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: 2002-03-14

Creator: Sandro R. Valentini, Jason M. Casolari, Carla C. Oliveira, Pamela A. Silver, Anne E., McBride

Access: Open access

The highly conserved eukaryotic translation initiation factor eIF5A has been proposed to have various roles in the cell, from translation to mRNA decay to nuclear protein export. To further our understanding of this essential protein, three temperature-sensitive alleles of the yeast TIF51A gene have been characterized. Two mutant eIF5A proteins contain mutations in a proline residue at the junction between the two eIFSA domains and the third, strongest allele encodes a protein with a single mutation in each domain, both of which are required for the growth defect. The stronger tif51A alleles cause defects in degradation of short-lived mRNAs, supporting a role for this protein in mRNA decay. A multicopy suppressor screen revealed six genes, the overexpression of which allows growth of a tif51A-1 strain at high temperature; these genes include PAB1, PKC1, and PKC1 regulators WSC1, WSC2, and WSC3. Further results suggest that eIFSA may also be involved in ribosomal synthesis and the WSC/PKC1 signaling pathway for cell wall integrity or related processes.

Date: 2004-08-15

Creator: Michael C. Yu, François Bachand, Anne E. McBride, Suzanne Komili, Jason M., Casolari, Pamela A. Silver

Access: Open access

Hmt1 is the major type I arginine methyltransferase in the yeast Saccharomyces cerevisiae and facilitates the nucleocytoplasmic transport of mRNA-binding proteins through their methylation. Here we demonstrate that Hmt1 is recruited during the beginning of the transcriptional elongation process. Hmt1 methylates Yra1 and Hrp1, two mRNA-binding proteins important for mRNA processing and export. Moreover, loss of Hmt1 affects interactions between mRNA-binding proteins and Tho2, a component of the TREX (transcription/export) complex that is important for transcriptional elongation and recruitment of mRNA export factors. Furthermore, RNA in situ hybridization analysis demonstrates that loss of Hmt1 results in slowed release of HSP104 mRNA from the sites of transcription. Genome-wide location analysis shows that Hmt1 is bound to specific functional gene classes, many of which are also bound by Tho2 and other mRNA-processing factors. These data suggest a model whereby Hmt1 affects transcriptional elongation and, as a result, influences recruitment of RNA-processing factors.

Date: 2021-01-01

Creator: Barry Logan

Access: Open access

Date: 2011-04-01

Creator: Hadley Wilson Horch, Elizabeth Sheldon, Claire C. Cutting, Claire R. Williams, Dana M., Riker, Hannah R. Peckler, Rohit B. Sangal

Access: Open access

The auditory system of the cricket has the unusual ability to respond to deafferentation by compensatory growth and synapse formation. Auditory interneurons such as ascending neuron 2 (AN-2) in the cricket Gryllus bimaculatus possess a dendritic arbor that normally grows up to, but not over, the midline of the prothoracic ganglion. After chronic deafferentation throughout larval development, however, the AN-2 dendritic arbor changes dramatically, and medial dendrites sprout across the midline where they form compensatory synapses with the auditory afferents from the contralateral ear. We quantified the extent of the effects of chronic, unilateral deafferentation by measuring several cellular parameters of 3 different neuronal components of the auditory system: the deafferented AN-2, the contralateral (or nondeafferented) AN-2 and the contralateral auditory afferents. Neuronal tracers and confocal microscopy were used to visualize neurons, and double-label experiments were performed to examine the cellular relationship between pairs of cells. Dendritic complexity was quantified using a modified Sholl analysis, and the length and volume of processes and presynaptic varicosities were assessed under control and deafferented conditions. Chronic deafferentation significantly influenced the morphology of all 3 neuronal components examined. The overall dendritic complexity of the deafferented AN-2 dendritic arbor was reduced, while both the contralateral AN-2 dendritic arbor and the remaining, intact, auditory afferents grew longer. We found no significant changes in the volume or density of varicosities after deafferentation. These complex cellular changes after deafferentation are interpreted in the light of the reported differential regulation of vesicle-associated membrane protein and semaphorin 2a. Copyright © 2011 S. Karger AG, Basel.

