Life Sciences Commons^™

The Replication Initiator Of The Cholera Pathogen’S Second Chromosome Shows Structural Similarity To Plasmid Initiators, Natalia Orlova, Matthew Gerding, Olha Ivashkiv, Paul Dominic B. Olinares, Brian T. Chait, Matthew K. Waldor, David Jeruzalmi

Publications and Research

The conserved DnaA-oriC system is used to initiate replication of primary chromosomes throughout the bacterial kingdom; however, bacteria with multipartite genomes evolved distinct systems to initiate replication of secondary chromosomes. In the cholera pathogen, Vibrio cholerae, and in related species, secondary chromosome replication requires the RctB initiator protein. Here, we show that RctB consists of four domains. The structure of its central two domains resembles that of several plasmid replication initiators. RctB contains at least three DNA binding winged-helix-turn-helix motifs, and mutations within any of these severely compromise biological activity. In the structure, RctB adopts a headto- head dimeric configuration …

A Machine Learning Approach For Using The Postmortem Skin Microbiome To Estimate The Postmortem Interval, Hunter R. Johnson, Donovan D. Trinidad, Stephania Guzman, Zenab Khan, James V. Parziale, Jennifer M. Debruyn, Nathan H. Lents

Publications and Research

Research on the human microbiome, the microbiota that live in, on, and around the human person, has revolutionized our understanding of the complex interactions between microbial life and human health and disease. The microbiome may also provide a valuable tool in forensic death investigations by helping to reveal the postmortem interval (PMI) of a decedent that is discovered after an unknown amount of time since death. Current methods of estimating PMI for cadavers discovered in uncontrolled, unstudied environments have substantial limitations, some of which may be overcome through the use of microbial indicators. In this project, we sampled the microbiomes …

Bioremoval Of Phenol From Aqueous Solutions Using Native Caribbean Seaweed, Abel E. Navarro, Anibal Hernandez-Vega, Md Emran Masud, Loretta M. Roberson, Liz M. Diaz-Vázquez

Publications and Research

Among several Puerto Rican algae, Sargassum sp. (SG) and Chaetomorpha (CM) showed the highest phenol adsorption capacity from aqueous solutions and were used in optimized adsorption batch experiments at room temperature. The effects of pH, adsorbent dose, phenol concentration, salinity and presence of interfering substances were evaluated. Initial solution pH exhibited a strong effect, mainly on the phenol aqueous chemistry; showing the maximum adsorption at pH 10. Sorption isotherm results were modelled according to the Langmuir, Tempkin and Freundlich equations. Isotherm modelling indicated a maximum adsorption capacity (qmax) of 82.10 and 17.7 mg of phenol per gram of SG and …

A Mineralized Alga And Acritarch Dominated Microbiota From The Tully Formation (Givetian) Of Pennsylvania, Usa, John A. Chamberlain Jr., Rebecca B. Chamberlain, James O. Brown

Publications and Research

Sphaeromorphic algal cysts, most probably of the prasinophyte Tasmanites, and acanthomorphic acritarch vesicles, most probably Solisphaeridium, occur in a single 20 cm thick bed of micritic limestone in the lower part of the Middle Devonian (Givetian) Tully Formation near Lock Haven, Pennsylvania. Specimens are composed of authigenic calcite and pyrite crystals about 5–10 µm in length. Some specimens are completely calcitic; some contain both pyrite and calcite; and many are composed totally of pyrite. The microfossils are about 80 to 150 µm in diameter. Many show signs of originally containing a flexible wall composed of at least two layers. Some …

The Vibrio Cholerae Minor Pilin Tcpb Initiates Assembly And Retraction Of The Toxin- Coregulated Pilus, Dixon Ng, Tony Harn, Tuba Altindal, Subramania Kolappan, Jarrad M. Marles, Rajan Lala, Ingrid Spielman, Yang Gao, Caitlyn A. Hauke, Gabriela Kovacikova, Zia Verjee, Ronald K. Taylor, Nicolas Biais, Lisa Craig

