Life Sciences Commons^™

Draft Nuclear Genome Sequence Of The Halophilic And Beta-Carotene- Accumulating Green Alga Dunaliella Salina Strain Ccap19/18, Juergen Polle, Kerrie Barry, John Cushman, Jeremy Schmutz, Duc Tran, Leyla T. Hathwaik, Won C. Yin, Jerry Jenkins, Zaid Mckie-Krisberg, Simon Prochnik, Erika Lindquist, Rhyan B. Dockter, Catherine Adam, Henrik Molina, Jakob Bunkenborg, Eonseon Jin, Mark Buchheim, Jon Magnuson

Publications and Research

The halotolerant alga Dunaliella salina is a model for stress tolerance and is used commercially for production of beta-carotene (pro-vitamin A). The presented draft genome of the genuine strain CCAP19/18 will allow investigations into metabolic processes involved in regulation of stress responses, including carotenogenesis and adaptations to life in high-salinity environments.

Synthesis, Crystal Structure, And Photoluminescent Properties Of 3,3′,4,4′-Tetraethyl-5,5′-Divinyl-2,2′-Bipyrrole Derivatives, Toru Okawara, Reo Kawano, Hiroya Morita, Alan Finkelstein, Renjiro Toyofuku, Kanako Matsumoto, Kenji Takehara, Toshihiko Nagamura, Seiji Iwasa, Sanjai Kumar

Publications and Research

Photoluminescent divinylbipyrroles were synthesized from 3,3′,4,4′-tetraetyl-2,2′-bipyrrole-5,5′-dicarboxaldehyde and activated methylene compounds via aldol condensation.For mechanistic clarity, molecular structures of Meldrum’s acid- and 1,3-dimethylbarbituricacid-derived divinylbipyrroles were determined by single-crystal X-ray diffraction. Photoluminescentproperties of the synthesized divinylbipyrroles in dichloromethane were found to be dependent onthe presence of electron withdrawing groups at the vinylic terminal. The divinylbipyrroles derivedfrom malononitrile, Meldrum’s acid, and 1,3-dimethylbarbituric acid showed fluorescent peaks at553, 576, and 602 nm respectively. Computational studies indicated that the alkyl substituents on thebipyrrole 3 and 3′positions increased energy level of the highest occupied molecular orbital (HOMO)compared to the unsubstituted derivatives and provided rationale for the …

Comparative Transcriptomics Reveal Developmental Turning Points During Embryogenesis Of A Hemimetabolous Insect, The Damselfly Ischnura Elegans, Sabrina Simon, Sven Sagasser, Edoardo Saccenti, Mercer R. Brugler, M. Eric Schranz, Heike Hadrys, George Amato, Rob Desalle

Publications and Research

Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a “core” set of 6,794 transcripts – shared by all embryonic stages – which are mainly involved …

Comparative Transcriptomics Reveal Developmental Turning Points During Embryogenesis Of A Hemimetabolous Insect, The Damselfly Ischnura Elegans, Sabrina Simon, Sven Sagasser, Edoardo Saccenti, Mercer R. Brugler, M. Eric Schranz, Heike Hadrys, George Amato, Rob Desalle

Publications and Research

Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a “core” set of 6,794 transcripts – shared by all embryonic stages – which are mainly involved …

Substitutions In Conserved Regions Preceding And Within The Linker Affect Activity And Flexibility Of Trnase Zl, The Long Form Of Trnase Z, Makensie Saoura, Kyla Pinnock, Maria Pujantell-Graell, Louis Levinger

Publications and Research

The enzyme tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes 3' trailers from precursor tRNAs, preparing them for CCA addition and aminoacylation. The short form of tRNase Z, tRNase ZS, functions as a homodimer and is found in all prokaryotes and some eukaryotes. The long form, tRNase ZL, related to tRNase ZS through tandem duplication and found only in eukaryotes, possesses ~2,000-fold greater catalytic efficiency than tRNase ZS. tRNase ZL consists of related but diverged amino and carboxy domains connected by a flexible linker (also referred to as a flexible tether) and functions as a monomer. The amino …

