Consolidation and Forced Elasticity in Double-Network Hydrogels

This paper discusses two observations that are unique with respect to the mechanics of double network (DN) hydrogels, forced elasticity driven by water diffusion and consolidation, which are analogous to the so-called Gough-Joule effects in rubbers. A series of DN hydrogels were synthesized from 2-acrylamido-2-methylpropane sulfuric acid (AMPS), 3-sulfopropyl acrylate potassium salt (SAPS) and acrylamide (AAm). Drying of AMPS/AAm DN hydrogels was monitored by extending the gel specimens to different stretch ratios and holding them until all the water evaporated. At high extension ratios, the gels underwent plastic deformation. Water diffusion measurements performed on AMPS/AAm DN hydrogels that were dried at different stretch ratios indicated that the diffusion mechanism deviated from Fickian behavior at extension ratios greater than two. Study of the mechanical behavior of AMPS/AAm and SAPS/AAm DN hydrogels during tensile and confined compression tests showed that despite their large water content, DN hydrogels can retain water during large-strain tensile or compression deformations.

Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site

Nanobodies can achieve remarkable neutralization of genetically diverse pathogens, including HIV-1. To gain insight into their recognition, we determined crystal structures of four llama nanobodies (J3, A12, C8, and D7), all of which targeted the CD4-binding site, in complex with the HIV-1 envelope (Env) gp120 core, and determined a cryoelectron microscopy (cryo-EM) structure of J3 with the Env trimer. Crystal and cryo-EM structures of J3 complexes revealed this nanobody to mimic binding to the prefusion-closed trimer for the primary site of CD4 recognition as well as a secondary quaternary site. In contrast, crystal structures of A12, C8, and D7 with gp120 revealed epitopes that included portions of the gp120 inner domain, inaccessible on the prefusion-closed trimer. Overall, these structures explain the broad and potent neutralization of J3 and limited neutralization of A12, C8, and D7, which utilized binding modes incompatible with the neutralization-targeted prefusion-closed conformation of Env.

Luc Montagnier (1932-2022)

Discoverer of the human immunodeficiency virus.

Emergence of epidemic diseases: zoonoses and other origins

Infectious diseases emerge via many routes and may need to overcome stepwise bottlenecks to burgeon into epidemics and pandemics. About 60% of human infections have animal origins, whereas 40% either co-evolved with humans or emerged from non-zoonotic environmental sources. Although the dynamic interaction between wildlife, domestic animals, and humans is important for the surveillance of zoonotic potential, exotic origins tend to be overemphasized since many zoonoses come from anthropophilic wild species (for example, rats and bats). We examine the equivocal evidence of whether the appearance of novel infections is accelerating and relate technological developments to the risk of novel disease outbreaks. Then we briefly compare selected epidemics, ancient and modern, from the Plague of Athens to COVID-19.

A perspective on the early days of RAS research

The name of the oncogene, ras, has its origin in studies of murine leukemia viruses in the 1960s by Jenny Harvey (H-ras) and by Werner Kirsten (K-ras) which, at high doses, produced sarcomas in rats. Transforming retroviruses were isolated, and its oncogene was named ras after rat sarcoma. From 1979, cellular ras sequences with transforming properties were identified by transfection of tumor DNA initially by Robert Weinberg from rodent tumors, and the isolation of homologous oncogenes from human tumors soon followed, including HRAS and KRAS, and a new member of the family named NRAS. I review these discoveries, placing emphasis on the pioneering research of Christopher Marshall and Alan Hall, who subsequently made immense contributions to our understanding of the functions of RAS and related small GTPases to signal transduction pathways, cell structure, and the behavior of normal and malignant cells.

Nanobodies that Neutralize HIV

Nanobodies or VHH (variable domains of heavy-chain only antibodies) are derived from camelid species such as llamas and camels. Nanobodies isolated and selected through phage display can neutralize a broad range of human immunodeficiency virus type 1 (HIV-1) strains. Nanobodies fit into canyons on the HIV envelope that may not be accessible to IgG (immunoglobulin G) containing both heavy and light chains, and they tend to have long CDR3 (complementarity-determining region 3) loops that further enhance recognition of otherwise cryptic epitopes. Nanobodies are readily expressed at high levels in bacteria and yeast, as well as by viral vectors, and they form relatively stable, heat-resistant molecules. Nanobodies can be linked to human Fc chains to gain immune effector functions. Bivalent and trivalent nanobodies recognizing the same or distinct epitopes on the envelope glycoproteins, gp120 and gp41, greatly increase the potency of HIV-1 neutralization. Nanobodies have potential applications for HIV-1 diagnostics, vaccine design, microbicides, immunoprophylaxis, and immunotherapy.

Super Potent Bispecific Llama VHH Antibodies Neutralize HIV via a Combination of gp41 and gp120 Epitopes

Broad and potent neutralizing llama single domain antibodies (VHH) against HIV-1 targeting the CD4 binding site (CD4bs) have previously been isolated upon llama immunization. Here we describe the epitopes of three additional VHH groups selected from phage libraries. The 2E7 group binds to a new linear epitope in the first heptad repeat of gp41 that is only exposed in the fusion-intermediate conformation. The 1B5 group competes with co-receptor binding and the 1F10 group interacts with the crown of the gp120 V3 loop, occluded in native Env. We present biophysical and structural details on the 2E7 interaction with gp41. In order to further increase breadth and potency, we constructed bi-specific VHH. The combination of CD4bs VHH (J3/3E3) with 2E7 group VHH enhanced strain-specific neutralization with potencies up to 1400-fold higher than the mixture of the individual VHHs. Thus, these new bivalent VHH are potent new tools to develop therapeutic approaches or microbicide intervention.