Date: 2015-04-01

Creator: Jeffrey C. Yu, Zachary D. Fox, James L. Crimp, Hana E. Littleford, Andrea L., Jowdry, William R. Jackman

Access: Open access

Intercellular communication by the hedgehog cell signaling pathway is necessary for tooth development throughout the vertebrates, but it remains unclear which specific developmental signals control cell behavior at different stages of odontogenesis. To address this issue, we have manipulated hedgehog activity during zebrafish tooth development and visualized the results using confocal microscopy. Results: We first established that reporter lines for dlx2b, fli1, NF-κB, and prdm1a are markers for specific subsets of tooth germ tissues. We then blocked hedgehog signaling with cyclopamine and observed a reduction or elimination of the cranial neural crest derived dental papilla, which normally contains the cells that later give rise to dentin-producing odontoblasts. Upon further investigation, we observed that the dental papilla begins to form and then regresses in the absence of hedgehog signaling, through a mechanism unrelated to cell proliferation or apoptosis. We also found evidence of an isometric reduction in tooth size that correlates with the time of earliest hedgehog inhibition. Conclusions: We hypothesize that these results reveal a previously uncharacterized function of hedgehog signaling during tooth morphogenesis, regulating the number of cells in the dental papilla and thereby controlling tooth size.

Date: 1998-05-07

Creator: Michael F. Palopoli, Nipam H. Patel

Access: Open access

Segmental identifies along the insect body depend on the activities of Hox genes [1,2]. In Drosophila melanogaster, one well-studied Hox regulatory target is Distal-less (DII), which Is required for the development of distel limb structures [3]. In abdominal segments, DII transcription is prevented when Hox proteins of the Bithorax Complex (BX-C) bind to cis-regulatory elements upstream of the DII transcription start site [4,5]. Previous evolutionary comparisons of gene expression patterns suggest that this direct repression is conserved between Diptera and Lepidoptera, but is absent in the Crustacea [6,7]. We examined gene expression patterns in three orders of hexapods, all of which develop abdominal appendages, in order to determine when the strong repressive interaction between BX-C proteins and DII appeared during evolution. In each of the species examined, DII expression was initiated in abdominal cells despite the presence of high levels of BX-C proteins. It appears that the strong repressive effects of BX-C proteins on DII expression arose relatively late in insect evolution. We suggest that the regulatory interaction between the BX-C genes and DII has evolved within the hexapods in a complex, segment-specific manner.

Date: 2004-01-01

Creator: Michael Butler, Amy S. Johnson

Access: Open access

Melanin has been associated with increased resistance to abrasion, decreased wear and lowered barb breakage in feathers. But, this association was inferred without considering barb position along the rachis as a potentially confounding variable. We examined the cross-sectional area, breaking force, breaking stress, breaking strain and toughness of melanized and unmelanized barbs along the entire rachis of a primary feather from an osprey (Pandion haliaetus). Although breaking force was higher for melanized barbs, breaking stress (force divided by cross-sectional area) was greater for unmelanized barbs. But when position was considered, all mechanical differences between melanized and unmelanized barbs disappeared. Barb breaking stress, breaking strain and toughness decreased, and breaking stiffness increased, distally along the rachis. These proximal-distal material property changes are small and seem unlikely to affect flight performance of barbs. Our observations of barb bending, breaking and morphology, however, lead us to propose a design principle for barbs. We propose that, by being thicker-walled dorso-ventrally, the barb's flexural stiffness is increased during flight; but, by allowing for twisting when loaded with dangerously high forces, barbs firstly avoid failure by bending and secondly avoid complete failure by buckling rather than rupturing.

Date: 1993-01-01

Creator: A. S. Johnson, K. P. Sebens

Access: Open access

Per polyp feeding rate was independent of the horizontal planform area of colonies. At the lowest velocities, most particles were captured on the upstream edge or in the middle of colonies, but all positional bias in capture rate disappeared at higher velocities. Particle capture and increasing flow speed were negatively associated. There were small, but measurable, differences in mean tentacle length between corals feeding at different velocities. Velocity-dependent feeding rate at most velocities was thus related to changes in flow rather than to changes in feeding behavior. Experiments in which corals were turned upside down revealed that the increased capture rate for rightside-up corals feeding at low velocity could be almost entirely accounted for by gravitational deposition of particles on the corals' tentacles. The tentacles form a canopy within which water movement was slowed, possibly facilitating gravitational deposition of non-buoyant or sinking food particles. -from Authors

