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1. Learning attentional templates for value-based decision-making

   https://doi.org/10.1016/j.cell.2024.01.041  

   Jahn, Caroline I; Markov, Nikola T; Morea, Britney; Daw, Nathaniel D; Ebitz, R Becket; Buschman, Timothy J (March 2024, Cell)

   Attention filters sensory inputs to enhance task-relevant information. It is guided by an “attentional template” that represents the stimulus features that are currently relevant. To understand how the brain learns and uses templates, we trained monkeys to perform a visual search task that required them to repeatedly learn new attentional templates. Neural recordings found that templates were represented across the prefrontal and parietal cortex in a structured manner, such that perceptually neighboring templates had similar neural representations. When the task changed, a new attentional template was learned by incrementally shifting the template toward rewarded features. Finally, we found that attentional templates transformed stimulus features into a common value representation that allowed the same decision-making mechanisms to deploy attention, regardless of the identity of the template. Altogether, our results provide insight into the neural mechanisms by which the brain learns to control attention and how attention can be flexibly deployed across tasks. 

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2. Overcoming nucleotide bias in the nonenzymatic copying of RNA templates

   https://doi.org/10.1093/nar/gkae982  

   Duzdevich, Daniel; Carr, Christopher E; Colville, Ben W F; Aitken, Harry R M; Szostak, Jack W (November 2024, Nucleic Acids Research)

   Abstract The RNA World hypothesis posits that RNA was the molecule of both heredity and function during the emergence of life. This hypothesis implies that RNA templates can be copied, and ultimately replicated, without the catalytic aid of evolved enzymes. A major problem with nonenzymatic template-directed polymerization has been the very poor copying of sequences containing rA and rU. Here, we overcome that problem by using a prebiotically plausible mixture of RNA mononucleotides and random-sequence oligonucleotides, all activated by methyl isocyanide chemistry, that direct the uniform copying of arbitrary-sequence templates, including those harboring rA and rU. We further show that the use of this mixture in copying reactions suppresses copying errors while also generating a more uniform distribution of mismatches than observed for simpler systems. We find that oligonucleotide competition for template binding sites, oligonucleotide ligation and the template binding properties of reactant intermediates work together to reduce product sequence bias and errors. Finally, we show that iterative cycling of templated polymerization and activation chemistry improves the yields of random-sequence products. These results for random-sequence template copying are a significant advance in the pursuit of nonenzymatic RNA replication. 

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3. Fast Constraint Synthesis for C++ Function Templates

   https://doi.org/10.1145/3720422  

   Ding, Shuo; Zhang, Qirun (April 2025, Proceedings of the ACM on Programming Languages)

   C++ templates are a powerful feature for generic programming and compile-time computations, but C++ compilers often emit overly verbose template error messages. Even short error messages often involve unnecessary and confusing implementation details, which are difficult for developers to read and understand. To address this problem, C++20 introduced constraints and concepts, which impose requirements on template parameters. The new features can define clearer interfaces for templates and can improve compiler diagnostics. However, manually specifying template constraints can still be non-trivial, which becomes even more challenging when working with legacy C++ projects or with frequent code changes. This paper bridges the gap and proposes an automatic approach to synthesizing constraints for C++ function templates. We utilize a lightweight static analysis to analyze the usage patterns within the template body and summarize them into constraints for each type parameter of the template. The analysis is inter-procedural and uses disjunctions of constraints to model function overloading. We have implemented our approach based on the Clang frontend and evaluated it on two C++ libraries chosen separately from two popular library sets: algorithm from the Standard Template Library (STL) and special functions from the Boost library, both of which extensively use templates. Our tool can process over 110k lines of C++ code in less than 1.5 seconds and synthesize non-trivial constraints for 30%-40% of the function templates. The constraints synthesized for algorithm align well with the standard documentation, and on average, the synthesized constraints can reduce error message lengths by 56.6% for algorithm and 63.8% for special functions. 

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4. A remodeled RNA polymerase II complex catalyzing viroid RNA-templated transcription

   https://doi.org/10.1371/journal.ppat.1010850  

   Dissanayaka Mudiyanselage, Shachinthaka D.; Ma, Junfei; Pechan, Tibor; Pechanova, Olga; Liu, Bin; Wang, Ying (September 2022, PLOS Pathogens)

   Daròs, José-Antonio (Ed.)

   Viroids, a fascinating group of plant pathogens, are subviral agents composed of single-stranded circular noncoding RNAs. It is well-known that nuclear-replicating viroids exploit host DNA-dependent RNA polymerase II (Pol II) activity for transcription from circular RNA genome to minus-strand intermediates, a classic example illustrating the intrinsic RNA-dependent RNA polymerase activity of Pol II. The mechanism for Pol II to accept single-stranded RNAs as templates remains poorly understood. Here, we reconstituted a robust in vitro transcription system and demonstrated that Pol II also accepts minus-strand viroid RNA template to generate plus-strand RNAs. Further, we purified the Pol II complex on RNA templates for nano-liquid chromatography-tandem mass spectrometry analysis and identified a remodeled Pol II missing Rpb4, Rpb5, Rpb6, Rpb7, and Rpb9, contrasting to the canonical 12-subunit Pol II or the 10-subunit Pol II core on DNA templates. Interestingly, the absence of Rpb9, which is responsible for Pol II fidelity, explains the higher mutation rate of viroids in comparison to cellular transcripts. This remodeled Pol II is active for transcription with the aid of TFIIIA-7ZF and appears not to require other canonical general transcription factors (such as TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH, and TFIIS), suggesting a distinct mechanism/machinery for viroid RNA-templated transcription. Transcription elongation factors, such as FACT complex, PAF1 complex, and SPT6, were also absent in the reconstituted transcription complex. Further analyses of the critical zinc finger domains in TFIIIA-7ZF revealed the first three zinc finger domains pivotal for RNA template binding. Collectively, our data illustrated a distinct organization of Pol II complex on viroid RNA templates, providing new insights into viroid replication, the evolution of transcription machinery, as well as the mechanism of RNA-templated transcription. 

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5. T7Max transcription system

   https://doi.org/10.1186/s13036-023-00323-1  

   Deich, Christopher; Cash, Brock; Sato, Wakana; Sharon, Judee; Aufdembrink, Lauren; Gaut, Nathaniel J.; Heili, Joseph; Stokes, Kaitlin; Engelhart, Aaron E.; Adamala, Katarzyna P. (December 2023, Journal of Biological Engineering)

   Abstract BackgroundEfficient cell-free protein expression from linear DNA templates has remained a challenge primarily due to template degradation. In addition, the yields of transcription in cell-free systems lag behind transcriptional efficiency of live cells. Most commonly used in vitro translation systems utilize T7 RNA polymerase, which is also the enzyme included in many commercial kits. ResultsHere we present characterization of a variant of T7 RNA polymerase promoter that acts to significantly increase the yields of gene expression withinin vitrosystems. We have demonstrated that T7Max increases the yield of translation in many types of commonly used in vitro protein expression systems. We also demonstrated increased protein expression yields from linear templates, allowing the use of T7Max driven expression from linear templates. ConclusionsThe modified promoter, termed T7Max, recruits standard T7 RNA polymerase, so no protein engineering is needed to take advantage of this method. This technique could be used with any T7 RNA polymerase- basedin vitroprotein expression system. 

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