Similar Substitution Research Articles

Influences of Similar Elements on Glass Forming Ability and Magnetic Properties in Al-Ni-La Amorphous Alloy

Similar element substitution has been applied for improving glass forming ability (GFA) in Al86Ni9La5 amorphous alloy. The effects of La-Ce and Ni-Co pairs on the GFA, magnetic properties and hardness of Al-Ni-La alloy were investigated by using X-ray diffraction (XRD), transmission electron microscopy (TEM), differential scanning calorimetry (DSC), magnetometer and hardness-tester. The results show the GFA of the samples in the order of Al86(Ni0.5Co0.5)9(La0.5Ce0.5)5<Al86Ni9La5<Al86Ni9(La0.5Ce0.5)5, implying that similar element substitution has a limited enhancing effect on the GFA of the present Al-Ni-La alloy. In addition, the measured samples display a diamagnetic behavior at room temperature. The variations of diamagnetic behavior as well as the microhardness of the samples are strongly dependent on the microstructure, i.e., the amounts of the icosahedral structure and precipitates, after the similar element substitution in the Al-Ni-La alloy.

Limited effects of among-lineage rate variation on the phylogenetic performance of molecular markers

Variation in substitution rates among evolutionary lineages (among-lineage rate variation or ALRV) has been reported to negatively affect the estimation of phylogenies. When the substitution processes underlying ALRV are modeled inadequately, non-sister taxa with similar substitution rates are estimated incorrectly as sister species due to long-branch attraction. Recent advances in modeling site-specific rate variation (heterotachy) have reduced the impacts of ALRV on phylogeny estimation in several empirical and simulated datasets. However, the addition of parameters to the substitution model reduces power to estimate each parameter correctly, which can also lead to incorrect phylogeny estimation. A potential solution to this problem is to identify the levels of ALRV that negatively impact phylogeny estimation such that molecular markers with non-deleterious levels of ALRV can be identified. To this end, we used analyses of empirical and simulated gene datasets to evaluate whether levels of ALRV identified in a mitochondrial genomic dataset for salamanders negatively impacted phylogeny estimation. We simulated data with and without ALRV, holding all other evolutionary parameters constant, and compared the phylogenetic performance of both simulated and empirical datasets. Overall, we found limited, positive effects of ALRV on phylogeny estimation in this dataset, the majority of which resulted from an increase in substitution rate on short branches. We conclude that ALRV does not always negatively impact phylogeny estimation. Therefore, ALRV can likely be disregarded as a criterion for marker selection in comparable phylogenetic studies.

Portability of a Common Nucleic Acid Hairpin Loop Motif Between RNA and DNA

Hairpins are common nucleic acid secondary structures that perform both structural and functional roles. Recently, we reported that r(UNCG) and r(GNRA) hairpin families use molecular mimicry and electrostatic factors to attain exceptional thermodynamic stability with a CG closing base pair (cbp) (J. Amer. Soc. 2009 131, 8474-8484). Although these loop families fold with different global structures, the tetraloops are stabilized by displaying the same functional groups and partial charges to the major groove edge of the CG cbp. Herein, we compare the r(GNRA) tetraloop family to the DNA triloop family d(GNA), which is also exceptionally stable with a CG cbp and possesses same sheared GA base pair between the first and last positions of the loop (Biochemistry2009 48, 8787-8794). Interactions of d(GNA) loops with the cbp were probed with nucleobase and functional group modifications and the resulting effects on stability were compared to those from similar substitutions in r(GNRA) hairpins. Interruption or deletion of loop-cbp interactions in d(GNA) was consistent with electrostatic interactions identified through nonlinear Poisson-Boltzmann (NLPB) calculations. Moreover, loop stability changed in a manner consistent with similar loop-cbp interactions for d(GNA) and r(GNRA) loops. We also compared the relationship of ΔG°37 and log[Na+] for d(GNA) and r(GNRA) loops and found a decreased salt dependence for both loop families with a CG cbp. Similarity of loop-cbp interactions shows portability of the loop-cbp motif across polymer type and loop size and indicates RNA and DNA converged on a similar molecular solution for stability.

