Direct antibody access to the HIV-1 membrane-proximal external region positively correlates with neutralization sensitivity.

On the prereceptor-engaged HIV-1 envelope glycoprotein (Env) spike, epitope access by the membrane-proximal external region (MPER)-directed broadly neutralizing antibodies 2F5 and 4E10 remains unresolved. Data on binding to cell surface Env and entry data using primary isolates suggest inaccessibility of the 2F5 and 4E10 epitopes on the viral spike prior to receptor engagement, but trimer gel shift analysis and slow kinetics of shedding induced by 2F5 and 4E10 indicate otherwise. Therefore, it remains unclear if the epitopes themselves are formed in their antibody-bound state (or at least sampled) prior to receptor/coreceptor engagement or if receptor interactions both expose and form the MPER epitopes, presumably in the putative prefusion transitional intermediate. Here, we performed antibody-virus "washout experiments" using both lab-adapted and a panel of clade B primary isolates to analyze MPER accessibility. The neutralization activity of 2F5 and 4E10 against lab-adapted viruses and sensitive and moderately resistant viruses was largely unaffected by relatively rapid antibody-virus washing, suggesting direct interaction with the "static" spike. However, for more neutralization-resistant viruses, the 2F5 and 4E10 antibodies could neutralize only under the "no antibody-virus wash" conditions, implying that the MPER epitopes were not accessible prior to receptor engagement. Accessibility in the washout conditions could be precisely predicted by the relative resistance to neutralization in a standard neutralization format. These data are consistent with a model in which the local MPER antibody epitope conformations may be sampled on the native spike but are occluded to antibody by local steric or distal quaternary constraints adopted by highly resistant HIV-1 isolates.

Dynamic critical behavior of failure and plastic deformation in the random fiber bundle model.

The random fiber bundle (RFB) model, with the strength of the fibers distributed uniformly within a finite interval, is studied under the assumption of global load sharing among all unbroken fibers of the bundle. At any fixed value of the applied stress sigma (load per fiber initially present in the bundle), the fraction U(t)(sigma) of fibers that remain unbroken at successive time steps t is shown to follow simple recurrence relations. The model is found to have stable fixed point U*, filled (sigma) for applied stress in the range 0 < or = sigma < or = sigma(c), beyond which total failure of the bundle takes place discontinuously [abruptly from U*, filled (sigma(c)) to 0]. The dynamic critical behavior near this sigma(c) has been studied for this model analyzing the recurrence relations. We also investigated the finite size scaling behavior near sigma(c). At the critical point sigma = sigma(c), one finds strict power law decay (with time t) of the fraction of unbroken fibers U(t)(sigma(c)) (as t--> infinity). The avalanche size distribution for this mean-field dynamics of failure at sigma < sigma(c) has been studied. The elastic response of the RFB model has also been studied analytically for a specific probability distribution of fiber strengths, where the bundle shows plastic behavior before complete failure, following an initial linear response.

Carboxy-terminal five amino acids of the nucleocapsid protein of vesicular stomatitis virus are required for encapsidation and replication of genome RNA.

The encapsidation of vesicular stomatitis virus (VSV) genome RNA, a prerequisite step to the replication process by the nucleocapsid protein (N) was studied by its ability to package VSV leader RNA in vitro in a RNase-resistant form. The VSV leader RNA was derived from the SP6 transcription vector while the N protein was made in rabbit reticulocyte lysate. The in vitro encapsidation was carried out by translating N mRNA in the presence of 32P-labeled presynthesized leader RNA. The RNA encapsidation property of the N protein was completely abrogated when the C-terminal five amino acids (VEFDK-COOH) were deleted. Systematic mutational analyses within the C-terminal five amino acid regions reveal that the RNA encapsidation activity was lost in all mutants except K --> A and K --> R, indicating that C-terminal five amino acids, in particular the lysine residue play critical role in genome RNA encapsidation. To correlate the in vitro encapsidation abilities of these mutant N proteins with genome RNA replication, we have used a full-length cDNA clone of VSV genome RNA to rescue infectious virions from cells expressing L, P, and wt or mutant N proteins and measured the recovery of plaque forming units. The results indicate that the N mutants that are defective in in vitro encapsidation of leader RNA do not support replication, establishing the requirement of C-terminal five amino acids of the N protein in viral replication.