The Pulse Vision & Change Rubrics, Version 1.0: A Valid And Equitable Tool To Measure Transformation Of Life Sciences Departments At All Institution Types, Loretta Brancaccio-Taras, Pamela Pape-Lindstrom, Marcy Peteroy-Kelly, Karen Aguirre, Judy Awong-Taylor, Teri Balser, Michael J. Cahill, Regina F. Frey, Thomas Jack, Michael Kelrick, Kate Marley, Kathryn G. Miller, Marcy Osgood, Sandra Romano, J. Akif Uzman, Jiuqing Zhao

Publications and Research

The PULSE Vision & Change Rubrics, version 1.0, assess life sciences departments’ progress toward implementation of the principles of the Vision and Change report. This paper reports on the development of the rubrics, their validation, and their reliability in measuring departmental change aligned with the Vision and Change recommendations. The rubrics assess 66 different criteria across five areas: Curriculum Alignment, Assessment, Faculty Practice/Faculty Support, Infrastructure, and Climate for Change. The results from this work demonstrate the rubrics can be used to evaluate departmental transformation equitably across institution types and represent baseline data about the adoption of the Vision and Change …

Early And Late Components Of Eeg Delay Activity Correlate Differently With Scene Working Memory Performance, Timothy M. Ellmore, Kenneth Ng, Chelsea P. Reichert

Publications and Research

Sustained and elevated activity during the working memory delay period has long been considered the primary neural correlate for maintaining information over short time intervals. This idea has recently been reinterpreted in light of findings generated from multiple neural recording modalities and levels of analysis. To further investigate the sustained or transient nature of activity, the temporal-spectral evolution (TSE) of delay period activity was examined in humans with high density EEG during performance of a Sternberg working memory paradigm with a relatively long six second delay and with novel scenes as stimuli. Multiple analyses were conducted using different trial window …

Ligand Modulation Of Sidechain Dynamics In A Wild-Type Human Gpcr, Lindsay D. Clark, Igor Dikiy, Karen Chapman, Karin Ej Rodstrom, James Aramini, Michael V. Levine, George Khelashvili, Soren Gf Rasmussen, Kevin H. Gardner, Daniel M. Rosenbaum

Publications and Research

GPCRs regulate all aspects of human physiology, and biophysical studies have deepened our understanding of GPCR conformational regulation by different ligands. Yet there is no experimental evidence for how sidechain dynamics control allosteric transitions between GPCR conformations. To address this deficit, we generated samples of a wild-type GPCR (A2AR) that are deuterated apart from 1H/13C NMR probes at isoleucine d1 methyl groups, which facilitated 1H/13C methyl TROSY NMR measurements with opposing ligands. Our data indicate that low [Na+] is required to allow large agonist-induced structural changes in A2AR, and that patterns of sidechain dynamics substantially differ between agonist (NECA) and …

Positive Interactions Among Foraging Seabirds, Marine Mammals And Fishes And Implications For Their Conservation, Richard R. Veit, Nancy M. Harrison

Publications and Research

There is increasing recognition of the importance of “positive interactions” among species in structuring communities. For seabirds, an important kind of positive interaction is the use of birds of the same species, birds of other species, and other marine predators such as cetaceans, seals and fishes as cues to the presence of prey. The process by which a single bird uses, say, a feeding flock of birds as a cue to the presence of prey is called “local enhancement” or “facilitation.” There are subtly different uses of each of these terms, but the issue we address here is the ubiquity …

Decreased Triple Network Connectivity In Patients With Recent Onset Post-Traumatic Stress Disorder After A Single Prolonged Trauma Exposure, Yang Liu, Liang Li, Baojuan Li, Na Feng, Lihong Li, Xi Zhang, Hongbing Lu, Hong Yin

