Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of SH-PTP2, a protein-tyrosine phosphatase with Src homology 2 domains, in insulin-stimulated Ras activation

SH-PTP2 is a nontransmembrane human protein-tyrosine phosphatase that contains two Src homology 2 (SH2) domains and binds to insulin receptor substrate 1 (IRS-1) via these domains in response to insulin. The expression of a catalytically inactive mutant of SH-PTP2 (containing the mutation Cys-459-->Ser) in Chinese hamster ovary cells that overexpress human insulin receptors (CHO-IR cells) markedly attenuated insulin-stimulated Ras activation. Expression of mutant SH-PTP2 also inhibited MAP kinase activation in response to insulin but not in response to 12-O-tetradecanoyl phorbol-13-acetate. In contrast, the insulin-induced association of phosphoinositide 3-kinase activity with IRS-1 was not affected by the expression of inactive SH-PTP2. Furthermore, the expression of mutant SH-PTP2 had no effect on the binding of Grb2 to IRS-1, on the tyrosine phosphorylation of Shc, or on the formation of the complex between Shc and Grb2 in response to insulin. However, the amount of SH-PTP2 bound to IRS-1 in insulin-treated CHO-IR cells expressing mutant SH-PTP2 was greater than that observed in CHO-IR cells overexpressing wild-type SH-PTP2. Recombinant SH-PTP2 specifically dephosphorylated a synthetic phosphopeptide corresponding to the sequence surrounding Tyr-1172 of IRS-1, a putative binding site for SH-PTP2. Additionally, phenylarsine oxide, an inhibitor of protein-tyrosine phosphatases, inactivated SH-PTP2 in vitro and increased the insulin-induced association of SH-PTP2 with IRS-1. These results suggest that SH-PTP2 may regulate an upstream element necessary for Ras activation in response to insulin and that this upstream element may be required for the Grb2- or Shc-dependent pathway. Furthermore, these results are consistent with the notion that SH-PTP2 may bind to IRS-1 through its SH2 domains in response to insulin and dephosphorylate the phosphotyrosine residue to which it binds, thereby regulating its association with IRS-1.
Shiga and Shiga-like toxins

Although Shigella dysenteriae serotype 1 (Shiga) toxin was discovered more than 80 years ago (18) and has long been recognized as one of the most potent bacterial toxins (18, 116), early efforts to characterize its structure, biologic activity, genetics, role in pathogenesis, and other properties were hindered by difficulties in preparing pure toxin, obtaining appropriate immunologic reagents, and conducting genetic studies with S. dysenteriae 1. The enterotoxicity of Shiga toxin was first reported in 1972 (59). Other important advances that have been made during the past decade include the following: (i) purification of Shiga toxin to homogeneity (7, 21, 81, 87, 120); (ii) identification of cell surface receptors for toxin (8, 45; A. A. Lindberg, J. E. Brown, N. Stromberg, M. Westling-Ryd, J. E. Schultz, and K. A. Karlson, J. Bliol. Chem., in press; A. A. Lindberg, J. E. Schultz, M. Westling, J. E. Brown, S. W. Rothman, K. A. Karlsson, and N. Stromberg, Proc. FEMS Meet. Mol. Biol. Pathogenic Microorganisms, in press); (iii) demonstration that the intracellular action of toxin causes an inhibition of protein synthesis (7, 8a, 97, 111; T. G. Obrig, T. P. Moran, and J. E. Brown, J. Biol. Chem., in press); (iv) recognition
Induction of mutation in mouse FM3A cells by N4-aminocytidine-mediated replicational errors

