Showing 51 - 100 of 116 Items

Date: 2020-01-01

Creator: William Allen

Access: Open access

Central pattern generators (CPGs) are neural circuits whose component neurons possess intrinsic properties and synaptic connections that allow them to generate rhythmic motor outputs in the absence of descending inputs. The cardiac ganglion (CG) is a nine-cell CPG located in the American lobster, Homarus americanus. Stretch of the myocardium feeds back to the CG through mechano-sensitive dendrites and is thought to play a role in maintaining regularity in the beating pattern of the heart. The novel peptide AMGSEFLamide has been observed to induce irregular beating patterns when applied at high concentrations. This study investigated the interaction between stretch-related feedback and AMGSEFLamide modulation in generating irregular beating patterns in the whole heart of Homarus americanus. It was hypothesized that greater longitudinal stretch of the heart would result in greater regularity in the instantaneous beat frequency, based on previous findings that stretch-sensitive dendrites play a role in the regulation of the heartbeat. Furthermore, it was predicted that the elimination of stretch feedback via deafferentation of the heart would augment the irregularity induced by AMGSEFLamide. Data showed significantly increased irregularity in beating in response to 10-6 M AMGSEFLamide application. Longitudinal stretch did not reliably alter baseline variability in frequency, nor did it influence the modulatory effect of AMGSEFLamide. Deafferentation did not significantly alter baseline irregularity. Deafferented preparations did exhibit a trend of responding to AMGSEFLamide with a greater percent increase in irregularity compared to when afferents were intact, suggesting a potential role of stretch-stabilization in response to modulatory perturbations in the Homarus heart.

Date: 2020-01-01

Creator: Jacob Salman Kazmi

Access: Open access

Neuromodulation may be a substrate for the evolution of behavioral diversity. The extent to which a central pattern generator is modulated could serve as a mechanism that enables variability in motor output dependent on an organism’s need for behavioral flexibility. The pyloric circuit, a central pattern generator in the crustacean stomatogastric nervous system (STNS), stimulates contractions of foregut muscles in digestion. Since neuromodulation enables variation in the movements of pyloric muscles, more diverse feeding patterns should be correlated with a higher degree of STNS neuromodulation. Previous data have shown that Cancer borealis, an opportunistic feeder, is sensitive to a wider array of neuromodulators than Pugettia producta, a specialist feeder. The observed difference in modulatory capacity may be coincidental since these species are separated by phylogeny. We predict that the difference in modulatory capacity is a product of a differential need for variety in foregut muscle movements. This study examined two members of the same superfamily as P. producta, the opportunistically feeding snow crab (Chionoecetes opilio) and portly spider crab (Libinia emarginata). Using extracellular recording methods, the responses of isolated STNS preparations to various neuromodulators were measured. Initial qualitative results indicate that the STNS of C. opilio is sensitive to all of these neuromodulators. Additionally, previous data on the neuromodulatory capacity of L. emarginata was supported through similar electrophysiological analysis of the isolated STNS. As a first step in determining the mechanism of differential sensitivity between species, tissue-specific transcriptomes were generated and mined for neuromodulators.

Date: 2020-01-01

Creator: Marie Marjorie Bergsund

Access: Access restricted to the Bowdoin Community

Date: 2023-01-01

Creator: Khushali N Patel

Access: Access restricted to the Bowdoin Community

Date: 2024-01-01

Creator: Zackery D. Reynolds

Access: Access restricted to the Bowdoin Community

Date: 2016-05-01

Creator: Michael M Kang

Access: Access restricted to the Bowdoin Community

Date: 2023-01-01

Creator: Lucia Marie O'Sullivan

Access: Access restricted to the Bowdoin Community

Date: 2025-01-01

Creator: Samantha McLemore

Access: Access restricted to the Bowdoin Community

Date: 2013-10-01

Creator: Brendan Eliot Depue, Nick Ketz, Matthew V. Mollison, Erika Nyhus, Marie T. Banich, Tim Curran

Access: Open access

Although investigations of memory and the dynamics of ERP components and neural oscillations as assessed through EEG have been well utilized, little research into the volitional nature of suppression over memory retrieval have used these methods. Oscillation analyses conducted on the Think/No-Think (TNT) task and volitional suppression of retrieval are of interest to broaden our knowledge of neural oscillations associated not only during successful memory retrieval but also when retrieval is unwanted or suppressed. In the current study, we measured EEG during a TNT task and performed ERP and EEG spectral power band analyses. ERP results replicated other researchers' observations of increases in 500-800 msec parietal effects for items where retrieval was instructed to be elaborated compared with being suppressed. Furthermore, EEG analyses indicated increased alpha (8-12 Hz) and theta (3-8 Hz) oscillations across parietal electrodes for items that were instructed to be suppressed versus those to be elaborated. Additionally, during the second half of the experiment (after repeated attempts at control), increases in theta oscillations were found across both frontal and parietal electrodes for items that were instructed to be suppressed and that were ultimately forgotten versus those ultimately remembered. Increased alpha power for items that were instructed to be suppressed versus elaborated may indicate reductions of retrieval attempts or lack of retrieval success. Increased theta power for items that were instructed to be suppressed versus elaborated may indicate increased or prolonged cognitive control to monitor retrieval events. © 2013 Massachusetts Institute of Technology.

Date: 2019-05-01

Creator: Katharine Torrey

Access: Open access

The peptide vasotocin (VT) and its mammalian homologue, vasopressin (VP), produce effects on social behavior that are highly species- and context-specific. We recently sequenced two genes for V1a-like receptors (VTR) in the goldfish brain, one that encodes for a fully-functioning canonical receptor and one that encodes for a non-functional truncated receptor. The current study is an investigation of whether social context may alter expression of these receptor types and thus, potentially, behavioral responses to VT. We used western blotting and immunohistochemistry with custom anti-VTR antibodies to characterize the distribution of VTR throughout the forebrain and the hindbrain. Western blot results showed bands close to the predicted sizes for truncated and canonical VTR constructs, suggesting that both genes are translated into protein in the brain, but the presence of additional bands suggested potential nonspecific binding. Immunohistochemistry data revealed VTR signal throughout the brain in regions associated with social behavior. We additionally examined whether visual and olfactory context alters behavioral responsiveness to VT, potentially by altering the expression of one or both receptors. Behavioral tests suggested that VT inhibits approach to males, but its effect on response to females in reproductive contexts is still undetermined, likely due to interference from a stress response during testing. Further characterization of VTR throughout the brain will clarify how social context might alter VT signaling through context-dependent modulation of its receptors. Additionally, future work should examine the behavioral consequences of such modulation by further studying whether VT’s effect on social approach behavior depends on context.

