Journal articles: 'Shadow protein'

1

Wang, Siqi, Hui Zhao, and Yaping Zhang. "Advances in research on Shadoo, shadow of prion protein." Chinese Science Bulletin 59, no. 9 (January 28, 2014): 821–27. http://dx.doi.org/10.1007/s11434-014-0129-5.

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Kaller, Markus, Balint Földesi, and Wolfgang Nellen. "Localization and organization of protein factors involved in chromosome inheritance in Dictyostelium discoideum." Biological Chemistry 388, no. 4 (April 1, 2007): 355–65. http://dx.doi.org/10.1515/bc.2007.047.

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Abstract Heterochromatin protein 1 (HP1) proteins are highly conserved heterochromatin components required for genomic integrity. We have previously shown that the two HP1 isoforms expressed in Dictyostelium, HcpA and HcpB, are mainly localized to (peri-)centromeric heterochromatin and have largely overlapping functions. However, they cause distinct phenotypes when overexpressed. We show here that these isoforms display quantitative differences in dimerization behavior. Dimerization preference, as well as the mutant phenotype in overexpression strains, depends on the C-terminus containing the hinge and chromo shadow domains. Both Hcp proteins are targeted to distinct subnuclear regions by different chromo shadow domain-dependent and -independent mechanisms. In addition, both proteins bind to DNA and RNA in vitro and binding is independent of the chromo shadow domain. Thus, this DNA and/or RNA binding activity may contribute to protein targeting. To further characterize heterochromatin, we cloned the Dictyostelium homolog of the origin recognition complex subunit 2 (OrcB). OrcB localizes to distinct subnuclear foci that were also targeted by HcpA. In addition, it is associated with the centrosome throughout the cell cycle. The results indicate that, similar to Orc2 homologs from other organisms, it is required for different processes in chromosome inheritance.

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Smothers, James F., and Steven Henikoff. "The Hinge and Chromo Shadow Domain Impart Distinct Targeting of HP1-Like Proteins." Molecular and Cellular Biology 21, no. 7 (April 1, 2001): 2555–69. http://dx.doi.org/10.1128/mcb.21.7.2555-2569.2001.

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ABSTRACT Drosophila heterochromatin-associated protein 1 (HP1) is an abundant component of heterochromatin, a highly condensed compartment of the nucleus that comprises a major fraction of complex genomes. Some organisms have been shown to harbor multiple HP1-like proteins, each exhibiting spatially distinct localization patterns within interphase nuclei. We have characterized the subnuclear localization patterns of two newly discovered DrosophilaHP1-like proteins (HP1b and HP1c), comparing them with that of the originally described fly HP1 protein (here designated HP1a). While HP1a targets heterochromatin, HP1b localizes to both heterochromatin and euchromatin and HP1c is restricted exclusively to euchromatin. All HP1-like proteins contain an amino-terminal chromo domain, a connecting hinge, and a carboxyl-terminal chromo shadow domain. We expressed truncated and chimeric HP1 proteins in vivo to determine which of these segments might be responsible for heterochromatin-specific and euchromatin-specific localization. Both the HP1a hinge and chromo shadow domain independently target heterochromatin, while the HP1c chromo shadow domain is implicated solely in euchromatin localization. Comparative sequence analyses of HP1 homologs reveal a conserved sequence block within the hinge that contains an invariant sequence (KRK) and a nuclear localization motif. This block is not conserved in the HP1c hinge, possibly accounting for its failure to function as an independent targeting segment. We conclude that sequence variations within the hinge and shadow account for HP1 targeting distinctions. We propose that these targeting features allow different HP1 complexes to be distinctly sequestered in organisms that harbor multiple HP1-like proteins.

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4

Service, R. F. "BIOCHEMISTRY: Protein Arrays Step Out of DNA's Shadow." Science 289, no. 5485 (September 8, 2000): 1673. http://dx.doi.org/10.1126/science.289.5485.1673.

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Sánchez-Salguero, C. A. "Food Protein-Induced Proctocolitis. The shadow of allergic disorders." Allergologia et Immunopathologia 46, no. 1 (January 2018): 1–2. http://dx.doi.org/10.1016/j.aller.2017.10.002.

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Kingston-Smith, Alison H., Joan E. Edwards, Sharon A. Huws, Eun J. Kim, and Michael Abberton. "Plant-based strategies towards minimising ‘livestock's long shadow’." Proceedings of the Nutrition Society 69, no. 4 (August 4, 2010): 613–20. http://dx.doi.org/10.1017/s0029665110001953.

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Ruminant farming is an important component of the human food chain. Ruminants can use offtake from land unsuitable for cereal crop cultivation via interaction with the diverse microbial population in their rumens. The rumen is a continuous flow fermenter for the digestion of ligno-cellulose, with microbial protein and fermentation end-products incorporated by the animal directly or during post-ruminal digestion. However, ruminal fermentation is inefficient in capturing the nutrient resource presented, resulting in environmental pollution and generation of greenhouse gases. Methane is generated as a consequence of ruminal fermentation and poor retention of ingested forage nitrogen causes nitrogenous pollution of water and land and contributes to the generation of nitrous oxide. One possible cause is the imbalanced provision of dietary substrates to the rumen micro-organisms. Deamination of amino acids by ammonia-producing bacteria liberates ammonia which can be assimilated by the rumen bacteria and used for microbial protein synthesis. However, when carbohydrate is limiting, microbial growth is slow, meaning low demand for ammonia for microbial protein synthesis and excretion of the excess. Protein utilisation can therefore be improved by increasing the availability of readily fermentable sugars in forage or by making protein unavailable for proteolysis through complexing with plant secondary products. Alternatively, realisation that grazing cattle ingest living cells has led to the discovery that plant cells undergo endogenous, stress-mediated protein degradation due to the exposure to rumen conditions. This presents the opportunity to decrease the environmental impact of livestock farming by using decreased proteolysis as a selection tool for the development of improved pasture grass varieties.

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7

Devitt, Elizabeth. "Sun sets on protein initiative, casting shadow over drug discovery." Nature Medicine 19, no. 11 (November 2013): 1352. http://dx.doi.org/10.1038/nm1113-1352.

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8

Luijsterburg, Martijn S., Christoffel Dinant, Hannes Lans, Jan Stap, Elzbieta Wiernasz, Saskia Lagerwerf, Daniël O. Warmerdam, et al. "Heterochromatin protein 1 is recruited to various types of DNA damage." Journal of Cell Biology 185, no. 4 (May 18, 2009): 577–86. http://dx.doi.org/10.1083/jcb.200810035.

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Heterochromatin protein 1 (HP1) family members are chromatin-associated proteins involved in transcription, replication, and chromatin organization. We show that HP1 isoforms HP1-α, HP1-β, and HP1-γ are recruited to ultraviolet (UV)-induced DNA damage and double-strand breaks (DSBs) in human cells. This response to DNA damage requires the chromo shadow domain of HP1 and is independent of H3K9 trimethylation and proteins that detect UV damage and DSBs. Loss of HP1 results in high sensitivity to UV light and ionizing radiation in the nematode Caenorhabditis elegans, indicating that HP1 proteins are essential components of DNA damage response (DDR) systems. Analysis of single and double HP1 mutants in nematodes suggests that HP1 homologues have both unique and overlapping functions in the DDR. Our results show that HP1 proteins are important for DNA repair and may function to reorganize chromatin in response to damage.

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9

Kaye, Frederic J. "The Retinoblastoma-Like Protein Family: Still in the Shadow of the RB Gene?" JNCI: Journal of the National Cancer Institute 90, no. 19 (October 7, 1998): 1418–19. http://dx.doi.org/10.1093/jnci/90.19.1418.

