Showing 1 - 50 of 274 Items

Date: 2012-09-17

Creator: Takahito Watanabe, Hiroshi Ochiai, Tetsushi Sakuma, Hadley W. Horch, Naoya, Hamaguchi, Taro Nakamura, Tetsuya Bando, Hideyo Ohuchi, Takashi Yamamoto, Sumihare Noji, Taro Mito

Access: Open access

Hemimetabolous, or incompletely metamorphosing, insects are phylogenetically relatively basal and comprise many pests. However, the absence of a sophisticated genetic model system, or targeted gene-manipulation system, has limited research on hemimetabolous species. Here we use zinc-finger nuclease and transcription activator-like effector nuclease technologies to produce genetic knockouts in the hemimetabolous insect Gryllus bimaculatus. Following the microinjection of mRNAs encoding zinc-finger nucleases or transcription activator-like effector nucleases into cricket embryos, targeting of a transgene or endogenous gene results in sequence-specific mutations. Up to 48% of founder animals transmit disrupted gene alleles after zinc-finger nucleases microinjection compared with 17% after microinjection of transcription activator-like effector nucleases. Heterozygous offspring is selected using mutation detection assays that use a Surveyor (Cel-I) nuclease, and subsequent sibling crosses create homozygous knockout crickets. This approach is independent from a mutant phenotype or the genetic tractability of the organism of interest and can potentially be applied to manage insect pests using a non-transgenic strategy. © 2012 Macmillan Publishers Limited. All rights reserved.

Date: 2017-12-01

Creator: Anne E. McBride

Access: Open access

Candida albicans, a common commensal fungus, can cause disease in immunocompromised hosts ranging from mild mucosal infections to severe bloodstream infections with high mortality rates. The ability of C. albicans cells to switch between a budding yeast form and an elongated hyphal form is linked to pathogenicity in animal models. Hyphal-specific proteins such as cell-surface adhesins and secreted hydrolases facilitate tissue invasion and host cell damage, but the specific mechanisms leading to asymmetric protein localization in hyphae remain poorly understood. In many eukaryotes, directional cytoplasmic transport of messenger RNAs that encode asymmetrically localized proteins allows efficient local translation at the site of protein function. Over the past two decades, detailed mechanisms for polarized mRNA transport have been elucidated in the budding yeast Saccharomyces cerevisiae and the filamentous fungus Ustilago maydis. This review highlights recent studies of RNA-binding proteins in C. albicans that have revealed intriguing similarities to and differences from known fungal mRNA transport systems. I also discuss outstanding questions that will need to be answered to reach an in-depth understanding of C. albicans mRNA transport mechanisms and the roles of asymmetric mRNA localization in polarized growth, hyphal function, and virulence of this opportunistic pathogen.

Date: 2015-05-01

Creator: Mary A. Rogalski

Access: Open access

Date: 2012-12-01

Creator: Pawat Seritrakul, Eric Samarut, Tenzing T.S. Lama, Yann Gibert, Vincent, Laudet, William R. Jackman

Access: Open access

Zebrafish lost anterior teeth during evolution but retain a posterior pharyngeal dentition that requires retinoic acid (RA) cell-cell signaling for its development. The purposes of this study were to test the sufficiency of RA to induce tooth development and to assess its role in evolution. We found that exposure of embryos to exogenous RA induces a dramatic anterior expansion of the number of pharyngeal teeth that later form and shifts anteriorly the expression patterns of genes normally expressed in the posterior tooth-forming region, such as pitx2 and dlx2b. After RA exposure, we also observed a correlation between cartilage malformations and ectopic tooth induction, as well as abnormal cranial neural crest marker gene expression. Additionally, we observed that the RA-induced zebrafish anterior teeth resemble in pattern and number the dentition of fish species that retain anterior pharyngeal teeth such as medaka but that medaka do not express the aldh1a2 RA-synthesizing enzyme in tooth-forming regions. We conclude that RA is sufficient to induce anterior ectopic tooth development in zebrafish where teeth were lost in evolution, potentially by altering neural crest cell development, and that changes in the location of RA synthesis correlate with evolutionary changes in vertebrate dentitions. © FASEB.

Date: 1996-11-20

Creator: Michael F. Palopoli, Andrew W. Davis, Chung I. Wu

Access: Open access

According to measures of molecular divergence, the three species of the Drosophila simulans clade are closely related to and essentially equidistant from each other. We introgressed 10% of the D. sechellia X chromosome into a pure D. simulans genetic background and found that males carrying this introgressed region were consistently fertile; in contrast, males carrying the same segment from D. mauritiana are sterile and suffer from incompatibilities at a minimum of four loci. Together with other recent results, these data suggest that D. simulans and D. sechellia are much more closely related to each other than either is to D. mauritiana. How can we reconcile the phylogeny inferred from the density of hybrid sterility genes with that inferred from molecular divergence? If the molecular phylogeny is correct, the discrepancy might be explained by uneven rates of functional evolution, resulting in the uneven accumulation of substitutions with corresponding negative effects in hybrids. If the functional phylogeny is correct, then low levels of gene flow across nascent species boundaries, particularly for loci not tightly linked to a hybrid sterility gene, may have erased the original pattern of lineage splitting. We propose tests that will allow us to discriminate between the hypotheses.

