gebhart/patrepeval huggingface dataset:
Cloning and expression in Escherichia coli of mature E1 beta subunit of bovine mitochondrial branched-chain alpha-keto acid dehydrogenase complex. Mapping of the E1 beta-binding region on E2. (1992)

A cDNA encoding the mature E1 beta subunit of the bovine branched-chain alpha-keto acid dehydrogenase complex was isolated from a lambda ZAP expression library. The bovine E1 beta cDNA is 1,393 base pairs in length. It encodes the entire mature E1 beta subunit consisting of 342 amino acid residues and a partial mitochondrial targeting presequence of 26 residues. The calculated molecular mass of the mature bovine E1 beta subunit is 37,776 daltons, and the calculated isoelectric point is pI 5.04. The mature bovine E1 beta subunit was expressed in Escherichia coli via the pKK233-2 vector in the presence of isopropyl beta-D-thiogalactopyranoside (IPTG). When expression was induced by IPTG at 37 degrees C, the soluble recombinant E1 beta subunit existed as a single high molecular weight form (Mr congruent to 3.5 x 10(5)), which sedimented during sucrose gradient ultracentrifugation at 2 x 10(5) x g. However, lowering the induction temperature to 25 degrees C resulted in the occurrence of both high and low molecular weight forms of the recombinant E1 beta protein. The low molecular weight form (Mr congruent to 9.1 x 10(4)) remained soluble after sucrose gradient centrifugation and was utilized in binding studies with a series of truncated recombinant E2 proteins. The results showed that the E1 beta subunit bound to the region between Ala-115 and Lys-150 of the E2 chain, which lay within the putative E3-binding domain. In contrast, the recombinant E1 alpha subunit did not bind the E2 component. The data suggest an apparent binding order of E2-E1 beta-E1 alpha, which supports and extends the model of E2 inner core deduced previously from the data of scanning transmission electron microscopy (Hackert, M.L., Xu, W.-X., Oliver, R.M., Wall, J.S., Hainfeld, J.F., Mullinax, T.R., and Reed, L.J. (1989) Biochemistry 28, 6816-6821). The relatively inaccessible topology of E1 beta may explain the lack of antigenicity and resistance to limited proteolysis of this subunit as it exists in the complex.
Hsp70 Inhibits Heat-induced Apoptosis Upstream of Mitochondria by Preventing Bax Translocation (2005)

Hsp70 overexpression can protect cells from stress-induced apoptosis. Our previous observation that Hsp70 inhibits cytochrome c release in heat-stressed cells led us to examine events occurring upstream of mitochondrial disruption. In this study we examined the effects of heat shock on the proapoptotic Bcl-2 family member Bax because of its central role in regulating cytochrome c release in stressed cells. We found that heat shock caused a conformational change in Bax that leads to its translocation to mitochondria, stable membrane association, and oligomerization. All of these events were inhibited in cells that had elevated levels of Hsp70. Hsp70 did not physically interact with Bax in control or heat-shocked cells, indicating that Hsp70 acts to suppress signals leading to Bax activation. Hsp70 inhibited stress-induced JNK activation and inhibition of JNK with SP600125 or by expression of a dominant negative mutant of JNK-blocked Bax translocation as effectively as Hsp70 overexpression. Hsp70 did not protect cells expressing a mutant form of Bax that has constitutive membrane insertion capability or cells treated with a small molecule activator of apoptosome formation, indicating that it is unable to prevent cell death after mitochondrial disruption and caspase activation have occurred. These results indicate that Hsp70 blocks heat-induced apoptosis primarily by inhibiting Bax activation and thereby preventing the release of proapoptotic factors from mitochondria. Hsp70, therefore, inhibits events leading up to mitochondrial membrane permeabilization in heat-stressed cells and thereby controls the decision to die but does not interfere with cell death after this event has occurred.
Identification of Urolithin A as a Metabolite Produced by Human Colon Microflora from Ellagic Acid and Related Compounds (2005)

