Mutations in CACNA1C, the gene encoding Cav1.2 voltage-gated calcium channels, are associated with a spectrum of disorders, including Timothy syndrome and other neurodevelopmental and cardiac conditions. In this study, we report a child with a de novo heterozygous missense variant (c.1973T > C; L658P) in CACNA1C, presenting with refractory epilepsy, global developmental delay, hypotonia, and multiple systemic abnormalities, but without overt cardiac dysfunction. Electrophysiological analysis of the recombinant Cav1.2 L658P variant revealed profound gating alterations, most notably a significant hyperpolarizing shift in the voltage dependence of activation and inactivation. Additionally, molecular modeling suggested that the L658P mutation disrupts interactions within the IIS5 transmembrane segment, reducing the energy barrier for state transitions and facilitating channel opening at more negative voltages. These findings establish L658P as a pathogenic CACNA1C variant primarily associated with severe neurological dysfunction and expands the phenotypic spectrum of CACNA1C-related disorders.
- MeSH
- dítě MeSH
- gating iontového kanálu * MeSH
- lidé MeSH
- missense mutace genetika MeSH
- molekulární modely MeSH
- neurovývojové poruchy * genetika MeSH
- předškolní dítě MeSH
- sekvence aminokyselin MeSH
- vápníkové kanály - typ L * genetika MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
BACKGROUND: In hospitals, decisions are often made under time pressure. There is, however, little evidence on how time pressure affects the quality of treatment and the documentation behaviour of physicians. SETTING: We implemented a controlled laboratory experiment with a healthcare framing in which international medical students in the Czech Republic treated patients in the role of hospital physicians. We varied the presence of time pressure and a documentation task. RESULTS: We observed worse treatment quality when individuals were faced with a combination of a documentation task and time pressure. In line with the concept of the speed-accuracy trade-off, we showed that quality changes are likely driven by less accuracy. Finally, we showed that while documentation quality was relatively high overall, time pressure significantly lowered the latter leading to a higher hypothetical profit loss for the hospital. CONCLUSIONS: Our results suggest that policy reforms aimed at increasing staffing and promoting novel technologies that facilitate physicians' treatment decisions and support their documentation work in the hospital sector might be promising means of improving the treatment quality and reducing inefficiencies potentially caused by documentation errors.
- MeSH
- časové faktory MeSH
- dokumentace * normy MeSH
- kvalita zdravotní péče * MeSH
- lékaři * psychologie MeSH
- lidé MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.
The overexpression of MYC genes is frequently found in many human cancers, including adult and pediatric malignant brain tumors. Targeting MYC genes continues to be challenging due to their undruggable nature. Using our prediction algorithm, the nine-amino-acid activation domain (9aaTAD) has been identified in all four Yamanaka factors, including c-Myc. The predicted activation function was experimentally demonstrated for all these short peptides in transactivation assay. We generated a set of c-Myc constructs (1-108, 69-108 and 98-108) in the N-terminal regions and tested their ability to initiate transcription in one hybrid assay. The presence and absence of 9aaTAD (region 100-108) in the constructs strongly correlated with their activation functions (5-, 3- and 67-times respectively). Surprisingly, we observed co-activation function of the myc region 69-103, called here acetyl-TAD, previously described by Faiola et al. (Mol Cell Biol 25:10220-10234, 2005) and characterized in this study as a new domain collaborating with the 9aaTAD. We discovered strong interactions on a nanomolar scale between the Myc-9aaTAD activation domains and the KIX domain of CBP coactivator. We showed conservation of the 9aaTADs in the MYC family. In summary for the c-Myc oncogene, the acetyl-TAD and the 9aaTAD domains jointly mediated activation function. The c-Myc protein is largely intrinsically disordered and therefore difficult to target with small-molecule inhibitors. For the c-Myc driven tumors, the strong c-Myc interaction with the KIX domain represents a promising druggable target.
