Synchrotron imaging and diffraction to investigate internal features of stable tearing fracture phenomenon in metallic specimens.

In situ synchrotron imaging and diffraction on beamline 1-ID-C at the Advanced Photon Source (APS) has been used to investigate the internal features present during the stable tearing fracture phenomenon in low-constraint metallic specimens. The results that are obtained from this investigation show that the internal features are identifiable with these techniques, and this initial investigation lays the groundwork for future, more in-depth investigations with some improvements to the methods.

Bioinformatic prediction of ultraviolet light mutagenesis sensitivity of human genes and a method for genetically engineering UVB resistance.

Living on earth, we are exposed to ultraviolet (UV) light as part of the solar radiation. UVB spectrum light exposure contributes to the development of skin cancer by interacting with pyrimidine pairs to create lesions called cyclobutane pyrimidine dimers. If these lesions are not removed by nucleotide excision repair, they often give rise to C to T transition mutations. Based on these observations, a bioinformatics approach was used to predict the vulnerability of human protein coding genes to UVB induced loss of function mutations. This data was used to evaluate in depth those genes associated with malignant melanoma. In addition, we demonstrate a method of genetically engineering genes that significantly improves resistance to UVB loss of function mutations.

Effect of a collateral ligament sparing surgical approach on mechanical properties of equine proximal interphalangeal joint arthrodesis constructs.

OBJECTIVE: To (1) compare the effect of a collateral ligament sparing surgical approach with an open surgical approach on mechanical properties of proximal interphalangeal joint (PIPJ) arthrodesis, and (2) to determine the percentage of articular cartilage surface removed by transarticular (TA) drilling with different diameter drill bits. STUDY DESIGN: Randomized paired limb design. SAMPLE POPULATION: Cadaveric equine limbs (n=76). METHODS: Cadaveric PIPJ were drilled using a 3.5, 4.5, or 5.5 mm drill bit at 80-84° to the dorsal plane to remove articular cartilage and subchondral bone from the distal articular surface of the proximal phalanx (P1) and the proximal articular surface of the middle phalanx (P2). Bone ends were photographed and the percentage of the projected surface area that was denuded of cartilage was measured. PIPJ arthrodesis constructs (3-hole dynamic compression plate [DCP], two 5.5 mm TA screws inserted in lag fashion, medial and lateral to the DCP; DCP-TA) were created using 2 surgical approaches in paired limbs. A conventional open approach was used in 1 limb and a collateral ligament sparing approach used in the other limb. Constructs were tested to failure in single-cycle 3-point dorsopalmar/plantar or lateromedial bending. Maximum load, yield load, and composite stiffness were compared between techniques. RESULTS: The 3.5, 4.5, and 5.5 mm drill bits removed 24±4%, 35±5%, and 45±7% of total PIPJ articular cartilage surface, respectively. Constructs with the collateral ligament sparing approach had significantly greater mean yield load (11.3±2.8 versus 7.68±1.1 kN, P=.008) and mean maximum load (13.5±3.1 versus 10.1±1.94 kN, P=.02) under lateromedial bending. Under dorsopalmar/plantar bending there was no significant difference between surgical approaches. The collateral ligament sparing arthrodesis technique had a shorter surgical time (19±3 minutes) compared with the open technique (31±3 minutes). CONCLUSION: A collateral ligament sparing surgical approach to the PIPJ with removal of articular cartilage by TA drilling and arthrodesis by DCP-TA was faster and stronger in mediolateral bending than arthrodesis constructs created with an open surgical approach. CLINICAL RELEVANCE: Preservation of the collateral ligaments and TA drilling for cartilage removal during PIPJ arthrodesis may be a superior approach to the conventional open approach and warrants clinical evaluation.

Bioinformatic identification of plant peptides.

