Approaching the Chemometric Modeling of Realistically Diverse Biochemical Data

2015 ◽  
pp. 283-298
Author(s):  
Jeffrey A. Cramer
Keyword(s):  
Biochemical Data

Discrimination of monomer from multimer DNA disk-shaped toruses by freezeetch TEM

1984 ◽  
Vol 42 ◽  
pp. 210-211
Author(s):  
George C. Ruben ◽  
Kenneth A. Marx
Keyword(s):  
Biochemical Data ◽  
Dna Structures ◽  
Ice Surface ◽  
Double Stranded Dna ◽  
Data Support ◽  
Dna Organization ◽  
Trivalent Cations

In vitro collapse of DNA by trivalent cations like spermidine produces torus (donut) shaped DNA structures thought to have a DNA organization similar to certain double stranded DNA bacteriophage and viruses. This has prompted our studies of these structures using freeze-etch low Pt-C metal (9Å) replica TEM. With a variety of DNAs the TEM and biochemical data support a circumferential DNA winding model for hydrated DNA torus organization. Since toruses are almost invariably oriented nearly horizontal to the ice surface one of the most accessible parameters of a torus population is annulus (ring) thickness. We have tabulated this parameter for populations of both nicked, circular (Fig. 1: n=63) and linear (n=40: data not shown) ϕX-174 DNA toruses. In both cases, as can be noted in Fig. 1, there appears to be a compact grouping of toruses possessing smaller dimensions separated from a dispersed population possessing considerably larger dimensions.

Evaluation of preoperative ultrasonographic parameters to predict renal recovery in long-term survivors after treatment of feline ureteral obstructions: 2012–2019

2021 ◽  
pp. 1098612X2110236
Author(s):  
Elisa P McEntee ◽  
Allyson C Berent ◽  
Chick Weisse ◽  
Alexandre Le Roux ◽  
Kenneth Lamb
Keyword(s):  
Serum Creatinine ◽  
Ultrasound Imaging ◽  
Ureteral Obstruction ◽  
Unilateral Ureteral Obstruction ◽  
Biochemical Data ◽  
Preoperative Imaging ◽  
Long Term Outcome ◽  
Preoperative Ultrasound ◽  
Imaging Characteristics

Objectives The aim of this study was to determine whether preoperative ultrasound imaging characteristic(s) in cats suffering from unilateral benign ureteral obstructions are predictive of outcome after successful renal decompression with a subcutaneous ureteral bypass (SUB) device. Methods This was a retrospective study of 37 cats with unilateral, benign ureteral obstruction. Preoperative imaging characteristics (including renal pelvis diameter, parenchymal thickness [transverse plane], renal length and pelvic size:overall renal size) and biochemical data were evaluated for all cats diagnosed with a unilateral ureteral obstruction treated with a SUB device. Any patient with bilateral obstructions or documented bacteriuria/infection in the data collection period was excluded. All patients were followed between 3 and 6 months postoperatively to obtain postoperative biochemical data. Long-term outcome was defined as serum creatinine concentration at 3–6 months postoperatively. Results No preoperative imaging characteristics or biochemical findings were found to be significantly associated with long-term serum creatinine concentrations. The length of the kidney was found to be associated with change in blood urea nitrogen and creatinine with decompression but not with long-term renal values. Conclusions and relevance In this study, long-term renal function based on preoperative ultrasound imaging findings could not be predicted in cats with unilateral ureteral obstruction, regardless of the severity of the biochemical parameters, renal pelvic dilation (large or small pelvis), kidney size or thickness of renal parenchyma assessed.

scholarly journals Crystal structures of an E1–E2–ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Lingmin Yuan ◽  
Zongyang Lv ◽  
Melanie J. Adams ◽  
Shaun K. Olsen
Keyword(s):  
Complex Formation ◽  
Crystal Structures ◽  
Molecular Mechanisms ◽  
Conformational State ◽  
Biochemical Data ◽  
Conformational States ◽  
Product Release ◽  
Closed Conformation ◽  
Open Conformation ◽  
Conjugating Enzymes

