Equine severe combined immunodeficiency: a defect in V(D)J recombination and DNA-dependent protein kinase activity.

V(D)J rearrangement is the molecular mechanism by which an almost infinite array of specific immune receptors are generated. Defects in this process result in profound immunodeficiency as is the case in the C.B-17 SCID mouse or in RAG-1 (recombination-activating gene 1) or RAG-2 deficient mice. It has recently become clear that the V(D)J recombinase most likely consists of both lymphoid-specific factors and ubiquitously expressed components of the DNA double-strand break repair pathway. The deficit in SCID mice is in a factor that is required for both of these pathways. In this report, we show that the factor defective in the autosomal recessive severe combined immunodeficiency of Arabian foals is required for (i) V(D)J recombination, (ii) resistance to ionizing radiation, and (iii) DNA-dependent protein kinase activity.

Involvement of the ALL-1 gene in a solid tumor.

Translocations involving chromosome band 11q23, found in 5-10% of human acute leukemias, disrupt the ALL-1 gene. This gene is fused by reciprocal translocation with a variety of other genes in acute lymphoblastic and myelogenous leukemias, and it undergoes self-fusion in acute myeloid leukemias with normal karyotype or trisomy 11. Here we report an alteration of the ALL-1 gene in a gastric carcinoma cell line (Mgc80-3). Characterization of this rearrangement revealed a three-way complex translocation, involving chromosomes 1 and 11, resulting in a partial duplication of the ALL-1 gene. Sequencing of reverse transcription-PCR products and Northern blot analysis showed that only the partially duplicated ALL-1 gene was transcribed, producing an mRNA with exon 8 fused to exon 2. This report of ALL-1 gene rearrangement in a solid tumor suggests that ALL-1 plays a role in the pathogenesis of some solid malignancies. The absence of the normal transcript in this cell line, in association with the loss-of-heterozygosity studies on chromosome 11q23 seen in solid tumors, suggests that ALL-1 is involved in tumorigenesis by a loss-of-function mechanism.

Caracterização de rearranjos cromossômicos citogeneticamente equilibrados associados a quadros clínicos

