Clone-structured graph representations enable flexible learning and vicarious evaluation of cognitive maps.

Cognitive maps are mental representations of spatial and conceptual relationships in an environment, and are critical for flexible behavior. To form these abstract maps, the hippocampus has to learn to separate or merge aliased observations appropriately in different contexts in a manner that enables generalization and efficient planning. Here we propose a specific higher-order graph structure, clone-structured cognitive graph (CSCG), which forms clones of an observation for different contexts as a representation that addresses these problems.

Lysine-specific acetylated proteome from the archaeon Thermococcus gammatolerans reveals the presence of acetylated histones.

Thermococcus gammatolerans EJ3 is an extremophile archaeon which was revealed as one of the most radioresistant organisms known on Earth, withstanding up to 30 kGy gamma-ray radiations. While its theoretical proteome is rather small, T. gammatolerans may enhance its toolbox by post-translational modification of its proteins.

Stabilization of a new nanocomposite family by reduction of gold nanoclusters with electron-reservoir complexes.

Four stable 19-electron Fe and Co sandwich electron-reservoirs and three hydride reservoir complexes reduce the prototypal nanocluster Au25(SR)18 (R = CH2CH2Ph) leading to a largely increased kinetic stabilization of the anionic nanocluster form compared to previously known nanocluster anion salts; these salts represent new and robust nanocomposite anionic gold clusters with 18-electron sandwich complexes as counter cations.

Role of AcrAB-TolC multidrug efflux pump in drug-resistance acquisition by plasmid transfer.

Drug-resistance dissemination by horizontal gene transfer remains poorly understood at the cellular scale. Using live-cell microscopy, we reveal the dynamics of resistance acquisition by transfer of the fertility factor-conjugation plasmid encoding the tetracycline-efflux pump TetA. The entry of the single-stranded DNA plasmid into the recipient cell is rapidly followed by complementary-strand synthesis, plasmid-gene expression, and production of TetA.

Loss of Msp1p in Schizosaccharomyces pombe induces a ROS-dependent nuclear mutator phenotype that affects mitochondrial fission genes.

Mitochondria continually fuse and divide to dynamically adapt to changes in metabolism and stress. Mitochondrial dynamics are also required for mitochondrial DNA (mtDNA) integrity; however, the underlying reason is not known. In this study, we examined the link between mitochondrial fusion and mtDNA maintenance in Schizosaccharomyces pombe, which cannot survive without mtDNA, by screening for suppressors of the lethality induced by loss of the dynamin-related large GTPase Msp1p.

Prioritizing targets for structural biology through the lens of proteomics: the archaeal protein TGAM_1934 from Thermococcus gammatolerans.

ORFans are hypothetical proteins lacking any significant sequence similarity with other proteins. Here, we highlighted by quantitative proteomics the TGAM_1934 ORFan from the hyperradioresistant Thermococcus gammatolerans archaeon as one of the most abundant hypothetical proteins. This protein has been selected as a priority target for structure determination on the basis of its abundance in three cellular conditions.

N- and O-acetylation of threonine residues in the context of proteomics.

The detection of post-translational modifications (PTMs) of proteins is a matter of intensive research. Among all possible pitfalls that may lead to misidentifications, the chemical stability of modified peptides is scarcely questioned. Global proteomic studies devoted to protein acetylation are becoming popular.

Major soluble proteome changes in Deinococcus deserti over the earliest stages following gamma-ray irradiation.

Background: Deinococcus deserti VCD115 has been isolated from Sahara surface sand. This radiotolerant bacterium represents an experimental model of choice to understand adaptation to harsh conditions encountered in hot arid deserts. We analysed the soluble proteome dynamics in this environmentally relevant model after exposure to 3 kGy gamma radiation, a non-lethal dose that generates massive DNA damages.

PPR8522 encodes a chloroplast-targeted pentatricopeptide repeat protein necessary for maize embryogenesis and vegetative development.

