268 Matching Annotations
  1. Oct 2021
  2. Sep 2021
  3. Aug 2021
    1. RRID:ZFIN_ZDB-GENO-060811-12

      DOI: 10.7554/eLife.22199

      Resource: (ZFIN Cat# ZDB-GENO-060811-12,RRID:ZFIN_ZDB-GENO-060811-12)

      Curator: @scibot

      SciCrunch record: RRID:ZFIN_ZDB-GENO-060811-12


      What is this?

  4. Jul 2021
  5. Jun 2021
  6. Mar 2021
    1. Results for individual PALB2 variants were normalized relative to WT-PALB2 and the p.Tyr551ter (p.Y551X) truncating variant on a 1:5 scale with the fold change in GFP-positive cells for WT set at 5.0 and fold change GFP-positive cells for p.Y551X set at 1.0. The p.L24S (c.71T>C), p.L35P (c.104T>C), p.I944N (c.2831T>A), and p.L1070P (c.3209T>C) variants and all protein-truncating frame-shift and deletion variants tested were deficient in HDR activity, with normalized fold change <2.0 (approximately 40% activity) (Fig. 1a).

      AssayResult: 4

      AssayResultAssertion: Indeterminate

      StandardErrorMean: 0.32

    2. A total of 84 PALB2 patient-derived missense variants reported in ClinVar, COSMIC, and the PALB2 LOVD database were selected

      HGVS: NM_024675.3:c.1226A>G p.(Tyr409Cys)

    1. SUPPLEMENTARY DATA

      AssayResult: 94.01

      AssayResultAssertion: Not reported

      PValue: > 0.9999

      Comment: Exact values reported in Table S3.

    2. To this end, 44 missense variants found in breast cancer patients were identified in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar) and/or selected by literature curation based on their frequency of description or amino acid substitution position in the protein (Supplemental Table S1).

      HGVS: NM_024675.3:c.280G>A p.(Glu94Lys)

    1. Source Data

      AssayResult: 23.96

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardErrorMean: 7.6

      Comment: Exact values reported in “Source Data” file.

    2. Source Data

      AssayResult: 7.75

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardDeviation: 2.59

      StandardErrorMean: 1.83

      Comment: Exact values reported in “Source Data” file.

    3. We, therefore, analyzed the effect of 48 PALB2 VUS (Fig. 2a, blue) and one synthetic missense variant (p.A1025R) (Fig. 2a, purple)29 on PALB2 function in HR.

      HGVS: NM_024675.3:c.1592delT p.(L531Cfs)

    1. Most Suspected Brugada Syndrome Variants Had (Partial) Loss of Function

      AssayResult: 68.1

      AssayResultAssertion: Indeterminate

      ReplicateCount: 18

      StandardErrorMean: 8.7

      Comment: This variant had mild loss of function (peak current >50% and <75% of wildtype), therefore it was considered inconclusive and neither abnormal nor normal in vitro function. (Personal communication: A. Glazer)

    2. we selected 73 previously unstudied variants: 63 suspected Brugada syndrome variants and 10 suspected benign variants

      HGVS: NM_198056.2:c.2200A>G p.(Met734Val)

  7. Feb 2021
    1. Supplemental material

      AssayResult: 94

      AssayResultAssertion: Normal

      Comment: See Table S3 for details; This variant was reported as c.323_235del but assumed to be c.323_325del, which corresponds to the reported protein change (p.(Gly108_Phe109delinsVal)).

    2. Supplemental material

      AssayResult: 3.8

      AssayResultAssertion: Abnormal

      Comment: See Table S3 for details; This variant was reported as c.323_235del but assumed to be c.323_325del, which corresponds to the reported protein change (p.(Gly108_Phe109delinsVal)).

    3. We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.

      HGVS: NM_000546.5:c.323_325del p.(Gly108_Phe109delinsVal)

  8. Dec 2020
    1. L’adoption de l’article 12 de la CIDE a marqué un tournant décisif dans l’avènement des droits de l’enfant. Il impose aux États une obligation de considérer l’enfant comme un acteur en capacité de contribuer à sa propre protection en participant aux décisions le concernant.

      à mettre en relation avec le rapport du DD sur la JADE

  9. Oct 2020
    1. For many amorphous and crystalline semiconductors,an exponential dependence of absorption coefficientα<104cm−1may take Urbach’s empirical formula [28]:av=a0exphv/EU,wherea0is a constant andEU(Urbachenergy) is an energy characterizing the degree of disorderintroduced from defects and grain boundaries; also, it is inter-preted as the width of the tail of localized states associated withthe amorphous states in forbidden band. Figure 12 representsthe logarithm of absorption coefficient as function of thephoton energy at different deposition times 20, 30, 40, and50 min. The value ofEUis calculated from the inverse slopeof the linear part of curves and also listed in Table 3

      Para muchos semiconductores amorfos y cristalinos, una dependencia exponencial del coeficiente de absorción puede tomar la formula empírica de Urbach [28]:

      donde es una constante y (la energía de Urbach) es una energía caracterizada por el grado de desorden introducido de defectos y los limites de grano; también es interpretado como el amplio de la cos estados localizados de la cola asociados con los estados amorfos en la banda prohibida. La figura 12 representa el logaritmo del coeficiente absorción como una función del fotón de energía a diferentes tiempos de deposición (20,30,40 y 50 min). El valor de la energía de Urbach es calculado desde la pendiente inversa de la parte linear de las las curvas y también enlistado en la Tabla 3.

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  10. Sep 2020
    1. “You are free to eat from any tree in the garden;(W) 17 but you must not eat from the tree of the knowledge of good and evil,(X) for when you eat from it you will certainly die.”

      God instructed Adam and Eve to eat whatever they desired, though prohibited them to eat from the tree of the knowledge of good and evil. In Robin Wall Kimmerer's "Skywoman Falling", she explained how in Indigenous culture, they follow Original Instructions. These "instructions" are not rules but rather guidelines for each person. Kimmerer explains how during Skywoman's time, the first people's understanding of the Original Instructions were to care for the and have respect for hunted animals, value family, and hold respectful ceremonies for their beliefs.