Strain rate dependent nanostructure of hydrogels with reversible hydrophobic associations during uniaxial extension

An energy dissipation mechanism during deformation is required to impart toughness to hydrogels. Here we describe how in situ small angle X-ray scattering (SAXS) provides insight into possible energy dissipation mechanisms for a tough hydrogel based on an amphiphilic copolymer where nanoscale associations of the hydrophobic moieties act as effective crosslinks. The mechanical properties of the hydrogels are intimately coupled with the nanostructure that provides reversible crosslinks and evolves during deformation. As the extension rate increases, more mechanical energy is dissipated from rearrangements of the crosslinks. The scattering is consistent with hopping of hydrophobes between the nanoscale aggregates as the primary rearrangement mechanism. This rearrangement changes the network conformation that leads to non-affine deformation, where the change in the nanostructure dimension from SAXS is less than 15% of the total macroscopic strain. These nanostructure changes are rate dependent and correlated with the relaxation time of the hydrogel. At low strain rate (0.15% s-1), no significant change of the nanostructure was observed, whereas at higher strain rates (1.5% s-1 and 8.4% s-1) significant nanostructure anisotropy occurred during extension. These differences are attributed to the ability for the network chains to rearrange on the time scale of the deformation; when the characteristic time for extension is longer than the average segmental relaxation time, no significant change in nanostructure occurs on uniaxial extension. These results illustrate the importance of strain rate in the mechanical characterization and consideration of relaxation time in the design of tough hydrogels with reversible crosslinks.

Open questions: knowing who's who in multicellular animals is not always as simple as we imagine

The ability of certain tumor cells of mammals and molluscs to spread from the original host to others reopens the question of distinguishing self from non-self. It is part of a wider phenomenon of cellular parasitism and cell chimerism including germ cells.

Remembering Jan Svoboda: A Personal Reflection

The Czech scientist Jan Svoboda was a pioneer of Rous sarcoma virus (RSV). In the 1960s, before the discovery of reverse transcriptase, he demonstrated the long-term persistence of the viral genome in non-productive mammalian cells, and he supported the DNA provirus hypothesis of Howard Temin. He showed how the virus can be rescued in the infectious form and elucidated the replication-competent nature of the Prague strain of RSV later used for the identification of the src oncogene. His studies straddled molecular oncology and virology, and he remained an active contributor to the field until his death last year. Throughout the 50 years that I was privileged to know Svoboda as my mentor and friend, I admired his depth of scientific inquiry and his steadfast integrity in the face of political oppression.

Molecular Signatures of Regression of the Canine Transmissible Venereal Tumor

The canine transmissible venereal tumor (CTVT) is a clonally transmissible cancer that regresses spontaneously or after treatment with vincristine, but we know little about the regression mechanisms. We performed global transcriptional, methylation, and functional pathway analyses on serial biopsies of vincristine-treated CTVTs and found that regression occurs in sequential steps; activation of the innate immune system and host epithelial tissue remodeling followed by immune infiltration of the tumor, arrest in the cell cycle, and repair of tissue damage. We identified CCL5 as a possible driver of CTVT regression. Changes in gene expression are associated with methylation changes at specific intragenic sites. Our results underscore the critical role of host innate immunity in triggering cancer regression.

Quantitative Rheometry of Thin Soft Materials Using the Quartz Crystal Microbalance with Dissipation

In the inertial limit, the resonance frequency of the quartz crystal microbalance (QCM) is related to the coupled mass on the quartz sensor through the Sauerbrey expression that relates the mass to the change in resonance frequency. However, when the thickness of the film is sufficiently large, the relationship becomes more complicated and both the frequency and damping of the crystal resonance must be considered. In this regime, a rheological model of the material must be used to accurately extract the adhered film's thickness, shear modulus, and viscoelastic phase angle from the data. In the present work we examine the suitability of two viscoelastic models, a simple Voigt model ( Physica Scripta 1999, 59, 391-396) and a more realistic power-law model ( Langmuir 2015, 31, 4008-4017), to extract the rheological properties of a thermoresponsive hydrogel film. By changing temperature and initial dry film thickness of the gel, the operation of QCM was traversed from the Sauerbrey limit, where viscous losses do not impact the frequency, through the regime where the QCM response is sensitive to viscoelastic properties. The density-shear modulus and the viscoelastic phase angle from the two models are in good agreement when the shear wavelength ratio, d/λ _n, is in the range of 0.05-0.20, where d is the film thickness and λ _n is the wavelength of the mechanical shear wave at the n^th harmonic. We further provide a framework for estimating the physical properties of soft materials in the megahertz regime by using the physical behavior of polyelectrolyte complexes. This provides the user with an approximate range of allowable film thicknesses for accurate viscoelastic analysis with either model, thus enabling better use of the QCM-D in soft materials research.

Human oncogenic viruses: nature and discovery

Seven kinds of virus collectively comprise an important cause of cancer, particularly in less developed countries and for people with damaged immune systems. Discovered over the past 54 years, most of these viruses are common infections of humankind for which malignancy is a rare consequence. Various cofactors affect the complex interaction between virus and host and the likelihood of cancer emerging. Although individual human tumour viruses exert their malignant effects in different ways, there are common features that illuminate mechanisms of oncogenesis more generally, whether or not there is a viral aetiology.This article is part of the themed issue 'Human oncogenic viruses'.