Dietary ellagic acid and related polyphenols are metabolized in humans to dibenzopyran-6-one derivatives, and the microbial origin of these metabolites has been suggested. However, this has not been demonstrated so far. Fecal samples donated by six volunteers were incubated under anaerobic conditions, and aliquots were used to evaluate the fecal metabolism of ellagic acid, the ellagitannin punicalagin, and an ellagitannin rich extract from walnuts. The isoflavone daidzein was also incubated with the same fecal samples to follow the production of the microbial metabolites previously reported (dihydrogenistein, O-demethylangolensin, and equol) as a positive control of the system and to evaluate similarities between isoflavone and ellagic acid fecal flora metabolism. After fermentation the metabolite "urolithin A" (3,8-dihydroxy-6H-dibenzo[b,d]pyran-6-one) was produced from ellagic acid, punicalagin, and the ellagitannin extract in all the fecal cultures from different volunteers, but with very different production rates and concentrations. This large variability in the concentration of metabolite and kinetics of metabolite production is consistent with the large variability found in the excretion of these metabolites in urine in vivo after human consumption of ellagitannins, and with differences in the composition of the fecal microflora. No correlation between isoflavone and ellagic acid metabolism by fecal microflora was observed. The present study confirms the microbial origin of the recently reported in vivo generated hydroxy-6H-dibenzo[b,d]pyran-6-one derivatives in humans and is a further step in the study of the bioavailability and metabolism of ellagic acid and ellagitannins.
Differential expression of cyclin-dependent kinase 6 in cortical thymocytes and T-cell lymphoblastic lymphoma/leukemia. (1998)

Cyclin-dependent kinase-6 (CDK6) is the earliest inducible member of the CDK family in human T lymphocytes, involved in growth factor stimulation and cell cycle progression. CDK6 is one of the targets of p16 and p15, CDK inhibitors encoded by MTS1 and MTS2, two tumor suppressor genes that are frequently deleted in T-cell leukemia. In this study we have investigated CDK6 expression in normal and neoplastic lymphoid tissues using immunohistochemistry and flow cytometry. In normal (six samples) and hyperplastic (four samples) thymuses, strong CDK6 expression was observed in a discrete proportion of cortical thymocytes (10 to 15%), mainly located in the peripheral (subcapsular) zone of the cortex. All tested cases of T-cell lymphoblastic lymphoma/leukemia (T-LBL/ALL) showed strong CDK6 expression in the majority (up to 100%) of neoplastic lymphoid cells. Western blot analysis confirmed the expected CDK6 protein size (40 kd). According to Southern blot analysis, CDK6 overexpression in neoplastic T lymphoblasts was not due to gene amplification. In all other lymphomas investigated (28 peripheral T-cell non-Hodgkin's lympohomas (T-NHLs), 7 CD30+ anaplastic NHLs, 22 high-grade B-NHLs, 15 low-grade B-NHLs, 25 B-cell precursor ALLs), CDK6 was not expressed or expressed at low levels, with the only exception of three nasal angiocentric T-NHLs, all exhibiting CDK6 immunoreactivity comparable to that observed in T-LBL/ALL. These data provide evidence that CDK6 is abnormally expressed in T-LBL/ALL and may be involved in the pathogenesis of this malignancy. In addition, the quantitative difference of CDK6 expression between neoplastic and non-neoplastic cortical thymocytes can be potentially useful in the differential diagnosis of thymic neoplasms on histological and cytological specimens.
Analysis of Topical Cyclosporine Treatment of Patients With Dry Eye Syndrome<subtitle>Effect on Conjunctival Lymphocytes</subtitle> (2000)

<h3>Objective</h3> To study the effect of topical cyclosporine on lymphocyte activation within the conjunctiva of patients with moderate to severe dry eye syndrome (Sjögren and non-Sjögren). <h3>Methods</h3> Biopsy specimens were obtained at baseline and after 6 months of cyclosporine treatment from eyes of 32 patients with moderate to severe dry eye syndrome; 19 were cyclosporine treated (0.05% cyclosporine, n = 13; 0.1% cyclosporine, n = 6) and 13 were vehicle treated. Within this group there were 12 with Sjögren syndrome and 20 with non–Sjögren syndrome. Biopsy tissue was analyzed using immunohistochemical localization of binding of monoclonal antibodies to lymphocytic markers CD3, CD4, and CD8 as well as lymphocyte activation markers CD11a and HLA-DR. <h3>Results</h3> In cyclosporine-treated eyes, biopsy results of conjunctivae showed decreases in the number of cells positive for CD3, CD4, and CD8, while in vehicle-treated eyes, results showed increases in these markers, although these differences were not statistically significant. Following treatment with 0.05% cyclosporine, there was a significant decrease in the number of cells expressing the lymphocyte activation markers CD11a (<i>P</i>&lt;.05) and HLA-DR (<i>P</i>&lt;.05), indicating less activation of lymphocytes as compared with vehicle treatment. Within the Sjögren patient subgroup, those treated with 0.05% cyclosporine also showed a significant decrease in the number of cells positive for CD11a (<i>P</i>&lt;.001) as well as CD3 (<i>P</i>&lt;.03), indicating a reduction in number of activated lymphocytes. <h3>Conclusion</h3> Treatment of dry eye syndrome with topical cyclosporine significantly reduced the numbers of activated lymphocytes within the conjunctiva.
BAC Microarray-Based Comparative Genomic Hybridization (2004)

