Relevant Sites Research Articles

Abstract 7073: Integrating fragment-based crystallographic screening with dTAG-PROTAC degradation and genetic rescue to explore the function of eIF4E

Abstract The translation initiation factor eIF4E is a rate-limiting factor for protein synthesis that binds the mRNA m7G-cap to initiate the recruitment and binding of eIF4F components such as eIF4G. Targeting eIF4E has long been considered a promising anticancer strategy but it has remained undruggable using conventional screening approaches. Fragment-based crystallographic screening is a powerful technique for probing the surface of proteins to identify potentially druggable binding sites. Here, we describe fragment-based screening using a combination of Xray crystallography and NMR to identify low affinity fragment hits binding to the mRNA cap-binding site or at an additional site of unknown functional relevance (site 2). Subsequent rounds of iterative structure-based design yielded a lead molecule, with 100nM binding potency for site 2, that could disrupt the eIF4E:eIF4G interaction and inhibit cap-dependent translation in cell lysates. To explore the functional relevance of site 2 we established a cell model expressing an eIF4E-FKBP12F36V fusion protein that was sensitive to degradation following treatment with the heterobifunctional dTAGV-1 molecule. Degradation of eIF4E resulted in inhibition of cell growth and reduced expression of MCL1 protein, that were rescued by re-expression of a non-degradable wild-type eIF4E. A mutation reported to block canonical eIF4G binding (W73F) disrupted binding to eIF4G but to our surprise retained the ability to rescue the eIF4E degradation phenotype. Mutation of site 2 (L85R and L134R) also disrupted the eIF4E:eIF4G interaction. The L85R mutant remained able to partially rescue the cellular responses, in contrast to the L134R mutant that could not rescue eIF4E loss. The W73F/L85R double mutant resulted in a combinatorial loss of eIF4E function. Despite disrupting eIF4E function in lysates, there was a significant drop-off of compound activity in cells. However, treatment of the W73F mutant with compound recapitulated the combination of the W73F canonical eIF4G binding mutation with the L85R site 2 mutation. This approach demonstrates the power of coupling fragment screening with target-degradation and genetic rescue approaches to find and explore novel functional pockets. Our data suggest it may be necessary to disrupt the extended protein-protein interaction made by both the canonical and non-canonical regions of eIF4E to drive a strong functional effect in cells. However, the discovery of a lead compound, the associated structural understanding, and the knowledge that one site 2 mutation inactivates eIF4E provides hope that a significantly more potent small molecule inhibitor or degrader could drive a more profound cellular effect which may lead to improved cellular activity and a deeper understanding of eIF4E biology. Citation Format: Paul A. Clarke, Swee Y. Sharp, Marianna Martella, Christopher I. Milton, Charlotte East, Mladen Vinkovic, Nicola Wallis, George Ward, Caroline Richardson, Andrew Woodhead. Integrating fragment-based crystallographic screening with dTAG-PROTAC degradation and genetic rescue to explore the function of eIF4E [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7073.

