Molecular Biology at IgMin Research | Biology Group

Since the initial identification of TBCK (formerly MGC16169) in 2010, significant advances have been made in understanding the role of TBCK mutations in neurodevelopmental disorders such as TBCK encephalopathy. However, the precise function and detailed mechanisms of TBCK remain largely unexplored. Previous studies, including our own, suggest that aberrant expression or mutations in TBCK can impact cell growth, division, and cytoskeleton assembly, contributing to both cancer and neurogenetic diseases. Despite this, the specific domains within T...BCK responsible for these functions are still unclear. Notably, mutations in the TBC domain have been implicated in disrupting mTOR pathways, linking TBCK dysfunction to neurogenetic disorders and cancers. Given TBCK’s diverse roles, we have focused on its putative kinase domain. Through comprehensive analysis using tools such as Kinase Tree, AlphaFold2, Clustal Omega, and SMART, we discovered that TBCK lacks the key “D” residue in the conserved “HRD” and “DFG” motifs typical of protein kinases like PKA and SRC, suggesting TBCK functions as a pseudokinase. Intriguingly, gene ontology analysis from recent RNA-seq data indicates TBCK’s involvement in regulating protein phosphorylation. This suggests that TBCK may influence protein phosphorylation either directly through its potential kinase domain or indirectly via interactions with other proteins. To uncover the full spectrum of TBCK’s roles in neurogenetic disorders and cancer, urgent high-throughput analyses are necessary to identify its interacting partners.Read more

The medicinal herb Asparagus racemosus has been used in traditional medicine to treat various diseases such as cough, diarrhoea, diabetes, gastric issues, gonorrhoea, headaches, piles, rheumatism, and even lactation enhancement. This study explores the genetic information and phytochemicals of the species native to Gia Lai province, Vietnam before its conservation and cultivation. Five species of A. racemosus were analyzed using the trnL-e/trnL-f regions sequence. A. racemosus roots were extracted by water then Ultra-High-Performance Liquid Chr...omatography coupled with Quadrupole/Time-Of-Flight Mass Spectrometry (UHPLC-Q-TOF-MS) spectroscopy was used to screen for their phytochemicals. We have confirmed the DNA genetics of A. racemosus species collected in Gia Lai, Vietnam. In water extract of A. racemosus roots, UHPLC-Q-TOF-MS tentatively identified two flavonoids (Quercetin-3-glucuronide, Rutin), five steroidal saponins (Shatavarin I, Shatavarin IV, Shatavarin IX, Asparacoside, Asparanin A), and two steroids (β-sitosterol, Daucosterol). The experimental findings confirm the A. racemosus species for conservation and cultivation in Vietnam and contribute the benefits to the chemical literature of Vietnamese natural flora. A. racemosus should be further studied for pharmaceutical activities.Read more

Uremic toxins (UTs) are compounds derived from the metabolism of dietary molecules such as tryptophan (Indossyl Sulphate, IS) and phenil-alanine (P-Cresyl Sulphate, PCS), that are normally eliminated by the kidneys of healthy patients. The accumulation of such toxins is an indicator of kidney disease at different degrees of severity, and the toxins can be found as free or protein bound in human biological samples. The toxicity of such compounds causes the loss of several biological functions, and the subjects suffering from such complications w...ill need, more often than not, hemodialysis to properly excrete these toxins. Despite this not being a resolutive, but rather a symptom managing clinical approach, this is the most common course of treatment. Two analytical methods are proposed to quantify both the protein-bound and free forms of IS and PCS (HPLC-UV for the former; LC-MS/MS with ESI negative ionization for the latter), with lower variability and higher robustness than what is currently proposed, allowing for a precise simultaneous determination of the aforementioned UTs.Read more

The aim of the study was to determine the incidence of laboratory aspirin resistance; and to study the associations of genetic markers and clinical and laboratory parameters (including parameters of the platelet hemostasis) in patients with non-cardioembolic ischemic stroke using machine learning methods to assess the prognosis of recurrent ischemic strokes. Clinical and laboratory data (including induced platelet aggregation) were analyzed from 296 patients with ischemic stroke who were treated in the stroke center of City Clinical Hospital No.... 1 named after. N.I. Pirogov. The frequencies of polymorphic variants of the ITGB3, GPIba, TBXA2R, ITGA2, PLA2G7, HMOX1, PTGS1, PTGS2, ADRA2A, ABCB1, PEAR1 genes and intergenic region 9p21.3) in patients with non-cardioembolic ischemic stroke, which were identified using hydrogel biochip technology, were determined. Using the developed machine learning model, additional clinical and genetic factors influencing the development of laboratory aspirin resistance and recurrent ischemic stroke were studied. In the future, the identified factors can be used for differentiated prevention of recurrent ischemic strokes.Read more

Upon dysfunction of the Endoplasmic Reticulum (ER), eukaryotic cells provoke a gene expression program, namely, the Unfolded Protein Response (UPR), leading to an increase in the size and function of the ER. In the yeast Saccharomyces cerevisiae, the UPR is modulated by the Hac1i protein, which is a transcription factor produced by ER stress. When the UPR is artificially triggered under non-stress conditions by artificial expression of the Hac1i protein, S. cerevisiae cells carry an enforced and enlarged ER, which allows us to obtain commercial...ly valuable materials such as secretory proteins and functional lipids abundantly.Read more

The finite Markov chain to which there correspond the qualities of the conformational dynamics of the K-Ras4B proteins in the catalytic reaction is written. The corresponding Markov-Sates models are studied. The properties of the K-Ras4B processes Markov chain allow one to define a new two-state MSM for the analytical description of the final-state transition. The time evolution of the eigenvalue corresponding to the final-state transition in the Galerkin description is written. The tools for the analytical calculations of the relative error ...are therefore prepared. New analytical formulations of the time evolution of the eigenvalue corresponding to the final-state transition are newly written from the experimental data and form the properties of the lag time in shaping the discretization error. The features of the discretization error are newly studied. A comparison with the experimental data is proposed.Read more

For the first time, a method for calculating formulas of homologous series of chemical compounds of the systems (Aa+ – Bb+ – Cc–) and {Zn2+ – Ge4+ – P3–} in a generalized form is presented. The calculation is confirmed by the literature experimentally obtained compounds: thirteen compounds of the system (Na+ – Ti4+ – O2–), seven – systems (Li+ – Ti4+ – O2–), five – systems (K+ – V5a+ –  – O2–), eight – systems (Ba2+ – Cu2...+ – O2*). Homological series in (Aa+ – Bb+ – Cc–) have the following generalized form: A{t – k·r + nr – r)bcBracC{t – k·r + nr)ab and AtbcB{r – k·t + nt – t}acC (r – k·t + nt)ab.In (Zn2+ – Ge4+ – P3–) systems for the m-group the formulas of homologous series, that develops towards Ge3P4, have the following generalized form: Zn6tGe(6r – 6kt + 6n – 6t)P(8r – 8kt + 8n)  and for αm-homologous series – Zn6Ge3nP4(n + 1). A method for calculating formulas of homologous series of chemical compounds in a generalized form can be used for any system of chemical elements.Read more