Aspect and modality in the interpretation of deverbal -<Emphasis Type="Italic">er</Emphasis> nominals in English

This article presents a corpus study of over 16,000 tokens of -er nominalizations on 62 verbal bases that were extracted from the Corpus of Contemporary American English and the British National Corpus. We show that an individual -er nominal can often be given a range of modal and aspectual readings and that a number of factors influence the availability of different readings for -er nominals, including verb type, syntactic context (verb tenses, adverbs), and encyclopedic information. On the basis of these data, we argue, contra Cohen (2016), that the core meaning of the affix -er (as in writer, printer, etc.) cannot be that of a dynamic modal. We show that neither Cohen’s (2016) analysis nor syntactic analyses such as that of Alexiadou and Schäfer (2010) can account for the range of readings we find. We conclude by sketching one possible analysis in terms of the Lexical Semantic Framework of Lieber (2004, 2016) that postulates underspecified lexical representations of the -er nominals and resolution of underspecification in context.     

Generation of Adenovirus Vectors Devoid of All Viral Genes by Recombination between Inverted Repeats

Direct or inverse repeated sequences are important functional features of prokaryotic and eukaryotic genomes. Considering the unique mechanism, involving single-stranded genomic intermediates, by which adenovirus (Ad) replicates its genome, we investigated whether repetitive homologous sequences inserted into E1-deleted adenoviral vectors would affect replication of viral DNA. In these studies we found that inverted repeats (IRs) inserted into the E1 region could mediate predictable genomic rearrangements, resulting in vector genomes devoid of all viral genes. These genomes (termed DeltaAd.IR) contained only the transgene cassette flanked on both sides by precisely duplicated IRs, Ad packaging signals, and Ad inverted terminal repeat sequences. Generation of DeltaAd.IR genomes could also be achieved by coinfecting two viruses, each providing one inverse homology element. The formation of DeltaAd.IR genomes required Ad DNA replication and appeared to involve recombination between the homologous inverted sequences. The formation of DeltaAd. IR genomes did not depend on the sequence within or adjacent to the inverted repeat elements. The small DeltaAd.IR vector genomes were efficiently packaged into functional Ad particles. All functions for DeltaAd.IR replication and packaging were provided by the full-length genome amplified in the same cell. DeltaAd.IR vectors were produced at a yield of approximately 10(4) particles per cell, which could be separated from virions with full-length genomes based on their lighter buoyant density. DeltaAd.IR vectors infected cultured cells with the same efficiency as first-generation vectors; however, transgene expression was only transient due to the instability of deleted genomes within transduced cells. The finding that IRs present within Ad vector genomes can mediate precise genetic rearrangements has important implications for the development of new vectors for gene therapy approaches.     

Passive mechanical properties of the lumbar multifidus muscle support its role as a stabilizer

The purpose of this study was to compare the passive mechanical properties and titin isoform sizes of the multifidus, longissimus, and iliocostalis muscles. Given our knowledge of each muscle's architecture and the multifidus’ operating range, we hypothesized that multifidus would have higher elastic modulus with corresponding smaller titin isoforms compared to longissimus or iliocostalis muscles. Single-fiber and fiber-bundle material properties were derived from passive stress–strain tests of excised biopsies (n=47). Titin isoform sizes were quantified via sodium dodecyl sulfate-vertical agarose gel electrophoresis (SDS-VAGE) analysis. We found that, at the single-fiber level, all muscles had similar material properties and titin isoform sizes. At the fiber-bundle level, however, we observed significantly increased stiffness (～45%) in multifidus compared to longissimus and iliocostalis muscles. These data demonstrate that each muscle may have a different scaling relationship between single-fiber and fiber-bundle levels, suggesting that the structures responsible for higher order passive mechanical properties may be muscle specific. Our results suggest that divergent passive material properties are observed at size scales larger than the single cell level, highlighting the importance of the extracellular matrix in these muscles. In addition to architectural data previously reported, these data further support the unique stabilizing function of the multifidus muscle. These data will provide key input variables for biomechanical modeling of normal and pathologic lumbar spine function and direct future work in biomechanical testing in these important muscles.     

A helper-dependent capsid-modified adenovirus vector expressing adeno-associated virus rep78 mediates site-specific integration of a 27-kilobase transgene cassette

Random integration of viral gene therapy vectors and subsequent activation or disruption of cellular genes poses safety risks. Major efforts in the field are aimed toward targeting vector integration to specific sites in the host genome. The adeno-associated virus (AAV) Rep78 protein is able to target AAV integration to a specific site on human chromosome 19, called AAVS1. We studied whether this ability could be harnessed to achieve site-specific integration of a 27-kb transgene cassette into a model cell line for human hematopoietic cells (Mo7e). To deliver rep78 and the transgene to Mo7e cells, we used helper-dependent adenovirus (Ad) vectors containing Ad serotype 35 fiber knob domains (HD-Ad). An HD-Ad vector containing the rep78 gene under the control of the globin locus control region (LCR) (Ad.LCR-rep78) conferred Rep78 expression on Mo7e cells. Upon coinfection of Ad.LCR-rep78 with an HD-Ad vector containing a 27-kb globin-LCR-green fluorescent protein (GFP) transgene cassette flanked by AAV inverted terminal repeats (ITRs) (Ad.AAV-LCR-GFP), transduced cells were cloned and expanded (without selection pressure), and vector integration was analyzed in clones with more than 30% GFP-positive cells. Vector integration into the AAVS1 region was seen in 30% of analyzed integration sites, and GFP expression from these integrants was stable over time. Of the remaining integration sites, 25% were within the genomic globin LCR. In almost 90% of sites, transgene integration occurred via the Ad ITR. This indicates that rescue of the AAV ITR-flanked transgene cassette from Ad.AAV-LCR-GFP is not required for Rep78-mediated integration into AAVS1 and that free ends within the vector genome can be created by breaks within the Ad ITRs, whose structure is apparently recognized by cellular "nicking" enzymes. The finding that 55% of all analyzed integration sites were either within the AAVS1 or globin LCR region demonstrates that a high frequency of targeted integration of a large transgene cassette can be achieved in human hematopoietic stem cell lines.     