Date: 2011-01-01

Creator: A. Forche, D. Abbey, T. Pisithkul, M. A. Weinzierl, T., Ringstrom, D. Bruck, K. Petersen, J. Berman

Access: Open access

Genetic diversity is often generated during adaptation to stress, and in eukaryotes some of this diversity is thought to arise via recombination and reassortment of alleles during meiosis. Candida albicans, the most prevalent pathogen of humans, has no known meiotic cycle, and yet it is a heterozygous diploid that undergoes mitotic recombination during somatic growth. It has been shown that clinical isolates as well as strains passaged once through a mammalian host undergo increased levels of recombination. Here, we tested the hypothesis that stress conditions increase rates of mitotic recombination in C. albicans, which is measured as loss of heterozygosity (LOH) at specific loci. We show that LOH rates are elevated during in vitro exposure to oxidative stress, heat stress, and antifungal drugs. In addition, an increase in stress severity correlated well with increased LOH rates. LOH events can arise through local recombination, through homozygosis of longer tracts of chromosome arms, or by whole-chromosome homozygosis. Chromosome arm homozygosis was most prevalent in cultures grown under conventional lab conditions. Importantly, exposure to different stress conditions affected the levels of different types of LOH events, with oxidative stress causing increased recombination, while fluconazole and high temperature caused increases in events involving whole chromosomes. Thus, C. albicans generates increased amounts and different types of genetic diversity in response to a range of stress conditions, a process that we term "stress-induced LOH" that arises either by elevating rates of recombination and/or by increasing rates of chromosome missegregation. IMPORTANCE Stress-induced mutagenesis fuels the evolution of bacterial pathogens and is mainly driven by genetic changes via mitotic recombination. Little is known about this process in other organisms. Candida albicans, an opportunistic fungal pathogen, causes infections that require adaptation to different host environmental niches. We measured the rates of LOH and the types of LOH events that appeared in the absence and in the presence of physiologically relevant stresses and found that stress causes a significant increase in the rates of LOH and that this increase is proportional to the degree of stress. Furthermore, the types of LOH events that arose differed in a stress-dependent manner, indicating that eukaryotic cells generate increased genetic diversity in response to a range of stress conditions. We propose that this "stress-induced LOH" facilitates the rapid adaptation of C. albicans, which does not undergo meiosis, to changing environments within the host. © 2011 Forche et al.

Date: 2007-10-01

Creator: Alix Coste, Anna Selmecki, Anja Forche, Dorothée Diogo, Marie Elisabeth, Bougnoux, Christophe D'Enfert, Judith Berman, Dominique Sanglard

Access: Open access

TAC1 (for transcriptional activator of CDR genes) is critical for the upregulation of the ABC transporters CDR1 and CDR2, which mediate azole resistance in Candida albicans. While a wild-type TAC1 allele drives high expression of CDR1/2 in response to inducers, we showed previously that TAC1 can be hyperactive by a gain-of-function (GOF) point mutation responsible for constitutive high expression of CDR1/2. High azole resistance levels are achieved when C. albicans carries hyperactive alleles only as a consequence of loss of heterozygosity (LOH) at the TAC1 locus on chromosome 5 (Chr 5), which is linked to the mating-type-like (MTL) locus. Both are located on the Chr 5 left arm along with ERG11 (target of azoles). In this work, five groups of related isolates containing azole-susceptible and -resistant strains were analyzed for the TAC1 and ERG11 alleles and for Chr 5 alterations. While recovered ERG11 alleles contained known mutations, 17 new TAC1 alleles were isolated, including 7 hyperactive alleles with five separate new GOF mutations. Single-nucleotide- polymorphism analysis of Chr 5 revealed that azole-resistant strains acquired TAC1 hyperactive alleles and, in most cases, ERG11 mutant alleles by LOH events not systematically including the MTL locus. TAC1 LOH resulted from mitotic recombination of the left arm of Chr 5, gene conversion within the TAC1 locus, or the loss and reduplication of the entire Chr 5. In one case, two independent TAC1 hyperactive alleles were acquired. Comparative genome hybridization and karyotype analysis revealed the presence of isochromosome 5L [i(5L)] in two azole-resistant strains. i(5L) leads to increased copy numbers of azole resistance genes present on the left arm of Chr 5, among them TAC1 and ERG11. Our work shows that azole resistance was due not only to the presence of specific mutations in azole resistance genes (at least ERG11 and TAC1) but also to their increase in copy number by LOH and to the addition of extra Chr 5 copies. With the combination of these different modifications, sophisticated genotypes were obtained. The development of azole resistance in C. albicans is therefore a powerful instrument for generating genetic diversity. Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Date: 2019-05-01

Creator: Anja Forche, Norma V. Solis, Marc Swidergall, Robert Thomas, Alison, Guyer, Annette Beach, Gareth A. Cromie, Giang T. Le, Emily Lowell, Norman Pavelka, Judith Berman, Aimeé M. Dudley, Anna Selmecki, Scott G. Filler

Access: Open access

When the fungus Candida albicans proliferates in the oropharyngeal cavity during experimental oropharyngeal candidiasis (OPC), it undergoes large-scale genome changes at a much higher frequency than when it grows in vitro. Previously, we identified a specific whole chromosome amplification, trisomy of Chr6 (Chr6x3), that was highly overrepresented among strains recovered from the tongues of mice with OPC. To determine the functional significance of this trisomy, we assessed the virulence of two Chr6 trisomic strains and a Chr5 trisomic strain in the mouse model of OPC. We also analyzed the expression of virulence-associated traits in vitro. All three trisomic strains exhibited characteristics of a commensal during OPC in mice. They achieved the same oral fungal burden as the diploid progenitor strain but caused significantly less weight loss and elicited a significantly lower inflammatory host response. In vitro, all three trisomic strains had reduced capacity to adhere to and invade oral epithelial cells and increased susceptibility to neutrophil killing. Whole genome sequencing of pre- and post-infection isolates found that the trisomies were usually maintained. Most post-infection isolates also contained de novo point mutations, but these were not conserved. While in vitro growth assays did not reveal phenotypes specific to de novo point mutations, they did reveal novel phenotypes specific to each lineage. These data reveal that during OPC, clones that are trisomic for Chr5 or Chr6 are selected and they facilitate a commensal-like phenotype.