  11. Jun 2020
    1. vous

      Pourquoi est ce que pour cette question il a fallu calculer a nouveau le rayon de la terre alors qu'elle était déjà donnée dans un document et que nous l'avons calculer dans la question 13 ? Et que les 3 valeurs ( valeur donnée dans le doc et dans les calculs ) ne sont pas les mêmes

  12. Mar 2020
    1. This source is presented by Google who is well-known by its platform to inform and provide technological advancers for others. This particular report highlights the major trends for K-12 classrooms worldwide. This analysis provides data and interviews gathered from students and teachers about the evolution of K-12 classrooms. Rating: 9/10

    1. Roles and Practices of Educators in Technology-Supported Learning

      This article examines how technology is used in classrooms by educators and students in the every-changing technology realm. I liked how this article addressed the professional development educators need in K-12 classrooms. There are multitude of ways educators can gain additional learning opportunities for themselves or their students via technology. K-12 Educators can share their skills with other educators via online platforms. Rate: 7/10

    1. This article explores how technology can be utilized in the K-12 classroom. Educators can consider this a professional development due to the content it covers. Technological language can be decoded and evaluated through instruction. Teacher can use what children, adolescents, and teenagers are interested in technology wise. Incorporating this into the classroom will be engaging for learners. Rate: 7/10

  13. Dec 2019
  14. Nov 2019
    1. Mary Lou Fulton Teachers College

      This site is the homepage of the Tech Infusion program at Arizona State University (ASU). Housed within ASU's Mary Lou Fulton Teachers College, Tech Infusion is a technology integration curriculum for Pre-K-12 teacher candidates. Through coursework and hands-on practices, teacher candidates are prepared to use technology fluently and innovatively for teaching and learning. The program integrates research, ISTE Standards, and the TPACK (Technological Pedagogical Content Knowledge) framework around effective technology integration. This website provides technology-infusion resources for course developers, instructors, and current and future educators. Examples include research articles, edtech tool tutorials, lesson plans, and outlines of the curriculum. Rating: 9/10

    1. Coffey argues the effectiveness of online literature discussions in the elementary classroom. Addressing both synchronous and asynchronous environments, she suggests that computer-based discussions can enhance understanding of literature and promote community within the classroom.

      10/10

    1. This manual, published by Hanover Research, outlines theory and practice of technology integration in the K-12 classroom and provides key strategies for professional development to equip teachers to successfully integrate technology.

      10/10

    1. The authors present the benefits of coaching in professional development for educators in today's technologically advanced classrooms. Of particular interest is the explanation of the different methods of coaching: executive, coactive, cognitive, and instructional. They suggest that coaching provides more successful outcomes than single workshops and stress that finding the correct method for each situation and organization is crucial.

      10/10

  15. Jul 2019
    1. regularly use data to continuously improve the supports, instruction, and learning students experience.

      Data from annotation informing teaching practices, understanding of learning, success, at admin level.

    2. real-time assessments for gauging student progress

      Real-time grading/assessment for reading = annotation

      And note just assessment, but presence: peer learning; teacher-student feedback, ...

  16. Jun 2019
    1. A Brief History of Reading Instruction. Includes references to studies that support phonics as the best method for teaching reading and writing. Free textbook for phonics instruction: https://elink.io/p/free-phonics-books-98c2d4e

