SHAKE34 was performed on all bonds including hydrogen with the AMBER default tolerance of 10−5 Å for NVT and 10−6 Å for NVE. Non-bonded interactions were calculated directly up to 8 Å. Beyond 8 Å, electrostatic interactions were treated with cubic spline switching and the particle-mesh Ewald approximation35 in explicit solvent, with direct sum tolerances of 10−5 for NVT or 10−6 for NVE. A continuum model correction for energy and pressure was applied to long-range van der Waals interactions. The production timesteps were 2 fs for NVT and 1 fs for NVE.
Vertebral Column
It consists of a series of interconnected vertebrae that provide support, flexibility, and protection for the spinal cord.
This complex system plays a crucial role in facilitating movement, transmitting forces, and safeguarding the delicate nervous system.
Ongoing research into the vertebral column explores advancements in areas such as biomechanics, spinal injuries, degenerative conditions, and surgical interventions.
By leveraging the power of data-driven comparisons, scientists can identify optimal solutions to enhance the understanding and treatment of vertebral column-related isssues, improving patient outcomes and advancing the field of musculoskeletal health.
Most cited protocols related to «Vertebral Column»
We also report accuracies using the r.m.s.d.95 (Cα r.m.s.d. at 95% coverage). We perform five iterations of (1) a least-squares alignment of the predicted structure and the PDB structure on the currently chosen Cα atoms (using all Cα atoms in the first iteration); (2) selecting the 95% of Cα atoms with the lowest alignment error. The r.m.s.d. of the atoms chosen for the final iterations is the r.m.s.d.95. This metric is more robust to apparent errors that can originate from crystal structure artefacts, although in some cases the removed 5% of residues will contain genuine modelling errors.
is satisfied for all dj,j+k that denotes the Cα distance between the jth and (j + k)th residues; otherwise, it is assigned to be a coil. The final assignment is further smoothed by merging and removing singlet SS states. We note that the set of eight parameters are optimized based on 100 non-homologous training proteins by maximizing the SS assignment similarity to the DSSP definition (20 (link)), which defines protein SS elements on the basis of hydrogen bond patterns and requires the full set of backbone atomic coordinates. The optimized parameters are , , , δα = 2.1 Å, , , , δβ = 1.42 Å. Using
The second type of initial alignment is based on the gapless matching of two structures. As in SAL (18 (link)), for the smaller of the two compared proteins, we perform gapless threading against the larger structure, but rather than use RMSD as the comparison metric as was done in SAL, now the alignment with the best TM-score is selected.
The third initial alignment is also obtained by DP using a gap-opening penalty of −1, but the score matrix is a half/half combination of the SS score matrix and the distance score matrix selected in the second initial alignment.
Most recents protocols related to «Vertebral Column»
Example 13
Molecular modeling study based upon the co-crystal structure of ALK with Alectinib (PDB: 3AOX) (Sakamoto, H. et al., Cancer Cell 2011, 19, 679) was performed to assess the structure-activity relationship of inhibition of ALK and/or ALK mutants by the compounds of the present application. The modeling showed that Compound 6 makes the same backbone hinge contact as Alectinib, however, Compound 6 forms two additional hydrogen bond interactions between the guanidine moiety of R1120 and the carbonyl group of the dimethyl acetamide group (
Example 6
Human multiple myeloma cancer cells are known to undergo increased cell division through IL-6-triggered STAT3 signaling. Numerous studies have shown that let7a-5p miRNA (SEQ ID NO:2) inhibits the activity of Signal Transducer and Activator of Transcription 3 (STAT3). Human multiple myeloma cells MM.1S were incubated for 48 hrs daily with 10 μg/ml polymer-modified let7a-5p miRNA as indicated and expression of the STAT3 target gene, oncogenic Bcl-xL gene, was analyzed by RT-PCR. As shown in
EXAMPLE 1
OCG was synthesized and the average molecular weight of OCG was confirmed by both gel permeation chromatography (GPC) and proton nuclear magnetic resonance (H NMR) spectroscopy (
Example 1
Expression strain generation. The TdT mouse gene may be generated from the pET28 plasmid described in [Boulé et al., 1998, Mol. Biotechnol. 10, 199-208]. For example, the gene may be amplified by using the following primers:
Expression. The Ec-CTdT and Ec-DSi or Ec-DSi′ strains may be used for inoculating 250 mL erlens with 50 mL of LB media supplemented with appropriate amount of kanamycin. After overnight growth at 37° C., appropriate volumes of these pre-cultures are used to inoculate 5 L erlens with 2 L LB media with kanamycin. The initial OD for the 5 L cultures is chosen to be 0.01. The erlens are put at 37° C. under strong agitation and the OD of the different cultures are regularly checked. After reaching an OD comprised between 0.6 and 0.9 each erlen is supplemented by the addition of 1 mL of 1M IPTG (Isopropyl β-D-1-thiogalactopyranoside, Sigma). The erlens are put back to agitation under a controlled temperature of 37° C. After overnight expression, the cells are harvested in several pellets. Pellets expressing the same variants are pooled and stored at −20° C., eventually for several months.
