gebhart/patrepeval huggingface dataset:
Comparison of multiple DNA dyes for real-time PCR: effects of dye concentration and sequence composition on DNA amplification and melting temperature (2007)

The importance of real-time polymerase chain reaction (PCR) has increased steadily in clinical applications over the last decade. Many applications utilize SYBR Green I dye to follow the accumulation of amplicons in real time. SYBR Green I has, however, a number of limitations that include the inhibition of PCR, preferential binding to GC-rich sequences and effects on melting curve analysis. Although a few alternative dyes without some of these limitations have been recently proposed, no large-scale investigation into the properties of intercalating dyes has been performed. In this study, we investigate 15 different intercalating DNA dyes for their inhibitory effects on PCR, effects on DNA melting temperature and possible preferential binding to GC-rich sequences. Our results demonstrated that in contrast to the results of SYBR Green I, two intercalating dyes SYTO-13 and SYTO-82 do not inhibit PCR, show no preferential binding to GC rich sequences and do not influence melting temperature, T(m), even at high concentrations. In addition, SYTO-82 demonstrated a 50-fold lower detection limit in a dilution series assay. In conclusion, the properties of SYTO-82 and SYTO-13 will simplify the development of multiplex assays and increase the sensitivity of real-time PCR.
Changes in association of the Xenopus origin recognition complex with chromatin on licensing of replication origins (1999)

During late mitosis and early G1, a series of proteins are assembled onto replication origins that results in them becoming 'licensed' for replication in the subsequent S phase. In Xenopus this first involves the assembly onto chromatin of the Xenopus origin recognition complex XORC, and then XCdc6, and finally the RLF-M component of the replication licensing system. In this paper we examine changes in the way that XORC associates with chromatin in the Xenopus cell-free system as origins become licensed. Restricting the quantity of XORC on chromatin reduced the extent of replication as expected if a single molecule of XORC is sufficient to specify a single replication origin. During metaphase, XOrc1 associated only weakly with chromatin. In early interphase, XOrc1 formed a strong complex with chromatin, as evidenced by its resistance to elution by 200 mM salt, and this state persisted when XCdc6 was assembled onto the chromatin. As a consequence of origins becoming licensed the association of XOrc1 and XCdc6 with chromatin was destabilised, and XOrc1 became susceptible to removal from chromatin by exposure to either high salt or high Cdk levels. At this stage the essential function for XORC and XCdc6 in DNA replication had already been fulfilled. Since high Cdk levels are required for the initiation of DNA replication, this 'licensing-dependent origin inactivation' may contribute to mechanisms that prevent re-licensing of replication origins once S phase has started.
Characterization of the d-Glucuronyl C5-epimerase Involved in the Biosynthesis of Heparin and Heparan Sulfate (2001)

The murine gene for the glucuronyl C5-epimerase involved in heparan sulfate biosynthesis was cloned, using a previously isolated bovine lung cDNA fragment (Li, J.-P., Hagner-McWhirter, A., Kjellén, L., Palgi, J., Jalkanen, M., and Lindahl, U. (1997) J. Biol. Chem. 272, 28158-28163) as probe. The approximately 11-kilobase pair mouse gene contains 3 exons from the first ATG to stop codon and is localized to chromosome 9. Southern analysis of the genomic DNA and chromosome mapping suggested the occurrence of a single epimerase gene. Based on the genomic sequence, a mouse liver cDNA was isolated that encodes a 618-amino acid residue protein, thus extending by 174 N-terminal residues the sequence deduced from the (incomplete) bovine cDNA. Comparison of murine, bovine, and human epimerase cDNA structures indicated 96-99% identity at the amino acid level. A cDNA identical to the mouse liver species was demonstrated in mouse mast cells committed to heparin biosynthesis. These findings suggest that the iduronic acid residues in heparin and heparan sulfate, despite different structural contexts, are generated by the same C5-epimerase enzyme. The catalytic activity of the recombinant full-length mouse liver epimerase, expressed in insect cells, was found to be >2 orders of magnitude higher than that of the previously cloned, smaller bovine recombinant protein. The approximately 52-kDa, similarly highly active, enzyme originally purified from bovine liver (Campbell, P., Hannesson, H. H., Sandbäck, D., Rodén, L., Lindahl, U., and Li, J.-P. (1994) J. Biol. Chem. 269, 26953-26958) was found to be associated with an approximately 22-kDa peptide generated by a single proteolytic cleavage of the full-sized protein.
“Black holes” and bacterial pathogenicity: A large genomic deletion that enhances the virulence of Shigella spp. and enteroinvasive Escherichia coli (1998)

