The 15th Infantry in China

 In 1921, my father received orders assigning him to U.S. 15th infantry which was based in Tientsin on the South China Sea, 90 miles from Peking. A few months after Capt. Cushman and his bride joined it, I was born into the regiment.       Since the mid-19th century, European powers had been in China with extraterritorial concessions wrung from the weak Manchu dynasty. The Boxer Rebellion of 1900 had brought an eight-nation allied force into Peking to restore Manchu rule. The Boxer Protocols, signed by the Chinese and by Western powers and japan, provided for foreign continents to be stationed, among other places, in Tientsin. This article previously appeared in the Command and General Staff College Foundation News, Number 11/fall 2011. Attempts to locate prior publications (if any) of this article were unsuccessful. Every effort has been made to trace and contact copyright holder. Permission to reprint the Foundation News version of this article had been granted

Suppression of 12-O-tetradecanoylphorbol-13-acetate-induced ornithine decarboxylase activity by resveratrol derivatives

As demonstrated previously, resveratrol (3,4',5-trihydroxy-trans-stilbene) inhibits 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced ornithine decarboxylase (ODC), the key rate limiting enzyme in mammalian polyamine synthesis. Using human bladder epithelial carcinoma HTB-24 cells in culture where resveratrol inhibits induction with an IC50 of 8.8 µM, we now report potential metabolites demonstrate greater activity [tetrabutylammonium (E)-4-(3,5-dihydroxystyryl)phenyl sulfate (IC50 1.2 µM), resveratrol tripotassium 3,5,4'-trisulfate (IC50 1.8 µM), resveratrol tripotassium 3,4'-disulfate (IC50 1.8 µM), and resveratrol tripotassium 3,5-disulfate (IC50 2.3 µM)]. Based on RT-PCR studies, ODC inhibition occurs at the transcriptional level, but this was not due to direct inhibition of protein kinase C (e.g., resveratrol IC50, 79 µM; resveratrol tripotassium 3,5-disulfate IC50, 49 µM). Additional work is underway to more fully investigate this potentially important observation. [This work was supported by program project P01 CA48112 awarded by the National Cancer Institute. SL acknowledges Indo-US Science and Technology Forum (IUSSTF), New Delhi for a Research Fellowship]

A Framework for Aggregating Private and Public Web Archives

Personal and private Web archives are proliferating due to the increase in the tools to create them and the realization that Internet Archive and other public Web archives are unable to capture personalized (e.g., Facebook) and private (e.g., banking) Web pages. We introduce a framework to mitigate issues of aggregation in private, personal, and public Web archives without compromising potential sensitive information contained in private captures. We amend Memento syntax and semantics to allow TimeMap enrichment to account for additional attributes to be expressed inclusive of the requirements for dereferencing private Web archive captures. We provide a method to involve the user further in the negotiation of archival captures in dimensions beyond time. We introduce a model for archival querying precedence and short-circuiting, as needed when aggregating private and personal Web archive captures with those from public Web archives through Memento. Negotiation of this sort is novel to Web archiving and allows for the more seamless aggregation of various types of Web archives to convey a more accurate picture of the past Web.Comment: Preprint version of the ACM/IEEE Joint Conference on Digital Libraries (JCDL 2018) full paper, accessible at the DO

An integrated approach to use genetic resources for resurrection plants to enhance drought tolerance in breeding-extension programs [abstract]

Only abstract of poster available.Track V: BiomassThe ultimate goals of this project are to gain a basic understanding of the unique gene and gene regulatory networks that are necessary and sufficient for vegetative tissues to withstand dehydration and then rapidly recover upon rehydration and to use the knowledge gained to develop crops, maize and forage grasses that maintain biomass production under drought condition. Our approach is to combine comparative genomics and phylogenetics to identify genes and gene networks that are adaptive and central to the tolerance of cellular dehydration. This involves the use of resurrection species as models for dehydration tolerance coupled with a suite of comparative bioinformatic tools that allows for the phylogenetic assessment of gene expression patterns in response to dehydration and rehydration. Once the key genetic elements have been identified and assessed we will use a transgenic functional assessment of their involvement in the phenotype, both at a molecular and physiological level, of drought tolerance. One of our key resurrection species is the South African grass Sporobolus stapfianus, which is capable of surviving -240 MPa of water deficit (a hundred times lower than most crop plants). This plant not only serves as a model for monocot crops such as maize and switchgrass, our major targets for crop improvement, but also serves as a direct possibility for an alternate forage grass and biomass source. The improvement of biomass production under drought conditions is not only important for sustainable biofuel production but also for food and energy security. Funded by a CSREES-NRI Grant of $450,000 over three years to PI Mel Oliver USDA-ARS-PGRU Columbia, CoPIs Robert Sharp, University of Missouri; John Cushman, University of Nevada, Reno; Paxton Payton, USDA-ARS-PSRU Lubbock

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible and used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. This freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.This work was supported by the Department of Energy (DOE), Office of Science, Genomic Science Program [DE-SC0008834 to JCC]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors would like to thank the Information Technology Department at the University of Nevada, Reno for the use of computing time on the High-Performance Computing Cluster (http://www.unr.edu/it/research-resources/the-grid) and Mary Ann Cushman and Pradeep Yerramsetty for providing helpful and clarifying comments on the manuscript