Syntheses and molecular structures of some tricobaltcarbonylclusters containing 2,4,6-trimethyl-1,3,5-trithiane

Reactions of CCo3 carbonyl clusters Co3(mu3-CR)(CO)9 with 2,4,6-trimethyl-1,3,5-trithiane (SMe3) have given Co3(mu3-CR)(mu3-SMe3)(CO)6 [R = H (1), C[triple bond]CSiMe3 (2)]. A small amount of the coupled-alkyne product Me3SiC2[Co2(CO)6]C2[Co2(mu-SMe3)(CO)4]C[triple bond]CSiMe3 (3) was isolated from the latter reaction. The reaction of Co3(mu3-CC[triple bond]CSiMe3)(mu3-SMe3)(CO)6 (2) with AuCl(PPh3) in the presence of NaOMe gave Co3{mu3-CC[triple bond]CAu(PPh3)}(mu3-SMe3)(CO)6 (4), which in turn reacts with Co3(mu3-CBr)(CO)9 in the presence of catalytic amounts of Pd(PPh3)4 and CuI to give {(OC)9Co3}(mu-C[triple bond]CC[triple bond]C){Co3(mu3-SMe3)(CO)6} (5). Further substitution of 5 with SMe3 gave symmetrical {Co3(mu3-SMe3)(CO)6}2(mu-C[triple bond]CC[triple bond]C) (6), also obtained from a reaction between {Co3(CO)9}2(mu-C[triple bond]CC[triple bond]C) and two equivalents of SMe3. Similar substitution of Co3{mu3-C(C[triple bond]C)2[Ru(dppe)Cp*]}(CO)9 with SMe3 gave Co3{mu3-C(C[triple bond]C)2[Ru(dppe)Cp*]}(mu3-SMe3)(CO)6 (7). In all of these compounds, the SMe3 ligand caps the basal face of the CCo3 cluster on the opposite side to the mu3-CR group. The three S donors occupy axial sites, with all CO groups being in equatorial sites. Reactions of Co3(mu3-CBr)(CO)9 with SMe3 gave only Co3(mu3-CX)(mu3-SMe3)(CO)6 [X = C(O)NMe2 (8), CO2H (9)]. The redox properties and electronic structure of the C4-bridged bis-cluster 6 have been investigated through a combination of cyclic voltammetry, IR spectroelectrochemistry and DFT calculations, with comparisons made with suitable model systems. Single-crystal X-ray diffraction structure determinations of 1, 2, 3, 4 and 8 are reported.

Korean speech sound development in children from bilingual Japanese-Korean environments

PurposeThis study investigates Korean speech sound development, including articulatory error patterns, among the Japanese-Korean children whose mothers are Japanese immigrants to Korea.MethodsThe subjects were 28 Japanese-Korean children with normal development born to Japanese women immigrants who lived in Jeonbuk province, Korea. They were assessed through Computerized Speech Lab 4500. The control group consisted of 15 Korean children who lived in the same area.ResultsThe values of the voice onset time of consonants /ph/, /t/, /th/, and /k*/ among the children were prolonged. The children replaced the lenis sounds with aspirated or fortis sounds rather than replacing the fortis sounds with lenis or aspirated sounds, which are typical among Japanese immigrants. The children showed numerous articulatory errors for /c/ and /l/ sounds (similar to Koreans) rather than errors on /p/ sounds, which are more frequent among Japanese immigrants. The vowel formants of the children showed a significantly prolonged vowel /o/ as compared to that of Korean children (P<0.05). The Japanese immigrants and their children showed a similar substitution /n/ for /ɧ/ [Japanese immigrants (62.5%) vs Japanese-Korean children (14.3%)], which is rarely seen among Koreans.ConclusionThe findings suggest that Korean speech sound development among Japanese-Korean children is influenced not only by the Korean language environment but also by their maternal language. Therefore, appropriate language education programs may be warranted not only or immigrant women but also for their children.

