Статті в журналах: "CopY-like"

1

Landau, Idan. "This Construction Looks Like a Copy Is Optional." Linguistic Inquiry 40, no. 2 (April 2009): 343–46. http://dx.doi.org/10.1162/ling.2009.40.2.343.

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2

Johns, M. A., J. Mottinger, and M. Freeling. "A low copy number, copia-like transposon in maize." EMBO Journal 4, no. 5 (May 1985): 1093–101. http://dx.doi.org/10.1002/j.1460-2075.1985.tb03745.x.

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3

Ishikawa, Asano, Yoel E. Stuart, Daniel I. Bolnick, and Jun Kitano. "Copy number variation of a fatty acid desaturase gene Fads2 associated with ecological divergence in freshwater stickleback populations." Biology Letters 17, no. 8 (August 2021): 20210204. http://dx.doi.org/10.1098/rsbl.2021.0204.

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Fitness of aquatic animals can be limited by the scarcity of nutrients such as long-chain polyunsaturated fatty acids, especially docosahexaenoic acid (DHA). DHA availability from diet varies among aquatic habitats, imposing different selective pressures on resident animals to optimize DHA acquisition and synthesis. For example, DHA is generally poor in freshwater ecosystems compared to marine ecosystems. Our previous work revealed that, relative to marine fishes, several freshwater fishes evolved higher copy numbers of the fatty acid desaturase2 ( Fads2 ) gene, which encodes essential enzymes for DHA biosynthesis, likely compensating for the limited availability of DHA in freshwater. Here, we demonstrate that Fads2 copy number also varies between freshwater sticklebacks inhabiting lakes and streams with stream fish having higher Fads2 copy number. Additionally, populations with benthic-like morphology possessed higher Fads2 copy number than those with planktivore-like morphology. This may be because benthic-like fish mainly feed on DHA-deficient prey such as macroinvertebrates whereas planktivore-like fish forage more regularly on DHA-rich prey, like copepods. Our results suggest that Fads2 copy number variation arises from ecological divergence not only between organisms exploiting marine and freshwater habitats but also between freshwater organisms exploiting divergent resources.

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4

Apesteguia, Jose, Jörg Oechssler, and Simon Weidenholzer. "Copy Trading." Management Science 66, no. 12 (December 2020): 5608–22. http://dx.doi.org/10.1287/mnsc.2019.3508.

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Copy trading allows traders in social networks to receive information on the success of other agents in financial markets and to directly copy their trades. Internet platforms like eToro, ZuluTrade, and Tradeo have attracted millions of users in recent years. The present paper studies the implications of copy trading for the risk taking of investors. Implementing a novel experimental financial asset market, we show that providing information on the success of others leads to a significant increase in risk taking of subjects. This increase in risk taking is even larger when subjects are provided with the option to directly copy others. We conclude that copy trading leads to excessive risk taking. This paper was accepted by Axel Ockenfels, decision analysis.

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5

Tandon, Ravi, Valentino Cattori, Barbara Willi, Marina L. Meli, Maria A. Gomes-Keller, Hans Lutz, and Regina Hofmann-Lehmann. "Copy number polymorphism of endogenous feline leukemia virus-like sequences." Molecular and Cellular Probes 21, no. 4 (August 2007): 257–66. http://dx.doi.org/10.1016/j.mcp.2007.01.003.

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6

Kapica, Steven S. "‘I don't feel like a copy’: posthuman legal personhood andCaprica." Griffith Law Review 23, no. 4 (October 2, 2014): 612–33. http://dx.doi.org/10.1080/10383441.2014.1014454.

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7

Portmann, Reto, Kristian R. Poulsen, Reinhard Wimmer, and Marc Solioz. "CopY-like Copper Inducible Repressors are Putative ‘Winged Helix’ Proteins." BioMetals 19, no. 1 (February 2006): 61–70. http://dx.doi.org/10.1007/s10534-005-5381-3.

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8

Gijsbers, Antoinet C. J., Barbara D’haene, Yvonne Hilhorst-Hofstee, Marcel Mannens, Beate Albrecht, Joerg Seidel, David R. Witt, et al. "Identification of copy number variants associated with BPES-like phenotypes." Human Genetics 124, no. 5 (October 25, 2008): 489–98. http://dx.doi.org/10.1007/s00439-008-0574-9.

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9

Kumagai, Jean. "Special report : Can we copy the brain? - Navigate like a rat." IEEE Spectrum 54, no. 6 (June 2017): 58–63. http://dx.doi.org/10.1109/mspec.2017.7934234.

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10

Roche, Peter J., Robert J. Crawford, and Geoffrey W. Tregear. "A single-copy relaxin-like gene sequence is present in sheep." Molecular and Cellular Endocrinology 91, no. 1-2 (February 1993): 21–28. http://dx.doi.org/10.1016/0303-7207(93)90250-n.

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11

Sekhar, Resmi, and R. S. Shaji. "A Methodological Review on Copy-Move Forgery Detection for Image Forensics." International Journal of Digital Crime and Forensics 6, no. 4 (October 2014): 34–49. http://dx.doi.org/10.4018/ijdcf.2014100103.

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Copy-Move forgery is the very prevalent form of image tampering. The powerful image processing tools available freely helps even the naive to tamper with images. A copy-move forgery is performed by copying a region in an image and pasting it in the same image most probably after applying some form of post-processing on the region like rotation, blurring, scaling, double JPEG compression etc. This makes it difficult to develop one common technique to detect copy-move forgery. As a result a considerable number of methods have been developed in view to detect different forms of copy-move forgeries. Those techniques can be classified generally as block based techniques and key- point based techniques. This paper presents an extensive survey on the very recent methods developed for copy-move forgery detection.

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12

Bruening, Benjamin. "Differences between the Wh-Scope-Marking and Wh-Copy Constructions in Passamaquoddy." Linguistic Inquiry 37, no. 1 (January 2006): 25–49. http://dx.doi.org/10.1162/002438906775321166.

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Several phenomena in Passamaquoddy clearly distinguish wh-scope marking with ‘what’ from an apparently similar wh-copy construction. These facts argue for a theory of wh-scope marking like that in Bruening 2004 (based on Dayal 1994), where the embedded question is the syntactic and semantic restriction on the matrix wh-word ‘what’. The wh-copy construction, in contrast, is best analyzed as spelling out multiple copies of a long-distance movement chain. This copy theory is extended to scope marking with tan and comparatives in Passamaquoddy.

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13

Asakura, Nobuaki, Shinya Yoshida, Naoki Mori, Ichiro Ohtsuka, and Chiharu Nakamura. "Sequence diversity and copy number variation of Mutator-like transposases in wheat." Genetics and Molecular Biology 31, no. 2 (2008): 539–46. http://dx.doi.org/10.1590/s1415-47572008000300022.

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14

Gogulamudi, Venkateswara Reddy, Indra Mani, Umadevi Subramanian, and Kailash N. Pandey. "Genetic disruption of Npr1 depletes regulatory T cells and provokes high levels of proinflammatory cytokines and fibrosis in the kidneys of female mutant mice." American Journal of Physiology-Renal Physiology 316, no. 6 (June 1, 2019): F1254—F1272. http://dx.doi.org/10.1152/ajprenal.00621.2018.