Alterations in DNA copy number underlie certain developmental abnormalities and are frequent in solid tumors. Microarray-based comparative genomic hybridization (array CGH) provides a high throughput means to measure and map copy number aberrations on a genome-wide scale and to link them directly to genome sequence. For applications involving the analysis of tumors, the technology must provide reliable detection of single copy gains and losses in mixed cell populations such as tumor and normal cells, accurate quantification of high level copy number gains, and confident interpretation of aberrations affecting only a single array element. Further, one would like to minimize the amount of specimen material required for an analysis. These requirements can be met if there are good signal-to-noise ratios in the hybridization.
Network-aware scheduling of mapreduce framework ondistributed clusters over high speed networks (2012)

Google's MapReduce has gained significant popularity as a platform for large scale distributed data processing. Hadoop [1] is an open source implementation of MapReduce [11] framework, originally it was developed to operate over single cluster environment and could not be leveraged for distributed data processing across federated clusters. At multiple federated clusters connected with high speed networks, computing resources are provisioned from any of the clusters from the federation. Placement of map tasks close to its data split is critical for performance of Hadoop. In this work, we add network awareness in Hadoop while scheduling the map tasks over federated clusters. We observe 12% to 15 % reduction of execution time in FIFO and FAIR schedulers of Hadoop for varying workloads.
Design of Comb-Type Polyamine Copolymers for a Novel pH-Sensitive DNA Carrier (1997)

The comb-type polycation consisting of a poly[2-(diethylamino)ethyl methacrylate] (PDEAEMA) backbone and poly(L-lysine) (PLL) side chains has been prepared as a novel pH-sensitive DNA carrier. The comb-type copolymer PDEAEMA-graft-PLL was prepared by using the macromonomer method, in which a poly(N epsilon-carbobenzoxy-L-lysine) macromonomer was radically copolymerized with DEAEMA. The comb-type copolymer exhibited a two-step proton dissociation and a dual ionic character owing to the two cationic segments in the copolymer, as determined by acid-base titration. In addition, the comb-type copolymer caused no significant turbidity even at pH 10, whereas PDEAEMA homopolymer suddenly precipitated out of the aqueous medium above pH 7.5 owing to the deprotonation of amino groups. Furthermore, a 1H NMR study proved that protonated PLL segments solubilized the comb-type copolymer with a hydrophobic PDEAEMA core at higher pH. Finally, the pH-dependent behavior of the DNA complex with the comb-type copolymer was evaluated. The discontinuous turbidity change of the DNA/PDEAEMA-graft-PLL mixture at pH 7.5 suggested that the solubility of the complex varied in response to pH. By circular dichroism measurement, we also found that the comb-type copolymer was capable of varying DNA compaction pH-dependently. In conclusion, we have demonstrated that the comb-type copolymer is capable of sensing a pH signal and outputting the nonlinear change of the physicochemical properties of DNA polyelectrolyte complexes.
Self-oscillating tapping mode atomic force microscopy (2003)

A piezoelectric microcantilever probe is demonstrated as a self-oscillator used for tapping mode atomic force microscopy. The integrated piezoelectric film on the cantilever serves as the frequency-determining component of an oscillator circuit; oscillation near the cantilever’s resonant frequency is maintained by applying positive feedback to the film via this circuit. This new mode, which is a step towards more compact and parallel tapping mode AFM imaging, is demonstrated by imaging an evaporated gold film on a silicon substrate. A self-oscillating frequency spectrum and a force–distance curve are also presented.
The promoter of the Arabidopsis thaliana Cel1 endo‐1,4‐β glucanase gene is differentially expressed in plant feeding cells induced by root‐knot and cyst nematodes (2004)