Publications and Research

Type IV pilus (T4P) systems are complex molecular machines that polymerize major pilin proteins into thin filaments displayed on bacterial surfaces. Pilus functions require rapid extension and depolymerization of the pilus, powered by the assembly and retraction ATPases, respectively. A set of low abundance minor pilins influences pilus dynamics by unknown mechanisms. The Vibrio cholerae toxin-coregulated pilus (TCP) is among the simplest of the T4P systems, having a single minor pilin TcpB and lacking a retraction ATPase. Here we show that TcpB, like its homolog CofB, initiates pilus assembly. TcpB co-localizes with the pili but at extremely low levels, equivalent …

Improved Genome-Scale Multitarget Virtual Screening Via A Novel Collaborative Filtering Approach To Cold-Start Problem, Hansaim Lim, Paul Gray, Lei Xie, Aleksandar Poleksic

Publications and Research

Conventional one-drug-one-gene approach has been of limited success in modern drug discovery. Polypharmacology, which focuses on searching for multi-targeted drugs to perturb disease-causing networks instead of designing selective ligands to target individual proteins, has emerged as a new drug discovery paradigm. Although many methods for single-target virtual screening have been developed to improve the efficiency of drug discovery, few of these algorithms are designed for polypharmacology. Here, we present a novel theoretical framework and a corresponding algorithm for genome-scale multitarget virtual screening based on the one-class collaborative filtering technique. Our method overcomes the sparseness of the protein-chemical interaction data by …

Photoassisted Oxidation Of Sulfides Catalyzed By Artificial Metalloenzymes Using Water As An Oxygen Source, Christian Herrero, Nhung Nguyen-Thi, Fabien Hammerer, Frédéric Banse, Donald Gagne, Nicolas Doucet, Jean-Pierre Mahy, Rémy Ricoux

Advanced Science Research Center

The Mn(TpCPP)-Xln10A artificial metalloenzyme, obtained by non-covalent insertion of Mn(III)-meso-tetrakis(p-carboxyphenyl)porphyrin [Mn(TpCPP), 1-Mn] into xylanase 10A from Streptomyces lividans (Xln10A) as a host protein, was found able to catalyze the selective photo-induced oxidation of organic substrates in the presence of [RuII(bpy)3] 2+ as a photosensitizer and [CoIII(NH3)5Cl]2+ as a sacrificial electron acceptor, using water as oxygen atom source.

Review Of The Cultivation Program Within The National Alliance For Advanced Biofuels And Bioproducts, Peter J. Lammers, Michael Huesemann, Wiebke Boeing, Daniel B. Anderson, Robert G. Arnold, Xuemei Bai, Manish Bhole, Yalini Brhanavan, Louis Brown, Jola Brown, Judith K. Brown, Stephen Chisholm, C. Meghan Downes, Scott Fulbright, Yufeng Ge, Jonathan E. Holladay, Balachandran Ketheesan, Avinash Khopkar, Ambica Koushik, Paul Laur, Babetta L. Marrone, John B. Mott, Nagamany Nirmalakhandan, Kimberly L. Ogden, Ronald L. Parsons, Juergen Polle, Randy D. Ryan, Tzachi Samocha, Richard T. Sayre, Mark Seger, Thinesh Selvaratnam, Ruixiu Sui, Alex Thomasson, Adrian Unc, Wayne Van Vorrhies, Peter Waller, Yao Yao, José A. Olivares

Publications and Research

The cultivation efforts within the National Alliance for Advanced Biofuels and Bioproducts (NAABB)were developed to provide four major goals for the consortium, which included biomass production for downstream experimentation, development of new assessment tools for cultivation, development of new cultivation reactor technologies, and development of methods for robust cultivation. The NAABB consortium test beds produced over 1500 kg of biomass for downstream processing. The biomass production included a number of model production strains, but also took into production some of the more promising strains found through the prospecting efforts of the consortium. Cultivation efforts at large scale are intensive and …

Siddhartha Mukherjee. The Gene. An Intimate History. New York: Scribner, 2016. 593 Pp. $32.00 Cloth (Isbn 978-1-4767-3350-0), Aldemaro Romero Jr.