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The present study was designed to determine the effects of gene knockout of guanylyl cyclase/natriuretic peptide receptor-A (GC-A/NPRA) on immunogenic responses affecting kidney function and blood pressure (BP) in Npr1 (coding for GC-A/NPRA)-null mutant mice. We used female Npr1 gene-disrupted ( Npr1−/−, 0 copy), heterozygous ( Npr1+/−, 1 copy), wild-type ( Npr1+/+, 2 copy), and gene-duplicated ( Npr1++/++, 4 copy) mice. Expression levels of Toll-like receptor (TLR)2/TLR4 mRNA were increased 4- to 5-fold in 1-copy mice and 6- to 10-fold in 0-copy mice; protein levels were increased 2.5- to 3-fold in 1-copy mice and 4- to 5-fold in 0-copy mice. Expression of proinflammatory cytokines and BP was significantly elevated in 1-copy and 0-copy mice compared with 2-copy and 4-copy mice. In addition, 0-copy and 1-copy mice exhibited drastic reductions in regulatory T cells (Tregs). After rapamycin treatment, Tregs were increased by 17% ( P < 0.001) in 0-copy mice and 8% ( P < 0.001) in 1-copy mice. Renal mRNA and protein levels of TLR2 and TLR4 were decreased by 70% in 0-copy mice and 50% in 1-copy mice. There were significantly higher levels of Tregs and very low levels of TLR2/TLR4 expression in 4-copy mice ( P < 0.001). These findings indicate that the disruption of Npr1 in female mice triggers renal immunogenic pathways, which transactivate the expression of proinflammatory cytokines and renal fibrosis with elevated BP in mutant animals. The data suggest that rapamycin treatment attenuates proinflammatory cytokine expression, dramatically increases anti-inflammatory cytokines, and substantially reduces BP and renal fibrosis in mutant animals.

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15

Naincy and Ashok Kumar Bathla. "Comparative Study and Survey on Copy Move Image Forgery Detection Approaches." Journal of Advance Research in Computer Science & Engineering (ISSN: 2456-3552) 2, no. 6 (June 30, 2015): 33–38. http://dx.doi.org/10.53555/nncse.v2i6.445.

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Nowadays the demand of digital images in various application areas is increasing and thus it is becoming important to ensure the authenticity of images. Due to easy availability of various image editing tools, continuous manipulations are done to create fake or forged images. Although various techniques like copy-move, splicing, resampling etc. for image forgery are present but copy move image forgery has received significant attention these days. Thus the focus of this paper is on copy-move image forgery detection techniques. We have presented a review of commonly used copy move image forgery detection techniques and the comparison of same is also showed to evaluate their performance on basis of various parameters.

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16

Naincy and Ashok Kumar Bathla. "Comparative Study and Survey on Copy Move Image Forgery Detection Approaches." Journal of Advance Research in Computer Science & Engineering (ISSN: 2456-3552) 2, no. 9 (September 30, 2015): 01–06. http://dx.doi.org/10.53555/nncse.v2i9.441.

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Nowadays the demand of digital images in various application areas is increasing and thus it is becoming important to ensure the authenticity of images. Due to easy availability of various image editing tools, continuous manipulations are done to create fake or forged images. Although various techniques like copy-move, splicing, resampling etc. for image forgery are present but copy move image forgery has received significant attention these days. Thus the focus of this paper is on copy-move image forgery detection techniques. We have presented a review of commonly used copy move image forgery detection techniques and the comparison of same is also showed to evaluate their performance on basis of various parameters.

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17

Hu, Kenneth H., Esmeralda Liu, Keith Dean, Monica Gingas, William DeGraff, and Nancy J. Trun. "Overproduction of Three Genes Leads to Camphor Resistance and Chromosome Condensation in Escherichia coli." Genetics 143, no. 4 (August 1, 1996): 1521–32. http://dx.doi.org/10.1093/genetics/143.4.1521.

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Abstract We isolated and characterized three genes, crcA, cspE and crcB, which when present in high copy confer camphor resistance on a cell and suppress mutations in the chromosomal partition gene mukB. Both phenotypes require the same genes. Unlike chromosomal camphor resistant mutants, high copy number crcA, cspE and crcB do not result in an increase in the ploidy of the cells. The cspE gene has been previously identified as a cold shock-like protein with homologues in all organisms tested. We also demonstrate that camphor causes the nucleoids to decondense in vivo and when the three genes are present in high copy, the chromosomes do not decondense. Our results implicate camphor and mukB mutations as interfering with chromosome condensation and high copy crcA, cspE and crcB as promoting or protecting chromosome folding.

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18

Pandey, Ramesh Chand, Sanjay Kumar Singh, and K. K. Shukla. "Passive Copy- Move Forgery Detection Using Speed-Up Robust Features, Histogram Oriented Gradients and Scale Invariant Feature Transform." International Journal of System Dynamics Applications 4, no. 3 (July 2015): 70–89. http://dx.doi.org/10.4018/ijsda.2015070104.

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Copy-Move is one of the most common technique for digital image tampering or forgery. Copy-Move in an image might be done to duplicate something or to hide an undesirable region. In some cases where these images are used for important purposes such as evidence in court of law, it is important to verify their authenticity. In this paper the authors propose a novel method to detect single region Copy-Move Forgery Detection (CMFD) using Speed-Up Robust Features (SURF), Histogram Oriented Gradient (HOG), Scale Invariant Features Transform (SIFT), and hybrid features such as SURF-HOG and SIFT-HOG. SIFT and SURF image features are immune to various transformations like rotation, scaling, translation, so SIFT and SURF image features help in detecting Copy-Move regions more accurately in compared to other image features. Further the authors have detected multiple regions COPY-MOVE forgery using SURF and SIFT image features. Experimental results demonstrate commendable performance of proposed methods.

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19

Tran, T. N., C. I. Selinger, B. Yu, C. C. Ng, M. R. J. Kohonen-Corish, B. McCaughan, C. Kennedy, S. A. O'Toole, and W. A. Cooper. "Alterations of insulin-like growth factor-1 receptor gene copy number and protein expression are common in non-small cell lung cancer." Journal of Clinical Pathology 67, no. 11 (August 12, 2014): 985–91. http://dx.doi.org/10.1136/jclinpath-2014-202347.

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AimsInsulin-like growth factor-1 receptor (IGF1R) is a tyrosine kinase membrane receptor involved in tumourigenesis that may be a potential therapeutic target. We aimed to investigate the incidence and prognostic significance of alterations in IGF1R copy number, and IGF1R protein expression in resected primary non-small cell lung cancer (NSCLC), and lymph node metastases.MethodsIGF1R gene copy number status was evaluated by chromogenic silver in situ hybridisation and IGF1R protein expression was evaluated by immunohistochemistry in tissue microarray sections from a retrospective cohort of 309 surgically resected NSCLCs and results were compared with clinicopathological features, including EGFR and KRAS mutational status and patient survival.ResultsIGF1R gene copy number status was positive (high polysomy or amplification) in 29.2% of NSCLC, and 12.1% exhibited IGF1R gene amplification. High IGF1R expression was found in 28.3%. There was a modest correlation between IGF1R gene copy number and protein expression (r=0.2, p<0.05). Alterations of IGF1R gene copy number and protein expression in primary tumours were significantly associated with alterations in lymph node metastases (p<0.01). High IGF1R gene copy number and protein expression was significantly higher in squamous cell carcinomas (SCC) compared with other subtypes of NSCLC (p<0.05). There were no other associations between IGF1R status and other clinicopathological features including patient age, gender, smoking status, tumour size, stage, grade, EGFR or KRAS mutational status or overall survival.ConclusionsHigh IGF1R gene copy number and protein overexpression are frequent in NSCLC, particularly in SCCs, but they are not prognostically relevant.