Date: 2013-09-27

Creator: Alexandra Pfister, Amy Johnson, Olaf Ellers, Hadley W. Horch

Access: Open access

Dendrite and axon growth and branching during development are regulated by a complex set of intracellular and external signals. However, the cues that maintain or influence adult neuronal morphology are less well understood. Injury and deafferentation tend to have negative effects on adult nervous systems. An interesting example of injury-induced compensatory growth is seen in the cricket, Gryllus bimaculatus. After unilateral loss of an ear in the adult cricket, auditory neurons within the central nervous system (CNS) sprout to compensate for the injury. Specifically, after being deafferented, ascending neurons (AN-1 and AN-2) send dendrites across the midline of the prothoracic ganglion where they receive input from auditory afferents that project through the contralateral auditory nerve (N5). Deafferentation also triggers contralateral N5 axonal growth. In this study, we quantified AN dendritic and N5 axonal growth at 30 h, as well as at 3, 5, 7, 14, and 20 days after deafferentation in adult crickets. Significant differences in the rates of dendritic growth between males and females were noted. In females, dendritic growth rates were non-linear; a rapid burst of dendritic extension in the first few days was followed by a plateau reached at 3 days after deafferentation. In males, however, dendritic growth rates were linear, with dendrites growing steadily over time and reaching lengths, on average, twice as long as in females. On the other hand, rates of N5 axonal growth showed no significant sexual dimorphism and were linear. Within each animal, the growth rates of dendrites and axons were not correlated, indicating that independent factors likely influence dendritic and axonal growth in response to injury in this system. Our findings provide a basis for future study of the cellular features that allow differing dendrite and axon growth patterns as well as sexually dimorphic dendritic growth in response to deafferentation. © 2013 Pfister, Johnson, Ellers and Horch.

Date: 2009-04-01

Creator: Rebecca Selden, Amy S. Johnson, Olaf Ellers

Access: Open access

Indirect predator-induced effects on growth, morphology and reproduction have been extensively studied in marine invertebrates but usually without consideration of size-specific effects and not at all in post-metamorphic echinoids. Urchins are an unusually good system, in which, to study size effects because individuals of various ages within one species span four orders of magnitude in weight while retaining a nearly isometric morphology. We tracked growth of urchins, Strongylocentrotus droebachiensis (0.013-161.385 g), in the presence or absence of waterborne cues from predatory Jonah crabs, Cancer borealis. We ran experiments at ambient temperatures, once for 4 weeks during summer and again, with a second set of urchins, for 22 weeks over winter. We used a scaled, cube-root transformation of weight for measuring size more precisely and for equalizing variance across sizes. Growth rate of the smallest urchins (summer: diameter; winter: diameter) decreased by 40-42% in response to crab cues. In contrast, growth rate of larger urchins was unaffected in the summer and increased in response to crab scent by 7% in the winter. At the end of the 22-week experiment, additional gonadal and skeletal variables were measured. Cue-exposed urchins developed heavier, thicker skeletons and smaller gonads, but no differences in spine length or jaw size. The differences depended on urchin size, suggesting that there are size-specific shifts in gonadal and somatic investment in urchins.

Date: 2021-04-01

Creator: Bruce D. Kohorn, Jacob Dexter-Meldrum, Frances D.H. Zorensky, Salem Chabout, Gregory, Mouille, Susan Kohorn

Access: Open access

The cellulose-and pectin-rich plant cell wall defines cell structure, mediates defense against pathogens, and facilitates plant cell adhesion. An adhesion mutant screen of Arabidopsis hypocotyls identified a new allele of QUASIMODO2 (QUA2), a gene required for pectin accumulation and whose mutants have reduced pectin content and adhesion defects. A suppressor of qua2 was also isolated and describes a null allele of SABRE (SAB), which encodes a previously described plasma membrane protein required for longitudinal cellular expansion that organizes the tubulin cytoskeleton. sab mutants have increased pectin content, increased levels of expression of pectin methylesterases and extensins, and reduced cell surface area relative to qua2 and Wild Type, con-tributing to a restoration of cell adhesion.

Date: 1994-01-01

Creator: A. S. Johnson, M. A.R. Koehl

Access: Open access

Date: 2000-01-01

Creator: Holly A. Leddy, Amy S. Johnson

Access: Open access

The podia of sea urchins function in locomotion, adhesion, feeding, and respiration; but different podia on a single urchin are often specialized to one or more of these tasks. We examined the morphology and material properties of podia of the green sea urchin, Strongylocentrotus droebachiensis, to determine whether, despite apparent similarities, they achieve functional specialization along the oral-aboral axis through the differentiation of distinct mechanical properties. We found that oral podia, which are used primarily for locomotion and adhesion, are stronger and thicker than aboral podia, which are used primarily for capturing drift material and as a respiratory surface. The functional role of ambital podia is more ambiguous; however, they are longer and are extended at a lower strain rate than other podial types. They are also stronger and stiffer than aboral podia. In addition, all podia become stronger and stiffer when extended at faster strain rates, in some cases by nearly an order of magnitude for an order of magnitude change in strain rate. This strain-rate dependence implies that resistance to rapid loading such as that imposed by waves is high compared to resistance to slower, self-imposed loads. Thus, the serially arranged podia of S. droebachiensis are functionally specialized along an oral-aboral axis by differences in their morphology and mechanical properties.

Date: 2012-01-01

Creator: Bruce D. Kohorn, Susan L. Kohorn, Tanya Todorova, Gillian Baptiste, Kevin, Stansky, Meghan McCullough

Access: Open access

The plant cell wall is composed of a matrix of cellulose fibers, flexible pectin polymers, and an array of assorted carbohydrates and proteins. The receptor-like Wall-Associated Kinases (WAKs) of Arabidopsis bind pectin in the wall, and are necessary both for cell expansion during development and for a response to pathogens and wounding. Mitogen Activated Protein Kinases (MPKs) form a major signaling link between cell surface receptors and both transcriptional and enzyme regulation in eukaryotes, and Arabidopsis MPK6 and MPK3 indeed have important roles in development and the response to stress and pathogens. A dominant allele of WAK2 requires kinase activity and activates a stress response that includes an increased ROS accumulation and the up-regulation of numerous genes involved in pathogen resistance, wounding, and cell wall biogenesis. This dominant allele requires a functional pectin binding and kinase domain, indicating that it is engaged in a WAK signaling pathway. A null mutant of the major plasma membrane ROS-producing enzyme complex, rbohd/f does not suppress the WAK2cTAP-induced phenotype. A mpk6, but not a mpk3, null allele is able to suppress the effects of this dominant WAK2 mutation, thus distinguishing MPK3 and MPK6, whose activity previously was thought to be redundant. Pectin activation of gene expression is abated in a wak2-null, but is tempered by the WAK-dominant allele that induces elevated basal stress-related transcript levels. The results suggest a mechanism in which changes to the cell wall can lead to a large change in cellular responses and help to explain how pathogens and wounding can have general effects on growth. The Author 2011. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPB and IPPE, SIBS, CAS.2011 © The Author 2011. Published by the Molecular Plant Shanghai Editorial Office in association with Oxford University Press on behalf of CSPB and IPPE, SIBS, CAS.

