E), that is, genetic variation in phenotypic plasticity, is a central concept in ecology and evolutionary biology. G×E has wide-ranging implications for trait development and for understanding how organisms will respond to environmental change. Although G × E has been extensively documented, its presence and magnitude vary dramatically across populations and traits. Despite this, we still know little about why G × E is so evident in some traits and populations, but minimal or absent in others. To encourage synthetic research in this area, we review diverse hypotheses for the underlying biological causes of variation in G × E. We extract common themes from these hypotheses to develop a more synthetic understanding of variation in G × E and suggest some important next steps., Keywords: Genetic variation, Genotype‐by‐environment interaction, Phenotypic plasticity, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6024136.

: Zika Virus Infects Human Cortical Neural Progenitors and Attenuates Their Growth.; The suspected link between infection by Zika virus (ZIKV), a re-emerging flavivirus, and microcephaly is an urgent global health concern. The direct target cells of ZIKV in the developing human fetus are not clear. Here we show that a strain of the ZIKV, MR766, serially passaged in monkey and mosquito cells efficiently infects human neural progenitor cells (hNPCs) derived from induced pluripotent stem cells. Infected hNPCs further release infectious ZIKV particles. Importantly, ZIKV infection increases cell death and dysregulates cell-cycle progression, resulting in attenuated hNPC growth. Global gene expression analysis of infected hNPCs reveals transcriptional dysregulation, notably of cell-cycle-related pathways. Our results identify hNPCs as a direct ZIKV target. In addition, we establish a tractable experimental model system to investigate the impact and mechanism of ZIKV on human brain development and provide a platform to screen therapeutic compounds., Grant Number: R37 NS047344, R21 AI111250, R21 NS095348, R21 AI119530, R56 NS047344, R01 NS048271, R01 NS047344, R01 MH102690, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299540.

: Zika virus and neural developmental defects; Publication Note: The publisher’s version of record is available at http://www.dx.doi.org/10.1007/s11427-016-5053-2

: Zika virus directly infects peripheral neurons and induces cell death.; Zika virus (ZIKV) infection is associated with neurological disorders of both the CNS and peripheral nervous systems (PNS), yet few studies have directly examined PNS infection. Here we show that intraperitoneally or intraventricularly injected ZIKV in the mouse can infect and impact peripheral neurons in vivo. Moreover, ZIKV productively infects stem-cell-derived human neural crest cells and peripheral neurons in vitro, leading to increased cell death, transcriptional dysregulation and cell-type-specific molecular pathology., Grant Number: P01 NS097206, U54 HD079123, R35 NS097370, R21 MH087874, R33 MH087874, P30 DK089502, R37 NS047344, U19 MH106434, R01 NS093213, R21 NS095348, R21 AI119530, R01 AR070751, R01 NS051630, U19 AI131130, R01 MH105128, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5575960.

: Zika-Virus-Encoded NS2A Disrupts Mammalian Cortical Neurogenesis by Degrading Adherens Junction Proteins.; Zika virus (ZIKV) directly infects neural progenitors and impairs their proliferation. How ZIKV interacts with the host molecular machinery to impact neurogenesis in vivo is not well understood. Here, by systematically introducing individual proteins encoded by ZIKV into the embryonic mouse cortex, we show that expression of ZIKV-NS2A, but not Dengue virus (DENV)-NS2A, leads to reduced proliferation and premature differentiation of radial glial cells and aberrant positioning of newborn neurons. Mechanistically, in vitro mapping of protein-interactomes and biochemical analysis suggest interactions between ZIKA-NS2A and multiple adherens junction complex (AJ) components. Functionally, ZIKV-NS2A, but not DENV-NS2A, destabilizes the AJ complex, resulting in impaired AJ formation and aberrant radial glial fiber scaffolding in the embryonic mouse cortex. Similarly, ZIKA-NS2A, but not DENV-NS2A, reduces radial glial cell proliferation and causes AJ deficits in human forebrain organoids. Together, our results reveal pathogenic mechanisms underlying ZIKV infection in the developing mammalian brain., Keywords: Zika virus, Adherens junction, Cortical neurogenesis, Flavivirus, Human organoid, Human protein microarray, Microcephaly, Neural stem cell, Neuronal migration, Radial glial cell, Grant Number: R01 GM111514, P01 NS097206, R35 NS097370, T32 GM007814, R21 MH087874, T32 GM007309, T32 GM007445, R33 MH087874, R37 NS047344, U19 MH106434, R25 NS065729, K12 NS098482, R21 ES021957, R21 NS095348, R21 AI119530, R56 NS047344, R01 NS048271, R01 NS051630, U19 AI131130, R01 MH105128, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5600197.

