Search

Conditional gene regulation inDrosophilathrough binary expression systems like theLexA-LexAopsystem provides a superb tool for investigating gene and tissue function. To increase the availability of defined LexA enhancer trap insertions, we present molecular, genetic and tissue expression studies of 301 novel Stan-X LexA enhancer traps derived from mobilization of the index SX4 line. This includes insertions into distinct loci on the X, II and III chromosomes that were not previously associated with enhancer traps or targeted LexA constructs, an insertion intoptc, and eleven insertions into natural transposons. A subset of enhancer traps was expressed in CNS neurons known to produce and secrete insulin, an essential regulator of growth, development and metabolism. Fly lines described here were generated and characterized through studies by students and teachers in an international network of genetics classes at public, independent high schools, and universities serving a diversity of students, including those underrepresented in science. Thus, a unique partnership between secondary schools and university-based programs has produced and characterized novel resources inDrosophila, establishing instructional paradigms devoted to unscripted experimental science.

I do not think you can start with anything precise. You have to achieve such precision as you can, as you go along. —Bertrand Russell

Horizontal gene transfer (HGT), the movement and genomic integration of DNA across species boundaries, is commonly associated with bacteria and other microorganisms, but functional HGT (fHGT) is increasingly being recognized in heterotrophic parasitic plants that obtain their nutrients and water from their host plants through direct haustorial feeding. Here, in the holoparasitic stem parasite Cuscuta, we identify 108 transcribed and probably functional HGT events in Cuscuta campestris and related species, plus 42 additional regions with host-derived transposon, pseudogene and non-coding sequences. Surprisingly, 18 Cuscuta fHGTs were acquired from the same gene families by independent HGT events in Orobanchaceae parasites, and the majority are highly expressed in the haustorial feeding structures in both lineages. Convergent retention and expression of HGT sequences suggests an adaptive role for specific additional genes in parasite biology. Between 16 and 20 of the transcribed HGT events are inferred as ancestral in Cuscuta based on transcriptome sequences from species across the phylogenetic range of the genus, implicating fHGT in the successful radiation of Cuscuta parasites. Genome sequencing of C. campestris supports transfer of genomic DNA-rather than retroprocessed RNA-as the mechanism of fHGT. Many of the C. campestris genes horizontally acquired are also frequent sources of 24-nucleotide small RNAs that are typically associated with RNA-directed DNA methylation. One HGT encoding a leucine-rich repeat protein kinase overlaps with a microRNA that has been shown to regulate host gene expression, suggesting that HGT-derived parasite small RNAs may function in the parasite-host interaction. This study enriches our understanding of HGT by describing a parasite-host system with unprecedented gene exchange that points to convergent evolution of HGT events and the functional importance of horizontally transferred coding and non-coding sequences.

Variation in translation-elongation kinetics along a transcript’s coding sequence plays an important role in the maintenance of cellular protein homeostasis by regulating co-translational protein folding, localization, and maturation. Translation-elongation speed is influenced by molecular factors within mRNA and protein sequences. For example, the presence of proline in the ribosome’s P- or A-site slows down translation, but the effect of other pairs of amino acids, in the context of all 400 possible pairs, has not been characterized. Here, we study Saccharomyces cerevisiae using a combination of bioinformatics, mutational experiments, and evolutionary analyses, and show that many different pairs of amino acids and their associated tRNA molecules predictably and causally encode translation rate information when these pairs are present in the A- and P-sites of the ribosome independent of other factors known to influence translation speed including mRNA structure, wobble base pairing, tripeptide motifs, positively charged upstream nascent chain residues, and cognate tRNA concentration. The fast-translating pairs of amino acids that we identify are enriched four-fold relative to the slow-translating pairs across Saccharomyces cerevisiae’s proteome, while the slow-translating pairs are enriched downstream of domain boundaries. Thus, the chemical identity of amino acid pairs contributes to variability in translation rates, elongation kinetics are causally encoded in the primary structure of proteins, and signatures of evolutionary selection indicate their potential role in co-translational processes.

