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- ArticleKnuesel RJ, Jacobs HO.Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):993-8.This paper introduces a method for self-assembling and electrically connecting small (20-60 micrometer) semiconductor chiplets at predetermined locations on flexible substrates with high speed (62500 chips/45 s), accuracy (0.9 micrometer, 0.14 degrees), and yield (> 98%). The process takes place at the triple interface between silicone oil, water, and a penetrating solder-patterned substrate. The assembly is driven by a stepwise reduction of interfacial free energy where chips are first collected and preoriented at an oil-water interface before they assemble on a solder-patterned substrate that is pulled through the interface. Patterned transfer occurs in a progressing linear front as the liquid layers recede. The process eliminates the dependency on gravity and sedimentation of prior methods, thereby extending the minimal chip size to the sub-100 micrometer scale. It provides a new route for the field of printable electronics to enable the integration of microscopic high performance inorganic semiconductors on foreign substrates with the freedom to choose target location, pitch, and integration density. As an example we demonstrate a fault-tolerant segmented flexible monocrystalline silicon solar cell, reducing the amount of Si that is used when compared to conventional rigid cells.
- ArticleLaothamatas I, Gao P, Wickramaratne A, Quintanilla CG, Dino A, Khan CA, Liou J, Green CB.Proc Natl Acad Sci U S A. 2020 01 14;117(2):993-999.An intimate link exists between circadian clocks and metabolism with nearly every metabolic pathway in the mammalian liver under circadian control. Circadian regulation of metabolism is largely driven by rhythmic transcriptional activation of clock-controlled genes. Among these output genes, Nocturnin (Noct) has one of the highest amplitude rhythms at the mRNA level. The Noct gene encodes a protein (NOC) that is highly conserved with the endonuclease/exonuclease/phosphatase (EEP) domain-containing CCR4 family of deadenylases, but highly purified NOC possesses little or no ribonuclease activity. Here, we show that NOC utilizes the dinucleotide NADP(H) as a substrate, removing the 2' phosphate to generate NAD(H), and is a direct regulator of oxidative stress response through its NADPH 2' phosphatase activity. Furthermore, we describe two isoforms of NOC in the mouse liver. The cytoplasmic form of NOC is constitutively expressed and associates externally with membranes of other organelles, including the endoplasmic reticulum, via N-terminal glycine myristoylation. In contrast, the mitochondrial form of NOC possesses high-amplitude circadian rhythmicity with peak expression level during the early dark phase. These findings suggest that NOC regulates local intracellular concentrations of NADP(H) in a manner that changes over the course of the day.
- ArticlePause A, Lee S, Lonergan KM, Klausner RD.Proc Natl Acad Sci U S A. 1998 Feb 03;95(3):993-8.The inactivation of the von Hippel-Lindau (VHL) tumor suppressor gene predisposes affected individuals to the human VHL cancer syndrome and is associated with sporadic renal cell carcinomas (RCC) and brain hemangioblastomas. VHL-negative 786-0 RCC cells are tumorigenic in nude mice which is suppressed by the reintroduction of VHL. Remarkably, this occurs without affecting the growth rate and cell cycle profile of these cells in culture. The 786-0 cell line, like many cancer cells, fails to exit the cell cycle upon serum withdrawal. Here, it is shown that reintroduction of the wild-type VHL gene restores the ability of VHL-negative RCC cancer cells to exit the cell cycle and enter G0/quiescence in low serum. Both VHL-positive and VHL-negative RCC cells exit the cell cycle by contact inhibition. The cyclin-dependent kinase inhibitor, p27, accumulates upon serum withdrawal, only in the presence of VHL, as a result of the stabilization of the protein. We propose that the loss of wild-type VHL gene results in a specific cellular defect in serum-dependent growth control, which may initiate tumor formation. This is corrected by the reintroduction of wild-type VHL, implicating VHL as the first tumor suppressor involved in the regulation of cell cycle exit, which is consistent with its gatekeeper function in the kidney.