Film Confinement Induced "Jump-Percolation" Wetting Transition in Amphiphilic Block Copolymer Films

We report a first-order like sharp surface wettability transition with varying film thickness dependent morphology in cast films of an amphiphilic triblock copolymer. Films composed of poly(2-(N-ethylperfluorooctanesulfonamido) ethyl methyl acrylate), poly(FOSM), and poly(N,N'-dimethyl acrylamide), poly(DMA), with thickness (h) in the transition-range, 200 < h < 300 nm, exhibited an abrupt hydrophobic to hydrophilic dynamic water contact angle transition. After an induction time, t_i ≈ 40 to 180 s, water contact angle varied as θ_c ≈ 116° to 40° with an ultrafast contact angle decay time constant, [Formula: see text] ≈ -18°/s. This behavior is a result of competing heterogeneous and antagonistic effects of bumpy poly(DMA) wetting domains against a nonwetting planar poly(FOSM) background, with a "jump percolation" wetting transition when the poly(DMA) domain density reaches unity. Outside of this film thickness range, relatively shallow decreasing water contact angle gradients were observed with a monotonically increasing poly(DMA) domain area coverage with increasing film thickness in the overall range of 40 nm (hydrophobic, θ_c ≈ 118°) < h < 500 nm (hydrophilic, θ_c ≈ 8°). The optical diffuse reflectance properties of these rough surfaces exhibit an onset of diffuse reflectance maxima correlated to the transition morphology film thickness.

Three-Dimensional Printed Shape Memory Objects Based on an Olefin Ionomer of Zinc-Neutralized Poly(ethylene-co-methacrylic acid)

Three-dimensional printing enables the net shape manufacturing of objects with minimal material waste and low tooling costs, but the functionality is generally limited by available materials, especially for extrusion-based printing, such as fused deposition modeling (FDM). Here, we demonstrate shape memory behavior of 3D printed objects with FDM using a commercially available olefin ionomer, Surlyn 9520, which is zinc-neutralized poly(ethylene-co-methacrylic acid). The initial fixity for 3D printed and compression-molded samples was similar, but the initial recovery was much lower for the 3D printed sample (R = 58%) than that for the compression-molded sample (R = 83%). The poor recovery in the first cycle is attributed to polyethylene crystals formed during programming that act to resist the permanent network recovery. This effect is magnified in the 3D printed part due to the higher strain (lower modulus in the 3D printed part) at a fixed programming stress. The fixity and recovery in subsequent shape memory cycles are greater for the 3D printed part than for the compression-molded part. Moreover, the programmed strain can be systematically modulated by inclusion of porosity in the printed part without adversely impacting the fixity or recovery. These characteristics enable the direct formation of complex shapes of thermoplastic shape memory polymers that can be recovered in three dimensions with the appropriate trigger, such as heat, through the use of FDM as a 3D printing technology.

Unravelling the Molecular Basis of High Affinity Nanobodies against HIV p24: In Vitro Functional, Structural, and in Silico Insights

Preventing the spread of infectious diseases remains an urgent priority worldwide, and this is driving the development of advanced nanotechnology to diagnose infections at the point of care. Herein, we report the creation of a library of novel nanobody capture ligands to detect p24, one of the earliest markers of HIV infection. We demonstrate that these nanobodies, one tenth the size of conventional antibodies, exhibit high sensitivity and broad specificity to global HIV-1 subtypes. Biophysical characterization indicates strong 690 pM binding constants and fast kinetic on-rates, 1 to 2 orders of magnitude better than monoclonal antibody comparators. A crystal structure of the lead nanobody and p24 was obtained and used alongside molecular dynamics simulations to elucidate the molecular basis of these enhanced performance characteristics. They indicate that binding occurs at C-terminal helices 10 and 11 of p24, a negatively charged region of p24 complemented by the positive surface of the nanobody binding interface involving CDR1, CDR2, and CDR3 loops. Our findings have broad implications on the design of novel antibodies and a wide range of advanced biomedical applications.

Tumour-inducing viruses

Virus infections are an important factor in the global burden of human cancer. The discovery and mode of action of human tumour viruses is briefly reviewed together with the promise of prevention through vaccination.

Efficient Polymer Solar Cells by Lithium Sulfonated Polystyrene as a Charge Transport Interfacial Layer

In this paper, we report the highly efficient bulk heterojunction (BHJ) polymer solar cells (PSCs) with an inverted device structure via utilizing an ultrathin layer of lithium sulfonated polystyrene (LiSPS) ionomer to reengineer the surface of the solution-processed zinc oxide (ZnO) electron extraction layer (EEL). The unique lithium-ionic conductive LiSPS contributes to enhanced electrical conductivity of the ZnO/LiSPS EEL, which not only facilitates charge extraction from the BHJ active layer but also minimizes the energy loss within the charge transport processes. In addition, the organic-inorganic LiSPS ionomer well circumvents the coherence issue of the organic BHJ photoactive layer on the ZnO EEL. Consequently, the enhanced charge transport and the lowered internal resistance between the BHJ photoactive layer and the ZnO/LiSPS EEL give rise to a dramatically reduced dark saturation current density and significantly minimized charge carrier recombination. As a result, the inverted BHJ PSCs with the ZnO/LiSPS EEL exhibit an approximatively 25% increase in power conversion efficiency. These results indicate our strategy provides an easy, but effective, approach to reach high performance inverted PSCs.

Exchange of Genetic Sequences Between Viruses and Hosts

Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes. Conversely, integration of proviruses into the host germ line has generated endogenous retroviral genomes (ERV) in all vertebrate genomes sequenced to date. Some of these genomes retain potential infectivity and upon reactivation may transmit to other host species. During mammalian evolution, sequences of retroviral origin have been repurposed to serve host functions, such as the viral envelope glycoproteins crucial to the development of the placenta. Beyond retroviruses, DNA viruses with complex genomes have acquired numerous genes of host origin which influence replication, pathogenesis and immune evasion, while host species have accumulated germline sequences of both DNA and RNA viruses. A codicil is added on lateral transmission of cancer cells between hosts and on migration of host mitochondria into cancer cells.