“I have no idea what’s awaiting me, or what will happen when this all ends. For the moment I know this: there are sick people and they need curing.” ―Albert Camus, The Plague

“Every day sadder and sadder news of its increase. In the City died this week 7496; and of them, 6102 of the plague. But it is feared that the true number of the dead this week is near 10,000 ....” —Samuel Pepys, 1665

“With one eye you are looking at the outside world, while with the other you are looking within yourself.” —Amedeo Modigliani

Context-dependent biological variation presents a unique challenge to the reproducibility of results in experimental animal research, because organisms’ responses to experimental treatments can vary with both genotype and environmental conditions. In March 2019, experts in animal biology, experimental design and statistics convened in Blonay, Switzerland, to discuss strategies addressing this challenge. In contrast to the current gold standard of rigorous standardization in experimental animal research, we recommend the use of systematic heterogenization of study samples and conditions by actively incorporating biological variation into study design through diversifying study samples and conditions. Here we provide the scientific rationale for this approach in the hope that researchers, regulators, funders and editors can embrace this paradigm shift. We also present a road map towards better practices in view of improving the reproducibility of animal research. In this Perspective, Hanno Wurbel and colleagues argue that a disregard for incorporating biological variation in study design is an important cause of poor reproducibility in animal research. They put the case for the use of systematic heterogenization of study samples and conditions in studies to improve reproducibility.

Background Parasitic plants engage in a complex molecular dialog with potential host plants to identify a host and overcome host defenses to initiate development of the parasitic feeding organ, the haustorium, invade host tissues, and withdraw water and nutrients. While one of two critical signaling events in the parasitic plant life cycle (germination via stimulant chemicals) has been relatively well-studied, the signaling event that triggers haustorium formation remains elusive. Elucidation of this poorly understood molecular dialogue will shed light on plant-plant communication, parasitic plant physiology, and the evolution of parasitism in plants. Results Here we present an experimental framework that develops easily quantifiable contrasts for the facultative generalist parasitic plant, Triphysaria, as it feeds across a broad range of diverse flowering plants. The contrasts, including variable parasite growth form and mortality when grown with different hosts, suggest a dynamic and host-dependent molecular dialogue between the parasite and host. Finally, by comparing transcriptome datasets from attached versus unattached parasites we gain insight into some of the physiological processes that are altered during parasitic behavior including shifts in photosynthesis-related and stress response genes. Conclusions This work sheds light on Triphysaria’s parasitic life habit and is an important step towards understanding the mechanisms of haustorium initiation factor perception, a unique form of plant-plant communication. Electronic supplementary material The online version of this article (10.1186/s12870-019-1856-1) contains supplementary material, which is available to authorized users.

“Everything we see hides another thing, we always want to see what is hidden by what we see” — Rene Magritte

You can look back there to explain things, but the explanation disappears. You’ll never find it there. Things are not explained by the past. They’re explained by what happens now. –Alan Watts

Robust regression generates more reliable estimates by detecting and downweighting outliers.

Simultaneous examination of multiple factors at two levels can reveal which have an effect.

International audience; Two major goals in the study of biological systems are inference andprediction. Inference creates a mathematical model of the datageneration process to formalize our understanding or test ahypothesis about how the system behaves. Prediction aims atforecasting unobserved outcomes or future behavior, such as whethera mouse with a given phenotype will have a disease. Prediction makesit possible to identify best courses of action (e.g. treatment choice)without requiring understanding of the underlying mechanisms. In atypical research project, both inference and prediction are of value—we want to know how biological processes work and what will happennext. For example, we might want to infer which biological processesare associated with the dysregulation of a gene in a disease as well asclassify whether a subject has the disease and predict the besttherapy, such as drug intervention or invasive surgery.

Supervised learning algorithms extract general principles from observed examples guided by a specific prediction objective.

Machine learning extracts general principles from observed examples without explicit instructions.

Customize the experiment for the setting instead of adjusting the setting to fit a classical design.

The initially published paper contained an error in Table 1: in the rightmost column (y), “0.09” should have been “–0.09.” This error has been corrected in the PDF and HTML versions of the article.

Understanding past relative sea-level changes is important to a number of social and scientific questions, including the effects of global climate change and future land-use planning under scenarios of accelerated sea-level rise with a concomitant increased threat to coastal areas around the world. In particular, accurately characterizing millennial sea-level changes is important in evaluating vertical movements of the Earth's crust that happen in response to the advances and retreats of ice sheets during long-term climatic cycles. In this paper, we analyze sea-level data from several Maine salt marshes previously reported in a paper from the geological literature. We address these data and questions of geological interest with a ‘smooth transition’ model. Copyright © 2013 John Wiley & Sons, Ltd.