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10

Anderson, M. S. "Projection of an Immunological Self Shadow Within the Thymus by the Aire Protein." Science 298, no. 5597 (October 10, 2002): 1395–401. http://dx.doi.org/10.1126/science.1075958.

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11

Pyne, Nigel J., and Susan Pyne. "Receptor tyrosine kinase–G-protein-coupled receptor signalling platforms: out of the shadow?" Trends in Pharmacological Sciences 32, no. 8 (August 2011): 443–50. http://dx.doi.org/10.1016/j.tips.2011.04.002.

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12

Gaudin, Valérie, Marc Libault, Sylvie Pouteau, Trine Juul, Gengchun Zhao, Delphine Lefebvre, and Olivier Grandjean. "Mutations in LIKE HETEROCHROMATIN PROTEIN 1 affect flowering time and plant architecture in Arabidopsis." Development 128, no. 23 (December 1, 2001): 4847–58. http://dx.doi.org/10.1242/dev.128.23.4847.

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In plants, recent studies have demonstrated links between the regulation of developmental processes and chromatin dynamics and organisation. Analysis of new mutations affecting overall plant architecture, leaf development and flowering time in Arabidopsis has allowed us to clone and characterise LHP1, the Drosophila heterochromatin protein 1 (HP1) homologue. LHP1 has the chromo and chromo shadow domains central to the function of animal proteins. Yeast two hybrid studies and in planta deletion experiments suggest similar modes of action in plants and animals via homodimer formation. In vivo localisation experiments revealed a specific subnuclear protein distribution in foci throughout the nucleus. Our data suggest that LHP1 may act as a main regulator of gene expression in plants, through formation of heterochromatin-like repressive complexes, to control developmental pathways involved in organ and cell size, and the vegetative to reproductive phase transition.

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13

Lipkin, Ehud, Mathias O. Mosig, Ariel Darvasi, Ephraim Ezra, A. Shalom, Adam Friedmann, and Morris Soller. "Quantitative Trait Locus Mapping in Dairy Cattle by Means of Selective Milk DNA Pooling Using Dinucleotide Microsatellite Markers: Analysis of Milk Protein Percentage." Genetics 149, no. 3 (July 1, 1998): 1557–67. http://dx.doi.org/10.1093/genetics/149.3.1557.

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Abstract “Selective DNA pooling” accomplishes quantitative trait locus (QTL) mapping through densitometric estimates of marker allele frequencies in pooled DNA samples of phenotypically extreme individuals. With poly(TG) microsatellites, such estimates are confounded by “shadow” (“stutter”) bands. A correction procedure was developed on the basis of an observed linear regression between shadow band intensity and allele TG repeat number. Using this procedure, a selective DNA pooling study with respect to milk protein percentage was implemented in Israel-Holstein dairy cattle. Pools were prepared from milk samples of high and low daughters of each of seven sires and genotyped with respect to 11 markers. Highly significant associations with milk protein percentage were found for 5 of the markers; 4 of these markers confirmed previous reports. Selective DNA pooling accessed 80.6 and 48.3%, respectively, of the information that would have been available through individual selective genotyping or total population genotyping. In effect, the statistical power of 45,600 individual genotypings was obtained from 328 pool genotypings. This methodology can make genome-wide mapping of QTL accessible to moderately sized breeding organizations.

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14

Won, Sae-Young, Yong-Chan Kim, Seon-Kwan Kim, and Byung-Hoon Jeong. "The First Report of Genetic and Structural Diversities in the SPRN Gene in the Horse, an Animal Resistant to Prion Disease." Genes 11, no. 1 (December 28, 2019): 39. http://dx.doi.org/10.3390/genes11010039.

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Prion diseases are fatal neurodegenerative diseases and are characterized by the accumulation of abnormal prion protein (PrPSc) in the brain. During the outbreak of the bovine spongiform encephalopathy (BSE) epidemic in the United Kingdom, prion diseases in several species were reported; however, horse prion disease has not been reported thus far. In previous studies, the shadow of prion protein (Sho) has contributed to an acceleration of conversion from normal prion protein (PrPC) to PrPSc, and the shadow of prion protein gene (SPRN) polymorphisms have been significantly associated with the susceptibility of prion diseases. We investigated the genotype, allele and haplotype frequencies of the SPRN gene using direct sequencing. In addition, we analyzed linkage disequilibrium (LD) and haplotypes among polymorphisms. We also investigated LD between PRNP and SPRN single nucleotide polymorphisms (SNPs). We compared the amino acid sequences of Sho protein between the horse and several prion disease-susceptible species using ClustalW2. To perform Sho protein modeling, we utilized SWISS-MODEL and Swiss-PdbViewer programs. We found a total of four polymorphisms in the equine SPRN gene; however, we did not observe an in/del polymorphism, which is correlated with the susceptibility of prion disease in prion disease-susceptible animals. The SPRN SNPs showed weak LD value with PRNP SNP. In addition, we found 12 horse-specific amino acids of Sho protein that can induce significantly distributional differences in the secondary structure and hydrogen bonds between the horse and several prion disease-susceptible species. To the best of our knowledge, this is the first report regarding the genetic and structural characteristics of the equine SPRN gene.

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15

Mueller, Jonathan W., and Peter Bayer. "Small Family with Key Contacts: Par14 and Par17 Parvulin Proteins, Relatives of Pin1, Now Emerge in Biomedical Research." Perspectives in Medicinal Chemistry 2 (January 2008): PMC.S496. http://dx.doi.org/10.4137/pmc.s496.

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The parvulin-type peptidyl-prolyl cis/trans isomerase Pin1 is subject of intense biochemical and clinical research as it seems to be involved in the pathogenesis of certain cancers and protein folding illnesses like Alzheimer's and Parkinson's disease. In addition to Pin1, the human genome only contains a single other parvulin locus encoding two protein species–-Par14 and Par17. Much less is known about these enzymes although their sequences are highly conserved in all metazoans. Parvulin has been proposed to function as Pin1 complementing enzyme in cell cycle regulation and in chromatin remodelling. Pharmaceutical modulation of Par14 might therefore have benefits for certain types of cancer. Moreover, the Par17 protein that has been shown to be confined to anthropoid primate species only might provide a deeper understanding for human-specific brain development. This review aims at stimulating further research on Par14 and Par17 that are overlooked drug targets in the shadow of an overwhelming plethora of Pin1 literature by summarising all current knowledge on these parvulin proteins.

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16

Muhammad Ikhwan. "PENGGUNAAN MESIN CROCKMETER UNTUK UJI GOSOK PADA KULIT PERKAMEN." Berkala Penelitian Teknologi Kulit, Sepatu, dan Produk Kulit 21, no. 2 (August 31, 2022): 202–11. http://dx.doi.org/10.58533/bptkspk.v21i2.173.

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One of the small industries that survives and needs to be developed is the shadow puppet industry. The shadow puppet industry uses parchment skin as the main raw material. As a laboratory institution, the author tested the quality of parchment skin dye paint for shadow puppet using a crockmeter machine. The test is carried out by adding an auxiliary material in the form of ethylene glycol to the dye paint which is expected to improve the quality of the rubbing resistance of the dye paint on the shadow puppets. In this test the author uses parchment skin from sun-dried buffalo skin with a transparent color and an even thickness of the skin and a large cross-sectional area so that no part is wasted. Furthermore, the parchment skin surface was sanded before staining. This sanding aims to level the parchment skin surface and remove the remaining collagen, protein and fat. The test was carried out using 3 samples. Sample I used coloring materials (mowilex paint, foxputih glue, water and finishing using mowilex clear). Sample II uses coloring materials (mowilex paint, white fox glue, water, Ethylen Glycol and finishing using mowilex clear). Sample III uses dyes (mowilex paint, white fox glue, water, Ethylen Glycol, finishing using mowilex clear and the addition of a clearing process using a sunlight wetting agent. From the experiments and tests carried out, better results were obtained for the use of Ethylen Glycol in the coloring and also the clearing process to improve the color quality of the wayang kulit products produced.

