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opennotspecifiedApr 2003View details →

F in Taxonomic revision of Amerus troisi (Berlese, 1883) (Acari, Oribatida, Ameridae) using morphological and biochemical characters

F. 1. Amerus troisi (Berlese, 1883): (a) detail of notogastral seta ms (×775); (b) anterolateral portion of the notogastral shield showing the humeral foramen, sensillus and the cerotegument on the proximal leg segments (×265); (c) dorsal view of topotypical specimen (×150); (d) detail of the marginal notogastral setae (×1500); (e) posterior portion of the notogastral shield (×220); (f) detail of the deep humeral foramen (×1100); (g) detail of the cerotegumental layer (×3400); (h) bothridial rim (×1150); (i) dorsal view of rostrum (×1050); (l) detail of exobothridial seta ex (×4200).

opencc-by-4.0May 2023View details →

Combined immune checkpoint blockade increases myocardial secretion of H-FABP, NT-Pro-BNP, NLRP-3 inflammasome, Interleukin-1β and Interleukin-6: biochemical implications in cardio-immuno-oncology

Background: Immune checkpoint inhibitors have transformed the treatment of several cancers by releasing restrained antitumor immune responses. Ipilimumab, an anti–cytotoxic T-lymphocyte–associated antigen 4 (CTLA-4) antibody, and nivolumab, an anti–programmed death-1 (PD-1) antibody, have individually improved survival in patients with melanoma, and their combination further enhances antitumor activity and survival. More recently, an anti-LAG3 human monoclonal antibody, Relatlimab, has been approved by FDA for combinatorial treatment with Nivolumab for metastatic melanoma and an anti-PD-L1 mAb,Atezolizumab, is undergoing clinical trials evaluation in combination with Ipilimumab for metastatic lung cancer.However,adverse events associated with these agents include dermatitis, endocrinopathies, colitis, hepatitis, and pneumonitis, which are all thought to arise from aberrant activation of autoreactive T cells. These toxic effects are more frequent and severe when immunomodulatory mAbs are used in combination.                       Methods: human cardiomyocytes co-cultured with hPBMC were exposed to monotherapy and combinatorial ICIs (PD-L1 and  CTLA-4 or PD-1 and  LAG-3 blocking agents, at 200 nM) for 48 h. After treatments, cardiac cell lysis and secretion of biomarkers of cardiotoxicity (H-FABP, NT-Pro-BNP), NLRP3-inflammasome and Interleukin 1 and 6 were determined through colorimetric and enzymatic assays.                                                                                                                                                    Results:Both Combinations of immune checkpoint inhibitors  exertmore potent cardiotoxic side effects compared to monotherapies against human cardiac cells co-cultured with human lymphocytes. LDH release from cardiac cells was 43% higher in PDL-1/CTLA-4 blocking agents, and 35.7% higher  in PD-1/LAG-3 blocking agents compared to monotherapies. Biomarkers of cardiotoxicity, such as  H-FABP and NT-Pro-BNP were also strongly increased in combination therapy than monotherapies. NLRP3 inflammasome, IL-1β and IL-6 levels were also increased by PDL-1/CTLA-4 and PD-1/LAG-3 combined blocking agents compared to untreated cells and monotherapies.                                                                    Conclusions:Data of the present study, although in vitro, indicate that combinatorial immune checkpoint blockade on co-cultures of hPBMCs and cardiac cells, including for the first time the anti LAG-3 monoclonal antibody, induce a pro- inflammatory phenotype, thus indicating that these therapies should be closely monitored by the multidisciplinary team consisting of oncologists, cardiologists and immunologists.

dryad32/100

Data for: Biochemical properties of naturally occurring human bloom helicase variants

