Formal Verification of the LDACS MAKE Protocol

In our talk, we present the first formal verification of the security properties of the updated LDACS 3-pass Mutual Authentication and Key Establishment (MAKE) protocol. This protocol allows AS and GS to establish shared keys via Diffie-Hellman or a Key Encapsulation Mechanism, and to mutually authenticate communication partners in a three-way handshake. There are two variants: (1) The LDACS IKEv2 based 3-pass MAKE protocol and (2) the LDACS ISO/IEC 11770-3:2021 key agreement mechanism 7 based 3-pass MAKE protocol. The verification is done with the Tamarin Prover. We present our approach, point out security features and highlight difficulties in modelling the protocol correctly. Our work supports the on-going design and standardization process of LDACS

Reducing 2-qubit gate count for ZX-calculus based quantum circuit optimization

In the near term, programming quantum computers will remain severely limited by low quantum volumes. Therefore, it is desirable to implement quantum circuits with the fewest resources possible. For the common Clifford+T circuits, most research is focused on reducing the number of T gates, since they are an order of magnitude more expensive than Clifford gates in quantum error corrected encoding schemes. However, this optimization sometimes leads to more 2-qubit gates, which, even though they are less expensive in terms of fault-tolerance, contribute significantly to the overall circuit cost. Approaches based on the ZX-calculus have recently gained some popularity in the field, but reduction of 2-qubit gates is not their focus. In this work, we present an alternative for improving 2-qubit gate count of a quantum circuit with the ZX-calculus by using heuristics in ZX-diagram simplification. Our approach maintains the good reduction of the T gate count provided by other strategies based on ZX-calculus, thus serving as an extension for other optimization algorithms. Our results show that combining the available ZX-calculus-based optimizations with our algorithms can reduce the number of 2-qubit gates by as much as 40 % compared to current approaches using ZX-calculus. Additionally, we improve the results of the best currently available optimization technique of Nam et. al [22] for some circuits by up to 15 %

Security in Digital Aeronautical Communications A Comprehensive Gap Analysis

Aeronautical communications still heavily depend on analog radio systems, despite the fact that digital communication has been introduced to aviation in the 1990's. Since then, the digitization of civil aviation has been continued, as considerable pressure to rationalize the aeronautical spectrum has built up. In any modern digital communications system, the threat of digital attacks needs to be considered carefully. This is especially true for safety-critical infrastructure, which aviation's operational communication services clearly are. In this article, we reverse the traditional approach in the aeronautical industry of looking at a system from the safety perspective and assume a security-oriented point of view. We use the lens of security properties to review the requirements and specifications of aeronautical communications infrastructure as of 2021 and observe that most standards lack cybersecurity as a key requirement. Furthermore, we review the academic literature to identify possible solutions for the lack of cybersecurity measures in aeronautical communications system. We observe that most systems have been thoroughly analyzed within the academic security community, some for decades even, with many papers proposing concrete solutions to missing cybersecurity features. We conclude that there is a systematic problem in the design process of aeronautical communication systems. We provide a list of eight key findings and recommendations to improve the process of specifying such systems in a secure manner

Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes

Motivation: Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins, UGA is recoded to Sec in presence of specific features on selenoprotein gene transcripts. Due to the dual role of the UGA codon, selenoprotein prediction and annotation are difficult tasks, and even known selenoproteins are often misannotated in genome databases

A Rodent Model for Dirofilaria Immitis, Canine Heartworm: Parasite Growth, Development, and Drug Sensitivity in NSG Mice

Heartworm disease, caused by Dirofilaria immitis, remains a significant threat to canines and felines. The development of parasites resistant to macrocyclic lactones (ML) has created a significant challenge to the control of the infection. The goal of this study was to determine if mice lacking a functional immune response would be susceptible to D. immitis. Immunodeficient NSG mice were susceptible to the infection, sustaining parasites for at least 15 weeks, with infective third-stage larvae molting and developing into the late fourth-stage larvae. Proteomic analysis of host responses to the infection revealed a complex pattern of changes after infection, with at least some of the responses directed at reducing immune control mechanisms that remain in NSG mice. NSG mice were infected with isolates of D. immitis that were either susceptible or resistant to MLs, as a population. The susceptible isolate was killed by ivermectin whereas the resistant isolate had improved survivability, while both isolates were affected by moxidectin. It was concluded that D. immitis survives in NSG mice for at least 15 weeks. NSG mice provide an ideal model for monitoring host responses to the infection and for testing parasites in vivo for susceptibility to direct chemotherapeutic activity of new agents

Mps1 regulates kinetochore-microtubule attachment stability via the ska complex to ensure error-free chromosome segregation

The spindle assembly checkpoint kinase Mps1 not only inhibits anaphase but also corrects erroneous attachments that could lead to missegregation and aneuploidy. However, Mps1’s error correction-relevant substrates are unknown. Using a chemically tuned kinetochore-targeting assay, we show that Mps1 destabilizes microtubule attachments (K fibers) epistatically to Aurora B, the other major error-correcting kinase. Through quantitative proteomics, we identify multiple sites of Mps1-regulated phosphorylation at the outer kinetochore. Substrate modification was microtubule sensitive and opposed by PP2A-B56 phosphatases that stabilize chromosome-spindle attachment. Consistently, Mps1 inhibition rescued K-fiber stability after depleting PP2A-B56. We also identify the Ska complex as a key effector of Mps1 at the kinetochore-microtubule interface, as mutations that mimic constitutive phosphorylation destabilized K fibers in vivo and reduced the efficiency of the Ska complex’s conversion from lattice diffusion to end-coupled microtubule binding in vitro. Our results reveal how Mps1 dynamically modifies kinetochores to correct improper attachments and ensure faithful chromosome segregation

