Showing papers by "University of Basel published in 1999"

Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis

Abstract: The functions of many open reading frames (ORFs) identified in genome-sequencing projects are unknown. New, whole-genome approaches are required to systematically determine their function. A total of 6925 Saccharomyces cerevisiae strains were constructed, by a high-throughput strategy, each with a precise deletion of one of 2026 ORFs (more than one-third of the ORFs in the genome). Of the deleted ORFs, 17 percent were essential for viability in rich medium. The phenotypes of more than 500 deletion strains were assayed in parallel. Of the deletion strains, 40 percent showed quantitative growth defects in either rich or minimal medium.

Plant diversity and productivity experiments in european grasslands

Abstract: At eight European field sites, the impact of loss of plant diversity on primary productivity was simulated by synthesizing grassland communities with different numbers of plant species. Results differed in detail at each location, but there was an overall log-linear reduction of average aboveground biomass with loss of species. For a given number of species, communities with fewer functional groups were less productive. These diversity effects occurred along with differences associated with species composition and geographic location. Niche complementarity and positive species interactions appear to play a role in generating diversity-productivity relationships within sites in addition to sampling from the species pool.

Motivation, Knowledge Transfer, and Organizational Forms

Abstract: Employees are motivated intrinsically as well as extrinsically. Intrinsic motivation is crucial when tacit knowledge in and between teams must be transferred. Organizational forms enable different kinds of motivation and have different capacities to generate and transfer tacit knowledge. Since knowledge generation and transfer are essential for a firm's sustainable competitive advantage, we ask specifically what kinds of motivation are needed to generate and transfer tacit knowledge, as opposed to explicit knowledge.

Quantum information processing using quantum dot spins and cavity QED

Abstract: The electronic spin degrees of freedom in semiconductors typically have decoherence times that are several orders of magnitude longer than other relevant time scales. A solid-state quantum computer based on localized electron spins as qubits is therefore of potential interest. Here, a scheme that realizes controlled interactions between two distant quantum dot spins is proposed. The effective long-range interaction is mediated by the vacuum field of a high finesse microcavity. By using conduction-band-hole Raman transitions induced by classical laser fields and the cavity-mode, parallel controlled-not operations, and arbitrary single qubit rotations can be realized.

On the origin of species by sympatric speciation

Abstract: Understanding speciation is a fundamental biological problem. It is believed that many species originated through allopatric divergence, where new species arise from geographically isolated populations of the same ancestral species. In contrast, the possibility of sympatric speciation (in which new species arise without geographical isolation) has often been dismissed, partly because of theoretical difficulties. Most previous models analysing sympatric speciation concentrated on particular aspects of the problem while neglecting others. Here we present a model that integrates a novel combination of different features and show that sympatric speciation is a likely outcome of competition for resources. We use multilocus genetics to describe sexual reproduction in an individual-based model, and we consider the evolution of assortative mating (where individuals mate preferentially with like individuals) depending either on an ecological character affecting resource use or on a selectively neutral marker trait. In both cases, evolution of assortative mating often leads to reproductive isolation between ecologically diverging subpopulations. When assortative mating depends on a marker trait, and is therefore not directly linked to resource competition, speciation occurs when genetic drift breaks the linkage equilibrium between the marker and the ecological trait. Our theory conforms well with mounting empirical evidence for the sympatric origin of many species.

Nucleosynthesis in Chandrasekhar Mass Models for Type Ia Supernovae and Constraints on Progenitor Systems and Burning-Front Propagation