Length and time scale divergences at the magnetization-reversal transition in the Ising model.

The divergences of both the length and time scales, at the magnetization-reversal transition in the Ising model under a pulsed field, have been studied in the linearized limit of the mean field theory. Both the length and time scales are shown to diverge at the transition point and it has been checked that the nature of the time scale divergence agrees well with the result obtained from the numerical solution of the mean field equation of motion. Similar growths in length and time scales are also observed, as one approaches the transition point, using Monte Carlo simulations. However, these are not of the same nature as the mean field case. Nucleation theory provides a qualitative argument that explains the nature of the time scale growth. To study the nature of growth of the characteristic length scale, we have looked at the cluster size distribution of the reversed spin domains and have defined a pseudocorrelation length that has been observed to grow at the phase boundary of the transition.

A live-virus "suicide" vaccine for human immunodeficiency virus.

A vaccine that uses a live, attenuated human immunodeficiency virus (HIV) may offer the best hope of a vaccine against acquired immunodeficiency syndrome (AIDS). A recent improvement should increase the safety of the live-virus approach: a "suicide gene" inserted into the viral RNA, which causes infected cells to die when treated with ganciclovir. We envision using this strategy not only to prevent AIDS, but also to treat it.

Characterization of Vibrio cholerae EIT or typing phage D10.

The Vibrio cholerae EITor typing phage D10 was characterized. The adsorption kinetics of the phage on V. cholerae MAK757 strain were biphasic in nature. Intracellular growth was characterized by an eclipse period, latent period and burst size which were 20 min, 25 min and 80 particles per cell respectively. The phage yield was dependent on the concentration and time of addition of DNA synthesis inhibitors such as nalidixic acid and novobiocin, and RNA synthesis inhibitors such as rifampicin. The 32+/-0.2 kb linear double-stranded DNA molecule has unique termini. A restriction map of the phage DNA was constructed with the enzymes BamHI, HindIII and PstI.

The nef Gene of SIVmac239 Is Necessary for Efficient Growth in H9 Cells.

AIDS viruses require an intact functional nef gene in order to induce disease. The nonpathogenic molecular cloned virus SIVmac239nef-deletion encodes a truncated nef gene. This attenuated reading frame is expressed both in vitro and in a virus-infected animal in vivo. Encoding the first 58 amino acids of Nef, the reading frame retained its ability to down-modulate CD4 from the surface of T cells. CD4-down-modulated stable cell lines expressing full-length and truncated nef genes were significantly less infected by SIV. SIVmac239nef-open and SIVmacnef-deletion encoding a truncated nef clearly differed in replication kinetics in H9 cells and H9-derived cell lines. SIVmac239nef-deletion replication was delayed in H9. Copyright 1996 S. Karger AG, Basel

A candidate live inactivatable attenuated vaccine for AIDS.

The recent discovery of long term AIDS nonprogressors who harbor nef-attenuated HIV suggests that a naturally occurring live vaccine for AIDS may already exist. Animal models have shown that a live vaccine for AIDS, attenuated in nef, is the best candidate vaccine. There are considerable risks, real and perceived, with the use of live HIV vaccines. We have introduced a conditional lethal genetic element into HIV-1 and simian immunodeficiency virus (SIV) molecular clones deleted in nef. The antiviral strategy we employed targets both virus replication and the survival of the infected cell. The suicide gene, herpes simplex virus thymidine kinase (tk), was expressed and maintained in HIV over long periods of time. Herpes simplex virus tk confers sensitivity to the antiviral activity of acyclic nucleosides such as ganciclovir (GCV). HIV-tk and SIV-tk replication were sensitive to GCV at subtoxic concentrations, and virus-infected cells were eliminated from tumor cell lines as well as primary cell cultures. We found the HIV-tk virus to be remarkably stable even after being cultured in media containing a low concentration of GCV and then challenged with the higher dose and that while GCV resistant escape mutants did arise, a significant fraction of the virus remained sensitive to GCV.