Genetics of osteopontin in patients with chronic kidney disease: The German chronic kidney disease study

Osteopontin (OPN), encoded by SPP1, is a phosphorylated glycoprotein predominantly synthesized in kidney tissue. Increased OPN mRNA and protein expression correlates with proteinuria, reduced creatinine clearance, and kidney fibrosis in animal models of kidney disease. But its genetic underpinnings are incompletely understood. We therefore conducted a genome-wide association study (GWAS) of OPN in a European chronic kidney disease (CKD) population. Using data from participants of the German Chronic Kidney Disease (GCKD) study (N = 4,897), a GWAS (minor allele frequency [MAF]>= 1%) and aggregated variant testing (AVT, MAFAuthor summaryOsteopontin (OPN) is involved in many (patho)physiological processes of the human body. Among others, it is known to be associated with adverse kidney outcomes. Since its genetic underpinnings are incompletely understood, we conducted a genome-wide association study of OPN in a European chronic kidney disease (CKD) population (N = 4,897). Of the three detected signals, two could be replicated within a population-based study of Finns. One locus is located upstream of SPP1 which encodes the OPN protein and is related to OPN production. This gene was also disclosed by an analysis of rare variants, all presumably effecting the gene product. Another locus maps into KLKB1 encoding prekallikrein (PK) that after processing to kallikrein (KAL) is implicated in blood pressure control and inflammation among others. Overall, our results highlight the multi-functional role of OPN and its possible pathological role in CKD. Further studies are needed to elucidate the complex role of OPN in humans.</p

Ex vivo correction of selenoprotein N deficiency in rigid spine muscular dystrophy caused by a mutation in the selenocysteine codon

Premature termination of translation due to nonsense mutations is a frequent cause of inherited diseases. Therefore, many efforts were invested in the development of strategies or compounds to selectively suppress this default. Selenoproteins are interesting candidates considering the idiosyncrasy of the amino acid selenocysteine (Sec) insertion mechanism. Here, we focused our studies on SEPN1, a selenoprotein gene whose mutations entail genetic disorders resulting in different forms of muscular diseases. Selective correction of a nonsense mutation at the Sec codon (UGA to UAA) was undertaken with a corrector tRNASec that was engineered to harbor a compensatory mutation in the anticodon. We demonstrated that its expression restored synthesis of a full-length selenoprotein N both in HeLa cells and in skin fibroblasts from a patient carrying the mutated Sec codon. Readthrough of the UAA codon was effectively dependent on the Sec insertion machinery, therefore being highly selective for this gene and unlikely to generate off-target effects. In addition, we observed that expression of the corrector tRNASec stabilized the mutated SEPN1 transcript that was otherwise more subject to degradation. In conclusion, our data provide interesting evidence that premature termination of translation due to nonsense mutations is amenable to correction, in the context of the specialized selenoprotein synthesis mechanism

Identification of a signature motif for the eIF4a3–SECIS interaction

eIF4a3, a DEAD-box protein family member, is a component of the exon junction complex which assembles on spliced mRNAs. The protein also acts as a transcript-selective translational repressor of selenoprotein synthesis during selenium deficiency. Selenocysteine (Sec) incorporation into selenoproteins requires a Sec Insertion Sequence (SECIS) element in the 3′ untranslated region. During selenium deficiency, eIF4a3 binds SECIS elements from non-essential selenoproteins, preventing Sec insertion. We identified a molecular signature for the eIF4a3-SECIS interaction using RNA gel shifts, surface plasmon resonance and enzymatic foot printing. Our results support a two-site interaction model, where eIF4a3 binds the internal and apical loops of the SECIS. Additionally, the stability of the complex requires uridine in the SECIS core. In terms of protein requirements, the two globular domains of eIF4a3, which are connected by a linker, are both critical for SECIS binding. Compared to full-length eIF4a3, the two domains in trans bind with a lower association rate but notably, the uridine is no longer important for complex stability. These results provide insight into how eIF4a3 discriminates among SECIS elements and represses translation

Novel structural determinants in human SECIS elements modulate the translational recoding of UGA as selenocysteine

The selenocysteine insertion sequence (SECIS) element directs the translational recoding of UGA as selenocysteine. In eukaryotes, the SECIS is located downstream of the UGA codon in the 3′-UTR of the selenoprotein mRNA. Despite poor sequence conservation, all SECIS elements form a similar stem-loop structure containing a putative kink-turn motif. We functionally characterized the 26 SECIS elements encoded in the human genome. Surprisingly, the SECIS elements displayed a wide range of UGA recoding activities, spanning several 1000-fold in vivo and several 100-fold in vitro. The difference in activity between a representative strong and weak SECIS element was not explained by differential binding affinity of SECIS binding Protein 2, a limiting factor for selenocysteine incorporation. Using chimeric SECIS molecules, we identified the internal loop and helix 2, which flank the kink-turn motif, as critical determinants of UGA recoding activity. The simultaneous presence of a GC base pair in helix 2 and a U in the 5′-side of the internal loop was a statistically significant predictor of weak recoding activity. Thus, the SECIS contains intrinsic information that modulates selenocysteine incorporation efficiency