Plasmids, bacteriophages, and pathogenicity islands are genomic additions that contribute to the evolution of bacterial pathogens. For example, Shigella spp., the causative agents of bacillary dysentery, differ from the closely related commensal Escherichia coli in the presence of a plasmid in Shigella that encodes virulence functions. However, pathogenic bacteria also may lack properties that are characteristic of nonpathogens. Lysine decarboxylase (LDC) activity is present in approximately 90% of E. coli strains but is uniformly absent in Shigella strains. When the gene for LDC, cadA, was introduced into Shigella flexneri 2a, virulence became attenuated, and enterotoxin activity was inhibited greatly. The enterotoxin inhibitor was identified as cadaverine, a product of the reaction catalyzed by LDC. Comparison of the S. flexneri 2a and laboratory E. coli K-12 genomes in the region of cadA revealed a large deletion in Shigella. Representative strains of Shigella spp. and enteroinvasive E. coli displayed similar deletions of cadA. Our results suggest that, as Shigella spp. evolved from E. coli to become pathogens, they not only acquired virulence genes on a plasmid but also shed genes via deletions. The formation of these "black holes," deletions of genes that are detrimental to a pathogenic lifestyle, provides an evolutionary pathway that enables a pathogen to enhance virulence. Furthermore, the demonstration that cadaverine can inhibit enterotoxin activity may lead to more general models about toxin activity or entry into cells and suggests an avenue for antitoxin therapy. Thus, understanding the role of black holes in pathogen evolution may yield clues to new treatments of infectious diseases.
The hrpA and hrpC operons of Erwinia amylovora encode components of a type III pathway that secretes harpin (1997)

A 6.2-kb region of DNA corresponding to complementation groups II and III of the Erwinia amylovora hrp gene cluster was analyzed. Transposon mutagenesis indicated that the two complementation groups are required for secretion of harpin, an elicitor of the hypersensitive reaction. The sequence of the region revealed 10 open reading frames in two putative transcription units: hrpA, hrpB, hrcJ, hrpD, and hrpE in the hrpA operon (group III) and hrpF, hrpG, hrcC, hrpT, and hrpV in the hrpC operon (group II). From promoter regions of the hrpA, hrpC, and hrpN operons, sequences similar to those of the HrpL-dependent promoters of Pseudomonas syringae pathovars were identified with a consensus sequence of 5'-GGAAC-N17-18-CACTNAA-3'. The protein products of seven genes, hrpA, hrcJ, hrpE, hrpF, hrpG, hrcC, and hrpV, were visualized with a T7 polymerase/promoter expression system. HrcC, HrcJ, and HrpT sequences contained potential signal peptides, and HrcC appeared to be envelope associated based on a TnphoA translational fusion. Comparison of deduced amino acid sequences indicated that many of the proteins are homologous to proteins that function in the type III protein secretion pathway. HrcC is a member of the YscC-containing subgroup in the PulD/pIV superfamily of outer membrane proteins. HrcJ is a member of a lipoprotein family that includes YscJ of Yersinia spp., MxiJ of Shigella flexneri, and NolT of Rhizobim fredii. Additional similarities were detected between HrpB and YscI and between HrpE and YscL. HrcJ and HrpE were similar to flagellar biogenesis proteins FliF and FliH, respectively. In addition, HrpA, HrpB, HrcJ, HrpD, HrpE, HrpF, and HrcC showed various degrees of similarity to corresponding proteins of P. syringae. Comparison of hrp clusters with respect to gene organization and similarity of individual proteins confirms that the hrp systems of E. amylovora and P. syringae are closely related to each other and distinct from those of Ralstonia (Pseudomonas) solanacearum and Xanthomonas campestris. Possible implications of extensive similarities between the E. amylovora and P. syringae hrp systems in pathogenesis mechanisms are discussed.
The role of growth factors in gastrointestinal cell proliferation. (1994)