Publications and Research

Heredity has always been, in one form or another, at the center of biological

research. There is little doubt that the first scientific experimentation took place

about fifteen thousand years ago, when humans started breeding plants and

animals in order to domesticate them. Today the science of genetics seems to

advance at such a pace that even the experts have trouble keeping up with all the

developments. Now we are witnessing the expansion of our understanding of this

realm of science to levels unimaginable just a few decades ago.

Comparative Phylogeography In The Atlantic Forest And Brazilian Savannas: Pleistocene Fluctuations And Dispersal Shape Spatial Patterns In Two Bumblebees, Elaine Françoso, Alexander Rizzo Zuntini, Ana Carolina Carnaval, Maria Cristina Arias

Publications and Research

Background: Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages.

Results: Results suggest that Pleistocene climatic oscillations directly influenced the population structure of both species. Correlative species distribution models predict that …

Control Of Gene Expression By Rna Binding Protein Action On Alternative Translation Initiation Sites, Angela Re, Levi Waldron, Alessandro Quattrone

Publications and Research

Transcript levels do not faithfully predict protein levels, due to post-transcriptional regulation of gene expression mediated by RNA binding proteins (RBPs) and non-coding RNAs. We developed a multivariate linear regression model integrating RBP levels and predicted RBP-mRNA regulatory interactions from matched transcript and protein datasets. RBPs significantly improved the accuracy in predicting protein abundance of a portion of the total modeled mRNAs in three panels of tissues and cells and for different methods employed in the detection of mRNA and protein. The presence of upstream translation initiation sites (uTISs) at the mRNA 5' untranslated regions was strongly associated with improvement …

Striatal Dopaminergic Innervation Regulates Subthalamic Beta-Oscillations And Cortical-Subcortical Coupling During Movements: Preliminary Evidence In Subjects With Parkinson’S Disease, Andrea Canessa, Nicolo G. Pozzi, Gabriele Arnulfo, Joachim Brumberg, Martin M. Reich, Gianni Pezzoli, Maria F. Ghilardi, Cordula Matthies, Frank Steigerwald, Jens Volkman, Ioannis U. Isais

Publications and Research

Activation of the basal ganglia has been shown during the preparation and execution of movement. However, the functional interaction of cortical and subcortical brain areas during movement and the relative contribution of dopaminergic striatal innervation remains unclear. We recorded local field potential (LFP) activity from the subthalamic nucleus (STN) and high-density electroencephalography (EEG) signals in four patients with Parkinson’s disease (PD) off dopaminergic medication during a multi-joint motor task performed with their dominant and non-dominant hand. Recordings were performed by means of a fully-implantable deep brain stimulation (DBS) device at 4 months after surgery. Three patients also performed a single-photon …

Efficient Method For Transfer Of Microinjected Eggs To Mouse Ampulla For Generating Transgenic Mice, Guang Wen, Jin Di, Qian Li, Jianling Chen, Ling Jin, Cheng Wang, Sanqing Xu

Publications and Research

Background: The new method described here is highly efficient in transferring microinjected mouse eggs (MEs) through the bursa membrane of a surrogate mother mouse to the ampulla of the oviduct without damaging the blood vessels on the bursa membrane.

Results: This method causes no loss of blood, and it produces newborn pups/founders from approximately 70% of the transferred MEs, because only a small hole is made on the blood vessel–free area of the bursa membrane and ampulla of the surrogate mother mouse. The infundibulum remains intact. The small hole on the bursa membrane/ ampulla may already heal up before the …

The Science Teaching Fellows Program: A Model For Online Faculty Development Of Early Career Scientists Interested In Teaching, Loretta Branacaccio-Taras, Kelly A. Gull, Claudia Ratti

Publications and Research

The American Society for Microbiology (ASM) has a history of providing a wide range of faculty development opportunities. Recently, ASM developed the Science Teaching Fellows Program (STF) for early career biologists and postdoctoral students to explore student-centered teaching and develop the skills needed to succeed in positions that have a significant teaching component. Participants were selected to STF through a competitive application process. The STF program consisted of a series of six webinars. In preparation for each webinar, participants completed a pre-webinar assignment. After each webinar, fellows practiced what they learned by completing a post-webinar assignment. In a survey used …

