A chromatin code for limb segment identity in axolotl limb regeneration

The salamander limb correctly regenerates missing limb segments because connective tissue cells have segment-specific identities, termed "positional information". How positional information is molecularly encoded at the chromatin level has been unknown. Here, we performed genome-wide chromatin profiling in mature and regenerating axolotl limb connective tissue cells. We find segment-specific levels of histone H3K27me3 as the major positional mark, especially at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. In the hand, the permissive chromatin state of the homeoprotein gene HoxA13 engages with the regeneration program bypassing the upper limb program. Comparison of regeneration regulatory elements with those found in other regenerative animals identified a core shared set of transcription factors, supporting an ancient, conserved regeneration program.

Cellular senescence promotes progenitor cell expansion during axolotl limb regeneration

Axolotl limb regeneration is accompanied by the transient induction of cellular senescence within the blastema, the structure that nucleates regeneration. The precise role of this blastemal senescent cell (bSC) population, however, remains unknown. Here, through a combination of gain- and loss-of-function assays, we elucidate the functions and molecular features of cellular senescence in vivo. We demonstrate that cellular senescence plays a positive role during axolotl regeneration by creating a pro-proliferative niche that supports progenitor cell expansion and blastema outgrowth. Senescent cells impact their microenvironment via Wnt pathway modulation. Further, we identify a link between Wnt signaling and senescence induction and propose that bSC-derived Wnt signals facilitate the proliferation of neighboring cells in part by preventing their induction into senescence. This work defines the roles of cellular senescence in the regeneration of complex structures.

Conserved enhancers control notochord expression of vertebrate Brachyury

The cell type-specific expression of key transcription factors is central to development and disease. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three conserved Brachyury-controlling notochord enhancers, T3, C, and I, in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, in cis deletion of all three enhancers in mouse abolishes Brachyury/T/Tbxt expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. The three Brachyury-driving notochord enhancers are conserved beyond mammals in the brachyury/tbxtb loci of fishes, dating their origin to the last common ancestor of jawed vertebrates. Our data define the vertebrate enhancers for Brachyury/T/TBXTB notochord expression through an auto-regulatory mechanism that conveys robustness and adaptability as ancient basis for axis development.

Conserved enhancer logic controls the notochord expression of vertebrate Brachyury

The cell type-specific expression of key transcription factors is central to development. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three Brachyury-controlling notochord enhancers T3, C, and I in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, deletion of all three enhancers in mouse abolishes Brachyury/T expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. Sequence and functional conservation of Brachyury-driving notochord enhancers with the brachyury/tbxtb loci from diverse lineages of fishes dates their origin to the last common ancestor of jawed vertebrates. Our data define the enhancers for Brachyury/T/TBXTB notochord expression as ancient mechanism in axis development.

Tig1 regulates proximo-distal identity during salamander limb regeneration

Salamander limb regeneration is an accurate process which gives rise exclusively to the missing structures, irrespective of the amputation level. This suggests that cells in the stump have an awareness of their spatial location, a property termed positional identity. Little is known about how positional identity is encoded, in salamanders or other biological systems. Through single-cell RNAseq analysis, we identified Tig1/Rarres1 as a potential determinant of proximal identity. Tig1 encodes a conserved cell surface molecule, is regulated by retinoic acid and exhibits a graded expression along the proximo-distal axis of the limb. Its overexpression leads to regeneration defects in the distal elements and elicits proximal displacement of blastema cells, while its neutralisation blocks proximo-distal cell surface interactions. Critically, Tig1 reprogrammes distal cells to a proximal identity, upregulating Prod1 and inhibiting Hoxa13 and distal transcriptional networks. Thus, Tig1 is a central cell surface determinant of proximal identity in the salamander limb.

The mechanisms by which cells determine their position within the 3D space are poorly understood. Research in salamanders offers fresh insights into this question, uncovering Tig1 as a central determinant of proximo-distal identity in regeneration.

Postembryonic development and aging of the appendicular skeleton in Ambystoma mexicanum

BACKGROUND

The axolotl is a key model to study appendicular regeneration. The limb complexity resembles that of humans in structure and tissue components; however, axolotl limbs develop postembryonically. In this work, we evaluated the postembryonic development of the appendicular skeleton and its changes with aging.

RESULTS

The juvenile limb skeleton is formed mostly by Sox9/Col1a2 cartilage cells. Ossification of the appendicular skeleton starts when animals reach a length of 10 cm, and cartilage cells are replaced by a primary ossification center, consisting of cortical bone and an adipocyte-filled marrow cavity. Vascularization is associated with the ossification center and the marrow cavity formation. We identified the contribution of Col1a2-descendants to bone and adipocytes. Moreover, ossification progresses with age toward the epiphyses of long bones. Axolotls are neotenic salamanders, and still ossification remains responsive to l-thyroxine, increasing the rate of bone formation.

CONCLUSIONS

In axolotls, bone maturation is a continuous process that extends throughout their life. Ossification of the appendicular bones is slow and continues until the complete element is ossified. The cellular components of the appendicular skeleton change accordingly during ossification, creating a heterogenous landscape in each element. The continuous maturation of the bone is accompanied by a continuous body growth.