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20

Saha, Agniva, Jessica A. Mitchell, Yuri Nishida, Jonathan E. Hildreth, Joshua A. Ariberre, Wendy V. Gilbert, and David J. Garfinkel. "Atrans-Dominant Form of Gag Restricts Ty1 Retrotransposition and Mediates Copy Number Control." Journal of Virology 89, no. 7 (January 21, 2015): 3922–38. http://dx.doi.org/10.1128/jvi.03060-14.

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ABSTRACTSaccharomyces cerevisiaeandSaccharomyces paradoxuslack the conserved RNA interference pathway and utilize a novel form of copy number control (CNC) to inhibit Ty1 retrotransposition. Although noncoding transcripts have been implicated in CNC, here we present evidence that a truncated form of the Gag capsid protein (p22) or its processed form (p18) is necessary and sufficient for CNC and likely encoded by Ty1 internal transcripts. Coexpression of p22/p18 and Ty1 decreases mobility more than 30,000-fold. p22/p18 cofractionates with Ty1 virus-like particles (VLPs) and affects VLP yield, protein composition, and morphology. Although p22/p18 and Gag colocalize in the cytoplasm, p22/p18 disrupts sites used for VLP assembly. GlutathioneS-transferase (GST) affinity pulldowns also suggest that p18 and Gag interact. Therefore, this intrinsic Gag-like restriction factor confers CNC by interfering with VLP assembly and function and expands the strategies used to limit retroelement propagation.IMPORTANCERetrotransposons dominate the chromosomal landscape in many eukaryotes, can cause mutations by insertion or genome rearrangement, and are evolutionarily related to retroviruses such as HIV. Thus, understanding factors that limit transposition and retroviral replication is fundamentally important. The present work describes a retrotransposon-encoded restriction protein derived from the capsid gene of the yeast Ty1 element that disrupts virus-like particle assembly in a dose-dependent manner. This form of copy number control acts as a molecular rheostat, allowing high levels of retrotransposition when few Ty1 elements are present and inhibiting transposition as copy number increases. Thus, yeast and Ty1 have coevolved a form of copy number control that is beneficial to both “host and parasite.” To our knowledge, this is the first Gag-like retrotransposon restriction factor described in the literature and expands the ways in which restriction proteins modulate retroelement replication.

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21

Gladyshev, E. A., and I. R. Arkhipova. "A Single-Copy IS5-Like Transposon in the Genome of a Bdelloid Rotifer." Molecular Biology and Evolution 26, no. 8 (May 14, 2009): 1921–29. http://dx.doi.org/10.1093/molbev/msp104.

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22

Schmid, C. W., E. F. K. Wong, and N. Deka. "Single copy sequences in galago DNA resemble a repetitive human retrotransposon-like family." Journal of Molecular Evolution 31, no. 2 (August 1990): 92–100. http://dx.doi.org/10.1007/bf02109478.

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23

Ashley, C. W., A. D. C. Paula, R. Kumar, D. Mandelker, X. Pei, N. Riaz, J. Reis-Filho, and B. Weigelt. "Homologous recombination DNA repair defects in copy-number high serous-like endometrial cancers." Gynecologic Oncology 154 (June 2019): 32. http://dx.doi.org/10.1016/j.ygyno.2019.04.077.

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24

Littell, Patrick W. "Kwak'wala "Agreement" as Partial Subject Copy." LSA Annual Meeting Extended Abstracts 3 (April 8, 2012): 11. http://dx.doi.org/10.3765/exabs.v0i0.583.

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In the literature on Kwak'wala, a Northern Wakashan language of British Columbia, the term "agreement" refers to a particular phenomenon in which a determiner-like enclitic agreeing with the subject can occur in clause-second position when the subject itself does not. Using subject topicalizations, conjoined predicates, and other structures, I will argue that this phenomenon is not "agreement" as ordinarily understood. Instead, I will propose an account of Kwak'wala agreement in which this enclitic is a partial copy of the subject; that is, that it is movement of the D head of the DP subject under a copy theory of movement.

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25

Schouten, Philip C., Sabine C. Linn, Sebastian Aulmann, Hans-Peter Sinn, Andreas Schneeweiss, and Frederik Marme. "BRCA1 like copy number profiles to predict benefit of intensified alkylating chemotherapy in breast cancer." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): 11023. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.11023.

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11023 Background: DNA copy number profiles can identify patients with a defect in BRCA1. We previously showed that patients with a BRCA1-like profile benefit from intensified alkylating chemotherapy (IA, 4 cycles 5-fluorouracyl, epirubicin, cyclophosphamide + 1 cycle carboplatin, thiotepa and cyclophosphamide with autologous stem cell transplantation (ASCT)). Presumably, this is because of the defect in error free homologous recombination DNA repair. Here we present an independent study of BRCA1-like profiles to predict benefit of IA chemotherapy (2 cycles induction chemotherapy consisting of 2500 mg/m2 ifosfamide and 40 mg/m2 epirubicin, followed by 12 g/m2 ifosfamide, 900 mg/m2 carboplatin, 180 mg/m2 epirubicin with ASCT) versus adriamycin-cyclophosphamide or cyclophosphamide-methotrexate-5-fluorouracyl regimens in high risk breast cancer. Methods: We isolated tumor DNA from 117 patients of a case-control study of high risk breast cancer patients to apply a marker by treatment interaction study design to assess overall survival. We generated copy number profiles and classified them to be BRCA1-like or non-BRCA1 like. We used Fisher Exact tests to calculate correlations and performed Kaplan-Meier and Cox regression analyses to investigate whether patients with a BRCA1-like tumor benefit from IA chemotherapy compared to an AC/CMF regimen. Results: 16 of 117 (14%) patients had a BRCA1-like profile. BRCA1-like status was associated with high tumor grade (p=0.03), triple negative status (p=0.0005) and high N stage (p=0.03). When corrected for hormone receptor and HER2 status, size, positive lymph nodes, and grade we found that BRCA1 like patients had a 6-fold decreased chance of death (HR: 0.15, 95% confidence interval: 0.03-0.80, p: 0.03) compared to non-BRCA1 like patients (HR: 0.94, 95% confidence interval: 0.53-1.67, p: 0.84). The interaction test between IA chemotherapy and marker status was significant (p: 0.04). Conclusions: We provide independent validation of the previous finding that breast cancer patients with a BRCA1 like copy number profile benefit highly from intensified alkylating chemotherapy.

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Yoshimura, Ayano, Kaoru Araki-Sasaki, Noriko Toyokawa, Rho Fujiwara, Nobuo Jho, and Fumi Gomi. "Relationships between the clinical characteristics and copy numbers of DNA of cytomegalovirus determined by real-time PCR." International Ophthalmology 40, no. 9 (May 16, 2020): 2297–305. http://dx.doi.org/10.1007/s10792-020-01412-6.