Specific amino acid substitutions cause distinct expression of JAL (RH48) and JAHK (RH53) antigens in RhCE and not in RhD

Westhoff and colleagues1 and Hustinx and coworkers2 have recently reported a total of three molecular causes for the low-prevalence Rh antigen JAL (RH48). Quantitative weakening and qualitative effects are documented for these variant RhCE proteins. Similar serological effects have been observed in the JAHK+ (RH53),3 ceSL,4 and RhCe(S122P)5 variants of the RhCE protein. We have observed 4 RhD variants harboring similar amino acid substitutions at positions 114 or 122 (Table 1). Table 1 RHD alleles encoding amino acid substitutions at positions 114 and 122 Most Rh antigens are known to be associated with molecular variants of either the RHD or RHCE gene. However, distinct Rh antigens, like c (RH4), G (RH12), Rh32 (RH32), Evans (RH37) and FPTT (RH50), can be expressed by RhD and RhCE variants (Table S1, available online). We collated all low-prevalence Rh antigens caused by single nucleotide substitutions and identified pairs of RHD and RHCE alleles that harbor identical substitutions (Table S2, available online).1–4,6 Only amino acid substitutions at positions 114 and 122 were currently found to fulfill both criteria. In RhCE these substitutions cause JAL or JAHK antigen expression. Hence, we assessed the possible expression of JAL and JAHK by RhD proteins harboring similar amino acids at positions 114 or 122. A DVII sample harboring a substitution at 110 was used as negative control. All RhD samples with amino acid substitutions at position 114, weak D type 17, type 25 and type 47, were negative for the JAL antigen (Table 2). The CeMA and Rhce(R114Q) control samples were JAL positive, as expected. Because the antigen density of weak D type 17 is very low (Table 1), we corroborated its lack of JAL expression by a negative adsorption-elution test (not shown). Table 2 Serologic results of RhD and RhCE variants with amino acid substitutions at positions 114 and 122 The weak D type 54 sample with an amino acid substitution at position 122 was negative for the JAHK antigen (Table 2). The RhCe(S122L) control sample was positive with the 3 anti-JAHK sera, as expected. ceSL has been reported to be JAHK negative.4 We confirmed this result with the original red blood cell (RBC) samples and the anti-JAHK P4.53A serum used previously. However, the two anti-JAHK sera of greater titer revealed that ceSL samples were in fact JAHK positive (Table 2). Both RhCe(S122P) samples were JAHK negative with all 3 sera. The two sera P4.53B and P4.53C were identified from a series of 138 samples collected from pregnant women with a positive antibody screen.7 Both women had neither been transfused nor were their newborns or the putative fathers positive for the JAHK antigen.7 Hence, anti-JAHK is possibly a rather frequent, naturally occurring antibody associated with pregnancy. The titers of anti-JAL (Table 2) determined with CeMA and Rhce(R114Q) differed in congruence with the known weaker expression of JAL in the Rhce variants Rhce(R114Q) and ces(340) compared to the RhCe variant CeMA.2 In contrast to Rhce(R114Q) harboring Gln114, ces(340) and CeMA are caused by mutations encoding for Trp114.1,2 The model presented by Westhoff et al.1 suggests conformational changes due to Trp114 that contribute to the expression pattern of the JAL antigen. The weak JAL expression in Rhce(R114Q) may be due to the different biochemical properties of Trp (W) and Gln (Q). However, the JAL expression in ces(340), which also harbors Trp114, is distinctly weaker than in CeMA and, hence, requires a different molecular explanation (Table S3, available online):1,2,8 The additional Leu245Val substitution, known to cause a weak expression of the e antigen,8 could also induce the weak expression of the JAL antigen. Currently observed alleles cannot exclude the possibility that the weak JAL expression in both Rhce variants is caused by the 4 amino acid residues at positions 48, 60, 68, and 103, which typically differ between the RhCe and Rhce proteins. We conclude that JAL and JAHK antigens are expressed by Ce and ce variants of the RhCE protein. We found that neither antigen was expressed by any of the 4 RhD protein variants possessing similar amino acid substitutions at positions 114 and 122.

SUBSTITUTIONS GENERATING THE FRACTAL MATRICES OF THE p-ADIC VALUATION OF THE BINOMIAL AND LEGENDRE-POLYNOMIAL COEFFICIENTS

We consider the fractal matrix which describes the divisibility properties of the coefficients of the Legendre polynomials by prime powers, and derive a block matrix substitution system that generates it. Central in the development is a similar substitution for a particular matrix of binomial coefficients.