Date: 2018-03-01

Creator: S. E. Kingston, P. Martino, M. Melendy, F. A. Reed, D. B., Carlon

Access: Open access

A key component to understanding the evolutionary response to a changing climate is linking underlying genetic variation to phenotypic variation in stress response. Here, we use a genome-wide association approach (GWAS) to understand the genetic architecture of calcification rates under simulated climate stress. We take advantage of the genomic gradient across the blue mussel hybrid zone (Mytilus edulis and Mytilus trossulus) in the Gulf of Maine (GOM) to link genetic variation with variance in calcification rates in response to simulated climate change. Falling calcium carbonate saturation states are predicted to negatively impact many marine organisms that build calcium carbonate shells – like blue mussels. We sampled wild mussels and measured net calcification phenotypes after exposing mussels to a ‘climate change’ common garden, where we raised temperature by 3°C, decreased pH by 0.2 units and limited food supply by filtering out planktonic particles >5 μm, compared to ambient GOM conditions in the summer. This climate change exposure greatly increased phenotypic variation in net calcification rates compared to ambient conditions. We then used regression models to link the phenotypic variation with over 170 000 single nucleotide polymorphism loci (SNPs) generated by genotype by sequencing to identify genomic locations associated with calcification phenotype, and estimate heritability and architecture of the trait. We identified at least one of potentially 2–10 genomic regions responsible for 30% of the phenotypic variation in calcification rates that are potential targets of natural selection by climate change. Our simulations suggest a power of 13.7% with our study's average effective sample size of 118 individuals and rare alleles, but a power of >90% when effective sample size is 900.

Date: 2020-12-01

Creator: J. Joe Hull, Melissa A. Stefanek, Patsy S. Dickinson, Andrew E. Christie

Access: Open access

Over the past decade, many new peptide families have been identified via in silico analyses of genomic and transcriptomic datasets. While various molecular and biochemical methods have confirmed the existence of some of these new groups, others remain in silico discoveries of computationally assembled sequences only. An example of the latter are the CCRFamides, named for the predicted presence of two pairs of disulfide bonded cysteine residues and an amidated arginine-phenylalanine carboxyl-terminus in family members, which have been identified from annelid, molluscan, and arthropod genomes/transcriptomes, but for which no precursor protein-encoding cDNAs have been cloned. Using routine transcriptome mining methods, we identified four Homarus americanus (American lobster) CCRFamide transcripts that share high sequence identity across the predicted open reading frames but more limited conservation in their 5′ terminal ends, suggesting the Homarus gene undergoes alternative splicing. RT-PCR profiling using primers designed to amplify an internal fragment common to all of the transcripts revealed expression in the supraoesophageal ganglion (brain), eyestalk ganglia, and cardiac ganglion. Variant specific profiling revealed a similar profile for variant 1, eyestalk ganglia specific expression of variant 2, and an absence of variant 3 expression in the cDNAs examined. The broad distribution of CCRFamide transcript expression in the H. americanus nervous system suggests a potential role as a locally released and/or circulating neuropeptide. This is the first report of the cloning of a CCRFamide-encoding cDNA from any species, and as such, provides the first non-in silico support for the existence of this invertebrate peptide family.

Date: 2019-10-01

Creator: Patsy S. Dickinson, Heidi M. Samuel, Elizabeth A. Stemmler, Andrew E. Christie

Access: Open access

The SIFamides are a broadly conserved arthropod peptide family characterized by the C-terminal motif –SIFamide. In decapod crustaceans, two isoforms of SIFamide are known, GYRKPPFNGSIFamide (Gly1-SIFamide), which is nearly ubiquitously conserved in the order, and VYRKPPFNGSIFamide (Val1-SIFamide), known only from members of the astacidean genus Homarus. While much work has focused on the identification of SIFamide isoforms in decapods, there are few direct demonstrations of physiological function for members of the peptide family in this taxon. Here, we assessed the effects of Gly1- and Val1-SIFamide on the cardiac neuromuscular system of two closely related species of Cancer crab, Cancer borealis and Cancer irroratus. In each species, both peptides were cardioactive, with identical, dose-dependent effects elicited by both isoforms in a given species. Threshold concentrations for bioactivity are in the range typically associated with hormonal delivery, i.e., 10−9 to 10−8 M. Interestingly, and quite surprisingly, while the predicted effects of SIFamide on cardiac output are similar in both C. borealis and C. irroratus, frequency effects predominate in C. borealis, while amplitude effects predominate in C. irroratus. These findings suggest that, while SIFamide is likely to increase cardiac output in both crabs, the mechanism through which this is achieved is different in the two species. Immunohistochemical/mass spectrometric data suggest that SIFamide is delivered to the heart hormonally rather than locally, with the source of hormonal release being midgut epithelial endocrine cells in both Cancer species. If so, midgut-derived SIFamide may function as a regulator of cardiac output during the process of digestion.