Date: 2020-01-01

Creator: Julianne Scholes

Access: Access restricted to the Bowdoin Community

Date: 2018-02-13

Creator: Robert S. Ross, Andrew Smolen, Tim Curran, Erika Nyhus

Access: Open access

A critical problem for developing personalized treatment plans for cognitive disruptions is the lack of understanding how individual differences influence cognition. Recognition memory is one cognitive ability that varies from person to person and that variation may be related to different genetic phenotypes. One gene that may impact recognition memory is the monoamine oxidase A gene (MAO-A), which influences the transcription rate of MAO-A. Examination of how MAO-A phenotypes impact behavioral and event-related potentials (ERPs) correlates of recognition memory may help explain individual differences in recognition memory performance. Therefore, the current study uses electroencephalography (EEG) in combination with genetic phenotyping of the MAO-A gene to determine how well-characterized ERP components of recognition memory, the early frontal old/new effect, left parietal old/new effect, late frontal old/new effect, and the late posterior negativity (LPN) are impacted by MAO-A phenotype during item and source memory. Our results show that individuals with the MAO-A phenotype leading to increased transcription have lower response sensitivity during both item and source memory. Additionally, during item memory the left parietal old/new effect is not present due to increased ERP amplitude for correct rejections. The results suggest that MAO-A phenotype changes EEG correlates of recognition memory and influences how well individuals differentiate between old and new items.

Date: 2009-08-04

Creator: Erika Nyhus, Tim Curran

Access: Open access

The present experiments examined how semantic vs. perceptual encoding and perceptual match affect the processes involved in recognition memory. Experiment 1 examined the effects of encoding task and perceptual match between study and test fonts on recognition discrimination for words. Font fan was used to determine the effect of distinctiveness on perceptual match. The semantic encoding task and perceptual match for distinctive items led to better recognition memory. Event-related brain potentials (ERPs) recorded from the human scalp during recognition memory experiments have revealed differences between old (studied) and new (not studied) items that are thought to reflect the activity of memory-related brain processes. In Experiment 2, the semantic encoding task and perceptual match for distinctive words led to better recognition memory by acting on both familiarity and recollection processes, as purportedly indexed by the FN400 and parietal old/new effects. Combined these results suggest that the semantic encoding task and perceptual match for distinctive items aid recognition memory by acting on both familiarity and recollection processes. © 2009 Elsevier B.V. All rights reserved.

Date: 2018-07-01

Creator: Anja Forche, Gareth Cromie, Aleeza C. Gerstein, Norma V. Solis, Tippapha, Pisithkul, Waracharee Srifa, Eric Jeffery, Darren Abbey, Scott G. Filler, Aimée M. Dudley, Judith Berman

Access: Open access

In vitro studies suggest that stress may generate random standing variation and that different cellular and ploidy states may evolve more rapidly under stress. Yet this idea has not been tested with pathogenic fungi growing within their host niche in vivo. Here, we analyzed the generation of both genotypic and phenotypic diversity during exposure of Candida albicans to the mouse oral cavity. Ploidy, aneuploidy, loss of heterozygosity (LOH), and recombination were determined using flow cytometry and double digest restriction site-associated DNA sequencing. Colony phenotypic changes in size and filamentous growth were evident without selection and were enriched among colonies selected for LOH of the GAL1 marker. Aneuploidy and LOH occurred on all chromosomes (Chrs), with aneuploidy more frequent for smaller Chrs and whole Chr LOH more frequent for larger Chrs. Large genome shifts in ploidy to haploidy often maintained one or more heterozygous disomic Chrs, consistent with random Chr missegregation events. Most isolates displayed several different types of genomic changes, suggesting that the oral environment rapidly generates diversity de novo. In sharp contrast, following in vitro propagation, isolates were not enriched for multiple LOH events, except in those that underwent haploidization and/or had high levels of Chr loss. The frequency of events was overall 100 times higher for C. albicans populations following in vivo passage compared with in vitro. These hyper-diverse in vivo isolates likely provide C. albicans with the ability to adapt rapidly to the diversity of stress environments it encounters inside the host.

Date: 2020-01-01

Creator: Benjamin Harley Wong

Access: Open access

Neuropeptides are important modulators of neural activity, allowing neural networks, such as the central pattern generators (CPGs) that control rhythmic movements, to alter their output and thus generate behavioral flexibility. Isoforms of a neuropeptide family vary in physical structure, allowing potentially distinct functional neuromodulatory effects on CPG systems. While some familial neuropeptide isoforms can differentially affect a system, others in the same family may elicit indistinguishable effects. Here, we examined the effects elicited by members of a novel family of six peptide hormone isoforms (GSEFLamides: I-, M-, AL-, AM-, AV-, and VM-GSEFLamide) on the pyloric filter and gastric mill CPGs in the stomatogastric nervous system (STNS) of the American lobster, Homarus americanus. Recent unpublished work from the Dickinson lab found that five of the six GSEFLamides elicited similar increases in contraction amplitude when perfused through the isolated lobster heart, while one (AVGSEFLamide) had virtually no effect. Using extracellular recordings, we found the pattern of GSEFLamide effects on the STNS gastric mill to be similar to the pattern observed in the lobster cardiac system; the gastric mill circuit was fairly consistently activated by all isoforms except AVGSEFLamide. The intrinsically active pyloric pattern was also significantly enhanced by three out of five peptide isoforms, and nearly significantly enhanced by two more, but was likewise non-responsive to AVGSEFLamide. While the reason AVGSEFLamide had no effect on either pattern is unknown, the similar phenomenon noted in the isolated whole heart potentially indicates that this isoform lacks any function in the lobster.