Tough Stretchable Physically-Cross-linked Electrospun Hydrogel Fiber Mats

Nature uses supramolecular interactions and hierarchical structures to produce water-rich materials with combinations of properties that are challenging to obtain in synthetic systems. Here, we demonstrate hierarchical supramolecular hydrogels from electrospun, self-associated copolymers with unprecedented elongation and toughness for high porosity hydrogels. Hydrophobic association of perfluoronated comonomers provides the physical cross-links for these hydrogels based on copolymers of dimethyl acrylamide and 2-(N-ethylperfluorooctane sulfonamido)ethyl methacrylate (FOSM). Intriguingly, the hydrogel fiber mats show an enhancement in toughness in comparison to compression molded bulk hydrogels. This difference is attributed to the size distribution of the hydrophobic aggregates where narrowing the distribution in the electrospun material enhances the toughness of the hydrogel. These hydrogel fiber mats exhibit extensibility more than double that of the bulk hydrogel and a comparable modulus despite the porosity of the fiber mat leading to >25 wt % increase in water content.

Human endogenous retroviruses: friend or foe?

The integration of proviral DNA into host chromosomal DNA as an obligatory step in the replication cycle of retroviruses is a natural event of genetic recombination between virus and host. When integration occurs in cells of the germ line, it results in mendelian inheritance of viral sequences that we call endogenous retroviruses (ERV) and HERV for humans. HERVs and host often establish a symbiotic relationship, especially in the placenta and in pluripotent embryonic stem cells, but HERVs occasionally have deleterious consequences for the host. This special issue of APMIS features the fascinating relationships between HERV and humans in health and disease.

Tailor-Made Fluorinated Copolymer/Clay Nanocomposite by Cationic RAFT Assisted Pickering Miniemulsion Polymerization

Fluorinated polymers in emulsion find enormous applications in hydrophobic surface coating. Currently, lots of efforts are being made to develop specialty polymer emulsions which are free from surfactants. This investigation reports the preparation of a fluorinated copolymer via Pickering miniemulsion polymerization. In this case, 2,2,3,3,3-pentafluoropropyl acrylate (PFPA), methyl methacrylate (MMA), and n-butyl acrylate (nBA) were copolymerized in miniemulsion using Laponite-RDS as the stabilizer. The copolymerization was carried out via reversible addition-fragmentation chain transfer (RAFT) process. Here, a cationic RAFT agent, S-1-dodecyl-S'-(methylbenzyltriethylammonium bromide) trithiocarbonate (DMTTC), was used to promote polymer-Laponite interaction by means of ionic attraction. The polymerization was much faster when Laponite content was 30 wt % or above with 1.2 wt % RAFT agent. The stability of the miniemulsion in terms of zeta potential was found to be dependent on the amount of both Laponite and RAFT agent. The miniemulsion had particle sizes in the range of 200-300 nm. Atomic force microscopy (AFM) and transmission electron microscopy (TEM) analyses showed the formation of Laponite armored spherical copolymer particles. The fluorinated copolymer films had improved surface properties because of polymer-Laponite interaction.

What's the host and what's the microbe? The Marjory Stephenson Prize Lecture 2015

The interchange between retroviruses and their hosts is an intimate one because retroviruses integrate proviral DNA into host chromosomal DNA as an obligate step in the replication cycle. This has resulted in the occasional transduction of host genes into retroviral genomes as oncogenes, and also led to the integration of viral genomes into the host germ line that gives rise to endogenous retroviruses. I shall reflect on the evolutionary consequences of these events for virus and host. Then, I shall discuss the emergence of non-viral infections of host origin, namely, how malignant cells can give rise to eukaryotic single cell 'parasites' that colonize new hosts and how these in turn have been colonized by host mitochondria.

The clammy grip of parasitic tumors

An epidemic of leukemia among bivalve molluscs is spreading along the Atlantic coast of North America, with a serious population decline of soft-shelled clams. In this issue of Cell, Metzger et al. use forensic DNA markers to demonstrate that the leukemia cells have a clonal origin and appear to be transmitted through sea water.

Neutralization properties of simian immunodeficiency viruses infecting chimpanzees and gorillas

Broadly cross-reactive neutralizing antibodies (bNabs) represent powerful tools to combat human immunodeficiency virus type 1 (HIV-1) infection. Here, we examined whether HIV-1-specific bNabs are capable of cross-neutralizing distantly related simian immunodeficiency viruses (SIVs) infecting central (Pan troglodytes troglodytes) (SIVcpzPtt) and eastern (Pan troglodytes schweinfurthii) (SIVcpzPts) chimpanzees (n = 11) as well as western gorillas (Gorilla gorilla gorilla) (SIVgor) (n = 1). We found that bNabs directed against the CD4 binding site (n = 10), peptidoglycans at the base of variable loop 3 (V3) (n = 5), and epitopes at the interface of surface (gp120) and membrane-bound (gp41) envelope glycoproteins (n = 5) failed to neutralize SIVcpz and SIVgor strains. In addition, apex V2-directed bNabs (n = 3) as well as llama-derived (heavy chain only) antibodies (n = 6) recognizing both the CD4 binding site and gp41 epitopes were either completely inactive or neutralized only a fraction of SIVcpzPtt strains. In contrast, one antibody targeting the membrane-proximal external region (MPER) of gp41 (10E8), functional CD4 and CCR5 receptor mimetics (eCD4-Ig, eCD4-Ig(mim2), CD4-218.3-E51, and CD4-218.3-E51-mim2), as well as mono- and bispecific anti-human CD4 (iMab and LM52) and CCR5 (PRO140, PRO140-10E8) receptor antibodies neutralized >90% of SIVcpz and SIVgor strains with low-nanomolar (0.13 to 8.4 nM) potency. Importantly, the latter antibodies blocked virus entry not only in TZM-bl cells but also in Cf2Th cells expressing chimpanzee CD4 and CCR5 and neutralized SIVcpz in chimpanzee CD4(+) T cells, with 50% inhibitory concentrations (IC50s) ranging from 3.6 to 40.5 nM. These findings provide new insight into the protective capacity of anti-HIV-1 bNabs and identify candidates for further development to combat SIVcpz infection.