Incidence of Nonkeratinocyte Skin Cancer After Breast Cancer Radiation Therapy

Previous studies have suggested that radiation therapy may contribute to an increased risk of subsequent nonkeratinocyte (ie, not squamous and basal cell) skin cancers. To test the hypothesis that radiation therapy for breast cancer increases the risk of subsequent nonkeratinocyte skin cancers, particularly when these cancers are localized to the skin of the breast or trunk. This population-based cohort study used longitudinal data from the Surveillance, Epidemiology, and End Results (SEER) Program for January 1, 2000, to December 31, 2019. The SEER database includes population-based cohort data from 17 registries. Patients with newly diagnosed breast cancer were identified and were evaluated for subsequent nonkeratinocyte skin cancer development. Data analysis was performed from January to August 2023. Radiation therapy, chemotherapy, or surgery for breast cancer. The primary outcomes were standardized incidence ratios (SIRs) for subsequent nonkeratinocyte skin cancer development from 2000 to 2019 based on treatment type (radiation therapy, chemotherapy, or surgery), skin cancer site on the body, and skin cancer subtype. Among the 875 880 patients with newly diagnosed breast cancer included in this study, 99.3% were women, 51.6% were aged older than 60 years, and 50.3% received radiation therapy. A total of 11.2% patients identified as Hispanic, 10.1% identified as non-Hispanic Black, and 69.5% identified as non-Hispanic White. From 2000 to 2019, there were 3839 patients with nonkeratinocyte skin cancer, including melanoma (3419 [89.1%]), Merkel cell carcinoma (121 [3.2%]), hemangiosarcoma (104 [2.7%]), and 32 other nonkeratinocyte skin cancers (195 [5.1%]), documented to occur after breast cancer treatment. The risk of nonkeratinocyte skin cancer diagnosis after breast cancer treatment with radiation was 57% higher (SIR, 1.57 [95% CI, 1.45-1.7]) than that of the general population when considering the most relevant site: the skin of the breast or trunk. When risk at this site was stratified by skin cancer subtype, the SIRs for melanoma and hemangiosarcoma were both statistically significant at 1.37 (95% CI, 1.25-1.49) and 27.11 (95% CI, 21.6-33.61), respectively. Receipt of radiation therapy was associated with a greater risk of nonkeratinocyte skin cancer compared with chemotherapy and surgical interventions. In this study of patients with breast cancer, an increased risk of melanoma and hemangiosarcoma after breast cancer treatment with radiation therapy was observed. Although occurrences of nonkeratinocyte skin cancers are rare, physicians should be aware of this elevated risk to help inform follow-up care.

Некоторые проблемы перевода политического анекдота (на материале немецкого языка)

The aim of the research is to identify potential problems in translating political German jokes into Russian. The research is based on jokes about the German Democratic Republic and the Federal Republic of Germany extracted from a printed collection and relevant German thematic Internet sites. The scientific novelty of the research lies in substantiating a comprehensive, interdisciplinary approach to the problems of translation (understanding) of a political joke, in which attention should be focused not only on interlingual, but also on intercultural differences between the two societies. The research conducted allows us to confirm that the structure of a (political) joke in German and Russian societies is similar. Translation problems usually arise due to insufficient linguistic competence, as well as to the lack of cultural background in conveying historical, political, cultural realia, which contain implicit cultural subcontext. To understand the latter, one should possess cultural knowledge close to that of a native speaker. So, to perceive a comic effect of a joke, a foreign recipient should first study culturally relevant information or it should be explained to them.

Synthesis of surgeon and rehabilitation therapist treatment methods of bicipital tenosynovitis in dogs allows development of an initial consensus therapeutic protocol.

To compare the therapeutic approach of surgical specialists, sports medicine and rehabilitation specialists, and veterinarians with rehabilitation certification when treating bicipital tendon disease or tenosynovitis in dogs and to combine this information with existing research to develop a treatment algorithm that provides a framework for treating bicipital tenosynovitis. 223 respondents to an internet survey of board-certified veterinary surgeons, board-certified sports medicine and rehabilitation therapists, and veterinarians with rehabilitation certification. The survey was promoted via multiple listservs, specialist college newsletters, and private relevant social media sites. Answers were compiled and submitted for statistical analysis. Compared to rehabilitation therapists (RTh), surgeons placed less value on the stabilizing function of the biceps tendon and its role in preventing other shoulder morbidities. Similarly, compared to RTh, surgeons were more inclined to select surgery as the primary therapeutic approach and attributed a less optimistic prognosis to conservative therapy outcomes. There were multiple differences between surgeons and RTh in executing a conservative therapy program, with RTh more likely to recommend therapeutic exercise, extracorporeal shockwave, regenerative medicine, therapeutic ultrasound, exercise restriction, photobiomodulation, and pulsed electromagnetic field therapy. RTh were less likely to prescribe NSAIDS or inject corticosteroids. Despite the above noted differences, there were also multiple areas of agreement. Consensus agreement, combined with existing research, was used to create a treatment algorithm suggesting how to best address multiple manifestations of bicipital tendinopathy. Such guidelines can be considered to direct therapeutic strategies for this common condition.