A conserved regulatory program initiates lateral plate mesoderm emergence across chordates

Cardiovascular lineages develop together with kidney, smooth muscle, and limb connective tissue progenitors from the lateral plate mesoderm (LPM). How the LPM initially emerges and how its downstream fates are molecularly interconnected remain unknown. Here, we isolate a pan-LPM enhancer in the zebrafish-specific draculin (drl) gene that provides specific LPM reporter activity from early gastrulation. In toto live imaging and lineage tracing of drl-based reporters captures the dynamic LPM emergence as lineage-restricted mesendoderm field. The drl pan-LPM enhancer responds to the transcription factors EomesoderminA, FoxH1, and MixL1 that combined with Smad activity drive LPM emergence. We uncover specific activity of zebrafish-derived drl reporters in LPM-corresponding territories of several chordates including chicken, axolotl, lamprey, Ciona, and amphioxus, revealing a universal upstream LPM program. Altogether, our work provides a mechanistic framework for LPM emergence as defined progenitor field, possibly representing an ancient mesodermal cell state that predates the primordial vertebrate embryo.

Numerous tissues are derived from the lateral plate mesoderm (LPM) but how this is specified is unclear. Here, the authors identify a pan-LPM reporter activity found in the zebrafish draculin (drl) gene that also shows transgenic activity in LPM-corresponding territories of several chordates, including chicken, axolotl, lamprey, Ciona, and amphioxus.

Application and optimization of CRISPR-Cas9-mediated genome engineering in axolotl (Ambystoma mexicanum)

Genomic manipulation is essential to the use of model organisms to understand development, regeneration and adult physiology. The axolotl (Ambystoma mexicanum), a type of salamander, exhibits an unparalleled regenerative capability in a spectrum of complex tissues and organs, and therefore serves as a powerful animal model for dissecting mechanisms of regeneration. We describe here an optimized stepwise protocol to create genetically modified axolotls using the CRISPR-Cas9 system. The protocol, which takes 7-8 weeks to complete, describes generation of targeted gene knockouts and knock-ins and includes site-specific integration of large targeting constructs. The direct use of purified CAS9-NLS (CAS9 containing a C-terminal nuclear localization signal) protein allows the prompt formation of guide RNA (gRNA)-CAS9-NLS ribonucleoprotein (RNP) complexes, which accelerates the creation of double-strand breaks (DSBs) at targeted genomic loci in single-cell-stage axolotl eggs. With this protocol, a substantial number of F0 individuals harboring a homozygous-type frameshift mutation can be obtained, allowing phenotype analysis in this generation. In the presence of targeting constructs, insertions of exogenous genes into targeted axolotl genomic loci can be achieved at efficiencies of up to 15% in a non-homologous end joining (NHEJ) manner. Our protocol bypasses the long generation time of axolotls and allows direct functional analysis in F0 genetically manipulated axolotls. This protocol can be potentially applied to other animal models, especially to organisms with a well-characterized transcriptome but lacking a well-characterized genome.

Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration

Amputation of the axolotl forelimb results in the formation of a blastema, a transient tissue where progenitor cells accumulate prior to limb regeneration. However, the molecular understanding of blastema formation had previously been hampered by the inability to identify and isolate blastema precursor cells in the adult tissue. We have used a combination of Cre-loxP reporter lineage tracking and single-cell messenger RNA sequencing (scRNA-seq) to molecularly track mature connective tissue (CT) cell heterogeneity and its transition to a limb blastema state. We have uncovered a multiphasic molecular program where CT cell types found in the uninjured adult limb revert to a relatively homogenous progenitor state that recapitulates an embryonic limb bud-like phenotype including multipotency within the CT lineage. Together, our data illuminate molecular and cellular reprogramming during complex organ regeneration in a vertebrate.

Author Correction: The axolotl genome and the evolution of key tissue formation regulators

In the originally published version of this Article, the sequenced axolotl strain (the homozygous white mutant) was denoted as 'D/D' rather than 'd/d' in Fig. 1a and the accompanying legend, the main text and the Methods section. The original Article has been corrected online.

Efficient gene knockin in axolotl and its use to test the role of satellite cells in limb regeneration

Salamanders exhibit extensive regenerative capacities and serve as a unique model in regeneration research. However, due to the lack of targeted gene knockin approaches, it has been difficult to label and manipulate some of the cell populations that are crucial for understanding the mechanisms underlying regeneration. Here we have established highly efficient gene knockin approaches in the axolotl (Ambystoma mexicanum) based on the CRISPR/Cas9 technology. Using a homology-independent method, we successfully inserted both the Cherry reporter gene and a larger membrane-tagged Cherry-ERT2-Cre-ERT2 (∼5-kb) cassette into axolotl Sox2 and Pax7 genomic loci. Depending on the size of the DNA fragments for integration, 5-15% of the F0 transgenic axolotl are positive for the transgene. Using these techniques, we have labeled and traced the PAX7-positive satellite cells as a major source contributing to myogenesis during axolotl limb regeneration. Our work brings a key genetic tool to molecular and cellular studies of axolotl regeneration.