A Conformation Change in the Extracellular Domain that Accompanies Desensitization of Acid-sensing Ion Channel (ASIC) 3

Acid-sensing ion channels (ASICs) are thought to trigger some forms of acid-induced pain and taste, and to contribute to stroke-induced neural damage. After activation by low extracellular pH, different ASICs undergo desensitization on time scales from 0.1 to 10 s. Consistent with a substantial conformation change, desensitization slows dramatically when temperature drops (Askwith, C.C., C.J. Benson, M.J. Welsh, and P.M. Snyder. 2001. PNAS. 98:6459–6463). The nature of this conformation change is unknown, but two studies showed that desensitization rate is altered by mutations on or near the first transmembrane domain (TM1) (Coric, T., P. Zhang, N. Todorovic, and C.M. Canessa. 2003. J. Biol. Chem. 278:45240–45247; Pfister, Y., I. Gautschi, A.-N. Takeda, M. van Bemmelen, S. Kellenberger, and L. Schild. 2006. J. Biol. Chem. 281:11787–11791). Here we show evidence of a specific conformation change associated with desensitization. When mutated from glutamate to cysteine, residue 79, which is some 20 amino acids extracellular to TM1, can be altered by cysteine-modifying reagents when the channel is closed, but not when it is desensitized; thus, desensitization appears to conceal the residue from the extracellular medium. D78 and E79 are a pair of adjacent acidic amino acids that are highly conserved in ASICs yet absent from epithelial Na+ channels, their acid-insensitive relatives. Despite large effects on desensitization by mutations at positions 78 and 79—including a shift to 10-fold lower proton concentration with the E79A mutant—there are not significant effects on activation

Volume reduction, cell washing and affinity cell selection using multi-dimensional acoustic standing wave technology

Acoustic Cell Processing is a unique acousto-fluidics platform technology for shear-free manipulation of cells using ultrasonic standing waves. The platform has broad applications in the field of cell and gene therapy, e.g., cell concentration and washing, cell culturing, microcarrier/cell separation, acoustic affinity cell selection and label-free cell selection. The acoustic radiation force exerted by the ultrasonic standing wave on the suspended cells in combination with fluid drag forces and gravitational forces is used to manipulate the cells and achieve a certain cell processing unit operation, e.g., separate, concentrate, or wash. The technology is single-use, continuous, and can be scaled up, down or out. It therefore allows for a flexible and modular approach that can be customized to process a desired cell count, cell culture volume or cell concentration within a given required process time. Utilizing its proprietary multi-dimensional standing wave platform, FloDesign Sonics (FD Sonics) has been developing two applications for cell and gene therapy manufacturing, an Acoustic Concentrate-Wash (ACW) and Acoustic Affinity Cell Selection (AACS) system for closed and shear free Cell and Gene Therapy manufacturing, namely CAR-T immunocellular therapies. The ACW technology has been applied to Jurkat T-cells and primary cultures of T-cells of 1-2 Liters (L) with cell concentrations ranging from 1 million cells per milliliter (ml) to 40 million cells per ml. The process flow rate varies from 2-3 L/hour with average cell recoveries of more than 80% in 60 to 90 minutes. The efficiency of the cell washing process ranges from 95-99% depletion of a model protein (BSA), depending on the wash methodology. The AACS technology is a scalable acoustic affinity cell selection method using acoustic (non-paramagnetic) affinity beads for positive or negative cell selection. A multi-dimensional acoustic standing wave is then used to separate the affinity bead-cell complexes from the unbound cells, thereby completing the process of a negative or positive cell selection. A population of 1 billion CAR-T cells containing 30% T-Cell Receptor positive (TCR+) and 70% T-cell Receptor Negative (TCR-) cells has been depleted of 99% of its TCR+ population. The TCR- cell recovery for this process was above 70% and the full process took less than 2 hours. When used for positive selection of CD3+ cells, AACS allowed for an enrichment of 2.5-fold in CD3+ population. ACW and AACS are powerful acoustic-based cell processing technologies that lower cost and risk while enabling a modular, automation-friendly manufacturing process for cell and gene therapy manufacturing. Please click Additional Files below to see the full abstract

The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

<p>Abstract</p> <p>Background</p> <p><it>Dunaliella salina </it>Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because <it>D. salina </it>can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of <it>D. salina </it>have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of <it>D. salina </it>and compares them with those of the model green algae <it>Chlamydomonas reinhardtii </it>and <it>Volvox carteri</it>.</p> <p>Results</p> <p>The <it>D. salina </it>organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the <it>D. salina </it>plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the <it>D. salina </it>ptDNA.</p> <p>Conclusions</p> <p>These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of <it>D. salina </it>and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the <it>D. salina </it>organelle DNA sequences will aid in the development of a viable plastid transformation system for this model alga, and they will complement the forthcoming <it>D. salina </it>nuclear genome sequence, placing <it>D. salina </it>in a group of a select few photosynthetic eukaryotes for which complete genome sequences from all three genetic compartments are available.</p