Non-Small Cell Lung Cancer Imaging Using a Phospholipase A2 Activatable Fluorophore.

Lung cancer, the most common cause of cancer-related death in the United States, requires advanced intraoperative detection methods to improve evaluation of surgical margins. In this study we employed DDAO-arachidonate (DDAO-A), a phospholipase A2 (PLA2) activatable fluorophore, designed for the specific optical identification of lung cancers in real-time during surgery. The fluorescence activation of DDAO-A by porcine sPLA2 was tested in various liposomal formulations, with 100 nm extruded EggPC showing the best overall characteristics.

Host control and species interactions jointly determine microbiome community structure.

The host microbiome can be considered an ecological community of microbes present inside a complex and dynamic host environment. The host is under selective pressure to ensure that its microbiome remains beneficial. The host can impose a range of ecological filters including the immune response that can influence the assembly and composition of the microbial community.

Naturally segregating genetic variants contribute to thermal tolerance in a Drosophila melanogaster model system.

Thermal tolerance is a fundamental physiological complex trait for survival in many species. For example, everyday tasks such as foraging, finding a mate, and avoiding predation are highly dependent on how well an organism can tolerate extreme temperatures. Understanding the general architecture of the natural variants within the genes that control this trait is of high importance if we want to better comprehend thermal physiology.

A minimal model of learning: quantifying the cost and benefit of learning in changing environments.

Many organisms have the ability to learn, but the costs and benefits of learning are difficult to quantify. We construct a minimal mathematical model of learning in which a forager attempts to maximize the amount of resources (food) it collects in a changing environment. Our model has two learning parameters: , corresponding to the duration of the forager's memory, and [Formula: see text], corresponding to how much the forager explores the environment to learn more about it.

The covalent nucleotide modifications within plant mRNAs: What we know, how we find them, and what should be done in the future.

Although covalent nucleotide modifications were first identified on the bases of transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), a number of these epitranscriptome marks have also been found to occur on the bases of messenger RNAs (mRNAs). These covalent mRNA features have been demonstrated to have various and significant effects on the processing (e.g.

Structures and consequences of pioneer factor binding to nucleosomes.

Pioneer transcription factors are able to bind a partially exposed motif on the surface of a nucleosome, enabling the proteins to target sites in silent regions of chromatin that have been compacted by linker histone. The targeting of nucleosomal DNA by pioneer factors has been observed in vitro and in vivo, where binding can promote local nucleosome exposure that allows other transcription factors, nucleosome remodelers, and histone modifiers to engage the chromatin and elicit gene activation or further repression. Pioneer factors thereby establish new gene expression programs during cell fate changes that occur during embryonic development, regeneration, and cancer.

Spatio-temporal variation in environmental features predicts the distribution and abundance of Ixodes scapularis.

Many species have experienced dramatic changes in both geographic range and population sizes in recent history. Increases in the geographic range or population size of disease vectors have public health relevance as these increases often precipitate the emergence of infectious diseases in human populations. Accurately identifying environmental factors affecting the biogeographic patterns of vector species is a long-standing analytical challenge, stemming from a paucity of data capturing periods of rapid changes in vector demographics.

Lonely at the top? Regulation of shoot apical meristem activity by intrinsic and extrinsic factors.

All the above-ground organs of a plant are derived from stem cells that reside in shoot apical meristems (SAM). Over the past 25 years, the genetic pathways that control the proliferation of stem cells within the SAM, and the differentiation of their progenitors into lateral organs, have been described in great detail. However, longstanding questions regarding the importance of communication between cells within the SAM and lateral organs have, until recently, remained unanswered.

regulates leaf identity independently of miR156-mediated translational repression.

In , loss of the carboxypeptidase ALTERED MERISTEM PROGRAM1 (AMP1) produces an increase in the rate of leaf initiation, an enlarged shoot apical meristem and an increase in the number of juvenile leaves. This phenotype is also observed in plants with reduced levels of miR156-targeted () transcription factors, suggesting that AMP1 might promote SPL activity. However, we found that the mutant phenotype is only partially corrected by elevated gene expression, and that has no significant effect on transcript levels, or on the level or the activity of miR156.

A species-level taxonomic review and host associations of (Hymenoptera, Braconidae, Microgastrinae) with an emphasis on 136 new reared species from Costa Rica and Ecuador.

The descriptive taxonomic study reported here is focused on , a species-rich genus of hymenopteran parasitoid wasps. The species were found within the framework of two independent long-term Neotropical caterpillar rearing projects: northwestern Costa Rica (Área de Conservación Guanacaste, ACG) and eastern Andes, Ecuador (centered on Yanayacu Biological Station, YBS). One hundred thirty-six new species of Ashmead are described and all of them are authored by Arias-Penna.

Infection from Outdoor Sporting Events-More Risk than We Think?

Competitive sports that involve extensive contact with mud are commonly held events and growing in popularity. However, the natural environment contributes to infection risks, and these events have been implicated in multiple infectious disease outbreaks. Soils and mud contain rich microbial communities and can include pathogens (including viruses, bacteria, and parasites), thereby offering risk of infection; there is also a risk of disease due to shedding, by participants, of pathogens directly into the environment.

Estimating C photosynthesis parameters by fitting intensive A/C curves.

Measurements of photosynthetic assimilation rate as a function of intercellular CO (A/C curves) are widely used to estimate photosynthetic parameters for C species, yet few parameters have been reported for C plants, because of a lack of estimation methods. Here, we extend the framework of widely used estimation methods for C plants to build estimation tools by exclusively fitting intensive A/C curves (6-8 more sampling points) for C using three versions of photosynthesis models with different assumptions about carbonic anhydrase processes and ATP distribution. We use simulation analysis, out of sample tests, existing in vitro measurements and chlorophyll-fluorescence measurements to validate the new estimation methods.