To explore the potential use of a nucleoside analog, N4-aminocytidine, in studies of cellular biology, the mechanism of mutation induced by this compound in mouse FM3A cells in culture was studied. On treatment of cells in suspension with N4-aminocytidine, the mutation to ouabain resistance was induced. The major DNA-replicating enzyme in mammalian cells, DNA polymerase alpha, was used to investigate whether the possible cellular metabolite of N4-aminocytidine, N4-aminodeoxycytidine 5'-triphosphate (dCamTP), can be incorporated into the DNA during replication. Using [3H]dCamTP in an in vitro DNA-synthesizing system, we were able to show that this nucleotide analog can be incorporated into newly formed DNA and that it can serve as a substitute for either dCTP or dTTP. dCamTP in the absence of dCTP maintained the activated calf thymus DNA-directed polymerization of deoxynucleoside triphosphates as efficiently as in its presence. Even in the presence of dCTP, dCamTP was incorporated into the polynucleotide. When dCamTP was used as a single substrate in the poly(dA)-oligo(dT)-directed polymerase reaction, it was incorporated into the polynucleotide fraction. The extent of incorporation was 4% of that of dTTP incorporation when dTTP was used as a single substrate. Even in the presence of dTTP, dCamTP incorporation was observed. A copolymer containing N4-aminocytosine residues was shown to incorporate guanine residues opposite the N4-aminocytosines. However, we were unable to observe adenine incorporation opposite N4-aminocytosine in templates. These cell-free experiments show that an AT-to-GC transition can take place in the presence of dCamTP during DNA synthesis, strongly suggesting that the mutation induced in the FM3A cells by N4-aminocytidine is due to replicational errors.
The Highly Conserved C-Terminal Dileucine Motif in the Cytosolic Domain of the Human Immunodeficiency Virus Type 1 Envelope Glycoprotein Is Critical for Its Association with the AP-1 Clathrin Adapter

Short amino acid sequences in the cytosolic domains of transmembrane proteins are recognized by special- ized adapter proteins which are part of coated vesicles utilized to transport membrane proteins between the trans-Golgi network (TGN) and the plasma membrane (forward and backward). Previously, we and others re- ported that the membrane-proximal tyrosine residues Y712 (human immunodeﬁciency virus [HIV]) and Y721 (simian immunodeﬁciency virus [SIV]) in the envelope glycoprotein (Env) of the primate lentiviruses are cru- cial for the association of Env with clathrin-associated adapter complex AP-2. The same tyrosine-based endocytosis motifs in the cytosolic domains (EnvCD) of transmembrane gp41 of HIV type 1 (HIV-1) and SIV, respec- tively, were also shown to modulate the interaction with TGN- and endosome-based clathrin-associated complex AP-1. Our ﬁndings suggested that EnvCD binding to AP-1, unlike the association of EnvCD with AP-2, is dependent largely on residues other than Y712 and Y721. Here, we tested if motifs downstream of Y712 affect HIV-1 EnvCD–AP-1 binding and Env trafﬁcking. Mutational analysis revealed that the C-terminal leucine-based mo- tif in Env was crucial for the recruitment of AP-1 in vitro and in Env-expressing cells. In addition to affecting Env–AP-1 association, mutations at the C terminus of Env also altered the subcellular localization of Env, sug- gesting that proper post-Golgi routing of Env depends on its recruitment of AP-1. Finally, the C-terminal dileucine was shown to assist the membrane-proximal Y712 motif in restricting the cell surface expression of Env. incubated anti-Env mono- or with from an infected individual in BSA-DMEM m per three times nonspeciﬁc secondary antibody binding blocked 20 and transfection of CD8-EnvCD chimeras. DNA fragment encoding EnvCD of HIV-1 LAI Env (amino acid residues 707 to 856) was obtained by PCR and cloned in-frame with the extracellular and transmembrane (TM) domains of human CD8 alpha chain (residues 1 to 211) into the pJ.CN vector (48) to generate the pCD8-HIV construct. The HIV-1 LAI Env dileucine motifs at positions 814 and 815 and
Thermo-mechanical properties of cubic titanium nitride

Abstract The equilibrium structure, elastic constants Cij and thermodynamic functions of cubic titanium nitride (TiN) were calculated within the temperature range of 0–3100 K and under a pressure range 0–60 GPa. Properties were computed using the generalised gradient approximations (GGA) exchange-correlation functional. Calculated mechanical properties (Elastic constants, Young’s modulus and shear modulus) and phonon spectra of TiN obtained via robust DFT-QHA algorithm, were generally in a good agreement with available experimental and theoretical analogous values. In particular, a well-examined quasi-harmonic approximation method implemented in the Gibbs2 code is utilised herein to provide accurate estimation of thermal expansion coefficients, entropies, heat capacity values (at different combinations of temperature/volume/pressure) and Debye’s temperature. Parameters calculated herein shall be useful to elucidate the superior performance of TiN at harsh operational conditions encompassing elevated temperatures and pressures pertinent to cutting machineries and surface coatings.
Loss of p53 protein during radiation transformation of primary human mammary epithelial cells