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Abstract Purpose To determine whether there is a correlation between the clinicals characteristics including various types of keratic precipitates and the copy numbers of the DNA of cytomegalovirus (CMV) in eyes with CMV corneal endotheliitis. Methods We reviewed the medical charts of four cases of corneal endotheliitis that were CMV-positive. We have classified types of clinical phenomenon into four types: coin-shaped KPs, sectoral corneal edema with or without Khodadoust line-like KPs, mutton-fat KPs, and fine KPs and have graded their severity. We also determined the copy numbers of the DNA of CMV in the aqueous humor by real-time polymerase chain reaction before and during the treatment. We evaluated the correlation between the patterns of clinical characteristics and copy number of the DNA of CMV. Results There were clinical improvements in all eyes following topical ganciclovir in conjunction with low dose of topical steroid treatment, with or without oral valganciclovir. The clinical characteristics and the copy numbers of the DNA of CMV varied during the treatment period. The presence of coin-shaped KPs was correlated with high copy numbers (105–103 copies/ml) of the DNA of CMV. The copy numbers of the DNA of CMV with sectoral corneal edema with or without Khodadoust line-like KPs ranged from 104 to 102 copies/ml, and it was occasionally accompanied by high intraocular pressure. Mutton-fat KPs were observed inferiorly, sometimes together with coin-shaped KPs and sectoral corneal edema, or solely. The copy numbers in eyes with mutton-fat KPs varied and occasionally less than the cutoff level. Fine-pigmented KPs were observed after the resolution of the endotheliitis, and no DNA of CMV was detected in the aqueous humor. Conclusions Careful observations of the clinical characteristics such as the KPs and corneal edema might be helpful in estimating the amount of the DNA of CMV in eyes with corneal endotheliitis.

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27

Marzanski, Marek, Padmapriya Musunuri, and Tim Coupe. "Copying letters to patients: a study of patients' views." Psychiatric Bulletin 29, no. 2 (February 2005): 56–58. http://dx.doi.org/10.1192/pb.29.2.56.

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Aims & MethodTo investigate patients' views on receiving copies of letters sent by their healthcare professionals, 72 patients were asked about their willingness to receive a copy of the letter sent to their general practitioner and about preferences for the type of information to be included in such letters. We also asked what concerns, if any, they had about the process.ResultsThree-quarters of the respondents (n=55) said they would like to receive a copy of the letter. Patients accepted the inclusion of information about their illness but were reluctant for data about their family, work and finances to be included.Clinical ImplicationsAlthough the majority of the patients we interviewed wished to have the copy letter, many of them expressed concerns about confidentiality, the risk of distress and the cost of the process to the National Health Service. The rights of those who do not want copy letters should also be respected.

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28

Daimon, Takaaki, Masao Mitsuhiro, Susumu Katsuma, Hiroaki Abe, Kazuei Mita, and Toru Shimada. "Recent transposition of yabusame, a novel piggyBac-like transposable element in the genome of the silkworm, Bombyx mori." Genome 53, no. 8 (August 2010): 585–93. http://dx.doi.org/10.1139/g10-035.

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On the W chromosome of the silkworm, Bombyx mori , we found a novel piggyBac-like DNA transposon that potentially encodes an intact transposase (610 amino acid residues), which is flanked by 16-bp perfect inverted terminal repeats and a duplicated TTAA target site. Interestingly, we also identified another intact copy of this transposon on an autosome (chromosome 21), which showed 99.6% identity in the DNA sequence of the transposase (99.3% amino acid identity). These features raised the possibility that this novel piggyBac-like DNA transposon, designated as yabusame, may retain transposition activity. Here we report the identification and characterization of yabusame transposons from the silkworm. We cloned the full length of the yabusame transposon on the W chromosome (yabusame-W) and its autosomal copy (yabusame-1). Southern blot analysis showed that there are interstrain polymorphisms in yabusame elements for their insertion sites and copy number. We also found strong evidence for the recent transposition of yabusame elements in the silkworm genome. Although our in vitro excision assays suggested that the transposition activity of yabusame-1 and yabusame-W has been lost almost entirely, our data will lead to a greater understanding of the characteristics of piggyBac superfamily elements.

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29

Fazio, A. R. "Cosmological correlators, In–In formalism and double copy." Modern Physics Letters A 35, no. 11 (January 30, 2020): 2050076. http://dx.doi.org/10.1142/s0217732320500765.

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We are investigating if the double copy structure as product of scattering amplitudes of gauge theories applies to cosmological correlators computed, in a class of theories for inflation, by the operatorial version of the In–In formalism of Schwinger–Keldysh. We consider tree-level momentum–space correlators involving primordial gravitational waves with different polarizations and the scalar curvature fluctuations on a three-dimensional fixed spatial slice. The correlators are sum of terms factorized in a time-dependent scalar factor, which takes into account the curved background where energy is not conserved, and in a so-called tensor factor, constructed by polarization tensors. In the latter, we recognize scattering amplitudes in four-dimensional Minkowski space spanned by three points gravitational amplitudes related by double copy to those of gauge theories. Our study indicates that gravitational waves are double copy of gluons and the primordial scalar curvature is double copy of a scalar with Higgs-like interactions.

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30

Hartert, Keenan, Saber Tadros, Alyssa Bouska, Dalia Moore, Christine Pak, Tayla Heavican, Chih Long Liu, et al. "DNA Copy Number Gains of TCF4 (E2-2) Are Associated with Poor Outcome in Diffuse Large B-Cell Lymphoma." Blood 128, no. 22 (December 2, 2016): 2686. http://dx.doi.org/10.1182/blood.v128.22.2686.2686.