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17

Assland, Rein, and Francls stewart. "The chromo shadow domain, a second chromo domain in heterochromatin-binding protein 1, HP1." Nucleic Acids Research 23, no. 16 (1995): 3168–73. http://dx.doi.org/10.1093/nar/23.16.3168.

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18

Delattre, M., A. Spierer, C. H. Tonka, and P. Spierer. "The genomic silencing of position-effect variegation in Drosophila melanogaster: interaction between the heterochromatin-associated proteins Su(var)3-7 and HP1." Journal of Cell Science 113, no. 23 (December 1, 2000): 4253–61. http://dx.doi.org/10.1242/jcs.113.23.4253.

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Position-effect variegation results from mosaic silencing by chromosomal rearrangements juxtaposing euchromatin genes next to pericentric heterochromatin. An increase in the amounts of the heterochromatin-associated Su(var)3-7 and HP1 proteins augments silencing. Using the yeast two-hybrid protein interaction trap system, we have isolated HP1 using Su(var)3-7 as a bait. We have then delimited three binding sites on Su(var)3-7 for HP1. On HP1, the C-terminal moiety, including the chromo shadow domain, is required for interaction. In vivo, both proteins co-localise not only in heterochromatin, but also in a limited set of sites in euchromatin and at telomeres. When delocalised to the sites bound by the protein Polycomb in euchromatin, HP1 recruits Su(var)3-7. Finally, and in contrast with euchromatin genes, a decrease in the amounts of both proteins enhances variegation of the light gene, one of the few genetic loci mapped within pericentric heterochromatin. This body of data supports a direct link between Su(var)3-7 and HP1 in the genomic silencing of position-effect variegation.

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Hay, Ronald T. "Decoding the SUMO signal." Biochemical Society Transactions 41, no. 2 (March 21, 2013): 463–73. http://dx.doi.org/10.1042/bst20130015.

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SUMO (small ubiquitin-like modifier) emerged from the shadow of the well-established ubiquitin some 15 years ago when it was shown that a distinct conjugation pathway was responsible for SUMO modification. Since then it has been established that SUMO modifies over a thousand substrates and plays diverse roles in many important biological processes. Recognition of SUMO is mediated by short peptide sequences known as SIMs (SUMO-interaction motifs) that allow effector proteins to engage SUMO-modified substrates. Like ubiquitin, SUMO can form polymeric chains, and these chains can be recognized by proteins containing multiple SIMs. One protein that contains such a sequence of SIMs also contains a RING (really interesting new gene) domain that is the hallmark of a ubiquitin E3 ligase. This ubiquitin ligase known as RNF4 (RING finger protein 4) has the unique property that it can recognize SUMO-modified proteins and target them for ubiquitin-mediated proteolysis. Structural and biochemical analyses of RNF4 has shed light on the long sought after mechanism of ubiquitin transfer and illustrates how its RING domain primes the ubiquitin-loaded E2 for catalysis.

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Amara, Amro A., and Nawal Abd El-Baky. "Fungi as a Source of Edible Proteins and Animal Feed." Journal of Fungi 9, no. 1 (January 3, 2023): 73. http://dx.doi.org/10.3390/jof9010073.

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It is expected that the world population will reach 9 billion by 2050. Thus, meat, dairy or plant-based protein sources will fail to meet global demand. New solutions must be offered to find innovative and alternative protein sources. As a natural gift, edible wild mushrooms growing in the wet and shadow places and can be picked by hand have been used as a food. From searching mushrooms in the forests and producing single cell proteins (SCP) in small scales to mega production, academia, United Nations Organizations, industries, political makers and others, play significant roles. Fermented traditional foods have also been reinvestigated. For example, kefir, miso, and tempeh, are an excellent source for fungal isolates for protein production. Fungi have unique criteria of consuming various inexpensive wastes as sources of carbon and energy for producing biomass, protein concentrate or amino acids with a minimal requirement of other environmental resources (e.g., light and water). Fungal fermented foods and SCP are consumed either intentionally or unintentionally in our daily meals and have many applications in food and feed industries. This review addresses fungi as an alternative source of edible proteins and animal feed, focusing mainly on SCP, edible mushrooms, fungal fermented foods, and the safety of their consumption.

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21

Lampo, Evelyne, Mario Van Poucke, Karine Hugot, Hélène Hayes, Alex Van Zeveren, and Luc J. Peelman. "Characterization of the genomic region containing the Shadow of Prion Protein (SPRN) gene in sheep." BMC Genomics 8, no. 1 (2007): 138. http://dx.doi.org/10.1186/1471-2164-8-138.

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22

Zhang, Xaioli, Xiangmei Zhou, Tianjian Ding, Wenqiang Gan, Lifeng Yang, Xiaomin Yin, and Deming Zhao. "Polymorphisms of SPRN (shadow of prion protein homology) in three breeds of sheep in China." Virus Genes 44, no. 3 (February 26, 2012): 548–50. http://dx.doi.org/10.1007/s11262-012-0727-8.

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23

Kim, Yong-Chan, Hyeon-Ho Kim, Kiwon Kim, An-Dang Kim, and Byung-Hoon Jeong. "Novel Polymorphisms and Genetic Characteristics of the Shadow of Prion Protein Gene (SPRN) in Cats, Hosts of Feline Spongiform Encephalopathy." Viruses 14, no. 5 (May 6, 2022): 981. http://dx.doi.org/10.3390/v14050981.

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Prion diseases are transmissible spongiform encephalopathies (TSEs) caused by pathogenic prion protein (PrPSc) originating from normal prion protein (PrPC) and have been reported in several types of livestock and pets. Recent studies have reported that the shadow of prion protein (Sho) encoded by the shadow of prion protein gene (SPRN) interacts with prion protein (PrP) and accelerates prion diseases. In addition, genetic polymorphisms in the SPRN gene are related to susceptibility to prion diseases. However, genetic polymorphisms in the feline SPRN gene and structural characteristics of the Sho have not been investigated in cats, a major host of feline spongiform encephalopathy (FSE). We performed amplicon sequencing to identify feline SPRN polymorphisms in the 623 bp encompassing the open reading frame (ORF) and a small part of the 3′ untranslated region (UTR) of the SPRN gene. We analyzed the impact of feline SPRN polymorphisms on the secondary structure of SPRN mRNA using RNAsnp. In addition, to find feline-specific amino acids, we carried out multiple sequence alignments using ClustalW. Furthermore, we analyzed the N-terminal signal peptide and glycosylphosphatidylinositol (GPI)-anchor using SignalP and PredGPI, respectively. We identified three novel SNPs in the feline SPRN gene and did not find strong linkage disequilibrium (LD) among the three SNPs. We found four major haplotypes of the SPRN polymorphisms. Strong LD was not observed between PRNP and SPRN polymorphisms. In addition, we found alterations in the secondary structure and minimum free energy of the mRNA according to the haplotypes in the SPRN polymorphisms. Furthermore, we found four feline-specific amino acids in the feline Sho using multiple sequence alignments among several species. Lastly, the N-terminal signal sequence and cutting site of the Sho protein of cats showed similarity with those of other species. However, the feline Sho protein exhibited the shortest signal sequence and a unique amino acid in the omega-site of the GPI anchor. To the best of our knowledge, this is the first report on genetic polymorphisms of the feline SPRN gene.