Bloom syndrome helicase (BLM) is a RecQ-family helicase implicated in a variety of cellular processes, including DNA replication, DNA repair, and telomere maintenance. Mutations in human BLM cause Bloom syndrome (BS), an autosomal recessive disorder that leads to myriad negative health impacts including a predisposition to cancer. BS-causing mutations in BLM often negatively impact BLM ATPase and helicase activity. While BLM mutations that cause BS have been well characterized both in vitro and in vivo, there are other less studied BLM mutations that exist in the human population that do not lead to BS. Two of these non-BS mutations, encoding BLM P868L and BLM G1120R, when homozygous, increase sister chromatid exchanges in human cells. To characterize these naturally occurring BLM mutant proteins in vitro, we purified the BLM catalytic core with either the P868L or G1120R substitution. We also purified a BLM K869A K870A mutant protein, which alters a lysine-rich loop proximal to the P868 residue. We found that BLM P868L and BLM G1120R were both able to hydrolyze ATP, bind diverse DNA substrates, and unwind G-quadruplex and duplex DNA structures. Molecular dynamics simulations suggest that the P868L substitution weakens the DNA interaction with the winged-helix domain of BLM and alters the orientation of lobe 1 of the ATPase domain. Because BLM P868L and BLM G1120R retain helicase function in vitro, it is likely that the increased genome instability is caused by specific impacts of the mutant proteins in vivo. Interestingly, we found that BLM K869A K870A has diminished ATPase activity compared to wild-type BLM, weakened binding to duplex DNA structures, and less robust helicase activity. Thus, the lysine-rich loop may have an important role in ATPase activity and specific binding and DNA unwinding functions in BLM.

opencc-zeroJun 2023View details →

opencc-by-4.0Jul 2023View details →

Archive of biochemical data sets contained in: Guanine-containing ssDNA and RNA induce dimeric and tetrameric SAMHD1 in cryo-EM and binding studies

This archive contains all the biochemical data for the study "Guanine-containing ssDNA and RNA induce dimeric and tetrameric SAMHD1 in cryo-EM and binding studies". Further data supporting the structural data in this study is found in pdb and EMD accession numbers PDB ID 8TDV and EMD-41174 (RNA complex SAMHD1-T*cl) and PDB ID 8TDW and EMD-41175 (RNA complex SAMHD1-T*op). Further proteomics data is found in the Protein Exchange Database (PXD043587).

Fig. 4. Amino acid sequences alignment between TCS1 and candidate N in Discovery and Biochemical Characterization of N-methyltransferase Genes Involved in Purine Alkaloid Biosynthetic Pathway of Camellia gymnogyna Hung T.Chang (Theaceae) from Dayao Mountain

Fig. 4. Amino acid sequences alignment between TCS1 and candidate N-methyltransferase genes (GCS1, GCS2, and GCS3).

Fig. 2 in Discovery and Biochemical Characterization of N-methyltransferase Genes Involved in Purine Alkaloid Biosynthetic Pathway of Camellia gymnogyna Hung T.Chang (Theaceae) from Dayao Mountain

Fig. 2. Purine alkaloid content in different leaf positions of C. gymnogyna and other tea plants. Bud, 1st, 2nd, 3rd, 4th, and 5th represent the apical bud, first leaf, second leaf, third leaf, and fourth leaf, respectively. Total purine alkaloid concentration is the sum of Tb, Cf, and Tc. Asterisk indicates not detected. A lack of sufficient Kucha bud samples prohibited the analysis of that component. Data represent the mean value ± SD of independent experiments performed in triplicate. Data with the same letter and numeric above SD bar in each column are not significantly different from each other at P ≦ 0.05. Data with alphabet are significantly different from the data with numeric above SD bar.

Fig. 6. N in Discovery and Biochemical Characterization of N-methyltransferase Genes Involved in Purine Alkaloid Biosynthetic Pathway of Camellia gymnogyna Hung T.Chang (Theaceae) from Dayao Mountain

Fig. 6. N-methyltransferase gene expression patterns in different leaf positions of C. gymnogyna and other tea plants. Bud, 1st, 2nd, 3rd, 4th, and 5th represent the apical bud, first leaf, second leaf, third leaf, and fourth leaf, respectively.