The causative factors leading to breast cancer are largely unknown. Increased incidence of breast cancer following diagnostic or therapeutic radiation suggests that radiation may contribute to mammary oncogenesis. This report describes the in vitro neoplastic transformation of a normal human mammary epithelial cell strain, 76N, by fractionated gamma-irradiation at a clinically used dose (30 Gy). The transformed cells (76R-30) were immortal, had reduced growth factor requirements, and produced tumors in nude mice. Remarkably, the 76R-30 cells completely lacked the p53 tumor suppressor protein. Loss of p53 was due to deletion of the gene on one allele and a 26-bp deletion within the third intron on the second allele which resulted in abnormal splicing out of either the third or fourth exon from the mRNA. PCR with a mutation-specific primer showed that intron 3 mutation was present in irradiated cells before selection for immortal phenotype. 76R-30 cells did not exhibit G1 arrest in response to radiation, indicating a loss of p53-mediated function. Expression of the wild-type p53 gene in 76R-30 cells led to their growth inhibition. Thus, loss of p53 protein appears to have contributed to neoplastic transformation of these cells. This unique model should facilitate analyses of molecular mechanisms of radiation-induced breast cancer and allow identification of p53-regulated cellular genes in breast cells.
Differential expression of the myocyte enhancer factor 2 family of transcription factors in development: the cardiac factor BBF-1 is an early marker for cardiogenesis

In the present study, we have used single chicken blastoderms of defined early developmental stages, beginning with the prestreak stage, stage 1 (V. Hamburger and H. L. Hamilton, J. Morphol. 88:49-92, 1951), to analyze the onset of cardiac myogenesis by monitoring the appearance of selected cardiac muscle tissue-specific gene transcripts and the functional expression of the myocyte enhancer factor 2 (MEF-2) proteins. Using gene-specific oligonucleotide primers in reverse transcriptase PCR assay, we have demonstrated that the cardiac myosin light-chain 2 (MLC2) and alpha-actin gene transcripts appear as early as stage 5, i.e., immediately after the cardiogenic fate assignment at stage 4. Consistent with this observation is the developmental expression pattern of DNA-binding activity of BBF-1, a cardiac muscle-specific member of the MEF-2 protein family, which also begins at stage 5 prior to MEF-2. Differential expression of DNA-binding complexes is also observed with another AT-rich DNA sequence (CArG box) as probe, but the binding pattern with the ubiquitous TATA-binding proteins remains unchanged during the same developmental period. Thus, the cardiogenic commitment and differentiation of the precardiac mesoderm, as exemplified by the appearance of cardiac MEF-2, MLC2, and alpha-actin gene products, occur earlier than previously thought and appear to be closely linked. The onset of skeletal myogenic program follows that of the cardiogenic program with the appearance of skeletal MLC2 at stage 8. We also observed that mRNA for the MEF-2 family of proteins appears as early as stage 2 and that for CMD-1, the chicken counterpart of MyoD, appears at stage 5. The temporal separation of activation of cardiac and skeletal MLC2 genes, which appears immediately after the respective fate assignments, and those of cardiac MEF-2 and CMD-1, which occur before, are consistent with the established appearance of the myogenic programs and with the acquisition pattern of the two tissue-specific morphological characteristics in the early embryo. The preferential appearance of BBF-1 activity in precardiac moesderm, relative to that of MEF-2, indicates that these two protein factors are distinct members of the MEF-2 family and provides a compelling argument in support of the potential role of BBF-1 as a regulator of the cardiogenic cell lineage determination, while cardiac MEF-2 might be involved in maintenance of the cardiac differentiative state.
Suppression of tropomyosin synthesis, a common biochemical feature of oncogenesis by structurally diverse retroviral oncogenes

To identify proteins whose production may be altered as a common event in the expression of structurally diverse oncogenes, we compared two-dimensional electropherograms of newly synthesized proteins from NIH/3T3 cell lines transformed by a variety of retroviral oncogenes, from cellular revertant lines, and from a line (433.3) which expresses the v-ras oncogene in response to corticosteroids. Most alterations in the synthesis of specific proteins detected by this approach appeared to be the result of selection during prolonged cultivation and were probably unrelated to the transformation process. However, we detected seven proteins whose synthesis was strongly suppressed in cell lines transformed by each of the six retroviral oncogenes we studied and whose production was fully or partially restored in two cellular revertant lines. Suppression of two of these proteins was also correlated with the initial appearance of morphological alteration during corticosteroid-induced oncogene expression in 433.3 cells. These proteins (p37/4.78 and p41/4.75) were identified as tropomyosins, a group of at least five cytoskeletal proteins. Transformation by the papovaviruses simian virus 40 and polyomavirus caused no suppression of synthesis of these tropomyosins. This indicates that suppression of tropomyosin synthesis is not a nonspecific response by cells to being forced to grow with the transformed phenotype but is specifically associated with oncogenesis by diverse retroviral oncogenes. The results are consistent with the hypothesis that the different biochemical processes initiated by expression of structurally diverse retroviral oncogenes may converge on a limited number of common targets, one of which is the mechanism which regulates the synthesis of tropomyosins.
The Saccharomyces cerevisiae checkpoint gene BUB1 encodes a novel protein kinase