• Embargo End Date: 2025-05-13

Date: 2020-01-01

Creator: Samuel G. Brill-Weil

Access: Embargoed

Date: 2014-05-01

Creator: Elizabeth A Owens

Access: Open access

The American lobster, Homarus americanus, inhabits a large oceanic range spanning from Labrador, Canada to North Carolina, USA. This geographic range varies in temperature by as much as 25ºC, and daily temperature fluctuations of up to 12ºC may occur at a single location depending on season, water depth, and tides. The cardiac system of the lobster is sensitive to these temperature changes, and has been shown to adjust its functioning over a large temperature range. A previous study showed that various functional parameters respond differently to temperature changes, but a stable cardiac output can be maintained over the range of 2-20ºC. The current study showed that the effects of temperature were exerted primarily through changes in the lobster heart central pattern generator, the cardiac ganglion. Similar patterns of change were seen in both semi-intact hearts and isolated cardiac ganglion preparations in response to increasing temperature. Specifically, with increasing temperature, the burst frequency showed a biphasic pattern in which frequency initially increased, then decreased rapidly at high temperatures. The burst duration, duty cycle, and number of spikes per burst generally decreased with increasing temperature, and spike frequency increased over the entire temperature range. Semi-intact hearts and isolated cardiac ganglia showed similar “crash” patterns, characterized by complete loss of function at high temperatures and complete recovery of function when temperature was returned to baseline. Feedback in the semi-intact heart provided some stabilization of bursting activity, but it did not provide the expected protection from high temperatures. The isolated CG had a significantly higher crash temperature than did the semi-intact system. This discrepancy in crash temperatures may be explained by considering factors at the level of the muscle and neuromuscular junction (NMJ), such as stretch and nitric oxide (NO) feedback and the balance of facilitation and depression at the NMJ. Stimulated preparations showed defacilitation of contraction amplitude at high temperatures despite the maintenance of constant burst parameters of stimulation. Therefore, several factors contributing to the relatively low crash temperature of the intact system may be a shift in the balance of facilitation and depression at the NMJ, a depression in ganglion function due to the release of NO by the muscle, or a combination of the two mechanisms.

Date: 2022-01-01

Creator: Hannah Tess Scotch

Access: Open access

The auditory system of the Mediterranean field cricket (Gryllus bimaculatus) is capable of profound compensatory plasticity. Following deafferentation due to the loss of an auditory organ, the dendrites of intermediate auditory neuron Ascending Neuron 2 (AN-2) grow across the midline and functionally connect to contralateral afferents. The loss of the auditory organ can be mimicked with reversible cold-deactivation, in which cooled Peltier elements silence the auditory organ and its afferents. Though this would presumably prevent AN-2 from firing, cooling instead induces a novel firing pattern called DOPE (delayed-onset, prolonged-excitation). In this study, intracellular physiological recordings were completed before, during, and after cooling in response to “chirp” and “pulse” sounds. Analysis was performed within and across crickets to characterize DOPE. Results revealed expected variability across individuals, as well as a wider spread of onset delay and a decrease in spike frequency and number of spikes per burst relative to baseline within individuals during cooling. Generally, subsequent warming only partially restored the neuronal responses to baseline as measured by all three parameters. This was particularly true in response to “pulse” stimuli. Future experiments will investigate if DOPE is caused by synaptic inputs or intrinsic properties of AN-2, as well as the role of inhibition in the circuit. Eventually, we hope to develop a complete model of the auditory circuit for future investigations of plasticity, with ramifications for treating human neuronal injury.

• Restriction End Date: 2025-06-01

Date: 2022-01-01

Creator: Seneca N. Ellis

Access: Access restricted to the Bowdoin Community

Date: 2015-05-01

Creator: Leigh A Andrews

Access: Access restricted to the Bowdoin Community

• Restriction End Date: 2028-06-01

Date: 2023-01-01

Creator: Sarah Lührmann

Access: Access restricted to the Bowdoin Community

• Embargo End Date: 2027-05-16

Date: 2024-01-01

Creator: Sam McClelland

Access: Embargoed

Date: 2025-01-01

Creator: Kyla Gary

Access: Access restricted to the Bowdoin Community

Date: 2015-11-01

Creator: Robert S. Ross, Paolo Medrano, Kaitlin Boyle, Andrew Smolen, Tim Curran, Erika Nyhus

Access: Open access

Recognition memory is defined as the ability to recognize a previously encountered stimulus and has been associated with spatially and temporally distinct event-related potentials (ERPs). Allelic variations of the serotonin transporter gene (SLC6A4) have recently been shown to impact memory performance. Common variants of the serotonin transporter-linked polymorphic region (5HTTLPR) of the SLC6A4 gene result in long (l) and short (s) allelic variants with carriers of the s allele having lowered transcriptional efficiency. Thus, the current study examines the effects polymorphisms of the SLC6A4 gene have on performance and ERP amplitudes commonly associated with recognition memory. Electroencephalogram (EEG), genetic, and behavioral data were collected from sixty participants as they performed an item and source memory recognition task. In both tasks, participants studied and encoded 200 words, which were then mixed with 200 new words during retrieval. Participants were monitored with EEG during the retrieval portion of each memory task. EEG electrodes were grouped into four ROIs, left anterior superior, right anterior superior, left posterior superior, and right posterior superior. ERP mean amplitudes during hits in the item and source memory task were compared to correctly recognizing new items (correct rejections). Results show that s-carriers have decreased mean hit amplitudes in both the right anterior superior ROI 1000-1500. ms post stimulus during the source memory task and the left anterior superior ROI 300-500. ms post stimulus during the item memory task. These results suggest that individual differences due to genetic variation of the serotonin transporter gene influences recognition memory. © 2015 Elsevier Ltd.