Abstract: The major uncertainties involved in the Chandrasekhar mass models for Type Ia supernovae (SNe Ia) are related to the companion star of their accreting white dwarf progenitor (which determines the accretion rate and consequently the carbon ignition density) and the flame speed after the carbon ignition. We calculate explosive nucleosynthesis in relatively slow deflagrations with a variety of deflagration speeds and ignition densities to put new constraints on the above key quantities. The abundance of the Fe group, in particular of neutron-rich species like 48Ca,50Ti,54Cr,54,58Fe, and 58Ni, is highly sensitive to the electron captures taking place in the central layers. The yields obtained from such a slow central deflagration, and from a fast deflagration or delayed detonation in the outer layers, are combined and put to comparison with solar isotopic abundances. To avoid excessively large ratios of 54Cr/56Fe and 50Ti/56Fe, the central density of the average white dwarf progenitor at ignition should be as low as 2 ? 109 g cm-3. To avoid the overproduction of 58Ni and 54Fe, either the flame speed should not exceed a few percent of the sound speed in the central low Ye layers or the metallicity of the average progenitors has to be lower than solar. Such low central densities can be realized by a rapid accretion as fast as -->img1.gif 1 ? 10-7 M? yr-1. In order to reproduce the solar abundance of 48Ca, one also needs progenitor systems that undergo ignition at higher densities. Even the smallest laminar flame speeds after the low-density ignitions would not produce sufficient amount of this isotope. We also found that the total amount of 56Ni, the Si-Ca/Fe ratio, and the abundance of some elements like Mn and Cr (originating from incomplete Si burning), depend on the density of the deflagration-detonation transition in delayed detonations. Our nucleosynthesis results favor transition densities slightly below 2.2 ? 107 g cm-3.

Coupled quantum dots as quantum gates

Abstract: We consider a quantum-gate mechanism based on electron spins in coupled semiconductor quantum dots. Such gates provide a general source of spin entanglement and can be used for quantum computers. We determine the exchange coupling $J$ in the effective Heisenberg model as a function of magnetic $(B)$ and electric fields, and of the interdot distance $a$ within the Heitler-London approximation of molecular physics. This result is refined by using $\mathrm{sp}$ hybridization, and by the Hund-Mulliken molecular-orbit approach, which leads to an extended Hubbard description for the two-dot system that shows a remarkable dependence on $B$ and $a$ due to the long-range Coulomb interaction. We find that the exchange $J$ changes sign at a finite field (leading to a pronounced jump in the magnetization) and then decays exponentially. The magnetization and the spin susceptibilities of the coupled dots are calculated. We show that the dephasing due to nuclear spins in GaAs can be strongly suppressed by dynamical nuclear-spin polarization and/or by magnetic fields.

Electrical conduction through DNA molecules

Abstract: The question of whether DNA is able to transport electrons has attracted much interest, particularly as this ability may play a role as a repair mechanism after radiation damage to the DNA helix1. Experiments addressing DNA conductivity have involved a large number of DNA strands doped with intercalated donor and acceptor molecules, and the conductivity has been assessed from electron transfer rates as a function of the distance between the donor and acceptor sites2,3. But the experimental results remain contradictory, as do theoretical predictions4. Here we report direct measurements of electrical current as a function of the potential applied across a few DNA molecules associated into single ropes at least 600 nm long, which indicate efficient conduction through the ropes. We find that the resistivity values derived from these measurements are comparable to those of conducting polymers, and indicate that DNA transports electrical current as efficiently as a good semiconductor. This property, and the fact that DNA molecules of specific composition ranging in length from just a few nucleotides to chains several tens of micrometres long can be routinely prepared, makes DNA ideally suited for the construction of mesoscopic electronic devices.

The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors

Abstract: The rapamycin-sensitive TOR signalling pathway in Saccharomyces cerevisiae activates a cell-growth program in response to nutrients such as nitrogen and carbon. The TOR1 and TOR2 kinases (TOR) control cytoplasmic protein synthesis and degradation through the conserved TAP42 protein. Upon phosphorylation by TOR, TAP42 binds and possibly inhibits type 2A and type-2A-related phosphatases; however, the mechanism by which TOR controls nuclear events such as global repression of starvation-specific transcription is unknown. Here we show that TOR prevents transcription of genes expressed upon nitrogen limitation by promoting the association of the GATA transcription factor GLN3 with the cytoplasmic protein URE2. The binding of GLN3 to URE2 requires TOR-dependent phosphorylation of GLN3. Phosphorylation and cytoplasmic retention of GLN3 are also dependent on the TOR effector TAP42, and are antagonized by the type-2A-related phosphatase SIT4. TOR inhibits expression of carbon-source-regulated genes by stimulating the binding of the transcriptional activators MSN2 and MSN4 to the cytoplasmic 14-3-3 protein BMH2. Thus, the TOR signalling pathway broadly controls nutrient metabolism by sequestering several transcription factors in the cytoplasm.

