scholarly journals Rapid CD4 cell loss is caused by specific CRF01_AE cluster with V3 signatures favoring CXCR4 usage

2018 ◽  
Author(s):  
Hongshuo Song ◽  
Weidong Ou ◽  
Yi Feng ◽  
Junli Zhang ◽  
Fan Li ◽  
...  
Keyword(s):  
Rapid Evolution ◽  
Cell Loss ◽  
Binding Model ◽  
Global Epidemic ◽  
Cxcr4 Usage ◽  
Phylogenetic Cluster ◽  
Similar Phenotype ◽  
Underlying Mechanisms ◽  
First Time ◽  
Hiv 1

AbstractHIV-1 evolved into various genetic subtypes and circulating recombinant forms (CRFs) in the global epidemic, with the same subtype or CRF usually having similar phenotype. Being one of the world’s major CRFs, CRF01_AE infection was reported to associate with higher prevalence of CXCR4 (X4) viruses and faster CD4 decline. However, the underlying mechanisms remain unclear. We identified eight phylogenetic clusters of CRF01_AE in China and hypothesized that they may have different phenotypes. In the national HIV molecular epidemiology survey, we discovered that people infected by CRF01_AE cluster 4 had significantly lower CD4 count (391 vs. 470,p< 0.0001) and higher prevalence of predicted X4-using viruses (17.1% vs. 4.4%,p< 0.0001) compared to those infected by cluster 5. In a MSM cohort, X4-using viruses were only isolated from sero-convertors infected by cluster 4, which associated with rapid CD4 loss within the first year of infection (141 vs. 440,p= 0.01). Using co-receptor binding model, we identified unique V3 signatures in cluster 4 that favor CXCR4 usage. We demonstrate for the first time that HIV-1 phenotype and pathogenicity can be determined at the phylogenetic cluster level in a single subtype. Since its initial spread to human from chimpanzee in 1930s, HIV-1 remains undergoing rapid evolution in larger and more diverse population. The divergent phenotype evolution of two major CRF01_AE clusters highlights the importance in monitoring the genetic evolution and phenotypic shift of HIV-1 to provide early warning for the appearance of more pathogenic strains such as CRF01_AE cluster 4.Significance StatementPast studies on HIV-1 evolution were mainly at the genetic level. This study provides well-matched genotype and phenotype data and demonstrates disparate pathogenicity of two major CRF01_AE clusters. While both CRF01_AE cluster 4 and cluster 5 are mainly spread through the MSM route, cluster 4 but not cluster 5 causes fast CD4 loss, which is associated with the higher prevalence CXCR4 viruses in cluster 4. The higher CXCR4 use tendency in cluster 4 is derived from its unique V3 loop favoring CXCR4 binding. This study for the first time demonstrates disparate HIV-1 phenotype between different phylogenetic clusters. It is important to monitor HIV-1 evolution at both the genotype and phenotype level to identify and control more pathogenic HIV-1 strains.

scholarly journals Disparate impact on CD4 T cell count by two distinct HIV-1 phylogenetic clusters from the same clade

2018 ◽  
Vol 116 (1) ◽  
pp. 239-244 ◽  
Author(s):  
Hongshuo Song ◽  
Weidong Ou ◽  
Yi Feng ◽  
Junli Zhang ◽  
Fan Li ◽  
...  
Keyword(s):  
Rapid Evolution ◽  
First Year ◽  
Binding Model ◽  
Global Epidemic ◽  
Phylogenetic Cluster ◽  
Coreceptor Binding ◽  
Similar Phenotype ◽  
Underlying Mechanisms ◽  
Phenotypic Shift ◽  
Hiv 1

HIV-1 evolved into various genetic subtypes and circulating recombinant forms (CRFs) in the global epidemic. The same subtype or CRF is usually considered to have similar phenotype. Being one of the world’s major CRFs, CRF01_AE infection was reported to associate with higher prevalence of CXCR4 (X4) viruses and faster CD4 decline. However, the underlying mechanisms remain unclear. We identified eight phylogenetic clusters of CRF01_AE in China and hypothesized that they may have different phenotypes. In the National HIV Molecular Epidemiology Survey, we discovered that people infected by CRF01_AE cluster 4 had significantly lower CD4 counts (391 vs. 470,P< 0.0001) and higher prevalence of X4-using viruses (17.1% vs. 4.4%,P< 0.0001) compared with those infected by cluster 5. In an MSM cohort, X4-using viruses were only isolated from seroconvertors in cluster 4, which was associated with low a CD4 count within the first year of infection (141 vs. 440,P= 0.003). Using a coreceptor binding model, we identified unique V3 signatures in cluster 4 that favor CXCR4 use. We demonstrate that the HIV-1 phenotype and pathogenicity can be determined at the phylogenetic cluster level in the same subtype. Since its initial spread to humans from chimpanzees, estimated to be the first half of the 20th century, HIV-1 continues to undergo rapid evolution in larger and more diverse populations. The divergent phenotype evolution of two major CRF01_AE clusters highlights the importance of monitoring the genetic evolution and phenotypic shift of HIV-1 to provide early warning of the appearance of more pathogenic strains.