Tissue- and time-directed electroporation of CAS9 protein-gRNA complexes in vivo yields efficient multigene knockout for studying gene function in regeneration

A rapid method for temporally and spatially controlled CRISPR-mediated gene knockout in vertebrates will be an important tool to screen for genes involved in complex biological phenomena like regeneration. Here we show that in vivo injection of CAS9 protein-guide RNA (gRNA) complexes into the spinal cord lumen of the axolotl and subsequent electroporation leads to comprehensive knockout of Sox2 gene expression in SOX2⁺ neural stem cells with corresponding functional phenotypes from the gene knockout. This is particularly surprising considering the known prevalence of RNase activity in cerebral spinal fluid, which apparently the CAS9 protein protects against. The penetrance/efficiency of gene knockout in the protein-based system is far higher than corresponding electroporation of plasmid-based CRISPR systems. We further show that simultaneous delivery of CAS9-gRNA complexes directed against Sox2 and GFP yields efficient knockout of both genes in GFP-reporter animals. Finally, we show that this method can also be applied to other tissues such as skin and limb mesenchyme. This efficient delivery method opens up the possibility for rapid in vivo genetic screens during axolotl regeneration and can in principle be applied to other vertebrate tissue systems.

Estimating surface NO2 and SO2 mixing ratios from fast-response total column observations and potential application to geostationary missions

Total-column nitrogen dioxide (NO₂) data collected by a ground-based sun-tracking spectrometer system (Pandora) and an photolytic-converter-based in-situ instrument collocated at NASA's Langley Research Center in Hampton, Virginia were analyzed to study the relationship between total-column and surface NO₂ measurements. The measurements span more than a year and cover all seasons. Surface mixing ratios are estimated via application of a planetary boundary-layer (PBL) height correction factor. This PBL correction factor effectively corrects for boundary-layer variability throughout the day, and accounts for up to ≈75 % of the variability between the NO₂ data sets. Previous studies have made monthly and seasonal comparisons of column/surface data, which has shown generally good agreement over these long average times. In the current analysis comparisons of column densities averaged over 90 s and 1 h are made. Applicability of this technique to sulfur dioxide (SO₂) is briefly explored. The SO₂ correlation is improved by excluding conditions where surface levels are considered background. The analysis is extended to data from the July 2011 DISCOVER-AQ mission over the greater Baltimore, MD area to examine the method's performance in more-polluted urban conditions where NO₂ concentrations are typically much higher.

Germline transgenic methods for tracking cells and testing gene function during regeneration in the axolotl

The salamander is the only tetrapod that regenerates complex body structures throughout life. Deciphering the underlying molecular processes of regeneration is fundamental for regenerative medicine and developmental biology, but the model organism had limited tools for molecular analysis. We describe a comprehensive set of germline transgenic strains in the laboratory-bred salamander Ambystoma mexicanum (axolotl) that open up the cellular and molecular genetic dissection of regeneration. We demonstrate tissue-dependent control of gene expression in nerve, Schwann cells, oligodendrocytes, muscle, epidermis, and cartilage. Furthermore, we demonstrate the use of tamoxifen-induced Cre/loxP-mediated recombination to indelibly mark different cell types. Finally, we inducibly overexpress the cell-cycle inhibitor p16 (INK4a) , which negatively regulates spinal cord regeneration. These tissue-specific germline axolotl lines and tightly inducible Cre drivers and LoxP reporter lines render this classical regeneration model molecularly accessible.

Comparative transcriptional profiling of the axolotl limb identifies a tripartite regeneration-specific gene program

Understanding how the limb blastema is established after the initial wound healing response is an important aspect of regeneration research. Here we performed parallel expression profile time courses of healing lateral wounds versus amputated limbs in axolotl. This comparison between wound healing and regeneration allowed us to identify amputation-specific genes. By clustering the expression profiles of these samples, we could detect three distinguishable phases of gene expression - early wound healing followed by a transition-phase leading to establishment of the limb development program, which correspond to the three phases of limb regeneration that had been defined by morphological criteria. By focusing on the transition-phase, we identified 93 strictly amputation-associated genes many of which are implicated in oxidative-stress response, chromatin modification, epithelial development or limb development. We further classified the genes based on whether they were or were not significantly expressed in the developing limb bud. The specific localization of 53 selected candidates within the blastema was investigated by in situ hybridization. In summary, we identified a set of genes that are expressed specifically during regeneration and are therefore, likely candidates for the regulation of blastema formation.

Connective tissue cells, but not muscle cells, are involved in establishing the proximo-distal outcome of limb regeneration in the axolotl

During salamander limb regeneration, only the structures distal to the amputation plane are regenerated, a property known as the rule of distal transformation. Multiple cell types are involved in limb regeneration; therefore, determining which cell types participate in distal transformation is important for understanding how the proximo-distal outcome of regeneration is achieved. We show that connective tissue-derived blastema cells obey the rule of distal transformation. They also have nuclear MEIS, which can act as an upper arm identity regulator, only upon upper arm amputation. By contrast, myogenic cells do not obey the rule of distal transformation and display nuclear MEIS upon amputation at any proximo-distal level. These results indicate that connective tissue cells, but not myogenic cells, are involved in establishing the proximo-distal outcome of regeneration and are likely to guide muscle patterning. Moreover, we show that, similarly to limb development, muscle patterning in regeneration is influenced by β-catenin signalling.