Effects Of An 18- Week Strength, Conditioning, And Circuit Training Program On Weight Loss In A Middle Aged Adult Male, Aryeh D. Spingarn

Publications and Research

Aryeh Spingarn Queens College, City University of New York Department of Family, Nutrition, and Exercise Sciences, Effects of an 18-week strength, conditioning, and circuit training program on weight loss in a middle-aged male. Purpose: The purpose of this study was to examine the effects of a strength, conditioning, and circuit training program on weight loss in a middle age adult. Methods: The subject participated in an 18-week strength and conditioning program 2 days per week for one hour per session, totaling 2 hours of training time per week. The first 12 weeks of the program included only strength training for …

Narrative Review Of Vitamin D And Its Specific Impact On Balance Capacity In Older Adults, Ray Marks

Publications and Research

Introduction and Aims: Falls injuries among older adults, a widespread well-established contributor to high disability levels, excess morbidity and mortality rates, have many causes. This review examines the association between vitamin D levels and postural stability or balance control—a fairly consistent predictor of falls among older adults.

Materials and Method: All relevant English language peer reviewed research publications detailing the relationship between vitamin D levels and balance control among the elderly were sought. Key words included “Vitamin D and Balance or Postural Control.” Databases used were Academic Search Complete, PubMed, Scopus, and Web of Science.

Results: Analysis showed no consistent …

The Power Of Associative Learning And The Ontogeny Of Optimal Behaviour, Magnus Enquist, Johan Lind, Stefano Ghirlanda

Publications and Research

Behaving efficiently (optimally or near-optimally) is central to animals’ adaptation to their environment. Much evolutionary biology assumes, implicitly or explicitly, that optimal behavioural strategies are genetically inherited, yet the behaviour of many animals depends crucially on learning. The question of how learning contributes to optimal behaviour is largely open. Here we propose an associative learning model that can learn optimal behaviour in a wide variety of ecologically relevant circumstances. The model learns through chaining, a term introduced by Skinner to indicate learning of behaviour sequences by linking together shorter sequences or single behaviours. Our model formalizes the concept of conditioned …

Gruber Explores The Living Lights Of The Oceans., Aldemaro Romero Jr.

Publications and Research

The ocean waters are full of creatures that produce light, from microscopic organisms to sharks and marine turtles. Sometimes human vision is not prepared to detect it, but that does not mean such phenomena, known as bioluminescence and biofluorescence, are unimportant.

“There’s so many different ways in which life perceives light, and trying to get inside these animals, to get behind their eyes, is almost like walking in someone else’s shoes,” says Dr. David Gruber, an associate professor of biology at Baruch College in New York City. “It’s like being someone else for a day.”

Statistical Learning In Songbirds: From Self-Tutoring To Song Culture, Olga Fehér, Iva Ljubičić, Kenta Suzuki, Kazuo Okanoya, Ofer Tchernichovski

Publications and Research

At the onset of vocal development, both songbirds and humans produce variable vocal babbling with broadly distributed acoustic features. Over development, these vocalizations differentiate into the well-defined, categorical signals that characterize adult vocal behaviour. A broadly distributed signal is ideal for vocal exploration, that is, for matching vocal production to the statistics of the sensory input. The developmental transition to categorical signals is a gradual process during which the vocal output becomes differentiated and stable. But does it require categorical input?We trained juvenile zebra finches with playbacks of their own developing song, produced just a few moments earlier, updated continuously …

Hiv Glycoprotein Gp120 Impairs Fast Axonal Transport By Activating Tak1 Signaling Pathways, Sarah H. Berth, Nichole Mesnard-Hoaglin, Bin Wang, Hajwa Kim, Yuyu Song, Maria Sapar, Gerardo Morfini, Scott T. Brady