Large-scale discovery and characterization of protein regulatory motifs in eukaryotes

The increasing ability to generate large-scale, quantitative proteomic data has brought with it the challenge of analyzing such data to discover the sequence elements that underlie systems-level protein behavior. Here we show that short, linear protein motifs can be efficiently recovered from proteome-scale datasets such as sub-cellular localization, molecular function, half-life, and protein abundance data using an information theoretic approach. Using this approach, we have identified many known protein motifs, such as phosphorylation sites and localization signals, and discovered a large number of candidate elements. We estimate that ~80% of these are novel predictions in that they do not match a known motif in both sequence and biological context, suggesting that post-translational regulation of protein behavior is still largely unexplored. These predicted motifs, many of which display preferential association with specific biological pathways and non-random positioning in the linear protein sequence, provide focused hypotheses for experimental validation.     

Elucidation of extracellular matrix mechanics from muscle fibers and fiber bundles

The importance of the extracellular matrix (ECM) in muscle is widely recognized, since ECM plays a central role in proper muscle development (Buck and Horwitz, 1987), tissue structural support (Purslow, 2002), and transmission of mechanical signals between fibers and tendon (Huijing, 1999). Since substrate biomechanical properties have been shown to be critical in the biology of tissue development and remodeling (Engler et al., 2006; Gilbert et al., 2010), it is likely that mechanics are critical for ECM to perform its function. Unfortunately, there are almost no data available regarding skeletal muscle ECM viscoelastic properties. This is primarily due to the impossibility of isolating and testing muscle ECM. Therefore, this note presents a new method to quantify viscoelastic ECM modulus by combining tests of single muscle fibers and fiber bundles. Our results demonstrate that ECM is a highly nonlinearly elastic material, while muscle fibers are linearly elastic.     

Moment arms of the human digital flexors

For the extrinsic hand flexors (flexor digitorum profundus, FDP; flexor digitorum superficialis, FDS; flexor pollicis longus, FPL), moment arm corresponds to the tendon's distance from the center of the metacarpalphalangeal (MP), proximal interphalangeal (PIP), or distal interphalangeal (DIP) joint. The clinical value of establishing accurate moment arms has been highlighted for biomechanical modeling, the development of robotic hands, designing rehabilitation protocols, and repairing flexor tendon pulleys (Brand et al., 1975; An et al., 1983; Thompson and Giurintano, 1989; Deshpande et al., 2010; Wu et al., 2010). In this study, we define the moment arms for all of the extrinsic flexor tendons of the hand across all digital joints for all digits in cadaveric hands.     

Muscle extracellular matrix applies a transverse stress on fibers with axial strain

It is widely assumed that skeletal muscle contraction is isovolumic. This assumption has been verified at the single fiber and at the myofibril level. Model development and mechanical analyses often exploit this assumption when investigating skeletal muscle and evaluating muscle mechanical properties. This communication describes a method whereby individual muscle fibers and bundles of fibers, which include their constituent extracellular matrix (ECM), were tested to define the change in volume with axial strain. The results demonstrate that fibers are isovolumic, but bundles decrease in volume with strain. The loss of volume implicates a transverse force being applied to the fibers by the ECM. The nature and importance of this transverse force warrant further investigation.     

Overexpression of Cu/Zn superoxide dismutase is lethal for mice lacking double-strand break repair

The non-homologous DNA end joining (NHEJ) pathway is a major double-strand DNA break repair pathway in cells of multicellular eukaryotes. Ku is a heterodimeric protein consisting of Ku70 and Ku86, and it is thought to be the first component to bind to a broken double-strand DNA end. Mice lacking Ku86 show features of premature aging, live about 6-12 months, and show a characteristic loss of neurons in the central nervous system during development. Cells from mice lacking Ku have increased numbers of chromosome breaks, a significant fraction of which are caused by oxidative metabolism. Overexpression of the cytoplasmic Cu/Zn superoxide dismutase (SOD1) from a transgene is known to increase the number of chromosome breaks in primary cells (presumably by increasing reactive oxygen species). Here we show that SOD1 overexpression in a Ku86-/- mouse results in embryonic lethality. This striking effect is, however, subject to a strain-specific modifier. Genome-wide marker analysis is most consistent with the modifier being on mouse chromosome 13. Analysis of 10 markers on chromosome 13 suggests that the modifier is within the same region as a modifier of the murine amyotropic lateral sclerosis (ALS) phenotype when it is caused by overexpression of a mutant form of SOD1. Based on these results, we propose a model in which oxidative metabolism causes chromosome breaks, leading to neuronal death; and this neuronal death may account for that seen in NHEJ mutant animals and in mammals with SOD1-mediated ALS.