The dimer initiation sequence stem-loop of human immunodeficiency virus type 1 is dispensable for viral replication in peripheral blood mononuclear cells

Human immunodeficiency virus type 1 (HIV-1) contains two copies of genomic RNA that are noncovalently linked via a palindrome sequence within the dimer initiation site (DIS) stem-loop. In contrast to the current paradigm that the DIS stem or stem-loop is critical for HIV-1 infectivity, which arose from studies using T-cell lines, we demonstrate here that HIV-1 mutants with deletions in the DIS stem-loop are replication competent in peripheral blood mononuclear cells (PBMCs). The DIS mutants contained either the wild-type (5′GCGCGC3′) or an arbitrary (5′ACGCGT3′) palindrome sequence in place of the 39-nucleotide DIS stem-loop (NLCGCGCG and NLACGCGT). These DIS mutants were replication defective in SupT1 cells, concurring with the current model in which DIS mutants are replication defective in T-cell lines. All of the HIV-1 DIS mutants were replication competent in PBMCs over a 40-day infection period and had retained their respective DIS mutations at 40 days postinfection. Although the stability of the virion RNA dimer was not affected by our DIS mutations, the RNA dimers exhibited a diffuse migration profile when compared to the wild type. No defect in protein processing of the Gag and GagProPol precursor proteins was found in the DIS mutants. Our data provide direct evidence that the DIS stem-loop is dispensable for viral replication in PBMCs and that the requirement of the DIS stem-loop in HIV-1 replication is cell type dependent.

Time-periodic perturbation of a Lienard equation with an unbounded homoclinic loop

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Frequency synthesizer using a hybrid analog/digital loop filter: A low complexity approach

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Variability of the conserved V3 loop tip motif in HIV-1 subtype B isolates collected from Brazilian and French patients

The diversity of the V3 loop tip motif sequences of HIV-1 subtype B was analyzed in patients from Botucatu (Brazil) and Montpellier (France). Overall, 37 tetrameric tip motifs were identified, 28 and 17 of them being recognized in Brazilian and French patients, respectively. The GPGR (P) motif was predominant in French but not in Brazilian patients (53.5% vs 31.0%), whereas the GWGR (W) motif was frequent in Brazilian patients (23.0%) and absent in French patients. Three tip motif groups were considered: P, W, and non-P non-W groups. The distribution of HIV-1 isolates into the three groups was significantly different between isolates from Botucatu and from Montpellier (P < 0.001). A higher proportion of CXCR4-using HIV-1 (X4 variants) was observed in the non-P non-W group as compared with the P group (37.5% vs 19.1%), and no X4 variant was identified in the W group (P < 0.001). The higher proportion of X4 variants in the non-P non-W group was essentially observed among the patients from Montpellier, who have been infected with HIV-1 for a longer period of time than those from Botucatu. Among patients from Montpellier, CD4+ cell counts were lower in patients belonging to the non-P non-W group than in those belonging to the P group (24 cells/µL vs 197 cells/µL; P = 0.005). Taken together, the results suggest that variability of the V3 loop tip motif may be related to HIV-1 coreceptor usage and to disease progression. However, as analyzed by a bioinformatic method, the substitution of the V3 loop tip motif of the subtype B consensus sequence with the different tip motifs identified in the present study was not sufficient to induce a change in HIV-1 coreceptor usage.

Visual detection of turkey coronavirus RNA in tissues and feces by reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynaphthol blue dye

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Force system evaluation of symmetrical beta-titanium T-loop springs preactivated by curvature and concentrated bends

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structure of BthA-I complexed with p-bromophenacyl bromide: possible correlations with lack of pharmacological activity