Extraction. Previously prepared pellets are thawed in 30 to 37° C. water bath. Once fully thawed, pellets are resuspended in lysis buffer composed of 50 mM tris-HCL (Sigma) pH 7.5, 150 mM NaCl (Sigma), 0.5 mM mercaptoethanol (Sigma), 5% glycerol (Sigma), 20 mM imidazole (Sigma) and 1 tab for 100 mL of protease cocktail inhibitor (Thermofisher). Careful resuspension is carried out in order to avoid premature lysis and remaining of aggregates. Resuspended cells are lysed through several cycles of French press, until full color homogeneity is obtained. Usual pressure used is 14,000 psi. Lysate is then centrifuged for 1 h to 1h30 at 10,000 rpm. Centrifugate is pass through a 0.2 μm filter to remove any debris before column purification.
Purification. A one-step affinity procedure is used to purify the produced and extracted polymerase enzymes. A Ni-NTA affinity column (GE Healthcare) is used to bind the polymerases. Initially the column has been washed and equilibrated with 15 column volumes of 50 mM tris-HCL (Sigma) pH 7.5, 150 mM NaCl (Sigma) and 20 mM imidazole (Sigma). Polymerases are bound to the column after equilibration. Then a washing buffer, composed of 50 mM tris-HCL (Sigma) pH 7.5, 500 mM NaCl (Sigma) and 20 mM imidazole (Sigma), is applied to the column for 15 column volumes. After wash the polymerases are eluted with 50 mM tris-HCL (Sigma) pH 7.5, 500 mM NaCl (Sigma) and 0.5M imidazole (Sigma). Fractions corresponding to the highest concentration of polymerases of interest are collected and pooled in a single sample. The pooled fractions are dialyzed against the dialysis buffer (20 mM Tris-HCl, pH 6.8, 200 mM Na Cl, 50 mM MgOAc, 100 mM [NH4]2SO4). The dialysate is subsequently concentrated with the help of concentration filters (Amicon Ultra-30, Merk Millipore). Concentrated enzyme is distributed in small aliquots, 50% glycerol final is added, and those aliquots are then frozen at −20° C. and stored for long term. 5 μL of various fraction of the purified enzymes are analyzed in SDS-PAGE gels.
Example 4
miRNAs with naturally occurring sequences were fused covalently to a phosphorothioated single-stranded abasic sugar-phosphate backbone (PS) 20meric polymer to facilitate cellular internalization targeting intracellular molecular targets. A non-phosphorothioated, phosphodiester single-stranded abasic sugar-phosphate backbone polymer (PO) extension of the miRNAs was employed as a non-internalizing control.
Applicants modified naturally occurring miRNAs, for example, let7a-5p (SEQ ID NO:2) by attaching a phosphorothioated single-stranded abasic sugar-phosphate backbone (PS) 20meric polymer to the 3′ end of the miRNAs via a chemical linker (
Top products related to «Vertebral Column»
More about "Vertebral Column"
The vertebral column, also known as the spine or backbone, is a central structural component of the human body.
This complex system of interconnected vertebrae plays a crucial role in facilitating movement, transmitting forces, and safeguarding the delicate nervous system.
Ongoing research into the vertebral column explores advancements in areas such as biomechanics, spinal injuries, degenerative conditions, and surgical interventions.
Synonyms and Related Terms:
The vertebral column is also referred to as the spinal column or rachis.
Other related terms include the cervical, thoracic, lumbar, sacral, and coccygeal regions of the spine, as well as conditions like scoliosis, kyphosis, and lordosis.
Key Subtopics:
Biomechanics of the Vertebral Column: Understanding the complex interplay of vertebrae, discs, and ligaments that enable spinal flexibility, load-bearing, and stability.
Spinal Injuries and Trauma: Investigating the causes, effects, and treatment options for injuries like herniated discs, fractures, and spinal cord damage.
Degenerative Conditions: Exploring the pathogenesis and management of age-related conditions affecting the vertebral column, such as osteoarthritis and intervertebral disc degeneration.
Surgical Interventions: Advancements in minimally invasive procedures, implants, and fusion techniques to address vertebral column-related issues and improve patient outcomes.
Tools and Techniques:
Lipofectamine 2000 and Lipofectamine 3000 are transfection reagents that can be used to study gene expression and signaling pathways in vertebral column-related cells and tissues.
The FD Rapid GolgiStain Kit is a histological technique that allows for the visualization of neuronal structures within the spinal cord.
Polybrene and T4 DNA ligase are commonly used in viral transduction and gene cloning experiments, which can contribute to our understanding of vertebral column development and disease.
FBS (Fetal Bovine Serum) is a essential supplement for cell culture media, enabling the growth and maintenance of vertebral column-derived cells in the laboratory.
The MAGNETOM Skyra is a high-field MRI scanner that can provide detailed imaging of the vertebral column, aiding in the diagnosis and monitoring of various spinal conditions.
PsPAX2 and GeneArt are tools used for lentiviral vector production and gene synthesis, respectively, which can be leveraged in vertebral column-related research.
DMEM (Dulbecco's Modified Eagle Medium) is a common cell culture medium used to support the growth and study of vertebral column-derived cell lines.
By leveraging the power of data-driven comparisons, scientists can identify optimal solutions to enhance the understanding and treatment of vertebral column-related issues, improving patient outcomes and advancing the field of musculoskeletal health.
OtherTerms: spine, backbone, rachis, cervical, thoracic, lumbar, sacral, coccygeal, scoliosis, kyphosis, lordosis, biomechanics, spinal injuries, degenerative conditions, surgical interventions, Lipofectamine, FD Rapid GolgiStain Kit, Polybrene, T4 DNA ligase, FBS, MAGNETOM Skyra, PsPAX2, GeneArt, DMEM