Cross-Sectional Dating of Novel Haplotypes of HERV-K 113 and HERV-K 115 Indicate These Proviruses Originated in Africa before Homo sapiens

The human genome, human endogenous retroviruses (HERV), of which HERV-K113 and HERV-K115 are the only known full-length proviruses that are insertionally polymorphic. Although a handful of previously published papers have documented their prevalence in the global population; to date, there has been no report on their prevalence in the United States population. Here, we studied the geographic distribution of K113 and K115 among 156 HIV-1+ subjects from the United States, including African Americans, Hispanics, and Caucasians. In the individuals studied, we found higher insertion frequencies of K113 (21%) and K115 (35%) in African Americans compared with Caucasians (K113 9% and K115 6%) within the United States. We also report the presence of three single nucleotide polymorphism sites in the K113 5′ long terminal repeats (LTRs) and four in the K115 5′ LTR that together constituted four haplotypes for K113 and five haplotypes for K115. HERV insertion times can be estimated from the sequence differences between the 5′ and 3′ LTR of each insertion, but this dating method cannot be used with HERV-K115. We developed a method to estimate insertion times by applying coalescent inference to 5′ LTR sequences within our study population and validated this approach using an independent estimate derived from the genetic distance between K113 5′ and 3′ LTR sequences. Using our method, we estimated the insertion dates of K113 and K115 to be a minimum of 800,000 and 1.1 million years ago, respectively. Both these insertion dates predate the emergence of anatomically modern Homo sapiens

The discovery of endogenous retroviruses

When endogenous retroviruses (ERV) were discovered in the late 1960s, the Mendelian inheritance of retroviral genomes by their hosts was an entirely new concept. Indeed Howard M Temin's DNA provirus hypothesis enunciated in 1964 was not generally accepted, and reverse transcriptase was yet to be discovered. Nonetheless, the evidence that we accrued in the pre-molecular era has stood the test of time, and our hypothesis on ERV, which one reviewer described as 'impossible', proved to be correct. Here I recount some of the key observations in birds and mammals that led to the discovery of ERV, and comment on their evolution, cross-species dispersion, and what remains to be elucidated

Breaking ‘128-bit Secure’ Supersingular Binary Curves

In late 2012 and early 2013 the discrete logarithm problem (DLP) in finite fields of small characteristic underwent a dramatic series of breakthroughs, culminating in a heuristic quasi-polynomial time algorithm, due to Barbulescu, Gaudry, Joux and Thomé. Using these developments, Adj, Menezes, Oliveira and Rodríguez-Henríquez analysed the concrete security of the DLP, as it arises from pairings on (the Jacobians of) various genus one and two supersingular curves in the literature, which were originally thought to be 128-bit secure. In particular, they suggested that the new algorithms have no impact on the security of a genus one curve over F21223 , and reduce the security of a genus two curve over F2367 to 94.6 bits. In this paper we propose a new field representation and efficient general descent principles which together make the new techniques far more practical. Indeed, at the ‘128-bit security level’ our analysis shows that the aforementioned genus one curve has approximately 59 bits of security, and we report a total break of the genus two curv

Adaptively Simulation-Secure Attribute-Hiding Predicate Encryption

This paper demonstrates how to achieve simulation-based strong attribute hiding against adaptive adversaries for predicate encryption (PE) schemes supporting expressive predicate families under standard computational assumptions in bilinear groups. Our main result is a simulation-based adaptively strongly partially-hiding PE (PHPE) scheme for predicates computing arithmetic branching programs (ABP) on public attributes, followed by an inner-product predicate on private attributes. This simultaneously generalizes attribute-based encryption (ABE) for boolean formulas and ABP’s as well as strongly attribute-hiding PE schemes for inner products. The proposed scheme is proven secure for any a priori bounded number of ciphertexts and an unbounded (polynomial) number of decryption keys, which is the best possible in the simulation-based adaptive security framework. This directly implies that our construction also achieves indistinguishability-based strongly partially-hiding security against adversaries requesting an unbounded (polynomial) number of ciphertexts and decryption keys. The security of the proposed scheme is derived under (asymmetric version of) the well-studied decisional linear (DLIN) assumption. Our work resolves an open problem posed by Wee in TCC 2017, where his result was limited to the semi-adaptive setting. Moreover, our result advances the current state of the art in both the fields of simulation-based and indistinguishability-based strongly attribute-hiding PE schemes. Our main technical contribution lies in extending the strong attribute hiding methodology of Okamoto and Takashima [EUROCRYPT 2012, ASIACRYPT 2012] to the framework of simulation-based security and beyond inner products