SUMMARY Transgenic tobacco and Arabidopsis thaliana carrying the Arabidopsis endo-1,4-beta-glucanase (EC 3.2.1.4) Cel1 promoter fused to the beta-glucuronidase (GUS) reporter gene were infected with the root-knot nematode, Meloidogyne incognita, and either the tobacco cyst nematode, Globodera tabacum (tobacco), or beet cyst nematode, Heterodera schachtii (Arabidopsis). Cel1-driven GUS expression was detected in cell elongation zones of noninfected plants and within feeding sites (giant-cells) induced in roots of both plant hosts by M. incognita. The first detectable signs of Cel1 expression within developing giant-cells occurred at the onset of giant-cell formation and continued throughout the M. incognita life cycle. UidA (Gus) transcripts were detectable within giant-cells induced in tobacco roots at 11-13 days postinoculation with M. incognita as determined by in situ mRNA hybridization. By contrast, expression of the Cel1 promoter was not detected within developing syncytia induced in tobacco or Arabidopsis roots by G. tabacum and H. schachtii, respectively, at any time point. The results demonstrate specific regulation of cell wall-degrading enzymes that may be required for cell wall modifications during feeding cell formation by sedentary endoparasitic nematodes. Differential expression of Cel1 by cyst and root-knot nematodes further supports underlying mechanistic differences in giant-cell and syncytium formation.
Immunophenotyping of melanomas for tyrosinase: implications for vaccine development. (1995)

Tyrosinase (EC 1.14.18.1), the key enzyme in melanin synthesis, has been shown to be one of the targets for cytotoxic T-cell recognition in melanoma patients. To develop serological reagents useful for immunophenotyping melanoma for tyrosinase, human tyrosinase cDNA was expressed in an Escherichia coli expression vector. The purified recombinant tyrosinase was used to generate mouse monoclonal and rabbit polyclonal antibodies. The prototype monoclonal antibody, T311, recognized a cluster of protein moieties ranging from 70 to 80 kDa in tyrosinase mRNA-positive melanoma cell lines and melanoma specimens as well as in L cells transfected with tyrosinase cDNA. Untransfected L cells and L cells transfected with tyrosinase-related protein 1, TRP-1(gp75), were nonreactive. Immunohistochemical analysis of melanomas with T311 showed tyrosinase in melanotic and amelanotic variants, and tyrosinase expression correlated with the presence of tyrosinase mRNA. Melanocytes in skin stained with T311, whereas other normal tissues tested were negative. The expression pattern of three melanosome-associated proteins--tyrosinase, TRP-1(gp75), and gp100--in melanoma was also compared. Tyrosinase and gp100 are expressed in a higher percentage of melanomas than TRP-1(gp75), and the expression of these three antigens was discordant. Tyrosinase expression within individual tumor specimen is usually homogenous, distinctly different from the commonly observed heterogeneous pattern of gp100 expression.
Identification of Nectin-4 Oncoprotein as a Diagnostic and Therapeutic Target for Lung Cancer (2009)

Gene expression profile analysis of lung cancers revealed the transactivation of an immunoglobulin-like molecule Nectin-4 in the majority of non-small cell lung cancers (NSCLC). Immunohistochemical staining of 422 NSCLCs showed that a high level of Nectin-4 expression was associated with poor prognosis for NSCLC patients (P < 0.0001), and multivariate analysis confirmed its independent prognostic value (P < 0.0001). We established an ELISA to measure serum Nectin-4 and found that serum Nectin-4 levels were significantly higher in NSCLC patients than in healthy volunteers. The proportion of the serum Nectin-4-positive cases was 88 of 164 (53.7%) NSCLCs, whereas only 3 of 131 (2.3%) healthy volunteers were falsely diagnosed as positive, which was superior to carcinoembryonic antigen (CEA) and cytokeratin 19-fragment (CYFRA21-1) in sensitivity and specificity. A combined ELISA for both Nectin-4 and CEA increased sensitivity and classified 65.0% of lung adenocarcinomas as positive with false-positive rate of 4.6%. The use of both Nectin-4 and CYFRA21-1 classified 68.3% of lung squamous cell carcinomas as positive with false-positive rate of 6.1%. Treatment of lung cancer cells with small interfering RNAs against Nectin-4 suppressed its expression and cell growth. In addition, exogenous expression of Nectin-4 increased the lamellipodia formation and the invasive ability of mammalian cells through activation of small GTPase Rac1. Nectin-4 might play a significant role in lung carcinogenesis, and it should be a new candidate serum and tissue biomarker, as well as a therapeutic target.
Evolutionary Constraints on the Norovirus Pandemic Variant GII.4_2006b over the Five-Year Persistence in Japan (2017)