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Sahar, Tahreem, Aruna Nigam, Shadab Anjum, Farheen Waziri, Shipie Biswas, Swatantra K. Jain, and Saima Wajid. "Interactome Analysis of the Differentially Expressed Proteins in Uterine Leiomyoma." Anti-Cancer Agents in Medicinal Chemistry 19, no. 10 (October 24, 2019): 1293–312. http://dx.doi.org/10.2174/1871520619666190206143523.

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Background: Recent advances in proteomics present enormous opportunities to discover proteome related disparities and thus understanding the molecular mechanisms related to a disease. Uterine leiomyoma is a benign monoclonal tumor, located in the pelvic region, and affecting 40% of reproductive aged female. Objective: Identification and characterization of the differentially expressed proteins associated with leiomyogenesis by comparing uterine leiomyoma and normal myometrium. Methods: Paired samples of uterine leiomyoma and adjacent myometrium retrieved from twenty-five females suffering from uterine leiomyoma (n=50) were submitted to two-dimensional electrophoresis (2-DE), matrixassisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and to reverse transcription polymerase chain reaction (RT-PCR). Results: Comparison of protein patterns revealed seven proteins with concordantly increased spot intensities in leiomyoma samples. E3 ubiquitin-protein ligase MIB2 (MIB2), Mediator of RNA polymerase II transcription subunit 10 (MED10), HIRA-interacting protein (HIRP3) and Fatty acid binding protein brain (FABP7) were found to be upregulated. While, Biogenesis of lysosome-related organelles complex 1 subunit 2 (BL1S2), Shadow of prion protein (SPRN) and RNA binding motif protein X linked like 2 (RMXL2) were found to be exclusively present in leiomyoma sample. The expression modulations of the corresponding genes were further validated which corroborated with the 2-DE result showing significant upregulation in leiomyoma. We have generated a master network showing the interactions of the experimentally identified proteins with their close neighbors and further scrutinized the network to prioritize the routes leading to cell proliferation and tumorigenesis. Conclusion: This study highlights the importance of identified proteins as potential targets for therapeutic purpose. This work provides an insight into the mechanism underlying the overexpression of the proteins but warrants further investigations.

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Gao, Yu, Yi Ding, Prim B. Singh, and Zihe Rao. "Crystallization and preliminary crystallographic studies on the chromo shadow domain (CSD) of mouse heterochromatin protein M31." Acta Crystallographica Section D Biological Crystallography 58, no. 6 (May 29, 2002): 1051–53. http://dx.doi.org/10.1107/s0907444902005863.

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Joppich, Christian, Sabrina Scholz, Günter Korge, and Alexander Schwendemann. "Umbrea, a chromo shadow domain protein in Drosophila melanogaster heterochromatin, interacts with Hip, HP1 and HOAP." Chromosome Research 17, no. 1 (January 2009): 19–36. http://dx.doi.org/10.1007/s10577-008-9002-1.

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Litt, Michael, Yi Qiu, and Suming Huang. "Histone arginine methylations: their roles in chromatin dynamics and transcriptional regulation." Bioscience Reports 29, no. 2 (February 18, 2009): 131–41. http://dx.doi.org/10.1042/bsr20080176.

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PRMTs (protein arginine N-methyltransferases) specifically modify the arginine residues of key cellular and nuclear proteins as well as histone substrates. Like lysine methylation, transcriptional repression or activation is dependent upon the site and type of arginine methylation on histone tails. Recent discoveries imply that histone arginine methylation is an important modulator of dynamic chromatin regulation and transcriptional controls. However, under the shadow of lysine methylation, the roles of histone arginine methylation have been under-explored. The present review focuses on the roles of histone arginine methylation in the regulation of gene expression, and the interplays between histone arginine methylation, histone acetylation, lysine methylation and chromatin remodelling factors. In addition, we discuss the dynamic regulation of arginine methylation by arginine demethylases, and how dysregulation of PRMTs and their activities are linked to human diseases such as cancer.

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Rybska, Marta, Sandra Knap, Maurycy Jankowski, Michal Jeseta, Dorota Bukowska, Paweł Antosik, Michał Nowicki, Maciej Zabel, Bartosz Kempisty, and Jędrzej M. Jaśkowski. "Cytoplasmic and nuclear maturation of oocytes in mammals – living in the shadow of cells developmental capability." Medical Journal of Cell Biology 6, no. 1 (January 1, 2018): 13–17. http://dx.doi.org/10.2478/acb-2018-0003.

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AbstractThe pig is a polyestrous animal in which the ovarian cycle lasts about 21 days and results in ovulation of 10-25 oocytes. Ovum reaches 120-150 μm in diameter, with the surrounding corona radiata providing communication with the environment. The zona pellucida is composed of glycoproteins: ZP1, ZP2, ZP3. In the course of oogenesis, RNA and protein accumulation for embryonic development occurs. Maternal mRNA is the template for protein production. Nuclear, cytoplasmic and genomic maturity condition the ability of the ovum to undergo fertilization. There are several differences in protein expression profiles observed between in vitro and in vivo conditions. Oogenesis is the process of differentiating female primary sex cells into gametes. During development gonocytes migrate from the yolk sac into the primary gonads with TGF-1, fibronectin, and laminin regulating this process. Cell cycle is blocked in dictyotene. Primary oocyte maturation is resumed before each ovulation and lasts until the next block in metaphase II. At the moment of penetration of the sperm into the ovum, the metaphase block is broken. The oocytes, surrounded by a single layer of granular cells, form the ovarian follicle. The exchange of signals between the oocyte and the cumulus cells done by gap-junctions, as well as various endo and paracrine signals. The contact between the corona radiata cells provides substances necessary for growth, through the same gap junctions. Studies on follicular cells can be used to amplify the knowledge of gene expression in these cells, in order to open way for potential clinical applications.

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Ssekyanzi, Athanasius, Nancy Nevejan, Dimitry Van der Zande, Molly E. Brown, and Gilbert Van Stappen. "Identification of Potential Surface Water Resources for Inland Aquaculture from Sentinel-2 Images of the Rwenzori Region of Uganda." Water 13, no. 19 (September 26, 2021): 2657. http://dx.doi.org/10.3390/w13192657.

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Aquaculture has the potential to sustainably meet the growing demand for animal protein. The availability of water is essential for aquaculture development, but there is no knowledge about the potential inland water resources of the Rwenzori region of Uganda. Though remote sensing is popularly utilized during studies involving various aspects of surface water, it has never been employed in mapping inland water bodies of Uganda. In this study, we assessed the efficiency of seven remote-sensing derived water index methods to map the available surface water resources in the Rwenzori region using moderate resolution Sentinel 2A/B imagery. From the four targeted sites, the Automated Water Extraction Index for urban areas (AWEInsh) and shadow removal (AWEIsh) were the best at identifying inland water bodies in the region. Both AWEIsh and AWEInsh consistently had the highest overall accuracy (OA) and kappa (OA > 90%, kappa > 0.8 in sites 1 and 2; OA > 84.9%, kappa > 0.61 in sites 3 and 4), as well as the lowest omission errors in all sites. AWEI was able to suppress classification noise from shadows and other non-water dark surfaces. However, none of the seven water indices used during this study was able to efficiently extract narrow water bodies such as streams. This was due to a combination of factors like the presence of terrain shadows, a dense vegetation cover, and the image resolution. Nonetheless, AWEI can efficiently identify other surface water resources such as crater lakes and rivers/streams that are potentially suitable for aquaculture from moderate resolution Sentinel 2A/B imagery.

