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1.
Nature ; 614(7947): 275-280, 2023 02.
Article in English | MEDLINE | ID: mdl-36473497

ABSTRACT

Oxygen-containing functional groups are nearly ubiquitous in complex small molecules. The installation of multiple C-O bonds by the concurrent oxygenation of contiguous C-H bonds in a selective fashion would be highly desirable but has largely been the purview of biosynthesis. Multiple, concurrent C-H bond oxygenation reactions by synthetic means presents a challenge1-6, particularly because of the risk of overoxidation. Here we report the selective oxygenation of two or three contiguous C-H bonds by dehydrogenation and oxygenation, enabling the conversion of simple alkylarenes or trifluoroacetamides to their corresponding di- or triacetoxylates. The method achieves such transformations by the repeated operation of a potent oxidative catalyst, but under conditions that are sufficiently selective to avoid destructive overoxidation. These reactions are achieved using electrophotocatalysis7, a process that harnesses the energy of both light and electricity to promote chemical reactions. Notably, the judicious choice of acid allows for the selective synthesis of either di- or trioxygenated products.

2.
Brief Bioinform ; 25(4)2024 May 23.
Article in English | MEDLINE | ID: mdl-38797969

ABSTRACT

In recent decades, antibodies have emerged as indispensable therapeutics for combating diseases, particularly viral infections. However, their development has been hindered by limited structural information and labor-intensive engineering processes. Fortunately, significant advancements in deep learning methods have facilitated the precise prediction of protein structure and function by leveraging co-evolution information from homologous proteins. Despite these advances, predicting the conformation of antibodies remains challenging due to their unique evolution and the high flexibility of their antigen-binding regions. Here, to address this challenge, we present the Bio-inspired Antibody Language Model (BALM). This model is trained on a vast dataset comprising 336 million 40% nonredundant unlabeled antibody sequences, capturing both unique and conserved properties specific to antibodies. Notably, BALM showcases exceptional performance across four antigen-binding prediction tasks. Moreover, we introduce BALMFold, an end-to-end method derived from BALM, capable of swiftly predicting full atomic antibody structures from individual sequences. Remarkably, BALMFold outperforms those well-established methods like AlphaFold2, IgFold, ESMFold and OmegaFold in the antibody benchmark, demonstrating significant potential to advance innovative engineering and streamline therapeutic antibody development by reducing the need for unnecessary trials. The BALMFold structure prediction server is freely available at https://beamlab-sh.com/models/BALMFold.


Subject(s)
Antibodies , Antibodies/chemistry , Antibodies/immunology , Computational Biology/methods , Protein Conformation , Humans , Models, Molecular , Deep Learning
3.
PLoS Biol ; 21(8): e3002227, 2023 08.
Article in English | MEDLINE | ID: mdl-37531320

ABSTRACT

Phosphoinositide-dependent kinase-1 (PDK1) is a master kinase of the protein A, G, and C (AGC) family kinases that play important roles in regulating cancer cell proliferation, survival, and metabolism. Besides phosphorylating/activating AKT at the cell membrane in a PI3K-dependent manner, PDK1 also exhibits constitutive activity on many other AGC kinases for tumor-promoting activity. In the latter case, PDK1 protein levels dominate its activity. We previously reported that MAPK4, an atypical MAPK, can PI3K-independently promote AKT activation and tumor growth. Here, using triple-negative breast cancer (TNBC) cell models, we demonstrate that MAPK4 can also enhance PDK1 protein synthesis, thus phosphorylate/activate PDK1 substrates beyond AKT. This new MAPK4-PDK1 axis alone lacks vigorous tumor-promoting activity but cooperates with our previously reported MAPK4-AKT axis to promote tumor growth. Besides enhancing resistance to PI3K blockade, MAPK4 also promotes cancer cell resistance to the more stringent PI3K and PDK1 co-blockade, a recently proposed therapeutic strategy. Currently, there is no MAPK4 inhibitor to treat MAPK4-high cancers. Based on the concerted action of MAPK4-AKT and MAPK4-PDK1 axis in promoting cancer, we predict and confirm that co-targeting AKT and PDK1 effectively represses MAPK4-induced cancer cell growth, suggesting a potential therapeutic strategy to treat MAPK4-high cancers.