Publications and Research

Sensory neuropathies are the most common neurological complication of HIV. Of these, distal sensory polyneuropathy (DSP) is directly caused by HIV infection and characterized by length-dependent axonal degeneration of dorsal root ganglion (DRG) neurons. Mechanisms for axonal degeneration in DSP remain unclear, but recent experiments revealed that the HIV glycoprotein gp120 is internalized and localized within axons of DRG neurons. Based on these findings, we investigated whether intra-axonal gp120 might impair fast axonal transport (FAT), a cellular process critical for appropriate maintenance of the axonal compartment. Significantly, we found that gp120 severely impaired both anterograde and retrograde FAT. Providing a …

Habitual Coffee Consumption And Risk Of Type 2 Diabetes, Ischemic Heart Disease, Depression And Alzheimer’S Disease: A Mendelian Randomization Study, Man Ki Kwok, Gabriel M. Leung, C. Mary Schooling

Publications and Research

Observationally, coffee is inversely associated with type 2 diabetes mellitus (T2DM), depression and Alzheimer’s disease, but not ischemic heart disease (IHD). Coffee features as possibly protective in the 2015 Dietary Guidelines for Americans. Short-term trials suggest coffee has neutral effect on most glycemic traits, but raises lipids and adiponectin. To clarify we compared T2DM, depression, Alzheimer’s disease, and IHD and its risk factors by genetically predicted coffee consumption using two-sample Mendelian randomization applied to large extensively genotyped case-control and cross-sectional studies. Childhood cognition was used as a negative control outcome. Genetically predicted coffee consumption was not associated with T2DM (odds …

Radiation Damage In Xfel: Case Study From The Oxygen-Evolving Complex Of Photosystem Ii, Muhamed Amin, Ashraf Badawi, S.S. Obayya

Publications and Research

Structural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10–50 fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II. In the model, the nuclei move classically in a fully quantum potential created by electron density under the effect of strong laser pulse …

Glucose-6-Phosphate Dehydrogenase Deficiency And Physical And Mental Health Until Adolescence, Man Ki Kwok, Gabriel M. Leung, C. Mary Schooling

Publications and Research

Background: To examine the association of glucose-6-phosphate dehydrogenase (G6PD) deficiency with adolescent physical and mental health, as effects of G6PD deficiency on health are rarely reported.

Methods: In a population-representative Chinese birth cohort: ªChildren of 1997º (n = 8,327), we estimated the adjusted associations of G6PD deficiency with growth using generalized estimating equations, with pubertal onset using interval censored regression, with hospitalization using Cox proportional hazards regression and with size, blood pressure, pubertal maturation and mental health using linear regression with multiple imputation and inverse probability weighting.

Results: Among 5,520 screened adolescents (66% follow-up), 4.8% boys and 0.5% girls had …

Memorable Audiovisual Narratives Synchronize Sensory And Supramodal Neural Responses, Samantha S. Cohen, Lucas C. Parra

Publications and Research

Our brains integrate information across sensory modalities to generate perceptual experiences and form memories. However, it is difficult to determine the conditions under which multisensory stimulation will benefit or hinder the retrieval of everyday experiences. We hypothesized that the determining factor is the reliability of information processing during stimulus presentation, which can be measured through intersubject correlation of stimulus-evoked activity. We therefore presented biographical auditory narratives and visual animations to 72 human subjects visually, auditorily, or combined, while neural activity was recorded using electroencephalography. Memory for the narrated information, contained in the auditory stream, was tested 3 weeks later. While …

The Potential Of Forest Biomass Inversion Based On Vegetation Indices Using Multi-Angle Chris/Proba Data, Qiang Wang, Yong Pang, Zengyuan Li, Guoqing Sun, Erxue Chen, Wenge Ni-Meister

Publications and Research

Multi-angle remote sensing can either be regarded as an added source of uncertainty for variable retrieval, or as a source of additional information, which enhances variable retrieval compared to traditional single-angle observation. However, the magnitude of these angular and band effects for forest structure parameters is difficult to quantify. We used the Discrete Anisotropic Radiative Transfer (DART) model and the Zelig model to simulate the forest canopy Bidirectional Reflectance Distribution Factor (BRDF) in order to build a look-up table, and eight vegetation indices were used to assess the relationship between BRDF and forest biomass in order to find the sensitive …

Improved Parental Dietary Quality Is Associated With Children’S Dietary Intake Through The Home Environment, Karen R. Flórez, A. S. Richardson, M. B. Ghosh-Dastidar, R. Beckman, C. Huang, L. Wagner, T. Dubowitz

Publications and Research

Background Improving access to supermarkets has been shown to improve some dietary outcomes, yet there is little evidence for such effects on children. Relatedly, there is a dearth of research assessing the impact of a structural change (i.e. supermarket in a former food desert) on the home environment and its relationship with children’s diet.