IMPORTANCE

SIVcpz is widespread in wild-living chimpanzees and can cause AIDS-like immunopathology and clinical disease. HIV-1 infection of humans can be controlled by antiretroviral therapy; however, treatment of wild-living African apes with current drug regimens is not feasible. Nonetheless, it may be possible to curb the spread of SIVcpz in select ape communities using vectored immunoprophylaxis and/or therapy. Here, we show that antibodies and antibody-like inhibitors developed to combat HIV-1 infection in humans are capable of neutralizing genetically diverse SIVcpz and SIVgor strains with considerable breadth and potency, including in primary chimpanzee CD4(+) T cells. These reagents provide an important first step toward translating intervention strategies currently developed to treat and prevent AIDS in humans to SIV-infected apes.

The prevention and eradication of smallpox: a commentary on Sloane (1755) 'An account of inoculation'

Sir Hans Sloane's account of inoculation as a means to protect against smallpox followed several earlier articles published in Philosophical Transactions on this procedure. Inoculation (also called 'variolation') involved the introduction of small amounts of infectious material from smallpox vesicles into the skin of healthy subjects, with the goal of inducing mild symptoms that would result in protection against the more severe naturally acquired disease. It began to be practised in England in 1721 thanks to the efforts of Lady Mary Wortley Montagu who influenced Sloane to promote its use, including the inoculation of the royal family's children. When Edward Jenner's inoculation with the cow pox ('vaccination') followed 75 years later as a safer yet equally effective procedure, the scene was set for the eventual control of smallpox epidemics culminating in the worldwide eradication of smallpox in 1977, officially proclaimed by WHO in 1980. Here, we discuss the significance of variolation and vaccination with respect to scientific, public health and ethical controversies concerning these 'weapons of mass protection'. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.

Defense-in-depth by mucosally administered anti-HIV dimeric IgA2 and systemic IgG1 mAbs: complete protection of rhesus monkeys from mucosal SHIV challenge

Although IgA is the most abundantly produced immunoglobulin in humans, its role in preventing HIV-1 acquisition, which occurs mostly via mucosal routes, remains unclear. In our passive mucosal immunizations of rhesus macaques (RMs), the anti-HIV-1 neutralizing monoclonal antibody (nmAb) HGN194, given either as dimeric IgA1 (dIgA1) or dIgA2 intrarectally (i.r.), protected 83% or 17% of the RMs against i.r. simian-human immunodeficiency virus (SHIV) challenge, respectively. Data from the RV144 trial implied that vaccine-induced plasma IgA counteracted the protective effector mechanisms of IgG1 with the same epitope specificity. We thus hypothesized that mucosal dIgA2 might diminish the protection provided by IgG1 mAbs targeting the same epitope. To test our hypothesis, we administered HGN194 IgG1 intravenously (i.v.) either alone or combined with i.r. HGN194 dIgA2. We enrolled SHIV-exposed, persistently aviremic RMs protected by previously administered nmAbs; RM anti-human IgG responses were undetectable. However, low-level SIV Gag-specific proliferative T-cell responses were found. These animals resemble HIV-exposed, uninfected humans, in which local and systemic cellular immune responses have been observed. HGN194 IgG1 and dIgA2 used alone and the combination of the two neutralized the challenge virus equally well in vitro. All RMs given only i.v. HGN194 IgG1 became infected. In contrast, all RMs given HGN194 IgG1+dIgA2 were completely protected against high-dose i.r. SHIV-1157ipEL-p challenge. These data imply that combining suboptimal defenses at the mucosal and systemic levels can completely prevent virus acquisition. Consequently, active vaccination should focus on defense-in-depth, a strategy that seeks to build up defensive fall-back positions well behind the fortified frontline.

Molecular evolution of broadly neutralizing Llama antibodies to the CD4-binding site of HIV-1

To date, no immunization of humans or animals has elicited broadly neutralizing sera able to prevent HIV-1 transmission; however, elicitation of broad and potent heavy chain only antibodies (HCAb) has previously been reported in llamas. In this study, the anti-HIV immune responses in immunized llamas were studied via deep sequencing analysis using broadly neutralizing monoclonal HCAbs as a guides. Distinct neutralizing antibody lineages were identified in each animal, including two defined by novel antibodies (as variable regions called VHH) identified by robotic screening of over 6000 clones. The combined application of five VHH against viruses from clades A, B, C and CRF_AG resulted in neutralization as potent as any of the VHH individually and a predicted 100% coverage with a median IC50 of 0.17 µg/ml for the panel of 60 viruses tested. Molecular analysis of the VHH repertoires of two sets of immunized animals showed that each neutralizing lineage was only observed following immunization, demonstrating that they were elicited de novo. Our results show that immunization can induce potent and broadly neutralizing antibodies in llamas with features similar to human antibodies and provide a framework to analyze the effectiveness of immunization protocols.