    1. All experiments were carried out on a Beckman XL-A analytical ultracentrifuge, equipped with absorbance optics, and an An60-Ti rotor, at 20 °C. Sedimentation velocity experiments were performed at 40,000 rpm. Data were collected at 540 nm and at a spacing of 0.005 em with three averages in a continuous scan mode. The protein concentration varied in the range 4-40 IJ.M (heme) in 50 mM phosphate buffer, pH 7.2
    2. Analytical Ultracentrifugation experiments
  17. May 2019
    1. suspension through a 26 gauge needle. Lysates were cleared by centrifugation at 14,000 g for 30 min at 4°C and supernatant was used for protein estimation using BCA protein estimation kit (Pierce)
    2. P. Jalciparum infected erythrocytes were lysed by the addition of 0.05 % (w/v) saponin to release parasites, followed by a 30 minute incubation on ice. To remove debris and lysed RBCs were washed with cold PBS followed by centrifugation at 8000g. The lysis buffer containing 10 mM Tris pH 7.5, 100 mM NaCl, 5 mM EDTA, 1% Triton X-100, and Ix complete protease inhibitor cocktail (Roche Applied Science) was added to the parasite pellet and homogenized by passing the
    3. Preparation of Parasite Cell Lysate
    1. at the acidic and basic endpoints of the titrations. Na+ free and HC03-free buffer were prepared as described by Khaled et al.
    2. Intracellular pH measurement was performed using the long-wavelength fluorescent pH indicator carboxy SNARF-1 AM. THP-1 macrophages were resuspended in serum-free and phenol-red free RPMI-1640 medium (106 cells/mL) and incubated at room temperature for 15 min with SNARF-1 AM at a final concentration of 1 f.!M. The cells were washed once in fresh serum-free media and incubated for 20 min for complete de-esterification of intracellular acetoxymethyl esters. In situ calibration ofSNARF-1 AM was performed to determine the pKa of the dye at 3 7°C by using the ionophore Nigericin (1 0 f.!M), which maintains the intracellular pH the same as that of the controlled extracellular medium in a buffer containing high-K+. Appropriate groups were subjected to different treatments and fluorescence measurements were commenced in a spectrofluorimeter (Perkin Elmer, Waltham, MA, USA) followed by kinetic analysis. The pH was calculated from the fluorescence measurements using the following formula: where pKa of carboxy SNARF-1 AM is 7.5 at 37 °C. R is the ratio of fluorescence intensities (F) measured at two emission wavelengths, 580 nm (AI) and 640 nm (A.2), with fixed excitation at 514 nm. The subscripts A and B represent the limiting values
    3. Measurement of intracellular pH
    1. The proteins were resolved on SDS-polyacrylamide gels and transferred onto a nitrocellulose membrane, in the transfer buffer, at a constant current of 300 rnA for 2 h. The membrane was incubated in blocking buffer for 45 min. at room temperature with continous shaking. The membrane was further incubated in anti-restrictocin antibody diluted in PBS, pH 7.4, containing 0.1% Tween 20 (PBST), for 45 min .. The membrane was washed thrice with PBST, followed by incubation in anti-rabbit IgG-HRP conjugate diluted in PBST for 30 min. with shaking. After repeated washings with PBS, colour was developed by incubating the membrane with the chromogenic substrate 0.5 mg/ml of DAB.4HCI (diaminobenzidine tetrahydrochloride dihydrate) and 1 f..ll/ml of H202 in PBS.
    2. Western Blotting
    1. eppendorf tube was put at the bottom of the column to collect the eluate. The column was respun as before and the purified probe collected in the eppendorf tube, the unincorporated nucleotides remaining within the column. One ul aliquot from the purified probe was diluted 100 fold, mixed well and 1 ul aliquots were put in triplicate into 3 ml scintillation fluid containing vials which were counted in a Beckman Liquid Scintillation Counter. The total radioactivity of the probe was calculated by multiplying the mean radioactivity of the three diluted samples with a factor of 104 ( dilution factor, 102, total reaction volume, 102 ). The specific activity of the probes ranged from 1 X 107 to 5 x·1o7 cpm 1 ug DNA. The probe purified by the above method did not require any further purification.
    2. The nick translated probe was purified by a spun column procedure to remove the unincorporated nucleotides. A sterile 1 ml syringe was plugged at the lower end with siliconised glass wool. The syringe was then filled with Bio-gel P-4 Bio Rad Laboratories, USA ) equilibrated in advance with TE. For doing this, 30 grammes of Bio-gel P-4 was slowly added into 250 ml of TE ensuring a good dispersion of the powder. This was then autoclaved at 15 psi for 20 minutes. After cooling, the supernate was decanted and replaced with an equal volume of sterile TE. The slurry was stored at 4°C. The slurry was poured upto the 1 ml mark in the syringe. The syringe was placed into a centrifuge tube and spun at 2000 · rpm for 3 minutes. The column was packed by repeating this process till the packed column volume reached 1 ml mark. Next, 50 ul of 2 mg 1 ml denatured salmon sperm DNA was loaded as carrier and the column spun as before. 100 ul of TE was then added to the column and it was respun as before. Finally, the nick translation reaction was diluted to 100 ul with TE and loaded on to the column. A sterile 1.5 ml
    3. Purification of the probe.
    4. 400 ci 1 mmole to 3000 ci 1 mmole. The nick translation reaction was set up as recommended by the manufacturer of the kit, using about 0.5 ug DNA. The reaction was incubated at 12 -14 °C for 90 minutes, except in the case of small fragments ( 500 bp ) when the reaction was incubated for 45 minutes only. The reaction was terminated by the addition of stop buffer supplied with the kit.
    5. DNA was labelled using the nick translation kits supplied by BRL or NEN, USA, or Amersham, UK. The 32P-deTP was from either NEN or Amersham, UK, at a concentration of 10 mei I ml. The specific activity of the label ranged from
    6. Nick translation.
    7. 32~ -labelling of DNA.
    1. TheO2carryingcapacity(Vol%)ofbloodwascalculatedby multiplyingtheHbcontentwith1.25O2combiningpowerofHb/g(Johansen,1970).
    2. TheO2carryingcapacity
    1. annealing at 25°C for 5 minutes, the reaction was incubated at 42°C for one hour.
    2. series of primers were designed to detect the levels of intact gene of interest or Rz in the cell lysate. The levels of RNA were quantitated by carrying out reverse transcriptase based-PCR using the Im.Prom-11™ Reverse Transcriptase system (Promega, U.S.A.). 1}lg of template RNA and 1}lM terminal primers were combined in 5pl reaction volume and the primer I template mix was thermally denatured at 70°C for 5 minutes and chilled on ice. A reverse transcription reaction mix of volume 15 pl was assembled on ice to contain nuclease-free water, 1X reaction buffer, 1pl reverse transcriptase, 6 mM magnesium chloride, 0.5 mM dNTPs and 1 U ribonuclease inhibitor RNasin. As a final step, the template-primer combination was added to the reaction mix on ice. Following an initia
    3. Reverse transcri.ptase polymerase chain reaction (RT-PCR)
    1. and fixed with 100μl of fixative solution per well, for 10 minutes at room temperature. The cells were then washed twice with PBS and 100μl of staining solution was added to each well. The plate was kept at 37° C, until the color development.
    2. 4x103-5x103 cells were plated in 96 well plate, well. Cells were transfected with reporter plasmid 18 -24 hrs after plating. After 48 hrs, cells were washed once with PBS
    3. Procedure:
    4. 1X PBS diluted in distilled water 1X fixative solution diluted in distilled water 2.4.12.3 Staining Solution25 μl Solution A 25 μl Solution B 25 μl Solution C 125 μl 20 mg/ml X-gal in DMF
    5. Working Solutions:
    6. 20 mg/ml X-gal in dimethylformamide Solution A as 40 mM potassium ferricyanide. Solution B as 40 mM potassium ferrocyanide. Solution C as 200mM magnesium chloride. 10X fixative (20% formaldehyde; 2% glutaraldehyde in 10X PBS) 10X PBS as 0.017 M KH2PO4, 0.05 M Na2HPO4, 1.5 M NaCl, pH 7