Mutational Hot Spot Potential of a Novel Base Pair Mutation of the CSPG2 Gene in a Family With Wagner Syndrome

To report a 3-generation white family clinically diagnosed variably with Wagner, Stickler, and Jansen syndromes and screened for sequence variants in the COL2A1 and CSPG2 genes. Wagner syndrome is an autosomal dominant vitreoretinopathy with a predisposition to retinal detachment and cataracts. It has significant phenotypic overlap with allelic Jansen syndrome and ocular Stickler syndrome type 1. Sticker syndrome type 1 maps to chromosome 12q13.11-q13.2, with associated COL2A1 gene mutations. Wagner syndrome maps to chromosome 5q13-q14 and is associated with mutations in CSPG2 encoding versican, a proteoglycan present in human vitreous. Genomic DNA samples derived from venous blood were collected from all family members. Complete sequencing of COL2A1 was performed on a proband. Primers for polymerase chain reaction and sequencing were designed to cover all exon and intron-exon boundaries. Direct sequencing of CSPG2 was performed on all family member samples. No detectable COL2A1 mutations were noted, making the diagnosis of ocular Stickler syndrome highly unlikely for this family. A unique base pair substitution (c.9265 + 1G>T) in intron 8 of the CSPG2 gene cosegregating with disease status was identified. This mutation occurred in a highly conserved previously reported splice site with a similar base pair substitution (G>A). Direct sequencing of this splice site mutation in 107 unrelated external controls revealed no variants, supporting the rarity of this base pair change and its causation in Wagner syndrome. This novel base pair substitution is thought to cause the deletion of exon 8 and formation of a truncated protein product. Mutation screening of CSPG2 in autosomal dominant vitreoretinopathy families is important for accurate diagnosis. This study underscores the importance of obtaining extensive pedigree information and comparative ophthalmologic clinical information, as the phenotypic findings may vary greatly among independent family members. The study also affirms the paradigm shift from diagnosis assignment based on eponyms to that based on gene mutation type.

Quantitative Photochemical Formation of [Ru(tpy)(bpy)H]+

Quantitative photochemical production of [Ru(tpy)(bpy)H](+) (Ru-H(+)) was achieved by irradiation of [Ru(tpy)(bpy)(DMF)](2+) (Ru-DMF(2+); DMF = N,N-dimethylformamide) in a tetrahydrofuran (THF) solution containing excess triethylamine (NEt(3)). The mechanism of the Ru-H(+) formation was investigated in detail. A photochemical ligand substitution reaction of Ru-DMF(2+) in THF proceeded to give [Ru(tpy)(bpy)(THF)](2+) (Ru-THF(2+)) with a quantum yield of (7.6 +/- 0.7) x 10(-2). In the presence of NEt(3), a similar photochemical ligand substitution reaction also proceeded quickly, but the products were an equilibrium mixture of Ru-THF(2+) and [Ru(tpy)(bpy)(NEt(3))](2+) (Ru-NEt(3)(2+)) with a considerable amount of Ru-H(+) even in the first stage of the photochemical reaction. The equilibrium constant between Ru-THF(2+) and Ru-NEt(3)(2+) was determined as 6.9 +/- 2.1. Irradiation to Ru-NEt(3)(2+) gave Ru-H(+) with a quantum yield of (9.1 +/- 0.5) x 10(-3). An important intermediate, Ru-NEt(3)(2+), was isolated, and its properties were investigated in detail.

Subgenotypes of hepatitis B virus genotype D (D1, D2, D3 and D5) in India: differential pattern of mutations, liver injury and occult HBV infection

Hepatitis B genotype D (HBV/D) is the most widespread genotype and exists as at least five subgenotypes (HBV/D1-D5). However, little is known about the association of virological characteristics with clinical differences among HBV/D subgenotypes. To investigate the virological characteristics of these subgenotypes and their clinical implications, we selected a cohort of 109 genotype D infected individuals from the state of West Bengal, India, including 68 HBsAg positive patients and 41 with occult HBV infection. Among the HBsAg positive subjects 28 had chronic hepatitis B virus infection, 40 were asymptomatic carriers based on clinical examination, liver function test and ultrasonograph results. Overall, HBV/D1 was found in 17%, HBV/D2 in 29%, HBV/D3 in 34% and HBV/D5 in 20% of the cases. HBV/D1 was significantly associated with chronic liver disease (P = 0.01), and in this subgenotype A1896 (PreC mutations) were most common. Although BCP mutations (A/C1753 and T1762/A1764) were found to be frequently associated with HBV/D2 (33% and 33%) and D5 (47% and 59%), no apparent clinical correlation was observed. On the other hand, occult HBV infection was significantly associated with HBV/D3 infection, along with low level of BCP and PreC mutations and several non-synonymous substitutions in the catalytic reverse transcriptase (RT) domain of polymerase gene. Similar nucleotide substitutions in the surface (S) gene region were observed from both northern and eastern Indian HBV/D3 isolates. In conclusion, HBV/D subgenotypes differ in their mutational patterns in the S, polymerase and the BCP/PreC regions that may influence their clinical outcomes.