Fig. 5 in Discovery and Biochemical Characterization of N-methyltransferase Genes Involved in Purine Alkaloid Biosynthetic Pathway of Camellia gymnogyna Hung T.Chang (Theaceae) from Dayao Mountain

Fig. 5. Phylogenetic tree of N-methyltransferase amino acid sequences. Substrates of the enzymes are indicated in parentheses. The following amino acid sequences were subjected to sequence alignment: TCS1, AB031280; CKCS, MN163829; TCS1d, KT215399; TCS1f, KT215398; TCS1e, KT215397; CkTcS, MN163831; CkTbS, MN163830; ICS1, AB056108; PCS1, AB207817; ICS2, AB207816; PCS2, AB207818; TCS2, AB031281; CkCS1, AB362884; CjCS1, AB297451; CgCS1, AB362882; CgCS2, AB362883; ClCS1, AB362885; CsSAMT, MG459470. Abbreviations of substrates are as follows: 7-mX, 7-methylxanthine; Tb, theobromine; Tc, theacrine; XR, xanthosine; CsSAMT as a outgroup.

Fig. 1 in Discovery and Biochemical Characterization of N-methyltransferase Genes Involved in Purine Alkaloid Biosynthetic Pathway of Camellia gymnogyna Hung T.Chang (Theaceae) from Dayao Mountain

Fig. 1. Main metabolic pathway for the biosynthesis and biodegradation of Cf. SAM = S-adenosyl- L -methionine, SAH = S-adenosyl- L -homo-cysteine. (b). Numbers (I, II, III, and IV) in (b) correspond to the reactions I, II, III, and IV in (a), respectively. TCS1 and CkCS have broad substrate specificities and catalyze the conversion of 7-mX to Cf via Tb [reactions II and III in (a)].

Fig. 3 in Discovery and Biochemical Characterization of N-methyltransferase Genes Involved in Purine Alkaloid Biosynthetic Pathway of Camellia gymnogyna Hung T.Chang (Theaceae) from Dayao Mountain

Fig. 3. Gene annotation. (a) Venn diagram; (b) The results of volcano plots of differential genes between the experimental groups; (c) GO annotation of DEGs; (d) The top 20 KEGG pathways of DEGs.

Fig. 4 in Molecular and biochemical characterization of Catharanthus roseus perivine-N -methyltransferase

Fig. 4. The organs of C. roseus display similar CrPeNMT and DhtNMT enzyme activities. A) Enzyme activity profiles of C. roseus leaf pairs 1(LP1), 2 (LP2), 3 (LP3), flowers (FL) and roots (RT) for CrPeNMT (A) and DhtNMT B) are displayed.

Fig. 3 in Molecular and biochemical characterization of Catharanthus roseus perivine-N -methyltransferase

Fig. 3. Recombinant CrPeNMT converts perivine to Vobasine. UPLC-MS analyses show that commercially available perivine (Rt 2.05, m/z+ 339) is not modified when assayed with empty vector (pET 30b) expressing bacterial extracts in the presence of 2 mM AdoMet. Perivine is completely converted to Vobasine (Rt 3.40, m/z+ 353) by bacterial extracts expressing recombinant CrPeNMT under the same conditions. The insets contain the UV and MS spectra of perivine and Vobasine, respectively.

Fig. 2 in Molecular and biochemical characterization of Catharanthus roseus perivine-N -methyltransferase

Fig. 2. Identification of MIAs in C. roseus MIA extracts that were methylated by recombinant CrPeNMT. Ultra performance liquid chromatography combined with MS showed that recombinant CrPeNMT converted an MIA (Rt 2.05, m/z+ 339) present in Catharanthus extracts into a methylated MIA (Rt 3.40, m/z+ 353) when assays are provided with 2 mM S-adenosyl-L-methionine. The UPLC elution and mass profiles of the MIA substrate and its methylated product suggested that perivine might be a possible substrate for CrPeNMT to generate a methylated form of this MIA.