      .4

    7. Stock Solutions:
    8. This protocol is for the detection of β-gal expression in fixed cells. It was performed on 96-well plates for initial screening of tTA transfected clone, and is a modification of Sanes et al., 1986
    9. In situβ-gal staining of Transfected Cells
    1. (ii) Stacking gel buffer: 1.0 M Tris-Cl pH 6.8 (iii) Resolving gel buffer: 1.5 M Tris-Cl pH 8.8 (iv) SDS stock: 10% (w/v) solution (v) Ammonium persulphate (APS) stock: 10% (w/v) solution made fresh (vi) Gel running buffer (1X) (vii) Loading dye (6X): (viii) Lysis buffer (RIPA) Gels of 1.5 mm thickness were cast in the Biorad small gel apparatus. Resolving gel of 10% (10 ml) was made by mixing 4.2 ml 10% acrylamide, 3.1 ml water, 2.5 ml of 1.5 M Tris-Cl pH 8.8 and 0.1 ml of 10% SDS. Stacking gel (2 ml) was made by mixing 0.33 ml of 30% acrylamide, 1.4 ml of water, 0.25 ml of 1 M Tris-Cl pH 6.8 and 0.02 ml of 10% SDS. Gels were polymerized by the addition of TEMED (N,N,N′, N′-tetramethyl ethylene diamine) and APS (1/100th volume of gel mix). Sample preparation for gel loading was done as follows. Mid log and late log phase 10 ml cultures were centrifuged at 26000g and the cell pellet was resuspended in 0.5 ml RIPA buffer. Cells were sonicated on ice for 1 min at output power of 5 to get a cleared lysate. The culture lysate was centrifuged at 26000g to recover the clear supernatant. Total cell protein was quantified in the lysates using BCA kit reagents (BioRad) using the manufacturers protocol. Appropriate volume of cell lysate was mixed with the loading dye in a final concentration of 1X and loaded onto the gel. The gel was run at constant voltage of 60 V for stacking and 80 V for resolving gel
    2. The method followed was as described in Sambrook and Russell (2001). The following solutions were used to cast and run SDS-PAGE gels. (i) Acrylamide stock: 29% (w/v) acrylamide and 1% N,N′-methylene bisacrylamide
    3. Sodium dodecyl sulphate-polyacrlyamide gel electrophoresis (SDS-PAGE)
    4. the phage (λ1098 for Tn10dTet transpositions and λNK1324 for Tn10dCm transpositions) at a multiplicity of infection (moi) of 0.05 in the presence of 5 mM MgSO4. This mixture was incubated for 15 min at 37°C to allow for phage adsorption. The unadsorbed phage was then removed by centrifugation and the pellet was resuspended in 10 ml of LB broth containing 5 mM sodium pyrophosphate. It was incubated without shaking at 37°C for 30 min for phenotypic expression. The rest of the mixture was diluted into 100 ml of LB broth with 5 mM sodium pyrophosphate carrying the required antibiotic and amplified overnight by growth at 30°C. This population of cells was used as a source of random transposon insertions. The λ lysates used for the transposition experiments carry amber mutations, and were propagated on a supE strain C600 by the protocol described below in section 2.14
    5. The method used was essentially the same as that described by Miller (Miller, 1992). The strain to be used for obtaining random Tn10dTet or Tn10dCm insertions was grown overnight in Z-broth containing 0.4% maltose. The culture was then diluted 50-fold in the same medium and grown to an A600 of 0.8. Two ml of the culture was infected with 107 pfu of
    6. Generation of random Tn10 insertions into the genome of E.coli
    1. he MTT Lysis buffer (20% SDS , 50% Dimethyl formamide) and the O.D.s7onm was measured. The standard curve was plotted and the equation derived, used to calculate the number of metabolically viable cells in experimental groups. Percentage of viable cells was calculated by comparing the number of viable cells in treated wells with that of untreated wells
    2. MTT micromethod is a colorimetric assay based upon the conversion of the (yellow) MTT reagent (3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide), a tetrazole to purple formazan in the mitochondria (succinate dehydrogenase) of the living cell which is quantified by measuring the optical density at 570nm. When the amount of purple formazan produced by untreated control cells is compared to that of treated cells, the effectiveness of the agent can be deduced through the production of a dose-response curve. Parasites in their log phase were harvested and the dead cells removed at 129 x g for 5min at RT. The live cells were resuspended in phenol red-free DMEM containing 10% FBS to a cell count of 2.5 X 107. 1mL of above culture was plated into each well of a 24 well plate and appropriate treatments were given for desired duration of time. Some untreated cells were also kept aside for generating the standard curve. After appropriate treatment, from each well of the 24 well plate 200pL was aliquotted into 4 wells of a 96 well plate. To each well of the 96 well plate, 10pL of MTT solution (5mg/ mL prepared in PBS and filtered with 0.22p filter) was added and the plate incubated at 23°C for 2-3 hours till colour develops in the control cells. A standard curve was also plated by taking different dilutions of untreated cells and processed similarly. Once colour developed, the reaction was stopped by lysing the cells using
    3. MTT assay to assess viability of Leishmania parasites
    4. Plasmid/Ligation mix was incubated with ultra-competent cells for 30 min on ice. This was followed by a heat shock at 42°C for exactly 45s after which the cells were chilled on ice for 2 min. lmL of LB (Luria Bertani) medium was added to the cells and incubated at 37°C in a shaker incubator for 45 min. Cells were then plated on LB agar plate containing appropriate antibiotic and/ or X-gal solution and incubated at 37°C overnight
    5. Transformation of competent cells with DNA
    1. Cells grown overnight in YNBmedium wereinoculated in fresh YNB mediumand incubated at 30 ̊C with shaking at 200 rpm. Cells were harvested when the cell density reached to an OD600of 0.6-0.8.Cells were consecutively washed with sterile MQ water and YNB without phosphate (YNB-Pi) medium. Washed cells were inoculated either in YNB orYNB-Pimediumto the initial OD600of 0.1. Cells were incubated at 30 ̊C for 3-4 h, harvested and resuspendedin 100 μlYNB-Pimedium. Radioactive P32-labelled o-phosphoric acid(Jonaki# LCP 32)was added to the cell suspension to a final concentration of 1 μCi/mlandcells were incubated for 30 min.For determining phosphate uptake, a10-12 μl cell suspensionaliquot,after every5 min,was removed and kept on ice.To this cell suspension, 500 μl ice-cold YNB-Pimediumwas addedand cells were harvested by centrifugation at 5,000 g for 5 minat 4 ̊C.These cells were washed with ice-cold YNB-Pimedium thrice and resuspendedin 100 μlPBS(1X). 10-20 μl of this cell suspension was added to5 ml scintillation fluid and β-decay counts were measured in ascintillation counter(Tri-Carb 2910 TR Liquid Scintillation Analyzer, PerkinElmer).Scintillation counts were normalized to total cell number and plotted with respect to time. Total phosphateuptake was expressed as P32c.p.m/OD600cellswhere c.p.m refers tocounts per min
    2. Phosphate uptake assay