Responses of tundra plants to experimental warming:meta‐analysis of the international tundra experiment

Abstract: The International Tundra Experiment (ITEX) is a collaborative, multisite experiment using a common temperature manipulation to examine variability in species response across climatic and geographic gradients of tundra ecosystems. ITEX was designed specifically to examine variability in arctic and alpine species response to increased temperature. We compiled from one to four years of experimental data from 13 different ITEX sites and used meta-analysis to analyze responses of plant phenology, growth, and reproduction to experimental warming. Results indicate that key phenological events such as leaf bud burst and flowering occurred earlier in warmed plots throughout the study period; however, there was little impact on growth cessation at the end of the season. Quantitative measures of vegetative growth were greatest in warmed plots in the early years of the experiment, whereas reproductive effort and success increased in later years. A shift away from vegetative growth and toward reproductive effort and success in the fourth treatment year suggests a shift from the initial response to a secondary response. The change in vegetative response may be due to depletion of stored plant reserves, whereas the lag in reproductive response may be due to the formation of flower buds one to several seasons prior to flowering. Both vegetative and reproductive responses varied among life-forms; herbaceous forms had stronger and more consistent vegetative growth responses than did woody forms. The greater responsiveness of the herbaceous forms may be attributed to their more flexible morphology and to their relatively greater proportion of stored plant reserves. Finally, warmer, low arctic sites produced the strongest growth responses, but colder sites produced a greater reproductive response. Greater resource investment in vegetative growth may be a conservative strategy in the Low Arctic, where there is more competition for light, nutrients, or water, and there may be little opportunity for successful germination or seedling development. In contrast, in the High Arctic, heavy investment in producing seed under a higher temperature scenario may provide an opportunity for species to colonize patches of unvegetated ground. The observed differential response to warming suggests that the primary forces driving the response vary across climatic zones, functional groups, and through time.

Cellular and molecular biology of the aquaporin water channels.

Abstract: The high water permeability characteristic of mammalian red cell membranes is now known to be caused by the protein AQP1 This channel freely permits movement of water across the cell membrane, but it is not permeated by other small, uncharged molecules or charged solutes AQP1 is a tetramer with each subunit containing an aqueous pore likened to an hourglass formed by obversely arranged tandem repeats Cryoelectron microscopy of reconstituted AQP1 membrane crystals has revealed the three-dimensional structure at 3-6 A AQP1 is distributed in apical and basolateral membranes of renal proximal tubules and descending thin limbs as well as capillary endothelia Ten mammalian aquaporins have been identified in water-permeable tissues and fall into two groupings Orthodox aquaporins are water-selective and include AQP2, a vasopressin-regulated water channel in renal collecting duct, in addition to AQP0, AQP4, and AQP5 Multifunctional aquaglyceroporins AQP3, AQP7, and AQP9 are permeated by water, glycerol, and some other solutes Aquaporins are being defined in numerous other species including amphibia, insects, plants, and microbials Members of the aquaporin family are implicated in numerous physiological processes as well as the pathophysiology of a wide range of clinical disorders

r-Process in Neutron Star Mergers

Abstract: The production site of the neutron-rich heavy elements that are formed by rapid neutron capture (the r-process) is still unknown despite intensive research. Here we show detailed studies of a scenario that has been proposed earlier by Lattimer & Schramm, Symbalisty & Schramm, Eichler et al., and Davies et al., namely the merger of two neutron stars. The results of hydrodynamic and full network calculations are combined in order to investigate the relevance of this scenario for r-process nucleosynthesis. Sufficient material is ejected to explain the amount of r-process nuclei in the Galaxy by decompression of neutron star material. Provided that the ejecta consist of matter with a proton-to-nucleon ratio of Ye approximately 0.1, the calculated abundances fit the observed solar r-pattern excellently for nuclei that include and are heavier than the A approximately 130 peak.