Este estudo teve como objetivos (a) identificar mecanismos pelos quais rearranjos cromossômicos citogeneticamente equilibrados possam estar associados de maneira causal a determinados quadros clínicos e (b) contribuir para a compreensão dos mecanismos de formação desses rearranjos. Para isso, foram estudados 45 rearranjos cromossômicos citogeneticamente equilibrados (29 translocações, 10 inversões e seis rearranjos complexos), detectados em pacientes que apresentavam malformações congênitas, comprometimento do desenvolvimento neuropsicomotor ou déficit intelectual. Foram 31 rearranjos cromossômicos esporádicos, três familiais que segregavam com o quadro clínico e mais 11 rearranjos cromossômicos herdados de genitores fenotipicamente normais. Inicialmente os pontos de quebra desses rearranjos foram mapeados por hibridação in situ fluorescente (FISH). A busca por microdeleções e duplicações genômicas foi realizada por a-CGH. A investigação dos pontos de quebra prosseguiu com a aplicação da técnica de Mate-Pair Sequencing (MPS), que permite localizar as quebras em segmentos de 100 pb - 1 kb, na maioria dos casos. Para obter os segmentos de junção das quebras no nível de pares de bases, os segmentos delimitados por MPS foram sequenciados pelo método de Sanger. A análise por aCGH revelou microdeleções ou microduplicações localizadas nos cromossomos rearranjados, em 12 dos 45 pacientes investigados (27%). A análise de 27 rearranjos por MPS permitiu a caracterização dos pontos de junção das quebras. MPS expandiu o número de pontos de quebra, detectados por análise do cariótipo ou aCGH, de 114 para 156 (em resolução < 2kb, na maioria dos casos). O número de pontos de quebra/rearranjo variou de 2 a 20. Os 156 pontos de quebra resultaram em 86 variantes estruturais equilibradas e outras 32 variantes não equilibradas. Perdas e ganhos de segmentos submiscroscópicos nos cromossomos rearranjados constituíram a principal causa ou, provavelmente, contribuíram para o quadro clínico de 12 dos 45 pacientes. Em cinco desses 12 rearranjos foram detectadas por MPS a interrupção de genes já relacionados à doença, ou provável alteração de sua região reguladora, contribundo para o quadro clínico. Em quatro dos 33 rearranjos não associados a perdas ou ganhos de segmentos, a análise por MPS revelou a interrupção de genes que já foram anteriormente relacionados a doenças, explicando-se, assim, as características clínicas dos portadores; outro rearranjo pode ter levando alteração da expressão gênica de gene sensível a dosagem e ao quadro clínico. Um rearranjo cromossômico familial, identificado na análise após bandamento G como uma translocação equilibrada, t(2;22)(p14;q12), segregava com quadro de atraso do desenvolvimento neuropsicomotor e dificuldade de aprendizado associados a dismorfismos. A combinação das análises por FISH, aCGH e MPS revelou que se tratava, na verdade, de rearranjo complexo entre os cromossomos 2, 5 e 22, incluindo 10 quebras. A segregação de diferentes desequilíbrios submicroscópicos em indivíduos afetados e clinicamente normais permitiu a compreensão da variabilidade clínica observada na família. Rearranjos equilibrados detectados em indivíduos afetados, mas herdados de genitores clinicamente normais, são, em geral, considerados como não tendo relação com o quadro clínico, apesar da possibilidade de desequilíbrios cromossômicos gerados por permuta desigual na meiose do genitor portador do rearranjo. Neste trabalho, a investigação de 11 desses rearranjos por aCGH não revelou perdas ou ganhos de segmentos nos cromossomos rearranjados. No entanto, a análise por aCGH da portadora de um desses rearranjos - inv(12)mat - revelou deleção de 8,7 Mb no cromossomo 8, como causa de seu fenótipo clínico. Essa deleção estava relacionada com outro rearranjo equilibrado também presente em sua mãe, independente da inversão. Para compreender os mecanismos de formação de rearranjos citogeneticamente equilibrados, investigamos os segmentos de junção no nível de pares de base. A análise por MPS que levou, na maioria dos casos, ao mapeamento dos pontos de quebras em segmentos <1kb permitiu o sequenciamento pelo método de Sanger de 51 segmentos de junções de 17 rearranjos. A ocorrência de blunt fusions ou inserções e deleções <10 pb, e a ausência de homologia ou a presença de micro homologia de 2 pb a 4 pb de extensão indicaram o mecanismo de junção de extremidades não homólogas (non-homologous end joinging; NHEJ), na maioria das 51 junções caracterizadas. As características de três dos quatro rearranjos mais complexos, com 17-20 quebras, indicaram sua formação pelo mecanismo de chromothripsis. Este estudo mostra a importância da análise genômica de variações de número de cópias por microarray, juntamente com o mapeamento dos pontos de quebra por MPS, para determinar a estrutura de rearranjos cromossômicos citogeneticamente equilibrados e seu impacto clínico. O mapeamento dos segmentos de junção por MPS, permitindo o sequenciamento pelo método de Sanger, foi essencial para a compreensão de mecanismos de formação desses rearranjos

Water adsorption in hydrophilic zeolites: experiment and simulation

We have measured experimental adsorption isotherms of water in zeolite LTA4A, and studied the regeneration process by performing subsequent adsorption cycles after degassing at different temperatures. We observed incomplete desorption at low temperatures, and cation rearrangement at successive adsorption cycles. We also developed a new molecular simulation force field able to reproduce experimental adsorption isotherms in the range of temperatures between 273 K and 374 K. Small deviations observed at high pressures are attributed to the change in the water dipole moment at high loadings. The force field correctly describes the preferential adsorption sites of water at different pressures. We tested the influence of the zeolite structure, framework flexibility, and cation mobility when considering adsorption and diffusion of water. Finally, we performed checks on force field transferability between different hydrophilic zeolite types, concluding that classical, non-polarizable water force fields are not transferable.

