Silicon Nanowire Field-Effect Transistor as Label-Free Detection of Hepatitis B Virus Proteins with Opposite Net Charges.

The prevalence of hepatitis B virus (HBV) is a global healthcare threat, particularly chronic hepatitis B (CHB) that might lead to hepatocellular carcinoma (HCC) should not be neglected. Although many types of HBV diagnosis detection methods are available, some technical challenges, such as the high cost or lack of practical feasibility, need to be overcome. In this study, the polycrystalline silicon nanowire field-effect transistors (pSiNWFETs) were fabricated through commercial process technology and then chemically functionalized for sensing hepatitis B virus surface antigen (HBsAg) and hepatitis B virus X protein (HBx) at the femto-molar level. These two proteins have been suggested to be related to the HCC development, while the former is also the hallmark for HBV diagnosis, and the latter is an RNA-binding protein. Interestingly, these two proteins carried opposite net charges, which could serve as complementary candidates for evaluating the charge-based sensing mechanism in the pSiNWFET. The measurements on the threshold voltage shifts of pSiNWFETs showed a consistent correspondence to the polarity of the charges on the proteins studied. We believe that this report can pave the way towards developing an approachable tool for biomedical applications.

Localization of SARS-CoV-2 Capping Enzymes Revealed by an Antibody against the nsp10 Subunit.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease-19 pandemic. One of the key components of the coronavirus replication complex are the RNA methyltransferases (MTases), RNA-modifying enzymes crucial for RNA cap formation. Recently, the structure of the 2'-O MTase has become available; however, its biological characterization within the infected cells remains largely elusive. Here, we report a novel monoclonal antibody directed against the SARS-CoV-2 non-structural protein nsp10, a subunit of both the 2'-O RNA and N7 MTase protein complexes. Using this antibody, we investigated the subcellular localization of the SARS-CoV-2 MTases in cells infected with the SARS-CoV-2.

Development of a Lateral Flow Strip Membrane Assay for Rapid and Sensitive Detection of the SARS-CoV-2.

The infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the coronavirus disease 2019 (COVID-19) has threatened public health worldwide. The easy human-to-human transmission of this virus has rapidly evolved into a global pandemic. Therefore, to control the community spread of the virus, it is crucial to identify the infected individuals, including asymptomatic people. Hence, a specific and rapid assay is crucial for the early diagnosis and active monitoring of individuals potentially exposed to SARS-CoV-2 for controlling the COVID-19 outbreak. In this study, we have developed the novel lateral flow strip membrane (LFSM) assay that allows the simultaneous detection of RdRp, ORF3a, and N genes using the PCR product obtained by using the single-tube reverse transcription polymerase chain reaction (RT-PCR). The LFSM assay allows detection of SARS-CoV-2 in 30 min at 25 °C after the RT-PCR with the detection limit of 10 copies/test for each gene. The clinical performance of the LFSM assay for the detection of SARS-Cov-2 was evaluated using 162 clinical samples previously detected by using the commercial assay. The percent positive agreement, percent negative agreement, and overall percent agreement of the LFSM assay with the commercial assay were 100% (94.2-100%), 99.0% (94.6-100%), and 99.4% (96.6-100%), respectively. Therefore, the results of the LFSM assay showed significantly high concordance with the commercial assay for the detection of SARS-CoV-2 in clinical specimens. Therefore, we conclude that the developed LFSM assay can be used alone or complementary to the RT-PCR or other methods for the diagnosis and monitoring of the patients to curb community transmission and the pandemic.

Identification of hepatitis B virus aetiologic antigens, HBx and Pre-S2, in diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) has been reported to have a significant association with the hepatitis B virus (HBV) infection. However, there has been no experimental evidence to determine whether the components of the hepatitis B virus are expressed in lymphoid cells. In this study, we used immunohistochemical methods to explore whether the antigens of hepatitis B virus are expressed in DLBCL lymphoma cells in HBsAg-positive DLBCL patients (HBsAg + DLBCL). HBx antigen was detected in 48.9% of HBsAg + DLBCL patients, and the expression rate of the Pre-S2 antigen was 57.2%. HBx expression was significantly associated with high-level expression of c-Myc, while the Pre-S2 antigen was not. In this study, we demonstrated that HBx antigen and Pre-S2 antigen could be detected in lymphoma cells, and HBx expression was related to c-Myc expression. Our findings provide a strong basis for further study of the HBV-infected DLBCL and molecular mechanism underlying the lymphomagenesis.