Norovirus GII.4 is a major cause of global outbreaks of viral gastroenteritis in humans, and has evolved by antigenic changes under the constantly changing human herd immunity. Major shift in the pandemic GII.4 strain periodically occurs concomitant with changes in the antigenic capsid protein VP1. However, how the newly emerged strain evolves after the onset of pandemic remains unclear. To address this issue, we examined molecular evolution of a pandemic lineage, termed the GII.4_2006b, by using the full-length viral genome and VP1 sequences (<i>n</i> = 317) from stools collected at 20 sites in Japan between 2006 and 2011. Phylogenetic tree showed a radial diversification of the genome sequences of GII.4_2006b, suggesting a rapid genetic diversification of the GII.4_2006b population from a few ancestral variants. Impressively, amino acid sequences of the variable VP1 in given seasons remained as homogeneous as those of viral enzymes under annual increase in the nucleotide diversity in the VP1 coding region. The Hamming distances between the earliest and subsequent variants indicate strong constraints on amino acid changes even for the highly variable P2 subdomain. These results show the presence of evolutionary constraints on the VP1 protein and viral enzymes, and suggest that these proteins gain near maximal levels of fitness benefits in humans around the onset of the outbreaks. These findings have implications for our understanding of molecular evolution, mechanisms of the periodic shifts in the pandemic NoV GII.4 strains, and control of the NoV GII.4 pandemic strain.
Oncogene-Induced Transformation of C3H 10T1/2 Cells Is Enhanced by Tumor Promoters (1984)

The tumor promoters 12-O-tetradecanoyl-phorbol-13-acetate and teleocidin markedly enhanced the transformation of C3H 10T1/2 mouse fibroblasts when these cells were transfected with the cloned human bladder cancer c-rasH oncogene. Transfection studies with the drug resistance marker gpt and time course studies indicate that this enhancement is not simply an effect on the process of DNA transfection. These findings, together with parallel studies with NIH 3T3 fibroblasts, also indicate that the competence of animal cells for DNA transfection is a function of the recipient cell line, the transfected marker, and the growth conditions. Our findings suggest that during multistage carcinogenesis tumor promoters may complement the function of activated cellular oncogenes.
Retroviral Transfer of Acid α -Glucosidase cDNA to Enzyme-Deficient Myoblasts Results in Phenotypic Spread of the Genotypic Correction by Both Secretion and Fusion (1997)

Myoblasts have properties that make them suitable vehicles for gene replacement therapy, and lysosomal storage diseases are attractive targets for such therapy. Type II Glycogen Storage Disease, a deficiency of acid alpha-glucosidase (GAA), results in the abnormal accumulation of glycogen in skeletal and cardiac muscle lysosomes. The varied manifestations of the enzyme deficiency in affected patient are ultimately lethal. We used a retroviral vector carrying the cDNA encoding for GAA to replace the enzyme in deficient myoblasts and fibroblasts and analyzed the properties of the transduced cells. The transferred gene was efficiently expressed, and the de novo-synthesized enzyme reached lysosomes where it digested glycogen. In enzyme-deficient myoblasts after transduction, enzyme activity rose to more than 30-fold higher than in normal myoblasts and increased about five-fold more when the cells were allowed to differentiate into myotubes. The transduced cells secreted GAA that was endocytosed via the mannose-6-phosphate receptor into lysosomes of deficient cells and digested glycogen. Moreover, the transduced myoblasts were able to fuse with and provide enzyme for GAA-deficient fusion partners. Thus, the gene-corrected cells, which appear otherwise normal, may ultimately provide phenotypic correction to neighboring GAA-deficient cells by fusion and to distant cells by secretion and uptake mechanisms.
Tissue Culture Methods of Watermelon (2012)

The plant tissue culture techniques are recognized as a creative, promising and feasible option for the multiplication and genetic modification of plant worldwide. As a tool of genetic engineering for plant, in vitro plant regeneration systems are taken a key part. Tissue culture systems are also used as alternative methods of vegetative plant propagation. While one cutting produces one plant by cutting propagation method and one seed produces one plant. In contrast, one explant (a piece of stem, leaf, bud, root, anther, or etc.) can produce an infinity number of plants using tissue culture system within a relatively short period. Somaclonal variation can be occurred in regenerated plant when plant regenerated from callus, which needs to be screened out of breeding programmes. Tissue culture systems have been now important and valuable for propagation and modification genetically in many plant species with immense potential in agriculture, horticulture and forestry. In this book, micropropagation, shoot organogenesis from callus and cell suspension culture are described in detailed, which are essential for improvement of watermelon.