: bright cyan-excitable orange fluorescent protein facilitates dual-emission microscopy and enhances bioluminescence imaging in vivo.; Orange-red fluorescent proteins (FPs) are widely used in biomedical research for multiplexed epifluorescence microscopy with GFP-based probes, but their different excitation requirements make multiplexing with new advanced microscopy methods difficult. Separately, orange-red FPs are useful for deep-tissue imaging in mammals owing to the relative tissue transmissibility of orange-red light, but their dependence on illumination limits their sensitivity as reporters in deep tissues. Here we describe CyOFP1, a bright, engineered, orange-red FP that is excitable by cyan light. We show that CyOFP1 enables single-excitation multiplexed imaging with GFP-based probes in single-photon and two-photon microscopy, including time-lapse imaging in light-sheet systems. CyOFP1 also serves as an efficient acceptor for resonance energy transfer from the highly catalytic blue-emitting luciferase NanoLuc. An optimized fusion of CyOFP1 and NanoLuc, called Antares, functions as a highly sensitive bioluminescent reporter in vivo, producing substantially brighter signals from deep tissues than firefly luciferase and other bioluminescent proteins., Grant Number: F32 GM117793, P50 GM107615, R01 HL064274, U01 NS090600, R01 GM105404, R01 MH080047, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4942401.

: functional significance of the last 5 residues of the C-terminus of cardiac troponin I.; The C-terminal region of cardiac troponin I (cTnI) is known to be important in cardiac function, as removal of the last 17 C-terminal residues of human cTnI has been associated with myocardial stunning. To investigate the C-terminal region of cTnI, three C-terminal deletion mutations in human cTnI were generated: Δ1 (deletion of residue 210), Δ3 (deletion of residues 208-210), and Δ5 (deletion of residues 206-210). Mammalian two-hybrid studies showed that the interactions between cTnI mutants and cardiac troponin C (cTnC) or cardiac troponin T (cTnT) were impaired in Δ3 and Δ5 mutants when compared to wild-type cTnI. Troponin complexes containing 2-[4'-(iodoacetamido) anilino] naphthalene-6-sulfonic acid (IAANS) labeled cTnC showed that the troponin complex containing cTnI Δ5 had a small increase in Ca(2+) affinity (P < 0.05); while the cTnI Δ1- and Δ3 troponin complexes showed no difference in Ca(2+) affinity when compared to wild-type troponin. In vitro motility assays showed that all truncation mutants had increased Ca(2+) dependent motility relative to wild-type cTnI. These results suggest that the last 5 C-terminal residues of cTnI influence the binding of cTnI with cTnC and cTnT and affect the Ca(2+) dependence of filament sliding, and demonstrate the importance of this region of cTnI., Keywords: Calcium, Heart, In vitro motility assay, Mammalian two-hybrid, Troponin I, Unloaded filament sliding, Grant Number: R01 HL063974, R01 HL096819, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4899223.

: genetics of venom ontogeny in the eastern diamondback rattlesnake ().; The same selective forces that give rise to rapid inter- and intraspecific divergence in snake venoms can also favor differences in venoms across life-history stages. Ontogenetic changes in venom composition are well known and widespread in snakes but have not been investigated to the level of unambiguously identifying the specific loci involved. The eastern diamondback rattlesnake was previously shown to undergo an ontogenetic shift in venom composition at sexual maturity, and this shift accounted for more venom variation than geography. To characterize the genetics underlying the ontogenetic venom compositional change in , we sequenced adult/juvenile pairs of venom-gland transcriptomes from five populations previously shown to have different adult venom compositions. We identified a total of 59 putative toxin transcripts for C. adamanteus, and 12 of these were involved in the ontogenetic change. Three toxins were downregulated, and nine were upregulated in adults relative to juveniles. Adults and juveniles expressed similar total levels of snake-venom metalloproteinases but differed substantially in their featured paralogs, and adults expressed higher levels of Bradykinin-potentiating and C-type natriuretic peptides, nerve growth factor, and specific paralogs of phospholipases A and snake venom serine proteinases. Juvenile venom was more toxic to mice, indicating that the expression differences resulted in a phenotypically, and therefore potentially ecologically, significant difference in venom function. We also showed that adult and juvenile venom-gland transcriptomes for a species with known ontogenetic venom variation were equally effective at individually providing a full characterization of the venom genes of a species but that any particular individual was likely to lack several toxins in their transcriptome. A full characterization of a species' venom-gene complement therefore requires sequencing more than one individual, although the ages of the individuals are unimportant., Keywords: Ontogeny, Transcriptome, Venom, Grant Number: P40 OD010960, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5410154.

: genome-wide phylogeny of jumping spiders (Araneae, Salticidae), using anchored hybrid enrichment.; We present the first genome-wide molecular phylogeny of jumping spiders (Araneae: Salticidae), inferred from Anchored Hybrid Enrichment (AHE) sequence data. From 12 outgroups plus 34 salticid taxa representing all but one subfamily and most major groups recognized in previous work, we obtained 447 loci totalling 96,946 aligned nucleotide sites. Our analyses using concatenated likelihood, parsimony, and coalescent methods (ASTRAL and SVDQuartets) strongly confirm most previous results, resolving as monophyletic the Spartaeinae, Salticinae (with the hisponines sister), Salticoida, Amycoida, Saltafresia, and Simonida. The agoriines, previously difficult to place beyond subfamily, are finally placed confidently within the saltafresians as relatives of the chrysillines and hasariines. Relationships among the baviines, astioids, marpissoids, and saltafresians remain uncertain, though our analyses tentatively conclude the first three form a clade together. Deep relationships, among the seven subfamilies, appear to be largely resolved, with spartaeines, lyssomanines, and asemoneines forming a clade. In most analyses, (representing the onomastines) is strongly supported as sister to the hisponines plus salticines. Overall, the much-improved resolution of many deep relationships despite a relatively sparse taxon sample suggests AHE is a promising technique for salticid phylogenetics., Keywords: Dionycha, Jumping spiders, Phylogenomics, Salticids, Systematics, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673835.