Portability of the GN(R)A Hairpin Loop Motif between RNA and DNA

Hairpins are common nucleic acid secondary structures that serve many structural and functional roles. Recently, we reported that r(UNCG) and r(GNRA) hairpin families use molecular mimicry and electrostatic factors to attain exceptional thermodynamic stability with a CG closing base pair (cbp). Despite having very different overall folds, these tetraloops present the same functionalities and partial charges to the major groove edge of the CG cbp to achieve stability. Herein, we compare the r(GNRA) tetraloop family to the DNA triloop family d(GNA), which is also exceptionally stable with a CG cbp and possesses the same base pairing between the first and last positions of the loop. Nucleobase and functional group modifications were used to investigate interactions of d(GNA) loops with the cbp, which provided for comparison with similar substitutions in r(GNRA) hairpins. Interruption or deletion of loop-cbp interactions in d(GNA) was consistent with electrostatic interactions identified through nonlinear Poisson-Boltzmann (NLPB) calculations, and loop stability changed in a manner consistent with similar loop-cbp interactions for d(GNA) and r(GNRA) loops. We also compared the relationship of DeltaG degrees (37) and log[Na+] for d(GNA) and r(GNRA) loops and found a decreased dependence of stability on salt for both loop families when a CG cbp was present. The similarity of the loop-cbp interactions shows portability of this loop-cbp motif across polymer type and loop size and indicates convergence on similar molecular solutions for stability in RNA and DNA.

Electronic Structure and Bonding in Neutral and Dianionic Boradiphospholes: R′BC2P2R2 (R=H, tBu, R′=H, Ph)

Classical and non-classical isomers of both neutral and dianionic BC(2)P(2)H(3) species, which are isolobal to Cp(+) and Cp(-), are studied at both B3LYP/6-311++G(d,p) and G3B3 levels of theory. The global minimum structure given by B3LYP/6-311++G(d,p) for BC(2)P(2)H(3) is based on a vinylcyclopropenyl-type structure, whereas BC(2)P(2)H(3)(2-) has a planar aromatic cyclopentadienyl-ion-like structure. However, at the G3B3 level, there are three low-energy isomers for BC(2)P(2)H(3): 1) tricyclopentane, 2) nido and 3) vinylcyclopropenyl-type structures, all within 1.7 kcal mol(-1) of each other. On the contrary, for the dianionic species the cyclic planar structure is still the minimum. In comparison to the isolobal Cp(+) and H(n)C(n)P(5-n)(+) isomers, BC(2)P(2)H(3) shows a competition between pi-delocalised vinylcyclopropenyl- and cluster-type structures (nido and tricyclopentane). Substitution of H on C by tBu, and H on B by Ph, in BC(2)P(2)H(3) increases the energy difference between the low-lying isomers, giving the lowest energy structure as a tricyclopentane type. Similar substitution in BC(2)P(2)H(3)(2-) merely favours different positional isomers of the cyclic planar geometry, as observed in 1) isoelectronic neutral heterodiphospholes EtBu(2)C(2)P(2) (E = S, Se, Te), 2) monoanionic heterophospholyl rings EtBu(2)C(2)P(2) (E = P(-), As(-), Sb(-)) and 3) polyphospholyl rings anions tBu(5-n)C(n)P(5-n) (n = 0-5). The principal factors that affect the stability of three-, four-, and five-membered ring and acyclic geometrical and positional isomers of neutral and dianionic BC(2)P(2)H(3) isomers appear to be: 1) relative bond strengths, 2) availability of electrons for the empty 2p boron orbital and 3) steric effects of the tBu groups in the HBC(2)P(2)tBu(2) systems.

