Performance Evaluation of Global Reading of Entire Databases

Using simulation and probabilistic analysis, we study the performance of an algorithm to read entire databases with locking concurrency control allowing multiple readers or an exclusive writer. The algorithm runs concurrently with the normal transaction processing (on-the-fly) and locks the entities in the database one by one (incremental). The analysis compares different strategies to resolve the conflicts between the global read algorithm and update. Since the algorithm is parallel in nature, its interference with normal transactions is minimized in parallel and distributed databases. A simulation study shows that one variant of the algorithm can read the entire database with very little overhead and interference with the updates

Genome Sequencing Reveals Widespread Virulence Gene Exchange among Human Neisseria Species

Commensal bacteria comprise a large part of the microbial world, playing important roles in human development, health and disease. However, little is known about the genomic content of commensals or how related they are to their pathogenic counterparts. The genus Neisseria, containing both commensal and pathogenic species, provides an excellent opportunity to study these issues. We undertook a comprehensive sequencing and analysis of human commensal and pathogenic Neisseria genomes. Commensals have an extensive repertoire of virulence alleles, a large fraction of which has been exchanged among Neisseria species. Commensals also have the genetic capacity to donate DNA to, and take up DNA from, other Neisseria. Our findings strongly suggest that commensal Neisseria serve as reservoirs of virulence alleles, and that they engage extensively in genetic exchange

Oncolytic Viruses for Multiple Myeloma Therapy

Although recent treatment advances have improved outcomes for patients with multiple myeloma (MM), the disease frequently becomes refractory to current therapies. MM thus remains incurable for most patients and new therapies are urgently needed. Oncolytic viruses are a promising new class of therapeutics that provide tumor-targeted therapy by specifically infecting and replicating within cancerous cells. Oncolytic therapy yields results from both direct killing of malignant cells and induction of an anti-tumor immune response. In this review, we will describe oncolytic viruses that are being tested for MM therapy with a focus on those agents that have advanced into clinical trials

The Pseudorabies Virus Us2 Protein, a Virion Tegument Component, Is Prenylated in Infected Cells

The Us2 gene is conserved among alphaherpesviruses, but its function is not known. We demonstrate here that the pseudorabies virus (PRV) Us2 protein is synthesized early after infection and localizes to cytoplasmic vesicles and to the plasma membrane, despite the lack of a recognizable signal sequence or membrane-spanning domain. Us2 protein is also packaged as part of the tegument of mature virions. The Us2 carboxy-terminal four amino acids comprise a CAAX motif, a well-characterized signal for protein prenylation. Treatment of infected cells with lovastatin, a drug that disrupts protein prenylation, changed the relative electrophoretic mobility of Us2 in sodium dodecyl sulfate-polyacrylamide gels. In addition, lovastatin treatment caused a dramatic relocalization of Us2 to cytoplasmic punctate structures associated with microtubules, which appeared to concentrate over the microtubule organizing center. When the CAAX motif was changed to GAAX and the mutant protein was synthesized from an expression plasmid, it concentrated in punctate cytoplasmic structures reminiscent of Us2 localization in infected cells treated with lovastatin. We suggest that prenylation of PRV Us2 protein is required for proper membrane association. Curiously, the Us2 protein isolated from purified virions does not appear to be prenylated. This is the first report to describe the prenylation of an alphaherpesvirus protein

Clostridium scindens exacerbates experimental necrotizing enterocolitis via upregulation of the apical sodium-dependent bile acid transporter

Supplemental Figure S1: https://doi.org/10.25422/azu.data.24208272Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in premature infants. Evidence indicates that bile acid homeostasis is disrupted during NEC: ileal bile acid levels are elevated in animals with experimental NEC, as is expression of the apical sodium-dependent bile acid transporter (Asbt). In addition, bile acids, which are synthesized in the liver, are extensively modified by the gut microbiome, including via the conversion of primary bile acids to more cytotoxic secondary forms. We hypothesized that the addition of bile acid-modifying bacteria would increase susceptibility to NEC in a neonatal rat model of the disease. The secondary bile acid-producing species Clostridium scindens exacerbated both incidence and severity of NEC. C. scindens upregulated the bile acid transporter Asbt and increased levels of intraenterocyte bile acids. Treatment with C. scindens also altered bile acid profiles and increased hydrophobicity of the ileal intracellular bile acid pool. The ability of C. scindens to enhance NEC requires bile acids, as pharmacological sequestration of ileal bile acids protects animals from developing disease. These findings indicate that bile acid-modifying bacteria can contribute to NEC pathology and provide additional evidence for the role of bile acids in the pathophysiology of experimental NEC.NEW & NOTEWORTHY Necrotizing enterocolitis (NEC), a life-threatening gastrointestinal emergency in premature infants, is characterized by dysregulation of bile acid homeostasis. We demonstrate that administering the secondary bile acid-producing bacterium Clostridium scindens enhances NEC in a neonatal rat model of the disease. C. scindens-enhanced NEC is dependent on bile acids and driven by upregulation of the ileal bile acid transporter Asbt. This is the first report of bile acid-modifying bacteria exacerbating experimental NEC pathology.NIH R01DK117652 NIH P30CA02307412 month embargo; first published 7 November 2023This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

