Stepwise Progression of Embryonic Patterning

It is long established that the graded distribution of Dorsal transcription factor influences spatial domains of gene expression along the dorsoventral (DV) axis of Drosophila melanogaster embryos. However, the more recent realization that Dorsal levels also change with time raises the question of whether these dynamics are instructive. An overview of DV axis patterning is provided, focusing on new insights identified through quantitative analysis of temporal changes in Dorsal target gene expression from one nuclear cycle to the next (‘steps’). Possible roles for the stepwise progression of this patterning program are discussed including (i) tight temporal regulation of signaling pathway activation, (ii) control of gene expression cohorts, and (iii) ensuring the irreversibility of the patterning and cell fate specification process

Individualized predictions of disease progression following radiation therapy for prostate cancer.

Background: Following treatment for localized prostate cancer, men are monitored with serial PSA measurements. Refining the predictive value of post-treatment PSA determinations may add to clinical management and we have developed a model that predicts for an individual patient future PSA values and estimates the time to future clinical recurrence. Methods: Data from 934 patients treated for prostate cancer between 1987 and 2000 were used to develop a comprehensive statistical model to fit the clinical recurrence events and pattern of PSA data. A logistic regression model was used for the probability of cure, non-linear hierarchical mixed models were used for serial PSA measurements and a time-dependent proportional hazards model was used for recurrences. Data available up to February 2001 and September 2003 was used to assess the performance of the model. Results: The model suggests that T-stage, baseline PSA, and radiotherapy dosage are all associated with probability of cure. The risk of clinical recurrence in those not cured by radiotherapy is most strongly affected by the slope of the long-transformed PSA values. We show how the model can be used for individual monitoring of a patient’s disease progression. For each patient the model predicts, based upon his baseline and all post-treatment PSA values, the probability of future clinical recurrence in the validation dataset and of 406 PSA measurements obtained 1-2 years after February 2001, 92.8% were within 95% prediction limits from the model. Conclusions: This statistical model presented accurately predicts future PSA values and risk of clinical relapse. This predictive information for each individual patient, which can be updated with each additional PSA value, may prove useful to patents and physicians in determining what post-treatment salvage should be employed

Genome Activation and Regulation of Signaling in the Rapidly Dividing Drosophila Embryo

Embryonic development of the fruit fly Drosophila melanogaster is unique among model organisms and animals in general, as rapid and syncytial nuclear divisions characterize the early stages before cell membranes form. These nuclear divisions occur every eight to fifteen minutes, culminating with a 45-minute cell cycle where cell membranes form and the 6000 nuclei become 6000 cells before the embryo undergoes gastrulation. At the beginning of development, maternally deposited transcripts define the major axes of the embryo and control all processes that occur. As the syncytial nuclear cycles slow and nuclei migrate to the periphery of the embryo, maternal transcripts are degraded and the zygotic genome is first activated. The rapid pace of nuclear divisions concurrent with the activation of the zygotic genome presents unique challenges to the developing embryo, as the constraints imposed by mitosis limit the ability to transcribe new genes. This switch of control, the Maternal to Zygotic Transition, has been the subject of studies at the molecular and genetic level for almost 30 years. Here, we use new tools and approaches to study the developing embryo at a time scale not previously achieved. We show how the gene regulatory network along the dorsal-ventral axis, including entire signaling pathways, is activated using time point intervals of 10 minutes. Using mutants, we show the contribution of individual genes in the process of development and the resulting changes in expression levels for the entire network. Finally, we examine the transcription of long genes during the rapid syncytial nuclear cycles, when time constraints limit the ability to transcribe the entire gene. We show how an RNA binding protein regulates the truncation of the transcripts into short isoforms with novel coding sequences, and how these short gene products code for functional proteins that regulate the spatiotemporal activation of key signaling pathways in the embryo.</p

Stepwise Progression of Embryonic Patterning

It is long established that the graded distribution of Dorsal transcription factor influences spatial domains of gene expression along the dorsoventral (DV) axis of Drosophila melanogaster embryos. However, the more recent realization that Dorsal levels also change with time raises the question of whether these dynamics are instructive. An overview of DV axis patterning is provided, focusing on new insights identified through quantitative analysis of temporal changes in Dorsal target gene expression from one nuclear cycle to the next (‘steps’). Possible roles for the stepwise progression of this patterning program are discussed including (i) tight temporal regulation of signaling pathway activation, (ii) control of gene expression cohorts, and (iii) ensuring the irreversibility of the patterning and cell fate specification process