AbstractE1 enzymes function as gatekeepers of ubiquitin (Ub) signaling by catalyzing activation and transfer of Ub to tens of cognate E2 conjugating enzymes in a process called E1–E2 transthioesterification. The molecular mechanisms of transthioesterification and the overall architecture of the E1–E2–Ub complex during catalysis are unknown. Here, we determine the structure of a covalently trapped E1–E2–ubiquitin thioester mimetic. Two distinct architectures of the complex are observed, one in which the Ub thioester (Ub(t)) contacts E1 in an open conformation and another in which Ub(t) instead contacts E2 in a drastically different, closed conformation. Altogether our structural and biochemical data suggest that these two conformational states represent snapshots of the E1–E2–Ub complex pre- and post-thioester transfer, and are consistent with a model in which catalysis is enhanced by a Ub(t)-mediated affinity switch that drives the reaction forward by promoting productive complex formation or product release depending on the conformational state.

scholarly journals Overlapping but distinct: a new model for G-quadruplex biochemical specificity

2021 ◽  
Author(s):  
Martin Volek ◽  
Sofia Kolesnikova ◽  
Katerina Svehlova ◽  
Pavel Srb ◽  
Ráchel Sgallová ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Drug Design ◽  
Solution Structure ◽  
Biochemical Data ◽  
Biological Regulation ◽  
New Model ◽  
G Quadruplex ◽  
Range Of Functions ◽  
Nucleic Acid Structures ◽  
Sequence Requirements

Abstract G-quadruplexes are noncanonical nucleic acid structures formed by stacked guanine tetrads. They are capable of a range of functions and thought to play widespread biological roles. This diversity raises an important question: what determines the biochemical specificity of G-quadruplex structures? The answer is particularly important from the perspective of biological regulation because genomes can contain hundreds of thousands of G-quadruplexes with a range of functions. Here we analyze the specificity of each sequence in a 496-member library of variants of a reference G-quadruplex with respect to five functions. Our analysis shows that the sequence requirements of G-quadruplexes with these functions are different from one another, with some mutations altering biochemical specificity by orders of magnitude. Mutations in tetrads have larger effects than mutations in loops, and changes in specificity are correlated with changes in multimeric state. To complement our biochemical data we determined the solution structure of a monomeric G-quadruplex from the library. The stacked and accessible tetrads rationalize why monomers tend to promote a model peroxidase reaction and generate fluorescence. Our experiments support a model in which the sequence requirements of G-quadruplexes with different functions are overlapping but distinct. This has implications for biological regulation, bioinformatics, and drug design.

scholarly journals A Role for MMS4 in the Processing of Recombination Intermediates During Meiosis in Saccharomyces cerevisiae

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1511-1525 ◽  
Author(s):  
Teresa de los Santos ◽  
Josef Loidl ◽  
Brittany Larkin ◽  
Nancy M Hollingsworth
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Meiotic Recombination ◽  
Biochemical Data ◽  
Dna Metabolism ◽  
Spore Viability ◽  
Vegetative Cells ◽  
Recombination Checkpoint

Abstract The MMS4 gene of Saccharomyces cerevisiae was originally identified due to its sensitivity to MMS in vegetative cells. Subsequent studies have confirmed a role for MMS4 in DNA metabolism of vegetative cells. In addition, mms4 diploids were observed to sporulate poorly. This work demonstrates that the mms4 sporulation defect is due to triggering of the meiotic recombination checkpoint. Genetic, physical, and cytological analyses suggest that MMS4 functions after the single end invasion step of meiotic recombination. In spo13 diploids, red1, but not mek1, is epistatic to mms4 for sporulation and spore viability, suggesting that MMS4 may be required only when homologs are capable of undergoing synapsis. MMS4 and MUS81 are in the same epistasis group for spore viability, consistent with biochemical data that show that the two proteins function in a complex. In contrast, MMS4 functions independently of MSH5 in the production of viable spores. We propose that MMS4 is required for the processing of specific recombination intermediates during meiosis.

scholarly journals Response to Comment on “Structural evidence for a dynamic metallocofactor during N2 reduction by Mo-nitrogenase”

Science ◽  
2021 ◽  
Vol 371 (6530) ◽  
pp. eabe5856
Author(s):  
Wonchull Kang ◽  
Chi Chung Lee ◽  
Andrew J. Jasniewski ◽  
Markus W. Ribbe ◽  
Yilin Hu
Keyword(s):  
Dynamic Structure ◽  
Structural Data ◽  
Biochemical Data ◽  
Structural Refinement

Peters et al. comment on our report of the dynamic structure of the nitrogenase metallocofactor during N2 reduction. Their claim that their independent structural refinement and consideration of biochemical data contradict our finding is incorrect and is strongly refuted by our biochemical and structural data that collectively and conclusively point to the binding of dinitrogen species to the nitrogenase cofactor.

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