A single locus determines sensitivity to bacterial flagellin in Arabidopsis thaliana

Abstract: Summary Peptides corresponding to the most conserved domain of eubacterial flagellin act as potent elicitors in cells of different plant species. In intact Arabidposis thaliana seedlings these peptides (flg22 and flg15) caused callose deposition, induction of genes coding for pathogenesis-related proteins and a strong inhibition of growth. Half-maximal growth inhibition occurred at peptide concentrations of approximately 100 nM. In contrast, peptides representing the corresponding flagellin domains of the plant-associated bacteria A. tumefaciens and R. meliloti were inactive even at concentrations of 10 μM. With the exception of Ws-0, all ecotypes of A. thaliana tested were sensitive to flg22. Crosses of Ws-0 with the sensitive ecotypes Col-0 and La-er, respectively, resulted in sensitive F1 seedlings. In the F2 generation of both crosses, sensitivity segregated as a single trait with markers of chromosome 5 and a ratio of 3:1. Dominance of the locus sensing flagellin, termed FLS-1, suggests that it encodes an element which is important for the perception of the flagellin signal.

Prevalence of hay fever and allergic sensitization in farmer's children and their peers living in the same rural community. SCARPOL team. Swiss Study on Childhood Allergy and Respiratory Symptoms with Respect to Air Pollution

Abstract: Introduction Lower prevalence rates of allergic diseases in rural as compared with urban populations have been interpreted as indicating an effect of air pollution. However, little is known about other factors of the rural environment which may determine the development of atopic sensitization and related diseases. Objective The authors tested the hypothesis that children growing up on a farm were less likely to be sensitized to common aerollergens and to suffer from allergic diseases than children living in the same villages but in nonfarming families. Materials and methods Three age groups of schoolchildren (6–7 years, 9–11 years, 13–15 years) living in three rural communities were included in the analyses. An exhaustive questionnaire was filled in by 1620 (86.0%) parents. A blood sample was provided by 404 (69.3%) of the 13–15 year olds to determine specific IgE antibodies against six common aeroallergens. Results Farming as parental occupation was reported for 307 children (19.0%). After adjustment for potential covariates such as family history of asthma and allergies, parental education, number of siblings, maternal smoking, pet ownership, indoor humidity and heating fuels, farming as parental occupation was significantly associated with lower rates of sneezing attacks during pollen season (adjusted OR 0.34, 95% CI 0.12–0.89) and atopic sensitization (adjusted OR 0.31, 95% CI 0.13–0.73) whereas the association with wheeze (adjusted OR 0.77 95% CI 0.38–1.58) and itchy skin rash (adjusted OR 0.86, 95% CI 0.49–1.50) was not statistically significant. The risk of atopic sensitization was lower in children from full-time farmers (adjusted OR 0.24, 95% CI 0.09–0.66) than from part-time farmers (adjusted OR 0.54, 95% CI 0.15–1.96). Conclusion Factors directly or indirectly related to farming as parental occupation decrease the risk of children becoming atopic and developing symptoms of allergic rhintis.

Aharonov–Bohm oscillations in carbon nanotubes

Abstract: When electrons pass through a cylindrical electrical conductor aligned in a magnetic field, their wave-like nature manifests itself as a periodic oscillation in the electrical resistance as a function of the enclosed magnetic flux1. This phenomenon reflects the dependence of the phase of the electron wave on the magnetic field, known as the Aharonov–Bohm effect2, which causes a phase difference, and hence interference, between partial waves encircling the conductor in opposite directions. Such oscillations have been observed in micrometre-sized thin-walled metallic cylinders3,4,5 and lithographically fabricated rings6,7,8. Carbon nanotubes9,10 are composed of individual graphene sheets rolled into seamless hollow cylinders with diameters ranging from 1 nm to about 20 nm. They are able to act as conducting molecular wires11,12,13,14,15,16,17,18, making them ideally suited for the investigation of quantum interference at the single-molecule level caused by the Aharonov–Bohm effect. Here we report magnetoresistance measurements on individual multi-walled nanotubes, which display pronounced resistance oscillations as a function of magnetic flux.We find that the oscillations are in good agreement with theoretical predictions for the Aharonov–Bohm effect in a hollow conductor with a diameter equal to that of the outermost shell of the nanotubes. In some nanotubes we also observe shorter-period oscillations, which might result from anisotropic electron currents caused by defects in the nanotube lattice.