The epithelial lining of the gastrointestinal (GI) tract is in a state of continuous cell renewal, and the proliferating and differentiating/differentiated cell populations are spatially clearly demarcated. Members of the epidermal growth factor (EGF) family of peptides, the trefoil peptides and enteroglucagon appear to be the most important enterotrophic molecules for both normal cell renewal and healing after cell damage. Transforming growth factor-a (TGF-a) appears to be the primary physiological ligand for the EGF receptor (EGFR), promoting normal cell renewal, and TGF-a/EGFR are part of an autocrine loop in many intestinal cancers. In response to damage, a differentiating cell lineage arises from adjacent epithelium secreting EGF, TGF-a and trefoil peptides; this may be viewed as part of a 'repair kit' in damaged endodermally-derived tissue.
Identification through overexpression and tagging of the variant type of the mouse H1e and H1c genes. (1993)

Multiple, nonallelic forms of histone H1 are found in most mammalian tissues. Attempts to determine a functional significance to this diversity is hindered by a paucity of primary amino acid sequence data. Although numerous H1 genes have been cloned, the type of variant they encode cannot be determined by sequence analysis alone. We used transformation and overexpression methods to determine that two cloned mouse H1 genes, MH143 and MH175, encode H1c and H1e, respectively. Since these genes have been completely sequenced, these results establish the amino acid sequence of these variants. Assignment was accomplished by mutagenically "tagging" the genes by incorporation of a codon for methionine, which is not found in the major somatic H1 variants. These genes were placed under the control of the mouse metallothionein I promoter and introduced into 3T3 cells. Products of these mutagenized genes were detected by [35S]methionine labeling and identified by high performance liquid chromatography and sodium dodecyl sulfate-acid polyacrylamide gel electrophoresis. We were also able to induce major alterations in the normal stoichiometry of chromatin-associated H1 variants through overproduction of H1c and H1e. This had little effect on the growth properties of these transformants.
Acyl-coenzyme A dehydrogenase from pig kidney. Purification and properties (1979)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAcyl-coenzyme A dehydrogenase from pig kidney. Purification and propertiesColin Thorpe, Rowena G. Matthews, and Charles H. Williams, Jr.Cite this: Biochemistry 1979, 18, 2, 331–337Publication Date (Print):January 23, 1979Publication History Published online1 May 2002Published inissue 23 January 1979https://pubs.acs.org/doi/10.1021/bi00569a016https://doi.org/10.1021/bi00569a016research-articleACS PublicationsRequest reuse permissionsArticle Views190Altmetric-Citations85LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Localization of the human tissue factor recognition determinant of human factor VIIa. (1991)

Tissue factor is an integral membrane glycoprotein that serves as an essential cofactor for the blood coagulation factor VIIa. Recent studies have attempted to localize the tissue factor recognition determinant of human factor VIIa. While several regions of factor VIIa have been implicated as important for tissue factor binding, the high affinity tissue factor recognition determinant of human factor VIIa is unknown. In order to define the determinant, we constructed a set of six chimeric proteins composed of portions of factor VII and factor IX. We then utilized the chimeras in competition experiments with 125I-labeled factor VIIa for recombinant tissue factor bound to an Immobilon-P membrane. The data indicate that the high affinity tissue factor recognition determinant of human factor VIIa is within the epidermal growth factor domains.
Pharmacophore Modeling, Virtual and In Vitro Screening for Acetylcholinesterase Inhibitors and their Effects on Amyloid-&beta; Self- Assembly (2013)

