Measurement of Electron-Neutrino Charged-Current Cross Sections on

Using an 185-kg NaI[Tl] array, COHERENT has measured the inclusive electron-neutrino charged-current cross section on ^{127}I with pion decay-at-rest neutrinos produced by the Spallation Neutron Source at Oak Ridge National Laboratory. Iodine is one the heaviest targets for which low-energy (≤50 MeV) inelastic neutrino-nucleus processes have been measured, and this is the first measurement of its inclusive cross section. After a five-year detector exposure, COHERENT reports a flux-averaged cross section for electron neutrinos of 9.2_{-1.8}^{+2.1}×10^{-40} cm^{2}. This corresponds to a value that is ∼41% lower than predicted using the MARLEY event generator with a measured Gamow-Teller strength distribution. In addition, the observed visible spectrum from charged-current scattering on ^{127}I has been measured between 10 and 55 MeV, and the exclusive zero-neutron and one-or-more-neutron emission cross sections are measured to be 5.2_{-3.1}^{+3.4}×10^{-40} and 2.2_{-0.5}^{+0.4}×10^{-40} cm^{2}, respectively.

Local kinetic interpretation of entropy production through reversed diffusion.

The time reversal of stochastic diffusion processes is revisited with emphasis on the physical meaning of the time-reversed drift and the noise prescription in the case of multiplicative noise. The local kinematics and mechanics of free diffusion are linked to the hydrodynamic description. These properties also provide an interpretation of the Pope-Ching formula for the steady-state probability density function along with a geometric interpretation of the fluctuation-dissipation relation. Finally, the statistics of the local entropy production rate of diffusion are discussed in the light of local diffusion properties, and a stochastic differential equation for entropy production is obtained using the Girsanov theorem for reversed diffusion. The results are illustrated for the Ornstein-Uhlenbeck process.

Propagation of fluctuations in biochemical systems, II: Nonlinear chains.

We consider biochemical reaction chains and investigate how random external fluctuations, as characterised by variance and coefficient of variation, propagate down the chains. We perform such a study under the assumption that the number of molecules is high enough so that the behaviour of the concentrations of the system is well approximated by differential equations. We conclude that the variances and coefficients of variation of the fluxes will decrease as one moves down the chain and, through an example, show that there is no corresponding result for the variances of the concentrations of the chemical species. We also prove that the fluctuations of the fluxes as characterised by their time averages decrease down reaction chains. The results presented give insight into how biochemical reaction systems are buffered against external perturbations solely by their underlying graphical structure and point out the benefits of studying the out-of-equilibrium dynamics of systems.

The folding of nascent mitochondrial aspartate aminotransferase synthesized in a cell-free extract can be assisted by GroEL and GroES.

At 30 degrees C, the precursor to mitochondrial aspartate aminotransferase (pmAspAT) cannot fold after synthesis in rabbit reticulocyte lysate (RRL), a model for studying intracellular protein folding. However, it folds rapidly once imported into mitochondria. Guanidinium chloride denatured pmAspAT likewise cannot refold at 30 degrees C in a defined in vitro system. However, it refolds rapidly and in good yield in the presence of the intramitochondrial chaperone homologues GroEL and GroES. In this report, we demonstrate that GroEL and GroES can also facilitate the folding of nascent pmAspAT in reticulocyte lysate under conditions where it otherwise would not. When added alone, GroEL arrests the slow folding of nascent pmAspAT and inhibits import into mitochondria. These effects are significantly reversed by adding GroES. These observations suggest that added GroEL participates in an equilibrium with endogenous chaperones in the cytosol which inhibit folding and promote import competence. Native gel electrophoresis suggests that nascent pmAspAT exists in RRL as a heterogeneous population of partially folded species, some of which bind to added GroEL more readily than others. The GroEL-trapped species appear to be among the productive pmAspAT folding intermediates formed in RRL or they at least appear to equilibrate with these intermediates, since they become import competent after GroES-stimulated release from GroEL.

Conformation of aspartate aminotransferase isozymes folding under different conditions probed by limited proteolysis.