Fig. 1 in Molecular and biochemical characterization of Catharanthus roseus perivine-N -methyltransferase

Fig. 1. The assembly of monoterpenoid indole alkaloids in different plant species involve substrate specific N-methylations catalysed by members of a recently described tocopherol-like methyltransferase gene family. The formation of strictosidine from secologanin and tryptamine involves the enzyme, strictosidine synthase (STR), while strictosidine-β-glucosidase (SGD) generates reactive intermediates, including 4, 21-dhydrogeissoschizine that is converted to 19Egeissoschizine by geissoschizine synthases (GS). This MIA is converted via multiple known enzyme reactions to 16-methoxy-2,3-dihydro-3-hydroxytabersonine which is N-methylated via dihydrotabersonine-N-methyltransferase (DhtNMT) to form 16-methoxy-2,3-dihydro-3-hydroxy-N-methyltabersonine that is ultimately converted into vindoline. While the conversion of 19E-geissoschizine to picrinine remains to be established, both Rauvolfia serpentina and Vinca minor express picrinine- N-methyltransferases (PiNMT) that converts picrinine to N-methypicrinine (ervincine). The formation of polyneuridine aldehyde from 19E-geissoschizine involves sarpagan bridge enzyme (SBE). Additional enzymes [polyneuridine aldehyde esterase (PNAE), vinorine synthase (VS), vinorine hydrolase, vinorine reductase and acetyajmaline esterase (AAE) convert vinorine to norajmaline. Two separate tocopherol-like methyltransferases (norajmaline N-methyltransferase (NNMT) and ajmaline N-methyltransferase convert norajmaline to ajmaline and Nβ-ajmaline, respectively. C. roseus and related species accumulate periformylene, an oxidixed form of Nβ-methylperivine. This MIA is derived from uncharacterized biochemical conversions of polyneuridine aldehyde to pericyclivine and to perivine. The formation of vobasine from perivine involves CrPeNMT found in C. roseus.

opennotspecifiedOct 2021View details →

Fig. 2 in Genetic diversity and biochemical analysis of Capsicum annuum (Bell pepper) in response to root and basal rot disease, Phytophthora capsici

Fig. 2. Three-dimensional analysis of the principal components derived from polymorphism pattern of 37 resistant and susceptible C. annuum genotypes to Phytophthora capsici by ISSR markers using NTSYS software, UPGMA algorithm and Jaccard similarity coefficient.

opennotspecifiedOct 2021View details →

Fig. 3 in Genetic diversity and biochemical analysis of Capsicum annuum (Bell pepper) in response to root and basal rot disease, Phytophthora capsici

Fig. 3. Activity of Peroxidase or Peroxide reductases (POX), (POX)(A), Superoxide dismutase (SOD) (B), Polyphenol oxidase (PPO) (C), Catalase (CAT) (D), Phenylalanine ammonia-lyase (PAL) (E), Glucanase (F) and Phenol contents (G) in inoculated resistant and susceptible pepper genotypes in comparison to controls, non-inoculated ones to damping-off disease, Phytophthora capcisi.

opennotspecifiedOct 2021View details →

Fig. 1 in Genetic diversity and biochemical analysis of Capsicum annuum (Bell pepper) in response to root and basal rot disease, Phytophthora capsici

Fig. 1. Two-dimensional diagram for principal coordinate analysis in C. annuum genotypes using ISSR markers. G1, G2, G3, G4 and G5: Genotype grouping. The results of PCA (Principal Coordinate Analysis) were largely consistent with those of ISSR markers. The studied genotypes were divided into five groups. There was no significant relationship between resistant and molecular markers in the present study (r = 0.020ns).

opennotspecifiedDec 2021View details →

Fig. 6 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 6. Characterization of Aa7DR1 as a 7-dehydrocholesterol reductase 1 from A. asphodeloides Bunge.

opennotspecifiedDec 2021View details →

Fig. 4 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 4. Transcriptional levels of candidate 7-DR genes involved in timosaponin biosynthesis by RT-qPCR. The characters on the X-axis indicate the roots (R), shortening stem (S) and leaves (L). The Y-axis represents the fold change in gene expression. The ubiquitin gene was used as an internal reference.