On the forbidden gap of finite graphene nanoribbons

The electronic structure of isolated finite graphene nanoribbons is investigated by solving, at the Hartree-Fock (HF) level, the Pariser, Parr and Pople (PPP) many-body Hamiltonian. The study is mainly focused on 7-AGNR and 13-AGNR (Armchair Graphene Nano-Ribbons), whose electronic structures have been recently experimentally investigated. Only paramagnetic solutions are considered. The characteristics of the forbidden gap are studied as a function of the ribbon length. For a 7-AGNR, the gap monotonically decreases from a maximum value of ~6.5 eV for short nanoribbons to a very small value of ~0.12 eV for the longer calculated systems. Gap edges are defined by molecular orbitals that are spatially localized near the nanoribbon extremes, that is, near both zig-zag edges. On the other hand, two delocalized orbitals define a much larger gap of about 5 eV. Conductance measurements report a somewhat smaller gap of ~3 eV. The small real gap lies in the middle of the one given by extended states and has been observed by STM and reproduced by DFT calculations. On the other hand, the length dependence of the gap is not monotonous for a 13-AGNR. It decreases initially but sharply increases for lengths beyond 30 Å remaining almost constant thereafter at a value of ~2.1 eV. Two additional states localized at the nanoribbon extremes show up at energies 0.31 eV below the HOMO (Highest Occupied Molecular Orbital) and above the LUMO (Lowest Unoccupied Molecular Orbital). These numbers compare favorably with those recently obtained by means of STS for a 13-AGNR sustained by a gold surface, namely 1.4 eV for the energy gap and 0.4 eV for the position of localized band edges. We show that the important differences between 7- and 13-AGNR should be ascribed to the charge rearrangement near the zig-zag edges obtained in our calculations for ribbons longer than 30 Å, a feature that does not show up for a 7-AGNR no matter its length.

[Draft of a committee report, 1790]

Two folio-sized leaves containing a handwritten draft of a report of a committee explaining proposed changes to the academic schedule of Harvard undergraduates. The report discusses the rearrangement of lectures, exercises, disputations, and recitations and the specific reasoning behind the changes. The first page of the report is written on the verso of an essay by student Henry Daingerfield titled, "Wishing of all employments is the worst," and the second page of the report is written on the verso of an essay on the importance of teaching morals to the young by Bradstreet Story (later known as Dudley Story Bradstreet, Harvard AB 1792), dated 1790.

Novel chromone and xanthone derivatives: Synthesis and ROS/RNS scavenging activities

Chromones and xanthones are oxygen-containing heterocyclic compounds acknowledged by their antioxidant properties. In an effort to develop novel agents with improved activity, a series of compounds belonging to these chemical classes were prepared. Their syntheses involve the condensation of appropriate 2-methyl-4H-chromen-4-ones, obtained via Baker-Venkataraman rearrangement, with (E)-3-(3,4-dimethoxyphenyl)acrylaldehyde to provide the corresponding 2-[(1E,3E)-4-(3,4-dimethoxyphenyl)buta-1,3-dien-1-yl]-4H-chromen-4-ones. Subsequent electrocyclization and oxidation of these compounds led to the synthesis of 1-aryl-9H-xanthen-9-ones. After cleavage of the protecting groups, hydroxylated chromones and xanthones were assessed as scavenging agents against both reactive oxygen species (ROS) [superoxide radical (O2(•-)), hydrogen peroxide (H2O2), hypochlorous acid (HOCl), singlet oxygen ((1)O2), and peroxyl radical (ROO(•))] and reactive nitrogen species (RNS) [nitric oxide ((•)NO) and peroxynitrite anion (ONOO(-))]. Generally, all the tested new hydroxylated chromones and xanthones exhibited scavenger effects dependent on the concentration, with IC50 values found in the micromolar range. Some of them were shown to have improved scavenging activity when compared with previously reported analogues, allowing the inference of preliminary conclusions on the structure-activity relationship.

Language lessons /

Cover title: Metcalf and Bright's language lessons.

Acyl glucuronide reactivity in perspective: biological consequences

The metabolic conjugation of exogenous and endogenous carboxylic acid substrates with endogenous glucuronic acid, mediated by the uridine diphosphoglucuronosyl transferase (UGT) superfamily of enzymes, leads to the formation of acyl glucuronide metabolites. Since the late 1970s, acyl glucuronides have been increasingly identified as reactive electrophilic metabolites, capable of undergoing three reactions: intramolecular rearrangement, hydrolysis, and intermolecular reactions with proteins leading to covalent drug-protein adducts. This essential dogma has been accepted for over a decade. The key question proposed by researchers, and now the pharmaceutical industry, is: does or can the covalent modification of endogenous proteins, mediated by reactive acyl glucuronide metabolites, lead to adverse drug reactions, perhaps idiosyncratic in nature? This review evaluates the evidence for acyl glucuronide-derived perturbation of homeostasis, particularly that which might result from the covalent modification of endogenous proteins and other macromolecules. Because of the availability of acyl glucuronides for test tube/in vitro experiments, there is now a substantial literature documenting their rearrangement, hydrolysis and covalent modification of proteins in vitro. It is certain from in vitro experiments that serum albumin, dipeptidyl peptidase IV, tubulin and UGTs are covalently modified by acyl glucuronides. However, these in vitro experiments have been specifically designed to amplify any interference with a biological process in order to find biological effects. The in vivo situation is not at all clear. Certainly it must be concluded that all humans taking carboxylate drugs that form reactive acyl glucuronides will form covalent drug-protein adducts, and it must also be concluded that this in itself is normally benign. However, there is enough in vivo evidence implicating acyl glucuronides, which, when backed up by in vivo circumstantial and documented in vitro evidence, supports the view that reactive acyl glucuronides may initiate toxicity/immune responses. In summary, though acyl glucuronide-derived covalent modification of endogenous macromolecules is well-defined, the work ahead needs to provide detailed links between such modification and its possible biological consequences. (C) 2003 Elsevier Science Ireland Ltd. All rights reserved.