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Kiefersauer, Reiner, Manuel E. Than, Holger Dobbek, Lothar Gremer, Marcos Melero, Stefan Strobl, João M. Dias, Tewfik Soulimane, and Robert Huber. "A novel free-mounting system for protein crystals: transformation and improvement of diffraction power by accurately controlled humidity changes." Journal of Applied Crystallography 33, no. 5 (October 1, 2000): 1223–30. http://dx.doi.org/10.1107/s0021889800008049.

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A novel device for capillary-free mounting of protein crystals is described. A controlled stream of air allows an accurate adjustment of the humidity at the crystal. The crystal is held on the tip of a micropipette. With a video system (CCD camera), the two-dimensional shadow projections of crystals can be recorded for optical analysis. Instead of the micropipette, a standard loop can also be used. Experiments and results for different crystal systems demonstrate the use of this method, also in combination with shock-freezing, to improve crystal order. Working with oxygen-free gases offers the possibility of crystal measurements under anaerobic conditions. Furthermore, the controlled application of arbitrary volatile substances with the gas stream is practicable.

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Saito, S., K. Suzuki, H. Shibuya, T. Yamaguchi, and T. Sato. "Melanocytic Matricoma in a Dog." Veterinary Pathology 42, no. 4 (July 2005): 499–502. http://dx.doi.org/10.1354/vp.42-4-499.

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We report a tumor that developed at the root of the tail in a male, 2-year-old Shih Tzu dog. Histologically, the tumor consisted of basaloid epithelial cells, with shadow cells and neoplastic melanocyte proliferation. immunohistochemically, epithelial components were positive for keratin/cytokeratin but basaloid cells were negative. Mononuclear or multinuclear melanocytes were positive for vimentin, S-100 protein, and HMB-45. In conclusion, this dog was diagnosed with canine melanocytic matricoma on the basis of the similarity of the histologic and immunohistochemical features in humans, and it may be the first case in an animal.

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Keene, Douglas R. "Rotary Shadowing Macromolecules." Microscopy Today 9, no. 1 (January 2001): 28–29. http://dx.doi.org/10.1017/s1551929500051348.

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I'm somewhat amazed by how many varied techniques there are for rotary shadowing, and how few seem to agree with what works for us. So, here is our method.We shadow biological molecules from the connective tissue matrix, usually ranging in size from 16 to 300 kilodaltons. Many are linear but some are globular. We spray the molecules in solution with 70% glycerol. The other 30% is 100 microgram/mL of protein, preferably in a volatile buffer such as 1% acetic acid or 0.1M ammonium bicarbonate, pH 7.8. Other buffers can be used, but salt crystals can be a big problem.

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Dobson, M. J., R. E. Pearlman, A. Karaiskakis, B. Spyropoulos, and P. B. Moens. "Synaptonemal complex proteins: occurrence, epitope mapping and chromosome disjunction." Journal of Cell Science 107, no. 10 (October 1, 1994): 2749–60. http://dx.doi.org/10.1242/jcs.107.10.2749.

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We have used polyclonal antibodies against fusion proteins produced from cDNA fragments of a meiotic chromosome core protein, Cor1, and a protein present only in the synapsed portions of the cores, Syn1, to detect the occurrence and the locations of these proteins in rodent meiotic prophase chromosomes. The 234 amino acid Cor1 protein is present in early unpaired cores, in the lateral domains of the synaptonemal complex and in the chromosome cores when they separate at diplotene. A novel observation showed the presence of Cor1 axial to the metaphase I chromosomes and substantial amounts of Cor1 in association with pairs of sister centromeres. The centromere-associated Cor1 protein becomes dissociated from the centromeres at anaphase II and it is not found in mitotic metaphase centromeres. The extended presence of Cor1 suggests that it may have a role in chromosome disjunction by fastening chiasmata at metaphase I and by joining sister kinetochores, which ensures co-segregation at anaphase I. Two-colour immunofluorescence of Cor1 and Syn1 demonstrates that synapsis between homologous cores is initiated at few sites but advances rapidly relative to the establishment of new initiation sites. If the rapid advance of synapsis deters additional initiation sites between pairs of homologues, it may provide a mechanism for positive recombination interference. Immunogold epitope mapping of antibodies to four Syn1 fusion proteins places the amino terminus of Syn1 towards the centre of the synaptonemal complex while the carboxyl terminus extends well into the lateral domain of the synaptonemal complex. The Syn1 fusion proteins have a non-specific DNA binding capacity. Immunogold labelling of Cor1 antigens indicates that the lateral domain of the synaptonemal complex is about twice as wide as the apparent width of lateral elements when stained with electron-dense metal ions. Electron microscopy of shadow-cast surface-spread SCs confirms the greater width of the lateral domain. The implication of these dimensions is that the proteins that comprise the synaptic domain overlap with the protein constituents of the lateral domains of the synaptonemal complex more than was apparent from earlier observations. This arrangement suggests that direct interactions might be expected between some of the synaptonemal complex proteins.

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Domokos-Szabolcsy, Éva, Nevien Elhawat, Geraldo Jorge Domingos, Zoltán Kovács, Judit Koroknai, Enikő Bodó, Miklós Gábor Fári, Tarek Alshaal, and Nóra Bákonyi. "Comparison of Wet Fractionation Methods for Processing Broccoli Agricultural Wastes and Evaluation of the Nutri-Chemical Values of Obtained Products." Foods 11, no. 16 (August 11, 2022): 2418. http://dx.doi.org/10.3390/foods11162418.

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The main objective of this study was to increase the economic value of broccoli green agro-waste using three wet fractionation methods in the shadow of green biorefinery and the circular economy. Product candidates were obtained directly by using a mechanical press, and indirectly by using microwave coagulation or via lactic acid fermentation of green juice. The leaf protein concentrates (LPC) fractions displayed significantly higher dry matter content and crude protein content (34–39 m/m% on average) than the green juice fraction (27.4 m/m% on average), without considerable changes in the amino acids composition ratio. UHPLC-ESI-ORBITRAP-MS/MS analysis showed that kaemferol and quercetin are the most abundant flavonols, forming complexes with glycosides and hydroxycinnamic acids in green juice. Lacto-ermentation induced a considerable increase in the quantity of quercetin (48.75 μg·g−1 dry weight) and kaempferol aglycons (895.26 μg·g−1 dry weight) of LPC. In contrast, chlorogenic acid isomers and sulforaphane disappeared from LPC after lactic acid fermentation, while microwave treatment did not cause significant differences. These results confirm that both microwave treatment and lacto-fermentation coagulate and concentrate most of the soluble proteins. Also, these two processes affect the amount of valuable phytochemicals differently, so it should be considered when setting the goals.

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Kim, Yong-Chan, and Byung-Hoon Jeong. "First report of prion-related protein gene (PRNT) polymorphisms in cattle." Veterinary Record 182, no. 25 (April 17, 2018): 717. http://dx.doi.org/10.1136/vr.104123.

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Prion diseases are caused by structural changes in normal prion protein (PrPC). The prion gene family includes four members: prion protein (PRNP), prion-like protein (PRND), shadow of PRNP (SPRN) and prion-related protein (PRNT). Genetic association studies of prion diseases and the other genes in the prion gene family, except for PRNT, have been performed in cattle. Our previous studies indicated that the distribution of PRNP promoter polymorphisms related with bovine spongiform encephalopathy susceptibility is significantly different in Hanwoo (Korean native cattle) and Holstein cattle. However, PRNT polymorphisms have not been reported thus far in cattle. Hence, we examined the PRNT single nucleotide polymorphisms (SNPs) in 315 Hanwoo and 140 Holstein cattle. We found a total of two SNPs, PRNT c.-87C>T and PRNT c.-37G>C, in the 5’ untranslated region of exon 2. The c.-87C>T and c.-37G>C genotype (P<0.0001) and allele (P<0.0001) frequencies exhibited significant differences in the distribution between Hanwoo and Holstein cattle. In addition, the c.-37G<C polymorphism was not found in Hanwoo. Interestingly, we did not find any polymorphisms in the ORF of bovine PRNT, which is in contrast with the highly polymorphic ovine PRNT ORF region. This is the first genetic research of the PRNT gene in cattle.