- MeSH
- aktivace transkripce MeSH
- lidé MeSH
- proteinové domény MeSH
- protoonkogenní proteiny c-myc * metabolismus genetika MeSH
- sekvence aminokyselin MeSH
- vazba proteinů * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Cíl: Molekulární klasifikace endometriálních karcinomů (EK) dělí tyto tumory do čtyř distinktních skupin definovaných genetickým pozadím. Vzhledem k prokázanému klinickému významu se genetické vyšetření EK stává nedílnou součástí dia gnostického postupu. Doporučený dia gnostický algoritmus zahrnuje molekulárně genetický průkaz mutace genu POLE, přičemž všechny další potřebné parametry se vyšetřují pouze imunohistochemicky. Cílem této studie je sdílet naše zkušenosti s molekulární klasifikací EK, která je na našem pracovišti prováděna pomocí imunohistochemie a následně sekvenování nové generace (NGS). Metodika: Do studie byly zařazeny všechny EK dia gnostikované na Šiklově ústavu patologie ve FN Plzeň a v Bioptické laboratoři, s. r. o., od roku 2020 do současnosti. Všechny EK byly prospektivně vyšetřeny nejprve imunohistochemicky (MMR proteiny, p53) a následně molekulárně geneticky pomocí NGS za použití „customizovaného Gyncore panelu“ (zahrnujícího geny POLE, POLD1, MSH2, MSH6, MLH1, PMS2, TP53, PTEN, ARID1A, PIK3CA, PIK3R1, CTNNB1, KRAS, NRAS, BRCA1, BRCA2, BCOR, ERBB2), na jehož základě byly rozčleněny do čtyř molekulárně distinktních skupin [POLE mutované EK (typ 1), hypermutované (MMR deficientní, typ 2), EK bez specifického molekulárního profilu (NSMP, typ 3) a TP53 mutované („copy number high“, typ 4) ]. Výsledky: Soubor zahrnuje celkem 270 molekulárně klasifikovaných EK. Osmnáct případů (6,6 %) bylo klasifikováno jako POLE mutované, 85 případů (31,5 %) jako hypermutované (MMR deficientní), 137 případů (50,7 %) jako EK bez specifického molekulárního profilu, 30 případů (11,1 %) jako TP53 mutované. Dvanáct případů (4,4 %) bylo zařazeno jako „multiple classifier“. Skupina NSMP se často vyznačovala mnohočetnými genetickými alteracemi, přičemž nejčastější byla mutace genu PTEN (44 % v rámci NSMP), následovaly PIK3CA (30 %), ARID1A (21 %) a KRAS (9 %). Závěr: Molekulární klasifikace EK pomocí metody NGS umožňuje v porovnání s doporučeným dia gnostickým algoritmem spolehlivější klasifikaci EK do jednotlivých molekulárních skupin. Kromě toho dovoluje NGS vyšetření odkrýt komplexní genetické pozadí jednotlivých EK, což má význam zvláště v rámci skupiny „bez specifického molekulárního profilu“, kde jsou tato data podkladem pro výzkum léčebných schémat s příslibem cílené terapie tohoto typu nádorů.
Objective: Molecular classification of endometrial carcinomas (EC) divides these neoplasms into four distinct subgroups defined by a molecular background. Given its proven clinical significance, genetic examination is becoming an integral component of the diagnostic procedure. Recommended diagnostic algorithms comprise molecular genetic testing of the POLE gene, whereas the remaining parameters are examined solely by immunohistochemistry. The aim of this study is to share our experiences with the molecular classification of EC, which has been conducted using immunohistochemistry and next-generation sequencing (NGS) at our department. Methods: This study includes all cases of EC diagnosed at Šikl's Department of Pathology and Biopticka Laboratory Ltd. from 2020 to the present. All ECs were prospectively examined by immunohistochemistry (MMR, p53), fol lowed by NGS examination using a customized Gyncore panel (including genes POLE, POLD1, MSH2, MSH6, MLH1, PMS2, TP53, PTEN, ARID1A, PIK3CA, PIK3R1, CTNNB1, KRAS, NRAS, BRCA1, BRCA2, BCOR, ERBB2), based on which the ECs were classified into four molecularly distinct groups [POLE mutated EC (type 1), hypermutated (MMR deficient, type 2), EC with no specific molecular profile (type 3), and TP53 mutated (“copy number high”, type 4)]. Results: The cohort comprised a total of 270 molecularly classified ECs. Eighteen cases (6.6%) were classified as POLE mutated EC, 85 cases (31.5%) as hypermutated EC (MMR deficient), 137 cases (50.7%) as EC of no specific molecular profile, and 30 cases (11.1%) as TP53 mutated EC. Twelve cases (4.4%) were classified as “multiple classifier” endometrial carcinoma. ECs of no specific molecular profile showed multiple genetic alterations, with the most common mutations being PTEN (44% within the group of NSMP), fol lowed by PIK3CA (30%), ARID1A (21%), and KRAS (9%). Conclusion: In comparison with recommended diagnostic algorithms, NGS provides a more reliable classification of EC into particular molecular subgroups. Furthermore, NGS reveals the complex molecular genetic background in individual ECs, which is especially significant within ECs with no specific molecular profile. These data can serve as a springboard for the research of therapeutic programs committed to targeted therapy in this type of tumor.