    1. To preclude the possibility of human RNA contamination, cDNA prepared from internalized yeast was examined for the presence of human transcripts encoding Ccl5 and histone H3. However,no amplification forhuman genes was observed, thus, eliminating any possiblecontamination of THP-1 RNA with yeast RNA
    2. Primersfor real-timePCR analysisweredesigned using Primer3 plus software and are listed in Table 4. To extractRNA from macrophage-ingested C. glabratacells, infected THP-1cells were washed twice with PBS and lysed in 1 ml ice-cold water. Lysate was centrifuged followed by two quick washes with DEPC-treated water andwashed yeast cell pellets were frozen on dry ice.For RNA extraction, yeast cells were disrupted with glass beads in trizol and total RNAwas isolated usingacid phenol extraction method described above.Optimal primer and cDNA concentrations were standardizedand qRT-PCR was performedusing ABI 7500 Fast Real-Time PCR System (Applied Biosystems).In brief, 0.5 μl cDNA,0.1 to 0.2picomoles of gene specific primers and 10 μl 2X MESA GREENqPCR™ Mastermix Plus containing SYBR green dye (Eurogentec)were mixed in thewellsof a 96-well PCRplate (Axygen). Final reaction volume was adjusted to 20 μl with DEPC-treated water. Transcript levels were quantified with an end-point value known as Ct(cyclethreshold). Expression of TDH3, which encodes CgGapdh,was used asaninternal control. The Ct defines the number of PCR cycles required for the fluorescent signalof SYBR green dye to cross beyondthe background level.Fold-change in transcript expression was determined usingfollowing formula.Fold change in expression = 2-ΔΔCtΔΔCt= ΔCttreated -ΔCtuntreatedΔCttreated = Ctvalue forthe gene of interest under treated condition -Ctvalue forthe internal control gene (TDH3) under treated conditionΔCt untreated = Ctvalue forthegene of interest under untreated condition -Ctvalue forthe internal control (TDH3) gene under untreated condition
    3. Quantitative real-timePCR
    4. 10 min at 4 ̊C and gently resuspended in 20 ml ice-cold Inoue transformation buffer. To this cell suspension, 1.5 ml sterile DMSO was added and swirled gently. Cell suspension was kept on ice for 10 min and 50 μl volume was aliquoted to chilled sterile microcentrifuge tubes. Cells were immediately snap-frozen in liquid nitrogen and stored at -80 ̊C
    5. A single colony of E. coli DH5α strain was inoculated in 10 ml LB medium and incubated at 37 ̊C for overnight. 4 ml overnight culture was inoculated in 2 lt SOB medium and incubated at 18 ̊C till the OD600 reached to 0.5. Cultures were centrifugedat 2,500 g for 10 min at 4 ̊C and harvested cells were washed gently with80 ml ice-cold Inoue transformation buffer. Cells were collected by centrifugation at 2,500 g for
    6. Preparation ofE. coli DH5α ultracompetent cells
    1. Retroviral based system was used for silencing of PTEN. BOSC23 packaging cells were grown in 100 mm culture dishes upto 80-85% confluency. Retroviral RNA vector containing either scrambled control shRNA or pool of PTEN shRNA along with a PCL-Ampho helper plasmid were co-transfected using Lipofectamine 2000 reagent to generate viral particles. After 48 h, supernatant containing viral particles were used to infect MDA-MB-231 cells in the presence of polybrene (8g/ml). For p53 gene knockdown, TP53 mission shRNAs obtained from Sigma Aldrich (St Louis, MO, USA) were transfected using Lipofectamine 2000 (Invitrogen, USA) and non-targeting shRNAs (Sigma) were used as controls. The cellular homogenates were prepared 36-48 h post transfection and were subjected to immunoblotting to check the levels of protein knockdown
    2. RNA interference
    1. labelled RNAs to N+Hybond membrane (GE Life Science), the radiolabelled rRNA was detected using a phosphorimager (Fuji Film FLA-9000)
    2. Overnight grown yeast were sub-cultured at 0.2 OD600and growntill 0.8 OD600.Cells equivalent to 1 OD600were harvested and were washed in SC-Ura medium, suspended in 1 mL of SC-Ura medium containing 3μCi/mL of [14C]uracil and pulselabelledfor 15 min at30°C.After incubation the cells were pelleted and a chase was performed by adding SC medium containing 240 mg/L unlabelled uracil. Samples were taken at 0, 1, 5, 10and 20min after the chase, centrifuged at 12000 x gfor 1 min at 4°C, and total RNA was isolated from cells by the hot-phenol techniquedescribed in Section 2.2.8.Equal total RNA was loaded on a 1.2% formaldehyde-agarose gel. After transfer of
    3. Pulse-chase analysis of rRNA synthesis
    1. Cells (HEK293T) were transfected with various combinations of plasmids/siRNAsor treated with cisplatin. Cells were washed first with 1X PBSand then with Met-/Cys-1X DMEM supplemented with dialyzed FBS(10%). Cells were then incubated with Met-/Cys-DMEM supplemented with dialyzed FBS in the incubatorfor 1h (met/cysstarvation). Cells were taken out from the incubator,and the culture media was removed. Cells were placed behind the radioactivity protective shield and DMEM supplemented with 35S met/cys (200μCi) was added to the cells. Plates containing radioactive media were then put into the acrylic box and incubated for 1h at 37°C in a CO2 incubator. Plates were taken out and kept behind the radioactivity protective shield;the radioactive media was disposedofin the radioactive liquid waste. One set of cells washarvested for 0 time point, other sets of cells were washed twice with 1X PBS and were incubated with normal medium containing 2mM each of cysteine and methionine. Cell plates were put in the acrylic box and incubated at 37°C in a CO2 incubator. Cells were harvested at different time points. Cells were collected in ice-cold PBS and were lysed using the standard cell lysis protocol. Cell lysate were subjected to immunoprecipitation(IP). IP complex is separated on SDS-gel using standard protocol. The gel was transferred onto PVDF membrane, and the membrane was dried. Dried membrane was exposed in a cassette and the signal was detected using phosphorimager. Later the same blots were probed with specific antibodies
    2. 35S met/cys pulse-chase assay
    1. Ferric-iron-reduction activity of Xanthomonas oryzaepv. oryzicolawas measured using ferrozine, a chromogenic ferrous iron chelator, as described previously (Velayudhan etal., 2000; Worst et al., 1998). For estimating the ferric reductase activity, Xanthomonas oryzaepv. oryzicolastrains were grown in 20 ml PS medium carrying appropriate antibiotics for 24 h to OD600 of 1. Cell free PS media was incubated under similarcondition to be used as control. Chromogenic ferrous iron chelator, ferrozine was added to a final concentration of 1 mM, and FeCl3was added as ferric iron source to a final concentration of 50 μM, and incubated at 28ºC. At regular time intervals, 1 ml aliquotes were taken from the test culture and control, centrifuged to remove the cells, and absorbance of the magenta coloured Fe2+-ferrozine complex in the cell free culture supernantant was measured at 535 nm by using control supernatant as reference. The Fe2+reduction activity was quantified as micromoles of Fe2+-Ferrozine complex formed
    2. Assay for ferric reductase activity