- ArticleOrban GA, Dupont P, De Bruyn B, Vogels R, Vandenberghe R, Mortelmans L.Proc Natl Acad Sci U S A. 1995 Feb 14;92(4):993-7.We have localized an area in the human brain involved in the processing of contours defined by motion differences (kinetic contours) by comparing with positron emission tomography the regional cerebral blood flow in tasks performed with kinetic and luminance-defined gratings. These tasks included passive viewing, counting the total number of grating stimuli, and counting the number of gratings of a given orientation. Comparison between the counting tasks and passive viewing with a given type of contour revealed a set of active areas that were similar for both luminance-defined and kinetic contours. Comparisons between these two types of contours revealed a single focus in the right hemisphere that did not overlap with the many regions activated by uniform motion. In particular this "kinetic focus" was clearly separated from the area previously defined as the human homologue of V5/middle temporal. Activity in this kinetic focus was stronger when orientation had to be processed than in the other two tasks. These results and control experiments with uniformly moving random dot patterns suggest the existence of an area in the human visual system that is activated much more by kinetic contours than by luminance contours or uniformly moving random dots. Up to now, such an area has not been described in the monkey visual system.
- ArticleYang Z, Kurpiewski MR, Ji M, Townsend JE, Mehta P, Jen-Jacobson L, Saxena S.Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):E993-1000.The relationship between DNA sequence recognition and catalytic specificity in a DNA-modifying enzyme was explored using paramagnetic Cu(2+) ions as probes for ESR spectroscopic and biochemical studies. Electron spin echo envelope modulation spectroscopy establishes that Cu(2+) coordinates to histidine residues in the EcoRI endonuclease homodimer bound to its specific DNA recognition site. The coordinated His residues were identified by a unique use of Cu(2+)-ion based long-range distance constraints. Double electron-electron resonance data yield Cu(2+)-Cu(2+) and Cu(2+)-nitroxide distances that are uniquely consistent with one Cu(2+) bound to His114 in each subunit. Isothermal titration calorimetry confirms that two Cu(2+) ions bind per complex. Unexpectedly, Mg(2+)-catalyzed DNA cleavage by EcoRI is profoundly inhibited by Cu(2+) binding at these hitherto unknown sites, 13 Å away from the Mg(2+) positions in the catalytic centers. Molecular dynamics simulations suggest a model for inhibition of catalysis, whereby the Cu(2+) ions alter critical protein-DNA interactions and water molecule positions in the catalytic sites. In the absence of Cu(2+), the Mg(2+)-dependence of EcoRI catalysis shows positive cooperativity, which would enhance EcoRI inactivation of foreign DNA by irreparable double-strand cuts, in preference to readily repaired single-strand nicks. Nonlinear Poisson-Boltzmann calculations suggest that this cooperativity arises because the binding of Mg(2+) in one catalytic site makes the surface electrostatic potential in the distal catalytic site more negative, thus enhancing binding of the second Mg(2+). Taken together, our results shed light on the structural and electrostatic factors that affect site-specific catalysis by this class of endonucleases.
- ArticleWu Q, Lahti JM, Air GM, Burrows PD, Cooper MD.Proc Natl Acad Sci U S A. 1990 Feb;87(3):993-7.The BP-1/6C3 antigen is a phosphorylated cell surface glycoprotein that can be identified by monoclonal antibodies on mouse pre-B cells, immature B cells, and certain stromal cell lines from bone marrow. Expression of this antigen is increased in stromal-dependent pre-B cell lines and retrovirally transformed pre-B cells. Expression of the BP-1/6C3 antigen thus correlates with proliferation and transformation of immature B-lineage cells. In this study, we report the isolation and characterization of cDNAs encoding the BP-1/6C3 antigen. Northern blot analysis revealed a major 4.1-kilobase mRNA in all BP-1/6C3+ mouse pre-B lines and in a human pre-B cell line. BP-1/6C3 mRNA was either absent or truncated in BP-1/6C3- cell lines. The cDNA sequence predicts a type II integral membrane protein of 945 amino acids with an intracytoplasmic amino terminus of only 17 amino acids and a typical zinc-binding motif in its extracellular domain. BP-1/6C3 has significant homology to aminopeptidase N and is the second member of the zinc-dependent metallopeptidase gene family to be found on the surface of early B-lineage cells.