Date: 2020-12-01

Creator: Andrew E. Christie, Cindy D. Rivera, Catherine M. Call, Patsy S. Dickinson, Elizabeth A., Stemmler, J. Joe Hull

Access: Open access

Over the past decade, in silico genome and transcriptome mining has led to the identification of many new crustacean peptide families, including the agatoxin-like peptides (ALPs), a group named for their structural similarity to agatoxin, a spider venom component. Here, analysis of publicly accessible transcriptomes was used to expand our understanding of crustacean ALPs. Specifically, transcriptome mining was used to investigate the phylogenetic/structural conservation, tissue localization, and putative functions of ALPs in decapod species. Transcripts encoding putative ALP precursors were identified from one or more members of the Penaeoidea (penaeid shrimp), Sergestoidea (sergestid shrimps), Caridea (caridean shrimp), Astacidea (clawed lobsters and freshwater crayfish), Achelata (spiny/slipper lobsters), and Brachyura (true crabs), suggesting a broad, and perhaps ubiquitous, conservation of ALPs in decapods. Comparison of the predicted mature structures of decapod ALPs revealed high levels of amino acid conservation, including eight identically conserved cysteine residues that presumably allow for the formation of four identically positioned disulfide bridges. All decapod ALPs are predicted to have amidated carboxyl-terminals. Two isoforms of ALP appear to be present in most decapod species, one 44 amino acids long and the other 42 amino acids in length, both likely generated by alternative splicing of a single gene. In carideans, a gene or terminal exon duplication appears to have occurred, with alternative splicing producing four ALPs, two 44 and two 42 amino acid isoforms. The identification of ALP precursor-encoding transcripts in nervous system-specific transcriptomes (e.g., Homarus americanus brain, eyestalk ganglia, and cardiac ganglion assemblies, finding confirmed using RT-PCR) suggests that members of this peptide family may serve as locally-released and/or hormonally-delivered neuromodulators in decapods. Their detection in testis- and hepatopancreas-specific transcriptomes suggests that members of the ALP family may also play roles in male reproduction and innate immunity/detoxification.

Date: 2020-06-01

Creator: Andrew E. Christie, J. Joe Hull, Patsy S. Dickinson

Access: Open access

Gap junctions are physical channels that connect adjacent cells, permitting the flow of small molecules/ions between the cytoplasms of the coupled units. Innexin/innexin-like proteins are responsible for the formation of invertebrate gap junctions. Within the nervous system, gap junctions often function as electrical synapses, providing a means for coordinating activity among electrically coupled neurons. While some gap junctions allow the bidirectional flow of small molecules/ions between coupled cells, others permit flow in one direction only or preferentially. The complement of innexins present in a gap junction determines its specific properties. Thus, understanding innexin diversity is key for understanding the full potential of electrical coupling in a species/system. The decapod crustacean cardiac ganglion (CG), which controls cardiac muscle contractions, is a simple pattern-generating neural network with extensive electrical coupling among its circuit elements. In the lobster, Homarus americanus, prior work suggested that the adult neuronal innexin complement consists of six innexins (Homam-Inx1-4 and Homam-Inx6-7). Here, using a H. americanus CG-specific transcriptome, we explored innexin complement in this portion of the lobster nervous system. With the exception of Homam-Inx4, all of the previously described innexins appear to be expressed in the H. americanus CG. In addition, transcripts encoding seven novel putative innexins (Homam-Inx8-14) were identified, four (Homam-Inx8-11) having multiple splice variants, e.g., six for Homam-Inx8. Collectively, these data indicate that the innexin complement of the lobster nervous system in general, and the CG specifically, is likely significantly greater than previously reported, suggesting the possibility of expanded gap junction diversity and function in H. americanus.

Date: 1982-11-11

Creator: Bruce D. Kohorn, Peter M.m. Rae

Access: Open access

Tandem repeats of ribosomal RNA transcription units in Drosophila melanogaster are separated by a nontranscribed spacer that is comprised in part of serial repeats of a 0.24 kb sequence. DNA sequence analysis shows that such repeats are imperfect copies of a region that includes the site of in vivo rRNA transcription initiation (ca. -240 to +30). Subclones of the rDNA spacer that are copies of the sequence extending from -34 through the initiation site support detectable in vitro transcription in a mixture involving a Drosophila cell-free extract, but accurate in vitro transcription is considerably enhanced when a nontranscribed spacer template includes a copy of the sequence extending upstream of -34. From a comparison of the sequence and transcription template-effectiveness of various rDNA subclones, we infer that a major promoter of RNA polymerase I activity lies between -150 and -30 in the rDNA nontranscribed spacer. The nontranscribed spacer copies of the initiation region are less effective templates for transcription than is the region of in vivo initiation and there are differences between spacer repeates and the authentic sequence downstream of -240 that may account for this. © 1982 IRL Press Limited.

• Embargo End Date: 2025-05-14

Date: 2020-01-01

Creator: Yujin Moon

Access: Embargoed

Date: 2009-12-01

Creator: Bruce D. Kohorn, Susan Johansen, Akira Shishido, Tanya Todorova, Rhysly, Martinez, Elita Defeo, Pablo Obregon

Access: Open access

The angiosperm extracellular matrix, or cell wall, is composed of a complex array of cellulose, hemicelluose, pectins and proteins, the modification and regulated synthesis of which are essential for cell growth and division. The wall associated kinases (WAKs) are receptor-like proteins that have an extracellular domain that bind pectins, the more flexible portion of the extracellular matrix, and are required for cell expansion as they have a role in regulating cellular solute concentrations. We show here that both recombinant WAK1 and WAK2 bind pectin in vitro. In protoplasts pectins activate, in a WAK2-dependent fashion, the transcription of vacuolar invertase, and a wak2 mutant alters the normal pectin regulation of mitogen-activated protein kinases. Microarray analysis shows that WAK2 is required for the pectin activation of numerous genes in protoplasts, many of which are involved in cell wall biogenesis. Thus, WAK2 plays a major role in signaling a diverse array of cellular events in response to pectin in the extracellular matrix. © 2009 Blackwell Publishing Ltd.