- MeSH
- imunohistochemie klasifikace metody MeSH
- klasifikace metody MeSH
- lidé MeSH
- molekulární patologie metody MeSH
- mutace genetika MeSH
- nádory endometria * diagnóza genetika klasifikace patologie MeSH
- vysoce účinné nukleotidové sekvenování * klasifikace metody MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- klinická studie MeSH
- práce podpořená grantem MeSH
Neurotropic pathogens, notably, herpesviruses, have been associated with significant neuropsychiatric effects. As a group, these pathogens can exploit molecular mimicry mechanisms to manipulate the host central nervous system to their advantage. Here, we present a systematic computational approach that may ultimately be used to unravel protein-protein interactions and molecular mimicry processes that have not yet been solved experimentally. Toward this end, we validate this approach by replicating a set of pre-existing experimental findings that document the structural and functional similarities shared by the human cytomegalovirus-encoded UL144 glycoprotein and human tumor necrosis factor receptor superfamily member 14 (TNFRSF14). We began with a thorough exploration of the Homo sapiens protein database using the Basic Local Alignment Search Tool (BLASTx) to identify proteins sharing sequence homology with UL144. Subsequently, we used AlphaFold2 to predict the independent three-dimensional structures of UL144 and TNFRSF14. This was followed by a comprehensive structural comparison facilitated by Distance-Matrix Alignment and Foldseek. Finally, we used AlphaFold-multimer and PPIscreenML to elucidate potential protein complexes and confirm the predicted binding activities of both UL144 and TNFRSF14. We then used our in silico approach to replicate the experimental finding that revealed TNFRSF14 binding to both B- and T-lymphocyte attenuator (BTLA) and glycoprotein domain and UL144 binding to BTLA alone. This computational framework offers promise in identifying structural similarities and interactions between pathogen-encoded proteins and their host counterparts. This information will provide valuable insights into the cognitive mechanisms underlying the neuropsychiatric effects of viral infections.
BACKGROUND: The mammalian Natural Killer Complex (NKC) harbors genes and gene families encoding a variety of C-type lectin-like proteins expressed on various immune cells. The NKC is a complex genomic region well-characterized in mice, humans and domestic animals. The major limitations of automatic annotation of the NKC in non-model animals include short-read based sequencing, methods of assembling highly homologous and repetitive sequences, orthologues missing from reference databases and weak expression. In this situation, manual annotations of complex genomic regions are necessary. METHODS: This study presents a manual annotation of the genomic structure of the NKC region in a high-quality reference genome of the domestic cat and compares it with other felid species and with representatives of other carnivore families. Reference genomes of Carnivora, irrespective of sequencing and assembly methods, were screened by BLAST to retrieve information on their killer cell lectin-like receptor (KLR) gene content. Phylogenetic analysis of in silico translated proteins of expanded subfamilies was carried out. RESULTS: The overall genomic structure of the NKC in Carnivora is rather conservative in terms of its C-type lectin receptor gene content. A novel KLRH-like gene subfamily (KLRL) was identified in all Carnivora and a novel KLRJ-like gene was annotated in the Mustelidae. In all six families studied, one subfamily (KLRC) expanded and experienced pseudogenization. The KLRH gene subfamily expanded in all carnivore families except the Canidae. The KLRL gene subfamily expanded in carnivore families except the Felidae and Canidae, and in the Canidae it eroded to fragments. CONCLUSIONS: Knowledge of the genomic structure and gene content of the NKC region is a prerequisite for accurate annotations of newly sequenced genomes, especially of endangered wildlife species. Identification of expressed genes, pseudogenes and gene fragments in the context of expanded gene families would allow the assessment of functionally important variability in particular species.