Neural crest does not contribute to the neck and shoulder in the axolotl (Ambystoma mexicanum)

BACKGROUND

A major step during the evolution of tetrapods was their transition from water to land. This process involved the reduction or complete loss of the dermal bones that made up connections to the skull and a concomitant enlargement of the endochondral shoulder girdle. In the mouse the latter is derived from three separate embryonic sources: lateral plate mesoderm, somites, and neural crest. The neural crest was suggested to sustain the muscle attachments. How this complex composition of the endochondral shoulder girdle arose during evolution and whether it is shared by all tetrapods is unknown. Salamanders that lack dermal bone within their shoulder girdle were of special interest for a possible contribution of the neural crest to the endochondral elements and muscle attachment sites, and we therefore studied them in this context.

RESULTS

We grafted neural crest from GFP+ fluorescent transgenic axolotl (Ambystoma mexicanum) donor embryos into white (d/d) axolotl hosts and followed the presence of neural crest cells within the cartilage of the shoulder girdle and the connective tissue of muscle attachment sites of the neck-shoulder region. Strikingly, neural crest cells did not contribute to any part of the endochondral shoulder girdle or to the connective tissue at muscle attachment sites in axolotl.

CONCLUSIONS

Our results in axolotl suggest that neural crest does not serve a general function in vertebrate shoulder muscle attachment sites as predicted by the "muscle scaffold theory," and that it is not necessary to maintain connectivity of the endochondral shoulder girdle to the skull. Our data support the possibility that the contribution of the neural crest to the endochondral shoulder girdle, which is observed in the mouse, arose de novo in mammals as a developmental basis for their skeletal synapomorphies. This further supports the hypothesis of an increased neural crest diversification during vertebrate evolution.

Gene expression profile of the regeneration epithelium during axolotl limb regeneration

Urodele amphibians are unique among adult vertebrates in their ability to regenerate missing limbs. The process of limb regeneration requires several key tissues including a regeneration-competent wound epidermis called the regeneration epithelium (RE). We used microarray analysis to profile gene expression of the RE in the axolotl, a Mexican salamander. A list of 125 genes and expressed sequence tags (ESTs) showed a ≥1.5-fold expression in the RE than in a wound epidermis covering a lateral cuff wound. A subset of the RE ESTs and genes were further characterized for expression level changes over the time-course of regeneration. This study provides the first large scale identification of specific gene expression in the RE.

Efficient regeneration by activation of neurogenesis in homeostatically quiescent regions of the adult vertebrate brain

In contrast to mammals, salamanders and teleost fishes can efficiently repair the adult brain. It has been hypothesised that constitutively active neurogenic niches are a prerequisite for extensive neuronal regeneration capacity. Here, we show that the highly regenerative salamander, the red spotted newt, displays an unexpectedly similar distribution of active germinal niches with mammals under normal physiological conditions. Proliferation zones in the adult newt brain are restricted to the forebrain, whereas all other regions are essentially quiescent. However, ablation of midbrain dopamine neurons in newts induced ependymoglia cells in the normally quiescent midbrain to proliferate and to undertake full dopamine neuron regeneration. Using oligonucleotide microarrays, we have catalogued a set of differentially expressed genes in these activated ependymoglia cells. This strategy identified hedgehog signalling as a key component of adult dopamine neuron regeneration. These data show that brain regeneration can occur by activation of neurogenesis in quiescent brain regions.

Cognitive evaluation in children and adolescents with Möbius sequence

BACKGROUND

Möbius sequence is a rare condition usually defined as uni- or bilateral congenital facial weakness with impairment of ocular abduction. Mental retardation is estimated to occur in 10-15% of cases, but at present there have been no studies focusing on the intellectual capacities of children and adolescents with Möbius sequence.

METHODS

Twenty-three children and adolescents aged 6-16 years could be recruited following a request of the German Möbius foundation. The primary caregivers of all subjects filled out a special questionnaire to compile personal, somatic and psychosocial history of the probands. All subjects had a physical examination. To assess intellectual capacities, the German version of the Wechsler Intelligence Test-III (WISC-III) was administered. In case of a severe mental retardation, the Vineland Adaptive Behavior Rating Form was used as an alternative.

RESULTS

Twenty-two subjects [12 males, 10 females; mean age: 11.3 (6-16) years] could be included; 21 could be examined with the WISC-III. Compared with the normative sample, Full Scale IQ (mean: 92.05; standard deviation: 14.84) was significantly lower (P = 0.023) which was the consequence of a very low Performance IQ (mean: 80.48; standard deviation: 15.84). Compared with the normative sample, the results of all performance subtests were significantly lower (P = 0.033-0.000), whereas verbal subtest scores did not differ or were even higher ['Similarities' (P = 0.026) and 'Vocabulary' (P = 0.019)]. Verbal IQ (mean: 106.24; standard deviation: 15.31) was not significantly different from the normative sample. Two boys met ICD-10 criteria for mental retardation. Full Scale IQ was not predictive for academic success.