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Abstract The development of B-cells is a complex process that proceeds through multiple stages and is regulated by a hierarchy of transcription factors and other physiologic signals. Each unique B-cell malignancy can be aligned with a 'normal counterpart' at one or more of these discrete developmental stages. However, with the exception of translocations of transcription factor genes, the genetic basis for this is not well defined. We performed an analysis of high-resolution single nucleotide polymorphism (SNP) microarrays from 694 diffuse large B-cell (DLBCL) tumors to identify significant somatic copy number alterations (SCNA). Through integrative analysis of 249 tumors with matched gene expression profiling (GEP) data, we identified the likely targets of these alterations and found that genes that were targeted by DNA copy number gain were significantly enriched for DNA binding activity and transcription factor function. We extended upon this observation by analyzing SNP microarray data of a further 2,716 tumors from 7 additional subtypes of B-cell malignancy. Through this analysis, we identified patterns of transcription factor alterations that aligned with the differentiation state of the 'normal B-cell counterpart' of each malignancy. This provides evidence that SCNA of B-cell transcription factors may underlie the differentiation state of B-cell malignancies. DLBCL can be divided into two subtypes based upon gene expression profiles that align with either the germinal center B-cell differentiation state (GCB-like) or a post-GCB activated B-cell state (ABC-like). Having observed an enrichment for transcription factor SCNAs in DLBCL, and an alignment between transcription factor alterations and differentiation states in other B-cell malignancies, we hypothesized that SCNAs of transcription factors may also underlie the etiology of these molecular subtypes. By testing for associations between SCNAs and cell of origin subtype, we identified three co-segregating DNA copy number gains that were significantly enriched in the ABC-like subtype. These included gains of the BCL6 and SPIB genes that have been previously observed to be associated with the ABC-like subtype. In addition, we found gains of the TCF4 (E2-2) gene to be significantly enriched in ABC-like tumors. In line with this, TCF4 alterations were significantly associated with reduced overall survival in cohorts of patients treated with either CHOP (n=232, P=0.009) or R-CHOP (n=197, P=0.041). B-cell receptor (BCR) signaling is a key survival pathway in ABC-like DLBCL, and the TCF4 gene has a defined role in promoting the expression of immunoglobulin (Ig) genes that encode the B-cell receptor (BCR). The analysis of paired SCNA and GEP data revealed a significantly higher expression of Ig genes in tumors with TCF4 DNA copy number gain compared to those without, suggesting that normal BCR expression may be deregulated by this genetic alteration. In addition, chromatin-immunoprecipitation sequencing (ChIP-seq) for TCF4 in ABC-like DLBCL cell lines also revealed binding of TCF4 to an Ig gene enhancer region. As BCR signaling can be altered by somatic mutations in the CARD11, CD79B and MYD88 genes, we evaluated the relative representation of these mutations and TCF4 DNA copy number gains using targeted deep sequencing of 124 DLBCL tumors. This revealed that TCF4 DNA copy number gains largely mutually excluded CARD11 mutations, but significantly co-segregated with both MYD88 (FDR=0.005) and CD79B (FDR=0.053) mutations. In addition, we observed significant co-segregation between CD79B and MYD88 mutations (FDR<0.001). This is particularly notable due to the preliminary associations between combined CD79B and MYD88 mutation status and response to an inhibitor of BCR signaling, Ibrutinib. Together these data highlight an association between SCNA of B-cell transcription factors and the differentiation state of the 'normal counterpart' of the respective malignant B-cell. In line with this, we show that DNA copy number gains of the TCF4 transcription factor are associated with the ABC-like subtype of DLBCL, significantly worse overall survival, and increased Ig expression. These characteristics, in addition to the co-association between TCF4 DNA copy number gains and somatic mutations of CD79B and MYD88, suggest that TCF4 may be an important modifier of BCR signaling and contribute to the etiology of ABC-like DLBCL. Disclosures Rosenquist: Gilead Sciences: Speakers Bureau. Lunning:TG Therapeutics: Consultancy; AbbVie: Consultancy; Gilead: Consultancy; Bristol-Myer-Squibb: Consultancy; Juno: Consultancy; Genentech: Consultancy; Spectrum: Consultancy; Celgene: Consultancy; Pharmacyclics: Consultancy. Rodig:Bristol-Myers Squibb: Honoraria, Research Funding; Perkin Elmer: Membership on an entity's Board of Directors or advisory committees. Levy:Kite Pharma: Consultancy; Five Prime Therapeutics: Consultancy; Innate Pharma: Consultancy; Beigene: Consultancy; Corvus: Consultancy; Dynavax: Research Funding; Pharmacyclics: Research Funding.

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31

Tanguay, Philippe, and Colette Breuil. "Transforming the sapstaining fungus Ophiostoma piceae with Agrobacterium tumefaciens." Canadian Journal of Microbiology 49, no. 4 (March 1, 2003): 301–4. http://dx.doi.org/10.1139/w03-036.

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A transformation protocol mediated by Agrobacterium tumefaciens is described for the sapstaining fungus Ophiostoma piceae. We compared transformants obtained from Agrobacterium with those obtained from yeast-like cells made into spheroplasts and treated with CaCl2. For all putative transformants analyzed, Southern hybridization confirmed that the hygromycin resistance gene had been integrated into the genomic DNA. While all transformants obtained from the treated spheroplasts had multiple copy vector insertion, 85% of the Agrobacterium-mediated transformants had single copy vector insertion.Key words: Ophiostoma piceae, genetic transformation, Ti plasmid.

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32

Taylor, Sean D., Hong Zhang, Jana S. Eaton, Matthew S. Rodeheffer, Maria A. Lebedeva, Thomas W. O'Rourke, Wolfram Siede, and Gerald S. Shadel. "The Conserved Mec1/Rad53 Nuclear Checkpoint Pathway Regulates Mitochondrial DNA Copy Number in Saccharomyces cerevisiae." Molecular Biology of the Cell 16, no. 6 (June 2005): 3010–18. http://dx.doi.org/10.1091/mbc.e05-01-0053.

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How mitochondrial DNA (mtDNA) copy number is determined and modulated according to cellular demands is largely unknown. Our previous investigations of the related DNA helicases Pif1p and Rrm3p uncovered a role for these factors and the conserved Mec1/Rad53 nuclear checkpoint pathway in mtDNA mutagenesis and stability in Saccharomyces cerevisiae. Here, we demonstrate another novel function of this pathway in the regulation of mtDNA copy number. Deletion of RRM3 or SML1, or overexpression of RNR1, which recapitulates Mec1/Rad53 pathway activation, resulted in an approximately twofold increase in mtDNA content relative to the corresponding wild-type yeast strains. In addition, deletion of RRM3 or SML1 fully rescued the ∼50% depletion of mtDNA observed in a pif1 null strain. Furthermore, deletion of SML1 was shown to be epistatic to both a rad53 and an rrm3 null mutation, placing these three genes in the same genetic pathway of mtDNA copy number regulation. Finally, increased mtDNA copy number via the Mec1/Rad53 pathway could occur independently of Abf2p, an mtDNA-binding protein that, like its metazoan homologues, is implicated in mtDNA copy number control. Together, these results indicate that signaling through the Mec1/Rad53 pathway increases mtDNA copy number by altering deoxyribonucleoside triphosphate pools through the activity of ribonucleotide reductase. This comprises the first linkage of a conserved signaling pathway to the regulation of mitochondrial genome copy number and suggests that homologous pathways in humans may likewise regulate mtDNA content under physiological conditions.

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Schouten, Philip C., Ewald van Dyk, Linde M. Braaf, Lennart Mulder, Esther H. Lips, Jorma J. de Ronde, Laura Holtman, et al. "Platform comparisons for identification of breast cancers with a BRCA-like copy number profile." Breast Cancer Research and Treatment 139, no. 2 (May 14, 2013): 317–27. http://dx.doi.org/10.1007/s10549-013-2558-2.

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34

Dmowski, Michał, Izabela Sitkiewicz та Piotr Cegłowski. "Characterization of a Novel Partition System Encoded by the δ and ω Genes from the Streptococcal Plasmid pSM19035". Journal of Bacteriology 188, № 12 (15 червня 2006): 4362–72. http://dx.doi.org/10.1128/jb.01922-05.

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ABSTRACT High segregational stability of the streptococcal plasmid pSM19035 is achieved by the concerted action of systems involved in plasmid copy number control, multimer resolution, and postsegregational killing. In this study, we demonstrate the role of two genes, δ and ω, in plasmid stabilization by a partition mechanism. We show that these two genes can stabilize the native pSM19035 replicon as well as other θ- and σ-type plasmids in Bacillus subtilis. In contrast to other known partition systems, in this case the two genes are transcribed separately; however, they are coregulated by the product of the parB-like gene ω. Analysis of mutants of the parA-like gene δ showed that the Walker A ATPase motif is necessary for plasmid stabilization. The ParB-like product of the ω gene binds to three regions containing repeated WATCACW heptamers, localized in the copS (regulation of plasmid copy number), δ, and ω promoter regions. We demonstrate that all three of these regions can cause partition-mediated incompatibility. Moreover, our data suggest that each of these could play the role of a centromere-like sequence. We conclude that δ and ω constitute a novel type of plasmid stabilization system.