Developing a vaccine against HIV-1 is a priority, but it remains unclear whether immunizations in humans can elicit potent broadly neutralizing antibodies able to prevent HIV-1 transmission. Llamas possess heavy chain only antibodies and conventional heavy and light chain antibodies. We previously reported the heavy chain only antibody J3, which potently neutralizes more than 95% of HIV strains, and was induced by immunization. Here we immunized two further llamas and elicited three novel broadly neutralizing heavy chain only antibodies, which were identified by high-throughput screening. These neutralizing llama antibodies target different areas of the CD4-binding site of the virus, therefore breadth and potency are increased when they are used in combination. To gain greater understanding of how the llama immunizations worked, deep sequencing of the HIV binding region of the antibodies was performed. This revealed that the antibodies were matured fully only in response to the protein immunogens. Furthermore, the VHH elicited in different animals, while sharing functional hallmarks, were encoded by distinct sequences and thus could not have been identified by a deep sequencing analysis alone. Our results show that immunization can potentially induce protective antibodies in llamas and provide a method to more extensively evaluate immunization studies.

Neutralisation of HIV-1 cell-cell spread by human and llama antibodies

BACKGROUND

Direct cell-cell spread of HIV-1 is a very efficient mode of viral dissemination, with increasing evidence suggesting that it may pose a considerable challenge to controlling viral replication in vivo. Much current vaccine research involves the study of broadly neutralising antibodies (bNabs) that arise during natural infection with the aims of eliciting such antibodies by vaccination or incorporating them into novel therapeutics. However, whether cell-cell spread of HIV-1 can be effectively targeted by bNabs remains unclear, and there is much interest in identifying antibodies capable of efficiently neutralising virus transmitted by cell-cell contact.

RESULTS

In this study we have tested a panel of bNAbs for inhibition of cell-cell spread, including some not previously evaluated for inhibition of this mode of HIV-1 transmission. We found that three CD4 binding site antibodies, one from an immunised llama (J3) and two isolated from HIV-1-positive patients (VRC01 and HJ16) neutralised cell-cell spread between T cells, while antibodies specific for glycan moieties (2G12, PG9, PG16) and the MPER (2F5) displayed variable efficacy. Notably, while J3 displayed a high level of potency during cell-cell spread we found that the small size of the llama heavy chain-only variable region (VHH) J3 is not required for efficient neutralisation since recombinant J3 containing a full-length human heavy chain Fc domain was significantly more potent. J3 and J3-Fc also neutralised cell-cell spread of HIV-1 from primary macrophages to CD4+ T cells.

CONCLUSIONS

In conclusion, while bNabs display variable efficacy at preventing cell-cell spread of HIV-1, we find that some CD4 binding site antibodies can inhibit this mode of HIV-1 dissemination and identify the recently described llama antibody J3 as a particularly potent inhibitor. Effective neutralisation of cell-cell spread between physiologically relevant cell types by J3 and J3-Fc supports the development of VHH J3 nanobodies for therapeutic or prophylactic applications.

Overcoming confinement limited swelling in hydrogel thin films using supramolecular interactions

The thin film behavior of poly(N-isopropylacrylamide-stat-2-(N-ethylperfluorooctane sulfonamido)ethyl acrylate) (NIPAAm-stat-FOSA) based hydrogels containing 5 mol% FOSA was elucidated using quartz crystal microbalance with dissipation (QCM-D) in combination with spectroscopic ellipsometry (SE) through examination of the lower critical solution temperature (LCST) and temperature dependent swelling for (dry) thicknesses ranging from 10 nm to 121 nm. For all thin films measured, the LCST was shown to slightly increase (>3 °C) in comparison to that of the bulk sample. However for these films, the increase in LCST was statistically identical, irrespective of thickness. Surprisingly, the volumetric swelling of the hydrogel in thin films, even at temperatures less than the LCST, was similar (within 20%) to the volumetric swelling of the bulk hydrogel, despite the expected significant decrease associated with the hydrogel being constrained by the substrate as predicted by one dimensional Flory-Rehner theory. We attribute this enhancement in swelling compared to theoretical expectations to the ability of the hydrophobic crosslinks to re-arrange under stress, which provides a mechanism to alleviate the decreased dimensionality imposed by the substrate; this mechanism is consistent with a large hysteresis in the swelling when cycling between 35 °C and 5 °C. Unlike the LCST, the swelling ratio increases with decreasing film thickness. At low temperatures (below the LCST), the volume swelling ratio increased from 3.9 to 4.9, while at temperatures above the LCST the swelling ratio increased from 1.5 to 2.5 when the film thickness decreased from 121 nm to 10 nm. The combination of facile processing through solution casting without the need for additional crosslinking chemistry and limited thickness dependent variation of swelling and LCST behavior in these physically crosslinked hydrogels makes these materials attractive for applications requiring thermoresponsive soft coatings.

Human immunodeficiency virus antibodies and the vaccine problem

Despite the great advances made in controlling human immunodeficiency virus type 1 (HIV-1) infection with antiretroviral drug treatment, a safe and efficacious HIV vaccine has yet to be developed. Here, we discuss why clinical trials and vaccine development for HIV have so far been disappointing, with an emphasis on the lack of protective antibodies. We review approaches for developing appropriate HIV immunogens and the stimulation of long-lasting B-cell responses with antibody maturation. We conclude that candidate reagents in the pipeline for HIV vaccine development are unlikely to be particularly effective. Although the major funders of HIV vaccine research and development are placing increasing emphasis on clinical product development, a genuine breakthrough in preventing HIV infection through vaccines is more likely to come from novel immunogen research.