CONCLUSIONS

The WISC-III is not an adequate predictor for academic success in Möbius patients; intelligence tests which are less dependant on time constraints should be preferred for subjects with Möbius sequence.

Axolotl (Ambystoma mexicanum) embryonic transplantation methods

A remarkable feature of axolotls (Ambystoma mexicanum) is their amenability to grafting at any stage of the lifecycle. The large size, slow development, and tensile properties of the axolotl embryo make it particularly easy to transplant different regions of the embryo at the neurula stage. Grafting of green fluorescent protein (GFP)-expressing tissue from a GFP germline transgenic animal to GFP-negative hosts has proven to be a powerful method for tracking cells during development and regeneration. In the following protocol, we describe the transplantation of epidermis, neural fold, presomitic mesoderm, and lateral plate mesoderm to produce specific labeling of limb epidermis, limb Schwann cells, limb muscle, and limb connective tissue, respectively.

The fluoride cleavable 2-(cyanoethoxy)methyl (CEM) group as reversible 3'-O-terminator for DNA sequencing-by-synthesis - synthesis, incorporation, and cleavage

A new and promising sequencing technology called sequencing-by-synthesis (SBS) enables fast determination of DNA sequences. 2'-Deoxynucleotides containing the (2-cyanoethoxy)methyl (CEM) group at the 3'-O-position are potential reversible terminators for the SBS technology. Herein we describe the synthesis, the incorporation by several polymerases, and the cleavage of this 3'-O-blocking group using 3'-O-CEM-thymidinyl-5'-O-triphosphate 7 as an example.

Neurotrophin receptor homolog (NRH1) proteins regulate mesoderm formation and apoptosis during early Xenopus development

Recent experiments suggest that Xenopus Neurotrophin Receptor Homolog 1 (NRH1) proteins act through the planar cell polarity pathway to regulate convergent extension movements during gastrulation and neurulation. We show in this paper that NRH1 proteins are also required for the proper expression of mesodermally expressed genes such as Xbra and Chordin, and to a lesser extent, of Xwnt11. Loss of NRH1 function is followed, during gastrula and neurula stages, by a dramatic increase in apoptosis. Apoptosis is delayed by injection of Xbra RNA, suggesting that cell death is a consequence, at least in part, of the down-regulation of this gene, and it is also delayed by expression of activated forms of Rho, Rac and Cdc42. These small GTPases have previously been implicated in the planar cell polarity pathway in Xenopus and, in other systems, in the regulation of apoptosis. We conclude that the effects of NRH1 proteins include the regulation of mesodermal gene expression and that the disruption of gastrulation that is caused by their loss of function is a consequence of the down-regulation of Xbra and other genes, in addition to direct interference with the planar cell polarity pathway. The apoptosis observed in embryos lacking NRH1 function is not an indirect consequence of the disruption of gastrulation, and indeed it may contribute to the observed morphological defects.

Identification and characterisation of the posteriorly-expressed Xenopus neurotrophin receptor homolog genes fullback and fullback-like

We have identified fullback and fullback-like, two Xenopus laevis neurotrophin receptor homolog (NRH1) genes. The sequences of Fullback and Fullback-like are very similar to that of the neurotrophin receptor p75NTR, in both their extracellular and their intracellular domains. As their names imply, fullback and fullback-like are expressed in essentially identical patterns in the posterior of the embryo from the early gastrula stage onward. At tailbud and tadpole stages transcripts are also present in dorsal somites and the head, in addition to the growing tailbud. This expression pattern differs from that of p75NTR, suggesting that fullback and fullback-like have different functions from p75NTR during early development.

Description and dosimetric verification of the PEREGRINE Monte Carlo dose calculation system for photon beams incident on a water phantom

PEREGRINE is a three-dimensional Monte Carlo dose calculation system written specifically for radiotherapy. This paper describes the implementation and overall dosimetric accuracy of PEREGRINE physics algorithms, beam model, and beam commissioning procedure. Particle-interaction data, tracking geometries, scoring, variance reduction, and statistical analysis are described. The BEAM code system is used to model the treatment-independent accelerator head, resulting in the identification of primary and scattered photon sources and an electron contaminant source. The magnitude of the electron source is increased to improve agreement with measurements in the buildup region in the largest fields. Published measurements provide an estimate of backscatter on monitor chamber response. Commissioning consists of selecting the electron beam energy, determining the scale factor that defines dose per monitor unit, and describing treatment-dependent beam modifiers. We compare calculations with measurements in a water phantom for open fields, wedges, blocks, and a multileaf collimator for 6 and 18 MV Varian Clinac 2100C photon beams. All calculations are reported as dose per monitor unit. Aside from backscatter estimates, no additional, field-specific normalization is included in comparisons with measurements. Maximum discrepancies were less than either 2% of the maximum dose or 1.2 mm in isodose position for all field sizes and beam modifiers.