Oxysterol-Induced Rearrangement of the Liquid-Ordered Phase: A Possible Link to Alzheimer’s Disease?

Nearest-neighbor recognition measurements have been made for an exchangeable phospholipid (A) interacting with an exchangeable form of cholesterol (B) in host membranes derived from 1, 2-dipalmitoyl-sn-glycero-3-phosphocholine and varying concentrations of cholesterol, 7beta-hydroxycholesterol (7beta-OH), and 25-hydroxycholesterol (25-OH). Whereas partial replacement of cholesterol with 7beta-OH strengthens the association between A and B, a similar substitution with 25-OH weakens this association. A model that accounts for this dichotomy, and the possible relevance of these findings to the cytotoxicity of 7beta-OH and to Alzheimer's disease are briefly discussed.

Weak preservation of local neutral substitution rates across mammalian genomes

BackgroundThe rate at which neutral (non-functional) bases undergo substitution is highly dependent on their location within a genome. However, it is not clear how fast these location-dependent rates change, or to what extent the substitution rate patterns are conserved between lineages. To address this question, which is critical not only for understanding the substitution process but also for evaluating phylogenetic footprinting algorithms, we examine ancestral repeats: a predominantly neutral dataset with a significantly higher genomic density than other datasets commonly used to study substitution rate variation. Using this repeat data, we measure the extent to which orthologous ancestral repeat sequences exhibit similar substitution patterns in separate mammalian lineages, allowing us to ascertain how well local substitution rates have been preserved across species.ResultsWe calculated substitution rates for each ancestral repeat in each of three independent mammalian lineages (primate – from human/macaque alignments, rodent – from mouse/rat alignments, and laurasiatheria – from dog/cow alignments). We then measured the correlation of local substitution rates among these lineages. Overall we found the correlations between lineages to be statistically significant, but too weak to have much predictive power (r2 <5%). These correlations were found to be primarily driven by regional effects at the scale of several hundred kb or larger. A few repeat classes (e.g. 7SK, Charlie8, and MER121) also exhibited stronger conservation of rate patterns, likely due to the effect of repeat-specific purifying selection. These classes should be excluded when estimating local neutral substitution rates.ConclusionAlthough local neutral substitution rates have some correlations among mammalian species, these correlations have little predictive power on the scale of individual repeats. This indicates that local substitution rates have changed significantly among the lineages we have studied, and are likely to have changed even more for more diverged lineages. The correlations that do persist are too weak to be responsible for many of the highly conserved elements found by phylogenetic footprinting algorithms, leading us to conclude that such elements must be conserved due to selective forces.

Potentiometric Stripping Analysis at Antimony Film Electrodes

AbstractNew procedures of potentiometric stripping analysis can be based on the use of antimony film electrodes and antimony(III) salts. In this paper, antimony films are generated onto carbon paste electrodes in situ and after electrolytic preconcentration of the metals to be determined, the excess antimony(III) serves as a chemical oxidant. Moreover in acidic solutions containing halide ions, the oxidation ability of antimony(III) is adequately limited because of formation of its corresponding halide complexes. Compared with similar total substitution of traditionally used mercury(II) by bismuth(III), the use of antimony(III) offers higher sensitivity in detection of heavy metals, namely, cadmium and lead.

Clonotypic density and cross-reactivity of the CD8+ memory T cell repertoire in adults. (83.12)

Abstract Adult memory T cell repertoires are populated by clonotypes that correspond to an individual's history of antigen exposures. The population density of clonotypes in the memory repertoire is important in light of the greatly reduced production of naïve T cells by the involuted thymus and the continuing need to respond to novel pathogens. We measure clonotypic density by comparing the recall response to the influenza-derived, HLA-A2 restricted, M158-66 peptide, with those to peptides substituted at positions 63 and 65 (TCR contact residues). The PBMC were from individuals who show a complex repertoire in recall response to the M158-66 peptide. All samples were obtained under an IRB approved protocol. Peptide-specific responses were identified by CDR3 spectratype analysis, and the clonotypes identified by sequencing the CDR3. As the substitutions became more pronounced, the M158-66 repertoire was lost and new responding clonotypes were revealed. However, the number of new clonotypes identified was lower than observed for M158-66. Structurally similar substitutions revealed a limited cross-reactivity in M158-66 repertoire. These data indicate that the adult repertoire is populated by T cells that can recognize structurally related epitopes. However, these T cells are sparsely distributed for the peptide:MHC structures generated by our substitutions.

