The chaining lemma and its application

We present a new information-theoretic result which we call the Chaining Lemma. It considers a so-called “chain” of random variables, defined by a source distribution X(0)with high min-entropy and a number (say, t in total) of arbitrary functions (T1,…, Tt) which are applied in succession to that source to generate the chain (Formula presented). Intuitively, the Chaining Lemma guarantees that, if the chain is not too long, then either (i) the entire chain is “highly random”, in that every variable has high min-entropy; or (ii) it is possible to find a point j (1 ≤ j ≤ t) in the chain such that, conditioned on the end of the chain i.e. (Formula presented), the preceding part (Formula presented) remains highly random. We think this is an interesting information-theoretic result which is intuitive but nevertheless requires rigorous case-analysis to prove. We believe that the above lemma will find applications in cryptography. We give an example of this, namely we show an application of the lemma to protect essentially any cryptographic scheme against memory tampering attacks. We allow several tampering requests, the tampering functions can be arbitrary, however, they must be chosen from a bounded size set of functions that is fixed a prior

Efficient public-key cryptography with bounded leakage and tamper resilience

We revisit the question of constructing public-key encryption and signature schemes with security in the presence of bounded leakage and tampering memory attacks. For signatures we obtain the first construction in the standard model; for public-key encryption we obtain the first construction free of pairing (avoiding non-interactive zero-knowledge proofs). Our constructions are based on generic building blocks, and, as we show, also admit efficient instantiations under fairly standard number-theoretic assumptions. The model of bounded tamper resistance was recently put forward by Damgård et al. (Asiacrypt 2013) as an attractive path to achieve security against arbitrary memory tampering attacks without making hardware assumptions (such as the existence of a protected self-destruct or key-update mechanism), the only restriction being on the number of allowed tampering attempts (which is a parameter of the scheme). This allows to circumvent known impossibility results for unrestricted tampering (Gennaro et al., TCC 2010), while still being able to capture realistic tampering attack

Cube Testers and Key Recovery Attacks On Reduced-Round MD6 and Trivium

CRYPTO 2008 saw the introduction of the hash function MD6 and of cube attacks, a type of algebraic attack applicable to cryptographic functions having a low-degree algebraic normal form over GF(2). This paper applies cube attacks to reduced round MD6, finding the full 128-bit key of a 14-round MD6 with complexity 2^22 (which takes less than a minute on a single PC). This is the best key recovery attack announced so far for MD6. We then introduce a new class of attacks called cube testers, based on efficient property-testing algorithms, and apply them to MD6 and to the stream cipher Trivium. Unlike the standard cube attacks, cube testers detect nonrandom behavior rather than performing key extraction, but they can also attack cryptographic schemes described by nonrandom polynomials of relatively high degree. Applied to MD6, cube testers detect nonrandomness over 18 rounds in 2^17 complexity; applied to a slightly modified version of the MD6 compression function, they can distinguish 66 rounds from random in 2^24 complexity. Cube testers give distinguishers on Trivium reduced to 790 rounds from random with 2^30 complexity and detect nonrandomness over 885 rounds in 2^27, improving on the original 767-round cube attack

An Electronic Analog of Synthetic Genetic Networks

An electronic analog of a synthetic genetic network known as the repressilator is proposed. The repressilator is a synthetic biological clock consisting of a cyclic inhibitory network of three negative regulatory genes which produces oscillations in the expressed protein concentrations. Compared to previous circuit analogs of the repressilator, the circuit here takes into account more accurately the kinetics of gene expression, inhibition, and protein degradation. A good agreement between circuit measurements and numerical prediction is observed. The circuit allows for easy control of the kinetic parameters thereby aiding investigations of large varieties of potential dynamics

Breaking The FF3 Format-Preserving Encryption Standard Over Small Domains

The National Institute of Standards and Technology (NIST) recently published a Format-Preserving Encryption standard accepting two Feistel structure based schemes called FF1 and FF3. Particularly, FF3 is a tweakable block cipher based on an 8-round Feistel network. In CCS~2016, Bellare et. al. gave an attack to break FF3 (and FF1) with time and data complexity $O(N^5\log(N))$, which is much larger than the code book (but using many tweaks), where $N^2$ is domain size to the Feistel network. In this work, we give a new practical total break attack to the FF3 scheme (also known as BPS scheme). Our FF3 attack requires $O(N^{\frac{11}{6}})$ chosen plaintexts with time complexity $O(N^{5})$. Our attack was successfully tested with $N\leq2^9$. It is a slide attack (using two tweaks) that exploits the bad domain separation of the FF3 design. Due to this weakness, we reduced the FF3 attack to an attack on 4-round Feistel network. Biryukov et. al. already gave a 4-round Feistel structure attack in SAC~2015. However, it works with chosen plaintexts and ciphertexts whereas we need a known-plaintext attack. Therefore, we developed a new generic known-plaintext attack to 4-round Feistel network that reconstructs the entire tables for all round functions. It works with $N^{\frac{3}{2}} \left( \frac{N}{2} \right)^{\frac{1}{6}}$ known plaintexts and time complexity $O(N^{3})$. Our 4-round attack is simple to extend to five and more rounds with complexity $N^{(r-5)N+o(N)}$. It shows that FF1 with $N=7$ and FF3 with $7\leq N\leq10$ do not offer a 128-bit security. Finally, we provide an easy and intuitive fix to prevent the FF3 scheme from our $O(N^{5})$ attack