scholarly journals Cobalt-based magnetic Weyl semimetals with high-thermodynamic stabilities

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Wei Luo ◽  
Yuma Nakamura ◽  
Jinseon Park ◽  
Mina Yoon
Keyword(s):  
Tight Binding ◽  
Three Dimensional ◽  
Interlayer Coupling ◽  
First Principles Calculation ◽  
Optimization Approach ◽  
Binding Model ◽  
Nodal Lines ◽  
Weyl Semimetal ◽  
Topological Quantum ◽  
First Time

AbstractRecent experiments identified Co3Sn2S2 as the first magnetic Weyl semimetal (MWSM). Using first-principles calculation with a global optimization approach, we explore the structural stabilities and topological electronic properties of cobalt (Co)-based shandite and alloys, Co3MM’X2 (M/M’ = Ge, Sn, Pb, X = S, Se, Te), and identify stable structures with different Weyl phases. Using a tight-binding model, for the first time, we reveal that the physical origin of the nodal lines of a Co-based shandite structure is the interlayer coupling between Co atoms in different Kagome layers, while the number of Weyl points and their types are mainly governed by the interaction between Co and the metal atoms, Sn, Ge, and Pb. The Co3SnPbS2 alloy exhibits two distinguished topological phases, depending on the relative positions of the Sn and Pb atoms: a three-dimensional quantum anomalous Hall metal, and a MWSM phase with anomalous Hall conductivity (~1290 Ω−1 cm−1) that is larger than that of Co2Sn2S2. Our work reveals the physical mechanism of the origination of Weyl fermions in Co-based shandite structures and proposes topological quantum states with high thermal stability.

scholarly journals Single-crystalline epitaxial TiO film: A metal and superconductor, similar to Ti metal

2021 ◽  
Vol 7 (2) ◽  
pp. eabd4248
Author(s):  
Fengmiao Li ◽  
Yuting Zou ◽  
Myung-Geun Han ◽  
Kateryna Foyevtsova ◽  
Hyungki Shin ◽  
...  
Keyword(s):  
Transition Metal ◽  
Density Functional ◽  
Tight Binding ◽  
Crystal Form ◽  
Titanium Monoxide ◽  
Binding Model ◽  
Functional Theory ◽  
Single Crystalline ◽  
First Time ◽  
Lattice Matched

Titanium monoxide (TiO), an important member of the rock salt 3d transition-metal monoxides, has not been studied in the stoichiometric single-crystal form. It has been challenging to prepare stoichiometric TiO due to the highly reactive Ti2+. We adapt a closely lattice-matched MgO(001) substrate and report the successful growth of single-crystalline TiO(001) film using molecular beam epitaxy. This enables a first-time study of stoichiometric TiO thin films, showing that TiO is metal but in proximity to Mott insulating state. We observe a transition to the superconducting phase below 0.5 K close to that of Ti metal. Density functional theory (DFT) and a DFT-based tight-binding model demonstrate the extreme importance of direct Ti–Ti bonding in TiO, suggesting that similar superconductivity exists in TiO and Ti metal. Our work introduces the new concept that TiO behaves more similar to its metal counterpart, distinguishing it from other 3d transition-metal monoxides.

scholarly journals From Capsids to Complexes: Expanding the Role of TRIM5α in the Restriction of Divergent RNA Viruses and Elements

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 446
Author(s):  
Kevin M. Rose ◽  
Stephanie J. Spada ◽  
Rebecca Broeckel ◽  
Kristin L. McNally ◽  
Vanessa M. Hirsch ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Molecular Basis ◽  
Human Population ◽  
Rna Viruses ◽  
Arms Race ◽  
Innate Immune ◽  
Immunodeficiency Virus ◽  
Underlying Mechanisms ◽  
Hiv 1