Date: 2000-01-01

Creator: B. D. Kohorn

Access: Open access

Date: 1990-01-01

Creator: Bruce D. Kohorn

Access: Open access

Eukaryotic light harvesting proteins (LHCPs) bind pigments and assemble into complexes (LHCs) that channel light energy into photosynthetic reaction centers. The structures of several prokaryotic LHCPs are known and histidines are important for the binding of the associated pigments. It has been difficult to predict how the eukaryotic LHCPs associate with pigments as the structure of the major LHCP of photosystem II is not yet known. While each LHCPII binds approximately 13 chlorophylls the protein contains only three histidines, one in each putative transmembrane helix. Experiments that use isolated pea (Pisum sativum L.) chloroplasts and mutant LHCPII synthesized in vitro show that the substitution of either an alanine or an arginine for each histidine residue inhibits some aspect of LHCII assembly. The histidine of the first membrane helix, but not the second or third, may be involved in the transport across the chloroplast envelope. No histidine alone is essential for the insertion of LHCP into thylakoid membranes, yet arginine substitutions are more inhibitory than those of alanine. The histidine replacements have their most pronounced effect on the assembly of LHCP into LHCII.

Date: 2012-05-01

Creator: Florence F. Sun, Justine E. Johnson, Martin P. Zeidler, Jack R. Bateman

Access: Open access

Balancer chromosomes are critical tools for Drosophila genetics. Many useful transgenes are inserted onto balancers using a random and inefficient process. Here we describe balancer chromosomes that can be directly targeted with transgenes of interest via recombinase-mediated cassette exchange (RMCE). ©2012 Sun et al.

Date: 2020-01-01

Creator: Hannah D. Konkel

Access: Access restricted to the Bowdoin Community

Date: 2016-01-27

Creator: V. Douhovnikoff, S. H. Taylor, E. L.G. Hazelton, C. M. Smith, J., O'Brien

Access: Open access

The fitness costs of reproduction by clonal growth can include a limited ability to adapt to environmental and temporal heterogeneity. Paradoxically, some facultatively clonal species are not only able to survive, but colonize, thrive and expand in heterogeneous environments. This is likely due to the capacity for acclimation (sensu stricto) that compensates for the fitness costs and complements the ecological advantages of clonality. Introduced Phragmites australis demonstrates great phenotypic plasticity in response to temperature, nutrient availability, geographic gradient, water depths, habitat fertility, atmospheric CO2, interspecific competition and intraspecific competition for light. However, no in situ comparative subspecies studies have explored the difference in plasticity between the non-invasive native lineage and the highly invasive introduced lineage. Clonality of the native and introduced lineages makes it possible to control for genetic variation, making P. australis a unique system for the comparative study of plasticity. Using previously identified clonal genotypes, we investigated differences in their phenotypic plasticity through measurements of the lengths and densities of stomata on both the abaxial (lower) and adaxial (upper) surfaces of leaves, and synthesized these measurements to estimate impacts on maximum stomatal conductance to water (gwmax). Results demonstrated that at three marsh sites, invasive lineages have consistently greater gwmax than their native congeners, as a result of greater stomatal densities and smaller stomata. Our analysis also suggests that phenotypic plasticity, determined as within-genotype variation in gwmax, of the invasive lineage is similar to, or exceeds, that shown by the native lineage.

Date: 2011-08-01

Creator: Kimberly A. Tice, D. B. Carlon

Access: Open access

Genome scans have identified candidate regions of the genome undergoing selection in a wide variety of organisms, yet have rarely been applied to broadly dispersing marine organisms experiencing divergent selection pressures, where high recombination rates can reduce the extent of linkage disequilibrium (LD) and the ability to detect genomic regions under selection. The broadly dispersing periwinkle Echinolittorina hawaiiensis exhibits a heritable shell sculpture polymorphism that is correlated with environmental variation. To elucidate the genetic basis of phenotypic variation, a genome scan using over 1000 AFLP loci was conducted on smooth and sculptured snails from divergent habitats at four replicate sites. Approximately 5% of loci were identified as outliers with Dfdist, whereas no outliers were identified by BayeScan. Closer examination of the Dfdist outliers supported the conclusion that these loci were false positives. These results highlight the importance of controlling for Type I error using multiple outlier detection approaches, multitest corrections and replicate population comparisons. Assuming shell phenotypes have a genetic basis, our failure to detect outliers suggests that the life history of the target species needs to be considered when designing a genome scan. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

• Embargo End Date: 2027-05-18

Date: 2022-01-01

Creator: Lauren Kanoelani Waters

Access: Embargoed

• Embargo End Date: 2028-05-16

Date: 2023-01-01

Creator: Brooke Asherman

Access: Embargoed

• Embargo End Date: 2025-05-17

Date: 2024-01-01

Creator: Eban Charles

Access: Embargoed

Date: 2014-05-01

Creator: Nicholas J Saba

Access: Access restricted to the Bowdoin Community

Date: 2013-04-24

Creator: Jack R. Bateman, Michael F. Palopoli, Sarah T. Dale, Jennifer E. Stauffer, Anita L., Shah, Justine E. Johnson, Conor W. Walsh, Hanna Flaten, Christine M. Parsons

Access: Open access

Site-specific recombinases (SSRs) are valuable tools for manipulating genomes. In Drosophila, thousands of transgenic insertions carrying SSR recognition sites have been distributed throughout the genome by several large-scale projects. Here we describe a method with the potential to use these insertions to make custom alterations to the Drosophila genome in vivo. Specifically, by employing recombineering techniques and a dual recombinase-mediated cassette exchange strategy based on the phiC31 integrase and FLP recombinase, we show that a large genomic segment that lies between two SSR recognition-site insertions can be "captured" as a target cassette and exchanged for a sequence that was engineered in bacterial cells. We demonstrate this approach by targeting a 50-kb segment spanning the tsh gene, replacing the existing segment with corresponding recombineered sequences through simple and efficient manipulations. Given the high density of SSR recognition-site insertions in Drosophila, our method affords a straightforward and highly efficient approach to explore gene function in situ for a substantial portion of the Drosophila genome. © 2013 by the Genetics Society of America.