The mitochondrial genomes of soft ticks have an arrangement of genes that has remained unchanged for over 400 million years

There are two major groups of ticks: soft ticks and hard ticks. The hard ticks comprise the prostriate ticks and the metastriate ticks. The mitochondrial (mt) genomes of one species of prostriate tick and two species of metastriate ticks had been sequenced prior to our study. The prostriate tick has the ancestral arrangement of mt genes of arthropods, whereas the two metastriate ticks have rearrangements of eight genes and duplicate control regions. However, the arrangement of genes in the mt genomes of soft ticks had not been studied. We sequenced the mt genomes of two species of soft ticks, Carios capensis and Ornithodoros moubata, and a metastriate tick, Haemaphysalis flava. We found that the soft ticks have the ancestral arrangement of mt genes of arthropods, whereas the metastriate tick, H. flava, shares the rearrangements of mt genes and duplicate control regions with the other two metastriate ticks that have previously been studied. Our study indicates that gene rearrangements and duplicate control regions in mt genomes occurred once in the most recent common ancestor of metastriate ticks, whereas the ancestral arrangement of arthropods has remained unchanged for over 400 million years in the lineages leading to the soft ticks and the prostriate ticks.

Synthesis of 1,3-diazepines and ring contraction to cyanopyrroles

Several tetrazolo[1,5-a] pyridines/2-azidopyridines undergo photochemical nitrogen elimination and ring expansion to 1,3-diazacyclohepta-1,2,4,6-tetraenes (7,10,13,16,19,22) as well as ring cleavage to cyanovinylketenimines (8,17,20b) in low temperature Ar matrices. 6,8-Dichlorotetrazolo[1,5-a] pyridine/2-azido-3,5-dichloropridine 6 undergoes ready exchange of the chlorine in position 8 (3) with ROH/RONa. 8-Chloro-6-trifluoromethyltetrazolo[1,5-a] pyridine 15 undergoes solvolysis of the CF3 group to afford 8-chloro-6-methoxycarbonyltetrazolo[1,5-a] pyridine 18. Several tetrazolopyridines/2-azidopyridines afford 1H- or 5H-1,3-diazepines in good yields on photolysis in the presence of alcohols or amines (11,14,23,25). 5-Chlorotetrazolo[1,5-a] pyridines/2-azido-6-chloropyridines 21 and 38 undergo a rearrangement to 1H- and 3H-3-cyanopyrroles 27 and 45, respectively. The mechanism of this rearrangement was investigated by N-15-labelling and takes place via transient 1,3-diazepines. The structures of 6,8-dichloro-tetrazolo[1,5-a] pyridine 6T, 6-chloro-8-ethoxytetrazolo[1,5-a] pyridine 9Tb, dipyrrolylmethane 28, and 2-isopropoxy-4-dimethylamino-5H-1,3-diazepine 25b were determined by X-ray crystallography. In the latter case, this represents the first reported X-ray crystal structure of a 5H-1,3-diazepine.