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Dou, Jun, Pengbo Liu, Jing Wang, and Xinjian Zhang. "Effect of hepatitis C virus core shadow protein expressed in human hepatoma cell line on human gene expression profiles." Journal of Gastroenterology and Hepatology 21, no. 12 (December 2006): 1794–800. http://dx.doi.org/10.1111/j.1440-1746.2006.04380.x.

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Matsuoka, Katsunari, Mitsuhiro Ueda, and Yoshihiro Miyamoto. "Mycobacterial granuloma on the staple line after pulmonary resection." Asian Cardiovascular and Thoracic Annals 26, no. 7 (September 2018): 540–45. http://dx.doi.org/10.1177/0218492318798228.

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Objective It has been reported previously that granulomas can occur around nonabsorbable sutures, but that granuloma formation around the staple line is very rare. However, the increased use of thoracoscopic surgery is creating more opportunities to use automatic mechanical suturing equipment for pulmonary surgery, and it is expected that the incidence of granuloma around the staple line will increase. Methods We retrospectively investigated the clinical records of 6 patients who developed nontuberculous mycobacterial granuloma on the staple line after pulmonary resection. We investigated their clinical characteristics and compared them with data in 16 cases of cancer recurrence. Results Fluorodeoxyglucose uptake was detected in all 6 patients. Laboratory data including white blood cell counts and C-reactive protein levels were within normal ranges in all patients. There was no evident tendency in terms of age, sex, maximal standardized uptake value, or radiological findings. However, compared to cancer recurrence, mycobacterial granuloma around the staple line appeared after a longer period of time, and the proportion of patients who had a segmentectomy as the initial surgery was significantly higher. Conclusion When growing shadows are observed near the staple line, it is difficult to differentiate between cancer recurrence and nontuberculous mycobacterial granuloma from computed tomography and laboratory findings. However, if a mass shadow around the staple line appears 2, 3, or more years after segmentectomy, it could be considered likely to be a granuloma. “Post-segmentectomy” and “late occurrence” are important attributes for distinguishing staple line granuloma from cancer recurrence.

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Kusumoto, K., K. Bessho, K. Fujimura, J. Akioka, Y. Okubo, Y. Wang, T. Iizuka, and Y. Ogawa. "Osteoinduction by Recombinant Human Bone Morphogenetic Protein-2 in Muscles of Non-Human Primates." Journal of International Medical Research 30, no. 3 (June 2002): 251–59. http://dx.doi.org/10.1177/147323000203000305.

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Heterotopic osteoinduction in a muscle of a medium-sized, non-human primate (Japanese macaque monkey; Macaca fuscata) was investigated with recombinant human bone morphogenetic protein-2 (rhBMP-2) mixed with atelopeptide type I collagen as the carrier. Nine monkeys were divided into three groups of three: groups I (1.25 mg rhBMP-2), II (250 μg rhBMP-2) and III (50 μg rhBMP-2). Four weeks after implanting into the calf muscle pouch, the implant was examined radiographically and histologically. In one specimen of three in group I, marked radio-opaque shadow, massive chondrogenesis and partial osteogenesis were observed. In the other two specimens, only microscopic calcification signs were recognized. In groups II and III, no findings of heterotopic osteoinduction were radiographically observed; however, nuclei from muscle bundles reacted to rhBMP-2 and were large and round, as in muscle bundles near the site of osteogenesis in group I. A positive control study using rats was carried out in parallel. This was a dose-finding study, with the monkeys in group III acting as a sub-effective dose (placebo) control, and rats acting as an active control, or verum, to show that the techniques are sufficiently sensitive. Bone morphogenetic protein appears to osteoinduce less bony material in soft tissue in primates than in rats.

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Gotow, T., T. Tanaka, Y. Nakamura, and M. Takeda. "Dephosphorylation of the largest neurofilament subunit protein influences the structure of crossbridges in reassembled neurofilaments." Journal of Cell Science 107, no. 7 (July 1, 1994): 1949–57. http://dx.doi.org/10.1242/jcs.107.7.1949.

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Phosphorylation-dependent change in electrophoretic mobility is the most unique characteristic of NF-H, the largest molecular mass subunit of the neurofilament. We dephosphorylated NF-H using Escherichia coli alkaline phosphatase, then reassembled it into neurofilaments with NF-M and NF-L, and into NF-H filaments with NF-H alone. We compared these dephosphorylated filaments with control: projections by low-angle rotary-shadow, crossbridges by quick-freeze deep-etch, and core filament packing density by thin-section electron microscopy. Projections in the dephosphorylated filaments were basically similar in structure to those in control, although there was a tendency for them to be wider and less dense, especially in NF-H filaments. Dephosphorylated filaments were still able to form crossbridges between core filaments, but their crossbridges were significantly wider, less dense, more branched and more irregular than crossbridges in control, and core filaments were more densely packed. These structural differences may be brought about by the removal of phosphate groups from NF-H tail and consequent reduction of electrostatic repulsion between adjacent crossbridges extending from the same core filament. The results indicate that phosphorylation of NF-H is necessary for forming well developed crossbridges, straight and at constant intervals, like those of in vivo axonal neurofilaments.

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Mosig, Mathias O., Ehud Lipkin, Galina Khutoreskaya, Elena Tchourzyna, Morris Soller, and Adam Friedmann. "A Whole Genome Scan for Quantitative Trait Loci Affecting Milk Protein Percentage in Israeli-Holstein Cattle, by Means of Selective Milk DNA Pooling in a Daughter Design, Using an Adjusted False Discovery Rate Criterion." Genetics 157, no. 4 (April 1, 2001): 1683–98. http://dx.doi.org/10.1093/genetics/157.4.1683.

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Abstract Selective DNA pooling was employed in a daughter design to screen all bovine autosomes for quantitative trait loci (QTL) affecting estimated breeding value for milk protein percentage (EBVP%). Milk pools prepared from high and low daughters of each of seven sires were genotyped for 138 dinucleotide microsatellites. Shadow-corrected estimates of sire allele frequencies were compared between high and low pools. An adjusted false discovery rate (FDR) method was employed to calculate experimentwise significance levels and empirical power. Significant associations with milk protein percentage were found for 61 of the markers (adjusted FDR = 0.10; estimated power, 0.68). The significant markers appear to be linked to 19–28 QTL. Mean allele substitution effects of the putative QTL averaged 0.016 (0.009–0.028) in units of the within-sire family standard deviation of EBVP% and summed to 0.460 EBVP%. Overall QTL heterozygosity was 0.40. The identified QTL appear to account for all of the variation in EBVP% in the population. Through use of selective DNA pooling, 4400 pool data points provided the statistical power of 600,000 individual data points.

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Won, Sae-Young, Yong-Chan Kim, Kyoungtag Do, and Byung-Hoon Jeong. "The First Report of Genetic Polymorphisms of the Equine SPRN Gene in Outbred Horses, Jeju and Halla Horses." Animals 11, no. 9 (September 1, 2021): 2574. http://dx.doi.org/10.3390/ani11092574.