    3. respectively. The resulting constructs pRR14 and pRR15 were transferred in E.coliDH5α. Through triparental mating using pRK600 helper plasmid the construct were transferred in E.coliS17-1. After confirming pRR14 and pRR15 constructs by sequencing, the constructs were then introduced into BXOR1 strain through biparental mating using E. coliS17-1. X. oryzaepv. oryzicolaGUS and GFP reporter strains were selected on PS medium plates containing suitable antibiotics. Since pVO155 cannot replicate in X. oryzaepv. oryzae, ampicillin and kanamycin-resistant colonies were obtained upon chromosomal integration of the plasmid using the cloned DNA sequence as a region of homology. pProbeGTcan replicate independently in Xanthomonasand report for the gene expression
    4. Glucuronidase (GUS) reporter gene fusion and GFP reporter fusion was created by using the suicide plasmid pVO155 having a promoterless gusAgene (Oke and Long, 1999), and pProbeGThaving a promoterless GFP (Miller et al., 2000). To construct the xsuA::gusAand xsuA::gfptranscriptional fusion, a 611-bp DNA fragment containing the putative promoter of the xssoperon (+213 to −398) was amplified by using the SCRsid_ pProbeGFP_F and SCRsid_ pProbeGFP_R primers (Table 2.2). This promoter fragment was subsequently digested with HindIII and BamHI,and directionally cloned upstream of the promoterless gusAand gfpgene in pVO155 and pProbeGTplasmids to create the xsuA::gusAand xsuA::pProbeGT(gfp) reporter constructs pRR1
    5. Construction of xsuA::gusAand xsuA::gfp strains in X. oryzaepv. oryzicola background
    1. To perform immunoblotting or western blotting, appropriate amounts of total protein(ranging from 20-40 μg) were separated ona SDS-PAGE gel of 12%acrylamide concentration in Tris-Glycine-SDS gel running buffer. Protein separation was done at 70-100 V for 2-3 h using a MINI PROTEAN®3 electrophoresis unit (Bio-Rad). Followingseparation, proteins weretransferredto polyvinylidene difluoride (PVDF) membrane, using a Bio-Rad Mini Trans-Blot electrophoretic transfer unit in Tris-Glycine transfer buffer at 4⁰C. Before setting transfer assembly, PVDF membrane was first activated in 100% methanolfollowedby washesin the transfer buffer. The transfer assembly was set inaBio-Rad Mini gel holder cassette (170-3931)according to manufacturer’s instructions. The transfer time and current settings varied depending on the size oftheprotein of interest. Post transfer, membranes wereseparated from the assembly and kept for blocking intheblocking buffer (0.1 % Tween-20, 5% w/v fat-free skimmed milk in 1X TBS) for 1 h at room temperature with shaking. Next,membranes wereincubated with appropriate dilutions of primary antibodiesin the blocking buffereitherfor 3-4 h at room temperature or overnight at 4°C with gentle shaking. Post incubation,membranes were washed thrice with 1X TBS-T, 10 min each,with constant agitation. After washes, membraneswere incubated with appropriate dilutions of secondary antibodiesconjugated with horseradish peroxidase (HRP) for 1 h at room temperature with gentle shaking. Next, membranes were washed thrice with 1X TBS-T, 10 min each,with constant agitation. To visualize proteins, membranes were removed from TBS-T, and theHRP substrate ECL plus (Amersham Biosciences, RPN2232) was uniformly added on top of the membrane. Chemiluminescent signalswere captured in the western blot imaging system (FluorChemTME system)
    2. For protein extraction, cells were spun down at 4,000 rpm for 5 min and washed with ice-cold water. The cell pellet was resuspended in 250-500 μl of homogenisation buffer which contained50 mM Tris (pH 7.5), 2 mM EDTA, 1 mM phenylmethylsulphonyl fluoride (PMSF) (serine protease inhibitor), 10 mM sodium fluoride (serine/threonine and acid phosphatases inhibitor), 1 mM sodium orthovanadate (Tyrosine and alakaline phosphatases inhibitor) and 1X protease inhibitor cocktail (Sigma, P 8215). The cell suspensison was transferred to a 1.5 ml centrifuge tube and equal amounts of glass beads (0.5 mm size) were added. Cells were lysed mechanically by bead-beatinghomogenizer (MP Biomedicals, FastPrep®-24) atthemaximum speed for 60 seconds, five times each,with intermittent cooling on ice.After lysis, tubes were punctured at the bottom with the helpofasurgical needle, and the lysed cell suspension was collected in a fresh microcentrifuge tubes by putting the punctured tubes on top of the fresh tubes and centrifuging them at 3,000 rpm for 10 min. The supernatant was transferred toafresh microcentrifugetubeandprotein concentrationwasestimated usingtheBCA protein assay kit (Thermo scientific). Protein preparations werestored at -20°C until use
    3. Total protein extraction and immunoblotting
    4. Total protein extraction and immunoblotting
    1. the selection marker.Knockdown was confirmed by immunoblot analysis with an IP6K1 specific antibody (Table 2.3) as described in Section 2.2.10
    2. lines were used for stable knockdown of IP6K1 expression. Viral particles harboring either non-targeting control or IP6K1directed shRNA were used to infect HeLa or HCT116 cell lines at 0.5 MOI, following treatment with polybrene (8 μg/mL)for 2 h.After 48 h, transduced cells were selected with 2 μg/mL puromycin. Medium was changed twice a week and observed for colony formation. After reaching the optimum growth, selected cells were maintained in DMEM supplemented with 10% FBS and 1 μg/mL puromycin as
    3. Generation of stable cell lines expressing shIP6K1-HeLa and HCT116 cell
    4. HEK293T packaging cellswere seeded at 30-40% confluency in 60 mm dishes. After 24 h, cells were co-transfected with three plasmids required for viral production i.e. VSV-G, psPAX2 (Addgene plasmid # 12260) and pLKO.1-puro-non-targeting and shIP6K1 clones using polyethyleniminereagent(PEI) and incubated at 37°C and 5% CO2 for virion formation. After 48 h, viral particles were harvested by collecting supernatant and filtered througha 0.45 μm syringe filter unit. Viral stock was aliquoted and stored at -80°C for further use. Viral titer was approximated on the number of cells plated for the production of lentivirus. Calculations were done as per Cell Bio Labs instruction. 2 x 106cells will yield 107infectious units/mL. All necessary precautions were taken while generating lentiviral particles such as wearing mask, double gloves, and sterile filter tips. All the consumables used were bleached (1% sodium hypochlorite solution) at least 1 h before being discarded
    5. Generation of lentiviral particle containing shRNAagainst human IP6K1-
    6. Generation of stable cells expressing shIP6K1 in HeLa and HCT116
  18. Apr 2019
  19. Mar 2019
    1. personalized mobile learning solutions to create effective learning paths This appears to blend personalized learning and mobile learning. It is prepared by a specific vendor, MagicBox, so they might be assumed to have their own agenda. This page describes some of the affordances of personalized mobile learning, such as the capacity to track and presumably respond to learner preferences. rating 2/5