Subject(s)
3-Phosphoinositide-Dependent Protein Kinases , Mitogen-Activated Protein Kinases , Neoplasms , Proto-Oncogene Proteins c-akt , Humans , 3-Phosphoinositide-Dependent Protein Kinases/metabolism , Mitogen-Activated Protein Kinases/metabolism , Neoplasms/drug therapy , Phosphatidylinositol 3-Kinases/metabolism , Proto-Oncogene Proteins c-akt/metabolism , Signal Transduction
4.
Proc Natl Acad Sci U S A ; 120(9): e2217256120, 2023 Feb 28.
Article in English | MEDLINE | ID: mdl-36802424

ABSTRACT

Crystallographic control of crystals as catalysts with precise geometrical and chemical features is significantly important to develop sustainable chemistry, yet highly challenging. Encouraged by first principles calculations, precise structure control of ionic crystals could be realized by introducing an interfacial electrostatic field. Herein, we report an efficient in situ dipole-sourced electrostatic field modulation strategy using polarized ferroelectret, for crystal facet engineering toward challenging catalysis reactions, which avoids undesired faradic reactions or insufficient field strength by conventional external electric field. Resultantly, a distinct structure evolution from tetrahedron to polyhedron with different dominated facets of Ag3PO4 model catalyst was obtained by tuning the polarization level, and similar oriented growth was also realized by ZnO system. Theoretical calculations and simulation reveal that the generated electrostatic field can effectively guide the migration and anchoring of Ag+ precursors and free Ag3PO4 nuclei, achieving oriented crystal growth by thermodynamic and kinetic balance. The faceted Ag3PO4 catalyst exhibits high performance in photocatalytic water oxidation and nitrogen fixation for valuable chemicals production, validating the effectiveness and potential of this crystal regulation strategy. Such an electrically tunable growth concept by electrostatic field provides new synthetic insights and great opportunity to effectively tailor the crystal structures for facet-dependent catalysis.

5.
Proc Natl Acad Sci U S A ; 120(20): e2218229120, 2023 05 16.
Article in English | MEDLINE | ID: mdl-37155905

ABSTRACT

Castration-resistant prostate cancer (CRPC) poses a major clinical challenge with the androgen receptor (AR) remaining to be a critical oncogenic player. Several lines of evidence indicate that AR induces a distinct transcriptional program after androgen deprivation in CRPCs. However, the mechanism triggering AR binding to a distinct set of genomic loci in CRPC and how it promotes CRPC development remain unclear. We demonstrate here that atypical ubiquitination of AR mediated by an E3 ubiquitin ligase TRAF4 plays an important role in this process. TRAF4 is highly expressed in CRPCs and promotes CRPC development. It mediates K27-linked ubiquitination at the C-terminal tail of AR and increases its association with the pioneer factor FOXA1. Consequently, AR binds to a distinct set of genomic loci enriched with FOXA1- and HOXB13-binding motifs to drive different transcriptional programs including an olfactory transduction pathway. Through the surprising upregulation of olfactory receptor gene transcription, TRAF4 increases intracellular cAMP levels and boosts E2F transcription factor activity to promote cell proliferation under androgen deprivation conditions. Altogether, these findings reveal a posttranslational mechanism driving AR-regulated transcriptional reprogramming to provide survival advantages for prostate cancer cells under castration conditions.


Subject(s)
Prostatic Neoplasms, Castration-Resistant , Receptors, Androgen , Male , Humans , Receptors, Androgen/genetics , Receptors, Androgen/metabolism , Prostatic Neoplasms, Castration-Resistant/genetics , Prostatic Neoplasms, Castration-Resistant/metabolism , Androgens , Androgen Antagonists , TNF Receptor-Associated Factor 4/metabolism , Cell Line, Tumor , Ubiquitination , Gene Expression Regulation, Neoplastic
6.
Proc Natl Acad Sci U S A ; 119(43): e2205350119, 2022 10 25.
Article in English | MEDLINE | ID: mdl-36251994