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Prion disease is a fatal infectious disease caused by the accumulation of pathogenic prion protein (PrPSc) in several mammals. However, to date, prion disease has not been reported in horses. The Sho protein encoded by the shadow of the prion protein gene (SPRN) plays an essential role in the pathomechanism of prion diseases. To date, the only genetic study of the equine SPRN gene has been reported in the inbred horse, Thoroughbred horse. We first discovered four SPRN single nucleotide polymorphisms (SNPs) in 141 Jeju and 88 Halla horses by direct DNA sequencing. In addition, we found that the genotype, allele and haplotype frequencies of these SNPs of Jeju horses were significantly different from those of Halla and Thoroughbred horses, this latter breed is also included in this study. Furthermore, we observed that the minimum free energy and mRNA secondary structure were significantly different according to haplotypes of equine SPRN polymorphisms by the RNAsnp program. Finally, we compared the SNPs in the coding sequence (CDS) of the SPRN gene between horses and prion disease-susceptible species. Notably, prion disease-susceptible animals had polymorphisms that cause amino acid changes in the open reading frame (ORF) of the SPRN gene, while these polymorphisms were not found in horses.

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Mendez, Deanna L., Rebecca E. Mandt, and Sarah C. R. Elgin. "Heterochromatin Protein 1a (HP1a) Partner Specificity Is Determined by Critical Amino Acids in the Chromo Shadow Domain and C-terminal Extension." Journal of Biological Chemistry 288, no. 31 (June 23, 2013): 22315–23. http://dx.doi.org/10.1074/jbc.m113.468413.

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Bhadha, Jehangir H., Nan Xu, Abul Rabbany, Naba R. Amgain, Jay Capasso, Kevin Korus, and Stewart Swanson. "On-farm Soil Health Assessment of Cover-cropping in Florida." Sustainable Agriculture Research 10, no. 2 (January 29, 2021): 17. http://dx.doi.org/10.5539/sar.v10n2p17.

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Conventional cropping systems on sandy soils require continuous application of large amounts of external nutrients and irrigation water yet remain vulnerable to loses of these inputs. Within the state of Florida, need exists to provide farmers with economically viable alternatives that harness ecological processes and improve soil health and biodiversity. Cover crops are proving to be vital in the development of soil health. As part of this study we conducted a comprehensive on-farm assessment involving nine collaborative growers (ten farms) across the state; with each individual farm following its unique cover-cropping practice. Our goal was to shadow their practice and determine its effect on soil health indicators such as soil pH, bulk density (BD), maximum water holding capacity (MWHC), organic matter (OM), active carbon, cation exchange capacity, soil protein, Total Kjeldahl nitrogen (TKN), total phosphorus (TP), Mehlich-3 P (M3P) and potassium (M3K). Compared to fallow, soil OM, MWHC, and soil protein showed increases in cover crop fields for most farms, which presented a positive change towards building up soil health. Although soil TKN level was significantly decreased due to cover crops, soil protein level building up over time was the most positive change for soil health. M3K decreased in cover-crop fields, which indicated that supplementary K would be necessary prior to planting subsequent cash crops.

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Simon, John C., and Stella Y. E. Pattipeilohy. "Pandangan Dunia Evolusioner dan Respon Iman Kristen." BIA': Jurnal Teologi dan Pendidikan Kristen Kontekstual 2, no. 1 (June 24, 2019): 94–107. http://dx.doi.org/10.34307/b.v2i1.66.

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Abstract: The evolutionary worldview confirms its position since the discovery of various ancient human sites, and continues to develop with various genetic engineerings and protein discoveries as well as advances in the field of artificial intelligence (AI) technology. Initially the religious community was the party who felt most attacked by the theory of evolution because it stripped the Bible of the truth about the creation of the world and humans. Later some Catholic Church appreciative statements about the theory of evolution and the big bang theory, including Pierre Teilhard de Chardin's attempt to explain the evolution of human consciousness towards the cosmic Christ, showed a change in religion towards acceptance of the diversity of world views: religion, culture and science. This evolutionary world development raises ethical questions about what is religion’s contribution. One of them is the awareness about shadow. The awareness is derived from religion which teaches that men are created by God that even though unique, but mortal and finite creations. Shadow is liberation so that men are not shackled to matter. He is a fragile human who longs to evolve to be a Christ as the perfect human image.Abstraksi:Pandangan dunia evolusioner meneguhkan kedudukannya sejak penemuan berbagai situs manusia purba, dan terus berkembang dengan berbagai penemuan rekayasa genetik dan protein dan kemajuan di bidang teknologi artificial intelligence (AI). Semula kalangan agama menjadi pihak yang merasa paling diserang dengan teori evolusi karena melucuti kebenaran Alkitab tentang penciptaan dunia dan manusia. Belakangan beberapa pernyataan apresiatif Gereja Katolik terhadap teori evolusi dan teori big bang, termasuk usaha Pierre Teilhard de Chardin menjelaskan tentang evolusi kesadaran manusia menuju Kristus kosmis, memperlihatkan perubahan agama menuju penerimaan akan keragaman pandangan dunia: agama, budaya dan ilmu pengetahuan. Perkembangan dunia evolusioner ini memperhadapkan berbagai pertanyaan etis tentang apa sumbangan agama. Salah satunya adalah kesadaran tentang bayangan. Kesadaran akan bayangan diperoleh dari agama yang mengajarkan bahwa manusia yang diciptakan Tuhan, sekalipun unik, adalah ciptaan yang fana dan terbatas. Bayangan adalah pembebasan agar manusia tidak tertambat pada materi. Ia adalah manusia yang rapuh yang merindukan berevolusi menuju Kristus sebagai gambaran manusia yang sempurna.

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Harnisch, Kim, Sarah Teuber-Hanselmann, Nicole Macha, Fabian Mairinger, Lena Fritsche, Daniel Soub, Edgar Meinl, and Andreas Junker. "Myelination in Multiple Sclerosis Lesions Is Associated with Regulation of Bone Morphogenetic Protein 4 and Its Antagonist Noggin." International Journal of Molecular Sciences 20, no. 1 (January 3, 2019): 154. http://dx.doi.org/10.3390/ijms20010154.

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Remyelination is a central aspect of new multiple sclerosis (MS) therapies, in which one aims to alleviate disease symptoms by improving axonal protection. However, a central problem is mediators expressed in MS lesions that prevent effective remyelination. Bone morphogenetic protein4 (BMP4) inhibits the development of mature oligodendrocytes in cell culture and also blocks the expression of myelin proteins. Additionally, numerous studies have shown that Noggin (SYM1)—among other physiological antagonists of BMP4—plays a prominent role in myelin formation in the developing but also the adult central nervous system. Nonetheless, neither BMP4 nor Noggin have been systematically studied in human MS lesions. In this study, we demonstrated by transcript analysis and immunohistochemistry that BMP4 is expressed by astrocytes and microglia/macrophages in association with inflammatory infiltrates in MS lesions, and that astrocytes also express BMP4 in chronic inactive lesions that failed to remyelinate. Furthermore, the demonstration of an increased expression of Noggin in so-called shadow plaques (i.e., remyelinated lesions with thinner myelin sheaths) in comparison to chronically inactive demyelinated lesions implies that antagonizing BMP4 is associated with successful remyelination in MS plaques in humans. However, although BMP4 is strongly overexpressed in inflammatory lesion areas, its levels are also elevated in remyelinated lesion areas, which raises the possibility that BMP4 signaling itself may be required for remyelination. Therefore, remyelination might be influenced by a small number of key factors. Manipulating these molecules, i.e., BMP4 and Noggin, could be a promising therapeutic approach for effective remyelination.