The partially homologous mitochondrial (mAAT) and cytosolic (cAAT) aspartate aminotransferase have nearly identical three-dimensional structures but differ in their folding rates in cell-free extracts and in their affinity for binding to molecular chaperones. In its native state, each isozyme is protease-resistant. Using limited proteolysis as an index of their conformational states, we have characterized these proteins (a) during the early stages of spontaneous refolding; (b) as species trapped in stable complexes with the chaperonin GroEL; or (c) as newly translated polypeptides in cell-free extracts. Treatment of the refolding proteins with trypsin generates reproducible patterns of large proteolytic fragments that are consistent with the formation of defined folding domains soon after initiating refolding. Binding to GroEL affords considerable protection to both isozymes against proteolysis. The tryptic fragments are similar in size for both isozymes, suggesting a common distribution of compact and flexible regions in their folding intermediates. cAAT synthesized in cell-free extracts becomes protease-resistant almost instantaneously, whereas trypsin digestion of the mAAT translation product produces a pattern of fragments qualitatively akin to that observed with the protein refolding in buffer. Analysis of the large tryptic peptides obtained with the GroEL-bound proteins reveals that the cleavage sites are located in analogous regions of the N-terminal portion of each isozyme. These results suggest that (a) binding to GroEL does not cause unfolding of AAT, at least to an extent detectable by proteolysis; (b) the compact folding domains identified in AAT bound to GroEL (or in mAAT fresh translation product) are already present at the early stages of refolding of the proteins in buffer alone; and (c) the two isozymes seem to bind in a similar fashion to GroEL, with the more compact C-terminal portion completely protected and the more flexible N-terminal first 100 residues still partially accessible to proteolysis.

Insight into the conformation of protein folding intermediate(s) trapped by GroEL.

Many aspects of the mechanism by which the GroEL/ES chaperonins mediate protein folding are still unclear, including the amount of structure present in the substrate bound to GroEL. To address this issue we have analyzed the susceptibility to limited proteolysis and to alkylation of cysteine residues of mitochondrial aspartate aminotransferase (mAAT) bound to GroEL. Several regions of the N-terminal portion of GroEL-bound mAAT are highly susceptible to proteolysis, whereas a large core of about 200 residues containing the C-terminal half of the polypeptide chain is protected in the complex. This protection does not extend to the mAAT sulfhydryl groups which in the GroEL-mAAT complex have similar reactivity as in fully unfolded mAAT. These results suggest that the mAAT species bound to GroEL represent folding intermediates with a conformation that is substantially more disorganized than that of the native state. The N-terminal half of the molecule is more flexible and lies exposed at the mouth of the central cavity of GroEL. The more compact C-terminal section of mAAT, which contains residues located at the subunit interface in the native dimer, appears to be hidden in the central cavity of GroEL. Thus, the bulk of the interactions in the GroEL.mAAT complex seems to involve residues from the more compact C-terminal section of the substrate.

Structural features of the precursor to mitochondrial aspartate aminotransferase responsible for binding to hsp70.

The precursor (pmAspAT) and mature (mAspAT) forms of mitochondrial aspartate aminotransferase interact with hsp70 very early during translation when synthesized in either rabbit reticulocyte lysate or wheat germ extract (Lain, B., Iriarte, A., and Martinez-Carrion. (1994) J. Biol. Chem. 269, 15588-15596). The nature of the structural elements responsible for recognition and binding of this protein to hsp70 has been studied by examining the folding and potential association with the chaperone of several engineered forms of this enzyme. Whereas pmAspAT and mAspAT bind hsp70 very early during translation, the cytosolic form of this enzyme (cAspAT) does not interact with hsp70. A fusion protein consisting of the mitochondrial presequence peptide attached to the amino terminus of cAspAT associates with hsp70 only after the protein has acquired its native-like conformation, apparently through binding to the presequence exposed on the surface of the folded protein. Deletion of the amino-terminal segment of mAspAT or its replacement with the corresponding domain from the cytosolic isozyme eliminates the cotranslational binding of hsp70 to the mitochondrial protein. We conclude that both the presequence and NH2-terminal region of pmAspAT represent recognition signals for binding of hsp70 to the newly synthesized mitochondrial precursor. Results from competition studies with synthetic peptides support this conclusion. The ability of hsp70 to discriminate between these two highly homologous proteins probably involves the recognition of specific sequence elements in the NH2-terminal portion of the mitochondrial protein and may relate to their separate localization in the cell. A slower folding rate and higher affinity for cytosolic chaperones may represent evolutionary adaptations of translocated mitochondrial proteins to ensure their efficient importation into the organelle.

Homologous proteins with different affinities for groEL. The refolding of the aspartate aminotransferase isozymes at varying temperatures.