The branching coral Acropora palmata is a foundation species of Caribbean reefs that has been decimated in recent decades by anthropogenic and natural stressors. Declines in population density and genotypic diversity likely reduce successful sexual reproduction in this self-incompatible hermaphrodite and might impede recovery. We investigated variation among genotypes in larval development under thermally stressful conditions. Six two-parent crosses and three four-parent batches were reared under three temperatures and sampled over time. Fertilization rates differed widely with two-parent crosses having lower fertilization rates (5–56 %, mean 22 % ± 22 SD) than batches (from 31 to 87 %, mean 59 % ± 28 SD). Parentage analysis of larvae in batch cultures showed differences in gamete compatibility among parents, coinciding with significant variation in both sperm morphology and egg size. While all larval batches developed more rapidly at increased water temperatures, rate of progression through developmental stages varied among batches, as did swimming speed. Together, these results indicate that loss of genotypic diversity exacerbates already severe limitations in sexual reproductive success of A. palmata. Nevertheless, surviving parental genotypes produce larvae that do vary in their phenotypic response to thermal stress, with implications for adaptation, larval dispersal and population connectivity in the face of warming sea surface temperatures.

It is often convenient to assume that X and X | Y are in the same exponential family. By considering X as the “parameter” and Y as the “data”, the problem becomes determining which exponential families X | Y have conjugate priors. We develop a necessary condition for conjugacy. One-dimensional exponential families can be conjugate only if they have exactly two support points.

Coral populations have declined worldwide largely due to increased sea surface temperatures. Recovery of coral populations depends in part upon larval recruitment. Many corals reproduce during the warmest time of year when further increases in temperature can lead to low fertilization rates of eggs and high larval mortality. Microarray experiments were designed to capture and assess variability in the thermal stress responses of Acropora palmata larvae from Puerto Rico. Transcription profiles showed a striking acceleration of normal developmental gene expression patterns with increased temperature. The transcriptional response to heat suggested rapid depletion of larval energy stores via peroxisomal lipid oxidation and included key enzymes that indicated the activation of the glyoxylate cycle. High temperature also resulted in expression differences in key developmental signalling genes including the conserved WNT pathway that is critical for pattern formation and tissue differentiation in developing embryos. Expression of these and other important developmental and thermal stress genes such as ferritin, heat shock proteins, cytoskeletal components, cell adhesion and autophagy proteins also varied among larvae derived from different parent colonies. Disruption of normal developmental and metabolic processes will have negative impacts on larval survival and dispersal as temperatures rise. However, it appears that variation in larval response to high temperature remains despite the dramatic population declines. Further research is needed to determine whether this variation is heritable or attributable to maternal effects.

Whole Exome Sequencing (WES) is a powerful clinical diagnostic tool for discovering the genetic basis of many diseases. A major shortcoming of WES is uneven coverage of sequence reads over the exome targets contributing to many low coverage regions, which hinders accurate variant calling. In this study, we devised two novel metrics, Cohort Coverage Sparseness (CCS) and Unevenness (UE) Scores for a detailed assessment of the distribution of coverage of sequence reads. Employing these metrics we revealed non-uniformity of coverage and low coverage regions in the WES data generated by three different platforms. This non-uniformity of coverage is both local (coverage of a given exon across different platforms) and global (coverage of all exons across the genome in the given platform). The low coverage regions encompassing functionally important genes were often associated with high GC content, repeat elements and segmental duplications. While a majority of the problems associated with WES are due to the limitations of the capture methods, further refinements in WES technologies have the potential to enhance its clinical applications.

Tabulating the number of objects in categories of interest dates back to the earliest records of commerce and population censuses.

A P value measures a sample's compatibility with a hypothesis, not the truth of the hypothesis.

The uncertainty in meteorological predictions is of interest for applications ranging from economic to recreational to public safety. One common method to estimate uncertainty is by using meteorological ensembles. These ensembles provide an easily quantifiable measure of the uncertainty in the forecast in the form of the ensemble variance. However, ensemble variance may not accurately reflect the actual uncertainty, so any measure of uncertainty derived from the ensemble should be calibrated to provide a more reliable estimate of the actual uncertainty in the forecast. A previous study introduced the linear variance calibration (LVC) as a simple method to determine the ensemble variance to error variance relationship and demonstrated this technique on real ensemble data. The LVC parameters, the slopes, and y intercepts, however, are generally different from the ideal values. This current study uses a stochastic model to examine the LVC in a controlled setting. The stochastic model is capable of simulating underdispersive and overdispersive ensembles as well as perfectly reliable ensembles. Because the underlying relationship is specified, LVC results can be compared to theoretical values of the slope and y intercept. Results indicate that all types of ensembles produce calibration slopes that are smaller than their theoretical values for ensemble sizes less than several hundred members, with corresponding y intercepts greater than their theoretical values. This indicates that all ensembles, even otherwise perfect ensembles, should be calibrated if the ensemble size is less than several hundred. In addition, it is shown that an adjustment factor can be computed for inadequate ensemble size. This adjustment factor is independent of the stochastic model and is applicable to any linear regression of error variance on ensemble variance. When applied to experiments using the stochastic model, the adjustment produces LVC parameters near their theoretical values for all ensemble sizes. Although the adjustment is unnecessary when applying LVC, it allows for a more accurate assessment of the reliability of ensembles, and a fair comparison of the reliability for differently sized ensembles.