Handmade microfluidic device for biochemical applications in emulsion.

A simple, inexpensive flow-focusing device has been developed to make uniform droplets for biochemical reactions, such as in vitro transcription and cell-free protein synthesis. The device was fabricated from commercially available components without special equipment. Using the emulsion droplets formed by the device, a class I ligase ribozyme, bcI 23, was successfully synthesized from DNA attached to magnetic microbeads by T7 RNA polymerase. It was also ligated with an RNA substrate on the same microbeads, and detected using flow cytometry with a fluorescent probe. In addition, a single-chain derivative of the lambda Cro protein was expressed using an Escherichia coli cell-free protein synthesis system in emulsion, which was prepared using the flow-focusing device. In both emulsified reactions, usage of the flow-focusing device was able to greatly reduce the coefficient of variation for the amount of RNA or protein displayed on the microbeads, demonstrating the device is advantageous for quantitative analysis in high-throughput screening.

A multi-scale mathematical modeling framework to investigate anti-viral therapeutic opportunities in targeting HIV-1 accessory proteins.

Human immunodeficiency virus-1 (HIV-1) employs accessory proteins to evade innate immune responses by neutralizing the anti-viral activity of host restriction factors. Apolipoprotein B mRNA-editing enzyme 3G (APOBEC3G, A3G) and bone marrow stromal cell antigen 2 (BST2) are host resistance factors that potentially inhibit HIV-1 infection. BST2 reduces viral production by tethering budding HIV-1 particles to virus producing cells, while A3G inhibits the reverse transcription (RT) process and induces viral genome hypermutation through cytidine deamination, generating fewer replication competent progeny virus. Two HIV-1 proteins counter these cellular restriction factors: Vpu, which reduces surface BST2, and Vif, which degrades cellular A3G. The contest between these host and viral proteins influences whether HIV-1 infection is established and progresses towards AIDS. In this work, we present an age-structured multi-scale viral dynamics model of in vivo HIV-1 infection. We integrated the intracellular dynamics of anti-viral activity of the host factors and their neutralization by HIV-1 accessory proteins into the virus/cell population dynamics model. We calculate the basic reproductive ratio (Ro) as a function of host-viral protein interaction coefficients, and numerically simulated the multi-scale model to understand HIV-1 dynamics following host factor-induced perturbations. We found that reducing the influence of Vpu triggers a drop in Ro, revealing the impact of BST2 on viral infection control. Reducing Vif׳s effect reveals the restrictive efficacy of A3G in blocking RT and in inducing lethal hypermutations, however, neither of these factors alone is sufficient to fully restrict HIV-1 infection. Interestingly, our model further predicts that BST2 and A3G function synergistically, and delineates their relative contribution in limiting HIV-1 infection and disease progression. We provide a robust modeling framework for devising novel combination therapies that target HIV-1 accessory proteins and boost antiviral activity of host factors.

Detection of human polyomavirus proteins, T-antigen and agnoprotein, in human tumor tissue arrays.

Expression of the human polyomavirus JCV genome in several experimental animals induces a variety of neural origin tumors. The viral proteins, T-antigen and Agnoprotein, contribute to the oncogenesis of JCV by associating with several tumor suppressor proteins and dysregulating signaling pathways, which results in uncontrolled cell proliferation. In addition, T-antigen and Agnoprotein have been associated with DNA damage and interfering with DNA repair mechanisms. In this study, we have utilized commercially available tissue arrays of human tumors of various origins and demonstrated the expression of both T-antigen and Agnoprotein in some, but not all, tumors of neural and non-neural origin. Most notably, more than 40% of human glioblastomas and greater than 30% of colon adenocarcinomas express viral proteins. The detection of viral transforming proteins, T-antigen and Agnoprotein in the absence of viral capsid proteins suggests a role for JCV in the development and/or progression of human tumors. These results invite further large-scale investigation on the role of polyomaviruses, particularly JCV in the pathogenesis of human cancer.

The absence of JC virus antigens in Indian children with medulloblastomas.