Date: 2024-01-01

Creator: Mary Alta Rogalski, Elizabeth S Baker, Clara M Benadon

Access: Open access

Increasing application of road deicing agents (e.g., NaCl) has caused widespread salinization of freshwater environments. Chronic exposure to toxic NaCl levels can impact freshwater biota at genome to ecosystem scales, yet the degree of harm caused by road salt pollution is likely to vary among habitats and populations. The background ion chemistry of freshwater environments may strongly impact NaCl toxicity, with greater harm occurring in ion-poor, soft water conditions. In addition, populations exposed to salinization may evolve increased NaCl tolerance. Notably, if organisms are adapted to their natal lake water chemistry, toxicity responses may also vary among populations in a given test medium. We examined how this evolutionary and environmental context may interact in shaping NaCl toxicity with a pair of laboratory reciprocal transplant toxicity experiments, using natural populations of the water flea Daphnia ambigua from three lakes differing in ion availability. The lake water environment strongly influenced NaCl toxicity in both trials. NaCl greatly reduced reproduction and r in lake water from a low-ion/ calcium-poor environment compared with water from both a calcium-rich lake and an ion-rich coastal lake. Daphnia from this coastal lake were most robust to the effects of NaCl. A significant population x environment interaction shaped survival in both trials, suggesting that local adaptation to the test waters used contributed to toxicity responses. Our findings that the lake water environment, adaptation to that environment, and adaptation to a focal contaminant may shape toxicity demonstrate the importance of considering environmental and biological complexity in mitigating pollution impacts.

Date: 2025-01-01

Creator: Roger M. Wilder

Access: Access restricted to the Bowdoin Community

Date: 2025-01-01

Creator: Annika Ruth Bell

Access: Access restricted to the Bowdoin Community

Date: 2025-01-01

Creator: Lucille Jean de Ferranti Dutton

Access: Access restricted to the Bowdoin Community

Date: 2020-08-24

Creator: Mary Alta Rogalski, Meghan A. Duffy

Access: Open access

Date: 2013-04-01

Creator: Chaiyaboot Ariyachet, Norma V. Solis, Yaoping Liu, Nemani V. Prasadarao, Scott G., Filler, Anne E. McBride

Access: Open access

Candida albicans causes both mucosal and disseminated infections, and its capacity to grow as both yeast and hyphae is a key virulence factor. Hyphal formation is a type of polarized growth, and members of the SR (serine-arginine) family of RNA-binding proteins influence polarized growth of both Saccharomyces cerevisiae and Aspergillus nidulans. Therefore, we investigated whether SR-like proteins affect filamentous growth and virulence of C. albicans. BLAST searches with S. cerevisiae SR-like protein Npl3 (ScNpl3) identified two C. albicans proteins: CaNpl3, an apparent ScNpl3 ortholog, and Slr1, another SR-like RNAbinding protein with no close S. cerevisiae ortholog. Whereas ScNpl3 was critical for growth, deletion of NPL3 in C. albicans resulted in few phenotypic changes. In contrast, the slr1δ/δ mutant had a reduced growth rate in vitro, decreased filamentation, and impaired capacity to damage epithelial and endothelial cells in vitro. Mice infected intravenously with the slr1δ/δ mutant strain had significantly prolonged survival compared to that of mice infected with the wild-type or slr1δ/δ mutant complemented with SLR1 (slr1δ/δ+SLR1) strain, without a concomitant decrease in kidney fungal burden. Histopathology, however, revealed differential localization of slr1δ/δ hyphal and yeast morphologies within the kidney. Mice infected with slr1δ/δ cells also had an increased brain fungal burden, which correlated with increased invasion of brain, but not umbilical vein, endothelial cells in vitro. The enhanced brain endothelial cell invasion was likely due to the increased surface exposure of the Als3 adhesin on slr1δ/δ cells. Our results indicate that Slr1 is an SR-like protein that influences C. albicans growth, filamentation, host cell interactions, and virulence. © 2013, American Society for Microbiology.

Date: 2019-11-04

Creator: Jack R. Bateman, Judith A. Kassis

Access: Open access

Homologous chromosomes pair in somatic cells in Drosophila, but how this occurs is poorly understood. In this issue of Developmental Cell, Viets et al. (2019) show that proteins and chromatin structure mediate pairing and argue against a DNA sequence-based mechanism.

Date: 2013-04-24

Creator: Jack R. Bateman, Michael F. Palopoli, Sarah T. Dale, Jennifer E. Stauffer, Anita L., Shah, Justine E. Johnson, Conor W. Walsh, Hanna Flaten, Christine M. Parsons

Access: Open access

Site-specific recombinases (SSRs) are valuable tools for manipulating genomes. In Drosophila, thousands of transgenic insertions carrying SSR recognition sites have been distributed throughout the genome by several large-scale projects. Here we describe a method with the potential to use these insertions to make custom alterations to the Drosophila genome in vivo. Specifically, by employing recombineering techniques and a dual recombinase-mediated cassette exchange strategy based on the phiC31 integrase and FLP recombinase, we show that a large genomic segment that lies between two SSR recognition-site insertions can be "captured" as a target cassette and exchanged for a sequence that was engineered in bacterial cells. We demonstrate this approach by targeting a 50-kb segment spanning the tsh gene, replacing the existing segment with corresponding recombineered sequences through simple and efficient manipulations. Given the high density of SSR recognition-site insertions in Drosophila, our method affords a straightforward and highly efficient approach to explore gene function in situ for a substantial portion of the Drosophila genome. © 2013 by the Genetics Society of America.

Date: 2006-08-01

Creator: David W. Stock, William R. Jackman, Josh Trapani

Access: Open access

The fossil record indicates that cypriniform fishes, a group including the zebrafish, lost oral teeth over 50 million years ago. Despite subsequent diversification of feeding modes, no cypriniform has regained oral teeth, suggesting the zebrafish as a model for studying the developmental genetic basis of evolutionary constraint. To investigate the mechanism of cypriniform tooth loss, we compared the oral expression of seven genes whose mammalian orthologs are involved in tooth initiation in the zebrafish and the Mexican tetra, Astyanax mexicanus, a related species retaining oral teeth. The most significant difference we found was an absence in zebrafish oral epithelium of expression of dlx2a and dlx2b, transcription factors that are expressed in early Astyanax odontogenic epithelium. Analysis of orthologous genes in the Japanese medaka (Oryzias latipes) and a catfish (Synodontis multipunctatus) suggests that expression was lost in cypriniforms, rather than gained in Astyanax. Treatment of Astyanaxwith an inhibitor of Fibroblast growth factor (Fgf) signaling produced a partial phenocopy of the zebrafish oral region, in that oral teeth, and expression of d1x2a and d1x2b, were lost, whereas shh and pitx2, genes whose expression is present in zebrafish oral epithelium, were unaffected. We hypothesize that a loss of Fgf signaling to oral epithelium was associated with cypriniform tooth loss.