Long-term survival and late deaths after allogeneic bone marrow transplantation. Late Effects Working Committee of the International Bone Marrow Transplant Registry.

Abstract: Background and Methods It is uncertain whether mortality rates among patients who have undergone bone marrow transplantation return to the level of the mortality rates of the general population. We analyzed the characteristics of 6691 patients listed in the International Bone Marrow Transplant Registry. All the patients were free of their original disease two years after allogeneic bone marrow transplantation. Mortality rates in this cohort were compared with those of an age-, sex-, and nationality-matched general population. Cox proportional-hazards regression was used to identify risk factors for death more than two years after transplantation (late death). Results Among patients who were free of disease two years after transplantation, the probability of living for five more years was 89 percent (95 percent confidence interval, 88 to 90 percent). Among patients who underwent transplantation for aplastic anemia, the risk of death by the sixth year after transplantation did not differ significantly from ...

Dynamic force spectroscopy of single DNA molecules

Abstract: To explore the analytic relevance of unbinding force measurements between complementary DNA strands with an atomic force microscope, we measured the forces to mechanically separate a single DNA duplex under physiological conditions by pulling at the opposite 5′-ends as a function of the loading rate (dynamic force spectroscopy). We investigated DNA duplexes with 10, 20, and 30 base pairs with loading rates in the range of 16–4,000 pN/s. Depending on the loading rate and sequence length, the unbinding forces of single duplexes varied from 20 to 50 pN. These unbinding forces are found to scale with the logarithm of the loading rate, which is interpreted in terms of a single energy barrier along the mechanical separation path. The parameters describing the energy landscape, i.e., the distance of the energy barrier to the minimum energy along the separation path and the logarithm of the thermal dissociation rate, are found to be proportional to the number of base pairs of the DNA duplex. These single molecule results allow a quantitative comparison with data from thermodynamic ensemble measurements and a discussion of the analytic applications of unbinding force measurements for DNA.

Polyomavirus Infection of Renal Allograft Recipients From Latent Infection to Manifest Disease

Abstract: . Polyomavirus (PV) exceptionally causes a morphologically manifest renal allograft infection. Five such cases were encountered in this study, and were followed between 40 and 330 d during persistent PV renal allograft infection. Transplant (Tx) control groups without PV graft infection were analyzed for comparison. Tissue and urine samples were evaluated by light microscopy, immunohistochemistry, electron microscopy, and PCR. The initial diagnosis of PV infection with the BK strain was made in biopsies 9 ± 2 mo (mean ± SD) post-Tx after prior rejection episodes and rescue therapy with tacrolimus. All subsequent biopsies showed persistent PV infection. Intranuclear viral inclusion bodies in epithelial cells along the entire nephron and the transitional cell layer were histologic hallmarks of infection. Affected tubular cells were enlarged and often necrotic. In two patients, small glomerular crescents were found. In 54% of biopsies, infection was associated with pronounced inflammation, which had features of cellular rejection. All patients were excreting PV-infected cells in the urine. PV infection was associated with 40% graft loss (2 of 5) and a serum creatinine of 484 ± 326 μmol/L (mean ± SD; 11 mo post-Tx). Tx control groups showed PV-infected cells in the urine in 5%. Control subjects had fewer rejection episodes ( P P = 0.01). It is concluded that a manifest renal allograft infection with PV (BK strain) can persist in heavily immunosuppressed patients with recurrent rejection episodes. PV mainly affects tubular cells and causes necrosis, a major reason for functional deterioration. A biopsy is required for diagnosis. Urine cytology can serve as an adjunct diagnostic tool.

