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The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery.

The objectives of this sabbatical were to examine the resilience of temperate corals (Astrangia poculata, Ellis & Solander 1787) and to address the following questions: 1. Do corals exhibit quiescence at warmer temperatures?; 2. Does Astrangia poculata exhibit quiescence across their geographic range?; 3. Does the microbial population on corals change during quiescence?; and 4. Does temperature cause a change in symbiotic state in A. poculata?

"Provides information about the habits and habitats of North America's 100 most common birds. Includes information on how to attract birds as well as how to identify their songs with a QR code that links directly to a recording of each bird's song"--

"This superb book, with its unique focus on the entire marine coastal environment, is the most comprehensive and up-to-date field guide available on the southeastern Atlantic Coast and the Gulf Coast. Not just for beachgoers, the book is essential for birders, whale watchers, fishers, boaters, scuba divers and snorkelers, and shoreline visitors" --Publisher description.

A Quantitative Trait Locus (QTL) analysis was performed using two novel Recombinant Inbred Line (RIL) populations, derived from the progeny between two Arabidopsis thaliana genotypes collected at the same site in Kyoto (Japan) crossed with the reference laboratory strain Landsberg erecta (Ler). We used these two RIL populations to determine the genetic basis of seed dormancy and flowering time, which are assumed to be the main traits controlling life history variation in Arabidopsis. The analysis revealed quantitative variation for seed dormancy that is associated with allelic variation at the seed dormancy QTL DOG1 (for Delay Of Germination 1) in one population and at DOG6 in both. These DOG QTL have been previously identified using mapping populations derived from accessions collected at different sites around the world. Genetic variation within a population may enhance its ability to respond accurately to variation within and between seasons. In contrast, variation for flowering time, which also segregated within each mapping population, is mainly governed by the same QTL. © 2011 Silady et al.

'Rauisuchia' comprises Triassic pseudosuchians that ranged greatly in body size, locomotor styles and feeding ecologies. Our concept of what constitutes a rauisuchian is changing as a result of discoveries over the last 15 years. New evidence has shown that rauisuchians are probably not a natural (monophyletic) group, but instead are a number of smaller clades (e.g. Rauisuchidae, Ctenosauriscidae, Shuvosauridae) that may not be each other's closest relatives within Pseudosuchia. Here, we acknowledge that there are still large gaps in the basic understanding in the alphalevel taxonomy and relationships of these groups, but good progress is being made. As a result of renewed interest in rauisuchians, an expanding number of recent studies have focused on the growth, locomotor habits, and biomechanics of these animals, and we review these studies here. We are clearly in the midst of a renaissance in our understanding of rauisuchian evolution and the continuation of detailed descriptions, the development of explicit phylogenetic hypotheses, and explicit palaeobiological studies are essential in advancing our knowledge of these extinct animals. © The Geological Society of London 2013.

Torpor is common in bats, but has historically been viewed as an energy-saving technique reserved for temperate and subarctic climates; however, torpor use is common across several tropical bat families. Central America hosts a great diversity of bats with approximately 150 species, yet data from this area are lacking compared with tropical Africa and Australia. We investigated thermoregulatory responses of bats from neotropical Belize and captured adult bats in the tropical forests of Lamanai Archeological Reserve, Belize. After a 12 h acclimation period, we recorded rectal temperature prior to and after exposing bats to an ambient temperature (Ta) of 7 °C forupto 2 h in anenvironmental chamber. All 11 species across four families expressed torpor to some degree upon exposure to cool temperatures. Individuals from Vespertilionidae defended the lowest resting body temperature (Tb) and showed the greatest decrease in Tb after acute exposure to low Ta. Our data help to establish a new spectrum of physiological ability for this group of mammals and shed light on the evolution of torpor and heterothermy. Weshow that energy conservation is important even in warm and energetically stable environmental conditions. Understanding how and why torpor is used in warm climates will help to better define paradigms in physiological ecology. © 2017, Canadian Science Publishing. All rights reserved.