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35

Mittapalli, O., R. H. Shukle, and I. L. Wise. "Identification of mariner-like elements in Sitodiplosis mosellana (Diptera: Cecidomyiidae)." Canadian Entomologist 138, no. 2 (April 2006): 138–46. http://dx.doi.org/10.4039/n05-007.

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AbstractMariner-like element sequences were recovered from the genome of the orange wheat midge, Sitodiplosis mosellana (Géhin), with degenerate PCR primers designed to conserved regions of mariner transposases. The deduced amino acid sequences of the mariner-like transposases from S. mosellana showed 67% to 78% identity with the peptide sequences of other mariner transposases. A phylogenetic analysis revealed that the mariner-like elements from S. mosellana grouped in the mauritiana subfamily of mariner transposons. Results from Southern blot analysis suggest mariner-like elements are at a moderate copy number in the genome of S. mosellana.

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Porokhovnik, Lev N., Natalia N. Veiko, Elizaveta S. Ershova, and Svetlana V. Kostyuk. "The Role of Human Satellite III (1q12) Copy Number Variation in the Adaptive Response during Aging, Stress, and Pathology: A Pendulum Model." Genes 12, no. 10 (September 28, 2021): 1524. http://dx.doi.org/10.3390/genes12101524.

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The pericentric satellite III (SatIII or Sat3) and II tandem repeats recently appeared to be transcribed under stress conditions, and the transcripts were shown to play an essential role in the universal stress response. In this paper, we review the role of human-specific SatIII copy number variation (CNV) in normal stress response, aging and pathology, with a focus on 1q12 loci. We postulate a close link between transcription of SatII/III repeats and their CNV. The accrued body of data suggests a hypothetical universal mechanism, which provides for SatIII copy gain during the stress response, alongside with another, more hypothetical reverse mechanism that might reduce the mean SatIII copy number, likely via the selection of cells with excessively large 1q12 loci. Both mechanisms, working alternatively like swings of the pendulum, may ensure the balance of SatIII copy numbers and optimum stress resistance. This model is verified on the most recent data on SatIII CNV in pathology and therapy, aging, senescence and response to genotoxic stress in vitro.

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Wajnberg, Gabriel, Benilton S. Carvalho, Carlos G. Ferreira, and Fabio Passetti. "Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/902419.

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Copy number variation is a class of structural genomic modifications that includes the gain and loss of a specific genomic region, which may include an entire gene. Many studies have used low-resolution techniques to identify regions that are frequently lost or amplified in cancer. Usually, researchers choose to use proprietary or non-open-source software to detect these regions because the graphical interface tends to be easier to use. In this study, we combined two different open-source packages into an innovative strategy to identify novel copy number variations and pathways associated with cancer. We used a mesothelioma and ependymoma published datasets to assess our tool. We detected previously described and novel copy number variations that are associated with cancer chemotherapy resistance. We also identified altered pathways associated with these diseases, like cell adhesion in patients with mesothelioma and negative regulation of glutamatergic synaptic transmission in ependymoma patients. In conclusion, we present a novel strategy using open-source software to identify copy number variations and altered pathways associated with cancer.

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Jain, Neeraj, Keenan Hartert, Saber Tadros, Warren Fiskus, Ondrej Havranek, Man Chun John Ma, Alyssa Bouska, et al. "Targetable genetic alterations of TCF4 (E2-2) drive immunoglobulin expression in diffuse large B cell lymphoma." Science Translational Medicine 11, no. 497 (June 19, 2019): eaav5599. http://dx.doi.org/10.1126/scitranslmed.aav5599.

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The activated B cell (ABC-like) subtype of diffuse large B cell lymphoma (DLBCL) is characterized by chronic activation of signaling initiated by immunoglobulin μ (IgM). By analyzing the DNA copy number profiles of 1000 DLBCL tumors, we identified gains of 18q21.2 as the most frequent genetic alteration in ABC-like DLBCL. Using integrative analysis of matched gene expression profiling data, we found that the TCF4 (E2-2) transcription factor gene was the target of these alterations. Overexpression of TCF4 in ABC-like DLBCL cell lines led to its occupancy on immunoglobulin (IGHM) and MYC gene enhancers and increased expression of these genes at the transcript and protein levels. Inhibition of TCF4 activity with dominant-negative constructs was synthetically lethal to ABC-like DLBCL cell lines harboring TCF4 DNA copy gains, highlighting these gains as an attractive potential therapeutic target. Furthermore, the TCF4 gene was one of the top BRD4-regulated genes in DLBCL cell lines. BET proteolysis-targeting chimera (PROTAC) ARV771 extinguished TCF4, MYC, and IgM expression and killed ABC-like DLBCL cells in vitro. In DLBCL xenograft models, ARV771 treatment reduced tumor growth and prolonged survival. This work highlights a genetic mechanism for promoting immunoglobulin signaling in ABC-like DLBCL and provides a functional rationale for the use of BET inhibitors in this disease.

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Choi, Hayoung, Hongseok Yoo, Jin Young Lee, Junseon Park, and Kyeongman Jeon. "Plasma Mitochondrial DNA and Necroptosis as Prognostic Indicators in Critically Ill Patients with Sepsis." Biomedicines 10, no. 10 (September 25, 2022): 2386. http://dx.doi.org/10.3390/biomedicines10102386.

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Mitochondrial DNA (mtDNA) has been identified as a biomarker for predicting sepsis mortality. Although preclinical studies suggested that necroptosis could explain the mechanistic link of mtDNA in sepsis, this is not yet evident in patients with sepsis. This study evaluated the association between mtDNA and essential necroptosis mediators in prospectively enrolled patients with sepsis. Plasma mtDNA copy number was measured using quantitative PCR assay and necroptosis mediators, including receptor-interacting protein kinase-3 (RIPK3), mixed lineage domain-like pseudokinase (MLKL), and high-mobility group box 1 (HMGB1), were measured by ELISA. Receiver operating characteristic (ROC) analysis was conducted to evaluate the predictive ability of mtDNA copy number as a predictor of hospital mortality. Among the 142 patients with sepsis, the mtDNA copy number was significantly higher in non-survivors than in survivors (median, 4040 copies/µL vs. 2585 copies/µL; p < 0.001), and the area under the ROC curve was 0.73 (95% CI, 0.64–0.82) for the relationship between mtDNA and hospital mortality. Furthermore, the correlation between mtDNA copy number and each necroptosis mediator was excellent (p < 0.001 for all): RIPK3 (r = 0.803), MLKL (r = 0.897), and HMGB1 (r = 0.603). The plasma mtDNA copy number was highly correlated with essential necroptosis mediators, suggesting that mtDNA propagates necroptosis and increases sepsis mortality.

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Raze, Dominique, Olivier Dardenne, Séverine Hallut, Manuel Martinez-Bueno, Jacques Coyette, and Jean-Marie Ghuysen. "The Gene Encoding the Low-Affinity Penicillin-Binding Protein 3r in Enterococcus hirae S185R Is Borne on a Plasmid Carrying Other Antibiotic Resistance Determinants." Antimicrobial Agents and Chemotherapy 42, no. 3 (March 1, 1998): 534–39. http://dx.doi.org/10.1128/aac.42.3.534.