An evolutionary arms race has been ongoing between retroviruses and their primate hosts for millions of years. Within the last century, a zoonotic transmission introduced the Human Immunodeficiency Virus (HIV-1), a retrovirus, to the human population that has claimed the lives of millions of individuals and is still infecting over a million people every year. To counteract retroviruses such as this, primates including humans have evolved an innate immune sensor for the retroviral capsid lattice known as TRIM5α. Although the molecular basis for its ability to restrict retroviruses is debated, it is currently accepted that TRIM5α forms higher-order assemblies around the incoming retroviral capsid that are not only disruptive for the virus lifecycle, but also trigger the activation of an antiviral state. More recently, it was discovered that TRIM5α restriction is broader than previously thought because it restricts not only the human retroelement LINE-1, but also the tick-borne flaviviruses, an emergent group of RNA viruses that have vastly different strategies for replication compared to retroviruses. This review focuses on the underlying mechanisms of TRIM5α-mediated restriction of retroelements and flaviviruses and how they differ from the more widely known ability of TRIM5α to restrict retroviruses.

scholarly journals Phenotypic Susceptibility to Bevirimat in Isolates from HIV-1-Infected Patients without Prior Exposure to Bevirimat

2010 ◽  
Vol 54 (6) ◽  
pp. 2345-2353 ◽  
Author(s):  
Nicolas A. Margot ◽  
Craig S. Gibbs ◽  
Michael D. Miller
Keyword(s):  
Recombinant Viruses ◽  
Gag Polyprotein ◽  
New Class ◽  
Major Mutation ◽  
Hiv Drugs ◽  
The Impact ◽  
First Time ◽  
Hiv 1

ABSTRACT Bevirimat (BVM) is the first of a new class of anti-HIV drugs with a novel mode of action known as maturation inhibitors. BVM inhibits the last cleavage of the Gag polyprotein by HIV-1 protease, leading to the accumulation of the p25 capsid-small peptide 1 (SP1) intermediate and resulting in noninfectious HIV-1 virions. Early clinical studies of BVM showed that over 50% of the patients treated with BVM did not respond to treatment. We investigated the impact of prior antiretroviral (ARV) treatment and/or natural genetic diversity on BVM susceptibility by conducting in vitro phenotypic analyses of viruses made from patient samples. We generated 31 recombinant viruses containing the entire gag and protease genes from 31 plasma samples from HIV-1-infected patients with (n = 21) or without (n = 10) prior ARV experience. We found that 58% of the patient isolates tested had a >10-fold reduced susceptibility to BVM, regardless of the patient's ARV experience or the level of isolate resistance to protease inhibitors. Analysis of mutants with site-directed mutations confirmed the role of the V370A SP1 polymorphism (SP1-V7A) in resistance to BVM. Furthermore, we demonstrated for the first time that a capsid polymorphism, V362I (CA protein-V230I), is also a major mutation conferring resistance to BVM. In contrast, none of the previously defined resistance-conferring mutations in Gag selected in vitro (H358Y, L363M, L363F, A364V, A366V, or A366T) were found to occur among the viruses that we analyzed. Our results should be helpful in the design of diagnostics for prediction of the potential benefit of BVM treatment in HIV-1-infected patients.

scholarly journals Elucidation of Early Evolution of HIV-1 Group M in the Congo Basin Using Computational Methods

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 517
Author(s):  
Marcel Tongo ◽  
Darren P. Martin ◽  
Jeffrey R. Dorfman
Keyword(s):  
Genetic Relatedness ◽  
Early Evolution ◽  
Congo Basin ◽  
Global Epidemic ◽  
The Past ◽  
History Of ◽  
Cold Spots ◽  
Genomic Regions ◽  
Basin Region ◽  
Hiv 1

The Congo Basin region is believed to be the site of the cross-species transmission event that yielded HIV-1 group M (HIV-1M). It is thus likely that the virus has been present and evolving in the region since that cross-species transmission. As HIV-1M was only discovered in the early 1980s, our directly observed record of the epidemic is largely limited to the past four decades. Nevertheless, by exploiting the genetic relatedness of contemporary HIV-1M sequences, phylogenetic methods provide a powerful framework for investigating simultaneously the evolutionary and epidemiologic history of the virus. Such an approach has been taken to find that the currently classified HIV-1 M subtypes and Circulating Recombinant Forms (CRFs) do not give a complete view of HIV-1 diversity. In addition, the currently identified major HIV-1M subtypes were likely genetically predisposed to becoming a major component of the present epidemic, even before the events that resulted in the global epidemic. Further efforts have identified statistically significant hot- and cold-spots of HIV-1M subtypes sequence inheritance in genomic regions of recombinant forms. In this review we provide ours and others recent findings on the emergence and spread of HIV-1M variants in the region, which have provided insights into the early evolution of this virus.