Differential Trends in the Codon Usage Patterns in HIV-1 Genes

Host-pathogen interactions underlie one of the most complex evolutionary phenomena resulting in continual adaptive genetic changes, where pathogens exploit the host's molecular resources for growth and survival, while hosts try to eliminate the pathogen. Deciphering the molecular basis of host–pathogen interactions is useful in understanding the factors governing pathogen evolution and disease propagation. In host-pathogen context, a balance between mutation, selection, and genetic drift is known to maintain codon bias in both organisms. Studies revealing determinants of the bias and its dynamics are central to the understanding of host-pathogen evolution. We considered the Human Immunodeficiency Virus (HIV) type 1 and its human host to search for evolutionary signatures in the viral genome. Positive selection is known to dominate intra-host evolution of HIV-1, whereas high genetic variability underlies the belief that neutral processes drive inter-host differences. In this study, we analyze the codon usage patterns of HIV-1 genomes across all subtypes and clades sequenced over a period of 23 years. We show presence of unique temporal correlations in the codon bias of three HIV-1 genes illustrating differential adaptation of the HIV-1 genes towards the host preferred codons. Our results point towards gene-specific translational selection to be an important force driving the evolution of HIV-1 at the population level

Candida albicans-produced farnesol stimulates Pseudomonas quinolone signal production in LasR-defective Pseudomonas aeruginosa strains

Candida albicans has been previously shown to stimulate the production of Pseudomonas aeruginosa phenazine toxins in dual-species colony biofilms. Here, we report that P. aeruginosa lasR mutants, which lack the master quorum sensing system regulator, regain the ability to produce quorum-sensing-regulated phenazines when cultured with C. albicans. Farnesol, a signalling molecule produced by C. albicans, was sufficient to stimulate phenazine production in LasR− laboratory strains and clinical isolates. P. aeruginosa ΔlasR mutants are defective in production of the Pseudomonas quinolone signal (PQS) due to their inability to properly induce pqsH, which encodes the enzyme necessary for the last step in PQS biosynthesis. We show that expression of pqsH in a ΔlasR strain was sufficient to restore PQS production, and that farnesol restored pqsH expression in ΔlasR mutants. The farnesol-mediated increase in pqsH required RhlR, a transcriptional regulator downstream of LasR, and farnesol led to higher levels of N-butyryl-homoserine lactone, the small molecule activator of RhlR. Farnesol promotes the production of reactive oxygen species (ROS) in a variety of species. Because the antioxidant N-acetylcysteine suppressed farnesol-induced RhlR activity in LasR− strains, and hydrogen peroxide was sufficient to restore PQS production in las mutants, we propose that ROS are responsible for the activation of downstream portions of this quorum sensing pathway. LasR mutants frequently arise in the lungs of patients chronically infected with P. aeruginosa. The finding that C. albicans, farnesol or ROS stimulate virulence factor production in lasR strains provides new insight into the virulence potential of these strains

On Randomizing Hash Functions to Strengthen the Security of Digital Signatures

Halevi and Krawczyk proposed a message randomization algorithm called RMX as a front-end tool to the hash-then-sign digital signature schemes such as DSS and RSA in order to free their reliance on the collision resistance property of the hash functions. They have shown that to forge a RMX-hash-then-sign signature scheme, one has to solve a cryptanalytical task which is related to finding second preimages for the hash function. In this article, we will show how to use Dean’s method of finding expandable messages for finding a second preimage in the Merkle-Damgård hash function to existentially forge a signature scheme based on a t-bit RMX-hash function which uses the Davies-Meyer compression functions (e.g., MD4, MD5, SHA family) in 2 t/2 chosen messages plus 2 t/2 + 1 off-line operations of the compression function and similar amount of memory. This forgery attack also works on the signature schemes that use Davies-Meyer schemes and a variant of RMX published by NIST in its Draft Special Publication (SP) 800-106. We discuss some important applications of our attack

Deciphering the universe of RNA structures and trans RNA-RNA interactions of transcriptomes in vivo: from experimental protocols to computational analyses

The last few years have seen an explosion of experimental and computational methods for investigating RNA structures of entire transcriptomes in vivo. Very recent experimental protocols now also allow trans RNA–RNA interactions to be probed in a transcriptome-wide manner. All of the experimental strategies require comprehensive computational pipelines for analysing the raw data and converting it back into actual RNA structure features or trans RNA–RNA interactions. The overall performance of these methods thus strongly depends on the experimental and the computational protocols employed. In order to get the best out of both worlds, both aspects need to be optimised simultaneously. This review introduced the methods and proposes ideas how they could be further improved