Nanopores: synergy from DNA sequencing to industrial filtration - small holes with big impact

Nanopores in thin membranes play important roles in science and industry. Single nanopores have provided a step-change in portable DNA sequencing and understanding nanoscale transport while multipore membranes facilitate food processing and purification of water and medicine. Despite the unifying use of nanopores, the fields of single nanopores and multipore membranes differ - to varying degrees - in terms of materials, fabrication, analysis, and applications. Such a partial disconnect hinders scientific progress as important challenges are best resolved together. This Viewpoint suggests how synergistic crosstalk between the two fields can provide considerable mutual benefits in fundamental understanding and the development of advanced membranes. We first describe the main differences including the atomistic definition of single pores compared to the less defined conduits in multipore membranes. We then outline steps to improve communication between the two fields such as harmonizing measurements and modelling of transport and selectivity. The resulting insight is expected to improve the rational design of porous membranes. The Viewpoint concludes with an outlook of other developments that can be best achieved by collaboration across the two fields to advance the understanding of transport in nanopores and create next-generation porous membranes tailored for sensing, filtration, and other applications

Exterior-Interior Duality for Discrete Graphs

The Exterior-Interior duality expresses a deep connection between the Laplace spectrum in bounded and connected domains in $\mathbb{R}^2$, and the scattering matrices in the exterior of the domains. Here, this link is extended to the study of the spectrum of the discrete Laplacian on finite graphs. For this purpose, two methods are devised for associating scattering matrices to the graphs. The Exterior -Interior duality is derived for both methods.Comment: 15 pages 1 figur

Single copy shRNA configuration for ubiquitous gene knockdown in mice

RNA interference through the expression of small hairpin RNA (shRNA) molecules has become a very promising tool in reverse mouse genetics as it may allow inexpensive and rapid gene function analysis in vivo. However, the prerequisites for ubiquitous and reproducible shRNA expression are not well defined. Here we show that a single copy shRNA-transgene can mediate body-wide gene silencing in mice when inserted in a defined locus of the genome. The most commonly used promoters for shRNA expression, H1 and U6, showed a comparably broad activity in this configuration. Taken together, the results define a novel approach for efficient interference with expression of defined genes in vivo. Moreover, we provide a rapid strategy for the production of gene knockdown mice combining recombinase mediated cassette exchange and tetraploid blastocyst complementation approaches

Nucleosomes in serum of patients with early cerebral stroke

Background: Nucleosomes are cell death products that are elevated in serum of patients with diseases that are associated with massive cell destruction. We investigated the kinetics of circulating nucleosomes after cerebral stroke and their correlation with the clinical status. Methods: In total, we analyzed nucleosomes by ELISA in sera of 63 patients with early stroke daily during the first week after onset. For correlation with the clinical pathology, patients were grouped into those with medium to slight functional impairment (Barthel Index BI >= 50) and those with severe functional impairment (BI = 50 showed a continuous increase in nucleosomes until day 5 (median: 523 arbitrary units, AU) followed by a slow decline. In contrast, patients with BI = 50 (497 AU; p = 0.031). Concerning the infarction volume, nucleosomes showed significant correlations for the concentrations on day 3 (r = 0.43; p = 0.001) and for the area under the curve (r = 0.34; p = 0.016). Conclusion: Even if nucleosomes are nonspecific cell death markers, their release into serum after cerebral stroke correlates with the gross functional status as well as with the infarction volume and can be considered as biochemical correlative to the severity of stroke. Copyright (c) 2006 S. Karger AG, Basel

Construction and composition of the squid pen from Doryteuthis pealeii

Author Posting. © University of Chicago Press, 2019. This article is posted here by permission of University of Chicago Press for personal use, not for redistribution. The definitive version was published in Messerli, M. A., Raihan, M. J., Kobylkevich, B. M., Benson, A. C., Bruening, K. S., Shribak, M., Rosenthal, J. J. C., & Sohn, J. J. Construction and composition of the squid pen from Doryteuthis pealeii. Biological Bulletin. 237(1), (2019): 1-15, doi:10.1086/704209.The pen, or gladius, of the squid is an internalized shell. It serves as a site of attachment for important muscle groups and as a protective barrier for the visceral organs. The pen’s durability and flexibility are derived from its unique composition of chitin and protein. We report the characterization of the structure, development, and composition of pens from Doryteuthis pealeii. The nanofibrils of the polysaccharide β-chitin are arranged in an aligned configuration in only specific regions of the pen. Chitin is secreted early in development, enabling us to characterize the changes in pen morphology prior to hatching. The chitin and proteins are assembled in the shell sac surrounded by fluid that has a significantly different ionic composition from squid plasma. Two groups of proteins are associated with the pen: those on its surface and those embedded within the pen. Only 20 proteins are identified as embedded within the pen. Embedded proteins are classified into six groups, including chitin associated, protease, protease inhibitors, intracellular, extracellular matrix, and those that are unknown. The pen proteins share many conserved domains with proteins from other chitinous structures. We conclude that the pen is one of the least complex, load-bearing, chitin-rich structures currently known and is amenable to further studies to elucidate natural construction mechanisms using chitin and protein.We thank John Dowling for financial support. We thank Kasia Hammar and Louie Kerr of the Marine Biological Laboratory Central Microscopy Facility for help obtaining scanning electron micrographs. We thank Bogdan Budnik and Renee Robinson from the Mass Spectrometry and Proteomics Resource Laboratory for their help and advice with protein identification. We thank Shin-Yi Marzano and Chenchen Feng of South Dakota State University for help with rapid amplification of cDNA ends. Funding for this work was provided by the Eugene and Millicent Bell Fellowship Fund in Tissue Engineering (MAM), an Agriculture and Biological Sciences Undergraduate Research Award (KSB), National Institutes of Health grant R01 GM101701 (MS), National Science Foundation grant IOS1557748 (JJCR), and Israel-United States Binational Science Foundation 2013094 (JJCR). Literature Cited2020-07-0

Prefetched Address Translation

With explosive growth in dataset sizes and increasing machine memory capacities, per-application memory footprints are commonly reaching into hundreds of GBs. Such huge datasets pressure the TLB, resulting in frequent misses that must be resolved through a page walk - a long-latency pointer chase through multiple levels of the in-memory radix tree-based page table.Anticipating further growth in dataset sizes and their adverse affect on TLB hit rates, this work seeks to accelerate page walks while fully preserving existing virtual memory abstractions and mechanisms - a must for software compatibility and generality. Our idea is to enable direct indexing into a given level of the page table, thus eliding the need to first fetch pointers from the preceding levels. A key contribution of our work is in showing that this can be done by simply ordering the pages containing the page table in physical memory to match the order of the virtual memory pages they map to. Doing so enables direct indexing into the page table using a base-plus-offset arithmetic.We introduce Address Translation with Prefetching (ASAP), a new approach for reducing the latency of address translation to a single access to the memory hierarchy. Upon a TLB miss, ASAP launches prefetches to the deeper levels of the page table, bypassing the preceding levels. These prefetches happen concurrently with a conventional page walk, which observes a latency reduction due to prefetching while guaranteeing that only correctly-predicted entries are consumed. ASAP requires minimal extensions to the OS and trivial microarchitectural support. Moreover, ASAP is fully legacy-preserving, requiring no modifications to the existing radix tree-based page table, TLBs and other software and hardware mechanisms for address translation. Our evaluation on a range of memory-intensive workloads shows that under SMT colocation, ASAP is able to reduce page walk latency by an average of 25% (42% max) in native execution, and 45% (55% max) under virtualization