Normal cell multiplication requires that the events of mitosis occur in a carefully ordered fashion. Cells employ checkpoints to prevent cycle progression until some prerequisite step has been completed. To explore the mechanisms of checkpoint enforcement, we previously screened for mutants of Saccharomyces cerevisiae which are unable to recover from a transient treatment with a benzimidazole-related microtubule inhibitor because they fail to inhibit subsequent cell cycle steps. Two of the identified genes, BUB2 and BUB3, have been cloned and described (M. A. Hoyt, L. Totis, and B. T. Roberts, Cell 66:507-517, 1991). Here we present the characterization of the BUB1 gene and its product. Genetic evidence was obtained suggesting that Bub1 and Bub3 are mutually dependent for function, and immunoprecipitation experiments demonstrated a physical association between the two. Sequence analysis of BUB1 revealed a domain with similarity to protein kinases. In vitro experiments confirmed that Bub1 possesses kinase activity; Bub1 was able to autophosphorylate and to catalyze phosphorylation of Bub3. In addition, overproduced Bub1 was found to localize to the cell nucleus.
urbs1, a gene regulating siderophore biosynthesis in Ustilago maydis, encodes a protein similar to the erythroid transcription factor GATA-1

Ustilago maydis secretes ferrichrome-type siderophores, ferric-ion-binding compounds, in response to iron starvation. TA2701, a non-enterobactin-producing, non-ferrichrome-utilizing mutant of Salmonella typhimurium LT-2, was employed as a biological indicator in a novel screening method to isolate three N-methyl-N'-nitro-N-nitrosoguanidine-induced U. maydis mutants defective in the regulation of ferrichrome-type siderophore biosynthesis. These mutants displayed a constitutive phenotype; they produced siderophores in the presence of iron concentrations that would typically repress siderophore synthesis in wild-type strains. A 4.8-kb fragment of U. maydis genomic DNA capable of restoring normal regulation of siderophore biosynthesis in the constitutive mutants was identified. This segment of DNA contains an intronless open reading frame that specifies a protein of 950 amino acids containing two finger motifs similar to those found in the erythroid transcription factor GATA-1. Disruption of this open reading frame in a wild-type strain gave rise to cells that produced siderophores constitutively. Genetic studies indicated that the disruption mutation was allelic to the chemically induced mutations, confirming that the structural gene for a regulator rather than a suppressor gene had been cloned. Northern (RNA) analysis of the gene revealed a 4.2-kb transcript that is expressed constitutively at low levels in wild-type cells. The data support the hypothesis that this gene, which we designate urbs1 (Ustilago regulator of biosynthesis of siderophores), acts directly or indirectly to repress biosynthesis of siderophores in U. maydis.
Isolation of Serratia marcescens on Deoxyribonuclease-Toluidine Blue-Cephalothin Agar

Serratia marcescens was isolated on a new medium—commercial deoxyribonuclease agar with the addition of cephalothin (1,000 μg/ml) and Toluidine Blue (1,000 μg/ml). It was detected in water samples even though it comprised only 0.1 to 0.0001% of the total bacterial population.
Abolition of Swarming of Proteus by p-Nitrophenyl Glycerin: Application to Blood Agar Media

Comparative plate counts were made of Staphylococcus aureus and Streptococcus pyogenes growing on blood agar supplemented with individual chemicals to abolish the swarming of Proteus. B-phenylethanol, sodium azide, and p-nitrophenyl glycerin (PNPG) were used as anti-swarm agents. Each anti-swarm agent effectively abolished swarming for 24 h, but azide failed to control swarming for longer periods of incubation. In addition, azide displayed growth inhibition towards the staphylococci and streptococci resulting in no hemolysis and reduced viable cell numbers with the streptococci. Phenylethanol showed reduced viable cell numbers with the streptococci and unreliable hemolytic reactions. At 0.1 to 0.3 mM, PNPG proved to be a superior anti-swarm agent in that it showed no growth inhibition and allowed normal hemolysis, but abolished swarming for extended periods of time. When laboratory strains of Streptococcus pneumoniae, Klebsiella pneumoniae, Pseudomonas aeruginosa. Listeria monocytogenes, and Vibrio cholerae were screened on a blood agar medium containing 0.1 mm PNPG, they displayed similar growth and hemolytic characteristics to the identical medium without PNPG.
Effect of Monosodium n-Alkylsalicylates on Spores of Bacillus subtilis

