Granulovirus PK-1 kinase activity relies on a side-to-side dimerization mode centered on the regulatory αC helix

The life cycle of Baculoviridae family insect viruses depends on the viral protein kinase, PK-1, to phosphorylate the regulatory protein, p6.9, to induce baculoviral genome release. Here, we report the crystal structure of Cydia pomenella granulovirus PK-1, which, owing to its likely ancestral origin among host cell AGC kinases, exhibits a eukaryotic protein kinase fold. PK-1 occurs as a rigid dimer, where an antiparallel arrangement of the αC helices at the dimer core stabilizes PK-1 in a closed, active conformation. Dimerization is facilitated by C-lobe:C-lobe and N-lobe:N-lobe interactions between protomers, including the domain-swapping of an N-terminal helix that crowns a contiguous β-sheet formed by the two N-lobes. PK-1 retains a dimeric conformation in solution, which is crucial for catalytic activity. Our studies raise the prospect that parallel, side-to-side dimeric arrangements that lock kinase domains in a catalytically-active conformation could function more broadly as a regulatory mechanism among eukaryotic protein kinases.

A parallel side graft—frontage graft—technique for intercostal artery reimplantation during thoraco-abdominal aorta replacement

In the conventional way of thoraco-abdominal aortic replacement, the intercostal arteries are reimplanted directly to the main aortic graft or by the interposition of branch grafts. To overcome the disadvantages of these techniques, we adopted a different technique using a parallel side graft. The good patency rate of reimplanted intercostal arteries achieved by this technique and its potential technical advantages can contribute to the improvement of the surgical outcome.

Jets in the magnetosheath: IMF control of where they occur

Magnetosheath jets are localized regions of plasma that move faster towards the Earth than the surrounding magnetosheath plasma. Due to their high velocities, they can cause indentations when colliding into the magnetopause and trigger processes such as magnetic reconnection and magnetopause surface waves. We statistically study the occurrence of these jets in the subsolar magnetosheath using measurements from the five Time History of Events and Macroscale Interactions during Substorms (THEMIS) spacecraft and OMNI solar wind data from 2008 to 2011. We present the observations in the BIMF–vSW plane and study the spatial distribution of jets during different interplanetary magnetic field (IMF) orientations. Jets occur downstream of the quasi-parallel bow shock approximately 9 times as often as downstream of the quasi-perpendicular shock, suggesting that foreshock processes are responsible for most jets. For an oblique IMF, with 30–60∘ cone angle, the occurrence increases monotonically from the quasi-perpendicular side to the quasi-parallel side. This study offers predictability for the numbers, locations, and magnetopause impact rates of jets observed during different IMF orientations, allowing us to better forecast the formation of these jets and their impact on the magnetosphere.

Self-Spectre, Write-Execute and the Hidden State

The recent Meltdown and Spectre vulnerabilities have highlighted a very present and real threat in the on-chip memory cache units which can ultimately provide a hidden state, albeit only readable via memory timing instructions [Kocher, P.—Genkin, D.— Gruss, D.— Haas, W.—Hamburg, M.—Lipp, M.–Mangard, S.—Prescher, T.—Schwarz, M.—Yarom, Y.: Spectre attacks: Exploiting speculative execution, CoRR, abs/1801.01203, 2018]. Yet the exploits, although having some complexity and slowness, are demonstrably reliable on nearly all processors produced for the last two decades. Moving out from looking at this strictly as a means of reading protected memory, as the large microprocessor companies move to close this security vulnerability, an interesting question arises. Could the inherent design of the processor give the ability to hide arbitrary calculations in this speculative and parallel side channel? Without even using protected memory and exploiting the vulnerability, as has been the focus, there could very well be a whole class of techniques which exploit the side-channel. It could be done in a way which would be largely un-preventable behavior as the technology would start to become self-defeating or require a more complicated and expensive on-chip cache memory system to properly post-speculatively clean itself. And the ability to train the branch predictor to incorrectly speculatively behave is almost certain given hardware limitations, andthusprovidesexactly this pathway. A novel approach looks at just how much computation can be done speculatively with a result store via indirect reads and available through the memory cache. A multi-threaded approach can allow a multi-stage computation pipeline where each computation is passed to a read-out thread and then to the next computation thread [Swanson, S.—McDowell, L. K.—Swift, M. M.—Eggers, S. J.–Levy H. M.: An evaluation of speculative instruction execution on simultaneous multithreaded processors, ACM Trans. Comput. Syst. 21 (2003), 314–340]. Through channels like this, an application can surreptitiously make arbitrary calculations, or even leak data without any standard tracing tools being capable of monitoring the subtle changes. Like a variation of the famous physics Heisenberg uncertainty principle, even a tool capable of reading the cache states would not only be incredibly inefficient, but thereby tamper with and modify the state. Tools like in-circuit emulators, or specially designed cache emulators would be needed to unmask the speculative reads, and it is further difficult to visualize with a linear time-line. Specifically, the AES and RSA algorithms will be studied with respect to these ideas, looking at success rates for various calculation batches with speculative execution, while having a summary view to see the rather severe performance penalties for using such methods. Either approaches could provide for strong white-box cryptography when considering a binary, non-source code form. In terms of white-box methods, both could be significantly challenging to locate or deduce the inner workings of the code. Further, both methods can easily surreptitiously leak or hide data within shared memory in a seemingly innocuous manner.

Jets in the Magnetosheath: IMF Control of Where They Occur

Magnetosheath jets are localized regions of plasma that move faster towards the Earth than the surrounding magnetosheath plasma. Due to their high velocities, they can cause indentations when colliding into the magnetopause and trigger processes such as magnetic reconnection and magnetopause surface waves. We statistically study the occurrence of these jets in the subsolar magnetosheath using measurements from the five Time History of Events and Macroscale Interactions during Substorms (THEMIS) spacecraft and OMNI solar wind data from 2008–2011. We present the observations in the BIMF-vSW plane and study the spatial distribution of jets during different interplanetary magnetic field (IMF) orientations. Jets occur downstream of the quasi-parallel bow shock approximately 9 times as often as downstream of the quasi-perpendicular shock, suggesting that foreshock processes are responsible for most jets. For oblique IMF, with 30°–60° cone angle, the occurrence increases monotonically from the quasi-perpendicular side to the quasi-parallel side. This study offers predictability for the numbers and locations of jets observed during different IMF orientations allowing us to better forecast the formation of these jets and their impact on the magnetosphere.