ABSTRACT

Androgen receptor (AR) signaling is crucial for driving prostate cancer (PCa), the most diagnosed and the second leading cause of death in male patients with cancer in the United States. Androgen deprivation therapy is initially effective in most instances of AR-positive advanced or metastatic PCa. However, patients inevitably develop lethal castration-resistant PCa (CRPC), which is also resistant to the next-generation AR signaling inhibitors. Most CRPCs maintain AR expression, and blocking AR signaling remains a main therapeutic approach. GATA2 is a pioneer transcription factor emerging as a key therapeutic target for PCa because it promotes AR expression and activation. While directly inhibiting GATA2 transcriptional activity remains challenging, enhancing GATA2 degradation is a plausible therapeutic strategy. How GATA2 protein stability is regulated in PCa remains unknown. Here, we show that constitutive photomorphogenesis protein 1 (COP1), an E3 ubiquitin ligase, drives GATA2 ubiquitination at K419/K424 for degradation. GATA2 lacks a conserved [D/E](x)xxVP[D/E] degron but uses alternate BR1/BR2 motifs to bind COP1. By promoting GATA2 degradation, COP1 inhibits AR expression and activation and represses PCa cell and xenograft growth and castration resistance. Accordingly, GATA2 overexpression or COP1 mutations that disrupt COP1-GATA2 binding block COP1 tumor-suppressing activities. We conclude that GATA2 is a major COP1 substrate in PCa and that COP1 promotion of GATA2 degradation is a direct mechanism for regulating AR expression and activation, PCa growth, and castration resistance.


Subject(s)
GATA2 Transcription Factor , Prostatic Neoplasms, Castration-Resistant , Prostatic Neoplasms , Ubiquitin-Protein Ligases , Humans , Male , Androgen Antagonists/therapeutic use , Androgens , Cell Line, Tumor , GATA2 Transcription Factor/genetics , GATA2 Transcription Factor/metabolism , Gene Expression Regulation, Neoplastic , Prostatic Neoplasms/genetics , Prostatic Neoplasms/metabolism , Prostatic Neoplasms, Castration-Resistant/drug therapy , Prostatic Neoplasms, Castration-Resistant/genetics , Prostatic Neoplasms, Castration-Resistant/pathology , Receptors, Androgen/genetics , Receptors, Androgen/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism
7.
Hum Genet ; 143(3): 385-399, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38502355

ABSTRACT

A certain proportion of genes are regulated by multiple, distinct promoters, revealing a dynamic landscape of the cancer transcriptome. However, the contribution of alternative promoters (APs) in breast cancer (BRCA) remains largely unexplored. Here, we identified 3654 genes with multiple promoters in BRCA patients, and 53 of them could generate distinct AP transcripts that are dysregulated and prognosis-related in BRCA, namely prognosis-related dysregulated AP (prdeAP) transcripts. Interestingly, when we searched for the genomic signatures of these prdeAP genes, we found that the promoter regions of 92% of the prdeAP genes were enriched with abundant DNA methylation signals. Through further bioinformatic analysis and experimental validation, we showed that AP selections of TANK, UNKL, CCL28, and MAP1LC3A were regulated by DNA methylation upon their corresponding promoter regions. Functionally, by overexpressing AP variants of TANK, we found that TANK|55731 could dramatically suppress MDA-MB-231 cell proliferation and migration. Meanwhile, pan-cancer survival analyses suggested that AP variants of TANK provided more accurate prognostic predictive ability than TANK gene in a variety of tumor types, including BRCA. Together, by uncovering the DNA methylation-regulated AP transcripts with tumor prognostic features, our work revealed a novel layer of regulators in BRCA progression and provided potential targets that served as effective biomarkers for anti-BRCA treatment.


Subject(s)
Breast Neoplasms , DNA Methylation , Gene Expression Regulation, Neoplastic , Promoter Regions, Genetic , Humans , Breast Neoplasms/genetics , Breast Neoplasms/pathology , Female , Prognosis , Genome-Wide Association Study , Cell Line, Tumor , Cell Proliferation/genetics , Transcriptome
8.
Biochem Biophys Res Commun ; 710: 149883, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38588611