Invasive crustacean species have been present in the Long Island Sound, northwestern Atlantic Ocean, for over two centuries. Three new records of introduction are recorded here from collections by local fishermen. Two records are for male Dungeness crabs, Metacarcinus magister (Dana, 1852), collected in the Western Long Island Sound (2017) and Cape Cod Bay (2018). The other record is that of a range extension documented by a single male Chinese mitten crab, Eriocheir sinensis (Milne-Edwards, 1853), found in New Haven Harbor, Connecticut. Both species could potentially harbor nonnative epibionts and endoparasites. Additionally, E. sinensis may be more likely to establish, as it has in numerous locations in the region and worldwide. © Hudson et al.

U.S. SEER (Surveillance Epidemiology and End Results) data for age-adjusted mortality rates for all cancers combined for all races show only a modest overall 13% decline over the past 35 years. Moreover, the greatest contributor to cancer mortality is treatment-resistant metastatic disease. The accepted therapeutic paradigm for the past half-century for the treatment of advanced cancers has involved the use of systemic chemotherapy drugs cytotoxic for cycling cells (both normal and malignant) during DNA synthesis and/or mitosis. The failure of this therapeutic modality to achieve high-level, consistent rates of disease-free survival for some of the most common cancers, including tumors of the lung, colon breast, brain, melanoma, and others is the focus of this paper. A retrospective assessment of critical milestones in cancer chemotherapy indicates that most successful therapeutic regimens use cytotoxic cell cycle inhibitors in combined, maximum tolerated, dose-dense acute treatment regimens originally developed to treat acute lymphoblastic leukemia and some lymphomas. Early clinical successes in this area led to their wholesale application to the treatment of solid tumor malignancies that, unfortunately, has not produced consistent, long-term high cure rates for many common cancers. Important differences in therapeutic sensitivity of leukemias/lymphomas versus solid tumors can be explained by key biological differences that define the treatment-resistant solid tumor phenotype. A review of these clinical outcome data in the context of recent developments in our understanding of drug resistance mechanisms characteristic of solid tumors suggests the need for a new paradigm for the treatment of chemotherapy-resistant cancers. In contrast to reductionist approaches, the systemic approach targets both microenvironmental and systemic factors that drive and sustain tumor progression. These systemic factors include dysregulated inflammatory and oxidation pathways shown to be directly implicated in the development and maintenance of the cancer phenotype. The paradigm stresses the importance of a combined preventive/therapeutic approach involving adjuvant chemotherapies that incorporate anti-inflammatory and anti-oxidant therapeutics.

Post-translational phosphorylation is essential to human cellular processes, but the transient, heterogeneous nature of this modification complicates its study in native systems. We developed an approach to interrogate phosphorylation and its role in protein-protein interactions on a proteome-wide scale. We genetically encoded phosphoserine in recoded E. coli and generated a peptide-based heterologous representation of the human serine phosphoproteome. We designed a single-plasmid library encoding >100,000 human phosphopeptides and confirmed the site-specific incorporation of phosphoserine in >36,000 of these peptides. We then integrated our phosphopeptide library into an approach known as Hi-P to enable proteome-level screens for serine-phosphorylation-dependent human protein interactions. Using Hi-P, we found hundreds of known and potentially new phosphoserine-dependent interactors with 14-3-3 proteins and WW domains. These phosphosites retained important binding characteristics of the native human phosphoproteome, as determined by motif analysis and pull-downs using full-length phosphoproteins. This technology can be used to interrogate user-defined phosphoproteomes in any organism, tissue, or disease of interest.

Fish and wildlife agencies produce a bounty of information aimed at the public. Under the right circumstances, that information can be compiled into scientifically useful data to complement full scientific studies. This poster describes some preliminary results from a project to compile mentions of gamefish species, locations, and sizes throughout the Long Island Sound and surrounding waters from the Weekly Fishing Report (2006, 2008-2018) and the Trophy Fish Report (2009-2017), both produced by the Connecticut Dept. of Energy and Environmental Protection. The dataset consists of more than 20,000 entries from the reports collected weekly by DEEP employees from tackle shops and charter companies. The current portion of the analysis is to determine the characteristics of the dataset, such as entry types, species counts, and some general trends. Presented at the 2019 NEAFWA Conference in Groton, CT and the 2019 CSCU Faculty Research Conference at SCSU in New Haven, CT.