The effects of several monosodium n-alkylsalicylates on washed spores of Bacillus subtilis have been examined. None of the compounds was sporicidal, but in general they prevented dormancy induced by incubating the spores in water. This effect was related to the position in the ring and size of the alkyl groups substituted on the salicylic acid nucleus.
A Course-Based Undergraduate Research Experience in CRISPR-Cas9 Experimental Design to Support Reverse Genetic Studies in Arabidopsis thaliana

Gene-editing tools such as CRISPR-Cas9 have created unprecedented opportunities for genetic studies in plants and animals. We designed a course-based undergraduate research experience (CURE) to train introductory biology students in the concepts and implementation of gene-editing technology as well as develop their soft skills in data management and scientific communication. ABSTRACT Gene-editing tools such as CRISPR-Cas9 have created unprecedented opportunities for genetic studies in plants and animals. We designed a course-based undergraduate research experience (CURE) to train introductory biology students in the concepts and implementation of gene-editing technology as well as develop their soft skills in data management and scientific communication. We present two versions of the course that can be implemented with twice-weekly meetings over a 5-week period. In the remote-learning version, students performed homology searches, designed guide RNAs (gRNAs) and primers, and learned the principles of molecular cloning. This version is appropriate when access to laboratory equipment or in-person instruction is limited, such as during closures that have occurred in response to the COVID-19 pandemic. In person, students designed gRNAs, cloned CRISPR-Cas9 constructs, and performed genetic transformation of Arabidopsis thaliana. Students learned how to design effective gRNA pairs targeting their assigned gene with an 86% success rate. Final exams tested students’ ability to apply knowledge of an unfamiliar genome database to characterize gene structure and to properly design gRNAs. Average final exam scores of ∼73% and ∼84% for in-person and remote-learning CUREs, respectively, indicated that students met learning outcomes. The highly parallel nature of the CURE makes it possible to target dozens to hundreds of genes, depending on the number of sections. Applying this approach in a sensitized mutant background enables focused reverse genetic screens for genetic suppressors or enhancers. The course can be adapted readily to other organisms or projects that employ gene editing.
UV radiation hardness of photovoltaic modules featuring crystalline Si solar cells with AlOx/p+‐type Si and SiNy/n+‐type Si interfaces

We report on the UV radiation hardness of photovoltaic modules with bifacial n‐type Passivated Emitter and Rear Totally diffused crystalline Si cells that are embedded in an encapsulation polymer with enhanced UV transparency. Modules with front junction cells featuring an AlOx/p+‐type Si passivation interface at the illuminated side are stable for a UV irradiation dose of 598 kWh m−2. In contrast, irradiating modules with back junction cells featuring an a‐SiNy/n+‐type Si passivation interface at the illuminated side reduces the output power by 15%. The quantum efficiency of the a‐SiNy‐passivated module degrades in the spectral range between 300 and 1000 nm, which we ascribe to a degradation of the surface passivation. Modeling the experimental data shows that photons with an energy above 3.4 eV contribute to the degradation effect and enhance the front surface recombination current density by a factor of 15.
Dietary element assessment of legumes originated from Tunceli province using different dissolving techniques

The objective of this study was to compare mineral contents of chickpeas and haricot bean using two different analytical digestion method including dry ashing and microwave digestion method. The levels of micronutrient (Cu, Fe, Mn, Zn) and macronutrient minerals (Ca, Mg, Na, K) in two different legumes, as chickpea ( Cicer arientinum L) and haricot bean ( Phaseolus vulgaris L. ) samples that are widely growing and consumed in Tunceli Province-Turkey were evaluated. The mineral composition of chickpea and haricot bean were determined by using FAAS after dissolving dry ashing and microwave digestion methods. In this way both the mineral composition of legume samples and the dissolving methods were compared. Results obtained from each group and each method was analyzed statistically using the SPSS statistic program. It was observed that in chickpea and haricot bean samples Ca, Cu and Zn concentrations using microwave digestion method were higher than dry ashing method (p<0.01).