Date: 2008-05-01

Creator: Anna Selmecki, Maryam Gerami-Nejad, Carsten Paulson, Anja Forche, Judith, Berman

Access: Open access

Acquired azole resistance is a serious clinical problem that is often associated with the appearance of aneuploidy and, in particular, with the formation of an isochromosome [i(5L)] in the fungal opportunist Candida albicans. Here we exploited a series of isolates from an individual patient during the rapid acquisition of fluconazole resistance (FluR). Comparative genome hybridization arrays revealed that the presence of two extra copies of Chr5L, on the isochromosome, conferred increased FluR and that partial truncation of Chr5L reduced FluR. In vitro analysis of the strains by telomere-mediated truncations and by gene deletion assessed the contribution of all Chr5L genes and of four specific genes. Importantly, ERG11 (encoding the drug target) and a hyperactive allele of TAC1 (encoding a transcriptional regulator of drug efflux pumps) made independent, additive contributions to FluR in a gene copy number-dependent manner that was not different from the contributions of the entire Chr5L arm. Thus, the major mechanism by which i(5L) formation causes increased azole resistance is by amplifying two genes: ERG11 and TAC1. © 2008 The Authors.

Date: 2019-11-01

Creator: Alberto Bellido, Toni Ciudad, Belén Hermosa, Encarnación Andaluz, Anja, Forche, Germán Larriba

Access: Open access

Candida albicans, the most common fungal pathogen, is a diploid with a genome that is rich in repeats and has high levels of heterozygosity. To study the role of different recombination pathways on direct-repeat recombination, we replaced either allele of the RAD52 gene (Chr6) with the URA-blaster cassette (hisG-URA3-hisG), measured rates of URA3 loss as resistance to 5-fluoroorotic acid (5FOAR) and used CHEF Southern hybridization and SNP-RFLP analysis to identify recombination mechanisms and their frequency in wildtype and recombination mutants. FOAR rates varied little across different strain backgrounds. In contrast, the type and frequency of mechanisms underlying direct repeat recombination varied greatly. For example, wildtype, rad59 and lig4 strains all displayed a bias for URA3 loss via pop-out/deletion vs. inter-homolog recombination and this bias was reduced in rad51 mutants. In addition, in rad51-derived 5FOAR strains direct repeat recombination was associated with ectopic translocation (5%), chromosome loss/truncation (14%) and inter-homolog recombination (6%). In the absence of RAD52, URA3 loss was mostly due to chromosome loss and truncation (80–90%), and the bias of retained allele frequency points to the presence of a recessive lethal allele on Chr6B. However, a few single-strand annealing (SSA)-like events were identified and these were independent of either Rad59 or Lig4. Finally, the specific sizes of Chr6 truncations suggest that the inserted URA-blaster could represent a fragile site.

Date: 2006-04-01

Creator: Alix Coste, Vincent Turner, Françoise Ischer, Joachim Morschhäuser, Anja, Forche, Anna Selmecki, Judith Berman, Jacques Bille, Dominique Sanglard

Access: Open access

TAC1, a Candida albicans transcription factor situated near the mating-type locus on chromosome 5, is necessary for the upregulation of the ABC-transporter genes CDR1 and CDR2, which mediate azole resistance. We showed previously the existence of both wild-type and hyperactive TAC1 alleles. Wild-type alleles mediate upregulation of CDR1 and CDR2 upon exposure to inducers such as fluphenazine, while hyperactive alleles result in constitutive high expression of CDR1 and CDR2. Here we recovered TAC1 alleles from two pairs of matched azole-susceptible (DSY294; FH1: heterozygous at mating-type locus) and azole-resistant isolates (DSY296; FH3: homozygous at mating-type locus). Two different TAC1 wild-type alleles were recovered from DSY294 (TAC1-3 and TAC1-4) while a single hyperactive allele (TAC1-5) was isolated from DSY296. A single amino acid (aa) difference between TAC1-4 and TAC1-5 (Asn977 to Asp or N977D) was observed in a region corresponding to the predicted activation domain of Tac1p. Two TAC1 alleles were recovered from FH1 (TAC1-6 and TAC1-7) and a single hyperactive allele (TAC1-7) was recovered from FH3. The N977D change was seen in TAC1-7 in addition to several other aa differences. The importance of N977D in conferring hyperactivity to TAC1 was confirmed by site-directed mutagenesis. Both hyperactive alleles TAC1-5 and TAC1-7 were codominant with wild-type alleles and conferred hyperactive phenotypes only when homozygous. The mechanisms by which hyperactive alleles become homozygous was addressed by comparative genome hybridization and single nucleotide polymorphism arrays and indicated that loss of TAC1 heterozygosity can occur by recombination between portions of chromosome 5 or by chromosome 5 duplication. Copyright © 2006 by the Genetics Society of America.

Date: 2005-01-01

Creator: Anja Forche, Georgiana May, P. T. Magee

Access: Open access

Candida albicans is a diploid yeast with a predominantly clonal mode of reproduction, and no complete sexual cycle is known. As a commensal organism, it inhabits a variety of niches in humans. It becomes an opportunistic pathogen in immunocompromised patients and can cause both superficial and disseminated infections. It has been demonstrated that genome rearrangement and genetic variation in isolates of C. albicans are quite common. One possible mechanism for generating genome-level variation among individuals of this primarily clonal fungus is mutation and mitotic recombination leading to loss of heterozygosity (LOH). Taking advantage of a recently published genome-wide single-nucleotide polymorphism (SNP) map (A. Forche, P. T. Magee, B. B. Magee, and G. May, Eukaryot. Cell 3:705-714, 2004), an SNP microarray was developed for 23 SNP loci residing on chromosomes 5, 6, and 7. It was used to examine 21 strains previously shown to have undergone mitotic recombination at the GAL1 locus on chromosome 1 during infection in mice. In addition, karyotypes and morphological properties of these strains were evaluated. Our results show that during in vivo passaging, LOH events occur at observable frequencies, that such mitotic recombination events occur independently in different loci across the genome, and that changes in karyotypes and alterations of phenotypic characteristics can be observed alone, in combination, or together with LOH.

Date: 2010-06-01

Creator: Erika Nyhus, Tim Curran

Access: Open access

The primary aim of this review is to examine evidence for a functional role of gamma and theta oscillations in human episodic memory. It is proposed here that gamma and theta oscillations allow for the transient interaction between cortical structures and the hippocampus for the encoding and retrieval of episodic memories as described by the hippocampal memory indexing theory (Teyler and DiScenna, 1986). Gamma rhythms can act in the cortex to bind perceptual features and in the hippocampus to bind the rich perceptual and contextual information from diverse brain regions into episodic representations. Theta oscillations act to temporally order these individual episodic memory representations. Through feedback projections from the hippocampus to the cortex these gamma and theta patterns could cause the reinstatement of the entire episodic memory representation in the cortex. In addition, theta oscillations could allow for top-down control from the frontal cortex to the hippocampus modulating the encoding and retrieval of episodic memories. © 2009.