BACKGROUND: The human polyoma virus, also known as the JC virus (JCV), replicates predominantly in the oligodendrocytes, the myelin producing cells in the central nervous system and results in the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML) especially in immunosuppressed patients with AIDS. Several investigators have also documented the presence of the viral genome and early and late antigens in a variety of brain tumors particularly in medulloblastomas, gliomas and ependymomas. Reports also indicate the presence of JCV in patients with colon cancer. The T antigen of JCV has been postulated to have oncogenic potential as substantiated by animal experiments. Although JCV infects 80% of the population, there are scant epidemiological studies regarding JCV from India. There are also reports of the low prevalence of PML in patients with AIDS from India and Africa. AIM: This study was undertaken to investigate if Indian children with medulloblastomas also show evidence of JCV. METHODS: Twenty-two consecutive cases of medulloblastomas were investigated for the presence of T antigen and agnoprotein of JCV in biopsy specimens by immunohistochemistry. Antibodies to the agnoprotein antigen raised in rabbits and a monoclonal antibody against SV40 T antigen raised in mice that cross-reacts with JCV T antigen were used. RESULTS: Out of 22 patients, 4 had desmoplastic tumors while the rest had classical tumors. All children were below the age of 10. Results indicate that while PML tissues showed consistent immunostaining both with antibody to T antigen and agnoprotein antibody, none of the tumors showed any positive staining for JC viral antigens. CONCLUSION: JCV antigens could not be detected by immunohistochemistry in the tumor tissues of Indian children with medulloblastomas.

Hepatitis B virus HBx protein localizes to mitochondria in primary rat hepatocytes and modulates mitochondrial membrane potential.

Over 350 million people are chronically infected with hepatitis B virus (HBV), and a significant number of chronically infected individuals develop primary liver cancer. HBV encodes seven viral proteins, including the nonstructural X (HBx) protein. The results of studies with immortalized or transformed cells and with HBx-transgenic mice demonstrated that HBx can interact with mitochondria. However, no studies with normal hepatocytes have characterized the precise mitochondrial localization of HBx or the effect of HBx on mitochondrial physiology. We have used cultured primary rat hepatocytes as a model system to characterize the mitochondrial localization of HBx and the effect of HBx expression on mitochondrial physiology. We now show that a fraction of HBx colocalizes with density-gradient-purified mitochondria and associates with the outer mitochondrial membrane. We also demonstrate that HBx regulates mitochondrial membrane potential in hepatocytes and that this function of HBx varies depending on the status of NF-kappaB activity. In primary rat hepatocytes, HBx activation of NF-kappaB prevented mitochondrial membrane depolarization; however, when NF-kappaB activity was inhibited, HBx induced membrane depolarization through modulation of the mitochondrial permeability transition pore. Collectively, these results define potential pathways through which HBx may act in order to modulate mitochondrial physiology, thereby altering many cellular activities and ultimately contributing to the development of HBV-associated liver cancer.

HIV-1 Vpu inhibits accumulation of the envelope glycoprotein within clathrin-coated, Gag-containing endosomes.

Several viruses encode ion channels that both modulate the trafficking of envelope glycoprotein(s) and stimulate the release of virions from cells. HIV-1 Vpu enhances virion release and inhibits the endosomal accumulation of the viral structural protein Gag. We investigated whether Vpu affects the subcellular distribution of Env as well as Gag. Env and Vpu colocalized with each other, in part within the trans-Golgi network. In the absence of Vpu, Env accumulated more extensively within clathrin-coated endosomal structures. These structures had several features consistent with an endosomal viral assembly domain: they contained Gag, including proteolytically processed viral matrix protein; the tetraspanins CD63 and CD81; the adaptor protein complex AP-3; and AIP1/ALIX, a cellular cofactor for viral budding. These endosomes labelled incompletely with Env derived from the cell surface, suggesting that some Env reaches this compartment without transiting the plasma membrane. Consistent with this, endosomal accumulation of Env was not blocked by dominant-negative Eps15, an inhibitor of AP-2-mediated endocytosis. Although these data are potentially explained by greater endocytosis of mature virions in the absence of Vpu, they also raise the possibility that Vpu inhibits the transport of Env and Gag to late endosomes, leading to viral assembly at the plasma membrane.

Analysis of HIV-2 Vpx by modeling and insertional mutagenesis.