: hPSC-Derived Tissue-Resident Macrophage Model Reveals Differential Responses of Macrophages to ZIKV and DENV Infection.; Zika virus (ZIKV) and dengue virus (DENV) are two closely related flaviviruses that lead to different clinical outcomes. The mechanism for the distinct pathogenesis of ZIKV and DENV is poorly understood. Here, we investigate ZIKV and DENV infection of macrophages using a human pluripotent stem cell (hPSC)-derived macrophage model and discover key virus-specific responses. ZIKV and DENV productively infect hPSC-derived macrophages. DENV, but not ZIKV, infection of macrophages strongly activates macrophage migration inhibitory factor (MIF) secretion and decreases macrophage migration. Neutralization of MIF leads to improved migratory ability of DENV-infected macrophages. In contrast, ZIKV-infected macrophages exhibit prolonged migration and express low levels of pro-inflammatory cytokines and chemokines. Mechanistically, ZIKV disrupts the nuclear factor κB (NF-κB)-MIF positive feedback loop by inhibiting the NF-κB signaling pathway. Our results demonstrate the utility of hPSC-derived macrophages in infectious disease modeling and suggest that the distinct impact of ZIKV and DENV on macrophage immune response may underlie different pathogenesis of Zika and dengue diseases., Keywords: MIF, NF-κB signaling, Zika virus, Dengue virus, Disease modeling, Dissemination, Human pluripotent stem cells, Immune response, Macrophage differentiation, Macrophage migration, Grant Number: R21 AI119530, U19 AI131130, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6092684.

: half-bridge component Kar1 promotes centrosome separation and duplication during budding yeast meiosis.; The budding yeast centrosome, often called the spindle pole body (SPB), nucleates microtubules for chromosome segregation during cell division. An appendage, called the half bridge, attaches to one side of the SPB and regulates SPB duplication and separation. Like DNA, the SPB is duplicated only once per cell cycle. During meiosis, however, after one round of DNA replication, two rounds of SPB duplication and separation are coupled with homologue segregation in meiosis I and sister-chromatid segregation in meiosis II. How SPB duplication and separation are regulated during meiosis remains to be elucidated, and whether regulation in meiosis differs from that in mitosis is unclear. Here we show that overproduction of the half-bridge component Kar1 leads to premature SPB separation during meiosis. Furthermore, excessive Kar1 induces SPB overduplication to form supernumerary SPBs, leading to chromosome missegregation and erroneous ascospore formation. Kar1--mediated SPB duplication bypasses the requirement of dephosphorylation of Sfi1, another half-bridge component previously identified as a licensing factor. Our results therefore reveal an unexpected role of Kar1 in licensing meiotic SPB duplication and suggest a unique mechanism of SPB regulation during budding yeast meiosis., Grant Number: R01 GM117102, R01 GM121443, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6085829.

: illustrated guide to seeds found in nests of the Florida harvester ant, Pogonomyrmex badius.; The Florida harvester ant, Pogonomyrmex badius collects the seeds of many plant species and stores them in underground nest chambers for later consumption. Seeds taken from multiple nests in 1989, 2014 and 2015 were separated by size and species and identified through published keys, comparison with herbarium specimens and with identified seed collections. Harvester ants stored at least 58 species of seeds from 20 plant families in their chambers. This paper presents images of each seed species in several aspects, their relative abundance in P. badius nests, their size relative to the smallest, and links to online data and images of the parent plant species, as well as to herbarium specimens. A number of seeds and plant families present at the site were not found in ant nests. These data and images will be valuable for future studies and experiments to untangle the choices the ants make in relation to what the plants and the seasons offer them., Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5331987.

: improved smaller biotin ligase for BioID proximity labeling.; The BioID method uses a promiscuous biotin ligase to detect protein-protein associations as well as proximate proteins in living cells. Here we report improvements to the BioID method centered on BioID2, a substantially smaller promiscuous biotin ligase. BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, and exhibits enhanced labeling of proximate proteins. Thus BioID2 improves the efficiency of screening for protein-protein associations. We also demonstrate that the biotinylation range of BioID2 can be considerably modulated using flexible linkers, thus enabling application-specific adjustment of the biotin-labeling radius., Grant Number: P20GM103620, R01EB014869, R01 GM102486, R01 EB014869, P20 GM103620, R01 GM102203, P30 CA030199, R01GM102486, R01GM102203, P20 GM103548, Publication Note: This NIH-funded author manuscript originally appeared in PubMed Central at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4831873.

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