ABSTRACT

Congenital heart diseases are the most common birth defects around the world. Emerging evidence suggests that mitochondrial homeostasis is required for normal heart development. In mitochondria, a series of molecular chaperones including heat shock protein 60 (HSP60) are engaged in assisting the import and folding of mitochondrial proteins. However, it remains largely obscure whether and how these mitochondrial chaperones regulate cardiac development. Here, we generated a cardiac-specific Hspd1 deletion mouse model by αMHC-Cre and investigated the role of HSP60 in cardiac development. We observed that deletion of HSP60 in embryonic cardiomyocytes resulted in abnormal heart development and embryonic lethality, characterized by reduced cardiac cell proliferation and thinner ventricular walls, highlighting an essential role of cardiac HSP60 in embryonic heart development and survival. Our results also demonstrated that HSP60 deficiency caused significant downregulation of mitochondrial ETC subunits and induced mitochondrial stress. Analysis of gene expression revealed that P21 that negatively regulates cell proliferation is significantly upregulated in HSP60 knockout hearts. Moreover, HSP60 deficiency induced activation of eIF2α-ATF4 pathway, further indicating the underlying mitochondrial stress in cardiomyocytes after HSP60 deletion. Taken together, our study demonstrated that regular function of mitochondrial chaperones is pivotal for maintaining normal mitochondrial homeostasis and embryonic heart development.


Subject(s)
Chaperonin 60 , Heart Defects, Congenital , Animals , Mice , Chaperonin 60/genetics , Chaperonin 60/metabolism , Heart Defects, Congenital/metabolism , Mitochondria/metabolism , Mitochondrial Proteins/metabolism , Molecular Chaperones/genetics , Molecular Chaperones/metabolism , Myocytes, Cardiac/metabolism
9.
Small ; : e2310072, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38470190

ABSTRACT

Flexible wearable sensors recently have made significant progress in human motion detection and health monitoring. However, most sensors still face challenges in terms of single detection targets, single application environments, and non-recyclability. Lipoic acid (LA) shows a great application prospect in soft materials due to its unique properties. Herein, ionic conducting elastomers (ICEs) based on polymerizable deep eutectic solvents consisting of LA and choline chloride are prepared. In addition to the good mechanical strength, high transparency, ionic conductivity, and self-healing efficiency, the ICEs exhibit swelling-strengthening behavior and enhanced adhesion strength in underwater environments due to the moisture-induced association of poly(LA) hydrophobic chains, thus making it possible for underwater sensing applications, such as underwater communication. As a strain sensor, it exhibits highly sensitive strain response with repeatability and durability, enabling the monitoring of both large and fine human motions, including joint movements, facial expressions, and pulse waves. Furthermore, due to the enhancement of ion mobility at higher temperatures, it also possesses excellent temperature-sensing performance. Notably, the ICEs can be fully recycled and reused as a new strain/temperature sensor through heating. This study provides a novel strategy for enhancing the mechanical strength of poly(LA) and the fabrication of multifunctional sensors.

10.
New Phytol ; 241(5): 2158-2175, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38098211

ABSTRACT

Rice OsBBX17 encodes a B-box zinc finger transcription factor in which the N-terminal B-box structural domain interacts with OsMPK1. In addition, it directly binds to the G-box of OsHAK2 and OsHAK7 promoters and represses their transcription. Under saline-alkaline conditions, the expression of OsBBX17 was inhibited. Meanwhile, activation of the OsMPK1-mediated mitogen-activated protein kinase cascade pathway caused OsMPK1 to interact with OsBBX17 and phosphorylate OsBBX17 at the Thr-95 site. It reduced OsBBX17 DNA-binding activity and enhanced saline-alkaline tolerance by deregulating transcriptional repression of OsHAK2 and OsHAK7. Genetic assays showed that the osbbx17-KO had an excellent saline-alkaline tolerance, whereas the opposite was in OsBBX17-OE. In addition, overexpression of OsMPK1 significantly improved saline-alkaline tolerance, but knockout of OsMPK1 caused an increased sensitivity. Further overexpression of OsBBX17 in the osmpk1-KO caused extreme saline-alkaline sensitivity, even a quick death. OsBBX17 was validated in saline-alkaline tolerance from two independent aspects, transcriptional level and post-translational protein modification, unveiling a mechanistic framework by which OsMPK1-mediated phosphorylation of OsBBX17 regulates the transcription of OsHAK2 and OsHAK7 to enhance the Na+ /K+ homeostasis, which partially explains light on the molecular mechanisms of rice responds to saline-alkaline stress via B-box transcription factors for the genetic engineering of saline-alkaline tolerant crops.