The homologous cytosolic and mitochondrial isozymes of aspartate aminotransferase (c- and mAspAT, respectively) seem to follow very different folding pathways after synthesis in rabbit reticulocyte lysate, suggesting that the nascent proteins interact differently with molecular chaperones (Mattingly, J. R., Jr., Iriarte, A., and Martinez-Carrion, M. (1993) J. Biol. Chem. 268, 26320-26327). In an attempt to discern the structural basis for this phenomenon, we have begun to study the effect of temperature on the refolding of the guanidine hydrochloride-denatured, purified proteins and their interaction with the groEL/groES molecular chaperone system from Escherichia coli. In the absence of chaperones, temperature has a critical effect on the refolding of the two isozymes, with mAspAT being more susceptible than cAspAT to diminishing refolding yields at increasing temperatures. No refolding is observed for mAspAT at physiological temperatures. The molecular chaperones groEL and groES can extend the temperature range over which the AspAT isozymes successfully refold; however, cAspAT can still refold at higher temperatures than mAspAT. In the absence of groES and MgATP, the two isozymes interact differently with groEL, groEL arrests the refolding of mAspAT throughout the temperature range of 0-45 degrees C. Adding only MgATP releases very little mAspAT from groEL; both groES and MgATP are required for significant refolding of mAspAT in the presence of groEL. On the other hand, the extent to which groEL inhibits the refolding of cAspAT depends upon the temperature of the refolding reaction, only slowing the reaction at 0 degrees C but arresting it completely at 30 degrees C. MgATP alone is sufficient to effect the release of cAspAT from groEL at any temperature examined; inclusion of groES along with MgATP has no effect on the refolding yield but does increase the refolding rate at temperatures greater than 15 degrees C. These results demonstrate that groEL can have significantly different affinities for proteins with highly homologous final tertiary and quarternary structures and suggest that dissimilarities in the primary sequence of the protein substrates may control the structure of the folding intermediates captured by groEL and/or the composition of the surfaces through which the folding proteins interact with groEL.

HSV-2 increases the mitochondrial aspartate amino transaminase characteristic of tumor cells.

A set of polypeptides has previously been described as being immunoprecipitated from tumor cell lysates by the sera of tumor-bearing animals (TBS) or by antisera raised to herpes simplex virus type 2 (HSV-2)-infected cells. These polypeptides were not immunoprecipitated from control cells. The principal polypeptides detected of MW 200, 90 (U90 and L90), 40, and 32 kDa were increased by HSV-2 infection. This communication describes the purification of the 40-kDa protein and its identification by amino acid sequence analysis as being homologous to the mature form of mitochondrial aspartate amino transaminase (mAAT). Two different forms of mAAT were purified and sequenced. One form, of low abundance, was immunoprecipitated by TBS and corresponded to the 40-kDa protein immunoprecipitated from tumor, but not control, cell lysates. Western blotting of the 40-kDa protein immunoprecipitated by TBS showed that it was a form of mAAT found only in tumor cells. The other abundant form reacted in Western blots with antibody to mAAT and was clearly the constitutive enzyme, present in all cells. In general, mAAT was increased up to fourfold after infection with HSV-2, HSV-2 infection also increased mAAT enzyme activity. Northern blotting and quantitative PCR showed that mAAT was induced by HSV-2 at the level of transcription. The specific form of mAAT immunoprecipitated from tumor, but not control, cell lysates could have a role in tumorigenesis, could be a putative tumor cell marker, or could be a target for antitumor drugs. HSV-2 probably induces enzymes of glutamine metabolism because HSV-2 requires glutamine for growth, thus revealing potential new antiviral targets.

Structural features which control folding of homologous proteins in cell-free translation systems. The effect of a mitochondrial-targeting presequence on aspartate aminotransferase.