- MeSH
- anotace sekvence MeSH
- buňky NK * imunologie metabolismus MeSH
- Carnivora * genetika MeSH
- fylogeneze * MeSH
- genom MeSH
- genomika * metody MeSH
- kočky genetika MeSH
- lektiny typu C genetika MeSH
- zvířata MeSH
- Check Tag
- kočky genetika MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics have generated genetic variants at an unprecedented scale. However, efficient tools and resources are needed to link disparate data types-to 'map' variants onto protein structures, to better understand how the variation causes disease, and thereby design therapeutics. Here we present the Genomics 2 Proteins portal ( https://g2p.broadinstitute.org/ ): a human proteome-wide resource that maps 20,076,998 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the Genomics 2 Proteins portal allows users to interactively upload protein residue-wise annotations (for example, variants and scores) as well as the protein structure beyond databases to establish the connection between genomics to proteins. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotypes.
The insulin-linked polymorphic region is a variable number of tandem repeats region of DNA in the promoter of the insulin gene that regulates transcription of insulin. This region is known to form the alternative DNA structures, i-motifs and G-quadruplexes. Individuals have different sequence variants of tandem repeats and although previous work investigated the effects of some variants on G-quadruplex formation, there is not a clear picture of the relationship between the sequence diversity, the DNA structures formed, and the functional effects on insulin gene expression. Here we show that different sequence variants of the insulin linked polymorphic region form different DNA structures in vitro. Additionally, reporter genes in cellulo indicate that insulin expression may change depending on which DNA structures form. We report the crystal structure and dynamics of an intramolecular i-motif, which reveal sequences within the loop regions forming additional stabilising interactions that are critical to formation of stable i-motif structures. The outcomes of this work reveal the detail in formation of stable i-motif DNA structures, with potential for rational based drug design for compounds to target i-motif DNA.
- MeSH
- DNA * chemie genetika MeSH
- G-kvadruplexy * MeSH
- inzulin * chemie genetika MeSH
- konformace nukleové kyseliny MeSH
- krystalografie rentgenová MeSH
- lidé MeSH
- molekulární modely MeSH
- nukleotidové motivy MeSH
- polymorfismus genetický MeSH
- promotorové oblasti (genetika) * MeSH
- reportérové geny MeSH
- sekvence nukleotidů MeSH
- tandemové repetitivní sekvence genetika MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Background: Prolonged Grief Disorder (PGD) has recently been included in both the ICD-11 and DSM-5-TR diagnostic manuals. Studying its prevalence and correlates across cultures is vital for more effective identification, treatment, and prevention.Objective: This study aimed to examine prevalence rates of ICD-11-based PGD, in a representative Slovakian sample in response to deaths of loved ones occurring during the previous year. Further aims were to examine the factor structure of PGD symptoms and correlates of summed PGD item scores and PGD 'caseness'.Method: Self-reported data on PGD, depression, anxiety, alcohol use, and descriptive characteristics were gathered from a representative sample of the Slovak population (N = 319).Results: Data were gathered from N = 1853 people; 319 participants (17.2%) reported a loss in the past year. The prevalence of probable PGD among these bereaved participants was 1.99% for recent losses (<6 months, n = 151) and 7.75% for more distant losses (6-12 months, n = 130). The most frequently endorsed symptoms included longing/yearning for the deceased, sadness, denial/unrealness, and difficulty accepting the death. PGD symptoms had a unitary factor structure which was consistent for subsamples bereaved 1-5 and 6-12 months. The severity of PGD varied with kinship. Depression and anxiety, but not alcohol misuse, were associated with PGD severity and PGD caseness.Conclusions: These findings underscore that a significant group of people develop PGD between 6-12 months following a loss. This emphasises the need for targeted psychological interventions.
- MeSH
- deprese epidemiologie psychologie MeSH
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mezinárodní klasifikace nemocí MeSH
- prevalence MeSH
- úzkost epidemiologie psychologie MeSH
- zármutek * MeSH
- ztráta blízké osoby * MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Slovenská republika MeSH