scholarly journals Natural alteration of HIV-1 co-receptor tropism by contemporaneous HIV-2 infection

2018 ◽  
Author(s):  
Joakim Esbjörnsson ◽  
Fredrik Månsson ◽  
Hans Norrgren ◽  
Sarah L. Rowland-Jones
Keyword(s):  
Late Stage ◽  
Stage Disease ◽  
Late Stage Disease ◽  
Underlying Mechanisms ◽  
Disease Understanding ◽  
Hiv 1 ◽  
The Way

In this study, we show that the pathogenic HIV-1 CXCR4-tropism is more common in HIV-1 single (79%) than in HIV-1 and HIV-2 dual-infected individuals (35%), suggesting that contemporaneous HIV-2 infection can affect HIV-1 co-receptor tropism in late-stage disease. Understanding the underlying mechanisms responsible for this natural alteration by HIV-2 could pave the way towards a deeper understanding of the AIDS pathogenesis.

scholarly journals A Three-Pool Model Dissecting Readily Releasable Pool Replenishment at the Calyx of Held

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Jun Guo ◽  
Jian-long Ge ◽  
Mei Hao ◽  
Zhi-cheng Sun ◽  
Xin-sheng Wu ◽  
...  
Keyword(s):  
Time Course ◽  
Current View ◽  
Vesicle Recycling ◽  
Releasable Pool ◽  
Readily Releasable Pool ◽  
Central Synapse ◽  
Pool Model ◽  
Underlying Mechanisms ◽  
First Time ◽  
Intense Stimulation

Abstract Although vesicle replenishment is critical in maintaining exo-endocytosis recycling, the underlying mechanisms are not well understood. Previous studies have shown that both rapid and slow endocytosis recycle into a very large recycling pool instead of within the readily releasable pool (RRP) and the time course of RRP replenishment is slowed down by more intense stimulation. This finding contradicts the calcium/calmodulin-dependence of RRP replenishment. Here we address this issue and report a three-pool model for RRP replenishment at a central synapse. Both rapid and slow endocytosis provide vesicles to a large reserve pool (RP) ~42.3 times the RRP size. When moving from the RP to the RRP, vesicles entered an intermediate pool (IP) ~2.7 times the RRP size with slow RP-IP kinetics and fast IP-RRP kinetics, which was responsible for the well-established slow and rapid components of RRP replenishment. Depletion of the IP caused the slower RRP replenishment observed after intense stimulation. These results establish, for the first time, a realistic cycling model with all parameters measured, revealing the contribution of each cycling step in synaptic transmission. The results call for modification of the current view of the vesicle recycling steps and their roles.

Centrosome cohesion is regulated by a balance of kinase and phosphatase activities

2001 ◽  
Vol 114 (20) ◽  
pp. 3749-3757 ◽  
Author(s):  
Patrick Meraldi ◽  
Erich A. Nigg
Keyword(s):  
Protein Phosphatase ◽  
Kinase Activity ◽  
Dominant Negative ◽  
Dominant Negative Mutant ◽  
Microtubule Depolymerization ◽  
Drug Induced ◽  
Microtubule Network ◽  
Similar Phenotype ◽  
Underlying Mechanisms

Centrosome cohesion and separation are regulated throughout the cell cycle, but the underlying mechanisms are not well understood. Since overexpression of a protein kinase, Nek2, is able to trigger centrosome splitting (the separation of parental centrioles), we have surveyed a panel of centrosome-associated kinases for their ability to induce a similar phenotype. Cdk2, in association with either cyclin A or E, was as effective as Nek2, but several other kinases tested did not significantly interfere with centrosome cohesion. Centrosome splitting could also be triggered by inhibition of phosphatases, and protein phosphatase 1α (PP1α) was identified as a likely physiological antagonist of Nek2. Furthermore, we have revisited the role of the microtubule network in the control of centrosome cohesion. We could confirm that microtubule depolymerization by nocodazole causes centrosome splitting. Surprisingly, however, this drug-induced splitting also required kinase activity and could specifically be suppressed by a dominant-negative mutant of Nek2. These studies highlight the importance of protein phosphorylation in the control of centrosome cohesion, and they point to Nek2 and PP1α as critical regulators of centrosome structure.

Sign in / Sign up

Export Citation Format

Share Document