Objective Assess the relative impact of the home environment on children’s diet after the introduction of a new supermarket in a food desert.

Methods Among a randomly selected cohort of households living in a food desert, parental diet was assessed before and after the opening of …

Sex And Seasonal Differences In Diet And Nutrient Intake In Verreaux's Sifakas (Propithecus Verreauxi), Flávia Koch, Joerg U. Ganzhorn, Jessica M. Rothman, Colin A. Chapman, Claudia Fichtel

Publications and Research

Fluctuations in food availability are a major challenge faced by primates living in seasonal climates. Variation in food availability can be especially challenging for females, because of the high energetic costs of reproduction. Therefore, females must adapt the particular demands of the different reproductive stages to the seasonal availability of resources. Madagascar has a highly seasonal climate, where food availability can be extremely variable. We investigated the seasonal changes in diet composition, nutrient and energy intake of female and male sifakas (Propithecus verreauxi) in a dry deciduous forest in western Madagascar. We examined how females adjust their diet to different …

Airborne Infectious Agents And Other Pollutants In Automobiles For Domestic Use: Potential Health Impacts And Approaches To Risk Mitigation, Syed A. Sattar, Kathryn E. Wright, Bahram Zargar, Joseph R. Rubino, M. Khalid Ijaz

Publications and Research

Theworld total of passenger cars is expected to go fromthe current one billion to >2.5 billion by 2050. Cars for domestic use account for ∼74% of the world’s yearly production ofmotorized vehicles. In North America, ∼80% of the commuters use their own car with another 5.6% travelling as passengers.With the current life-expectancy of 78.6 years, the average North American spends 4.3 years driving a car! This equates to driving 101 minutes/day with a lifetime driving distance of nearly 1.3 million km inside the confined and often shared space of the car with exposure to a mix of potentially harmful pathogens, …

Molecular Mechanisms Of Stress-Induced Increases In Fear Memory Consolidation Within The Amygdala, Antonio V. Aubry, Peter A. Serrano, Nesha S. Burghardt

Publications and Research

Stress can significantly impact brain function and increase the risk for developing various psychiatric disorders. Many of the brain regions that are implicated in psychiatric disorders and are vulnerable to the effects of stress are also involved in mediating emotional learning. Emotional learning has been a subject of intense investigation for the past 30 years, with the vast majority of studies focusing on the amygdala and its role in associative fear learning. However, the mechanisms by which stress affects the amygdala and amygdala-dependent fear memories remain unclear. Here we review the literature on the enhancing effects of acute and chronic …

Cooperative Stimulation Of Megakaryocytic Differentiation By Gfi1b Gene Targets Kindlin3 And Talin1, Divya Singh, Ghanshyam Upadhyay, Ananya Sengupta, Mohammed A. Biplob, Shaleen Chakyayil, Tiji George, Shireen Saleque

Publications and Research

Understanding the production and differentiation of megakaryocytes from progenitors is crucial for realizing the biology and functions of these vital cells. Previous gene ablation studies demonstrated the essential role of the transcriptional repressor Gfi1b (growth factor independence 1b) in the generation of both erythroid and megakaryocytic cells. However, our recent work has demonstrated the down-regulation of this factor during megakaryocytic differentiation. In this study we identify two new gene targets of Gfi1b, the cytoskeletal proteins Kindlin3 and Talin1, and demonstrate the inverse expression and functions of these cytoskeletal targets relative to Gfi1b, during megakaryocytic differentiation. Both kindlin3 and talin1 promoters …