Identiflcation of a Proenkephalin Precursor in Striatal Tissue

Recent studies have supported the suggestion that proenkephalin is the same in both adrenal medulla and brain. However, although previous investigations have characterized enkephalin-containing adrenal intermediates derived from proenkephalin, as yet no such intermediates have been isolated from the brain. This has led to the belief that the processing of proenkephalin in the brain is extremely rapid and enkephalin-containing intermediates do not accumulate. In this investigation Sephacryl-300 gel filtration chromatography of guinea pig striata, extracted in 8 M urea, demonstrated several peaks of both bioactive and immunoreactive enkephalin-like peptides after enzymatic digest (trypsin followed by carboxypeptidase B). Comparable profiles were obtained using rat and bovine striatal tissue. In guinea pig the major species emerging from gel filtration, eluting with an apparent molecular weight of 29,000, represented approximately 9% of the total (methionine) enkephalin immunoreactivity. It had an apparent pI of 5.0 when subjected to chromatofocusing. This species was further characterized using sodium dodecyl sulphate-polyacrylamide gel electrophoresis and nitrocellulose blotting techniques as well as highly specific radioimmunoassays to (Met5)-enkephalin, (Leu5)-enkephalin, and (Met5)-enkephalin-Arg6-Phe7. This species was found to contain these opioid peptides in an approximately 6:1:1 ratio, respectively, and to have an apparent molecular weight of 31,000. It was also indicated that (Met5)-enkephalin-Arg6-Phe7 constituted the C-terminal seven residues of this molecule.     

Processing of Rat Preprocortistatin in Mouse AtT-20 Cells

Preprocortistatin (PPCST) has been recently identified as a novel somatostatin (SST)-related gene expressed only in brain. PPCST shares 11 of 14 residues with SST-14 at its C-terminal segment, where it features Lys-Lys and Lys-Arg basic sites for cleavage to putative cortistatin (CST)-14 and CST-29 peptides, respectively. Although synthetic replicates of the two putative CST peptides interact with SST receptors, they also display novel effects suggesting independent biological functions. Nothing is currently known about the naturally occurring mature cleavage products of PPCST posttranslational processing. Here we have cloned rat PPCST cDNA, stably expressed it in AtT-20 pituitary cells, and characterized the cellular and releasable products of PPCST processing by HPLC and radioimmunoassay using a SST-14 antibody that recognizes synthetic CST-14 and CST-29. Transfected cells released 120 +/- 21 pg of total CST-LI per plate basally, with an increase to 204 +/- 33 pg per plate with forskolin stimulation (p < 0.05). HPLC chromatograms of cell extracts revealed three peaks corresponding to CST-14, CST-29, and unprocessed PPCST (ratio, 41:55:4.5). CST was released preferentially as CST-14 (63-70%) compared with CST-29 (30-37%) under basal and forskolin-stimulated conditions. These studies demonstrate efficient processing of PPCST to both CST-14 and CST-29 through putative cleavage at both C-terminal dibasic sites of PPCST. Although the two peptides are synthesized approximately equally, CST-14 is released preferentially via the regulated secretory pathway.     

5'-Cleavage site of D. melanogaster 18 S rRNA

We determined the nucleotide sequence of the DNA region around the 5'-terminus of 18 S rRNA in two cloned rDNA gene units of Drosophila melanogaster. The 5'-base is within a sequence CATTATT which is present also at the 3'-terminus of the 18 S rRNA coding region. In this case it is known that the situation is CATTA3' . TT. With various methods we determined that the precise 5'-cleavage site is CATT . 5'ATT.     

