Wireless Sensor Networks for monitoring underwater sediment transport.

Monitoring of the coastline and coastal processes, in particular sediment movement, is vital to ensure that erosion response is appropriate given the dynamic nature of coastal systems. This should take place regularly over long periods and it is important that data are collected from submerged portions of the littoral zone, as well as the visible beach. This highlights two limitations in existing coastal monitoring techniques: 1. they require largely manual operation and 2. are limited to the visible beach, which results in an incomplete picture of what is happening in the coastal zone. Due to the current difficulties in gathering data beneath the sea surface, this paper reviews wireless sensor network (WSN) technology as a means to overcome these limitations. Analysis showed that WSNs are a promising technology for coastal monitoring, not only in terms of overcoming limitations, but also in terms of cost, safety, and the size of areas they are able to monitor. Previous work using WSNs in this environment is somewhat limited, especially as most current methods are largely limited to the visible beach, and do not consider submerged areas of the coastal zone. From consideration of the physical environment, geological and geographical processes, and informed by advances in technology, research gaps are identified, discussed and evaluated to provide strategies for implementation of WSNs to monitor sediment transport.

Simulation of TTT Curves for Additively Manufactured Inconel 625.

The ability to use common computational thermodynamic and kinetic tools to study the microstructure evolution in Inconel 625 (IN625) manufactured using the additive manufacturing (AM) technique of laser powder-bed fusion is evaluated. Solidification simulations indicate that laser melting and re-melting during printing produce highly segregated interdendritic regions. Precipitation simulations for different degrees of segregation show that the larger the segregation, i.e., the richer the interdendritic regions are in Nb and Mo, the faster the δ-phase (Ni3Nb) precipitation. This is in accordance with the accelerated d precipitation observed experimentally during post-build heat treatments of AM IN625 compared to wrought IN625. The δ-phase may be undesirable since it can lead to detrimental effects on the mechanical properties. The results are presented in the form of a TTT diagram and agreement between the simulated diagram and the experimental TTT diagram demonstrate how these computational tools can be used to guide and optimize post-build treatments of AM materials.

The Influence of Annealing Temperature and Time on the Formation of δ-Phase in Additively-Manufactured Inconel 625.

This research evaluated the kinetics of δ-phase growth in laser powder bed additively-manufactured (AM) Inconel 625 during post-build stress-relief heat treatments. The temperatures ranged between 650°C and 1050°C, and the times from 0.25 to 168 hours. The presence of δ-phase was verified for each temperature/time combination through multiple techniques. A conventional time-temperature-transformation diagram was constructed from the time-temperature data. Comparison to the growth in wrought IN625 with a similar nominal composition revealed that δ-phase formation occurred at least two orders of magnitude faster in the AM IN625. The results of this study also revealed that the segregated microstructure in the as-built condition has a strong influence on the kinetics of δ-phase formation in AM IN625 as compared to a homogenized material. Since control of the δ-phase growth is essential for reliable prediction of the performance of IN625 components in service, avoiding heat treatments that promote the formation of δ-phase in AM components that are not homogenized is highly recommended. This will be particularly true at elevated temperatures where the microstructural stability and the consistency of mechanical properties are more likely to be affected by the presence of δ-phase.

Valence-bond crystalline order in the s = 1/2 J1-J2 model on the honeycomb lattice.

Using the coupled cluster method we study the phase diagram of the spin-1/2 Heisenberg antiferromagnet on a honeycomb lattice with nearest-neighbour exchange coupling J1 > 0 and frustrating next-nearest-neighbour coupling J2 ≡ xJ1 > 0. In the range 0 < x < 1 we find four phases exhibiting respectively Néel, 6-spin plaquette, staggered dimer and Néel-II orderings, with quantum critical points at xc1 ≈ 0.207(3), xc2 ≈ 0.385(10) and xc3 ≈ 0.65(5). The transitions at xc1 and xc3 appear to be continuous (and hence deconfined) ones, while that at xc2 appears to be a direct first-order one.

The frustrated Heisenberg antiferromagnet on the honeycomb lattice: J1-J2 model.

