Genetic Signatures in the Envelope Glycoproteins of HIV-1 that Associate with Broadly Neutralizing Antibodies

A steady increase in knowledge of the molecular and antigenic structure of the gp120 and gp41 HIV-1 envelope glycoproteins (Env) is yielding important new insights for vaccine design, but it has been difficult to translate this information to an immunogen that elicits broadly neutralizing antibodies. To help bridge this gap, we used phylogenetically corrected statistical methods to identify amino acid signature patterns in Envs derived from people who have made potently neutralizing antibodies, with the hypothesis that these Envs may share common features that would be useful for incorporation in a vaccine immunogen. Before attempting this, essentially as a control, we explored the utility of our computational methods for defining signatures of complex neutralization phenotypes by analyzing Env sequences from 251 clonal viruses that were differentially sensitive to neutralization by the well-characterized gp120-specific monoclonal antibody, b12. We identified ten b12-neutralization signatures, including seven either in the b12-binding surface of gp120 or in the V2 region of gp120 that have been previously shown to impact b12 sensitivity. A simple algorithm based on the b12 signature pattern was predictive of b12 sensitivity/resistance in an additional blinded panel of 57 viruses. Upon obtaining these reassuring outcomes, we went on to apply these same computational methods to define signature patterns in Env from HIV-1 infected individuals who had potent, broadly neutralizing responses. We analyzed a checkerboard-style neutralization dataset with sera from 69 HIV-1-infected individuals tested against a panel of 25 different Envs. Distinct clusters of sera with high and low neutralization potencies were identified. Six signature positions in Env sequences obtained from the 69 samples were found to be strongly associated with either the high or low potency responses. Five sites were in the CD4-induced coreceptor binding site of gp120, suggesting an important role for this region in the elicitation of broadly neutralizing antibody responses against HIV-1

The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain:Bridging within and among Host Evolutionary Rates

Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the 'store and retrieve' hypothesis positing that viruses stored early in latently infected cells preferentially transmit or establish new infections upon reactivation.status: publishe

Successful cemented femoral arthroplasties reveal very often stiffened bone structures

Background: PMMA bone cements represent one of the oldest biomaterials used in general and orthopedic surgery since 1938. The use and application still raise questions with respect to osseointegration and long-lasting behavior in combination with artificial implants. Objectives: The study focuses on the following questions: Why do some implants last for many years and others do not, can bone embedded in bone cement survive, will heat gener- ated by the exothermic reaction yield a necrosis of the bony trabeculae, can the once obstructed medullary canal be remodeled for full revascularization, can preserved cancellous bone stiffened by bone cement carry the load and finally, is the so-called cemented-press-fit really an improvement as indicated? Purpose: The purpose of the study is to define the necessities for the long-lasting success of cemented components by scientifically answering the stated questions. Material and Methods: Twelve human specimens were selected. Long-lasting results between two and 20 years, an average of 8.2 years, were gathered from four female and eight male patients who died from causes other than arthroplasty. Inclusion criteria were the intact cement-to-bone transition without radiolucent line, and full-load bearing, with the exception of one amputee for comparison and the pain-free wearing until death. The well-preserved specimens were processed and fixated with a buffered Karnovsky solution cut into a series of sections using a special saw which thus guaranteed the preservation of the soft tissue together with metal and plastic, as well as bone cement. Documentation included the new HIIFL microscope, embedding in cross-linked polymers, and thinly ground cross-sec- tions documented in transmitted and polarized light, as well as freeze-dried and sputtered with gold for the scanning electron microscopy. Documentation was carried out with the PSEM 500 and Rollei Flex, as well as Leitz Orthoplan and Ploemopak. Results: The standardized cemented components revealed similar histo-pathological find- ings. All specimens presented enlarged areas with preserved cancellous bone, partly stiffened with bone cement. All specimens showed vital bone, signs of fracture healing and new bone formations immediately on or beside the bone cement. Furthermore, in all specimens, the medullary cavity was rebuilt by a complicated remodeling process resulting in a secondarily built medullary canal. It was obvious that heat necrosis plays no role in long-lasting symbiosis and it was proven that cancellous bone stiffened by bone cement can carry the load. The unloaded implantation revealed extreme bone atrophy in addition to stable implantation, recognizable by the lack of any fibrous encapsulation and the support by trabeculae oriented perpendicularly towards the implant. The cemented press-fit anchorage showed aggressive granulomata penetrating the interface and destroying the osseointegration. Conclusion: Preserved cancellous bone stiffened by bone cement can carry the load, heat necrosis plays no role, and bone cement is biocompatible and stable for 20 years and cer- tainly longer. It will be destroyed mechanically, however, by a press-fit implant anchoring directly with the bone which characterizes the principle of a mill and results in the finest bone-cement debris, a self-destroying system

Short MRI Protocol for Excluding Traumatic Lesions of the Scaphoid Bone in Children

Management of scaphoid trauma includes imaging with repeated X-rays whose interpretation is difficult and often ambivalent. The aim of the study was to propose a fast magnetic resonance imaging (MRI) protocol permitting exclusion of traumatic lesions of the scaphoid bone in children, which would avoid unnecessary immobilization and irradiation in negative cases