Terapia fonológica em irmãos com diferentes graus de gravidade do desvio fonológico

TEMA: terapia fonológica em irmãos com desvio fonológico. PROCEDIMENTOS: participaram da pesquisa dois irmãos, S1 e S2, do sexo masculino e feminino, respectivamente. O S1, 6:6 de idade, apresentava desvio fonológico de grau severo e foi tratado pelo modelo de Oposições Mínimas e o S2, 4:8 de idade, com desvio fonológico de grau moderado-severo foi tratado pelo Modelo de Oposições Máximas. Ambos os sujeitos realizaram 25 sessões de fonoterapia. RESULTADOS: o S2 obteve uma melhor evolução terapêutica comparado ao S1. O S1 apresentou generalização a itens não utilizados no tratamento e o S2 apresentou generalização dentro de uma classe de sons. CONCLUSÃO: os modelos utilizados são eficazes, pois proporcionaram a ocorrência de generalizações e a melhora do sistema fonológico de ambos os sujeitos. No entanto os fatores ambientais podem ter limitado a evolução do tratamento, uma vez que as crianças apresentavam substituições semelhantes na fala o que favorecia a manutenção da alteração.

Synthesis of isothiazol-3-one derivatives as inhibitors of histone acetyltransferases (HATs)

High-throughput screening led to the identification of isothiazolones 1 and 2 as inhibitors of histone acetyltransferase (HAT) with IC50s of 3 μM and 5 μM, respectively. Analogues of these hit compounds with variations of the N-phenyl group, and with variety of substituents at C-4, C-5 of the thiazolone ring, were prepared and assayed for inhibition of the HAT enzyme PCAF. Potency is modestly favoured when the N-aryl group is electron deficient (4-pyridyl derivative 10 has IC 50 = 1.5 μM); alkyl substitution at C-4 has little effect, whilst similar substitution at C-5 causes a significant drop in potency. The ring–fused compound 38 has activity (IC 50 = 6.1 μM) to encourage further exploration of this bicyclic structure. The foregoing SAR is consistent with an inhibitory mechanism involving cleavage of the S–N bond of the isothiazolone ring by a catalytically important thiol residue.

Evolutionary Dynamics of Variant Genomes of Human Papillomavirus Types 18, 45, and 97

Human papillomavirus type 18 (HPV18) and HPV45 account for approximately 20% of all cervix cancers. We show that HPV18, HPV45, and the recently discovered HPV97 comprise a clade sharing a most recent common ancestor within HPV alpha7 species. Variant lineages of these HPV types were classified by sequence analysis of the upstream regulatory region/E6 region among cervical samples from a population-based study in Costa Rica, and 27 representative genomes from each major variant lineage were sequenced. Nucleotide variation within HPV18 and HPV45 was 3.82% and 2.39%, respectively, and amino acid variation was 4.73% and 2.87%, respectively. Only 18 nucleotide variations, of which 10 were nonsynonymous, were identified among three HPV97 genomes. Full-genome comparisons revealed maximal diversity between HPV18 African and non-African variants (2.6% dissimilarity), whereas HPV18 Asian-American [E1 (AA)] and European (E2) variants were closely related (less than 0.5% dissimilarity); HPV45 genomes had a maximal difference of 1.6% nucleotides. Using a Bayesian Markov chain Monte Carlo (MCMC) method, the divergence times of HPV18, -45, and -97 from their most recent common ancestors indicated that HPV18 diverged approximately 7.7 million years (Myr) ago, whereas HPV45 and HPV97 split off around 5.7 Myr ago, in a period encompassing the divergence of the great ape species. Variants within the HPV18/45/97 lineages were estimated to have diverged from their common ancestors in the genus Homo within the last 1 Myr (<0.7 Myr). To investigate the molecular basis of HPV18, HPV45, and HPV97 evolution, regression models of codon substitution were used to identify lineages and amino acid sites under selective pressure. The E5 open reading frame (ORF) of HPV18 and the E4 ORFs of HPV18, HPV45, and HPV18/45/97 had nonsynonymous/synonymous substitution rate ratios (d(N)/d(S)) over 1 indicative of positive Darwinian selection. The L1 ORF of HPV18 genomes had an increased proportion of nonsynonymous substitutions (4.93%; average d(N)/d(S) ratio [M3] = 0.3356) compared to HPV45 (1.86%; M3 = 0.1268) and HPV16 (2.26%; M3 = 0.1330) L1 ORFs. In contrast, HPV18 and HPV16 genomes had similar amino acid substitution rates within the E1 ORF (2.89% and 3.24%, respectively), while HPV45 E1 was highly conserved (amino acid substitution rate was 0.77%). These data provide an evolutionary history of this medically important clade of HPVs and identify an unexpected divergence of the L1 gene of HPV18 that may have clinical implications for the long-term use of an L1-virus-like particle-based prophylactic vaccine.