Lithium-end-capped polylactide thin films influence osteoblast progenitor cell differentiation and mineralization

End-capping by covalently binding functional groups to the ends of polymer chains offers potential advantages for tissue engineering scaffolds, but the ability of such polymers to influence cell behavior has not been studied. As a demonstration, polylactide (PLA) was end-capped with lithium carboxylate ionic groups (hPLA13kLi) and evaluated. Thin films of the hPLA13kLi and PLA homopolymer were prepared with and without surface texturing. Murine osteoblast progenitor cells from collagen 1α1 transgenic reporter mice were used to assess cell attachment, proliferation, differentiation, and mineralization. Measurement of green fluorescent protein expressed by these cells and xylenol orange staining for mineral allowed quantitative analysis. The hPLA13kLi was biologically active, increasing initial cell attachment and enhancing differentiation, while reducing proliferation and strongly suppressing mineralization, relative to PLA. These effects of bound lithium ions (Li(+) ) had not been previously reported, and were generally consistent with the literature on soluble additions of lithium. The surface texturing generated here did not influence cell behavior. These results demonstrate that end-capping could be a useful approach in scaffold design, where a wide range of biologically active groups could be employed, while likely retaining the desirable characteristics associated with the unaltered homopolymer backbone.

Transmissible [corrected] dog cancer genome reveals the origin and history of an ancient cell lineage

Canine transmissible venereal tumor (CTVT) is the oldest known somatic cell lineage. It is a transmissible cancer that propagates naturally in dogs. We sequenced the genomes of two CTVT tumors and found that CTVT has acquired 1.9 million somatic substitution mutations and bears evidence of exposure to ultraviolet light. CTVT is remarkably stable and lacks subclonal heterogeneity despite thousands of rearrangements, copy-number changes, and retrotransposon insertions. More than 10,000 genes carry nonsynonymous variants, and 646 genes have been lost. CTVT first arose in a dog with low genomic heterozygosity that may have lived about 11,000 years ago. The cancer spawned by this individual dispersed across continents about 500 years ago. Our results provide a genetic identikit of an ancient dog and demonstrate the robustness of mammalian somatic cells to survive for millennia despite a massive mutation burden.

On the concept and elucidation of endogenous retroviruses

Endogenous retrovirus (ERV) genomes integrated into the chromosomal DNA of the host were first detected in chickens and mice as Mendelian determinants of Gag and Env proteins and of the release of infectious virus particles. The presence of ERV was confirmed by DNA hybridization. With complete host genomes available for analysis, we can now see the great extent of viral invasion into the genomes of numerous vertebrate species, including humans. ERVs are found at many loci in host DNA and also in the genomes of large DNA viruses, such as herpesviruses and poxviruses. The evolution of xenotropism and cross-species infection is discussed in the light of the dynamic relationship between exogenous and endogenous retroviruses.

Virology. Our viral inheritance

Viruses incorporated into vertebrate genomes may reemerge after long periods of dormancy to play a range of biological roles in their host.

Neutralizing antibodies to HIV-1 induced by immunization

Most neutralizing antibodies act at the earliest steps of viral infection and block interaction of the virus with cellular receptors to prevent entry into host cells. The inability to induce neutralizing antibodies to HIV has been a major obstacle to HIV vaccine research since the early days of the epidemic. However, in the past three years, the definition of a neutralizing antibody against HIV has been revolutionized by the isolation of extremely broad and potent neutralizing antibodies from HIV-infected individuals. Considerable hurdles remain for inducing neutralizing antibodies to a protective level after immunization. Meanwhile, novel technologies to bypass the induction of antibodies are being explored to provide prophylactic antibody-based interventions. This review addresses the challenge of inducing HIV neutralizing antibodies upon immunization and considers notable recent advances in the field. A greater understanding of the successes and failures for inducing a neutralizing response upon immunization is required to accelerate the development of an effective HIV vaccine.

A gp41 MPER-specific llama VHH requires a hydrophobic CDR3 for neutralization but not for antigen recognition

The membrane proximal external region (MPER) of the HIV-1 glycoprotein gp41 is targeted by the broadly neutralizing antibodies 2F5 and 4E10. To date, no immunization regimen in animals or humans has produced HIV-1 neutralizing MPER-specific antibodies. We immunized llamas with gp41-MPER proteoliposomes and selected a MPER-specific single chain antibody (VHH), 2H10, whose epitope overlaps with that of mAb 2F5. Bi-2H10, a bivalent form of 2H10, which displayed an approximately 20-fold increased affinity compared to the monovalent 2H10, neutralized various sensitive and resistant HIV-1 strains, as well as SHIV strains in TZM-bl cells. X-ray and NMR analyses combined with mutagenesis and modeling revealed that 2H10 recognizes its gp41 epitope in a helical conformation. Notably, tryptophan 100 at the tip of the long CDR3 is not required for gp41 interaction but essential for neutralization. Thus bi-2H10 is an anti-MPER antibody generated by immunization that requires hydrophobic CDR3 determinants in addition to epitope recognition for neutralization similar to the mode of neutralization employed by mAbs 2F5 and 4E10.