Identification of germline transcriptional regulatory elements in Aedes aegypti

The mosquito Aedes aegypti is the principal vector for the yellow fever and dengue viruses, and is also responsible for recent outbreaks of the alphavirus chikungunya. Vector control strategies utilizing engineered gene drive systems are being developed as a means of replacing wild, pathogen transmitting mosquitoes with individuals refractory to disease transmission, or bringing about population suppression. Several of these systems, including Medea, UD^MEL, and site-specific nucleases, which can be used to drive genes into populations or bring about population suppression, utilize transcriptional regulatory elements that drive germline-specific expression. Here we report the identification of multiple regulatory elements able to drive gene expression specifically in the female germline, or in the male and female germline, in the mosquito Aedes aegypti. These elements can also be used as tools with which to probe the roles of specific genes in germline function and in the early embryo, through overexpression or RNA interference

The Developmental Transcriptome of the Mosquito Aedes aegypti, an Invasive Species and Major Arbovirus Vector

Mosquitoes are vectors of a number of important human and animal diseases. The development of novel vector control strategies requires a thorough understanding of mosquito biology. To facilitate this, we used RNA-seq to identify novel genes and provide the first high-resolution view of the transcriptome throughout development and in response to blood feeding in a mosquito vector of human disease, Aedes aegypti, the primary vector for Dengue and yellow fever. We characterized mRNA expression at 34 distinct time points throughout Aedes development, including adult somatic and germline tissues, by using polyA+ RNA-seq. We identify a total of 14,238 novel new transcribed regions corresponding to 12,597 new loci, as well as many novel transcript isoforms of previously annotated genes. Altogether these results increase the annotated fraction of the transcribed genome into long polyA+ RNAs by more than twofold. We also identified a number of patterns of shared gene expression, as well as genes and/or exons expressed sex-specifically or sex-differentially. Expression profiles of small RNAs in ovaries, early embryos, testes, and adult male and female somatic tissues also were determined, resulting in the identification of 38 new Aedes-specific miRNAs, and ~291,000 small RNA new transcribed regions, many of which are likely to be endogenous small-interfering RNAs and Piwi-interacting RNAs. Genes of potential interest for transgene-based vector control strategies also are highlighted. Our data have been incorporated into a user-friendly genome browser located at www.Aedes.caltech.edu, with relevant links to Vectorbase (www.vectorbase.org

Dependencies in language: On the causal ontology of linguistic systems

Dependency is a fundamental concept in the analysis of linguistic systems. The many if-then statements offered in typology and grammar-writing imply a causally real notion of dependency that is central to the claim being made—usually with reference to widely varying timescales and types of processes. But despite the importance of the concept of dependency in our work, its nature is seldom defined or made explicit. This book brings together experts on language, representing descriptive linguistics, language typology, functional/cognitive linguistics, cognitive science, research on gesture and other semiotic systems, developmental psychology, psycholinguistics, and linguistic anthropology to address the following question: What kinds of dependencies exist among language-related systems, and how do we define and explain them in natural, causal terms

Dependencies in language: On the causal ontology of linguistic systems

Dependency is a fundamental concept in the analysis of linguistic systems. The many if-then statements offered in typology and grammar-writing imply a causally real notion of dependency that is central to the claim being made—usually with reference to widely varying timescales and types of processes. But despite the importance of the concept of dependency in our work, its nature is seldom defined or made explicit. This book brings together experts on language, representing descriptive linguistics, language typology, functional/cognitive linguistics, cognitive science, research on gesture and other semiotic systems, developmental psychology, psycholinguistics, and linguistic anthropology to address the following question: What kinds of dependencies exist among language-related systems, and how do we define and explain them in natural, causal terms

Dependencies in language: On the causal ontology of linguistic systems

Dependency is a fundamental concept in the analysis of linguistic systems. The many if-then statements offered in typology and grammar-writing imply a causally real notion of dependency that is central to the claim being made—usually with reference to widely varying timescales and types of processes. But despite the importance of the concept of dependency in our work, its nature is seldom defined or made explicit. This book brings together experts on language, representing descriptive linguistics, language typology, functional/cognitive linguistics, cognitive science, research on gesture and other semiotic systems, developmental psychology, psycholinguistics, and linguistic anthropology to address the following question: What kinds of dependencies exist among language-related systems, and how do we define and explain them in natural, causal terms