Subject(s)
Oryza , Transcription Factors , Transcription Factors/genetics , Transcription Factors/metabolism , Oryza/metabolism , Phosphorylation , Salt Tolerance/genetics , MAP Kinase Signaling System , Plant Proteins/metabolism , Gene Expression Regulation, Plant
11.
Ann Neurol ; 93(5): 881-892, 2023 05.
Article in English | MEDLINE | ID: mdl-36627836

ABSTRACT

OBJECTIVE: The objective of this study was to use a novel combined pharmacoepidemiologic and amyotrophic lateral sclerosis (ALS) mouse model approach to identify potential motor neuron protective medications. METHODS: We constructed a large, population-based case-control study to investigate motor neuron disease (MND) among US Medicare beneficiaries aged 66 to 90 in 2009. We included 1,128 incident MND cases and 56,400 age, sex, race, and ethnicity matched controls. We calculated MND relative risk for >1,000 active ingredients represented in Part D (pharmacy) claims in 2006 to 2007 (>1 year before diagnosis/reference). We then applied a comprehensive screening approach to select medications for testing in SOD1G93A mice: sulfasalazine, telmisartan, and lovastatin. We treated mice with the human dose equivalent of the medication or vehicle via subcutaneous osmotic pump before onset of weakness. We then assessed weight, gait, and survival. In additional mice, we conducted histological studies. RESULTS: We observed previously established medical associations for MND and an inverse dose-response association between lovastatin and MND, with 28% reduced risk at 40 mg/day. In SOD1G93A mouse studies, sulfasalazine and telmisartan conferred no benefit, whereas lovastatin treatment delayed onset and prolonged survival. Lovastatin treated mice also had less microgliosis, misfolded SOD1, and spinal motor neuron loss in the ventral horn. INTERPRETATION: Lovastatin reduced the risk of ALS in humans, which was confirmed in an ALS mouse model by delayed symptom onset, prolonged survival, and preservation of motor neurons. Although further studies to understand the mechanism are required, lovastatin may represent a potential neuroprotective therapy for patients with ALS. These data demonstrate the utility of a combined pharmacoepidemiologic and mouse model approach. ANN NEUROL 2023;93:881-892.


Subject(s)
Amyotrophic Lateral Sclerosis , Motor Neuron Disease , Aged , United States , Humans , Mice , Animals , Amyotrophic Lateral Sclerosis/drug therapy , Amyotrophic Lateral Sclerosis/genetics , Amyotrophic Lateral Sclerosis/pathology , Superoxide Dismutase-1 , Sulfasalazine/therapeutic use , Case-Control Studies , Telmisartan/therapeutic use , Spinal Cord/pathology , Mice, Transgenic , Superoxide Dismutase/therapeutic use , Medicare , Disease Models, Animal
12.
Chemistry ; : e202401812, 2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38887976

ABSTRACT

Diketopyrrolopyrrole (DPP)-based polymer semiconductors have drawn great attention in the field of organic electronics due to the planar structure, decent solubilizing capability, and high crystallinity. However, the electron-deficient capacity of DPP derivatives are not strong enough, leading to relatively high-lying lowest unoccupied molecular orbital (LUMO) energy levels of the corresponding polymers. As a result, n-type and ambipolar DPP-based polymers are rare and their electron mobilities also lag far behind the p-type counterparts, which limits the development of important p-n-junction-based electronic devices. Therefore, new design strategies have been proposed recent years to develop n-type/ambipolar DPP-based polymers with improved performances. In this view, these molecular design strategies are summarized, including copolymerization of DPP with different acceptors and weak donors, DPP flanked aromatic ring modification, DPP-core ring expansion and DPP dimerization. The relationship between the chemical structures and organic thin-film transistor performances is intensively discussed. Finally, a perspective on future trends in the molecular design of DPP-based n-type/ambipolar polymers is also proposed.

13.
Chemistry ; 30(10): e202302959, 2024 Feb 16.
Article in English | MEDLINE | ID: mdl-38012090

ABSTRACT

A two-enzyme cascade system containing ω-transaminase (ω-TA) and L-threonine aldolase (L-ThA) was reported for the synthesis of 3-Phenylserine starting from benzylamine, and PLP was utilized as the only cofactor in these both two enzymes reaction system. Based on the transamination results, benzylamine was optimized as an advantageous amino donor as confirmed by MD simulation results. This cascade reaction system could not only facilitate the in situ removal of the co-product benzaldehyde, enhancing the economic viability of the reaction, but also establish a novel pathway for synthesizing high-value phenyl-serine derivatives. In our study, nearly 95 % of benzylamine was converted, yielding over 54 % of 3-Phenylserine under the optimized conditions cascade reaction.