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Miesfeld, Joel B., Noor M. Ghiasvand, Brennan Marsh-Armstrong, Nicholas Marsh-Armstrong, Eric B. Miller, Pengfei Zhang, Suman K. Manna, Robert J. Zawadzki, Nadean L. Brown, and Tom Glaser. "TheAtoh7remote enhancer provides transcriptional robustness during retinal ganglion cell development." Proceedings of the National Academy of Sciences 117, no. 35 (August 17, 2020): 21690–700. http://dx.doi.org/10.1073/pnas.2006888117.

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The retinal ganglion cell (RGC) competence factor ATOH7 is dynamically expressed during retinal histogenesis.ATOH7transcription is controlled by a promoter-adjacent primary enhancer and a remote shadow enhancer (SE). Deletion of theATOH7human SE causes nonsyndromic congenital retinal nonattachment (NCRNA) disease, characterized by optic nerve aplasia and total blindness. We used genome editing to model NCRNA in mice. Deletion of the murine SE reducesAtoh7messenger RNA (mRNA) fivefold but does not recapitulate optic nerve loss; however, SEdel/knockout (KO)transheterozygotes have thin optic nerves. By analyzingAtoh7mRNA and protein levels, RGC development and survival, and chromatin landscape effects, we show that the SE ensures robustAtoh7transcriptional output. Combining SE deletion and KO and wild-type alleles in a genotypic series, we determined the amount ofAtoh7needed to produce a normal complement of adult RGCs, and the secondary consequences of graded reductions inAtoh7dosage. Together, these data reveal the workings of an evolutionary fail-safe, a duplicate enhancer mechanism that is hard-wired in the machinery of vertebrate retinal ganglion cell genesis.

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Baker, T. S., N. H. Olson, M. Gingery, and F. A. Eiserling. "Three-Dimensional Structure of Isometric Capsids of Bacteriophage T4." Microscopy and Microanalysis 6, S2 (August 2000): 254–55. http://dx.doi.org/10.1017/s1431927600033766.

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Coliphage T4 is a large, double-stranded DNA virus (family Myoviridae) which infects Escherichia coli. It is the classic example of a contractile-tailed phage and a wealth of information on viral morphogenesis processes have been obtained on it. Extensive studies of T4 by negative-stain and metal-shadow electron microscopy have shown that mature virions, which contain over 40 different polypeptides, have a prolate capsid that encapsidates the genome (∼175 × 106Da), and several other structural components, including the collar with whiskers, neck, a contractile sheath, and a baseplate with fibers. A complete understanding of processes such as assembly of the viral capsids will require atomic-scale knowledge of the various protein interactions. Details of the process can be extrapolated from knowledge of the initial, transitional, and final states of a structure.We have initiated an examination of T4 head morphogenesis by studying mutant, isometric capsids ('isometrics’) using cryo-electron microscopy and three-dimensional (3D) image reconstruction methods as applied to particles with icosahedral symmetry.

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Zhang, X., J. Spence, W. Qian, D. Taylor, and K. Taylor. "Fresnel interference in point-projection imaging of purple membrane." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 846–47. http://dx.doi.org/10.1017/s0424820100140609.

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Experimental point-projection shadow microscope (PPM) images of uncoated, unstained purple membrane (PM, bacteriorhodopsin, a membrane protein from Halobacterium holobium) were obtained recently using 100 volt electrons. The membrane thickness is about 5 nm and the hexagonal unit cell dimension 6 nm. The images show contrast around the edges of small holes, as shown in figure 1. The interior of the film is opaque. Since the inelastic mean free path for 100V electrons in carbon (about 6 Å) is much less than the sample thickness, the question arises that how much, if any, transmission of elastically scattered electrons occurs. A large inelastic contribution is also expected, attenuated by the reduced detection efficiency of the channel plate at low energies. Quantitative experiments using an energy-loss spectrometer are planned. Recently Shedd has shown that at about 100V contrast in PPM images of thin gold films can be explained as Fresnel interference effects between different pinholes in the film, separated by less than the coherence width.

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Kim, Yong-Chan, and Byung-Hoon Jeong. "The first report of prion-related protein gene (PRNT) polymorphisms in goat." Acta Veterinaria Hungarica 65, no. 2 (June 2017): 291–300. http://dx.doi.org/10.1556/004.2017.028.

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Prion protein is encoded by the prion protein gene (PRNP). Polymorphisms of several members of the prion gene family have shown association with prion diseases in several species. Recent studies on a novel member of the prion gene family in rams have shown that prion-related protein gene (PRNT) has a linkage with codon 26 of prion-like protein (PRND). In a previous study, codon 26 polymorphism of PRND has shown connection with PRNP haplotype which is strongly associated with scrapie vulnerability. In addition, the genotype of a single nucleotide polymorphism (SNP) at codon 26 of PRND is related to fertilisation capacity. These findings necessitate studies on the SNP of PRNT gene which is connected with PRND. In goat, several polymorphism studies have been performed for PRNP, PRND, and shadow of prion protein gene (SPRN). However, polymorphism on PRNT has not been reported. Hence, the objective of this study was to determine the genotype and allelic distribution of SNPs of PRNT in 238 Korean native goats and compare PRNT DNA sequences between Korean native goats and several ruminant species. A total of five SNPs, including PRNT c.-114G > T, PRNT c.-58A > G in the upstream of PRNT gene, PRNT c.71C > T (p.Ala24Val) and PRNT c.102G > A in the open reading frame (ORF) and c.321C > T in the downstream of PRNT gene, were found in this study. All five SNPs of caprine PRNT gene in Korean native goat are in complete linkage disequilibrium (LD) with a D’ value of 1.0. Interestingly, comparative sequence analysis of the PRNT gene revealed five mismatches between DNA sequences of Korean native goats and those of goats deposited in the GenBank. Korean native black goats also showed 5 mismatches in PRNT ORF with cattle. To the best of our knowledge, this is the first genetic research of the PRNT gene in goat.

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Kang, Jungseog, Jaideep Chaudhary, Hui Dong, Soonjoung Kim, Chad A. Brautigam, and Hongtao Yu. "Mitotic centromeric targeting of HP1 and its binding to Sgo1 are dispensable for sister-chromatid cohesion in human cells." Molecular Biology of the Cell 22, no. 8 (April 15, 2011): 1181–90. http://dx.doi.org/10.1091/mbc.e11-01-0009.

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Abstract:

Human Shugoshin 1 (Sgo1) protects centromeric sister-chromatid cohesion during prophase and prevents premature sister-chromatid separation. Heterochromatin protein 1 (HP1) has been proposed to protect centromeric sister-chromatid cohesion by directly targeting Sgo1 to centromeres in mitosis. Here we show that HP1α is targeted to mitotic centromeres by INCENP, a subunit of the chromosome passenger complex (CPC). Biochemical and structural studies show that both HP1–INCENP and HP1–Sgo1 interactions require the binding of the HP1 chromo shadow domain to PXVXL/I motifs in INCENP or Sgo1, suggesting that the INCENP-bound, centromeric HP1α is incapable of recruiting Sgo1. Consistently, a Sgo1 mutant deficient in HP1 binding is functional in centromeric cohesion protection and localizes normally to centromeres in mitosis. By contrast, INCENP or Sgo1 mutants deficient in HP1 binding fail to localize to centromeres in interphase. Therefore, our results suggest that HP1 binding by INCENP or Sgo1 is dispensable for centromeric cohesion protection during mitosis of human cells, but might regulate yet uncharacterized interphase functions of CPC or Sgo1 at the centromeres.

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Journal articles on the topic 'Shadow protein'

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