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1. Cooperative actin filament nucleation by the Arp2/3 complex and formins maintains the homeostatic cortical array in Arabidopsis epidermal cells

   https://doi.org/10.1093/plcell/koad301  

   Xu, Liyuan; Cao, Lingyan; Li, Jiejie; Staiger, Christopher J (December 2023, The Plant Cell)

   Abstract Precise control over how and where actin filaments are created leads to the construction of unique cytoskeletal arrays within a common cytoplasm. Actin filament nucleators are key players in this activity and include the conserved actin-related protein 2/3 (Arp2/3) complex as well as a large family of formins. In some eukaryotic cells, these nucleators compete for a common pool of actin monomers and loss of one favors the activity of the other. To test whether this mechanism is conserved, we combined the ability to image single filament dynamics in the homeostatic cortical actin array of living Arabidopsis (Arabidopsis thaliana) epidermal cells with genetic and/or small molecule inhibitor approaches to stably or acutely disrupt nucleator activity. We found that Arp2/3 mutants or acute CK-666 treatment markedly reduced the frequency of side-branched nucleation events as well as overall actin filament abundance. We also confirmed that plant formins contribute to side-branched filament nucleation in vivo. Surprisingly, simultaneous inhibition of both classes of nucleator increased overall actin filament abundance and enhanced the frequency of de novo nucleation events by an unknown mechanism. Collectively, our findings suggest that multiple actin nucleation mechanisms cooperate to generate and maintain the homeostatic cortical array of plant epidermal cells. 

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2. Mitigating Voltage Drop in Resistive Memories by Dynamic RESET Voltage Regulation and Partition RESET

   https://doi.org/10.1109/HPCA47549.2020.00031  

   Zokaee, Farzaneh; Jiang, Lei (February 2020, IEEE International Symposium on High Performance Computer Architecture)

   The emerging resistive random access memory (ReRAM) technology has been deemed as one of the most promising alternatives to DRAM in main memories, due to its better scalability, zero cell leakage and short read latency. The cross-point (CP) array enables ReRAM to obtain the theoretical minimum 4F^2 cell size by placing a cell at the cross-point of a word-line and a bit-line. However, ReRAM CP arrays suffer from large sneak current resulting in significant voltage drop that greatly prolongs the array RESET latency. Although prior works reduce the voltage drop in CP arrays, they either substantially increase the array peripheral overhead or cannot work well with wear leveling schemes. In this paper, we propose two array micro-architecture level techniques, dynamic RESET voltage regulation (DRVR) and partition RESET (PR), to mitigate voltage drop on both bit-lines and word-lines in ReRAM CP arrays. DRVR dynamically provides higher RESET voltage to the cells far from the write driver and thus encountering larger voltage drop on a bit-line, so that all cells on a bit-line share approximately the same latency during RESETs. PR decides how many and which cells to reset online to partition the CP array into multiple equivalent circuits with smaller word-line resistance and voltage drop. Because DRVR and PR greatly reduce the array RESET latency, the ReRAM-based main memory lifetime under the worst case non-stop write traffic significantly decreases. To increase the CP array endurance, we further upgrade DRVR by providing lower RESET voltage to the cells suffering from less voltage drop on a word-line. Our experimental results show that, compared to the combination of prior voltage drop reduction techniques, our DRVR and PR improve the system performance by 11.7% and decrease the energy consumption by 46% averagely, while still maintaining >10-year main memory system lifetime. 

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3. A bioinspired, passive microfluidic lobe filtration system

   https://doi.org/10.1039/D1LC00449B  

   Clark, Andrew S.; San-Miguel, Adriana (September 2021, Lab on a Chip)

   Size-based microfluidic filtration systems can be affected by clogging, which prevents their use in high-throughput and continuous applications. To address these concerns, we have developed two microfluidic lobe filters bioinspired by the filtration mechanism of two species of manta ray. These chips enable filtration of particles around 10–30 μm with precise control and high throughput by using two arrays of equally spaced filter lobes. For each filter design, we investigated multiple inlet flow rates and particle sizes to identify successful operational parameters. Filtration efficiency increases with fluid flow rate, suggesting that particle inertial effects play a key role in lobe filter separation. Microparticle filtration efficiencies up to 99% were obtainable with inlet flow rates of 20 mL min −1 . Each filter design successfully increased microparticle concentrations by a factor of two or greater at different inlet flow rates ranging from 6–16 mL min −1 . At higher inlet flow rates, ANSYS Fluent simulations of each device revealed a complex velocity profile that contains three local maxima and two inflection points. Ultimately, we show that distances from the lobe array to the closest local maxima and inflection point of the velocity profile can be used to successfully estimate lobe filtration efficiency at each operational flow rate. 