Graphene polyimide nanocomposites; thermal, mechanical, and high-temperature shape memory effects

Flexible graphene polyimide nanocomposites (0.1-4 wt %) with superior mechanical properties over those of neat polyimide resin have been prepared by solution blending. Imide moieties were grafted to amine-functionalized graphene using a step-by-step condensation and thermal imidization method. The imide-functionalized graphene exhibited excellent compatibility with N-methyl-2-pyrrolidone. The dynamic storage moduli of the graphene polyimide nanocomposites increased linearly with increasing graphene content for both unmodified graphene and imidized graphene. Moduli of the imidized graphene nanocomposites were 25-30% higher than those of unmodified graphene nanocomposites. Both neat polyimide and polyimide nanocomposites exhibited shape memory effects with a triggering temperature of 230 °C. where addition of graphene improved the recovery rate. Addition of graphene improved thermal stability of the polyimide nanocomposites for both graphene and modified graphene.

Potent and broad neutralization of HIV-1 by a llama antibody elicited by immunization

A heavy chain–only antibody isolated from a llama repeatedly immunized with trimeric HIV-1 Env neutralizes 96% of tested HIV-1 strains.

Llamas (Lama glama) naturally produce heavy chain–only antibodies (Abs) in addition to conventional Abs. The variable regions (VHH) in these heavy chain–only Abs demonstrate comparable affinity and specificity for antigens to conventional immunoglobulins despite their much smaller size. To date, immunizations in humans and animal models have yielded only Abs with limited ability to neutralize HIV-1. In this study, a VHH phagemid library generated from a llama that was multiply immunized with recombinant trimeric HIV-1 envelope proteins (Envs) was screened directly for HIV-1 neutralization. One VHH, L8CJ3 (J3), neutralized 96 of 100 tested HIV-1 strains, encompassing subtypes A, B, C, D, BC, AE, AG, AC, ACD, CD, and G. J3 also potently neutralized chimeric simian-HIV strains with HIV subtypes B and C Env. The sequence of J3 is highly divergent from previous anti–HIV-1 VHH and its own germline sequence. J3 achieves broad and potent neutralization of HIV-1 via interaction with the CD4-binding site of HIV-1 Env. This study may represent a new benchmark for immunogens to be included in B cell–based vaccines and supports the development of VHH as anti–HIV-1 microbicides.

A facile method for preparing sticky, hydrophobic polymer surfaces

Textured surfaces consisting of nanometer- to micrometer-sized lightly sulfonated polystyrene ionomer (SPS) particles were prepared by rapid evaporation of the solvent from a dilute polymer solution-cast onto silica. The particle textured ionomer surfaces were prepared by either spin-coating or solution-casting ionomer solutions at controlled evaporation rates. The effects of the solvent used to spin-coat the film, the molecular weight of the ionomer, and the rate of solvent evaporation on the surface morphology of cast films were investigated. The surface morphologies were consistent with a spinodal decomposition mechanism, where the surface first existed as a percolated-like structure and then ripened into droplets if molecular mobility was retained for sufficient time. The SPS particles or particle aggregates were robust and resisted separation from the surface even after annealing at 120 °C for 1 week. The water contact angles on as-prepared surfaces were relatively low, ∼90°, due to the polar groups in the ionomer, but when the surface was modified by chemical vapor deposition of 1H,1H,2H,2H-perfluorooctyltrichlorosilane, the surface contact angles increased to ∼109° on smooth surfaces and up to ∼140° on the textured surfaces. Although the surfaces were hydrophobic, the contact angle hysteresis was relatively high and water droplets stuck to these surfaces even when the surface was turned upside down.

100 years of Rous sarcoma virus

The discovery of Rous sarcoma virus, which was reported by Peyton Rous in the Journal of Experimental Medicine 100 years ago, opened the field of tumor virology. It showed that some cancers have infectious etiology, led to the discovery of oncogenes, and laid the foundation for the molecular mechanisms of carcinogenesis. Rous spent his entire research career at The Rockefeller Institute, and he was the JEM's longest serving editor. Here, we comment briefly on the life of this remarkable scientist and on the importance of his discoveries.

Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women

BACKGROUND

The Duffy-null trait and ethnic netropenia are both highly prevalent in Africa. The influence of pre-seroconversion levels of peripheral blood cell counts (PBCs) on the risk of acquiring human immunodeficiency virus (HIV)-1 infection among Africans is unknown.

METHODS

The triangular relationship among pre-seroconversion PBC counts, host genotypes, and risk of HIV acquisition was determined in a prospective cohort of black South African high-risk female sex workers. Twenty-seven women had seroconversion during follow-up, and 115 remained HIV negative for 2 years, despite engaging in high-risk activity.

RESULTS

Pre-seroconversion neutrophil counts in women who subsequently had seroconversion were significantly lower, whereas platelet counts were higher, compared with those who remained HIV negative. Comprising 27% of the cohort, subjects with pre-seroconversion neutrophil counts of <2500 cells/mm(3) had a ∼3-fold greater risk of acquiring HIV infection. In a genome-wide association analyses, an African-specific polymorphism (rs2814778) in the promoter of Duffy Antigen Receptor for Chemokines (DARC -46T > C) was significantly associated with neutrophil counts (P = 7.9 × 10(-11)). DARC -46C/C results in loss of DARC expression on erthyrocytes (Duffy-null) and resistance to Plasmodium vivax malaria, and in our cohort, only subjects with this genotype had pre-seroconversion neutrophil counts of <2500 cells/mm(3). The risk of acquiring HIV infection was ∼3-fold greater in those with the trait of Duffy-null-associated low neutrophil counts, compared with all other study participants.

CONCLUSIONS

Pre-seroconversion neutrophil and platelet counts influence risk of HIV infection. The trait of Duffy-null-associated low neutrophil counts influences HIV susceptibility. Because of the high prevalence of this trait among persons of African ancestry, it may contribute to the dynamics of the HIV epidemic in Africa.