Publications and Research

The triple network model provides a common framework for understanding affective and neurocognitive dysfunctions across multiple disorders, including central executive network (CEN), default mode network (DMN), and salience network (SN). Considering the effect of traumatic experience on post-traumatic stress disorder (PTSD), this study aims to explore the alteration of triple network connectivity in a specific PTSD induced by a single prolonged trauma exposure. With an arterial spin labeling sequence, three networks were first identified using independent component analysis among 10 PTSD patients and 10 healthy survivors, who experienced the same coal mining flood disaster. Then, the triple network connectivity was …

Learning About Women In Stem For First-Year Students [Liberal Arts: Math And Science], Reem Jaafar, Ian Alberts

Open Educational Resources

This assignment was designed for students in the first year seminar and aligns with the Inquiry and Problem Solving core competency, with a focus on “framing the issues” (identifies and/or addresses questions problems and/or hypothesis informed by knowledge of context) and “evidence gathering” (assembles, reviews and synthesizes evidence from diverse sources of relevant knowledge). Both assignments rely on writing and one may include an oral component. In writing, the focus is on “Content Development and Organization,” as well as “Control of Language, Syntax, and Mechanics.”

LaGuardia’s Core Competencies and Communication Abilities

Main Course Learning Objectives:

• The LMF course for Liberal …

Fundamentals Of Biology Research Project [Biology], Ana Lucia Fuentes, Maria Entezari

Open Educational Resources

1. The goal of this initiative is to improve students’ learning of the subject while developing their Inquiry and Problem-Solving competencies as well as their numeracy, written, digital and oral communication abilities.
2. A “flipped-class” approach will be taken to present different topics ahead of the practical laboratory experiences. Topics will be presented with PowerPoints and/or videos posted on Blackboard.
3. Students will be given a “low stakes” quiz at the beginning of each laboratory session to assess their knowledge and understanding of the posted material.
4. A research project, introduced at the beginning of the semester, will be used as the backbone to …

Lim Protein Ajuba Directly Interacts With Replication Protein A To Prevent Atr Dna Damage Response, Sandy Wan Shan Fowler

Dissertations, Theses, and Capstone Projects

Integrity of the human genome is essential for viability and proliferation of human cells. Intrinsic (endogenous replication stress) or extrinsic (UV, chemotherapy drugs) agents threaten the stability of the genome by generation of single stranded (ss) DNA or double stranded (ds) DNA breaks. The DNA damage response (DDR) pathways are conserved in evolution and constitute systems that perform the surveillance, signaling, and repair of the damage in the nucleus. Unchecked and accumulation of DNA damage can lead to deleterious effects such as replication fork collapse, chromosome fusion and breakage. The dysregulations of DNA damage response pathways are hallmarks of tumorigenesis. …

Pharmacological Antagonism And The Olfactory Code, Mihwa Na

Dissertations, Theses, and Capstone Projects

Mammals can detect and discriminate uncountable odors through their odorant receptors. To accommodate the countless and diverse odors, exceptionally large numbers of odorant receptor (OR) genes are expressed in mammals. In addition, the mammals utilize a combinatorial code, where an odorant molecule can activate multiple ORs; an OR also responds to a set of multiple odorants. In nature, an odor is often a complex mixture of multiple odorant molecules. The combination of the ORs activated by each constituent generates the unique olfactory code for the particular odor.

Some odorants can antagonize select ORs, as discussed in Chapter 1. An antagonist …

Structural And Biochemical Studies Of The Dna Replication Initiation Mechanism Of The Second Chromosome Of Vibrio Cholerae, Natalia Orlova

Dissertations, Theses, and Capstone Projects

Transmission of genetic information through DNA replication is one of the key processes for any living organism. Despite the extensive effort put into studies of the mechanism of DNA replication, the understanding of the process on the molecular level is still incomplete. Specifically the molecular details of the very first events of DNA replication initiation are not sufficiently understood.