Current understanding of floral developmental genetics comes primarily from the core eudicot model Arabidopsis thaliana. Here, we explore the floral transcriptome of the basal angiosperm, Nuphar advena (water lily), for insights into the ancestral developmental program of flowers. We identify several thousand Nuphar genes with significantly upregulated floral expression, including homologs of the well-known ABCE floral regulators, deployed in broadly overlapping transcriptional programs across floral organ categories. Strong similarities in the expression profiles of different organ categories in Nuphar flowers are shared with the magnoliid Persea americana (avocado), in contrast to the largely organ-specific transcriptional cascades evident in Arabidopsis, supporting the inference that this is the ancestral condition in angiosperms. In contrast to most eudicots, floral organs are weakly differentiated in Nuphar and Persea, with staminodial intermediates between stamens and perianth in Nuphar, and between stamens and carpels in Persea. Consequently, the predominantly organ-specific transcriptional programs that characterize Arabidopsis flowers (and perhaps other eudicots) are derived, and correlate with a shift towards morphologically distinct floral organs, including differentiated sepals and petals, and a perianth distinct from stamens and carpels. Our findings suggest that the genetic regulation of more spatially discrete transcriptional programs underlies the evolution of floral morphology.

Apple trees (Malus x domestica) do not reproduce true-to-type from seed. Therefore, desirable cultivars are clonally propagated by grafting vegetative material onto rootstocks. Although cloned cultivars are genetically identical, rootstocks influence horticulturally important cultivar traits, including tree size, disease resistance, and abiotic stress tolerance. Here, ‘Gala’ scions were grafted to seven different rootstocks that produce a range of tree sizes and grown in a greenhouse. Global gene expression patterns in the scions were compared using a DNA microarray representing 55,230 apple transcripts. Each rootstock triggered a distinct, reproducible scion gene expression pattern. Two thousand nine hundred thirty-four scion transcripts were differentially regulated, by a factor of two or greater, by one or more rootstocks. Transcripts from genes predicted to be involved in responses to stress and biotic and abiotic stimuli were disproportionately represented among the rootstock-regulated transcripts. Microarray data analysis based on tree size identified 116 transcripts whose expression levels were correlated with tree size. The correlation of transcript level with tree size was tested for 14 of these transcripts using quantitative polymerase chain reaction in a population of orchard-grown ‘Mutsu’ cultivar trees grafted onto rootstocks from a breeding population of multiple crosses. Of those tested, transcripts encoding predicted sorbitol dehydrogenase, homeobox-leucine zipper, and hevein-like proteins were confirmed as being expressed at higher levels in larger trees, while a transcript predicted to encode an extensin-like protein was confirmed as being expressed at higher levels in smaller trees. This study illustrates the utility of using rootstock-regulated phenotypes to identify genes potentially associated with horticulturally important traits.

The debate on the origin and evolution of flowers has recently entered the field of developmental genetics, with focus on the design of the ancestral floral regulatory program. Flowers can differ dramatically among angiosperm lineages, but in general, male and female reproductive organs surrounded by a sterile perianth of sepals and petals constitute the basic floral structure. However, the basal angiosperm lineages exhibit spectacular diversity in the number, arrangement, and structure of floral organs, whereas the evolutionarily derived monocot and eudicot lineages share a far more uniform floral ground plan. Here we show that broadly overlapping transcriptional programs characterize the floral transcriptome of the basal angiosperm Persea americana (avocado), whereas floral gene expression domains are considerably more organ specific in the model eudicot Arabidopsis thaliana . Our findings therefore support the “fading borders” model for organ identity determination in basal angiosperm flowers and extend it from the action of regulatory genes to downstream transcriptional programs. Furthermore, the declining expression of components of the staminal transcriptome in central and peripheral regions of Persea flowers concurs with elements of a previous hypothesis for developmental regulation in a gymnosperm “floral progenitor.” Accordingly, in contrast to the canalized organ-specific regulatory apparatus of Arabidopsis , floral development may have been originally regulated by overlapping transcriptional cascades with fading gradients of influence from focal to bordering organs.