Date: 2009-06-04

Creator: Geraldine Butler, Matthew D. Rasmussen, Michael F. Lin, Manuel A.S. Santos, Sharadha, Sakthikumar, Carol A. Munro, Esther Rheinbay, Manfred Grabherr, Anja Forche, Jennifer L. Reedy, Ino Agrafioti, Martha B. Arnaud, Steven Bates, Alistair J.P. Brown, Sascha Brunke, Maria C. Costanzo, David A. Fitzpatrick, Piet W.J. De Groot, David Harris, Lois L. Hoyer, Bernhard Hube, Frans M. Klis, Chinnappa Kodira, Nicola Lennard, Mary E. Logue, Ronny Martin, Aaron M. Neiman, Elissavet Nikolaou, Michael A. Quail, Janet Quinn, Maria C. Santos

Access: Open access

Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/α2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes. © 2009 Macmillan Publishers Limited. All rights reserved.

Date: 2015-01-01

Creator: Michael J. Frank, Chris Gagne, Erika Nyhus, Sean Masters, Thomas V., Wiecki, James F. Cavanagh, David Badre

Access: Open access

What are the neural dynamics of choice processes during reinforcement learning? Two largely separate literatures have examined dynamics of reinforcement learning (RL) as a function of experience but assuming a static choice process, or conversely, the dynamics of choice processes in decision making but based on static decision values. Here we show that human choice processes during RL are well described by a drift diffusion model (DDM) of decision making in which the learned trial-by-trial reward values are sequentially sampled, with a choice made when the value signal crosses a decision threshold. Moreover, simultaneous fMRI and EEG recordings revealed that this decision threshold is not fixed across trials but varies as a function of activity in the subthalamic nucleus (STN) and is further modulated by trial-by-trial measures of decision conflict and activity in the dorsomedial frontal cortex (pre-SMABOLDand mediofrontal theta in EEG). These findings provide converging multimodal evidence for a model in which decision threshold in reward-based tasks is adjusted as a function of communication from pre-SMA to STN when choices differ subtly in reward values, allowing more time to choose the statistically more rewarding option.

Date: 2020-01-01

Creator: Audrey J. Muscato

Access: Open access

Central pattern generators (CPGs) produce patterned outputs independent of sensory input. The cardiac neuromuscular system of the American lobster (Homarus americanus) is driven by a CPG called the cardiac ganglion (CG), which is composed of nine neurons, making it a model system of study. Modulation of CPGs allows for functional flexibility. One neuropeptide family that modulates the CG is C-type allatostatin (AST-C I-III). Previous research has shown variation in the responses of the CG across the three isoforms and among individuals. First, we investigated why AST-C I and III elicit responses that are more similar to each other than they are to the responses elicited by AST-C II. We hypothesized that an amino acid difference in the conserved sequence was responsible for the observed variation in responses. We synthesized isoforms of AST-C that replaced the endogenous amino acid and recorded responses to these isoforms. The identity of one particular amino acid in the conserved sequence seems to be responsible for variations in responses in frequency. Next, we focused on variation among individuals in their responses to AST-C I and III. We hypothesized that the mechanism behind this individual variation is differential expression of AST-C receptors and/or their downstream targets. We recorded physiological responses of the cardiac system to AST-C and then sequenced CG RNA from the same lobsters. Differential expression of one of the AST-C receptors and a number of downstream factors is correlated with physiological response. These findings inspire further experimentation investigating molt cycle as the underlying cause.

Date: 2020-01-01

Creator: Leah B Kratochvil

Access: Access restricted to the Bowdoin Community

Date: 2008-01-01

Creator: Melanie Legrand, Anja Forche, Anna Selmecki, Christine Chan, David T., Kirkpatrick, Judith Berman

Access: Open access

Haplotype maps (HapMaps) reveal underlying sequence variation and facilitate the study of recombination and genetic diversity. In general, HapMaps are produced by analysis of Single-Nucleotide Polymorphism (SNP) segregation in large numbers of meiotic progeny. Candida albicans, the most common human fungal pathogen, is an obligate diploid that does not appear to undergo meiosis. Thus, standard methods for haplotype mapping cannot be used. We exploited naturally occurring aneuploid strains to determine the haplotypes of the eight chromosome pairs in the C. albicans laboratory strain SC5314 and in a clinical isolate. Comparison of the maps revealed that the clinical strain had undergone a significant amount of genome rearrangement, consisting primarily of crossover or gene conversion recombination events. SNP map haplotyping revealed that insertion and activation of the UAU1 cassette in essential and non-essential genes can result in whole chromosome aneuploidy. UAU1 is often used to construct homozygous deletions of targeted genes in C. albicans; the exact mechanism (trisomy followed by chromosome loss versus gene conversion) has not been determined. UAU1 insertion into the essential ORC1 gene resulted in a large proportion of trisomic strains, while gene conversion events predominated when UAU1 was inserted into the non-essential LRO1 gene. Therefore, induced aneuploidies can be used to generate HapMaps, which are essential for analyzing genome alterations and mitotic recombination events in this clonal organism. © 2008 Legrand et al.

Date: 2008-02-01

Creator: Kenneth A. Norman, Katharine Tepe, Erika Nyhus, Tim Curran

Access: Open access

The question of interference (how new learning affects previously acquired knowledge and vice versa) is a central theoretical issue in episodic memory research, but very few human neuroimaging studies have addressed this question. Here, we used event-related potentials (ERPs) to test the predictions of the complementary learning systems (CLS) model regarding how list strength manipulations (strengthening some, but not all, items on a study list) affect recognition memory. Our analysis focused on the FN400 old-new effect, a hypothesized ERP correlate of familiarity-based recognition, and the parietal old-new effect, a hypothesized ERP correlate of recollection-based recognition. As is predicted by the CLS model, increasing list strength selectively reduced the ERP correlate of recollection-based discrimination, leaving the ERP correlate of familiarity-based discrimination intact. In a second experiment, we obtained converging evidence for the CLS model's predictions, using a remember/know test: Increasing list strength reduced recollection-based discrimination but did not reduce familiarity-based discrimination. Copyright 2008 Psychonomic Society, Inc.