The majority of bacteria possess a single circular chromosome, and in order to initiate DNA replication these organisms utilize a conserved system, consisting of a specific DNA sequence - replication origin, called oriC, and replication initiator protein DnaA. However, bacteria …

Regulation Of The Amyloid Precursor Protein By Prostaglandin J2, A Mediator Of Inflammation: Relevance To Alzheimer’S Disease, Teneka L. Jean-Louis

Dissertations, Theses, and Capstone Projects

Inflammation plays a major role in Alzheimer’s disease (AD). Investigating how specific mediators of inflammation contribute to neurodegeneration in AD is crucial. Our studies focused on cyclooxygenases, which are key enzymes in inflammation and highly relevant to AD. Cyclooxygenases (COX -1, constitutive; COX-2, inducible) have emerged as important determinants of AD pathogenesis and progression. COX-2 is highly induced in AD, correlating with AD severity, and COX-1 is also involved in AD. Cyclooxygenases are the rate-limiting enzymes that convert arachidonic acid into prostaglandins (PGs), the principal mediators of CNS neuroinflammation.

The overall GOAL of these studies was to address the mechanisms …

The Role Of Glutamate Neurotransmission In The Ventral Tegmental Area In The Expression Of Conditioned Approach Learning, Priscila Hachimine-Merli

Dissertations, Theses, and Capstone Projects

Conditioned stimuli (CSs) come to function as CSs by acquiring the capacity to activate the same mesocorticolimbic dopamine (DA) neurons activated by primary rewards, producing conditioned activation of these neurons and their associated motivational states. This model stipulates that CSs activate mesocorticolimbic DA systems through the activation of glutamate receptors on DA neurons in the ventral tegmental area (VTA). We tested the hypothesis that glutamate receptor stimulation in the VTA is necessary for the expression of conditioned approach. Rats were tested in a conditioned approach protocol that consisted of 7 consecutive conditioning sessions (light presentations and food were paired), one …

The Role Of Pitx Proteins In Early Xenopus Development, Ye Jin

Dissertations, Theses, and Capstone Projects

Embryos of the African clawed frog Xenopus laevis are widely used for the study of early vertebrate development. The cement gland, which secrets mucus to help tadpoles attach to solid supports and live in relative safety, has long been used as a model to study the interplay between cell signaling pathways and transcription factors. It has been proposed that an intermediate level of Bone Morphogenetic Protein (BMP) signaling is essential for cement gland formation. In addition, several transcription factors have been linked to cement gland development. Among them, the homeodomain proteins Pitx1 and the closely related Pitx2c can generate ectopic …

Cellular Mechanisms Of Cortisol-Induced Changes In Mauthner-Cell Excitability In The Startle Circuit Of Goldfish, Daniel R. Bronson, Thomas Preuss

Publications and Research

Predator pressure and olfactory cues (alarm substance) have been shown to modulate Mauthner cell (M-cell) initiated startle escape responses (C-starts) in teleost fish. The regulation of such adaptive responses to potential threats is thought to involve the release of steroid hormones such as cortisol. However, the mechanism by which cortisol may regulate M-cell excitability is not known. Here, we used intrasomatic, in vivo recordings to elucidate the acute effects of cortisol on M-cell membrane properties and sound evoked post-synaptic potentials (PSPs). Cortisol tonically decreased threshold current in the M-cell within 10 min before trending towards baseline excitability over an hour …

Divergent Neural Responses To Narrative Speech In Disorders Of Consciousness, Ivan Iotzov, Brian C. Fidali, Agustin Petroni, Mary M. Conte, Nicholas D. Schiff, Lucas C. Parra

Publications and Research

Objective: Clinical assessment of auditory attention in patients with disorders of consciousness is often limited by motor impairment. Here, we employ intersubject correlations among electroencephalography responses to naturalistic speech in order to assay auditory attention among patients and healthy controls.