We study the ground-state phase diagram of the frustrated spin-[Formula: see text] antiferromagnet with J(2) = xJ(1) > 0 (J(1) > 0) on the honeycomb lattice, using the coupled-cluster method. We present results for the ground-state energy, magnetic order parameter and plaquette valence-bond crystal (PVBC) susceptibility. We find a paramagnetic PVBC phase for x(c(1)) < x < x(c(2)), where x(c(1)) ≈ 0.207 ± 0.003 and x(c(2)) ≈ 0.385 ± 0.010. The transition at x(c(1)) to the Néel phase seems to be a continuous deconfined transition (although we cannot exclude a very narrow intermediate phase in the range 0.21 ≲ x ≲ 0.24), while that at x(c(2)) is of first-order type to another quasiclassical antiferromagnetic phase that occurs in the classical version of the model only at the isolated and highly degenerate critical point [Formula: see text]. The spiral phases that are present classically for all values x > 1/6 are absent for all x ≲ 1.

A virus-like agent associated with neurofibromatosis in damselfish.

Damselfish neurofibromatosis (DNF) is a transmissible disease involving neurofibromas and chromatophoromas affecting bicolor damselfish Stegastes partitus on Florida reefs. Analysis of genomic DNA by Southern blotting techniques demonstrated the presence of a group of extrachromosomal DNAs in tumors from fish affected with DNF but not in healthy individuals. Cell lines obtained from tumors contained identical DNAs and were shown to be tumorigenic in vivo, while lines established from healthy fish did not contain such DNA and were not tumorigenic. These DNA patterns were also observed in experimentally induced tumors. A DNase resistant component of this DNA was isolated from both tumor cells and conditioned media of tumor cell lines suggesting that these sequences were encapsulated in viral particles. These data support the hypothesis that one or more of these extrachromosomal DNA forms is the genome of an unusual virus and that this virus is the etiologic agent of DNF. We have tentatively termed this agent the damselfish virus-like agent (DVLA).

A dominant repression domain in Tbx3 mediates transcriptional repression and cell immortalization: relevance to mutations in Tbx3 that cause ulnar-mammary syndrome.

Mutations in Tbx3 are responsible for ulnar-mammary syndrome (UMS), an autosomal dominant disorder affecting limb, tooth, hair, apocrine gland and genital development. Tbx3 is a member of a family of transcription factors that share a highly conserved DNA-binding domain known as the T-domain. UMS-causing mutations in Tbx3 have been found at numerous sites within the TBX3 gene, with many occurring downstream from the N-terminally located T-domain. The occurrence of mutations downstream of the DNA-binding domain raises the possibility that there exist important functional domains in C-terminal portions of the Tbx3 protein that affect its behavior as a transcription factor. To determine if and how such C-terminal mutations affect transcription we have mapped regions that confer transcriptional activity and nuclear localization and characterized the DNA binding properties of Tbx3. We find that Tbx3 binds the canonical Brachyury binding site as a monomer and represses transcription. We show that a key repression domain (RD1) resides in the Tbx3 C-terminus that can function as a portable repression domain. Most UMS-associated C-terminal mutants lack the RD1 and exhibit decreased or loss of transcriptional repression activity. In addition, we identify a domain responsible for nuclear localization of Tbx3 and show that two C-terminal mutants of Tbx3 have increased rates of protein decay. Finally, we show that Tbx3 can immortalize primary embryo fibroblasts and that the RD1 repression domain is required for this activity. Our results identify critical functional domains within the Tbx3 protein and facilitate interpretation of the functional consequences of present and future UMS mutations.

Progression of infection and tumor development in damselfish.

The bicolor damselfish (Stegastes partitus) is a tropical marine teleost naturally affected by multiple neurofibromas and chromatophoromas on South Florida reefs. Damselfish neurofibromatosis is a transmissible disease caused by a subcellular agent. Development of tumors is associated with the appearance of a series of extrachromosomal DNAs ranging in size from 1.2 to 7 kb that appear to be the genome of a small virus-like agent which we termed the damselfish virus-like agent (DVLA). This DNA was found at high copy number in most spontaneous and experimentally induced tumors. An essentially identical pattern of DNA, but with lower copy numbers, was observed in non-tumor-bearing tissue from diseased fish. Copy numbers of DVLA DNA in tumors and nontumorous tissues increased as the disease progressed from early to late stages. In healthy fish in which DVLA DNA was detected, the quantities were much lower than those in diseased fish. Healthy fish from populations with a high prevalence of disease exhibited more infected tissues than fish from populations with low levels.

A biomechanical evaluation of the Christensen temporomandibular joint implant.

The Christensen TMJ implant is often used clinically as a total joint replacement of the temporomandibular joint. The system consists of a thin fossa component and a condylar component with a polished articular head. In this study, we analyzed the surface finish and the metal structure of the components. We also measured the contact areas between the two components for different load levels. Such information may be useful in evaluating clinical performance as well as in making future improvements in the design of these implants.