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ABSTRACT Two plasmid-derived NcoI DNA fragments of 14 and 4.5 kb, respectively, have been isolated from the multidrug-resistant strain Enterococcus hirae S185R and analyzed. The 14-kb fragment contains two inverted (L and R) IS1216 insertion modules of the ISS1 family. These modules define a Tn5466 transposon-like structure that contains one copy of the methylase-encoding ermAMconferring erythromycin resistance and one copy of the adenylyl-transferase-encoding aadE conferring streptomycin resistance. Immediately on the left side of IS1216L there occurs a copy of pbp3r encoding the low-affinity penicillin-binding protein (PBP) PBP3r, itself preceded by apsr-like gene (psr3r) that controls the synthesis of PBP3r. ermAM, aadE, and the transposase gene (tnp) of IS1216R have the same polarities, and these are opposite those of psr3r,pbp3r, and the tnp gene of IS1216L. The 4.5-kb fragment is a copy of the 4.5-kb sequence at the 5′ end of the 14-kb fragment, although it is not a restriction product of the 14-kb fragment. It contains three genes with the same polarity:psr3r, pbp3r, and tnp in an IS1216 element. Because of the very high degree of identity (99%) with the chromosomal psrfm and pbp5fmgenes of Enterococcus faecium D63R, it is proposed that both the psr3r and pbp3r genes were transferred from an E. faecium strain and inserted in a plasmid ofE. hirae. E. hirae is the first known bacterial species in which a low-affinity PBP-encoding gene has been found to be plasmid borne.

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Downey, Rodney G., Bart Kastermans, and Steffen Lempp. "On computable self-embeddings of computable linear orderings." Journal of Symbolic Logic 74, no. 4 (December 2009): 1352–66. http://dx.doi.org/10.2178/jsl/1254748695.

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AbstractWe solve a longstanding question of Rosenstein, and make progress toward solving a long-standing open problem in the area of computable linear orderings by showing that every computable η-like linear ordering without an infinite strongly η-like interval has a computable copy without nontrivial computable self-embedding.The precise characterization of those computable linear orderings which have computable copies without nontrivial computable self-embedding remains open.

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Cullen, R., G. A. Fairburn, and K. F. D. Hughey. "COPY: A new technique for evaluation of biodiversity protection projects." Pacific Conservation Biology 5, no. 2 (1999): 115. http://dx.doi.org/10.1071/pc990115.

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New Zealand, like many other countries, is troubled by introduced animal and plant species which attack, damage, or displace indigenous species. Considerable amounts of taxpayer funds are spent each year attempting to combat these invasive species and some research has been conducted into the "cost effectiveness" and the efficiency of various conservation activities. Research into the cost effectiveness of biodiversity protection projects is hindered by the absence of satisfactory measures of output. A new output measure, Conservation Output Protection Years (COPY) is proposed for use in a cost utility evaluation of biodiversity protection projects. This paper outlines this approach and reports on the use of COPY in evaluation of six New Zealand biodiversity protection projects. The paper demonstrates that COPY provides a practical output measure, and reports on the comparative output per dollar spent on each biodiversity protection project.

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Johnston, M. J. G., P. McVeigh, S. McMaster, C. C. Fleming, and A. G. Maule. "FMRFamide-like peptides in root knot nematodes and their potential role in nematode physiology." Journal of Helminthology 84, no. 3 (October 21, 2009): 253–65. http://dx.doi.org/10.1017/s0022149x09990630.

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AbstractFMRFamide-like peptides (FLPs) are a diverse group of neuropeptides that are expressed abundantly in nematodes. They exert potent physiological effects on locomotory, feeding and reproductive musculature and also act as neuromodulators. However, little is known about the specific expression patterns and functions of individual peptides. The current study employed rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR) to characterizeflpgenes from infective juveniles of the root knot nematodes,Meloidogyne incognitaandMeloidogyne minor. The peptides identified from these transcripts are sequelogs of FLPs from the free-living nematode,Caenorhabditis elegans; the genes have therefore been designated asMi-flp-1,Mi-flp-7,Mi-flp-12,Mm-flp-12andMi-flp-14.Mi-flp-1encodes five FLPs with the common C-terminal moiety, NFLRFamide.Mi-flp-7encodes two copies of APLDRSALVRFamide and APLDRAAMVRFamide and one copy of APFDRSSMVRFamide.Mi-flp-12andMm-flp-12encode the novel peptide KNNKFEFIRFamide (a longer version of RNKFEFIRFamide found inC. elegans).Mi-flp-14encodes a single copy of KHEYLRFamide (commonly known as AF2 and regarded as the most abundant nematode FLP), and a single copy of the novel peptide KHEFVRFamide. These FLPs share a high degree of conservation betweenMeloidogynespecies and nematodes from other clades, including those of humans and animals, perhaps suggesting a common neurophysiological role which may be exploited by novel drugs. FLP immunoreactivity was observed for the first time inMeloidogyne, in the circumpharyngeal nerve ring, pharyngeal nerves and ventral nerve cord. Additionally,in situhybridization revealedMi-flp-12expression in an RIR-like neuron andMi-flp-14expression in SMB-like neurons‡, respectively. These localizations imply physiological roles for FLP-12 and FLP-14 peptides, including locomotion and sensory perception.

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Dobson, Melanie J., Andrew J. Pickett, Soundarapandian Velmurugan, Jordan B. Pinder, Lori A. Barrett, Makkuni Jayaram та Joyce S. K. Chew. "The 2μm Plasmid Causes Cell Death in Saccharomyces cerevisiae with a Mutation in Ulp1 Protease". Molecular and Cellular Biology 25, № 10 (15 травня 2005): 4299–310. http://dx.doi.org/10.1128/mcb.25.10.4299-4310.2005.

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ABSTRACT The 2μm circle plasmid confers no phenotype in wild-type Saccharomyces cerevisiae but in a nib1 mutant, an elevated plasmid copy number is associated with cell death. Complementation was used to identify nib1 as a mutant allele of the ULP1 gene that encodes a protease required for removal of a ubiquitin-like protein, Smt3/SUMO, from protein substrates. The nib1 mutation replaces conserved tryptophan 490 with leucine in the protease domain of Ulp1. Complete deletion of ULP1 is lethal, even in a strain that lacks the 2μm circle. Partial deletion of ULP1, like the nib1 mutation, results in clonal variations in plasmid copy number. In addition, a subset of these mutant cells produces lineages in which all cells have reduced proliferative capacity, and this phenotype is dependent upon the presence of the 2μm circle. Segregation of the 2μm circle requires two plasmid-encoded proteins, Rep1 and Rep2, which were found to colocalize with Ulp1 protein in the nucleus and interact with Smt3 in a two-hybrid assay. These associations and the observation of missegregation of a fluorescently tagged 2μm circle reporter plasmid in a subset of ulp1 mutant cells suggest that Smt3 modification plays a role in both plasmid copy number control and segregation.

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45

Banaszkiewicz, Sylwia, Ewa Wałecka-Zacharska, Justyna Schubert, Aleksandra Tabiś, Jarosław Król, Tadeusz Stefaniak, Ewelina Węsierska, and Jacek Bania. "Staphylococcal Enterotoxin Genes in Coagulase-Negative Staphylococci—Stability, Expression, and Genomic Context." International Journal of Molecular Sciences 23, no. 5 (February 25, 2022): 2560. http://dx.doi.org/10.3390/ijms23052560.