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4. Distinct Chemotaxis Protein Paralogs Assemble into Chemoreceptor Signaling Arrays To Coordinate Signaling Output

   https://doi.org/10.1128/mBio.01757-19  

   O’Neal, Lindsey; Gullett, Jessica M.; Aksenova, Anastasia; Hubler, Adam; Briegel, Ariane; Ortega, Davi; Kjær, Andreas; Jensen, Grant; Alexandre, Gladys; Peter Greenberg, E. (October 2019, mBio)

   ABSTRACT Most chemotactic motile bacteria possess multiple chemotaxis signaling systems, the functions of which are not well characterized. Chemotaxis signaling is initiated by chemoreceptors that assemble as large arrays, together with chemotaxis coupling proteins (CheW) and histidine kinase proteins (CheA), which form a baseplate with the cytoplasmic tips of receptors. These cell pole-localized arrays mediate sensing, signaling, and signal amplification during chemotaxis responses. Membrane-bound chemoreceptors with different cytoplasmic domain lengths segregate into distinct arrays. Here, we show that a bacterium, Azospirillum brasilense , which utilizes two chemotaxis signaling systems controlling distinct motility parameters, coordinates its chemotactic responses through the production of two separate membrane-bound chemoreceptor arrays by mixing paralogs within chemotaxis baseplates. The polar localization of chemoreceptors of different length classes is maintained in strains that had baseplate signaling proteins from either chemotaxis system but was lost when both systems were deleted. Chemotaxis proteins (CheA and CheW) from each of the chemotaxis signaling systems (Che1 and Che4) could physically interact with one another, and chemoreceptors from both classes present in A. brasilense could interact with Che1 and Che4 proteins. The assembly of paralogs from distinct chemotaxis pathways into baseplates provides a straightforward mechanism for coordinating signaling from distinct pathways, which we predict is not unique to this system given the propensity of chemotaxis systems for horizontal gene transfer. IMPORTANCE The assembly of chemotaxis receptors and signaling proteins into polar arrays is universal in motile chemotactic bacteria. Comparative genome analyses indicate that most motile bacteria possess multiple chemotaxis signaling systems, and experimental evidence suggests that signaling from distinct chemotaxis systems is integrated. Here, we identify one such mechanism. We show that paralogs from two chemotaxis systems assemble together into chemoreceptor arrays, forming baseplates comprised of proteins from both chemotaxis systems. These mixed arrays provide a straightforward mechanism for signal integration and coordinated response output from distinct chemotaxis systems. Given that most chemotactic bacteria encode multiple chemotaxis systems and the propensity for these systems to be laterally transferred, this mechanism may be common to ensure chemotaxis signal integration occurs. 

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5. Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae)

   https://doi.org/10.1111/tpj.15676  

   Choi, In‐Su; Wojciechowski, Martin F.; Steele, Kelly P.; Hunter, Sarah G.; Ruhlman, Tracey A.; Jansen, Robert K. (February 2022, The Plant Journal)

   SUMMARY Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31Medicagotaxa we detected exceptionally high post‐IGT amplification of mitochondrial (mt) DNA sequences containingrps10in the nuclear genome ofMedicago polymorphaand closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in theM. polymorphanuclear genome. The mtrps10‐like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6–3.0% of total genomic DNA, a value approximately three‐fold greater than the entire mitogenome inM. polymorpha. Compared to a typical mt gene, the mtrps10‐like sequence coverage level was 691.5–7198‐fold higher inM. polymorphaand closely related species. In addition to the post‐IGT amplification, our analysis identified the canonical telomeric repeat and the species‐specific satellite arrays that are likely attributable to an ancestral chromosomal fusion inM. polymorpha. A possible relationship between chromosomal instability and the mtrps10‐like tandem repeat family in theM. polymorphaclade is discussed. 

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