One of the most promising methods of unveiling the pharmacology of marketed drugs is to screen them against new biological targets. In an attempt to find inhibitors for acetylcholinesterase (AChE), the Drug Bank Database and natural alkaloids with other known medicinal values were screened through a four-point pharmacophore built in this study. The development of the pharmacophore was based on a structurally diverse set of reported AChE inhibitors and was validated using a separate set of known inhibitors. The developed pharmacophore indicated that the presence of one H-acceptor motif, one H-donor motif, one positively charged group and one aromatic ring is needed for AChE inhibition. Selected hits were further investigated by molecular docking and in vitro testing. The assays revealed that the majority of these compounds showed reasonable inhibition, indicating that the developed pharmacophore can indeed reliably screen molecules for potential AChE inhibitors. It appears that several commercially available marketed drugs have further potential as AChE inhibitors. To extend our study the same compounds have been tested in the fibrillogenesis inhibition of amyloidβ (Aβ) peptide to explore the possibility of their dual-function therapeutic activity in Alzheimer's disease.
Hemopoietic responses in mice injected with purified recombinant murine GM-CSF. (1987)

Normal adult BALB/c, C57BL, and C3H/HeJ mice were injected intraperitoneally three times daily for six days with 6-200 ng purified, bacterially synthesized, murine recombinant GM-CSF. Mice injected with 200 ng rGM-CSF developed a twofold increase in blood neutrophils. In the peritoneal cavity, a dose-related rise was observed in macrophages (up to 15-fold), neutrophils (10- to 100-fold) and eosinophils (10- to 100-fold). Peritoneal macrophages exhibited 15-fold increased mitotic activity (to 7.6/10(3) cells) and increased phagocytic activity for antibody-coated erythrocytes. Increased numbers of infiltrating neutrophils and monocytes were observed in the liver and lung. Dose-related rises were observed in spleen weight (up to 50%) and the spleen content of monocytes (twofold) and nonerythroid progenitor cells (up to fourfold). A dose-related fall occurred in total marrow cellularity (40%) and total nonerythroid progenitor cells (37%-66%), but levels of neutrophils and monocytes remained constant. The data indicate that the injection of rGM-CSF to normal mice increases overall numbers of granulocytes and macrophages and the phagocytic activity of macrophages and provides direct evidence for the conclusion that GM-CSF is likely to function in vivo as a regulator of these cell populations.
Platelets secrete stromal cell–derived factor 1α and recruit bone marrow–derived progenitor cells to arterial thrombi in vivo (2006)

The accumulation of smooth muscle and endothelial cells is essential for remodeling and repair of injured blood vessel walls. Bone marrow-derived progenitor cells have been implicated in vascular repair and remodeling; however, the mechanisms underlying their recruitment to the site of injury remain elusive. Here, using real-time in vivo fluorescence microscopy, we show that platelets provide the critical signal that recruits CD34+ bone marrow cells and c-Kit+ Sca-1+ Lin- bone marrow-derived progenitor cells to sites of vascular injury. Correspondingly, specific inhibition of platelet adhesion virtually abrogated the accumulation of both CD34+ and c-Kit+ Sca-1+ Lin- bone marrow-derived progenitor cells at sites of endothelial disruption. Binding of bone marrow cells to platelets involves both P-selectin and GPIIb integrin on platelets. Unexpectedly, we found that activated platelets secrete the chemokine SDF-1alpha, thereby supporting further primary adhesion and migration of progenitor cells. These findings establish the platelet as a major player in the initiation of vascular remodeling, a process of fundamental importance for vascular repair and pathological remodeling after vascular injury.
Conflict-free data access of arrays and trees in parallel memory systems (2002)