HLA-DRB1*1101-Restricted T Cells from Two Unrelated Mild Hemophilia a Inhibitor Subjects with Missense Genotype R593C Respond to the Same Minimal Epitope.

The development of inhibitory anti-FVIII antibodies in hemophilia A patients, referred to clinically as “inhibitors”, results from stimulation of T cells when the infused FVIII is recognized as foreign. T-cell stimulation follows the binding of specific epitopes within FVIII-derived peptides to HLA-DR molecules on the surface of antigen-presenting cells. We are investigating the HLA dependence of immune responses to FVIII and characterizing T-cell epitopes to better understand the process of T-cell stimulation leading to anti-FVIII antibody production. Inhibitors are less common in mild/moderately severe patients than in severe hemophilia A, but an elevated risk of inhibitor formation has been noted for patients with missense mutation R593C in the FVIII A2 domain. CD4+ T cells were isolated from two unrelated hemophilic subjects with this missense genotype, one Dutch and one American. Both had a DRB1*1101 haplotype and longstanding low- to moderate-titer inhibitors. Antigen-specific T cells from both subjects were identified by staining with fluorescent, peptide-loaded MHC Class II tetramers. The tetramer staining was carried out after stimulating the cells with synthetic peptides corresponding to the FVIII A2 domain sequence. Both hemophilic subjects, but not an HLA-matched healthy control, had a DRB1*1101-restricted response to peptide FVIII589-608, which contained the wild-type R593 sequence. Single-cell sorting and expansion with PHA facilitated the isolation of A2-specific T-cell clones from both subjects. A polyclonal population of A2-specific T cells was also isolated from the American subject's CD4+ T cells. All T-cell clones and the polyclonal T-cell line proliferated in response to the FVIII589-608 peptide and to FVIII. However, the cytokine profiles were somewhat different for peptide-stimulated cells from the two subjects. The single clone obtained from the Dutch subject produced modest levels (<750 pg/mL) of IFN-g, TNF-a, IL-4 and IL-10, while the cloned and polyclonal T cells from the American subject secreted similar levels of the latter three cytokines but had a much more pronounced Th1 polarization, secreting >10,000 pg/mL of IFN-g. Somewhat surprisingly, all of the cloned and polyclonal A2-specific cultured cells proliferated in response to the hemophilic peptide FVIII589-608,593C, despite the fact that this peptide elicited no response from primary T-cell cultures isolated from the American subject. FVIII589-608 bound to recombinant, monomeric DRB1*1101 protein with high affinity, while the affinity of the hemophilic peptide FVIII589-608,593C was threefold lower. FVIII residues 594-602 (FLPNPAGVQ) comprise a predicted high-affinity DRB1*1101-binding motif. Proliferation assays carried out with truncated peptides (FVIII592-608, FVIII593-608, and FVIII594-608) confirmed the responsiveness of the clones and polyclonal T-cell line to peptides containing this predicted motif, but proliferation decreased markedly when residue R593 was removed. The immunogenicity of this FVIII region with respect to other HLA types was evaluated by binding assays utilizing several recombinant DR molecules, in order to determine the relative promiscuity of this T-cell epitope. The effects of modifying amino acid residues within this epitope are also under investigation, as substitutions at “anchor” positions should decrease the immunogenicity of the corresponding peptides. Similar substitutions in recombinant FVIII may allow development of less immunogenic variants of human FVIII proteins.