Differential DNA binding and transcription modulation by three T-box proteins, T, TBX1 and TBX2.

T-box genes encode a family of phylogenetically conserved DNA-binding proteins that regulate gene expression during embryogenesis. While the developmental importance of many T-box genes has been well documented, little is known about how family members differ in their DNA binding properties and ability to modulate transcription. Here we show that although TBX1, TBX2 and the Xenopus T protein (Xbra) share only 50-60% identity within their DNA-binding domains they can bind the same DNA sequence in vitro. However, the proteins differ in three important respects. While TBX1 protein binds a palindromic T oligonucleotide as a dimer, as had been previously reported for Xbra, TBX2 appears to bind the same DNA sequence as a monomer. Also, T protein/DNA complexes are stabilized in vitro by the addition of specific antibodies, whereas TBX2/DNA complexes are not stabilized by antibodies. Most importantly, TBX2 represses while Xbra activates transcription of the same chimeric reporter plasmid. TBX1, although capable of binding to the chimeric promoter, has no effect on transcription. Thus, while the DNA binding domains of T-box proteins share substantial homology, these proteins differ in both their DNA binding and transcriptional modulation properties. These results suggest that the various T-box proteins, while highly conserved, likely use different mechanisms to modulate transcription and may have different targets in vivo.

Different brain networks mediate task performance in normal aging and AD: defining compensation.

OBJECTIVE: To determine whether the pathologic mechanisms of AD alter the brain networks subserving performance of a verbal recognition task. BACKGROUND: Functional imaging studies comparing task-related activation in AD patients and controls generally have not used network analysis and have not controlled for task difficulty. METHODS: H2 15O PET was used to measure regional cerebral blood flow in 14 patients and 11 healthy elders during the performance of a serial verbal recognition task under two conditions: low demand, with study list size (SLS) equal to one; and titrated demand, with SLS adjusted so that each subject recognized words at 75% accuracy. The Scaled Subprofile Model was used to identify networks of regionally covarying activity across these task conditions. RESULTS: In the elders, higher SLS was associated with the recruitment of a network of brain areas involving left anterior cingulate and anterior insula (R2 = 0.94; p < 0.0001). Three patients also expressed this network. In the remaining patients, higher SLS was associated with the recruitment of an alternate network consisting of left posterior temporal cortex, calcarine cortex, posterior cingulate, and the vermis (R2 = 0.81, p < 0.001). Expression of this network was unrelated to SLS in the elders and more intact AD patients. CONCLUSIONS: The patients' use of the alternate network may indicate compensation for processing deficits. The transition from the normal to the alternate network may indicate a point where brain disease has irreversibly altered brain function and thus may have important implications for therapeutic intervention.

Molecular characterization of a urea transporter in the gill of the gulf toadfish (Opsanus beta).

Urea excretion by the gulf toadfish (Opsanus beta) has been shown in previous studies to be a highly pulsatile facilitated transport, with excretion probably occurring at the gill. The present study reports the isolation of an 1800 base pair (kb) cDNA from toadfish gill with one open reading frame putatively encoding a 475-residue protein, the toadfish urea transporter (tUT). tUT, the first teleostean urea transporter cloned, has high homology with UTs (facilitated urea transporters) cloned from mammals, an amphibian and a shark, and most closely resembles the UT-A subfamily. When expressed in Xenopus laevis oocytes, tUT increased urea permeability (as measured by [(14)C]urea uptake) five- to sevenfold, and this permeability increase was abolished by phloretin, a common inhibitor of other UTs. Northern analysis using the 1.8 kb clone was performed to determine the tissue distribution and dynamics of tUT mRNA expression. Of six tissues examined (gill, liver, red blood cells, kidney, skin and intestine), only gill showed expression of tUT mRNA, with a predominant band at 1.8 kb and a minor band at 3.5 kb. During several points in the urea pulse cycle of toadfish (0, 4, 6, 12 and 18 h post-pulse), measured by excretion of [(14)C]urea into the water, gill mRNA samples were obtained. Expression of tUT mRNA was found to be largely invariant relative to expression of beta-actin mRNA over the pulse cycle. These results further confirm the gill localization of urea transport in the toadfish and suggest that tUT regulation (and the regulation of pulsatile urea excretion) is probably not at the level of mRNA control. The results are discussed in the context of the mechanisms of vasopressin-regulated UT-A in mammalian kidney and morphological data for the toadfish gill.