The crystal structure of an acidic phospholipase A(2) isolated from Bothrops jararacussu venom (BthA-I) chemically modified with p-bromophenacyl bromide (BPB) has been determined at 1.85 angstrom resolution. The catalytic, platelet-aggregation inhibition, anticoagulant and hypotensive activities of BthA-I are abolished by ligand binding. Electron-density maps permitted unambiguous identification of inhibitor covalently bound to His48 in the substrate-binding cleft. The BthA-I-BPB complex contains three structural regions that are modified after inhibitor binding: the Ca2+-binding loop, ss-wing and C-terminal regions. Comparison of BthA-I-BPB with two other BPB-inhibited PLA(2) structures suggests that in the absence of Na+ ions at the Ca2+- binding loop, this loop and other regions of the PLA(2)s undergo structural changes. The BthA-I-BPB structure reveals a novel oligomeric conformation. This conformation is more energetically and conformationally stable than the native structure and the abolition of pharmacological activities by the ligand may be related to the oligomeric structural changes. A residue of the `pancreatic' loop (Lys69), which is usually attributed as providing the anticoagulant effect, is in the dimeric interface of BthA-I-BPB, leading to a new hypothesis regarding the abolition of this activity by BPB.

Comparison between apo and complexed structures of bothropstoxin-I reveals the role of Lys122 and Ca2+-binding loop region for the catalytically inactive Lys49-PLA(2)s

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Crystal structure of a phospholipase A(2) homolog complexed with p-bromophenacyl bromide reveals important structural changes associated with the inhibition of myotoxic activity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

General massive one-loop off-shell three-point functions

In this work we compute the most general massive one-loop off-shell three-point vertex in D-dimensions, where the masses, external momenta and exponents of propagators are arbitrary. This follows our previous paper in which we have calculated several new hypergeometric series representations for massless and massive (with equal masses) scalar one-loop three-point functions, in the negative dimensional approach.

One loop conformal invariance of the superstring in an AdS(5) x S-5 background

It is proven that the pure spinor superstring in an AdS(5) x S-5 background remains conformally invariant at one loop level in the sigma model perturbation theory.

Massless and massive one-loop three-point functions in negative dimensional approach

In this article we present the complete massless and massive one-loop triangle diagram results using the negative dimensional integration method (NDIM). We consider the following cases: massless internal fields; one massive, two massive with the same mass m and three equal masses for the virtual particles. Our results are given in terms of hypergeometric and hypergeometric-type functions of the external momenta (and masses for the massive cases) where the propagators in the Feynman integrals are raised to arbitrary exponents and the dimension of the space-time is D. Our approach reproduces the known results; it produces other solutions as yet unknown in the literature as well. These new solutions occur naturally in the context of NDIM revealing a promising technique to solve Feynman integrals in quantum field theories.

One-loop n-point equivalence among negative-dimensional, Mellin-Barnes and Feynman parametrization approaches to Feynman integrals

We show that at one-loop order, negative-dimensional, Mellin-Barnes (MB) and Feynman parametrization (FP) approaches to Feynman loop integral calculations are equivalent. Starting with a generating functional, for two and then for n-point scalar integrals, we show how to reobtain MB results, using negative-dimensional and FP techniques. The n-point result is valid for different masses, arbitrary exponents of propagators and dimension.

A systematization for one-loop 4D Feynman integrals

We present a strategy for the systematization of manipulations and calculations involving divergent (or not) Feynman integrals, typical of the one-loop perturbative solutions of QFT, where the use of an explicit regularization is avoided. Two types of systematization are adopted. The divergent parts are put in terms of a small number of standard objects, and a set of structure functions for the finite parts is also defined. Some important properties of the finite structures, specially useful in the verification of relations among Green's functions, are identified. We show that, in fundamental (renormalizable) theories, all the finite parts of two-, three- and four-point functions can be written in terms of only three basic functions while the divergent parts require (only) five objects. The final results obtained within the proposed strategy can be easily converted into those corresponding to any specific regularization technique providing an unified point of view for the treatment of divergent Feynman integrals. Examples of physical amplitudes evaluation and their corresponding symmetry relations verification are presented as well as generalizations of our results for the treatment of Green's functions having an arbitrary number of points are considered.