Date: 1991-07-01

Creator: David L. Murray, Bruce D. Kohorn

Access: Open access

Date: 2020-03-01

Creator: Zoe M. Wood, Patricia L. Jones

Access: Open access

Philaenus spumarius (Meadow Spittlebug, Homoptera: Cercopoidea) is a cosmopolitan generalist insect that feeds on a wide repertoire of host plants in the field. We studied density and growth of Meadow Spittlebugs on a range of host plants on Kent Island, a boreal island in the Bay of Fundy, NB, Canada. The highest spittlebug densities were on Cirsium arvense (Canadian Thistle), although spittlebugs had larger body sizes on Solidago rugosa (Rough-stemmed Goldenrod) and Anaphalis margaritacea (Pearly Everlasting). We fertilized plots of Rough-stemmed Goldenrod in the field over 3 weeks to examine the effects of plant quality on development of Meadow Spittlebugs. Following fertilization, there were fewer nymphs present in fertilized plots than in unfertilized plots, indicating faster nymph maturation to adulthood on fertilized plants. This study offers an initial report of the host plants used by Meadow Spittlebugs in northeastern boreal habitat, variation in density and performance of the species on a range of host plants, and the effects of plant fertilization on spittlebug life history.

Date: 1983-01-01

Creator: B. D. Kohorn, P. M.M. Rae

Access: Open access

Date: 2006-01-24

Creator: Aimee M. Eldridge, Wayne A. Halsey, Deborah S. Wuttke

Access: Open access

The single-strand overhang present at telomeres plays a critical role in mediating both the capping and telomerase regulation functions of telomeres. The telomere end-binding proteins, Cdc13 in Saccharomyces cerevisiae, Pot1 in higher eukaryotes, and TEBP in the ciliated protozoan Oxytricha nova, exhibit sequence-specific binding to their respective single-strand overhangs. S. cerevisiae telomeres are composed of a heterogeneous mixture of GT-rich telomeric sequence, unlike in higher eukaryotes which have a simple repeat that is maintained with high fidelity. In yeast, the telomeric overhang is recognized by the essential protein Cdc13, which coordinates end-capping and telomerase activities at the telomere. The Cdc13 DNA-binding domain (Cdc13-DBD) binds these telomere sequences with high affinity (3 pM) and sequence specificity. To better understand the basis for this remarkable recognition, we have investigated the binding of the Cdc13-DBD to a series of altered DNA substrates. Although an 11-mer of GT-rich sequence is required for full binding affinity, only three of these 11 bases are recognized with high specificity. This specificity differs from that observed in the other known telomere end-binding proteins, but is well suited to the specific role of Cdc13 at yeast telomeres. These studies expand our understanding of telomere recognition by the Cdc13-DBD and of the unique molecular recognition properties of ssDNA binding. © 2006 American Chemical Society.

Date: 2007-09-01

Creator: Benjamin R. Williams, Jack R. Bateman, Natasha D. Novikov, C. Ting Wu

Access: Open access

Homolog pairing refers to the alignment and physical apposition of homologous chromosomal segments. Although commonly observed during meiosis, homolog pairing also occurs in nonmeiotic cells of several organisms, including humans and Drosophila. The mechanism underlying nonmeiotic pairing, however, remains largely unknown. Here, we explore the use of established Drosophila cell lines for the analysis of pairing in somatic cells. Using fluorescent in situ hybridization (FISH), we assayed pairing at nine regions scattered throughout the genome of Kc167 cells, observing high levels of homolog pairing at all six euchromatic regions assayed and variably lower levels in regions in or near centromeric heterochromatin. We have also observed extensive pairing in six additional cell lines representing different tissues of origin, different ploidies, and two different species, demonstrating homolog pairing in cell culture to be impervious to cell type or culture history. Furthermore, by sorting Kc167 cells into G1, S, and G2 subpopulations, we show that even progression through these stages of the cell cycle does not significantly change pairing levels. Finally, our data indicate that disrupting Drosophila topoisomerase II (Top2) gene function with RNAi and chemical inhibitors perturbs homolog pairing, suggesting Top2 to be a gene important for pairing. Copyright © 2007 by the Genetics Society of America.