Reproducibility of alternative probe synthesis approaches for gene expression profiling with arrays.

Before gene expression profiling with microarray technology can be transferred to the diagnostic setting, we must have alternative approaches for synthesizing probe from limited RNA samples, and we must understand the limits of reproducibility in interpreting gene expression results. The current gold standard of probes for use with both microarrays and high-density filter arrays are synthesized from 1 microg of purified poly(A)+ RNA. We evaluated two approaches for synthesizing cDNA probes from total RNA with subsequent hybridization to high-density filter arrays: 1) reverse transcription (RT) of 5 microg total RNA and 2) RT-polymerase chain reaction (RT-PCR) of 1 microg total RNA, using the SMART system. The reproducibility of these two approaches was compared to the current gold standard. All three methods were highly reproducible. Triplicate experiments resulted in the following concordance correlation coefficients to evaluate reproducibility: 0.88 for the gold standard, 0.86 for cDNA probe synthesized by RT from total RNA, and 0.96 for the SMART cDNA probe synthesized from total RNA. We also compared the expression profile of 588 genes for the total RNA methods to that obtained with the gold standard. Of 150 positive genes detected by the gold standard, 97 (65%) were detected by cDNA probe synthesized by RT of total RNA, and 122 (81%) were detected by the SMART cDNA probe. We conclude that SMART cDNA probe produces highly reproducible results and yields gene expression profiles that represent the majority of transcripts detected with the gold standard.

Disruption of the murine nuclear factor I-A gene (Nfia) results in perinatal lethality, hydrocephalus, and agenesis of the corpus callosum.

The phylogenetically conserved nuclear factor I (NFI) family of transcription/replication proteins is essential both for adenoviral DNA replication and for the transcription of many cellular genes. We showed previously that the four murine NFI genes (Nfia, Nfib, Nfic, and Nfix) are expressed in unique but overlapping patterns during mouse development and in adult tissues. Here we show that disruption of the Nfia gene causes perinatal lethality, with >95% of homozygous Nfia(-/-) animals dying within 2 weeks after birth. Newborn Nfia(-/-) animals lack a corpus callosum and show ventricular dilation indicating early hydrocephalus. Rare surviving homozygous Nfia(-/-) mice lack a corpus callosum, show severe communicating hydrocephalus, a full-axial tremor indicative of neurological defects, male-sterility, low female fertility, but near normal life spans. These findings indicate that while the Nfia gene appears nonessential for cell viability and DNA replication in embryonic stem cells and fibroblasts, loss of Nfia function causes severe developmental defects. This finding of an NFI gene required for a developmental process suggests that the four NFI genes may have distinct roles in vertebrate development.

Transcription repression by Xenopus ET and its human ortholog TBX3, a gene involved in ulnar-mammary syndrome.

T box (Tbx) genes are a family of developmental regulators with more than 20 members recently identified in invertebrates and vertebrates. Mutations in Tbx genes have been found to cause several human diseases. Our understanding of functional mechanisms of Tbx products has come mainly from the prototypical T/Brachyury, which is a transcription activator. We previously discovered ET, a Tbx gene expressed in Xenopus embryos. We report here that ET is an ortholog of the human Tbx3 and that ET is a repressor of basal and activated transcription. Functional dissection of the ET protein reveals a novel transcription-repression domain highly conserved among ET, human TBX3, and TBX2. These results reveal a new transcription repressor domain, show the existence of a subfamily of transcription repressors in the Tbx superfamily, and provide a basis for understanding etiology of diseases caused by Tbx3 mutations.

The spectrum of mutations in TBX3: Genotype/Phenotype relationship in ulnar-mammary syndrome.

Ulnar-mammary syndrome (UMS) is a pleiotropic disorder affecting limb, apocrine-gland, tooth, hair, and genital development. Mutations that disrupt the DNA-binding domain of the T-box gene, TBX3, have been demonstrated to cause UMS. However, the 3' terminus of the open reading frame (ORF) of TBX3 was not identified, and mutations were detected in only two families with UMS. Furthermore, no substantial homology outside the T-box was found among TBX3 and its orthologues. The subsequent cloning of new TBX3 cDNAs allowed us to complete the characterization of TBX3 and to identify alternatively transcribed TBX3 transcripts, including one that interrupts the T-box. The complete ORF of TBX3 is predicted to encode a 723-residue protein, of which 255 amino acids are encoded by newly identified exons. Comparison of other T-box genes to TBX3 indicates regions of substantial homology outside the DNA-binding domain. Novel mutations have been found in all of eight newly reported families with UMS, including five mutations downstream of the region encoding the T-box. This suggests that a domain(s) outside the T-box is highly conserved and important for the function of TBX3. We found no obvious phenotypic differences between those who have missense mutations and those who have deletions or frameshifts.