Vpx facilitates HIV-2 nuclear localization by a poorly understood mechanism. We have compared Vpx to an NMR structure HIV-1 Vpr in a central helical domain and probed regions of Vpx by insertional mutagenesis. A predicted loop between helices two and three appears to be unique, overlapping with a known novel nuclear localization signal. Overall, Vpx was found to be surprisingly flexible, tolerating a series of large insertions. We found that insertion within the polyproline-containing C-terminus destabilizes nuclear localization, whereas mutating a second helix in the central domain disrupts viral packaging. Other insertional mutants in the predicted loop and in a linker region between the central domain and the C-terminus may be useful as sites of intramolecular tags as they could be packaged adequately and retained preintegration complex associated integration activity in a serum starvation assay. An unexpected result was found within a previously defined nuclear localization motif near aa 71. This mutant retained robust nuclear localization in a GFP fusion assay and was competent for preintegration complex associated nuclear import. In summary, we have modeled helical content in Vpx and assessed potential sites of intramolecular tags which may prove useful for protein-protein interactions studies.

Identification of the nuclear localization signal of human immunodeficiency virus type 2 Vpx.

The Vpx protein of human immunodeficiency virus type 2 (HIV-2) is a viral accessory protein related to, but distinct from, the Vpr protein of HIV-1. Vpx is packaged into virions and, as a component of the viral preintegration complex (PIC), Vpx is required for efficient virus replication in nondividing cells. Therefore, the localization of Vpx in cells is dynamic and dependent upon discrete domains of the protein. Expressed in the absence of other viral proteins, Vpx localizes to the nucleus of cells. However, if expressed with the Gag protein of HIV-2, Vpx localizes to the plasma membrane of cells. To further understand the regulation of Vpx localization, we fused regions of Vpx to beta-galactosidase to identify regions of the protein sufficient to mediate nuclear localization. The minimal transferable region of Vpx that conferred nuclear localization in these assays was aa 65 to 72. Alanine substitution of K(68) and R(70) in a GFP-Vpx construct abolished nuclear localization, suggesting that the basic residues in this region are important for nuclear import. Analysis of the membrane transport of several GFP-Vpx alanine mutants demonstrated that while separable, the domains of Vpx required for nuclear localization are not distinct from the domains required for membrane transport. The results of heterokaryon shuttling assays indicated that Vpx is not a shuttling protein; however, HIV-2 Vpr did shuttle similar to HIV-1 Vpr.

HIV type 2 Vpx interaction with Gag and incorporation into virus-like particles.

The domain of HIV-2 Vpx previously shown to be important for virion incorporation has been mapped to residues 73--89. Mutational analysis of this domain was employed to further define the sequences important for incorporation into virus-like particles, using a vaccinia virus expression system. Deletion of residues 73--89 did not abrogate Vpx packaging, but substitution with alanines markedly reduced incorporation into virus-like particles. Moreover, alanine substitution also disrupted Vpx interaction with Gag, as demonstrated with glutathione S-transferase fusion proteins and the yeast two-hybrid system.

Targeting a foreign protein into virion particles by fusion with the Vpx protein of simian immunodeficiency virus.

The Vpx and Vpr proteins of the primate immunodeficiency viruses are stoichiometrically incorporated into virion particles. The chloramphenicol acetyltransferase (CAT) enzyme, when fused to a sufficient portion of the simian immunodeficiency virus (SIVmac239) Vpx protein, was incorporated into virions and retained enzymatic activity. An analysis of the replication of this virus compared with the replication of revertants and control viruses encoding nonpackageable Vpx-CAT fusion proteins suggested that the observed delay in replication was due to cis-acting effects of the CAT gene insertion rather than to the presence of the Vpx-CAT fusion protein in the virions. These studies indicate that, in host cells where Vpx and Vpr function is not required for efficient SIVmac replication, functional enzymes can be incorporated into virions by fusion with the Vpx protein. This approach could be utilized for study of the function and localization of Vpx and/or Vpr proteins during virus replication and for attempts to disrupt virus replication by the incorporation of foreign proteins.

Protein stability influences human immunodeficiency virus type 2 Vpr virion incorporation and cell cycle effect.