Mapping the nodes of a data structure to a given set of memory modules so that different sets of nodes (called templates) can be accessed in parallel without conflicts is an important problem. We consider two useful data structures, namely trees and arrays. The most commonly used templates of a tree are the subtrees of a given height or the nodes in any given level. We present a recursive memory module assignment algorithm for complete k-ary trees, allowing conflict-free access to any complete subtree of height h. Our scheme uses k/sup h-1/-1/k-1 memory modules which is the same as the number of nodes in the subtree and hence the memory utilization is optimal. The number of conflicts in accessing nodes in different levels or subtrees of different heights for these schemes are presented. For accessing arrays, the templates of interest are rows, columns, diagonals, different subblocks, distributed blocks and so on. We propose a new scheme for conflict-free access to all of these templates with the help of quasigroups. The multiplication table of a quasigroup will be used to map the array elements to different memory modules.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bandwidth and latency guarantees in low-cost, high-performance networks (1997)

Network service guarantees not only provide significant performance benefits to distributed computing systems (more balanced resource utilization, fast fault recovery, and fair network access), but they are also essential for many new applications requiring realtime communications with continuous data types (audio/video). Unfortunately, existing multicomputer network routers, which use simple arbitration techniques such as first-comefirst-serve or round-robin, have fundamental limitations in supporting these needs. Most algorithms that have been suggested for network service guarantees in long-haul, real-time communication networks are too complicated to be feasible in high-speed, low-cost switches for multicomputer networks. The simpler algorithms proposed, so far, provide only limited service guarantees or waste significant network resources. In this dissertation, we show that a variety of traffic types, both real-time communications as well as best-effort communications, can be supported efficiently in fast and inexpensive switches. After analyzing limitations of existing solutions, we present a novel, cost-effective resource control algorithm for service guarantees. Such cost-effective service guarantees not only provide substantial benefits to overall system performance, but can also further expand the domain of multicomputer applications to encompass distributed multimedia applications requiring guaranteed services.
Reduced Incretin Effect in Type 2 Diabetes (2007)

We aimed to investigate whether the reduced incretin effect observed in patients with type 2 diabetes is a primary event in the pathogenesis of type 2 diabetes or a consequence of the diabetic state. Eight patients with chronic pancreatitis and secondary diabetes (A1C mean [range] of 6.9% [6.2-8.0]), eight patients with chronic pancreatitis and normal glucose tolerance (NGT; 5.3 [4.9-5.7]), eight patients with type 2 diabetes (6.9 [6.2-8.0]); and eight healthy subjects (5.5 [5.1-5.8]) were studied. Blood was sampled over 4 h on 2 separate days after a 50-g oral glucose load and an isoglycemic intravenous glucose infusion, respectively. The incretin effect (100% x [beta-cell secretory response to oral glucose tolerance test - intravenous beta-cell secretory response]/beta-cell secretory response to oral glucose tolerance test) was significantly (P < 0.05) reduced (means +/- SE) in patients with chronic pancreatitis and secondary diabetes (31 +/- 4%) compared with patients with chronic pancreatitis and NGT (68 +/- 3) and healthy subjects (60 +/- 4), respectively. In the type 2 diabetes group, the incretin effect amounted to 36 +/- 6%, significantly (P < 0.05) lower than in chronic pancreatitis patients with NGT and in healthy subjects, respectively. These results suggest that the reduced incretin effect is not a primary event in the development of type 2 diabetes, but rather a consequence of the diabetic state.
KAI1 , a Metastasis Suppressor Gene for Prostate Cancer on Human Chromosome 11p11.2 (1995)

A gene from human chromosome 11p11.2 was isolated and was shown to suppress metastasis when introduced into rat AT6.1 prostate cancer cells. Expression of this gene, designated KAI1, was reduced in human cell lines derived from metastatic prostate tumors. KAI1 specifies a protein of 267 amino acids, with four hydrophobic and presumably transmembrane domains and one large extracellular hydrophilic domain with three potential N-glycosylation sites. KAI1 is evolutionarily conserved, is expressed in many human tissues, and encodes a member of a structurally distinct family of leukocyte surface glycoproteins. Decreased expression of this gene may be involved in the malignant progression of prostate and other cancers.