Constitutive expression of the Wilms tumor suppressor gene (WT1) in renal cell carcinoma.

The expression of the Wilms tumor suppressor gene WT1 is largely restricted to elements of the developing urogenital system. In the fetal kidney, WT1 transcripts are present at low levels in the condensing mesenchyme and at much higher levels in differentiating glomerular epithelium and are not detected in other mesenchymal-derived epithelial structures such as the proximal and distal tubules. However, WT1 expression is observed in tubule-like elements found in some Wilms tumors. As renal cell carcinoma (RCC) of the clear cell type is one of the most prevalent adult tumors of the kidney, and is thought to originate from the epithelial cells of the proximal tubules, we studied WT1 expression in RCCs. Despite the absence of WT1 in normal primary epithelial cells derived from proximal tubules, RCC tumors and tumor-derived cell lines expressed WT1 RNA. Immunocytochemical analyses of tumor cryosections showed widespread expression throughout the poorly differentiated epithelial components of the tumor. Immunoblots of RCC samples detected a normal size WT I protein and reciprocal antibody immunoprecipitations of RCC cell extracts indicated that WT I interacts with p53 as has been demonstrated for normal human fetal kidney. The aberrant expression of functional WT1 in RCC may represent a reversion to a more de-differentiated phenotype and may contribute to the tumorigenic phenotype by inappropriately activating or repressing genes involved in growth regulation.

Genomic structure of TBX2 indicates conservation with distantly related T-box genes.

TBX2 is a member of a recently discovered gene family of transcription factors, named T-box genes after the Brachyury or T gene. Mutations in two of these family members, TBX5 and TBX3, have recently been shown to be responsible for the congenital abnormalities associated with Holt Oram syndrome and ulnar-mammary syndrome respectively, while mutations in T-box genes in other species also result in developmental abnormalities in the tissues where the gene is normally expressed. Thus, it likely that other T-box genes are responsible for additional human developmental anomalies. Here we report the exon/intron boundaries of TBX2 and a polymorphism within intron 2 of TBX2 that should be useful for exploring the involvement of this gene in human genetic disease. We further note that the exon/intron boundaries of TBX2 are highly conserved within the T-box domain with those of both T and TBX5, as well as with a new human T-box gene and more distantly related genes from Caenorhabditis elegans and Drosophila. This observation should facilitate the analysis of the genomic structure of other members of this gene family. It is also of interest that several members of this gene family have an additional intron that is variably present within members of at least two different lineages of the T-box family. This observation has implications regarding the evolution of T-box genes.

Tissue-specific regulation of the WT1 locus.

The 11p13 Wilms' tumor locus consists of two coordinately regulated transcripts, WT1 and WIT-1. These genes are highly expressed in the developing urogenital system, beginning with the urogenital ridge at day 10.5, the metanephric blastema at day 11.5, and during glomerular formation at day 13.5, becoming ultimately restricted to the podocytes. Stromal cells of the gonad also show abundant expression. WT1 is expressed at lower levels in spleen, uterus, mesothelial linings of organs in the abdominal and thoracic cavities, and the ependymal layer of the ventral aspect of the spinal cord. WIT-1 mRNA is about 10-fold less abundant than WT1, but appears to be expressed in the same tissue-restricted manner. Expression of the WT1 protein is required for kidney development, although its physiological function remains to be determined. The function of WIT-1 is similarly unknown but one intriguing possibility is that it is an antisense regulator of WT1. An understanding of events controlling spatial and temporal regulation of these genes will greatly improve our ability to study the role of WT1 and WIT-1 in urogenital development. We have found that while chimeric reporter constructs containing 0.6-2.5 kb of the 5' region of the WT1 gene direct transcription in many different cell lines, we were unable to detect expression in 13.5-day mouse embryos. However, a cosmid containing about 42 kb encompassing this region was able to direct the expression of abundant levels of mRNA from the appropriate transcription initiation sites in both stable transfectants of mouse Leydig cells (TM3) or in transgenic embryos. We are currently localizing the DNA elements required for this expression.