Content Validity-Based Evaluation Criteria System for Siting Wind-Solar Plants

The spatial assessment criteria system for hybridizing renewable energy sources, such as hybrid solar-wind farms, is critical in selecting ideal installation sites that maximize benefits, reduce costs, protect the environment, and serve the community. However, a systematic approach to designing indicator systems is rarely used in relevant site selection studies. Therefore, the current paper attempts to present an inclusive framework based on content validity to create an effective criteria system for siting wind-solar plants. To this end, the criteria considered in the related literature are captured, and the top 10 frequent indicators are identified. The Delphi technique is used to subject commonly used factors to expert judgments. Other factors are considered according to expert recommendations. In this context, the assessment tool was a combination of questionnaires and interviews with experts from scientific backgrounds that reflect the measurement target. The item-level content validity index (I-CVI) is applied along with the modified Kappa statistic (k*) to analyze expert ratings and suggestions. The results demonstrate the superiority of 9 and 4 commonly used factors and the suggested factors, respectively. The 13 criteria have achieved high agreement among experts at I-CVIs ≥ 0.78 and k*s > 0.76. The conclusion can be drawn that the modified Kappa statistic used in this analysis has a more significant effect on eliminating irrelevant factors. The current methodology and consequences might pave the way for making informed decisions to locate wind and solar farms.

Abstract A085: First-in-class humanized antibody targeting alternatively spliced tissue factor augments anti-metastatic efficacy of chemotherapy in a preclinical model of pancreatic ductal adenocarcinoma

Abstract Introduction. Alternatively spliced tissue factor (asTF) promotes progression of pancreatic ductal adenocarcinoma (PDAC) via activating b1-integrins on PDAC cell surfaces. hRabMab1, a humanized inhibitory anti-asTF antibody we recently developed, can suppress PDAC primary tumor growth as a single agent. Whether hRabMab1 has the potential to suppress metastases in PDAC is unknown. Aim. To test hRabMab1’s ability to suppress metastatic spread in combination with chemotherapy. Methods. asTF-proficient, KRAS G12V-mutant human PDAC cell line PaCa44 yields aggressive primary orthotopic tumors that spread spontaneously to the relevant anatomical sites, accompanied by severe leukocytosis. 5 × 105 PaCa44 cells were implanted into the pancreata of NOD-SCID mice (n=40). 10 days post-implantation, mice were randomized into 4 cohorts: vehicle; hRabMab1 administered IV at 18 mg/kg; gemcitabine/paclitaxel (gem/paclitaxel, 50 mg/kg/3 mg/kg); and hRabMab1+gem/paclitaxel. Results. Post-mortem analysis of tumor tissue and luciferase imaging of the abdominal cavity showed that gem/paclitaxel alone reduced primary tumor volume, but not metastatic spread; only the combination of hRabMab1 and gem/paclitaxel significantly reduced metastatic spread (p=0.0114 vs vehicle, 1-way ANOVA). RNAseq analysis of primary tumor tissue followed by gene set enrichment of differentially expressed genes showed that the addition of hRabMab1 to gem/paclitaxel downregulated tubulin binding and microtubule motor activity. Genes involved in extracellular matrix/collagen production and neovascularization were upregulated in response to gem/paclitaxel; addition of hRabMab1 to gem/paclitaxel tentatively reduced this compensatory effect. In the liver, hRabMab1 reduced liver metastasis as a single agent (p=0.031 vs vehicle) and in combination with gem/paclitaxel (p=0.0054 vs vehicle, 1-way ANOVA). In the surgical incision site, metastatic penetrance was as follows: vehicle, 100%; hRabMab1, 100%; gem/paclitaxel, 44% (4/9); hRabMab1+gem/paclitaxel, 0% (p=0.037715, gem/paclitaxel vs hRabMab1+gem/paclitaxel, Chi square test). Only the combination of hRabMab1 and gem/paclitaxel eliminated leukocytosis; levels of neutrophils, monocytes, eosinophils, and basophils were significantly lower in the hRabMab1+gem/paclitaxel cohort vs gem/paclitaxel cohort (p=0.035, p=0.051, p=0.032, and p=0.026, respectively). Leukocytes recruited from the circulation fuel tumor progression in PDAC. To address the potential significance of white blood cell (WBC) count normalization in our model, we performed correlation analysis between WBC counts and tumor volumes across all cohorts; there was a highly significant positive correlation between these two parameters (R=0.682, p=0.00002). Conclusions. This is the first study demonstrating that hRabMab1 can suppress metastasis in PDAC. hRabMab1’s ability to improve anti-metastatic efficacy of chemotherapy is potentially significant and warrants further investigation. Citation Format: Clayton S. Lewis, Charles Backman, Sabahat Ahsan, Ashley Cliff, Arthi Hariharan, Jen Jen Yeh, Davendra P. S. Sohal, Vladimir Y. Bogdanov. First-in-class humanized antibody targeting alternatively spliced tissue factor augments anti-metastatic efficacy of chemotherapy in a preclinical model of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A085.