Date: 2021-01-01

Creator: Hannah L. Randazzo

Access: Open access

Anthropogenic CO2 is changing the pCO2, temperature, and carbonate chemistry of seawater. These processes are termed ocean acidification (OA) and ocean warming. Previous studies suggest two opposing hypotheses for the way in which marine climate stress will influence echinoderm calcification, metabolic efficiency, and reproduction: either an additive or synergistic effect. Sea stars have a regenerative capacity, which may be particularly affected while rebuilding calcium carbonate arm structures, leading to changes in arm growth and calcification. In this study, Asterias forbesi were exposed to ocean water of either ambient, high temperature, high pCO2, or high temperature and high pCO2 for 60 days, and the regeneration length of the amputated arm was measured weekly. Ocean acidification conditions (pCO2 ~1180 μatm) had a negative impact on regenerated arm length, and an increase in temperature of +4°C above ambient conditions (Fall, Southern Gulf of Maine) had a positive effect on regenerated arm length, but the additive effects of these two factors resulted in smaller regenerated arms compared to ambient conditions. Sea stars regenerating under high pCO2 exhibited a lower proportion of calcified mass, which could be the result of a more energetically demanding calcification process associated with marine climate stress. These results indicate that A. forbesi calcification is sensitive to increasing pCO2, and that climate change will have an overall net negative effect on sea star arm regeneration. Such effects could translate into lower predation rates by a key consumer in the temperate rocky intertidal of North America.

Date: 2020-10-01

Creator: Emily R. Oleisky, Meredith E. Stanhope, J. Joe Hull, Andrew E. Christie, Patsy S., Dickinson

Access: Open access

The American lobster, Homarus americanus, cardiac neuromuscular system is controlled by the cardiac ganglion (CG), a central pattern generator consisting of four premotor and five motor neurons. Here, we show that the premotor and motor neurons can establish independent bursting patterns when decoupled by a physical ligature. We also show that mRNA encoding myosuppressin, a cardioactive neuropeptide, is produced within the CG. We thus asked whether myosuppressin modulates the decoupled premotor and motor neurons, and if so, how this modulation might underlie the role(s) that these neurons play in myosuppressin's effects on ganglionic output. Although myosuppressin exerted dose-dependent effects on burst frequency and duration in both premotor and motor neurons in the intact CG, its effects on the ligatured ganglion were more complex, with different effects and thresholds on the two types of neurons. These data suggest that the motor neurons are more important in determining the changes in frequency of the CG elicited by low concentrations of myosuppressin, whereas the premotor neurons have a greater impact on changes elicited in burst duration. A single putative myosuppressin receptor (MSR-I) was previously described from the Homarus nervous system. We identified four additional putative MSRs (MSR-II-V) and investigated their individual distributions in the CG premotor and motor neurons using RT-PCR. Transcripts for only three receptors (MSR-II-IV) were amplified from the CG. Potential differential distributions of the receptors were observed between the premotor and motor neurons; these differences may contribute to the distinct physiological responses of the two neuron types to myosuppressin. NEW & NOTEWORTHY Premotor and motor neurons of the Homarus americanus cardiac ganglion (CG) are normally electrically and chemically coupled, and generate rhythmic bursting that drives cardiac contractions; we show that they can establish independent bursting patterns when physically decoupled by a ligature. The neuropeptide myosuppressin modulates different aspects of the bursting pattern in these neuron types to determine the overall modulation of the intact CG. Differential distribution of myosuppressin receptors may underlie the observed responses to myosuppressin.

Date: 2013-10-22

Creator: Kristin M.K. Halbert, Erica Goetze, David B. Carlon

Access: Open access

Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate the global diversity within Pleuromamma piseki and P. gracilis, two dominant members of the migratory zooplankton assemblage in subtropical and tropical waters worldwide. Using DNA sequence data from the mitochondrial gene cytochrome c oxidase subunit II (mtCOII) from 522 specimens collected across the Pacific, Atlantic and Indian Oceans, we discover twelve well-resolved genetically distinct clades in this species complex (Bayesian posterior probabilities >0.7; 6.3-17% genetic divergence between clades). The morphologically described species P. piseki and P. gracilis did not form monophyletic groups, rather they were distributed throughout the phylogeny and sometimes co-occurred within well-resolved clades: this result suggests that morphological characters currently used for taxonomic identification of P. gracilis and P. piseki may be inaccurate as indicators of species' boundaries. Cryptic clades within the species complex ranged from being common to rare, and from cosmopolitan to highly restricted in distribution across the global ocean. These novel lineages appear to be ecologically divergent, with distinct biogeographic distributions across varied pelagic habitats. We hypothesize that these mtDNA lineages are distinct species and suggest that resolving their systematic status is important, given the ecological significance of the genus Pleuromamma in subtropical-tropical waters worldwide. © 2013 Halbert et al.