Meniscal lesion detection and characterization in adult knee MRI: A deep learning model approach with external validation

PurposeEvaluation of a deep learning approach for the detection of meniscal tears and their characterization (presence/absence of migrated meniscal fragment).MethodsA large annotated adult knee MRI database was built combining medical expertise of radiologists and data scientists’ tools. Coronal and sagittal proton density fat suppressed-weighted images of 11,353 knee MRI examinations (10,401 individual patients) paired with their standardized structured reports were retrospectively collected. After database curation, deep learning models were trained and validated on a subset of 8058 examinations. Algorithm performance was evaluated on a test set of 299 examinations reviewed by 5 musculoskeletal specialists and compared to general radiologists’ reports. External validation was performed using the publicly available MRNet database. Receiver Operating Characteristic (ROC) curves results and Area Under the Curve (AUC) values were obtained on internal and external databases.ResultsA combined architecture of meniscal localization and lesion classification 3D convolutional neural networks reached AUC values of 0.93 (95% CI 0.82, 0.95) for medial and 0.84 (95% CI 0.78, 0.89) for lateral meniscal tear detection, and 0.91 (95% CI 0.87, 0.94) for medial and 0.95 (95% CI 0.92, 0.97) for lateral meniscal tear migration detection. External validation of the combined medial and lateral meniscal tear detection models resulted in an AUC of 0.83 (95% CI 0.75, 0.90) without further training and 0.89 (95% CI 0.82, 0.95) with fine tuning.ConclusionOur deep learning algorithm demonstrated high performance in knee menisci lesion detection and characterization, validated on an external database.     

E. coli cardiolipin synthase: Function of N-terminal conserved residues

The E. coli cls open reading frame (ORF) predicts a 54.8 kDa polypeptide, whereas mature cardiolipin (CL) synthase is 46 kDa. The N-terminal region extending to residue 60 contains several conserved residues but is not essential for enzyme activity. A deletion mutant that is missing residues 2-60 produces a fully active protein. These findings raise the question of why several residues in a region that is not required for enzyme activity are conserved. Recombinant DNA technology was used to introduce an EYMPE epitope (EE) tag into the interior of CL synthase. The EE tagged polypeptide retained the biological properties of wild type CL synthase, including full enzymatic activity. Site-directed mutagenesis was used to alter conserved residues in the N-terminal region. An EE tagged CL synthase in which Leu-7 and Val-8 were both replaced by Ser residues retains in vitro activity but loses most of its in vivo activity. Furthermore, the mutant protein has a higher apparent molecular mass than its parent protein. Taken together, these findings suggest that conserved residues L7 and V8 play a role in polypeptide processing, topology, or both.     

Smart de novo Macromolecular Structure Modeling from Cryo-EM Maps

The study of macromolecular structures has expanded our understanding of the amazing cell machinery and such knowledge has changed how the pharmaceutical industry develops new vaccines in recent years. Traditionally, X-ray crystallography has been the main method for structure determination, however, cryogenic electron microscopy (cryo-EM) has increasingly become more popular due to recent advancements in hardware and software. The number of cryo-EM maps deposited in the EMDataResource (formerly EMDatabase) since 2002 has been dramatically increasing and it continues to do so. De novo macromolecular complex modeling is a labor-intensive process, therefore, it is highly desirable to develop software that can automate this process. Here we discuss our automated, data-driven, and artificial intelligence approaches including map processing, feature extraction, modeling building, and target identification. Recently, we have enabled DNA/RNA modeling in our deep learning-based prediction tool, DeepTracer. We have also developed DeepTracer-ID, a tool that can identify proteins solely based on the cryo-EM map. In this paper, we will present our accumulated experiences in developing deep learning-based methods surrounding macromolecule modeling applications.     

Cost Comparison of Protein Capture from Cultivation Broths by Expanded and Packed Bed Adsorption

In the downstream processing of recombinant protein production, the reduction of unit operations required for product capture and purification, is of the utmost priority due to its cost diminishing effect. In this regard, target protein capture from cell suspensions in a fluidized bed of affinity particles with different sizes (expanded bed adsorption (EBA) with classified particles), presents an efficient tool since EBA may substitute cell disintegration, separation by centrifugation or filtration, and packed bed adsorption. However, as illustrated by experiments with the BSA/yeast cells system, the entire broth processing used in EBA also has detrimental influences due to the cell (or cell debris) binding on the affinity carrier. In particular, external mass transfer may become more dominant, and the lifetime of the affinity particles may reduce as a result of other cleaning procedures. Using simulations performed with a commercial software package, the cost superiority of alternate process routes (EBA or packed bed adsorption with preceding steps) can be evaluated. This elucidates the favorable application range for each route.