A central region in the minor capsid protein of papillomaviruses facilitates viral genome tethering and membrane penetration for mitotic nuclear entry

<div><p>Incoming papillomaviruses (PVs) depend on mitotic nuclear envelope breakdown to gain initial access to the nucleus for viral transcription and replication. In our previous work, we hypothesized that the minor capsid protein L2 of PVs tethers the incoming vDNA to mitotic chromosomes to direct them into the nascent nuclei. To re-evaluate how dynamic L2 recruitment to cellular chromosomes occurs specifically during prometaphase, we developed a quantitative, microscopy-based assay for measuring the degree of chromosome recruitment of L2-EGFP. Analyzing various HPV16 L2 truncation-mutants revealed a central chromosome-binding region (CBR) of 147 amino acids that confers binding to mitotic chromosomes. Specific mutations of conserved motifs (IVAL286AAAA, RR302/5AA, and RTR313EEE) within the CBR interfered with chromosomal binding. Moreover, assembly-competent HPV16 containing the chromosome-binding deficient L2(RTR313EEE) or L2(IVAL286AAAA) were inhibited for infection despite their ability to be transported to intracellular compartments. Since vDNA and L2 were not associated with mitotic chromosomes either, the infectivity was likely impaired by a defect in tethering of the vDNA to mitotic chromosomes. However, L2 mutations that abrogated chromatin association also compromised translocation of L2 across membranes of intracellular organelles. Thus, chromatin recruitment of L2 may in itself be a requirement for successful penetration of the limiting membrane thereby linking both processes mechanistically. Furthermore, we demonstrate that the association of L2 with mitotic chromosomes is conserved among the alpha, beta, gamma, and iota genera of <i>Papillomaviridae</i>. However, different binding patterns point to a certain variance amongst the different genera. Overall, our data suggest a common strategy among various PVs, in which a central region of L2 mediates tethering of vDNA to mitotic chromosomes during cell division thereby coordinating membrane translocation and delivery to daughter nuclei.</p></div

Chromosomal association of point mutants of HPV16 L2.

<p>(A) Full-length L2 is depicted with N-terminal, middle and C-terminal functional domains. The minimal chromosomal binding region (CBR) is highlighted in orange. Within the CBR (insert) the nuclear retention signal and the SUMO interaction motif are indicated at their relative location with the CBR. Conserved regions within the CBR are depicted in red, whereas regions with lower conservation are white. Single conserved residues are highlighted. The sites of the point mutations in the CBR are color-coded according to their impact on chromosomal association (black = interfering; grey = silent). (B) The alignment of the amino acid (aa) sequences of the NRS and upstream residues of HPV16, 18, 5, BPV1 and MnPV L2 are written in the single-letter code. The aa residue numbers, and mutated residues (bold font) are denoted for HPV16 L2. The conservation between the indicated L2 aa sequences was scored by PRALINE [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006308#ppat.1006308.ref078" target="_blank">78</a>], and obtained scores were grouped into five categories: no (white), low (blue), intermediate-low (green), intermediate-high (orange) and high (red) conservation. (C), (D) The aa substitutions IVAL286AAAA, RR297EE, RR302/5AA and RTR313EEE in HPV16 L2-EGFP were analyzed for chromosomal association during mitosis as in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006308#ppat.1006308.g002" target="_blank">Fig 2C and 2D</a>. (C) Images of wild-type and mutant HPV16 L2-EGFP (upper row, green), H2B-mCherry (center row, red), and merges (lower row) are shown for representative cells. (D) The chromosomal association indices are depicted in a dot plot as in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006308#ppat.1006308.g002" target="_blank">Fig 2D</a>. Statistical significances (two-tailed Student’s t-test) relative to wild-type HPV16 L2-EGFP were assessed (**P < 0.01, ***P < 0.001).</p

HPV16 vDNA and L2-EGFP associate with mitotic chromosomes.

<p>(A) HeLa cells and HaCaT cells were infected with EdU-HPV16, fixed at 20 h p.i., and stained for host DNA and vDNA using Hoechst and EdU-click chemistry, respectively. Cells were analyzed by CLSM. Shown is a representative confocal section of a metaphase cell with the host DNA (left, red), vDNA (center, green), and merge (right). (B) HeLa cells were infected with HPV16 PsV, fixed at 20 h p.i., and stained for incoming L2 protein using K1L2 and host DNA with Hoechst. Shown is a representative confocal section of a metaphase cell as above. (C) HeLa H2B-mCherry cells were transiently transfected with a HPV16 L2-EGFP expression plasmid, and synchronized by a single thymidine block. High magnification images of fixed cells were acquired using a spinning disc microscope. Depicted are representative images of the subcellular localization of L2-EGFP during the different cell cycle phases as determined by the histone marker.</p