Spatial representations of virtual mazes: the role of visual fidelity and individual differences

Twenty-four people learned three versions of a room-sized maze: a wire-frame desktop virtual environment (VE), a normal surface-rendered desktop VE, and a real-world maze. Differences among the mental representations formed from each environment were measured with pointing and distance estimation tasks in a real-world version of each maze. People were more accurate at pointing after having learned the real and wire-frame VE maze than the surface-rendered VE maze; however, this effect was small compared with the effect of individual differences. Differences in gender, spatial ability, and prior computer experience were significantly related to the ability to acquire spatial information from the desktop VE. There was a high correlation between spatial knowledge when it was measured in the VE and spatial knowledge measured in the real world. Actual or potential applications include the design of effective VE training systems.

"True" color surface anatomy: mapping the Visible Human to patient-specific CT data

The mapping of "true" color and texture information into traditional medical imaging modality data can add considerable information and aid in diagnostics. One of the goals of this work has been to create CT color lookup tables for all visually well-defined structures in the Visible Human male cryosection data set which then can be used to color patient-specific CT data. The primary goal has been to develop a method for stripping textures from a volumetric data set for polygonal models and non-uniform rational B-spline (NURBS) models generated from a volumetric data set. It is believed that these methods can eventually be used to provide clinicians with 3D models with physiologically accurate color textures.

Subcellular immunolocalization of protein kinase CK2 in normal and carcinoma cells

CK2 is a messenger-independent protein serine/threonine kinase that has been implicated in cell growth and proliferation. Our recent analysis of squamous cell carcinomas of the head and neck (SCCHN) revealed a significant elevation in CK2 activity in these tumor cells relative to normal mucosa of the upper aerodigestive tract and suggested a correlation with aggressive tumor behavior and poor clinical outcome. In order to further define the distribution of CK2 in these tissues, we have examined the immunohistochemical staining pattern of surgical specimens of both SCCHN tumors and normal upper aerodigestive tract mucosa using a monoclonal antibody directed against the catalytic subunit CK2-alpha of the kinase, and have compared these data with the subcellular distribution of CK2 activity in these same tissues. These measurements showed that CK2 is predominantly localized to the nuclei of the tumor cells, which agreed closely with the immunohistochemical staining pattern of CK2-alpha in tumor cells. The chiefly nuclear distribution of CK2-alpha immunostaining found consistently in SCCHN tumor cells and tumor-infiltrating lymphocytes contrasted with a relatively more predominant cytosolic staining pattern exhibited by various cellular constituents of normal oropharyngeal mucosa. The immunostaining pattern of CK2-alpha revealed that staining was observed in the cells stained for the proliferation-marker Ki-67; however, strong distinct immunostaining for CK2-alpha was also observed in large numbers of other cells in these same tumors, suggesting that CK2 elevation in these tumors is not a reflection of proliferative activity alone, but may also relate to the pathobiological behavior of the tumor.

Comparison of the characteristics and features of pressure garments used in the management of burn scars

Two companies provide custom-made pressure garments to clients with burn scars at Westmead Hospital. This prospective study was completed in order to make objective decisions about which garments were most appropriate and cost effective to provide to clients. Issues such as cost, durability, fit and client preferences were investigated. Data were collected from 43 clients; at the time of initial fitting, at a follow-up appointment 4-6 weeks later, and at the time one of the garments required replacement. One Second Skin and one Jobst garment were provided to each client and the garments were compared using therapists' evaluation and clients' perspectives on a number of variables. Second Skin garments had significantly more favourable results on the variables of time for delivery, fit at follow-up, garment design, quality of fabric and seams, overall satisfaction and garment preference for ongoing wear. On all other variables there was no significant difference between the garments. Second Skin provided the most optimal and appropriate option for pressure garments in the management of burn scars for our clients.

[Rupture of the pectoralis major muscle--case study and review of the literature]

Rupture of the pectoralis major muscle is a rare injury. In total 125 cases of complete and uncomplete ruptures are reported. This injury is the result of excessive muscle tension, a direct blow or a combination of both. In a case study the aetiology, diagnostic, treatment and functional outcome of complete muscle ruptures are shown. The reported results of 14 cases who underwent conservative and 51 cases with surgical treatment were classified and analysed. Conservative management is recommended for partial and proximal ruptures. Distal ruptures of the musculo-tendinous or tendinous insertion in active patients should be treated surgically to return previous muscle strength and contour.

Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs

In eukaryotic cells, firing of DNA replication origins normally does not recur until after M phase. This characteristic is thought to be due to the properties of "initiation" proteins like Orc, Cdc6, and Mcms. Using formaldehyde cross-linking, we show that Cdc6p and Mcm7p associate specifically with replication origins during G1 but not during G2 in S. cerevisiae. Mcm7p's association with origins depends on Cdc6p. Ectopic expression of Cdc6p enables it to associate with origins during G2, but this fails to recruit Mcm7p. Our data suggest that the loading of Mcm proteins onto origins is regulated by two mechanisms: first, by Cdc6p occupancy, and second, by S- and M-CDKs, whose activity during S, G2, and M phases prevents Mcm loading.

Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis

BACKGROUND

During the cell cycle, cells progress through four distinct phases, G1, S, G2 and M; transcriptional controls play an important role at the transition between these phases. MCB-binding factor (MBF), a transcription factor from budding yeast, binds to the so-called MCB (MluI cell-cycle box) elements found in the promoters of many DNA synthesis genes, and activates the transcription of those at the G1-->S phase transition. MBF is comprised of two proteins, Mbp1 and Swi6.