• Restriction End Date: 2026-06-01

Date: 2021-01-01

Creator: Brandon S Lee

Access: Access restricted to the Bowdoin Community

Date: 2021-01-01

Creator: Audrey Elizabeth Jordan

Access: Open access

Networks of neurons known as central pattern generators (CPGs) generate rhythmic patterns of output to drive behaviors like locomotion. CPGs are relatively fixed networks that produce consistent patterns in the absence of other inputs. The heart contractions of the Homarus americanus are neurogenic and controlled by the CPG known as the cardiac ganglion. Neuromodulators can enable flexibility in CPG motor output, and also on muscle contractions by acting on the neuromuscular junction and the muscle itself. A tissue-specific transcriptome gleaned from the cardiac ganglion and cardiac muscle of the American lobster was used to predict the sites and sources of a variety of crustacean neuromodulators. If corresponding receptors were predicted to be expressed in the cardiac muscle, then it was hypothesized that the neuropeptide had peripheral effects. One peptide for which a cardiac muscle receptor was identified is myosuppressin. Myosuppressin has been shown to have modulatory effects at the cardiac neuromuscular system of the American lobster. In previous research, myosuppressin had modulatory effects on the periphery of cardiac neuromuscular system alone. It remains an open question of whether myosuppressin acts on the cardiac muscle directly, if it is exerting its effects at the neuromuscular junction (NMJ), or both. To test this, I performed physiological experiments on the isolated NMJ. Myosuppressin did not modulate the amplitude of the excitatory junction potentials. Since no modulatory effects were seen at the NMJ, the cardiac muscle was isolated from the cardiac ganglion and then glutamate-evoked contractions were stimulated. I showed that myosuppressin increased glutamate-evoked contraction amplitude. These data suggest myosuppressin exerts its peripheral effects at the cardiac muscle and not the NMJ.

• Restriction End Date: 2026-06-01

Date: 2023-01-01

Creator: Eliza M. Rhee

Access: Access restricted to the Bowdoin Community

Date: 2024-01-01

Creator: Katrina Carrier

Access: Open access

The ability of nervous systems to maintain function when exposed to global perturbations in temperature and salinity is a non-trivial task. The nervous system of the American lobster (H. americanus), a marine osmoconformer and poikilotherm, must be robust to these stressors, as they frequently experience fluctuations in both. I characterized the effects of temperature on the output of the pyloric circuit, a central pattern generator in the stomatogastric nervous system (STNS) that controls food filtration and established the maximum temperature that neurons in this circuit can withstand without “crashing” (ceasing to function but recovering when returned to normal conditions). I established a range of saline concentrations that did not cause the system to crash, and then determined whether combinatorial changes in temperature and salinity concentrations alter the maximum temperature the system tolerated. Even as burst frequency increased as temperature increased, phase constancy was observed. Interestingly, the system crashed at higher temperatures upon exposure to lower saline concentrations and lower temperatures in higher saline concentrations. I also established the range of saline concentrations that the lobster’s whole heart and cardiac ganglion (CG), the nervous system that controls the lobster’s heartbeat, can withstand. Then, I examined whether exposure to altered salinity and elevated temperature alters the crash temperature of the whole heart and CG. The CG crashed at higher temperatures than the whole heart in each saline concentration. Like the STNS, the whole heart and CG both crashed at higher temperatures in lower saline concentrations and higher temperatures in lower saline concentrations.

Date: 2023-01-01

Creator: Isabel Stella Petropoulos

Access: Open access

A substantial factor for behavioral flexibility is modulation — largely via neuropeptides — which occurs at multiple sites including neurons, muscles, and the neuromuscular junction (NMJ). Complex modulation distributed across multiple sites provides an interesting question: does modulation at multiple locations lead to greater dynamics than one receptor site alone? The cardiac neuromuscular system of the American lobster (Homarus americanus), driven by a central pattern generator called the cardiac ganglion (CG), is a model system for peptide modulation. The peptide myosuppressin (pQDLDHVFLRFamide) has been shown in the whole heart to decrease contraction frequency, largely due to its effects on the CG, as well as increase contraction amplitude by acting on periphery of the neuromuscular system, either at the cardiac muscle, the NMJ, or both. This set of experiments addresses the location(s) at which myosuppressin exerts its effects at the periphery. To elucidate myosuppressin’s effects on the cardiac muscle, the CG was removed, and muscle contractions were stimulated with L-glutamate while superfusing myosuppressin. Myosuppressin increased glutamate-evoked contraction amplitude in the isolated muscle, suggesting that myosuppressin exerts its peripheral effects directly on the cardiac muscle. To examine effects on the NMJ, excitatory junction potentials were evoked by stimulating of the motor nerve and intracellularly recording a single muscle fiber both in control saline and in the presence of myosuppressin. Myosuppressin did not modulate the amplitude of EJPs suggesting myosuppressin acts at the muscle and not at the NMJ, to cause an increase in contraction amplitude.

Date: 2024-01-01

Creator: Grant Griesman

Access: Open access

Central pattern generators (CPGs) are neuronal networks that produce rhythmic motor output in the absence of sensory stimuli. Invertebrate CPGs are valuable models of neural circuit dynamics and neuromodulation because they continue to generate fictive activity in vitro. For example, the cardiac ganglion (CG) of the Jonah crab (Cancer borealis) and American lobster (Homarus americanus) contains nine electrochemically coupled neurons that fire bursts of action potentials to trigger a heartbeat. The CG is modulated by neuropeptides, amines, small molecule transmitters, gases, and mechanosensory feedback pathways that enable flexibility and constrain output. One such modulator, the SLY neuropeptide family, was previously shown to be expressed in hormonal release sites and within the CG itself and has unusual processing features. However, its physiological effect was unknown. Here, I performed dose-response experiments in the crab and lobster whole heart and isolated CG to determine the threshold concentration of SLY neuropeptides to which these systems respond. The crab isoform had strong, excitatory effects in the crab whole heart and weakly modulated the crab CG. The lobster isoform weakly modulated the lobster whole heart and CG. Surprisingly, the crab isoform exerted large, variable effects on the lobster system, which suggests that SLY neuropeptides, their receptors, and their signaling pathways may be evolutionarily conserved across these two species. This research contributes to our understanding of how neural circuits can generate flexible output in response to modulation. It may also offer insight into processes influenced by peptidergic neurotransmission in the nervous systems of other animals, including mammals.