Date: 2006-12-19

Creator: William R. Jackman, David W. Stock

Access: Open access

It has been considered a "law" that a lost structure cannot reappear in evolution. The common explanation, that genes required for the development of the lost structure degrade by mutation, remains largely theoretical, however. Additionally, the extent to which this mechanism applies to systems of repeated parts, where individual modules are likely to exhibit few unique aspects of genetic control, is unclear. We investigated reversibility of evolution in one such system, the vertebrate dentition, using as a model loss of oral teeth in cypriniform fishes, which include the zebra fish. This evolutionary event, which occurred >50 million years ago, has not been reversed despite subsequent diversification of feeding modes and retention of pharyngeal teeth. We asked whether the cis-regulatory region of a gene whose expression loss parallels cypriniform tooth loss, Dlx2b, retains the capacity for expression in oral teeth. We first created a zebrafish reporter transgenic line that recapitulates endogenous dlx2b expression. We then showed that this zebrafish construct drives reporter expression in oral teeth of the related characiform Astyanax mexicanus. This result, along with our finding that Dlx genes are required for normal tooth development, suggests that changes in trans-acting regulators of these genes were responsible for loss of cypriniform oral teeth. Preservation of oral enhancer function unused for >50 million years could be the result of pleiotropic function in the pharyngeal dentition. If enhancers of other genes in the tooth developmental pathway are similarly preserved, teeth lost from specific regions may be relatively easy to reacquire in evolution. © 2006 by The National Academy of Sciences of the USA.

Date: 2001-01-01

Creator: T. A. Wagner, B. D. Kohorn

Access: Open access

The mechanism by which events in the angiosperm cell wall are communicated to the cytoplasm is not well characterized. A family of five Arabidopsis wall-associated kinases (WAKs) have the potential to provide a physical and signaling continuum between the cell wall and the cytoplasm. The WAKs have an active cytoplasmic protein kinase domain, span the plasma membrane, and contain an N terminus that binds the cell wall. We show here that WAKs are expressed at organ junctions, in shoot and root apical meristems, in expanding leaves, and in response to wall disturbances. Leaves expressing an antisense WAK gene have reduced WAK protein levels and exhibit a loss of cell expansion. WAKs are covalently bound to pectin in the cell wall, providing evidence that the binding of a structural carbohydrate by a receptor-like kinase may have significance in the control of cell expansion.

Date: 1996-09-05

Creator: Zheng Hui He, Masaaki Fujiki, Bruce D. Kohorn

Access: Open access

Physical connections between higher plant cell walls and the plasma membrane have been identified visually, but the molecules involved in the contact are unknown. We describe here an Arabidopsis thaliana protein kinase, designated Wak1 for wall-associated kinase, whose predicted extracytoplasmic domain contains several epidermal growth factor repeats and identity with a viral movement protein. Wak1 fractionates with insoluble material when plant tissue is ground in a variety of buffers and detergents, suggesting a tight association with the plant extracellular matrix. Immunocytochemistry confirms that Wak1 is associated with the cell wall. Enzymatic digestion of the cell wall allows the release of Wak1 from the insoluble cell wall fraction, and protease experiments indicate that Wak1 likely has a cytoplasmic kinase domain, and the EGF containing domain is extracellular. Wak1 is found in all vegetative tissues of Arabidopsis, and has relatives in other angiosperms, but not Chlamydomonas. We suggest that Wak1 is a good candidate for a physical continuum between the cell wall and the cytoplasm, and since the kinase is cytoplasmic, it also has the potential to mediate signals to the cytoplasm from the cell wall.

Date: 1986-01-01

Creator: B. D. Kohorn, E. Harel, P. R. Chitnis, J. P. Thornber, E. M., Tobin

Access: Open access

The precursor for a Lemna light-harvesting chlorophyll a/b protein (pLHCP) has been synthesized in vitro from a single member of the nuclear LHCP multigene family. We report the sequence of this gene. When incubated with Lemna chloroplasts, the pLHCP is imported and processed into several polypeptides, and the mature form is assembled into the light-harvesting complex of photosystem II (LHC II). The accumulation of the processed LHCP is enhanced by the addition to the chloroplasts of a precursor and a co-factor for chlorophyll biosynthesis. Using a model for the arrangement of the mature polypeptide in the thylakoid membrane as a guide, we have created mutations that lie within the mature coding region. We have studied the processing, the integration into thylakoid membranes, and the assembly into light-harvesting complexes of six of these deletions. Four different mutant LHCPs are found as processed proteins in the thylakoid membrane, but only one appears to have an orientation in the membrane that is similar to that of the wild type. No mutant LHCP appears in LHC II. The other two mutant LHCPs cannot be detected within the chloroplasts. We conclude that stable complex formation is not required for the processing and insertion of altered LHCPs into the thylakoid membrane. We discuss the results in light of our model.