  20. Feb 2019
    1. They can evaluate web content, and identify what is useful and trustworthy

      This should be taught throughout k-12 schooling. Learnng this in college was super helpful but it was taught a little late for me. I know now how to choose sources that present good information but growing up I wouldnt have been able to do that

  21. Nov 2018
    1. What K–12 Administrators Should Think About When Integrating Classroom Tech

      This article describes how school districts who wish to integrate more technology into their classrooms should approach the integration. Rating: 4/5

  22. Oct 2018
    1. Evaluation, when it is not asked for, and when it has consequences as it does in school, is a threat. It narrows the mind... it inhibits new learning, new insights, and creative thought—the very processes that some people think school is supposed to promote. -- Peter Gray

      . . .

      Why is it clear to us that it's degrading and objectifying to measure and rank a girl’s physical body on a numeric scale, but we think it’s perfectly okay to measure and rank her mind that way?

      . . .

      what an oak tree actually needs is not your opinion but soil and water and light and air, and what a child needs is love and stories and tools and conversation and support and guidance and access to nature and culture and the world. If a kid asks for your feedback, by all means you can give it; it would be impolite not to. But what we should be measuring and comparing is not our children but the quality of the learning environments we provide for them.

  23. Sep 2018
    1. bishop gave judgment, declaring the marriage null in a canonical sense. Regarded in a civil point of view, the marriage was still valid until it should have been declared null by a civil tribunal. It became necessary, therefore, to carry the cause before the Superior Court, and my honorable friend, the member for Because, who took the case in hand with his usual zeal and legal address, obtained from the court, after a suitable inquiry, a judgment declaring the marred null in a civil sense, and ordering that it should be registered as such in all places where it should be needful. If this affair had occurred in Upper Canada, what recourse would the parties have had ? The parties being Catholics, the case would have been brought before the bishop, who would also have declared the marriage null after suitable inquiry; but the cause would not have had the same conclusion in the civil court, particularly had it depended on certain impediments which have force in Lower Canada, but none in Upper Canada. It would have become necessary to go to Parliament to pray for an act, which, in a Catholic point of view, would be a mere decree of separation, but which the Parliament would have termed an act of divorce. This power to grant a separation is therefore necessarily vested in the Parliament, by whatever names such separation may be designated, and we are not to be reproached for the interpretation which others may give to such name, different from that which we assign to it. I thought it right to make myself understood on this point, because I do not choose that people should be able to say we are afraid of explaining our position with regard to the question of divorce and marriage, and I believe that I have shown that our position is consistent with our religious laws and our principles as Catholics. I regret that I have dwelt so long on the matters touched upon by the honorable member for Hochelaga ; but after his speech, and considering the position he assumed, he must have expected an answer.

      §§.91(26) and 92(12) of the Constitution Act, 1867.