RESULTS

The three-dimensional structure of the N-terminal DNA-binding domain of Mbp1 has been determined by multiwavelength anomalous diffraction from crystals of the selenomethionyl variant of the protein. The structure is composed of a six-stranded beta sheet interspersed with two pairs of alpha helices. The most conserved core region among Mbp1-related transcription factors folds into a central helix-turn-helix motif with a short N-terminal beta strand and a C-terminal beta hairpin.

CONCLUSIONS

Despite little sequence similarity, the structure within the core region of the Mbp1 N-terminal domain exhibits a similar fold to that of the DNA-binding domains of other proteins, such as hepatocyte nuclear factor-3gamma and histone H5 from eukaryotes, and the prokaryotic catabolite gene activator. However, the structure outside the core region defines Mbp1 as a larger entity with substructures that stabilize and display the helix-turn-helix motif.

Specimen adequacy of ThinPrep sample preparations in a direct-to-vial study

OBJECTIVE

To assess specimen adequacy of the ThinPrep slide preparation method in routine use.

STUDY DESIGN

Two studies, a feasibility study of 299 women and a clinical study of 499 women, were conducted. A broom-type collection device was used and rinsed directly into Pre-servCyt vials. Slides were prepared with the ThinPrep 2000 device, screened and classified according to the Bethesda System. The proportion of ThinPrep slides described as "Satisfactory But Limited By: No Endocervical Component (SBLB:No ECC)" was then compared to the proportion of SBLB: No ECC slides found on conventional smears in a previously conducted clinical trial of over 7,000 patients.

RESULTS

For the feasibility study the proportion of ThinPrep slides described as SBLB: No ECC was 9.36% as compared to the clinical trial combined rate of 9.4% for conventional smears. For the clinical study, 4.96% of ThinPrep slides were SBLB:No ECC as compared to the 4.4% SBLB:No ECC rate for conventional smears from the same clinical trial. The proportions were statistically equivalent for both studies.

CONCLUSION

It is expected that the rate of representing endocervical component will be maintained when the ThinPrep preparation method is used routinely in place of the conventional cytologic smear method.

Patient specific color texture mapping of CT-based anatomical surface models utilizing cryosection data

In traditional medical imaging modalities, color and texture information can add considerable information for diagnostics. Presently, multimodal images of a patient are unregistered and referenced independent of each other, or registered and fused into a single hybrid volume. Doctors and other medical professionals need to be able to visualize and interrogate, on a per-patient basis, a wide variety of 2D and 3D data representations that can be created from non-invasive imaging modalities, such as MRI and CT. In addition, any colorization that may be applied to the image data is strictly based on tissue density, radiation emission, or magnetic signature, and not on any physiological foundation. In order for "true-to-life" color information to be incorporated with non-invasive imaging techniques, and for it to be of consistent quality across the entire body, a single whole-body cryosection specimen with associated medical image data is needed. The National Library of Medicine's Visible Human Project offers just such a specimen. Using the full-body medical image data along with the cryosection images of the Visible Human subject, a set of color lookup tables for all visually well defined structures and organs can be created. As a result, patient-specific colorization based on real tissue color and characteristics can be incorporated into traditional intensity-based imaging modalities. The primary goal of this work has been to create CT color lookup tables for all visually well-defined structures in the Visible Human male cryosection data set. The subsequent goal has been to develop a method for stripping textures from a volumetric data set for polygonal models and non-uniform rational B-spline (NURBS) models, also generated from the volumetric data.

The transcription factor Swi5 regulates expression of the cyclin kinase inhibitor p40SIC1

DNA replication in budding yeast cells depends on the activation of the Cdc28 kinase (Cdk1 of Saccharomyces cerevisiae) associated with B-type cyclins Clb1 to Clb6. Activation of the kinase depends on proteolysis of the Cdk inhibitor p40SIC1 in late G1, which is mediated by the ubiquitin-conjugating enzyme Cdc34 and two other proteins, Cdc4 and Cdc53. Inactivation of any one of these three proteins prevents p40SIC1 degradation and causes cells to arrest in G1 with active Cln kinases but no Clb-associated Cdc28 kinase activity. Deletion of SIC1 allows these mutants to replicate. p40SIC1 disappears at the G1/S transition and reappears only after nuclear division. Cell cycle-regulated proteolysis seems largely responsible for this pattern, but transcriptional control could also contribute; SIC1 RNA accumulates to high levels as cells exit M phase. To identify additional factors necessary for the inhibition of the Cdk1/Cdc28 kinase in G1, we isolated mutants that can replicate DNA in the absence of Cdc4 function. Mutations in three loci (SIC1, SWI5, and RIC3) were identified. We have shown that high SIC1 transcript levels at late M phase depend on Swi5. Swi5 accumulates in the cytoplasm during S, G2, and M phases of the cell cycle but enters the nuclei at late anaphase. Our data suggest that cell cycle-regulated nuclear accumulation of Swi5 is responsible for the burst of SIC1 transcription at the end of anaphase. This transcriptional control may be important for inactivation of the Clb/Cdk1 kinase in G2/M transition and during the subsequent G1 period.