Tissue Microarrays for Gene Amplification Surveys in Many Different Tumor Types

Abstract: Gene amplifications are common in many different tumor types and may confer diagnostic, prognostic, or therapeutic information for patient management. Tedious experiments are often required to determine which tumor types have amplifications of a specific oncogene. To facilitate rapid screening for molecular alterations in many different malignancies, a tissue microarray consisting of samples from 17 different tumor types was generated. Altogether, 397 individual tumors were arrayed in a single paraffin block. To determine whether results from the literature can be reproduced on minute tissue samples (diameter, 0.6 mm), amplification of three extensively studied oncogenes (CCND1, CMYC, and ERBB2) was analyzed in three fluorescence in situ hybridization experiments from consecutive sections cut from the tissue microarray. Amplification of CCND1 was found in breast, lung, head and neck, and bladder cancer, as well as in melanoma. ERBB2 was amplified in bladder, breast, colon, stomach, testis, and lung cancer. CMYC was amplified in breast, colon, kidney, lung, ovary, bladder, head and neck, and endometrial cancer. These results confirm and even extend existing data in the literature on such amplifications. In summary, we applied three fluorescence in situ hybridization experiments to analyze amplifications of three oncogenes in three x 397 tumors within a week. This demonstrates the power of using minute arrayed tissue specimens for tumor screening.

Polyomavirus disease under new immunosuppressive drugs: a cause of renal graft dysfunction and graft loss.

Abstract: Background Manifest polyomavirus (PV) renal graft infection is a rare complication. We diagnosed 5 cases among 70 kidney recipients undergoing transplants since December 1995; however, there were no cases at our institution before December 1995. Method. To identify risk factors promoting manifest PV graft infection, we compared those 5 patients with kidney recipients who had signs of PV replication but no manifest graft infection (n=23, control group). PV replication was judged by the presence of intranuclear inclusion cells in the urine. Results. Before the infection, five of five patients had recurrent rejection episodes. All were switched from cyclosporine A to high dose tacrolimus as rescue therapy. Infection was diagnosed histologically 9±2 months posttransplantation; it persisted and led to graft loss in four of five patients. In control patients, graft function was stable, 1 of 23 patients were switched to tacrolimus as rescue therapy, and graft loss occurred in 4 of 23 patients. Conclusion. Recurrent rejection episodes and high dose immunosuppressive therapy, including tacrolimus, are risk factors for manifest PV kidney graft infection, which has an ominous prognosis.

A new crystal structure, Ca2+ dependence and mutational analysis reveal molecular details of E-cadherin homoassociation.

Abstract: Electron microscopy of ECADCOMP, a recombinant E-cadherin ectodomain pentamerized by the assembly domain of cartilage oligomeric matrix protein, has been used to analyze the role of cis-dimerization and trans-interaction in the homophilic association of this cell adhesion molecule. The Ca2+ dependency of both interactions was investigated. Low Ca2+ concentrations (50 microM) stabilized the rod-like structure of E-cadherin. At medium Ca2+ concentration (500 microM), two adjacent ectodomains in a pentamer formed cis-dimers. At high Ca2+ concentration (>1 mM), two cis-dimers from different pentamers formed a trans-interaction. The X-ray structure of an N-terminal domain pair of E-cadherin revealed two molecules per asymmetric unit in an intertwisted X-shaped arrangement with closest contacts in the Ca2+-binding region between domains 1 and 2. Contrary to previous data, Trp2 was docked in the hydrophobic cavity of its own molecule, and was therefore not involved in cis-dimerization of two molecules. This was supported further by W2A and A80I (a residue involved in the hydrophobic cavity surrounding Trp2) mutations in ECADCOMP which both led to abrogation of the trans- but not the cis-interaction. Structural and biochemical data suggest a link between Ca2+ binding in the millimolar range and Trp2 docking, both events being essential for the trans-association.

Neuronal overexpression of mutant amyloid precursor protein results in prominent deposition of cerebrovascular amyloid

Abstract: Transgenic mice that overexpress mutant human amyloid precursor protein (APP) exhibit one hallmark of Alzheimer’s disease pathology, namely the extracellular deposition of amyloid plaques. Here, we describe significant deposition of amyloid β (Aβ) in the cerebral vasculature [cerebral amyloid angiopathy (CAA)] in aging APP23 mice that had striking similarities to that observed in human aging and Alzheimer’s disease. Amyloid deposition occurred preferentially in arterioles and capillaries and within individual vessels showed a wide heterogeneity (ranging from a thin ring of amyloid in the vessel wall to large plaque-like extrusions into the neuropil). CAA was associated with local neuron loss, synaptic abnormalities, microglial activation, and microhemorrhage. Although several factors may contribute to CAA in humans, the neuronal origin of transgenic APP, high levels of Aβ in cerebrospinal fluid, and regional localization of CAA in APP23 mice suggest transport and drainage pathways rather than local production or blood uptake of Aβ as a primary mechanism underlying cerebrovascular amyloid formation. APP23 mice on an App-null background developed a similar degree of both plaques and CAA, providing further evidence that a neuronal source of APP/Aβ is sufficient to induce cerebrovascular amyloid and associated neurodegeneration.