When the precursor to mitochondrial aspartate aminotransferase (pmAspAT) is synthesized in a rabbit reticulocyte lysate translation system (RRL), its properties are quite unlike those of the purified protein (Mattingly, J.R., Jr., Youssef, J., Iriarte, A., and Martinez-Carrion, M. (1993) J. Biol. Chem. 268, 3925-3937). These results suggest that molecular chaperones present in RRL modulate the folding of pmAspAT. To investigate the structural basis for this, we have used protease resistance to monitor the extent of folding for several related AspATs after synthesis in RRL and in wheat germ extract (WGE). In addition to pmAspAT, the following proteins were examined: the mature form of pmAspAT (delta 2-28 pmAspAT), its cytosolic counterpart (cAspAT), a chimeric protein consisting of the presequence of pmAspAT attached to the amino terminus of cAspAT (pcAspAT), and a pmAspAT variant in which the presequence and the amino-terminal domain of the mature enzyme are deleted (delta 2-57 pmAspAT). In RRL, delta 2-28 pmAspAT folds somewhat faster than intact pmAspAT, whereas the truncated delta 2-57 pmAspAT is unable to fold. In contrast, cAspAT and pcAspAT both fold with extreme rapidity. After synthesis in WGE, pmAspAT and delta 2-28 pmAspAT never acquire a protease-resistant conformation, whereas the folding of cAspAT and pcAspAT still occurs rapidly. We conclude that the presequence has only a minor role in determining the folding rate of the pmAspAT mitochondrial precursor protein in RRL or WGE and has no influence on the folding of the homologous cAspAT. Rather, the primary sequence of the mature part of the protein seems to dictate whether or how molecular chaperones regulate folding events.

Protein folding in a cell-free translation system. The fate of the precursor to mitochondrial aspartate aminotransferase.

The precursor to rat mitochondrial aspartate aminotransferase (pmAspAT) can be expressed in and purified from Escherichia coli as a fully active enzyme with remarkable trypsin resistance. Only two sites within the presequence are readily hydrolyzed (Martinez-Carrion, M., Altieri, F., Iriarte, A., Mattingly, J. R., Youssef, J., and Wu, T. (1990) Ann. N.Y. Acad. Sci. 585, 346-356). In contrast, pmAspAT freshly synthesized in rabbit reticulocyte lysate is significantly less resistant to proteolysis and is completely digested by trypsin. Extended incubation of the pmAspAT translation product slowly converts it to a species with qualitatively the same trypsin resistance as the purified pmAspAT. In addition, this species binds pyridoxal 5'-phosphate, exhibits catalytic activity, and loses its ability to be imported into mitochondria. This process appears to reflect protein folding. The rate of folding is unaffected by the addition of cofactor or the depletion of endogenous cofactor and is not significantly affected by the concentration of translation product in the reaction. Agents that decrease the availability of ATP partially inhibit the folding, whereas the sulfhydryl alkylating reagent N-ethylmaleimide and the detergent Triton X-100 completely prevent the conversion. Although the folding of pmAspAT in reticulocyte lysate is slow, folding is rapid once the translation product is sequestered within the mitochondria as the mature form of the enzyme. These results are presented as a model for the in vivo folding of pyridoxal-dependent, oligomeric mitochondrial precursors in the presence of cytoplasmic components and for the fate of true mitochondrial precursor proteins when not imported.

Teaching multiplication facts to students with learning problems.

The present study investigated the effectiveness of a constant time delay procedure in teaching multiplication facts to fifth- and sixth-grade students identified as learning disabled, behavior disordered, or educable mentally handicapped. Four students were taught oral responses to 30 multiplication facts using a constant 5-second (s) delay procedure. Data on the number of minutes of direct instruction time, as well as the number and percent of errors, trials, and sessions to criterion, were collected. Results indicated that the near-errorless learning procedure was effective in teaching multiplication facts to students placed in special education.

Isolation and properties of a liver mitochondrial precursor protein to aspartate aminotransferase expressed in Escherichia coli.

The precursor to rat liver mitochondrial aspartate aminotransferase has been expressed in Escherichia coli JM105 using the pKK233-2 expression vector. This mammalian natural precursor has been isolated as a soluble dimeric protein. The amino-terminal sequence and the amino acid composition of the isolated protein correspond to those predicted from the inserted cDNA (Mattingly, J. R., Jr., Rodriguez-Berrocal, F. J., Gordon, J., Iriarte, A., and Martinez-Carrion, M. (1987) Biochem. Biophys. Res. Commun. 149, 859-865). The isolated precursor contains bound pyridoxal phosphate and shows catalytic activity with a specific activity equal to that of the mature form of the enzyme. This precursor can also be processed by mitochondria into a form with the sodium dodecyl sulfate-polyacrylamide gel electrophoresis mobility of mature enzyme. The isolation of this precursor as a stable and catalytically active entity indicates that the presequence peptide does not necessarily interfere with much of the folding and basic structural properties of the mature protein component.

Monoclonal antibodies which identify a genus-specific Listeria antigen.