Methods: Electroencephalographic data were recorded from 20 subjects with disorders of consciousness and 14 healthy controls during of two narrative audio stimuli, presented both forwards and time-reversed. Intersubject correlation of evoked electroencephalography signals were calculated, comparing responses of both groups to those of the healthy control subjects. This analysis was performed blinded and subsequently compared to the diagnostic status of …

Association Of Body Shape Index (Absi) With Cardio-Metabolic Risk Factors: A Crosssectional Study Of 6081 Caucasian Adults, Simona Bertoli, Alessandro Leone, Nir Y. Krakauer, Giorgio Bedogni, Angelo Vanzulli, Valentino Ippocrates Redaelli, Ramona De Amicis, Laila Vignati, Jesse C. Krakauer, Alberto Battezzati

Publications and Research

A Body Shape Index (ABSI) was specifically developed as a transformation of waist circumference (WC), statistically independent of BMI to better evaluate the relative contribution of WC to central obesity and clinical outcomes. Previous studies have found ABSI is associated with total mortality and cardiovascular events. However, no study has specifically evaluated the joint contribution of ABSI and BMI to cardio-metabolic outcomes (high triglycerides, low HDL, high fasting glucose and high blood pressure). With this aim, we performed a retrospective study on 6081 Caucasian adults. Subjects underwent a medical interview, anthropometric measurements, blood sampling, measurement of blood pressure, and measurement …

Zarnoch Studies The Health Of Our Waters, Aldemaro Romero Jr.

Publications and Research

Some people look at scientists and think of them as narrowly focused on obscure issues, but that is not the case with Dr. Chester Zarnoch. “You’re not just exploring the biology and the chemistry associated with the problem you’re working on, but also thinking about social implications, about economic implications,” he says.

A native of Manhattan, Zarnoch has studied and worked his entire life in New York, from receiving his bachelor’s degree at Southampton College of Long Island University, his master’s in the philosophy of biology at the City University of New York (CUNY) Graduate Center, a master’s in biology …

A First Linkage Map And Downy Mildew Resistance Qtl Discovery For Sweet Basil (Ocimum Basilicum) Facilitated By Double Digestion Restriction Site Associated Dna Sequencing (Ddradseq), Robert M. Pyne, Josh Honig, Jennifer Vaiciunas, Adolfina R. Koroch, Christian Wyenandt, Stacy Bonos, James Simon

Publications and Research

Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed …

Can Squirrel Monkeys Learn An Abna Grammar? A Re-Evaluation Of Ravignani Et Al. (2013), Stefano Ghirlanda

Publications and Research

Ravignani et al. (2013) habituated squirrel monkeys to sound sequences conforming to an ABnA grammar (nD1;2;3), then tested them for their reactions to novel gram- matical and non-grammatical sequences. Although they conclude that the monkeys ``consistently recognized and generalized the sequence ABnA,'' I remark that this conclusion is not robust. The statistical significance of results depends on specific choices of data analysis, namely dichotomization of the response variable and omission of specific data points. Additionally, there is little evidence of generalization to novel patterns (n D 4;5), which is important to conclude that the monkeys recognized the ABnA grammar beyond …

Chloride Intracellular Channel Proteins Respond To Heat Stress In Caenorhabditis Elegans, Jun Liang, Yakov Shaulov, Cathy Savage-Dunn, Stéphane Boissinot, Tasmia Hoque

Publications and Research

Chloride intracellular channel proteins (CLICs) are multi-functional proteins that are expressed in various cell types and differ in their subcellular location. Two CLIC homologs, EXL-1 (excretory canal abnormal like-1) and EXC-4 (excretory canal abnormal± 4), are encoded in the Caenorhabditis elegans genome, providing an excellent model to study the functional diversification of CLIC proteins. EXC-4 functions in excretory canal formation during normal animal development. However, to date, the physiological function of EXL-1 remains largely unknown. In this study, we demonstrate that EXL-1 responds specifically to heat stress and translocates from the cytoplasm to the nucleus in intestinal cells and body …