Subject(s)
Glycine Hydroxymethyltransferase , Serine , Serine/analogs & derivatives , Serine/metabolism , Glycine Hydroxymethyltransferase/metabolism , Benzylamines , Pyridoxal Phosphate
14.
Hum Genomics ; 17(1): 76, 2023 08 17.
Article in English | MEDLINE | ID: mdl-37587523

ABSTRACT

BACKGROUND: As one of the most common intestinal inflammatory diseases, celiac disease (CD) is typically characterized by an autoimmune disorder resulting from ingesting gluten proteins. Although the incidence and prevalence of CD have increased over time, the diagnostic methods and treatment options are still limited. Therefore, it is urgent to investigate the potential biomarkers and targeted drugs for CD. METHODS: Gene expression data was downloaded from GEO datasets. Differential gene expression analysis was performed to identify the dysregulated immune-related genes. Multiple machine algorithms, including randomForest, SVM-RFE, and LASSO, were used to select the hub immune-related genes (HIGs). The immune-related genes score (IG score) and artificial neural network (ANN) were constructed based on HIGs. Potential drugs targeting HIGs were identified by using the Enrichr platform and molecular docking method. RESULTS: We identified the dysregulated immune-related genes at a genome-wide level and demonstrated their roles in CD-related immune pathways. The hub genes (MR1, CCL25, and TNFSF13B) were further screened by integrating several machine algorithms. Meanwhile, the CD patients were divided into distinct subtypes with either high- or low-immunoactivity using single-sample gene set enrichment analysis (ssGSEA) and consensus clustering. By constructing IG score based on HIGs, we found that patients with high IG score were mainly attributed to high-immunoactivity subgroups, which suggested a strong link between HIGs and immunoactivity of CD patients. In addition, the novel constructed ANN model showed the sound diagnostic ability of HIGs. Mechanistically, we validated that the HIGs play pivotal roles in regulating CD's immune and inflammatory state. Through targeting the HIGs, we also found potential drugs for anti-CD treatment by using the Enrichr platform and molecular docking method. CONCLUSIONS: This study unveils the HIGs and elucidates the networks regulated by these genes in the context of CD. It underscores the pivotal significance of HIGs in accurately predicting the presence or absence of CD in patients. Consequently, this research offers promising prospects for the development of diagnostic biomarkers and therapeutic targets for CD.


Subject(s)
Celiac Disease , Humans , Celiac Disease/genetics , Molecular Docking Simulation , Neural Networks, Computer , Algorithms , Biomarkers
15.
Theor Appl Genet ; 137(5): 113, 2024 Apr 28.
Article in English | MEDLINE | ID: mdl-38678511

ABSTRACT

KEY MESSAGE: The rust resistance genes Lr53 and Yr35 were introgressed into bread wheat from Aegilops longissima or Aegilops sharonensis or their S-genome containing species and mapped to the telomeric region of chromosome arm 6BS. Wheat leaf and stripe rusts are damaging fungal diseases of wheat worldwide. Breeding for resistance is a sustainable approach to control these two foliar diseases. In this study, we used SNP analysis, sequence comparisons, and cytogenetic assays to determine that the chromosomal segment carrying Lr53 and Yr35 was originated from Ae.longissima or Ae. sharonensis or their derived species. In seedling tests, Lr53 conferred strong resistance against all five Chinese Pt races tested, and Yr35 showed effectiveness against Pst race CYR34 but susceptibility to race CYR32. Using a large population (3892 recombinant gametes) derived from plants homozygous for the ph1b mutation obtained from the cross 98M71 × CSph1b, both Lr53 and Yr35 were successfully mapped to a 6.03-Mb telomeric region of chromosome arm 6BS in the Chinese Spring reference genome v1.1. Co-segregation between Lr53 and Yr35 was observed within this large mapping population. Within the candidate region, several nucleotide-binding leucine-rich repeat genes and protein kinases were identified as candidate genes. Marker pku6B3127 was completely linked to both genes and accurately predicted the absence or presence of alien segment harboring Lr53 and Yr35 in 87 tetraploid and 149 hexaploid wheat genotypes tested. We developed a line with a smaller alien segment (< 6.03 Mb) to reduce any potential linkage drag and demonstrated that it conferred resistance levels similar to those of the original donor parent 98M71. The newly developed introgression line and closely linked PCR markers will accelerate the deployment of Lr53 and Yr35 in wheat breeding programs.