- ArticleWu MC, Shanks RD, Lewin HA.Proc Natl Acad Sci U S A. 1989 Feb;86(3):993-6.Genetic potentials (pedigree-estimated breeding value) for milk and for fat were compared in cows grouped according to subclinical stage of bovine leukemia virus infection. Genetic potential for milk production was significantly greater in seropositive cows with persistent lymphocytosis (622 +/- 72 kg) and in seropositive hematologically normal cows (554 +/- 34 34 kg) than in seronegative herdmates (418 +/- 53 kg). When 305-day twice-daily-milking mature equivalent milk production records for the current lactation were adjusted for genetic potential, bovine leukemia virus-infected cows that were hematologically normal had significantly greater milk production than did seronegative herdmates, suggesting that early bovine leukemia virus infection was positively associated with milk yield. Genetic potential for fat production was significantly greater for cows with persistent lymphocytosis (21 +/- 2 kg) than for other seropositive (16 +/- 1 kg) and seronegative herdmates (13 +/- 2 kg); however, 305-day twice-daily-milking mature equivalent fat production for the current lactation was not significantly different between the groups. Thus, cows with persistent lymphocytosis did not produce fat according to their genetic potential. As an apparent consequence of tendencies for greater milk yield and less fat production, milk fat percentage was significantly reduced in cows with persistent lymphocytosis (3.33 +/- 0.09%) and other seropositive cows (3.48 +/- 0.05%) relative to seronegative herdmates (3.67 +/- 0.07%). These results suggest a need to reevaluate the economic impact of bovine leukemia virus infection on the dairy industry.
- ArticleGelmann EP, Franchini G, Manzari V, Wong-Staal F, Gallo RC.Proc Natl Acad Sci U S A. 1984 Feb;81(4):993-7.Human T-cell leukemia virus IIMo (HTLV-IIMo) is a human retrovirus isolated from a patient with a T-cell hairy cell leukemia. This virus has been shown to have core protein (gag) antigens similar to, but distinct from, those of all known isolates of the prototype human T-cell leukemia virus (HTLV-I). We have used a subgenomic clone of the HTLV-I env-pX region to detect and characterize HTLV-IIMo proviral sequences by performing Southern blot hybridization under conditions of low stringency. Using the HTLV-I probe, we cloned a partial integrated HTLV-IIMo provirus from a genomic library of the producer Mo cell line. These sequences could be characterized by low stringency hybridization with different subgenomic clones of HTLV-I. An HTLV-IIMo-specific subclone was made by isolating a 3.6-kilobase BamHI fragment of the partial provirus. This was used to clone two full-length integrated viral genomes. Using the HTLV-IIMo viral probe, we also showed by hybridization under stringent conditions to DNA and RNA of various infected and uninfected cell lines that these HTLV-IIMo sequences are unique.
- ArticleFollicle-stimulating hormone-dependent phosphorylation of vimentin in cultures of rat Sertoli cells.Spruill WA, Steiner AL, Tres LL, Kierszenbaum AL.Proc Natl Acad Sci U S A. 1983 Feb;80(4):993-7.Endogenous protein phosphorylation was investigated in cultured rat Sertoli cells after treatment with follicle-stimulating hormone (FSH) and pharmacological agents that activate cAMP-dependent protein kinases. In intact Sertoli cells, both phosphorylation and dephosphorylation of proteins occurred in response to treatment with these agents. Studies using cell-free preparations suggest that four phosphoproteins phosphorylated by cAMP or the catalytic subunit of cAMP-dependent protein kinase were also phosphorylated in a FSH-dependent manner in intact cells. These data suggest that FSH-dependent phosphorylation in Sertoli cells occurs through activation of a cAMP-dependent protein kinase. A FSH-dependent phosphoprotein with a molecular weight of 58,000 was identified as the intermediate filament protein vimentin, based on its migration in two-dimensional gels and its peptide map. The cellular distribution of vimentin was monitored by immunofluorescence in Sertoli cells after treatment with FSH. Results of this study support a role for intermediate filaments in FSH-dependent events in Sertoli cells.
- ArticleStraus SE, Owens J, Ruyechan WT, Takiff HE, Casey TA, Vande Woude GF, Hay J.Proc Natl Acad Sci U S A. 1982 Feb;79(4):993-7.Varicella-zoster virus (VZV) DNA was cleaved with restriction endonuclease EcoRI, and most of the resulting fragments were successfully cloned in the phage vector lambda gtWES . lambda B. Double digestions of cloned fragments with EcoRI and BamHI and hybridizations to blot-transferred BamHI digests of VZV DNA were used to construct a physical map of the genome. The molecular termini of the DNA were identified by restriction enzyme analysis after exonuclease III digestion. The data indicate that VZV DNA exists in two isomeric forms that differ by inversion of one short terminal genome segment. Electron microscopic studies revealed that the short genome segment consists of a terminal revealed that the short genome segment consists of a terminal sequence of about 3.4 X 10(6) daltons that is separated from an internal inverted repeat of itself by a 5.8 X 10(60)-dalton unique DNA segment.