Immunohistochemical staining for markers of future neoplastic progression in the larynx

We performed a retrospective, longitudinal study to determine whether abnormalities in immunohistochemical staining for the epidermal growth factor receptor (EGFR), p53, or cyclin D1 occur before the development of laryngeal carcinoma. Staining was performed on 63 paraffin-embedded biopsies from 18 patients who subsequently developed carcinoma in situ (CIS) or invasive carcinoma of the larynx. These were compared to 71 biopsies from 20 patients who did not develop CIS/cancer (minimum follow-up period, 4 years). Also studied were the 34 biopsies containing CIS and/or carcinoma from those patients who progressed and 22 biopsies obtained concurrently. The two patient groups did not differ significantly in terms of tobacco and alcohol use. Distinct patterns of staining correlated with malignant progression. These included EGFR staining of two thirds or more of the epithelium thickness, a linear basal p53 staining pattern, and strong (3+) staining for cyclin D1 (P < 0.01 for each). These staining patterns also correlated with increasing atypia. In our study population, linear basal staining for p53 and strong staining for cyclin D1 had higher specificity for progression than did EGFR overexpression, which was also seen in association with inflammation and chronic irritation. Marked site-to-site variation was seen in the immunohistochemical staining and in the degree of atypia, suggesting that multiple biopsies are necessary to properly assess risk. These immunohistochemical staining patterns may be clinically useful to predict patients at risk for neoplastic progression.

Vergleich einer standardisierten Ernährungslösung (ZPE-Glukose/Elektrolyte^®) mit einer üblichen Ernährung im Intensivbereich

<i>Ziel:</i> Vergleich einer standardisierten Ernährungslösung mit einer selbst-gemischten Infusionstherapie bei Intensivpatienten einer chirurgischen Intensivstation; Untersuchung der standardisierten Ernährungstherapie auf Praktikabilität und Effizienz. <i>Design:</i> Prospektive randomisierte Studie. <i>Rahmen:</i> Chirurgisch-traumatologische Intensivstation einer Universitätsklinik. <i>Patienten:</i> Chirurgisch-traumatologische Patienten, die länger als 6 Tage auf der Intensivstation lagen. <i>Interventionen:</i> Gabe einer standardisierten Ernährungslösung im Ein-Liter-System (ZPE-GE) bzw. Gabe einer herkömmlichen, selbstgemischten Infusionslösung (hER). Bestim-mung von Stoffwechselparametern und Serum- bzw. Harnelektrolyten, zusätzlich Bestimmung von Blut- und Harnglukose, Harnstoffproduktionsrate, Triglyzeriden. <i>Ergebnisse:</i> Die beiden Patientengruppen waren sowohl in ihren physiologischen Daten als auch in der Schwere der Erkrankung miteinander vergleichbar, Komplikationen und Unverträglichkeiten konnten unter den angegebenen Regimen nicht beobachtet werden. Die Energie- (durchschnittlich 1202 kcal/Tag in der Gruppe hER versus 1331 kcal/Tag in der Gruppe ZPE-GE) und Substratzufuhren (Glukose: 228 versus 252 g/Tag; Aminosäuren: 56 versus 64 g/Tag) sind als ausge-glichen zu betrachten, es konnten keine Stoffwechselentgleisungen beobachtet werden. Die Elektrolytzufuhr (Natrium: 56 mmol/Tag in der Gruppe hER versus 92 mmol/Tag in der Gruppe ZPE-GE; Kalium: 65 versus 68 mmol/Tag; Phosphat: 15 versus 19 mmol/Tag) scheint in der Vollperiode nicht ganz optimal zu sein. <i>Schlussfolgerungen:</i> Die standardisierte Lösung scheint gegenüber den herkömmlichen Mischungen Vorteile zu haben: Sie erleichtert das Handling im Intensiv- und Postoperativbereich und verbessert Genauigkeit, Zeitersparnis und hygienische Bedingungen beim Umgang mit diesen Lösungen. Eine Infusionsmenge von 2000 ml (300 g Glukose und 100 g Aminosäuren) dieser Lösung erscheint als ausreichend, bei höherer Zufuhr könnte die Kohlenhydrat- und Aminosäurenzufuhr zu hoch liegen. Auch bei der Elektrolytzufuhr ist eine Begrenzung auf 2000 ml (120 mmol Natrium) angezeigt. Der Natriumanteil könnte auf 50 mmol/l reduziert werden, um ein entsprechendes Natriumloading zu verhindern, bei der Phosphatzufuhr ware eine Erhöhung auf 12 mmol/l empfehlenswert. Die Lösung kann zur standardisierten parenteralen Ernährung bei einem Großteil (ca. 80%) der postoperativen und posttraumatischen Patienten herangezogen werden, nur bei Extremsituationen müssen weiterhin die Einzelkomponenten (Glukose, Aminosäuren, Fette und Elektrolyte) speziell zusammengemischt werden, um metabolische Komplikationen zu verhindern.