In the developing nervous system, neurotrophin 3 (NT3) and brain-derived neurotrophic factor (BDNF) have been shown to interact with each other and with different parts of a neuron or glia and over considerable distances in time and space. The auditory system provides a useful model for analyzing these events, insofar as it is subdivided into well-defined groups of specific neuronal types that are readily related to each other at each stage of development. Previous work in our laboratory suggested that NT3 and its receptor TrkC in the mouse cochlear nucleus (CN) may be involved in directing neuronal migration and initial targeting of inputs from cochlear nerve axons in the embryo. NT3 is hard to detect soon after birth, but TrkC lingers longer. Here we found NT3 and TrkC around P8 and the peak around P30. Prominent in ventral CN, associated with globular bushy cells and stellate cells, they were localized to different subcellular sites. The TrkC immunostain was cytoplasmic, and that of NT3 was axonal and perisomatic. TrkC may be made by CN neurons, whereas NT3 has a cochlear origin. The temporal pattern of their development and the likelihood of activity-dependent release of NT3 from cochlear axons suggest that it may not be critical in early synaptogenesis; it may provide long-term trophic effects, including stabilization of synapses once established. Activity-related regulation could coordinate the supply of NT3 with inner ear activity. This may require interaction with other neurotrophins, such as BDNF.

To study the mechanisms of noise-induced hearing loss and the phantom noise, or tinnitus, often associated with it, we used a mouse model of noise damage designed for reproducible and quantitative structural analyses. We selected the posteroventral cochlear nucleus, which has shown considerable plasticity in past studies, and correlated its changes with the distribution of neurotrophin 3 (NT3). We used volume change, optical density analysis, and microscopic cluster analysis to measure the degeneration after noise exposure. There was a fluctuation pattern in the reorganization of nerve terminals. The data suggest that the source and size of the nerve terminals affect their capacity for regeneration. We hypothesize that the deafferentation of ventral cochlear nucleus is the structural basis of noise-induced tinnitus. In addition, the immunofluorescent data show a possible connection between NT3 and astrocytes. There appears to be a compensatory process in the supporting glial cells during this degeneration. Glia may play a role in the mechanisms of noise-induced hearing loss. © 2011 Wiley Periodicals, Inc.

Aims: Loline alkaloids produced by Epichloë spp. are known to deter feeding by insect herbivores while also serving as a significant carbon source for certain epiphytic bacteria on tall fescue leaves. In this study we examined the role of loline alkaloids in attracting certain bacteria to the rhizosphere of tall fescue plants that harbor loline producing fungal endophytes. Methods: Population studies were used to compare the fitness of known loline catabolizing strains to other rhizosphere bacteria. Pyrosequencing of 16S rRNA fragments compared the composition of bacterial communities inhabiting the endophyte infected tall fescue (Festuca arundinacea) rhizosphere to those of endophyte free fescue plants. Results: Rhizosphere population studies demonstrated that loline catabolizing strains Burkholderia ambifaria 7R and Pseudomonas aureofaciens outcompete and suppress the growth of non-loline catabolizing strains. Pyrosequencing of 16S rRNA fragments showed greater percentages of certain plant growth promoting bacteria in rhizosperes seeded with B. ambifaria 7R than non-inoculated soils. Rhizospheres of endophyte infected plants showed higher species richness (Shannon diversity index = 4.03) over endophyte free rhizospheres (Shannon diversity index = 3.08) and a greater percentage of Firmicutes. Conclusions: The differences in microbial community composition between endophyte-infected and endophyte-free rhizospheres suggest that the presence of fungal endophytes influences microbial community structure. Loline alkaloid production may be one proxy by which the fungal endophyte shapes microbial communities, as evidenced by increased fitness of loline catabolizing bacteria in the tall fescue rhizosphere. © 2015, Springer International Publishing Switzerland.