Fifteen murine monoclonal antibodies (MAbs) which react specifically with a protein antigen found in all species of Listeria were developed and characterized. These MAbs were tested extensively by both enzyme-linked immunosorbent assay and Western blot (immunoblot) analyses for cross-reaction with non-Listeria organisms, such as Staphylococcus, Streptococcus, Citrobacter, Pseudomonas, and Salmonella species, and were found to be nonreactive. The genus-specific antigen was identified as a heat-stable protein with a molecular weight in the range of 30,000 to 38,000 (under both reducing and nonreducing conditions), depending on the species of Listeria tested. In Listeria monocytogenes, L. innocua, L. ivanovii, and L. seeligeri the antigen has a molecular weight of approximately 30,000 to 34,000. In L. grayi and L. murrayi it has a molecular weight of approximately 35,000 to 38,000. In addition, several of the MAbs recognize lower-molecular-weight protein bands. There appear to be at least two groups of Listeria-specific MAbs based upon isotype and results of enzyme-linked immunosorbent assay and Western blot analyses. These MAbs have proven to be useful in the development of a diagnostic assay for Listeria species in food products.

Rapid monoclonal antibody-based enzyme-linked immunosorbent assay for detection of Listeria in food products.

A rapid diagnostic test for the detection of Listeria in food products has been created. This test, known as Listeria-Tek, uses 2 monoclonal antibodies specific for Listeria in an enzyme-linked immunosorbent assay (ELISA) format. The test requires only 40 h of broth enrichment with no culturing on solid media. It is extremely simple to perform and easy to interpret, and is at least as sensitive and accurate as the best of the culture methods. The test can be used with dairy products, meat products, and environmental samples. The ELISA test is safely performed on the open bench of the laboratory because no live cultures, no radioactivity, no phage, etc., are necessary. There is no need for special licenses or reserved laboratory space, and no waste disposal problems are encountered. If necessary, one technician could easily perform hundreds of assays per day. A printed data sheet is available for permanent records.

Evaluation of abbreviated enzyme immunoassay method for detection of Salmonella in low-moisture foods.

A modified enzyme immunoassay method (EIA) utilizing an 18 h pre-enrichment, a 6-8 h selective enrichment, and a 14 h M-broth post-enrichment is compared to the standard culture method (AOAC/BAM) on selected low-moisture foods. Tested samples included 238 inoculated, 30 naturally contaminated, and 30 uninoculated foods. By EIA, 235 samples were positive (optical densities greater than 0.2 at 405 nm), 233 of which were confirmed culturally. By the culture methods, 221 samples were positive. The EIA method was more productive in detecting salmonellae in inoculated samples of dry cheese powder, chocolate, and nonfat dry milk, whereas the culture method gave better recovery from naturally contaminated meat and bone meal. The modified EIA could be completed in 40 h and required no centrifugation.

Molecular cloning and in vivo expression of a precursor to rat mitochondrial aspartate aminotransferase.

A 2.4 kilobase cDNA for rat mitochondrial aspartate aminotransferase (E.C. 2.6.1.1.) was isolated and sequenced. The predicted presequence is 93% homologous to the presequences of the enzyme from pig and mouse. The predicted amino acid sequence of the mature enzyme differs from that determined directly by amino acid sequencing (Huynh, Q.K., Sakakibara, R., Watanabe, T., and Wada, H. (1981) J. Biochem. (Tokyo) 90, 863-875) at 13 amino acids residues. The most important difference is at position 140 where the cDNA encodes a tryptophanyl residue rather than the previously reported glycine. This critical residue is now seen to be conserved in all aspartate aminotransferases. The coding region of this cDNA was inserted into the plasmid cloning vector pKK233-2 and used to stably express an unfused precursor in Escherichia coli JM105.

Enzyme immunoassay for detection of Salmonella in low-moisture foods: collaborative study.

A collaborative study was performed in 15 laboratories to evaluate a modification of the enzyme immunoassay (EIA) method for detection of Salmonella in foods (46.B21-46.B29). The modified EIA requires 18-24 h pre-enrichment, 6-8 h selective enrichment, and 14-18 h M-broth post-enrichment prior to performing the assay, which requires 1-2 h. Total assay time is 40-52 h. The modified method was compared with the standard culture method for detection of Salmonella in 5 low-moisture foods: nonfat dry milk, milk chocolate, meat and bone meal, dry whole egg, and ground pepper. The modified method has been adopted official first action for use with low-moisture foods.