Crystal structures of the DsbG disulfide isomerase reveal an unstable disulfide

Dsb proteins control the formation and rearrangement of disulfide bonds during the folding of secreted and membrane proteins in bacteria. DsbG, a member of this family, has disulfide bond isomerase and chaperone activity. Here, we present two crystal structures of DsbG at 1.7- and 2.0-Angstrom resolution that are meant to represent the reduced and oxidized forms, respectively. The oxidized structure, however, reveals a mixture of both redox forms, suggesting that oxidized DsbG is less stable than the reduced form. This trait would contribute to DsbG isomerase activity, which requires that the active-site Cys residues are kept reduced, regardless of the highly oxidative environment of the periplasm. We propose that a Thr residue that is conserved in the cis-Pro loop of DsbG and DsbC but not found in other Dsb proteins could play a role in this process. Also, the structure of DsbG reveals an unanticipated and surprising feature that may help define its specific role in oxidative protein folding. Thus, the dimensions and surface features of DsbG show a very large and charged binding surface that is consistent with interaction with globular protein substrates having charged surfaces. This finding suggests that, rather than catalyzing disulfide rearrangement in unfolded substrates, DsbG may preferentially act later in the folding process to catalyze disulfide rearrangement in folded or partially folded proteins.

Imidoylketene-alpha-oxoketenimine and alpha-oxoketene-alpha-oxoketene rearrangements. 1,3-Shifts of substituted phenyl groups

1,3-Phenyl shifts interconvert imidoylketenes 1 and alpha-oxoketenimines 2 and, likewise, alpha-oxoketenes 3 automerize by this 1,3-shift. These rearrangements usually take place in the gas phase under conditions of. ash vacuum thermolysis. Energy profiles calculated at the B3LYP/6-31G(d, p) and B3LYP/6311 + G(3df,2p)//B3LYP/6-31G(d,p) levels demonstrate that electron donating substituents ( D) in the migrating phenyl group and electron withdrawing ones ( W) in the non-migrating phenyl group, can stabilise the transition states TS1 and TS2 to the extent that activation barriers of ca. 100 kJ mol(-1) or less are obtained; i.e. enough to make these reactions potentially observable in solution at ordinary temperatures. The calculated transition state energies Delta G(TS1) show an excellent correlation with the Hammett constants sigma(p)(W) and sigma(p) +(D).

Energy profiles for ketene cyclizations. interconversion of 1,3-oxazin-6-ones, mesoionic 1,3-oxazinium olates and acylketenes, imidoylketenes, oxoketenimines, and cyclization products

The energy surface connecting oxazinium olates 9, several possible conformers of ketenes 10 and 11, and the final cyclization products 12, 13 and 14, as well as the isomeric 1,3-oxazine-6-ones 15, ring opening of the latter to N-acylimidoylketenes 16, and subsequent rearrangement of 16 to oxoketenimines 17, azetinones 18, and the cyclization products 19 and 20 are evaluated computationally at the B3LYP/6-31G* and B3LYP/6-311+G*//B3LYP/6-31G* levels. The cyclizations of ketenes to oxazinium olates 9 and oxazines 15 have the characteristics of pseudopericyclic reactions. Plots of the energy vs internal reaction coordinate for the cyclization of transoid acylketenes such as 10 to 9 (via TS1) and 16 to 15 (via TS7) feature two inflection points and indicate that the part of the energy surface above the lower inflection points describe internal rotation of the acyl function in the ketene moiety, and the part below this point describes the cyclization of the cisoid ketene to the planar mesoionic oxazinium olate 9 or oxazinone 15. The 1,3-shifts of the OR group that interconvert ketenes 16 and ketenimines 17 via four-membered cyclic transition states TS8 behave similarly, the first portion (from the ketenimine side) of the activation barrier being due largely to internal rotation of substituents, and the top part being due to the 1,3-shift proper.

Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite, Leptotrombidium pallidum

To better understand the evolution of mitochondrial (mt) genomes in the Acari (mites and ticks), we sequenced the mt genome of the chigger mite, Leptotrombidium pallidum (Arthropoda: Acari: Acariformes). This genome is highly rearranged relative to that of the hypothetical ancestor of the arthropods and the other species of Acari studied. The mt genome of L. pallidum has two genes for large subunit rRNA, a pseudogene for small subunit rRNA, and four nearly identical large noncoding regions. Nineteen of the 22 tRNAs encoded by this genome apparently lack either a T-arm or a D-arm. Further, the mt genome of L. pallidum has two distantly separated sections with identical sequences but opposite orientations of transcription. This arrangement cannot be accounted for by homologous recombination or by previously known mechanisms of mt gene rearrangement. The most plausible explanation for the origin of this arrangement is illegitimate inter-mtDNA recombination, which has not been reported previously in animals. In light of the evidence from previous experiments on recombination in nuclear and mt genomes of animals, we propose a model of illegitimate inter-mtDNA recombination to account for the novel gene content and gene arrangement in the mt genome of L. pallidum.