Date: 2025-01-01

Creator: Yanevith A. Peña

Access: Access restricted to the Bowdoin Community

Date: 2025-01-01

Creator: Yasemin Altug

Access: Open access

In order to maintain circuit stability through environmental perturbations, such as increases in temperature, neural circuits are able to adjust their output via modulatory and ion channel regulation. For instance, peptide modulators enable the lobster cardiac neuromuscular system to sustain physiological function at temperatures that surpass the crash temperature of the organ in the absence of modulation. Crash temperature is defined as the temperature at which neural activity ceases. For a crash, this temperature induced loss of activity is recovered when temperature is returned within the permissible range. Thus, it is hypothesized that there are underlying physiological mechanisms employed by the nervous system that compensates for changes in temperature and provides stability within acute temperature fluctuations. Neuromodulatory mechanisms have been proposed as one hypothesis that provide this temperature compensation. In accordance with previously collected data (Lemus 2022), I hypothesized that myosuppressin, a crustacean neuropeptide, provides stability during acute temperature variations. Because myosuppressin acts on the cardiac neurons and muscles separately, we hypothesized that the myosuppressin-induced increase in heart contraction amplitude, and decrease in contraction period can offset each other to provide system stability as temperature is increased. To test whether or not myosuppressin stabilizes circuit output as temperature is increased, myosuppressin was applied to the lobster whole heart at 7ºC, 10ºC, 13ºC and 16ºC, for 20 minutes. Changes in cardiac output in response to temperature and modulation were assessed by measuring the contraction force, heart beat frequency, and minimum contraction force. Interestingly, and contrary to previous results, in this data set, the cardiac neuromuscular system was temperature compensated in saline alone (control), and was not temperature compensated when perfused with myosuppressin (10-6 M). These findings seemed to differ from Lemus’ data (2023), where the cardiac neuromuscular system was not temperature compensated in control conditions and became temperature compensated when perfused with myosuppressin. The seasons at which each data set was collected (June-August vs November-March) could underlie these observed discrepancies.

Date: 2025-01-01

Creator: Jasmine Jia

Access: Access restricted to the Bowdoin Community

Date: 2009-12-01

Creator: Erika Nyhus, Francisco Barceló

Access: Open access

For over four decades the Wisconsin Card Sorting Test (WCST) has been one of the most distinctive tests of prefrontal function. Clinical research and recent brain imaging have brought into question the validity and specificity of this test as a marker of frontal dysfunction. Clinical studies with neurological patients have confirmed that, in its traditional form, the WCST fails to discriminate between frontal and non-frontal lesions. In addition, functional brain imaging studies show rapid and widespread activation across frontal and non-frontal brain regions during WCST performance. These studies suggest that the concept of an anatomically pure test of prefrontal function is not only empirically unattainable, but also theoretically inaccurate. The aim of the present review is to examine the causes of these criticisms and to resolve them by incorporating new methodological and conceptual advances in order to improve the construct validity of WCST scores and their relationship to prefrontal executive functions. We conclude that these objectives can be achieved by drawing on theory-guided experimental design, and on precise spatial and temporal sampling of brain activity, and then exemplify this using an integrative model of prefrontal function [i.e., Miller, E. K. (2000). The prefrontal cortex and cognitive control. Nature Reviews Neuroscience, 1, 59-65.] combined with the formal information theoretical approach to cognitive control [Koechlin, E., & Summerfield, C. (2007). An information theoretical approach to prefrontal executive function. Trends in Cognitive Sciences, 11, 229-235.]. © 2009 Elsevier Inc.

Date: 2017-09-01

Creator: Christina A. Cuomo, Terrance Shea, Bo Yang, Reeta Rao, Anja, Forche

Access: Open access

Candida krusei is a diploid, heterozygous yeast that is an opportunistic fungal pathogen in immunocompromised patients. This species also is utilized for fermenting cocoa beans during chocolate production. One major concern in the clinical setting is the innate resistance of this species to the most commonly used antifungal drug fluconazole. Here, we report a high-quality genome sequence and assembly for the first clinical isolate of C. krusei, strain 81-B-5, into 11 scaffolds generated with PacBio sequencing technology. Gene annotation and comparative analysis revealed a unique profile of transporters that could play a role in drug resistance or adaptation to different environments. In addition, we show that, while 82% of the genome is highly heterozygous, a 2.0 Mb region of the largest scaffold has undergone loss of heterozygosity. This genome will serve as a reference for further genetic studies of this pathogen.

Date: 2009-07-01

Creator: Anja Forche, P. T. Magee, Anna Selmecki, Judith Berman, Georgiana, May

Access: Open access

The mechanisms and rates by which genotypic and phenotypic variation is generated in opportunistic, eukaryotic pathogens during growth in hosts are not well understood. We evaluated genomewide genetic and phenotypic evolution in Candida albicans, an opportunistic fungal pathogen of humans, during passage through a mouse host (in vivo) and during propagation in liquid culture (in vitro). We found slower population growth and higher rates of chromosome-level genetic variation in populations passaged in vivo relative to those grown in vitro. Interestingly, the distribution of long-range loss of heterozygosity (LOH) and chromosome rearrangement events across the genome differed for the two growth environments, while rates of short-range LOH were comparable for in vivo and in vitro populations. Further, for the in vivo populations, there was a positive correlation of cells demonstrating genetic alterations and variation in colony growth and morphology. For in vitro populations, no variation in growth phenotypes was detected. Together, our results demonstrate that passage through a living host leads to slower growth and higher rates of genomic and phenotypic variation compared to in vitro populations. Results suggest that the dynamics of population growth and genomewide rearrangement contribute to the maintenance of a commensal and opportunistic life history of C. albicans. Copyright © 2009 by the Genetics Society of America.