    2. HON. SOL. GEN. LANGEVIN—I beg your pardon, it means that a marriage contracted in no matter what part of the Confederacy, will be valid in Lower Canada, if contracted according to the laws of the country in which it takes place ; but also, when a marriage is contracted in any province contrary to its laws, although in conformity with the laws of another province, it will not be considered valid. Let us now examine the question of divorce. We do not intend either to establish or to recognize a new right ; we do not mean to admit a thing to which we have constantly refused to assent, but at the Conference the question arose, which legislature should exercise the different powers which already exist in the constitutions of the different provinces. Now, among these powers which have been already and frequently exercised de facto, is this of divorce. As a member of the Conference, without admitting or creating any new right in this behalf, and while declaring, as I now do, that as Catholics we acknowledge BO power of divorce, I found that we were to decide in what legislative body the authority should be lodged which we found in our Constitutions. After mature consideration, we resolved to leave it in the Central Legislature, thinking thereby to increase the difficulties of a procedure which is at present so easy. We thought then, as we still think, that in this we took the most prudent course. The following illustration will prove this still more forcibly. I t is known to the House how zealous a partisan the honorable member for Brome (Mr. DUNKIN) is of the cause of temperance. Well, we will suppose that the honorable gentleman were present as a member of a municipal council in which it was to be decided whether all the taverns in a very populous part of the parish, which could not be suppressed, should be banished to a remote corner of the parish, where they would no longer be a temptation and a stumbling-block ; would he not vote for such a measure ? Would he not send them to a place where they would be least accessible to the population, and would he not think he had done a meritorious act, an act worthy of a good friend of the temperance cause ? Just so in a question of divorce ; the case is exactly analogous. We found this power existing in the constitutions of the different provinces, and not being able to get rid of it, we wished to banish it as far from us as possible. One thing it would be vain to deny, namely, that although we, as Catholics, do not admit the liberty of divorce, although we hold the marriage bond to be indissoluble, yet there are cases in which we both admit and require the annulling of the marriage tie—in cases, for instance, where a marriage has been contracted within the prohibited degrees without the necessary dispensations. An instance of this occurred very recently. A few months since, an individual belonging to my county, who had married a young girl of a neighboring parish, without being aware at the time of his marriage of the relationship which existed between him and his wife, found out several months afterwards that they were related in such a degree that they required a dispensation from the bishop. That dispensation had not been obtained. He spoke of it to his wife, who refused to apply for a dispensation, as a step towards the legal celebration of their marriage. It became necessary, therefore, to have the marriage annulled. The affair was brought before the Ecclesiastical Court, and, after a minute investigation, the diocesan

      §§.91(26) and 92(12) of the Constitution Act, 1867.

    3. HON. SOL. GEN. LANGEVIN—The honorable member for Verchères does not choose to be convinced ; so I will make no further attempt to convince him. The resolution in question signifies just what I have stated.

      §§.91(26) and 92(12) of the Constitution Act, 1867.

    4. may be summed up as follows :—The Central Parliament may decide that any marriage contracted in Upper Canada, or in any other of the Confederated Provinces, in accordance with the laws of the country in which it was contracted, although that law might be different from ours, should be deemed valid in Lower Canada in case the parties should come to reside there, and vice versa.

      §§.91(26) and 92(12) of the Constitution Act, 1867.

    5. The honorable gentleman has asked the Government what meaning was to be attached to the word ” marriage,” where it occurred in the Constitution. He desired to know whether the Government proposed to leave to the Central Government the right of deciding at what age, for example, marriage might be contracted. I will now answer the honorable gentleman as categorically as possible, for I am anxious to be understood, not only in this House, but also by all those who may hereafter read the report of our proceedings. And first of all I will prove that civil rights form part of those which, by article 43 (paragraph 15) of the resolutions, are guaranteed to Lower Canada. This paragraph reads as follows :— 15. Property and civil rights, excepting those portions thereof assigned to the General Parliament. Well, amongst these rights are all the civil laws of Lower Canada, and among these latter those which relate to marriage; now it was of the highest importance that it should be so under the proposed system, and therefore the members from Lower Canada at the Conference took great care to obtain the reservation to the Local Government of this important right, and in consent-‘ ing to allow the word ” marriage ” after the word “divorce,” the delegates have not proposed to take away with one hand from the Local Legislature what they had reserved to it by the other. So that the word ” marriage,” placed where it is among the powers of the Central Parliament, has not the extended signification which was sought to be given to it by the honorable member. With the view of being more explicit, I now propose to read how the word marriage is proposed to be understood :— The word marriage has been placed in the draft of the proposed Constitution to invest the Federal Parliament with the right of declaring what marriages shall be held and deemed to be valid throughout the whole extent of the Confederacy, without, however, interfering in any particular with the doctrines or rites of the religious creeds to which the contracting parties may belong. This is a point of great importance, and the French Canadian members ought to rejoice to see that their fellow-countrymen in the Government have not failed in their duty on a question of so serious a nature. On many other points many of them will doubtless claim that we have not thoroughly fufilled our duty, but as regards the matter in question there can be no difference of opinion, as I we have all a common rule to guide us ; and I repeat that they ought to rejoice that their co-religionists in the Conference have not been found wanting on this occasion. The whole

      §§.91(26) and 92(12) of the Constitution Act, 1867.

    1. Remarks have also been made about the laws of divorce and marriage, and the honorable member for the division of DeLanaudière (Hon. Mr. OLIVIER) told us that the Conference had done well in transferring the power of divorce to the General Government. On his part, I think this was a wise view of the question, and I am glad to have the opportunity of now telling him so. He was, however, very uneasy about the word ” marriage.” Well, I will try to put him right and at his ease on that point; and I will give him the answer as I find it put down in writing, so that no possible misunderstanding may continue to exist. If the honorable gentleman will but take his pen, he will be able to note my answer :—” The word ‘ marriage’ has been inserted to give the General Legislature the right to decide what form of marriage will be legal in all parts of the Confederation, without in any way interfering with the rules and prescriptions of the Church to which the contracting parties belong.”

      §§.91(26) and 92(12) of the Constitution Act, 1867.

    2. One of them is a matter in which Lower Canada is somewhat peculiarly interested— the system of marriage and divorce, which, I see, is to be left in the hands of the Federal Government.

      §§.91(26) and 92(12) of the Constitution Act, 1867.

    1. what is meant by the regulation of the law of divorce ; but what is meant by the regulation of the marriage question ? Is the General Government to be at liberty to set aside all that we have been in the habit of doing in Lower Canada in this respect ? Will the General Government have the power to determine the degree of relationship and the age beyond which parties may marry, as well as the consent which will be required to make a marriage valid ?

      §§.91(26) and 92(12) of the Constitution Act, 1867.