- ArticleUiterkamp AJ, Mason HS.Proc Natl Acad Sci U S A. 1973 Apr;70(4):993-6.The T(r) and T[unk] states of tyrosinase were treated with NO. EPR spectra of the products observed at 14 degrees K and at 113 degrees K showed mixtures of two signals. One had components in the region of g = 2, about 1200 G wide, and in the region of g = 4, showing hyperfine splitting. The other signal was similar to that arising from isolated Cu(II) ions in an axially symmetric environment. The first signal was indicative of Deltam = 1 and Deltam = 2 transitions arising from magnetic dipole-dipole coupled Cu(II) ion pairs. It closely resembled previously reported EPR spectra obtained from NO-treated hemocyanin, which were confirmed in this study. The normal Curie behavior of the signals between 230 degrees K and 14 degrees K ruled out significant exchange coupling between the ion pairs. The Deltam = 2 signals were not saturable up to 350 mW at 14 degrees K. The broad Deltam = 1 signals could be separated from accompanying signals by the saturation characteristics of the latter at about 10 mW at 14 degrees K. The results establish the presence of a pair of copper ions at the active site of tyrosinase, and a clsoe structural relationship between this active site and that of hemocyanin.
- ArticleNeumann E, Katchalsky A.Proc Natl Acad Sci U S A. 1972 Apr;69(4):993-7.Electric impulses are capable of inducing long-lived conformational changes in (metastable) biopolymers. Results of experiments with poly(A).2 poly(U) and ribosomal RNA, which are known to develop metastabilities, are reported. A polarization mechanism is proposed to explain the structural transitions observed in the biopolymers exposed to the impulses. In accordance with this idea, the applied electric field (of about 20 kV/cm and decaying exponentially, with a decay time of about 10 musec) induces large dipole moments by shifting the ionic atmosphere of multistranded polynucleotide helices. This shift, in turn, causes strand repulsion and partial unwinding. The fields used in our experiments are of the same order of magnitude as those in nerve impulses. The significance of the impulse experiments with regard to the question of biological memory recording is briefly discussed.
- ArticleRodrigues JL, Pellizari VH, Mueller R, Baek K, Jesus Eda C, Paula FS, Mirza B, Hamaoui GS, Tsai SM, Feigl B, Tiedje JM, Bohannan BJ, Nüsslein K.Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):988-93.The Amazon rainforest is the Earth's largest reservoir of plant and animal diversity, and it has been subjected to especially high rates of land use change, primarily to cattle pasture. This conversion has had a strongly negative effect on biological diversity, reducing the number of plant and animal species and homogenizing communities. We report here that microbial biodiversity also responds strongly to conversion of the Amazon rainforest, but in a manner different from plants and animals. Local taxonomic and phylogenetic diversity of soil bacteria increases after conversion, but communities become more similar across space. This homogenization is driven by the loss of forest soil bacteria with restricted ranges (endemics) and results in a net loss of diversity. This study shows homogenization of microbial communities in response to human activities. Given that soil microbes represent the majority of biodiversity in terrestrial ecosystems and are intimately involved in ecosystem functions, we argue that microbial biodiversity loss should be taken into account when assessing the impact of land use change in tropical forests.
- ArticleAnders N, Wilkinson MD, Lovegrove A, Freeman J, Tryfona T, Pellny TK, Weimar T, Mortimer JC, Stott K, Baker JM, Defoin-Platel M, Shewry PR, Dupree P, Mitchell RA.Proc Natl Acad Sci U S A. 2012 Jan 17;109(3):989-93.Xylan, a hemicellulosic component of the plant cell wall, is one of the most abundant polysaccharides in nature. In contrast to dicots, xylan in grasses is extensively modified by α-(1,2)- and α-(1,3)-linked arabinofuranose. Despite the importance of grass arabinoxylan in human and animal nutrition and for bioenergy, the enzymes adding the arabinosyl substitutions are unknown. Here we demonstrate that knocking-down glycosyltransferase (GT) 61 expression in wheat endosperm strongly decreases α-(1,3)-linked arabinosyl substitution of xylan. Moreover, heterologous expression of wheat and rice GT61s in Arabidopsis leads to arabinosylation of the xylan, and therefore provides gain-of-function evidence for α-(1,3)-arabinosyltransferase activity. Thus, GT61 proteins play a key role in arabinoxylan biosynthesis and therefore in the evolutionary divergence of grass cell walls.