Methylation-associated Silencing of the Tissue Inhibitor of Metalloproteinase-3 Gene Suggests a Suppressor Role in Kidney, Brain, and Other Human Cancers

Abstract: Tissue inhibitor of metalloproteinase-3 (TIMP-3) antagonizes matrix metalloproteinase activity and can suppress tumor growth, angiogenesis, invasion, and metastasis. Loss of TIMP-3 has been related to the acquisition of tumorigenesis. Herein, we show that TIMP-3 is silenced in association with aberrant promoter-region methylation in cell lines derived from human cancers. TIMP-3 expression was restored after 5-aza-2'deoxycytidine-mediated demethylation of the TIMP-3 proximal promoter region. Genomic bisulfite sequencing revealed that TIMP-3 silencing was related to the overall density of methylation and that discrete regions within the TIMP-3 CpG island may be important for the silencing of this gene. Aberrant methylation of TIMP-3 occurred in primary cancers of the kidney, brain, colon, breast, and lung, but not in any of 41 normal tissue samples. The most frequent TIMP-3 methylation was found in renal cancers, which originate in the tissue that normally expresses the highest TIMP-3 levels. This methylation correlated with a lack of detectable TIMP-3 protein in these tumors. Together, these data show that methylation-associated inactivation of TIMP-3 is frequent in many human tumors.

Antisense Repression of Vacuolar and Cell Wall Invertase in Transgenic Carrot Alters Early Plant Development and Sucrose Partitioning

Abstract: To unravel the functions of cell wall and vacuolar invertases in carrot, we used an antisense technique to generate transgenic carrot plants with reduced enzyme activity. Phenotypic alterations appeared at very early stages of development; indeed, the morphology of cotyledon-stage embryos was markedly changed. At the stage at which control plantlets had two to three leaves and one primary root, shoots of transgenic plantlets did not separate into individual leaves but consisted of stunted, interconnected green structures. When transgenic plantlets were grown on media containing a mixture of sucrose, glucose, and fructose rather than sucrose alone, the malformation was alleviated, and plantlets looked normal. Plantlets from hexose-containing media produced mature plants when transferred to soil. Plants expressing antisense mRNA for cell wall invertase had a bushy appearance due to the development of extra leaves, which accumulated elevated levels of sucrose and starch. Simultaneously, tap root development was markedly reduced, and the resulting smaller organs contained lower levels of carbohydrates. Compared with control plants, the dry weight leaf-to-root ratio of cell wall invertase antisense plants was shifted from 1:3 to 17:1. Plants expressing antisense mRNA for vacuolar invertase also had more leaves than did control plants, but tap roots developed normally, although they were smaller, and the leaf-to-root ratio was 1.5:1. Again, the carbohydrate content of leaves was elevated, and that of roots was reduced. Our data suggest that acid invertases play an important role in early plant development, most likely via control of sugar composition and metabolic fluxes. Later in plant development, both isoenzymes seem to have important functions in sucrose partitioning.

The speed limit for protein folding measured by triplet-triplet energy transfer.

Abstract: A direct measure of intramolecular chain diffusion is obtained by the determination of triplet–triplet energy-transfer rates between a donor and an acceptor chromophore attached at defined points on a polypeptide chain. Single exponential kinetics of contact formation are observed on the nanosecond time scale for polypeptides in which donor and acceptor are linked by repeating units of glycine and serine residues. The rates depend on the number of peptide bonds (N) separating donor and acceptor and show a maximum for the shortest peptides (N = 3) with a time constant (τ = 1/k) of 20 ns. This sets an upper limit for the speed of formation of the first side-chain contacts during protein folding.