Subject(s)
Aegilops , Chromosome Mapping , Disease Resistance , Genes, Plant , Puccinia , Aegilops/genetics , Aegilops/microbiology , Chromosomes, Plant/genetics , Disease Resistance/genetics , Genetic Introgression , Genetic Linkage , Genetic Markers , Plant Breeding , Plant Diseases/genetics , Plant Diseases/microbiology , Polymorphism, Single Nucleotide , Puccinia/physiology , Triticum/genetics , Triticum/microbiology
16.
Analyst ; 149(8): 2236-2243, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38414418

ABSTRACT

Cadmium poisoning is a chronic accumulation process, and long-term drinking of even low cadmium content water will cause kidney damage, so an ultra-low detection limit is particularly important. However, at the present stage, the traditional detection method cannot reach a sufficiently low detection limit, the response time is too long, and the cost of detection is very high, so that real-time measurement cannot be realized. Therefore, the traditional cadmium ion detection method has a slow response and an insufficient detection limit. This paper presents a fiber optic cadmium ion sensor functionalized based on an Fe3O4@SiO2@CS magnetic ion imprinting polymer (M-IIP). The sensor is based on the coupling characteristics of the optical microfiber coupler (OMC) cone region to achieve a highly sensitive response to the change in the cadmium ion concentration. M-IIP materials were prepared by surface imprinting polymerization to achieve low cross-sensitivity and thus improve the detection limit of the sensor. The results show that the developed fiber sensor has high specificity and a rapid response to cadmium ions. The experimental limit of detection (LOD) reached 0.051 nM within 0-1 µM with a response time of less than 50 s. Moreover, the proposed fiber cadmium ion sensor exhibits excellent performance in terms of sensitivity, stability, repeatability and biocompatibility.

17.
J Chem Inf Model ; 64(3): 575-583, 2024 Feb 12.
Article in English | MEDLINE | ID: mdl-38265916

ABSTRACT

Discovery of small-molecule antibiotics with novel chemotypes serves as one of the essential strategies to address antibiotic resistance. Although a considerable number of computational tools committed to molecular design have been reported, there is a deficit in holistic and efficient tools specifically developed for small-molecule antibiotic discovery. To address this issue, we report AutoMolDesigner, a computational modeling software dedicated to small-molecule antibiotic design. It is a generalized framework comprising two functional modules, i.e., generative-deep-learning-enabled molecular generation and automated machine-learning-based antibacterial activity/property prediction, wherein individually trained models and curated datasets are out-of-the-box for whole-cell-based antibiotic screening and design. It is open-source, thus allowing for the incorporation of new features for flexible use. Unlike most software programs based on Linux and command lines, this application equipped with a Qt-based graphical user interface can be run on personal computers with multiple operating systems, making it much easier to use for experimental scientists. The software and related materials are freely available at GitHub (https://github.com/taoshen99/AutoMolDesigner) and Zenodo (https://zenodo.org/record/10097899).


Subject(s)
Artificial Intelligence , Software , Computer Simulation
18.
BMC Endocr Disord ; 24(1): 98, 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38926806

ABSTRACT

BACKGROUND: Advanced maternal age may affect the intrauterine environment and increase the risk of neurodevelopmental disorders in offspring. Thyroid hormones are critical for fetal neurological development but whether maternal age influences fetal thyroid hormone levels in euthyroid mothers is unknown. OBJECTIVE: This study evaluated the association between cord blood thyroid hormones and maternal age, fetal sex, maternal thyroid function, and other perinatal factors. METHODS: The study population consisted of 203 healthy women with term singleton pregnancies who underwent elective cesarean section. Maternal levels of free T3 (fT3), free T4 (fT4) and TSH before delivery, and cord levels of fT3, fT4 and TSH were measured. Spearman's correlation coefficient and multiple linear regression analyses were performed to determine the correlation between cord thyroid hormone parameters and maternal characteristics. RESULTS: There were no significant differences in maternal serum or cord blood thyroid hormone levels between male and female births. In multivariate linear regression analysis, maternal age and maternal TSH values were negatively associated with the cord blood levels of fT3 in all births, after adjusting for confounding factors. Maternal age was more closely associated with the cord blood levels of fT3 in female than in male births. CONCLUSION: The inverse association between maternal age and cord blood levels of fT3 in euthyroid pregnant women suggested an impact of maternal aging on offspring thyroid function.