Using recombinant proteins as standards, we calculated the amount of Vpr and Vpx present in HIV-2ROD particles. We find 2000-3000 copies of Vpx per particle but only 40-50 copies of Vpr. We investigated the reasons for this discrepancy between Vpx and Vpr and found that viral factors, including HIV-2 Vpx, do not restrict its incorporation. Instead, the accumulation of HIV-2ROD Vpr during infection is restricted by a short protein half-life which acts to limit its virion incorporation. The half-life of HIV-2 Vpr was calculated to be about 90 min, while HIV-2 Vpx and HIV-1 Vpr had half-lifes of 36 and 20 hr, respectively. Moreover, while both HIV-1 Vpr and HIV-2 Vpr cause cells to accumulate in G2 of the cell cycle, the effect of HIV-2 Vpr is attenuated relative to HIV-1 Vpr. Thus, protein stability correlates with both the function of Vpr and its virion incorporation.

Presence of virion protein x (Vpx) of simian immunodeficiency virus SIVmac 251 in target cells in vivo.

Localization of virion-associated protein x (Vpx) of SIVmac 251 was studied in lymph nodes and liver of six SIVmac-infected monkeys. Vpx was found associated with the network of follicular dendritic cells and macrophages in lymph nodes and/or livers from five out of six animals by immunohistochemistry. Although the humoral response to Vpx occurs in only 50% of the animals, the presence of Vpx in target cell or antibodies to Vpx in all the monkeys studied, suggests that Vpx may be necessary for viral replication in vivo.

Intracellular localization and DNA-binding activity of a class of viral early phosphoproteins in human fibroblasts infected with human cytomegalovirus (Towne strain).

Indirect immunofluorescence (IF) with monoclonal antibody M23 prepared against the nuclei of human embryo lung (HEL) cells infected with human cytomegalovirus (HCMV) Towne strain showed that the M23 antigen reactive with the M23 antibody was localized within distinct foci throughout the nucleus of infected HEL cells shortly after infection, even at 2 h post-infection (p.i.). The foci increased in size by 24 h p.i. and then the IF patterns changed to show the nuclear inclusion body-like structures at 72 h p.i. Treatment with phosphono-acetic acid, a HCMV DNA replication inhibitor, resulted in a nuclear pattern similar to that observed shortly after infection. The double-labelled IF test revealed that the HCMV UL44 antigen essential for viral DNA replication colocalized with the M23 antigen in the same intranuclear structure shortly after infection whereas neither viral antigen appeared to colocalize in most cells later after infection. The M23 antibody immunoprecipitated four proteins. 34K, 43K, 50K and 84K, in infected cells. To examine whether these proteins correspond to four early phosphoproteins encoded by the HCMV strain AD169 genome, the Towne strain DNA sequence corresponding to that encoding both the 34K and 43K proteins of strain AD169 was determined and transiently expressed in COS-7, Vero and HEL cells. These proteins were detected by the M23 antibody within the foci of these nuclei as found in the nuclei of productively infected cells shortly after infection. In addition, the 34K, 43K and 50K proteins at least were shown to be DNA-binding proteins by double- and single-stranded DNA-cellulose column chromatography. The relationship of these proteins to the status of viral DNA replication is discussed.

Localization of viral protein X in simian immunodeficiency virus macaque strain and analysis of its packaging requirements.

Simian immunodeficiency virus (SIV) and human immunodeficiency virus type 2 (HIV-2) encode the accessory viral protein X (Vpx) known to be incorporated into virions in amounts comparable to those of the Gag proteins. The localization of Vpx within SIVmac-infected HUT-78 cells and SIVmac virions was studied by immunoelectron microscopy. Vpx appeared to be associated with extracellular virions as well as budding viral particles at the surface of infected cells. Immunolabelling of purified viral cores suggested that Vpx was a component of the amorphous material surrounding the core structure. Furthermore, a detergent insoluble fraction containing SIV core proteins was devoid of Vpx. To investigate the protein requirement for packaging of Vpx, BHK-21 cells were co-infected with vaccinia virus recombinants encoding Vpx and other SIV proteins able to assemble into virus-like particles. Analysis by immunoprecipitation of the extracellular particulate material as well as immunoelectron microscopy demonstrated that co-expression of Vpx with the Pr56gag polyprotein was sufficient for the formation of pseudo-virions containing Vpx. Virus-like particles that appeared upon expression of p16gag did not contain Vpx. The results suggest that Vpx is packaged into viral particles through its binding to the Gag polyprotein. The precise positioning of Vpx within the space separating the viral envelope from the core structure is postulated to result from the reorganization of viral proteins that occurs upon Gag polyprotein cleavage and budding.