The pentatricopeptide repeat (PPR) domain is an RNA binding domain allowing members of the PPR superfamily to participate in post-transcriptional processing of organellar RNA. Loss of PPR8522 from maize (Zea mays) confers an embryo-specific (emb) phenotype. The emb8522 mutation was isolated in an active Mutator (Mu) population and co-segregation analysis revealed that it was tightly linked to a MuDR insertion in the first exon of PPR8522.

Mechanical stress acts via katanin to amplify differences in growth rate between adjacent cells in Arabidopsis.

The presence of diffuse morphogen gradients in tissues supports a view in which growth is locally homogenous. Here we challenge this view: we used a high-resolution quantitative approach to reveal significant growth variability among neighboring cells in the shoot apical meristem, the plant stem cell niche. This variability was strongly decreased in a mutant impaired in the microtubule-severing protein katanin.

PPR2263, a DYW-Subgroup Pentatricopeptide repeat protein, is required for mitochondrial nad5 and cob transcript editing, mitochondrion biogenesis, and maize growth.

RNA editing plays an important role in organelle gene expression in various organisms, including flowering plants, changing the nucleotide information at precise sites. Here, we present evidence that the maize (Zea mays) nuclear gene Pentatricopeptide repeat 2263 (PPR2263) encoding a DYW domain-containing PPR protein is required for RNA editing in the mitochondrial NADH dehydrogenase5 (nad5) and cytochrome b (cob) transcripts at the nad5-1550 and cob-908 sites, respectively. Its putative ortholog, MITOCHONDRIAL EDITING FACTOR29, fulfills the same role in Arabidopsis thaliana.

Revisiting iodination sites in thyroglobulin with an organ-oriented shotgun strategy.

Thyroglobulin (Tg) is secreted by thyroid epithelial cells. It is essential for thyroid hormonogenesis and iodine storage. Although studied for many years, only indirect and partial surveys of its post-translational modifications were reported.

T4 colorectal cancer: is laparoscopic resection contraindicated?

Aim: T4 colorectal cancer remains a contraindication for laparoscopy. It is argued that the risk of incomplete resection could be higher than in open surgery. Furthermore, difficulty in dissection could lead to a very high rate of conversion.

Laparoscopic enucleation of pancreatic neoplasm.

Background: Enucleation is an alternative procedure for treating benign and borderline neoplasms of the pancreas, which preserves healthy parenchyma and pancreatic function. This study aimed to evaluate the postoperative and long-term results after laparoscopic enucleation.

Methods: Data collected prospectively from 23 consecutive patients who underwent laparoscopic pancreatic enucleation were analyzed.

Palladium motion in cyclomeric compounds: a theoretical study.

Density functional theory (DFT)/B3LYP calculations have been carried out to study successive intramolecular 1,n palladium shifts (n = 3-5) in palladium complexes of organic cyclomers. Such shifts of the PdBr(phosphine) moiety, which is bound to the cyclomer and which exchanges concomitantly with a hydrogen atom distant by n carbon atoms from palladium, might lead to an endless motion around the cyclomer. The cyclomers that have been analyzed are either the [1,1,1,1]paracyclophane 1, a THF-based 16-crown-4 structure 2, or the THF-ethylene cyclic dimer 3 (THF = tetrahydrofuran).

Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons.

Deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. To achieve a comprehensive and accurate annotation of the Deinococcus deserti genome, we performed an N terminus-oriented characterization of its proteome. For this, we used a labeling reagent, N-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein N termini.

Identification of uranyl binding proteins from human kidney-2 cell extracts by immobilized uranyl affinity chromatography and mass spectrometry.

To improve our knowledge on protein targets of uranyl ion (UO(2)(2+)), we set up a proteomic strategy based on immobilized metal-affinity chromatography (IMAC). The successful enrichment of UO(2)(2+)-interacting proteins from human kidney-2 (HK-2) soluble cell extracts was obtained using an ion-exchange chromatography followed by a dedicated IMAC process previously described and designed for the uranyl ion. By mass spectrometry analysis we identified 64 proteins displaying varied functions.