Studying The Mechanisms Of Developmental Vocal Learning And Adult Vocal Performance In Zebra Finches Through Lentiviral Injection, Zhimin Shi, Ofer Tchernichovski, Xiaoching Li

Publications and Research

Here we provide a detailed step-by-step protocol for using lentivirus to manipulate miRNA expression in Area X of juvenile zebra finches and for analyzing the consequences on song learning and song performance. This protocol has four parts: 1) making the lentiviral construct to overexpress miRNA miR-9; 2) packaging the lentiviral vector; 3) stereotaxic injection of the lentivirus into Area X of juvenile zebra finches; 4) analysis of song learning and song performance in juvenile and adult zebra finches. These methods complement the methods employed in recent works that showed changing FoxP2 gene expression in Area X with lentivirus or adeno-associated …

Combined Mnemonic Strategy Training And High-Definition Transcranial Direct Current Stimulation For Memory Deficits In Mild Cognitive Impairment, Benjamin M. Hampstead, Krishnankutty Sathian, Marom Bikson, Anthony Y. Stringer

Publications and Research

Introduction: Memory deficits characterize Alzheimer’s dementia and the clinical precursor stage known as mild cognitive impairment. Nonpharmacologic interventions hold promise for enhancing functioning in these patients, potentially delaying functional impairment that denotes transition to dementia. Previous findings revealed that mnemonic strategy training (MST) enhances long-term retention of trained stimuli and is accompanied by increased blood oxygen level–dependent signal in the lateral frontal and parietal cortices as well as in the hippocampus. The present study was designed to enhance MST generalization, and the range of patients who benefit, via concurrent delivery of transcranial direct current stimulation (tDCS).

Methods: This protocol describes …

Comparative Phylogeographic, Population Genomic, And Selection Inference With Development Of Hierarchical Co-Demographic Models, Alexander Xue

Dissertations, Theses, and Capstone Projects

Comparing demographic histories across assemblages of populations, species, and sister pairs has been a focus in phylogeography since its inception. Initial approaches utilized organelle genetic data and involved qualitative comparisons of genetic patterns for evaluating hypotheses of shared evolutionary responses to past environmental changes. This endeavor has progressed with coalescent model-based statistical techniques and advances in next-generation sequencing, yet there remains a need for methods that can analyze aggregated genomic-scale data from non-model organisms within a unified framework that considers individual taxon uncertainty and variance. To this end, the aggregate site frequency spectrum (aSFS), an expansion of the site frequency …

Climate-Driven Habitat Shifts In South America: Biogeography, Historical Demography, And Population Genomics Of Anole Lizards, Ivan Prates

Dissertations, Theses, and Capstone Projects

Shifts in the geographic distribution of habitats over time can promote dispersal and vicariance, thereby influencing large-scale biogeographic patterns and ecological processes. The establishment of corridors of suitable habitat across previously disjunct yet ecologically similar regions has been widely linked to climate change over time. Such climate-mediated habitat changes may have played a key role in the assembly of tropical biotas, including those of Amazonia and the coastal Atlantic Forest in South America, two of the most diverse ecosystems on Earth. The history of biogeographic associations between tropical rainforest habitats in response to former climatic shifts, as well as their …

Song Rhythm Development In Zebra Finches, Julia Hyland Bruno

Dissertations, Theses, and Capstone Projects

This dissertation investigates song-rhythm learning in songbirds. Songbirds have been studied extensively in mechanistic investigations into the sensorimotor underpinnings of the cultural transmission of learned vocalizations. While several studies identified forebrain song-system neurons that generate rhythmic song patterns, we know little about how song rhythms are learned. The first part of the dissertation describes methods for detecting and analyzing birdsong rhythm patterns, and demonstrates their utility for identifying the role of song rhythms in social interactions. Results suggest that rhythm plasticity in zebra finch song may provide a potential vehicle for communication. Controlled song-learning experiments further found that developing zebra …