Subject(s)
Fetal Blood , Maternal Age , Triiodothyronine , Humans , Female , Adult , Male , Pregnancy , Fetal Blood/chemistry , Fetal Blood/metabolism , Infant, Newborn , Triiodothyronine/blood , Sex Factors , Thyroid Function Tests , Thyrotropin/blood
19.
Bioorg Chem ; 144: 107092, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38271825

ABSTRACT

KRAS is the most frequently mutated oncogene and drives the development and progression of malignancies, most notably non-small cell lung cancer (NSCLS), pancreatic ductal adenocarcinoma (PDAC) and colorectal cancer (CRC). However, KRAS proteins have maintained the reputation of being "undruggable" due to the lack of suitable deep pockets on its surface. One major milestone for KRAS inhibition was the discovery of the covalent inhibitors bond to the allosteric switch-II pocket of the KRASG12C protein. To date, the FDA has approved two KRASG12C inhibitors, sotorasib and adagrasib, for the treatment of patients with KRASG12C-driven cancers. Researchers have paid close attention to the development of inhibitors for other KRAS mutations and upstream regulatory factors. The KRAS targeted drug discovery has entered a state of rapid development. This article has aimed to present the current state of the art of drug development in the KRAS field. We systematically summarize recent advances in the discovery and optimization processes of direct KRAS inhibitors (including KRASG12C, KRASG12D, KRASG12A and KRASG12R inhibitors), indirect KRAS inhibitors (SOS1 and SHP2 inhibitors), pan-KRAS inhibitors, as well as proteolysis-targetingchimeras degrades and molecular chaperone modulators from the perspective of medicinal chemistry. We also discuss the current challenges and opportunities of KRAS inhibition and hope to shed light on future KRAS drug discovery.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , Chemistry, Pharmaceutical , Proto-Oncogene Proteins p21(ras)/genetics , Drug Development , Mutation
20.
Graefes Arch Clin Exp Ophthalmol ; 262(1): 267-279, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37606824

ABSTRACT

BACKGROUND: To describe clinical features and intraoperative findings of the patients with exotropia who presented mild V-pattern or vertical deviation, and to investigate the surgical outcomes of anatomical relocation of inferiorly displaced lateral rectus (LR) muscle insertion. METHODS: Detailed ophthalmological evaluations were obtained in 42 consecutive patients, and the horizontal rectus muscle insertions were detected intraoperatively. The displaced insertion of LR muscle was corrected accompanied with classic recession-resection procedure. RESULTS: The inferiorly displaced LR muscle insertions were detected in 19 patients (Group A), while the remaining 23 patients (Group B) had normal insertions. The mean distance of displaced insertion from the normal position was 2.92 ± 1.05 mm (range: 1.0-4.0). Mild V-pattern was more common in Group A (78.9%, 15/19) than Group B (47.8%, 11/23), and the magnitude of V-pattern in Group A (6.16 ± 3.91 PD) was also greater than Group B (3.43 ± 3.92 PD). The fundus extorsions of the affected eyes (9.68 ± 4.77 °) were greater than the contralateral eyes (5.91 ± 5.82 °) in Group A. At the 2 months follow-up, mild V-pattern and mild vertical deviation were corrected by upward transposition. The significant correlations were identified between the pre-operative misalignments and the amounts of misalignments correction. CONCLUSIONS: Nearly half of the cases with mild V-pattern or vertical deviation resulted from the inferiorly displaced LR muscle insertion, so the intraoperative exploration of the LR muscle insertion is strongly suggested. Upward transposition may effectively correct both the mild V-pattern and vertical deviation.


Subject(s)
Exotropia , Humans , Exotropia/diagnosis , Exotropia/surgery , Ophthalmologic Surgical Procedures/methods , Retrospective Studies , Oculomotor Muscles/surgery , Fundus Oculi , Treatment Outcome , Vision, Binocular/physiology
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