Simulating the component counts of combinatorial structures.

This article describes and compares methods for simulating the component counts of random logarithmic combinatorial structures such as permutations and mappings. We exploit the Feller coupling for simulating permutations to provide a very fast method for simulating logarithmic assemblies more generally. For logarithmic multisets and selections, this approach is replaced by an acceptance/rejection method based on a particular conditioning relationship that represents the distribution of the combinatorial structure as that of independent random variables conditioned on a weighted sum.

Rapid seasonal evolution in innate immunity of wild .

Understanding the rate of evolutionary change and the genetic architecture that facilitates rapid adaptation is a current challenge in evolutionary biology. Comparative studies show that genes with immune function are among the most rapidly evolving genes across a range of taxa. Here, we use immune defence in natural populations of to understand the rate of evolution in natural populations and the genetics underlying rapid change.

Female Songbirds: The unsung drivers of courtship behavior and its neural substrates.

Songbirds hold a prominent role in the fields of neurobiology, evolution, and social behavior. Many of these fields have assumed that females lacked the ability to produce song and have therefore treated song as a male-specific behavior. Consequently, much of our understanding regarding the evolution and neural control of song behavior has been driven by these assumptions.

riboviz: analysis and visualization of ribosome profiling datasets.

Background: Using high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009, this technique has played a key role in driving biological discovery, and yet it requires a rigorous computational toolkit for widespread adoption.

Description: We have developed a database and a browser-based visualization tool, riboviz, that enables exploration and analysis of riboseq datasets.

A resource on latitudinal and altitudinal clines of ecologically relevant phenotypes of the Indian Drosophila.

The unique geography of the Indian subcontinent has provided diverse natural environments for a variety of organisms. In this region, many ecological indices such as temperature and humidity vary predictably as a function of both latitude and altitude; these environmental parameters significantly affect fundamental dynamics of natural populations. Indian drosophilids are diverse in their geographic distribution and climate tolerance, possibly as a result of climatic adaptation.

tipdatingbeast: an r package to assist the implementation of phylogenetic tip-dating tests using beast.

Molecular tip dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to coestimate the timing of evolutionary events with rates of molecular evolution. In this context, beast, a program for Bayesian analysis of molecular sequences, is the most widely used phylogenetic tool. Here, we introduce tipdatingbeast, an r package built to assist the implementation of various phylogenetic tip-dating tests using beast.

A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer).

Background: RNA molecules fold into complex three-dimensional shapes, guided by the pattern of hydrogen bonding between nucleotides. This pattern of base pairing, known as RNA secondary structure, is critical to their cellular function. Recently several diverse methods have been developed to assay RNA secondary structure on a transcriptome-wide scale using high-throughput sequencing.

The role of small RNAs in vegetative shoot development.

Shoot development consists of the production of lateral organs in predictable spatial and temporal patterns at the shoot apex. To properly integrate such programs of growth across different cell and tissue types, plants require highly complex and robust genetic networks. Over the last twenty years, the roles of small, non-coding RNAs (sRNAs) in these networks have become increasingly apparent, not least in vegetative shoot growth.

Haemophilus influenzae LicB contributes to lung damage in an aged mice co-infection model.

Phosphorylcholine (ChoP) decoration of lipopolysaccharides is an important virulence strategy adopted by Haemophilus influenzae to establish a niche on the mucosal surface and to promote adherence to the host cells. The incorporation of ChoP on the LPS surface involves the lic1 operon, which consists of the licA, licB, licC, and licD genes. Among which, licB is a choline transporter gene required for acquisition of choline from environmental sources.

Bacterial community composition and diversity in an ancestral ant fungus symbiosis.

Fungus-farming ants (Hymenoptera: Formicidae, Attini) exhibit some of the most complex microbial symbioses because both macroscopic partners (ants and fungus) are associated with a rich community of microorganisms. The ant and fungal microbiomes are thought to serve important beneficial nutritional and defensive roles in these symbioses. While most recent research has investigated the bacterial communities in the higher attines (e.

High-throughput nuclease-mediated probing of RNA secondary structure in plant transcriptomes.

Empirical measurement of RNA secondary structure is an invaluable tool that has provided a more complete understanding of the RNA life cycle and functionality of this extremely important molecule. In general, methods for probing structural information involve treating RNA with either a chemical or an enzyme that preferentially targets regions of the RNA in a single- or double-stranded conformation (ssRNA and dsRNA, respectively). Here, we describe an approach that utilizes a combination of ssRNA- and dsRNA-specific nuclease (ss- and dsRNase, respectively) treatments along with high-throughput sequencing technology to provide comprehensive and robust measurements of RNA secondary structure across entire plant transcriptomes.

Reconstructing the δ(18) O of atmospheric water vapour via the CAM epiphyte Tillandsia usneoides: seasonal controls on δ(18) O in the field and large-scale reconstruction of δ(18) Oa.

Using both oxygen isotope ratios of leaf water (δ(18) OL ) and cellulose (δ(18) OC ) of Tillandsia usneoides in situ, this paper examined how short- and long-term responses to environmental variation and model parameterization affected the reconstruction of the atmospheric water vapour (δ(18) Oa ). During sample-intensive field campaigns, predictions of δ(18) OL matched observations well using a non-steady-state model, but the model required data-rich parameterization. Predictions from the more easily parameterized maximum enrichment model (δ(18) OL-M ) matched observed δ(18) OL and observed δ(18) Oa when leaf water turnover was less than 3.