A blueprint most wonderful, the homeobox discovery.

This is a personal, non-linear summary of the discovery of the homeobox, a short DNA sequence encoding a DNA-binding domain conserved in developmental control genes. It is based on our recollections, a few decaying lab notebooks and letters, the early research papers we published, and conversations with a few colleagues who were in Basel at the time. It presents a simple story, when the research we did was anything but, with failed experiments, blind alleys and dumb ideas.

The expression of Drosophila melanogaster Hox gene Ultrabithorax is not overtly regulated by the intronic long noncoding RNA lncRNA:PS4 in a wild-type genetic background.

Long noncoding RNAs (lncRNAs) have been implicated in a variety of processes in development, differentiation, and disease. In Drosophila melanogaster, the bithorax Hox cluster contains three Hox genes [Ultrabithorax (Ubx), abdominal-A, and Abdominal-B], along with a number of lncRNAs, most with unknown functions. Here, we investigated the function of a lncRNA, lncRNA:PS4 that originates in the second intron of Ubx and is transcribed in the antisense orientation to Ubx.

High-resolution in situ analysis of Cas9 germline transcript distributions in gene-drive Anopheles mosquitoes.

Gene drives are programmable genetic elements that can spread beneficial traits into wild populations to aid in vector-borne pathogen control. Two different drives have been developed for population modification of mosquito vectors. The Reckh drive (vasa-Cas9) in Anopheles stephensi displays efficient allelic conversion through males but generates frequent drive-resistant mutant alleles when passed through females.

Dissecting the evolutionary role of the gene in mouthpart diversification by full locus replacement.

genes determine positional codes along the head-to-tail axis. Here, we replaced the entire () locus, which controls the development of the proboscis and maxillary palps, with that from , a related species with highly modified mouthparts. The replacement rescues most aspects of adult proboscis morphology; however, the shape and orientation of maxillary palps were modified, resembling and closely related species.

Toll pathway is required for wound-induced expression of barrier repair genes in the epidermis.

The epidermis serves as a protective barrier in animals. After epidermal injury, barrier repair requires activation of many wound response genes in epidermal cells surrounding wound sites. Two such genes in encode the enzymes dopa decarboxylase () and tyrosine hydroxylase ().

Long-Term Results of a Trial of Concurrent Chemotherapy and Escalating Doses of Radiation for Unresectable Non-Small Cell Lung Cancer: NCCTG N0028 (Alliance).

Introduction: This phase I/II trial was designed to determine the maximally tolerated dose of thoracic radiotherapy as part of a combined modality approach. This report includes the long-term outcomes of patients treated on this study. The phase II portion was never completed, as RTOG-0617 opened before it was concluded.

Serine proteolytic pathway activation reveals an expanded ensemble of wound response genes in Drosophila.

After injury to the animal epidermis, a variety of genes are transcriptionally activated in nearby cells to regenerate the missing cells and facilitate barrier repair. The range and types of diffusible wound signals that are produced by damaged epidermis and function to activate repair genes during epidermal regeneration remains a subject of very active study in many animals. In Drosophila embryos, we have discovered that serine protease function is locally activated around wound sites, and is also required for localized activation of epidermal repair genes.

Three Drosophila Hox complex microRNAs do not have major effects on expression of evolutionarily conserved Hox gene targets during embryogenesis.

The discovery of microRNAs has resulted in a major expansion of the number of molecules known to be involved in gene regulation. Elucidating the functions of animal microRNAs has posed a significant challenge as their target interactions with messenger RNAs do not adhere to simple rules. Of the thousands of known animal microRNAs, relatively few microRNA:messenger RNA regulatory interactions have been biologically validated in an normal organismal context.

Duox, Flotillin-2, and Src42A are required to activate or delimit the spread of the transcriptional response to epidermal wounds in Drosophila.

The epidermis is the largest organ of the body for most animals, and the first line of defense against invading pathogens. A breach in the epidermal cell layer triggers a variety of localized responses that in favorable circumstances result in the repair of the wound. Many cellular and genetic responses must be limited to epidermal cells that are close to wounds, but how this is regulated is still poorly understood.

Gene length may contribute to graded transcriptional responses in the Drosophila embryo.

An important question in developmental biology is how relatively shallow gradients of morphogens can reliably establish a series of distinct transcriptional readouts. Current models emphasize interactions between transcription factors binding in distinct modes to cis-acting sequences of target genes. Another recent idea is that the cis-acting interactions may amplify preexisting biases or prepatterns to establish robust transcriptional responses.

Phosphorylation of Grainy head by ERK is essential for wound-dependent regeneration but not for development of an epidermal barrier.

Grainy head (GRH) is a key transcription factor responsible for epidermal barrier formation and repair, whose function is highly conserved across diverse animal species. However, it is not known how GRH function is reactivated to repair differentiated epidermal barriers after wounding. Here, we show that GRH is directly regulated by extracellular signal-regulated kinase (ERK) phosphorylation, which is required for wound-dependent expression of GRH target genes in epidermal cells.