Targeted therapies and the consequent adoption of "personalized" oncology have achieved notable successes in some cancers; however, significant problems remain with this approach. Many targeted therapies are highly toxic, costs are extremely high, and most patients experience relapse after a few disease-free months. Relapses arise from genetic heterogeneity in tumors, which harbor therapy-resistant immortalized cells that have adopted alternate and compensatory pathways (i.e., pathways that are not reliant upon the same mechanisms as those which have been targeted). To address these limitations, an international task force of 180 scientists was assembled to explore the concept of a low-toxicity "broad-spectrum" therapeutic approach that could simultaneously target many key pathways and mechanisms. Using cancer hallmark phenotypes and the tumor microenvironment to account for the various aspects of relevant cancer biology, interdisciplinary teams reviewed each hallmark area and nominated a wide range of high-priority targets (74 in total) that could be modified to improve patient outcomes. For these targets, corresponding low-toxicity therapeutic approaches were then suggested, many of which were phytochemicals. Proposed actions on each target and all of the approaches were further reviewed for known effects on other hallmark areas and the tumor microenvironment. Potential contrary or procarcinogenic effects were found for 3.9% of the relationships between targets and hallmarks, and mixed evidence of complementary and contrary relationships was found for 7.1%. Approximately 67% of the relationships revealed potentially complementary effects, and the remainder had no known relationship. Among the approaches, 1.1% had contrary, 2.8% had mixed and 62.1% had complementary relationships. These results suggest that a broad-spectrum approach should be feasible from a safety standpoint. This novel approach has potential to be relatively inexpensive, it should help us address stages and types of cancer that lack conventional treatment, and it may reduce relapse risks. A proposed agenda for future research is offered. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Cancer arises in the context of an in vivo tumor microenvironment. This microenvironment is both a cause and consequence of tumorigenesis. Tumor and host cells co-evolve dynamically through indirect and direct cellular interactions, eliciting multiscale effects on many biological programs, including cellular proliferation, growth, and metabolism, as well as angiogenesis and hypoxia and innate and adaptive immunity. Here we highlight specific biological processes that could be exploited as targets for the prevention and therapy of cancer. Specifically, we describe how inhibition of targets such as cholesterol synthesis and metabolites, reactive oxygen species and hypoxia, macrophage activation and conversion, indoleamine 2,3-dioxygenase regulation of dendritic cells, vascular endothelial growth factor regulation of angiogenesis, fibrosis inhibition, endoglin, and Janus kinase signaling emerge as examples of important potential nexuses in the regulation of tumorigenesis and the tumor microenvironment that can be targeted. We have also identified therapeutic agents as approaches, in particular natural products such as berberine, resveratrol, onionin A, epigallocatechin gallate, genistein, curcumin, naringenin, desoxyrhapontigenin, piperine, and zerumbone, that may warrant further investigation to target the tumor microenvironment for the treatment and/or prevention of cancer. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Quantitative Threshold Exposure (QTE) hypothesis is a multifactorial threshold model that accounts for the cumulative effects of risk factor exposure in both the causation of autism spectrum disorder (ASD) and its dramatic increase over the past 30 years. The QTE hypothesis proposes that ASD is triggered by the cumulative effects of high-level exposure to endogenous and environmental factors that act as antigens to impair normal immune system (IS) and associated central nervous system (CNS) functions during critical developmental stages. The quantitative threshold parameters that comprise a cumulative risk for the development of ASD are identified by the assessment of documented epidemiological factors that, in sum, determine the likelihood that ASD will occur as a result of their effects on critically integrated IS and CNS pathways active during prenatal, neo-natal and early childhood brain maturation. The model proposes an explanation for the relationship between critical developmental stages of brain/immune system development in conjunction with the quantitative effects of genetic and environmental risk factors that may interface with these critical developmental windows. This model may be useful even when the individual contributions of specific risk factors cannot be quantified, as it proposes that the combined quantitative level of exposure to risk factors for ASD rather than exposure to any one risk factor per se defines threshold occurrence rates. Copyright © 2015 Elsevier Ltd. All rights reserved.