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In the current study, we screened a collection of coagulase-negative staphylococci (CoNS) isolates for orthologues of staphylococcal enterotoxins (SEs) involved in S. aureus-related staphylococcal food poisoning (SFP). The amplicons corresponding to SEs were detected in S. chromogenes, S. epidermidis, S. haemolyticus, S. borealis, S. pasteuri, S. saprophyticus, S. vitulinus, S. warneri, and S. xylosus. All amplicons were sequenced and identified as parts of known S. aureus or S. epidermidis SE genes. Quantitative real-time PCR allowed determining the relative copy number of each SE amplicon. A significant portion of the amplicons of the sea, seb, sec, and seh genes occurred at low copy numbers. Only the amplicons of the sec gene identified in three isolates of S. epidermidis displayed relative copy numbers comparable to sec in the reference enterotoxigenic S. aureus and S. epidermidis strains. Consecutive passages in microbiological media of selected CoNS isolates carrying low copy numbers of sea, seb, sec, and seh genes resulted in a decrease of gene copy number. S. epidermidis isolates harbored a high copy number of sec, which remained stable over the passages. We demonstrated that enterotoxin genes may occur at highly variable copy numbers in CoNS. However, we could identify enterotoxin genes only in whole-genome sequences of CoNS carrying them in a stable form at high copy numbers. Only those enterotoxins were expressed at the protein level. Our results indicate that PCR-based detection of enterotoxin genes in CoNS should always require an additional control, like analysis of their presence in the bacterial genome. We also demonstrate S. epidermidis as a CoNS species harboring SE genes in a stable form at a specific chromosome site and expressing them as a protein.

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Cozen, Wendy, Amie Hwang, Vickie Marshall, Thomas M. Mack, and Denise Whitby. "EBV Copy Number Variation in Twins Discordant for Young Adult Hodgkin Lymphoma." Blood 118, no. 21 (November 18, 2011): 2631. http://dx.doi.org/10.1182/blood.v118.21.2631.2631.

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Abstract Abstract 2631 Background: Epstein-Barr Virus (EBV) is a risk factor for some types of Hodgkin lymphoma (HL). Host response to the virus may play a role in pathogenesis and is in part determined by genetic factors. Therefore, using only traditional unrelated controls may not be appropriate. Methods: We compared EBV DNA copy number in peripheral blood mononuclear cells (PBMCs) collected from 63 young adult HL patients in remission and their unaffected co-twins, and 43 spouse controls. Viral load was measured with TaqMan quantitative PCR assays, tested in triplicate and reported as viral copies per million cells. Samples positive in all 3 replicates were classified as positive, and those positive in 1–2 samples were classified as qualitative positive (QP). EBV copy number was log-transformed for some analyses. A binomial proportion test was used to compare EBV copy number in cases and their unaffected co-twins (n=50 like-sex pairs). Conditional (case vs. unaffected co-twin) and unconditional logistic regression (case and unaffected co-twin vs. spouse controls) were used to estimate the effect of EBV copy number on risk as a categorical (positive, QP, or negative) or continuous variable (SAS 9.1). Unconditional logistic regression analyses were adjusted for sex and age. Results: 26% of case, 18% of unaffected co-twins and 9% of spouse controls had positive EBV copy number measurements. Like-sex young adult HL cases had higher EBV copy numbers compared to their unaffected co-twins (P = 0.04). When EBV copy number was considered as a categorical variable, both cases and monozygotic unaffected co-twins were more likely to be positive compared to controls (cases v. controls: Odds Ratio [OR] = 3.2, 95% confidence intervals [CI] = 0.9, 11.1; unaffected co-twins v. controls: OR= 3.6, 95% CI= 0.9, 14.6). However, there was little difference between dizygotic unaffected co-twins and controls (OR= 0.7, 95% CI = 0.5, 5.5). Conclusions: That young adult HL cases had higher EBV DNA copies than their unaffected co-twins implies that an acquired pre-disease factor or disease affect altered the host response to EBV. However, that both cases and unaffected co-twins had higher EBV DNA copies compared to controls suggests that there is also a heritable component to the host response to EBV. HL cases > co-twins (acquired or disease effect) HL cases and co-twins > controls (heritable effect) Disclosures: No relevant conflicts of interest to declare.

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47

Bora, Gamze, Şulenur Subaşı-Yıldız, Ayşe Yeşbek-Kaymaz, Numan Bulut, İpek Alemdaroğlu, Öznur Tunca-Yılmaz, Haluk Topaloğlu, Aynur Ayşe Karaduman, and Hayat Erdem-Yurter. "Effects of Arm Cycling Exercise in Spinal Muscular Atrophy Type II Patients: A Pilot Study." Journal of Child Neurology 33, no. 3 (January 12, 2018): 209–15. http://dx.doi.org/10.1177/0883073817750500.

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Exercise studies in neuromuscular diseases like spinal muscular atrophy (SMA), a devastating disease caused by survival of motor neuron 1 ( SMN1) gene mutations, are drawing attention due to its beneficial effects. In this study, we presented a constructed arm cycling exercise protocol and evaluated the benefits on SMA patients. Five SMA type II patients performed 12 weeks of supervised arm cycling exercise. The physical functions were evaluated together with the SMN2 copy numbers, SMN protein levels, insulin-like growth factor 1(IGF1) and binding protein 3 (IGFBP3) levels. The active cycling distance and duration of patients significantly improved. Significant changes could not have detected either SMN or IGF1 and IGFBP3 levels in response to exercise. The findings demonstrated that the patients tolerated the exercise protocol and gained a benefit from arm cycling but benefits could not be associated with SMN2 copy number, SMN protein level, IGF1, or IGFBP3 levels.

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Blevins, Juliette, and Ander Egurtzegi. "Unexpected obstruent loss in initial obstruent–sonorant clusters: an apparent example from Basque." Phonology 34, no. 3 (December 2017): 507–22. http://dx.doi.org/10.1017/s0952675717000264.

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The apparent loss of initial obstruents in Basque borrowings from Romance (e.g.laru≪ Lat.claru) is striking. While Proto-Basque is generally reconstructed as lacking initial clusters, the expected repair in loans, based on typology, phonology and phonetics, is copy-vowel epenthesis, not obstruent loss. Indeed, there is evidence for a vowel-copy process in Basque in other loans with obstruent–sonorant clusters (e.g.gurutze≪ Lat.cruce). We suggest that initial obstruent loss before /l/ but not /r/ is related to Romance developments. In the Romance varieties in contact with Basque, /fl pl bl kl gl/ all show evidence of neutralisation to /ʎ/ word-initially. We hypothesise that obstruent loss in words like Basquelarureflects influence from local Romance languages at a time when Basque lacked /ʎ/. In contrast, vowel copy conforming to Basque syllable structure was the norm in Romance loanwords with clusters not affected by this process.

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49

Saab, Jad, Ian M. Rosenthal, Lu Wang, Klaus J. Busam, Kishwer S. Nehal, Mark A. Dickson, Meera R. Hameed, and Travis J. Hollmann. "Dermatofibrosarcoma Protuberans-Like Tumor With COL1A1 Copy Number Gain in the Absence of t(17;22)." American Journal of Dermatopathology 39, no. 4 (April 2017): 304–9. http://dx.doi.org/10.1097/dad.0000000000000746.

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50

Rep, Martijn, H. Charlotte van der Does, and Ben J. C. Cornelissen. "Drifter, a novel, low copy hAT-like transposon in Fusarium oxysporum is activated during starvation." Fungal Genetics and Biology 42, no. 6 (June 2005): 546–53. http://dx.doi.org/10.1016/j.fgb.2005.03.007.

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