- ArticleColebrook LD, Tarbell DS.Proc Natl Acad Sci U S A. 1961 Jul;47(7):993-6.
- ArticleParsons PA, Green MM.Proc Natl Acad Sci U S A. 1959 Jul;45(7):993-6.
- ArticleBrady RO.Proc Natl Acad Sci U S A. 1958 Oct 15;44(10):993-8.
- ArticleDufner A, Pownall S, Mak TW.Proc Natl Acad Sci U S A. 2006 Jan 24;103(4):988-93.Proteins containing a caspase recruitment domain (CARD) play pivotal roles in signal transduction leading to apoptosis and NF-kappaB activation and inflammation. Here we identify and characterize human and mouse CARD protein 6 (CARD6), CARD-containing proteins of unique structure. CARD6 associates with microtubules and interacts with receptor-interacting protein (RIP)-like interacting caspase-like apoptosis regulatory protein kinase (RICK), a CARD-containing member of the RIP family of protein kinases. These kinases are involved in multiple NF-kappaB signaling pathways important for innate and adaptive immune responses. Surprisingly, the CARDs of CARD6 and RICK were not required for their interaction; instead, mutational analysis revealed that the CARD of CARD6 negatively controls the association of these molecules. CARD6 also binds to RIP1, a RIP kinase homologue that lacks a CARD but contains a C-terminal death domain. Coexpression of RICK targets CARD6 to aggresomes via a mechanism that requires the CARD of RICK. Importantly, CARD6 expression has a synergistic effect on NF-kappaB activation induced by several independent signal transduction pathways. In summary, our results indicate that CARD6 is a regulator of NF-kappaB activation that modulates the functions of RIP kinase family members.
- ArticleSwairjo MA, Schimmel PR.Proc Natl Acad Sci U S A. 2005 Jan 25;102(4):988-93.The genetic code is fixed in aminoacylation reactions catalyzed by aminoacyl-tRNA synthetases. Amino acid discrimination occurs at two sites: one for amino acid activation and aminoacylation and one for editing misactivated amino acids. Although the active site sieves out bulkier amino acids, misactivation occurs with substrates whose side chains are smaller than the cognate one. Paradoxically, although alanyl-tRNA synthetase activates glycine as well as alanine, the sterically larger (than alanine) serine is also misactivated. Here, we report crystal structures of an active fragment of Aquifex aeolicus alanyl-tRNA synthetase complexed, separately, with Mg2+-ATP, alanine, glycine, and serine. Ala and Gly are bound in similar orientations in a side-chain-accommodating pocket, where alpha-amino and carboxyl groups are stabilized by salt bridges, and the carboxyl by an H-bond from the side chain NH2 of Asn-194. In contrast, whereas the same two salt bridges stabilize bound Ser, H-bonding of the highly conserved (among class II tRNA synthetases) Asn-194 side chain NH2 to the Ser OH, instead of to the carboxyl, forces pocket expansion. Significantly, in the Mg2+-ATP complex, Asn-194 coordinates a Mg2+-alpha-phosphate bridge. Thus, the sieve for Ser exclusion is broken because of selective pressure to retain Asn-194 for Mg2+-ATP and Ala binding.
- ArticleStollar V, Stollar BD.Proc Natl Acad Sci U S A. 1970 Apr;65(4):993-1000.A quantitative complement fixation assay which specifically measures double-stranded RNA has been used to study this RNA extracted from uninfected and arbovirus-infected cells. The double-straned RNA of the uninfected BHK-21 cells sedimented in the 12S region in sucrose gradients. The double-stranded RNA of Sinbis virus-infected cells, as measured immunochemically, included a predominant peak at 12S, a smaller 18S peak, and polydisperse material extending into the 26-30S region. All classes of this RNA detected immunochemically showed a sharp thermal denaturation curve, and increased in amount progressively during infection, with the 12S peak predominant at all times.