Floral stem cell termination involves the direct regulation of AGAMOUS by PERIANTHIA.

In Arabidopsis, the population of stem cells present in young flower buds is lost after the production of a fixed number of floral organs. The precisely timed repression of the stem cell identity gene WUSCHEL (WUS) by the floral homeotic protein AGAMOUS (AG) is a key part of this process. In this study, we report on the identification of a novel input into the process of floral stem cell regulation.

Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti.

To better understand adaptation to harsh conditions encountered in hot arid deserts, we report the first complete genome sequence and proteome analysis of a bacterium, Deinococcus deserti VCD115, isolated from Sahara surface sand. Its genome consists of a 2.8-Mb chromosome and three large plasmids of 324 kb, 314 kb, and 396 kb.

Autophosphorylated residues involved in the regulation of human chk2 in vitro.

Human checkpoint kinase 2 is a major actor in checkpoint activation through phosphorylation by ataxia telangiectasia mutated in response to DNA double-strand breaks. In the absence of de novo DNA damage, its autoactivation, reported in the event of increased Cds1/checkpoint kinase 2 (Chk2) expression, has been attributed to oligomerization. Here we report a study performed on autoactivated recombinant Chk2 proteins that aims to correlate kinase activity and phosphorylation status.

Specific capture of uranyl protein targets by metal affinity chromatography.

To improve general understanding of biochemical mechanisms in the field of uranium toxicology, the identification of protein targets needs to be intensified. Immobilized metal affinity chromatography (IMAC) has been widely developed as a powerful tool for capturing metal binding proteins from biological extracts. However uranyl cations (UO2(2+)) have particular physico-chemical characteristics which prevent them from being immobilized on classical metal chelating supports.

Through-space intramolecular palladium rearrangement in substituted aryl complexes: theoretical study of the aryl to alkylpalladium migration process.

DFT/B3LYP calculations have been carried out to study intramolecular 1,n palladium shifts (n = 3-5) between sp2 and sp3 carbon atoms in alkylarylpalladium systems. Such shifts, which also involve a concomitant exchange with a hydrogen atom of the alkylaryl ligand, are quite often a pivotal step of several organic transformations mediated by palladium complexes. We show that the intimate mechanism for the 1,3 shift corresponds to a Pd(IV) pathway, whereas a Pd(II) pathway is favored in the case of 1,5 migrations.

THUMP from archaeal tRNA:m22G10 methyltransferase, a genuine autonomously folding domain.

The tRNA:m2(2)G10 methyltransferase of Pyrococus abyssi (PAB1283, a member of COG1041) catalyzes the N2,N2-dimethylation of guanosine at position 10 in tRNA. Boundaries of its THUMP (THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases)--containing N-terminal domain [1-152] and C-terminal catalytic domain [157-329] were assessed by trypsin limited proteolysis. An inter-domain flexible region of at least six residues was revealed.

Can weak interactions modify the binding properties of a strong nitrogen donor? Unusual N-coordination of a phosphoranylidene-substituted pyrazolone unit towards palladium(II) centres: an experimental and theoretical study.

Selective N(2)-binding of 3-methyl-1-phenyl-4-(triphenylphosphoranylidene)-2-pyrazolin-5-one (L) has been found in two palladium(II) complexes, [PdCl(2)L(2)](2) and [Pd(o-C(6)H(4)CH(2)NMe(2))Cl](3). X-Ray diffraction studies show that the pyrazole rings lie almost perpendicular to the coordination plane. In both complexes the metal atom is located out of the plane defined by the pyrazole ring(s)(dihedral angle between the plane and the Pd-N vector approximately 30 degrees).

Screening of human serum proteins for uranium binding.

About 20% of uranyl ions in serum are associated with the protein pool. A few of them such as transferrin have been characterized, but most still have to be identified to obtain a better explanation of the biochemical toxicology and kinetics of uranium. We designed an in vitro sensitive procedure involving a combination of bidimensional chromatography with time-resolved fluorescence, coupled with proteomic analysis, to identify uranium-binding proteins in human serum fractions.