Plant peptides play a number of important roles in defence, development and many other aspects of plant physiology. Identifying additional peptide sequences provides the starting point to investigate their function using molecular, genetic or biochemical techniques. Due to their small size, identifying peptide sequences may not succeed using the default bioinformatic approaches that work well for average-sized proteins. There are two general scenarios related to bioinformatic identification of peptides to be discussed in this paper. In the first scenario, one already has the sequence of a plant peptide and is trying to find more plant peptides with some sequence similarity to the starting peptide. To do this, the Basic Local Alignment Search Tool (BLAST) is employed, with the parameters adjusted to be more favourable for identifying potential peptide matches. A second scenario involves trying to identify plant peptides without using sequence similarity searches to known plant peptides. In this approach, features such as protein size and the presence of a cleavable amino-terminal signal peptide are used to screen annotated proteins. A variation of this method can be used to screen for unannotated peptides from genomic sequences. Bioinformatic resources related to Arabidopsis thaliana will be used to illustrate these approaches.

The Arabidopsis unannotated secreted peptide database, a resource for plant peptidomics.

In the era of genomics, if a gene is not annotated, it is not investigated. Due to their small size, genes encoding peptides are often missed in genome annotations. Secreted peptides are important regulators of plant growth, development, and physiology. Identification of additional peptide signals by sequence homology searches has had limited success due to sequence heterogeneity. A bioinformatics approach was taken to find unannotated Arabidopsis (Arabidopsis thaliana) peptides. Arabidopsis chromosome sequences were searched for all open reading frames (ORFs) encoding peptides and small proteins between 25 and 250 amino acids in length. The translated ORFs were then sequentially queried for the presence of an amino-terminal cleavable signal peptide, the absence of transmembrane domains, and the absence of endoplasmic reticulum lumenal retention sequences. Next, the ORFs were filtered against the The Arabidopsis Information Resource 6.0 annotated Arabidopsis genes to remove those ORFs overlapping known genes. The remaining 33,809 ORFs were placed in a relational database to which additional annotation data were deposited. Genome-wide tiling array data were compared with the coordinates of the ORFs, supporting the possibility that many of the ORFs may be expressed. In addition, clustering and sequence similarity analyses revealed that many of the putative peptides are in gene families and/or appear to be present in the rice (Oryza sativa) genome. A subset of the ORFs was evaluated by reverse transcription-PCR and, for one-fifth of those, expression was detected. These results support the idea that the number and diversity of plant peptides is broader than currently assumed. The peptides identified and their annotation data may be viewed or downloaded through a searchable Web interface at peptidome.missouri.edu.

A petal breakstrength meter for Arabidopsis abscission studies.

BACKGROUND: Abscission is the regulated dropping of plant organs, such as leaves or flower petals. This process involves a break down of the cell wall between layers of cells in the abscission zone, causing the organ to become detached. The model plant Arabidopsis thaliana undergoes floral organ abscission. Various experimental methods have been used to study Arabidopsis floral organ abscission, including measuring the petal breakstrength, or the amount of force required to pull a petal from the receptacle. Petal breakstrength provides a quantitative insight into the physical integrity of the petal abscission zone. RESULTS: We developed a petal breakstrength meter that allows rapid data acquisition on a personal computer. We present the design of the device and show its utility in measuring Arabidopsis petal breakstrength for abscission studies. CONCLUSION: This petal breakstrength meter should enable researchers to perform the petal breakstrength assay as a routine part of the characterization of environmental and genetic factors affecting abscission.

A "bottom-counting" video system for measuring cocaine-induced behaviors in Drosophila.

Cocaine exposure elicits a set of stereotypic behaviors in Drosophila that are strikingly similar to the cocaine-induced behaviors observed in vertebrates. This provides a valuable model for the study of cocaine abuse and has led to the discovery of a connection between the cocaine response pathway and the circadian system. This article describes a simplified assessment of cocaine-induced behavior combined with an image acquisition system, which allows the assay to be semiautomated. With this new system, cocaine response can be evaluated in a fraction of the time required by the previous assay, and subjectivity in scoring is reduced dramatically.

A novel method of cocaine delivery to fruit flies using a graphic arts airbrush.