Date: 2014-09-01

Creator: Wouter Halfwerk, Marjorie M. Dixon, Kristina J. Ottens, Ryan C. Taylor, Michael J., Ryan, Rachel A. Page, Patricia L. Jones

Access: Open access

Many sexual displays contain multiple components that are received through a variety of sensory modalities. Primary and secondary signal components can interact to induce novel receiver responses and become targets of sexual selection as complex signals. However, predators can also use these complex signals for prey assessment, which may limit the evolution of elaborate sexual signals. We tested whether a multimodal sexual display of the male túngara frog (Physalaemus pustulosus) increases predation risk from the fringe-lipped bat (Trachops cirrhosus) when compared with a unimodal display. We gave bats a choice to attack one of two frog models: a model with a vocal sac moving in synchrony with a mating call (multisensory cue), or a control model with the call but no vocal sac movement (unimodal cue). Bats preferred to attack the model associated with the multimodal display. Furthermore, we determined that bats perceive the vocal sac using echolocation rather than visual cues. Our data illustrate the costs associated with multimodal signaling and that sexual and natural selection pressures on the same trait are not always mediated through the same sensory modalities. These data are important when considering the role of environmental fluctuations on signal evolution as different sensory modalities will be differentially affected.

Date: 1996-10-07

Creator: Benoit Baillet, Bruce D. Kohorn

Access: Open access

The integral membrane protein cytochrome f contains an amino-terminal signal sequence that is required for translocation into the thylakoid membrane. The signal sequence contains a hydrophobic core neighbored by an amino-terminal charged residue. Mutations that introduce charged amino acids into the hydrophobic core are inhibitory to cytochrome f translocation, and thus render cells non-photosynthetic. We have isolated both nuclear and chloroplast suppressors of these mutations by selecting for restoration of photosynthetic growth of Chlamydomonas. Here we describe the characterization of two chloroplast, second site suppressor mutations. Both suppressors remove the positively charged amino acid that borders the amino terminus of the hydrophobic core, and replace this arginine with either a cysteine or a leucine. The existence of these suppressors suggests that the hydrophobic core can be shifted in position within the signal sequence, and analysis of triple mutants in the signal confirms this hypothesis. Thus this signal that mediates translocation into the thylakoid membrane is characterized by a hydrophobic region whose exact amino acid content is not critical, and that need not be flanked on its amino terminus by a charged residue.

Date: 1992-01-01

Creator: Bruce D. Kohorn, Steven Lane, Tracy A. Smith

Access: Open access

A number of molecules have recently been described that effect the correct transport and assembly of cytoplasmically synthesized proteins to cellular membranes. To identify proteins that bind or modify other proteins during the process of membrane translocation, we developed a yeast selection scheme that employs the yeast transcriptional activator GAL4. This selection facilitates the isolation of cDNAs that encode proteases and binding proteins for known target peptide sequences. We report the isolation of an Arabidopsis cDNA encoding a polypeptide that can interact with the amino terminus of a light-harvesting chlorophyll a/b-binding protein (LHCP), a cytoplasmically synthesized protein that is integral to the chloroplast thylakoid membrane. The cDNA was selected in yeast from an Arabidopsis expression library for its ability to inhibit a transcriptional activator GAL4-LHCP fusion protein, but not inhibit native GAL4 protein. The LHCP aminoterminal sequences included in the fusion protein are known to regulate LHCP biogenesis and function. The Arabidopsis cDNA encodes a 595-amino acid protein with at least two functional domains, one with similarity to the family of proteinserine/threonine kinases and another that contains an epidermal growth factor repeat. The identification of an EGF repeat in Arabidopsis indicates that the motif is conserved between the plant and animal kingdoms. Hybridization studies indicate that this gene is likely to be present in other genera of plants. Its mRNA is detected in green leaves but not in other plant tissues or in etiolated plants. The specificity in yeast and the expression pattern in plants together are suggestive of a role for this protein kinase in the assembly or regulation of LHCP.

• Embargo End Date: 2025-05-13

Date: 2020-01-01

Creator: Emma Beane

Access: Embargoed

Date: 2016-10-01

Creator: Patricia L. Jones, Anurag A. Agrawal

Access: Open access

Attraction of mutualists and defense against antagonists are critical challenges for most organisms and can be especially acute for plants with pollinating and non-pollinating flower visitors. Secondary compounds in flowers have been hypothesized to adaptively mediate attraction of mutualists and defense against antagonists, but this hypothesis has rarely been tested. The tissues of milkweeds (Asclepias spp.) contain toxic cardenolides that have long been studied as chemical defenses against herbivores. Milkweed nectar also contains cardenolides, and we have examined the impact of manipulating cardenolides in nectar on the foraging choices of two flower visitors: generalist bumble bees, Bombus impatiens, which are mutualistic pollinators, and specialist monarch butterflies, Danaus plexippus, which are herbivores as larvae and ineffective pollinators as adults. Although individual bumble bees in single foraging bouts showed no avoidance of cardenolides at the highest natural concentrations reported for milkweeds, a pattern of deterrence did arise when entire colonies were allowed to forage for several days. Monarch butterflies were not deterred by the presence of cardenolides in nectar when foraging from flowers, but laid fewer eggs on plants paired with cardenolide-laced flowers compared to controls. Thus, although deterrence of bumble bees by cardenolides may only occur after extensive foraging, a primary effect of nectar cardenolides appears to be reduction of monarch butterfly oviposition.

Date: 2018-07-01

Creator: Rachel L. Kendal, Neeltje J. Boogert, Luke Rendell, Kevin N. Laland, Mike, Webster, Patricia L. Jones

Access: Open access

While social learning is widespread, indiscriminate copying of others is rarely beneficial. Theory suggests that individuals should be selective in what, when, and whom they copy, by following 'social learning strategies’ (SLSs). The SLS concept has stimulated extensive experimental work, integrated theory, and empirical findings, and created impetus to the social learning and cultural evolution fields. However, the SLS concept needs updating to accommodate recent findings that individuals switch between strategies flexibly, that multiple strategies are deployed simultaneously, and that there is no one-to-one correspondence between psychological heuristics deployed and resulting population-level patterns. The field would also benefit from the simultaneous study of mechanism and function. SLSs provide a useful vehicle for bridge-building between cognitive psychology, neuroscience, and evolutionary biology.

Date: 1998-01-01

Creator: L. A. Lipscomb, N. C. Gassner, S. D. Snow, A. M. Eldridge, W. A., Baase, D. L. Drew, B. W. Matthews

Access: Open access