Co-option of an anteroposterior head axis patterning system for proximodistal patterning of appendages in early bilaterian evolution.

The enormous diversity of extant animal forms is a testament to the power of evolution, and much of this diversity has been achieved through the emergence of novel morphological traits. The origin of novel morphological traits is an extremely important issue in biology, and a frequent source of this novelty is co-option of pre-existing genetic systems for new purposes (Carroll et al., 2008).

Silencing of an abdominal Hox gene during early development is correlated with limb development in a crustacean trunk.

We tested whether Artemia abd-A could repress limbs in Drosophila embryos, and found that although abd-A transcripts were produced, ABD-A protein was not. Similarly, developing Artemia epidermal cells showed expression of abd-A transcripts without accumulation of ABD-A protein. This finding in Artemia reveals a new variation in Hox gene function that is associated with morphological evolution.

Minimizing off-target signals in RNA fluorescent in situ hybridization.

Fluorescent in situ hybridization (FISH) techniques are becoming extremely sensitive, to the point where individual RNA or DNA molecules can be detected with small probes. At this level of sensitivity, the elimination of 'off-target' hybridization is of crucial importance, but typical probes used for RNA and DNA FISH contain sequences repeated elsewhere in the genome. We find that very short (e.

Visualization of individual Scr mRNAs during Drosophila embryogenesis yields evidence for transcriptional bursting.

The detection and counting of transcripts within single cells via fluorescent in situ hybridization (FISH) has allowed researchers to ask quantitative questions about gene expression at the level of individual cells. This method is often preferable to quantitative RT-PCR, because it does not necessitate destruction of the cells being probed and maintains spatial information that may be of interest. Until now, studies using FISH at single-molecule resolution have only been rigorously carried out in isolated cells (e.

Multiple transcription factor codes activate epidermal wound-response genes in Drosophila.

Wounds in Drosophila and mouse embryos induce similar genetic pathways to repair epidermal barriers. However, the transcription factors that transduce wound signals to repair epidermal barriers are largely unknown. We characterize the transcriptional regulatory enhancers of 4 genes-Ddc, ple, msn, and kkv-that are rapidly activated in epidermal cells surrounding wounds in late Drosophila embryos and early larvae.

Context-dependent regulation of Hox protein functions by CK2 phosphorylation sites.

Variations in Hox protein sequences and functions have been proposed to contribute to evolutionary changes in appendage shape and number in crustaceans and insects. One model is that insect Hox proteins of the Ultrabithorax (UBX) ortholog class evolved increased abilities to repress Distal-less (Dll) transcription and appendage development in part through the loss of serine and threonine residues in casein kinase 2 (CK2) phosphorylation sites. To explore this possibility, we constructed and tested the appendage repression function of chimeric proteins with insertions of different CK2 consensus sites or phosphomimetics of CK2 sites in C-terminal regions of Drosophila melanogaster UBX.

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans.

Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans.

The value of combined-modality therapy in elderly patients with stage III nonsmall cell lung cancer.

Background: The objective of this study was to assess the value of combined-modality therapy in elderly patients by comparing the differences in outcome between patients who received radiotherapy (RT) alone and patients who received RT plus chemotherapy for stage III nonsmall cell lung cancer (NSCLC).

Methods: The North Central Cancer Treatment Group performed 2 recent Phase III trials for stage III NSCLC. The first trial, NCCTG 90-24-51, included 3 arms: once-daily RT (QDRT) alone, twice-daily RT (BIDRT) alone, and concurrent chemotherapy plus BIDRT.

Genomic evolution of Hox gene clusters.

The family of Hox genes, which number 4 to 48 per genome depending on the animal, control morphologies on the main body axis of nearly all metazoans. The conventional wisdom is that Hox genes are arranged in chromosomal clusters in colinear order with their expression patterns on the body axis. However, recent evidence has shown that Hox gene clusters are fragmented, reduced, or expanded in many animals-findings that correlate with interesting morphological changes in evolution.

Gap peptides: A new way to control embryonic patterning?

Gap genes encode transcription factors involved in the patterning of the head-tail axis of insect embryos. In this issue of Cell, Savard et al. (2006) identify a beetle gap gene, mille-pattes, that encodes an unusual polycistronic transcript predicted to produce four conserved peptides.

Results of a Phase I trial of concurrent chemotherapy and escalating doses of radiation for unresectable non-small-cell lung cancer.

Purpose: This trial was performed to determine the maximum tolerated dose (MTD) of radiation that can be administered with carboplatin and paclitaxel.

Methods And Materials: This trial included 15 patients with unresectable non-small-cell lung cancer. Paclitaxel (50 mg/m2) and carboplatin (area under the curve=2) were given weekly during radiation therapy (RT).