The fruit fly Drosophila melanogaster is a model system for studying pathways regulating responses to cocaine. We describe a new method for delivering cocaine to Drosophila. Freebase cocaine dissolved in ethanol is sprayed onto cold-anaesthetized flies using a graphic arts airbrush modified to reproducibly control the drug dosage. Cocaine dose response curves were generated to characterize the behavioral responses of flies using the airbrush method or the established cocaine smoke method of drug delivery. The stereotypic responses observed with the airbrush showed a dose-dependent increase and were qualitatively similar to those elicited by cocaine smoke. The variation in behaviors of flies dosed with the airbrush was smaller than that of the smoke-dosed flies, indicating that the airbrush method gives better reproducibility. Since flies are exposed to alcohol as well as cocaine in the airbrush behavioral paradigm, it was important to control for possible effects of ethanol. Control experiments indicated that none of the stereotypies elicited with cocaine were caused by vehicle alone and very little ethanol remains in the flies following this protocol. The utility of the airbrush method was demonstrated by its use in a pilot genetic screen that identified a cocaine resistant mutant.

DVL, a novel class of small polypeptides: overexpression alters Arabidopsis development.

Small polypeptides can act as important regulatory molecules that coordinate cellular responses required for differentiation, growth, and development. In a gain-of-function genetic screen for genes that influence fruit development in Arabidopsis, we identified a novel gene -DEVIL1 (DVL1) - encoding a small protein. Overexpression of DVL1 results in pleiotropic phenotypes featured by shortened stature, rounder rosette leaves, clustered inflorescences, shortened pedicles, and siliques with pronged tips. cDNA analysis indicates that DVL1 has a 153-nucleotide (nt) open-reading frame (ORF) encoding a 51-amino acid polypeptide that shares no significant similarity to previously identified proteins. Sequence alignment shows that DVL1 belongs to a family of related genes that are limited to angiosperm plants. Ectopic overexpression of each of the five closely related Arabidopsis DVL genes causes similar phenotypic changes, suggesting overlapping function in the DVL gene family. Point mutations of conserved amino acids in the C-terminal region of the DVL1 polypeptide reveal that these conserved residues are required for DVL1-overexpression phenotypes. Our results show that the DVL family is a novel class of small polypeptides and the overexpression phenotypes suggest that these polypeptides may have a role in plant development.

BAK1, an Arabidopsis LRR receptor-like protein kinase, interacts with BRI1 and modulates brassinosteroid signaling.

Brassinosteroids regulate plant growth and development through a protein complex that includes the leucine-rich repeat receptor-like protein kinase (LRR-RLK) brassinosteroid-insensitive 1 (BRI1). Activation tagging was used to identify a dominant genetic suppressor of bri1, bak1-1D (bri1-associated receptor kinase 1-1Dominant), which encodes an LRR-RLK, distinct from BRI1. Overexpression of BAK1 results in elongated organ phenotypes, while a null allele of BAK1 displays a semidwarfed phenotype and has reduced sensitivity to brassinosteroids (BRs). BAK1 is a serine/threonine protein kinase, and BRI1 and BAK1 interact in vitro and in vivo. Expression of a dominant-negative mutant allele of BAK1 causes a severe dwarf phenotype, resembling the phenotype of null bri1 alleles. These results indicate BAK1 is a component of BR signaling.

Receptor serine/threonine protein kinases in signalling: analysis of the erecta receptor-like kinase of Arabidopsis thaliana.

The Arabidopsis ERECTA (ER) gene regulates elongation of above-ground organs. ER encodes a member of the leucine-rich repeats-receptor-like protein kinases (LRR-RLK) gene family, with the predicted protein containing a signal peptide, 20 leucine-rich repeats in the extracellular domain, a transmembrane domain, and a cytoplasmic serine/threonine protein kinase domain. The structural features of the predicted ER protein suggest its role in cell-cell signalling is through phosphorylating serine/threonine residues. Consistent with this hypothesis, in vitro protein kinase analysis indicates that ER is a functional serine/threonine protein kinase. Furthermore, a large-scale genetic screen was conducted to analyse new mutations in the erecta gene; 16 new er alleles were isolated, all of which were recessive. Here we present the identification of molecular lesions of seven alleles of er, which suggests the hypothesis that ERECTA might employ a mode of action distinct from other RLKs such as Xa21 or CLAVATA1, which function in disease resistance and developmental pathways, respectively.