The nef gene from a long-term HIV type 1 nonprogressor.

We examined the nef gene of HIV-1 in a long-term nonprogressor to look for evidence suggesting an attenuated virus. The nef gene was previously shown to be required for induction of AIDS. Simian immunodeficiency virus (SIV) deleted in nef, while infectious, fails to sustain the high viral loads necessary for the induction of AIDS in infected adult rhesus monkeys. The human subject of this report was found to harbor virus (HIV-1 Sur25) encoding open-nef reading frames. However, the nef genes of this subject bore a signature point mutation: a cysteine at amino acid 138. The sequence at this position was identical in all clones examined over a 3-year period. When this sequence was compared to the sequence database for AIDS and human retroviruses at Los Alamos, New Mexico, several isolates from other asymptomatic individuals were also found to encode nef genes with a cysteine at position 138. Furthermore, Cys-138 was found in chimpanzee immunodeficiency virus (CIV), a lentivirus that is similar to HIV but does not cause AIDS in chimpanzees. Multiple cysteines are also found in the nef gene of African green monkey virus, SVIagm, including cysteine at the position analogous to Cys-138. While seroprevalence of SIVagm is high in the wild, there is no known disease associated with this virus. The pathogenic virus isolated from Asian macaques, SIVmac, encodes a Nef protein that has few cysteines. Although the virus HIVSur25 encodes a completely open-nef gene, the virus from this individual is similar to attenuated SIVmac (SIVmac239/nef-deletion) as well as HIV deleted in nef in its growth properties in H9 cells. Nef containing a cysteine at position 138 was shown to be responsible for determining the ability to grow in H9.

Vibriophage D10 contains non-permuted DNA with cohesive ends.

Phage D10, a Vibrio cholerae O-1 El Tor group X phage, is one of the five newly isolated phages used in the phage typing scheme developed for V. cholerae O-1 biotype El Tor and belongs to the Myoviridae family. From electron microscopic studies it is shown that phage D10 has a DNA genome of 32 +/- 0.2 kb. This is the first report where it has been shown by the construction of a partial denaturation map that this vibriophage genome is nonpermuted and has cohesive ends. The location of the ends of the DNA in the phage head has also been inferred.

New phage typing scheme for Vibrio cholerae O1 biotype El Tor strains.

The conventional phage typing scheme proposed by S. Basu and S. Mukerjee (Experientia 24:299-300, 1968) has been used routinely for identification of the strains at the Vibrio Phage Reference Laboratory since 1968. However, because of limitations of this scheme, a new phage typing scheme using five newly isolated phages was incorporated into the conventional scheme. A different definition of routine test dilution (almost confluent lysis) was found to be more useful than the one previously used (confluent lysis). The 1,000 strains tested could be clustered into 27 types with the five new phages. With the new scheme of 10 phages (5 new phages and 5 phages of Basu and Mukerjee), the 1,000 strains could be grouped into 146 types. The new phages were different from each other and also from those of Basu and Mukerjee, as revealed by lytic pattern, electron microscopy, restriction endonuclease digestion, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and antiphage antiserum studies. With the new typing scheme, 99.6% of the strains were typeable. Phage type 115 was the most common and includes 119 (11.9%) of the 1,000 strains tested. Next most common were phage types 142 (9.4%), 143 (7.0%), 104 and 116 (both 5.4%), 3 (5.3%), 5 (4.1%), 4 (3.9%), 24 (2.1%), and 100 (1.7%). The larger number of types would be useful for further classification of the strains for epidemiological purposes. This newly developed scheme is highly applicable to, and could be widely adopted for, phage typing of Vibrio cholerae O1 biotype El Tor strains.