Exploring the Complex Relationship Between Childhood Trauma and Self-Harm

ABSTRACT Previous research has linked self-harm to adverse childhood experiences (i.e. abuse and neglect). Despite the extensive literature on self-harm, it remains of high importance to examine psychological predictors of repetitive self-harming behaviors in those who report childhood trauma. This study explored the role of maladaptive emotion regulation strategies, dissociation proneness, and borderline personality (BP) features. An international sample with n = 374 participants (N = 287, 77%, reporting intentional use of self-harm), was recruited online via relevant mental health platforms and research sites. Within an anonymous survey, participants completed the Self-harm Inventory, Childhood Trauma Questionnaire, Dissociative Experience Scale, Cognitive Emotion Regulation Questionnaire, and Personality Assessment Inventory-Borderline Personality Features Scale. Structural equation modeling (SEM) was used to explore direct and indirect effects. Self-harm was positively correlated to severity of childhood trauma, maladaptive emotion regulation strategies, dissociation, and BP features. In the path-analytical model, independent indirect effects of childhood trauma severity via self-blame, catastrophizing, dissociation, as well as BP features on self-harm were found. Maladaptive emotion regulation, dissociation proneness, and BP features all seem to be important intermediary agents in the close association between childhood trauma and self-harm.

Characterization of multi-copy C3 genes and association analysis of C3.1 polymorphism with GCRV resistance traits in Ctenopharyngodon idella

Molecular-assisted breeding plays an essential role in the selection of high disease -resistant fish in grass carp (Ctenopharyngodon idella) aquaculture. Complement 3 (C3) is a central molecule in the complement cascade and plays a polyfunctional role in immune defense, complement activation, and the inflammatory response. In this study, 9 copies of the C3 gene (named C3.1-C3.9) were identified in C. idella, and their structure, genomic location, phylogeny, expression patterns, and genetic characteristics were systematically analyzed. Phylogenetic analysis indicates that nine copies of grass carp C3 (hereafter called CiC3) cluster in the branch of Osteichthyes together with that of other fish, forming a different evolutionary branch distinct from other vertebrates. CiC3 are constitutively expressed in all examined tissues, among which CiC3.1 is the dominant C3 molecule. At 14 days of grass carp reovirus (GCRV) challenge, the CiC3s expression patterns share a similar expression trend. Furthermore, the comparison of the level of C3 protein, the mRNA expression level of dominant CiC3 (C3.1), and the mortality after GCRV challenge between the Xiangjiang River and Yangtze River grass carp indicate that the C3 protein exhibits distribution of polymorphism in a population, and the expression level of C3 is heritable and positively correlated with GCRV resistance. Furthermore, we identified 10 SNPs (named SNP1–10) of the C3.1 gene between GCRV-resistant and GCRV-susceptible grass carp groups. Inspiringly, SNP7 (g.76773C/T), SNP8 (g.76945 T/C), SNP1 (g.7065C/T), SNP9 (g.77153 A/C) and SNP10 (g.77252 T/C) have been verified to be significantly associated with the GCRV-resistant trait. Collectively, our findings provide potential molecular markers and relevant SNP sites for future grass carp breeding with respect to GCRV resistance.

Implementation and Optimization of Smart Pariri Assistance at the Elementary School Level in West Sumbawa Regency

The limited access to education because of many underprivileged communities has an impact to their children in which they could not obtain such a proper education. The Policy of Pariri Cerdas Assistance Program has been existed as one of the regional government innovations that aimed at achieving equal distribution and expansion of educational access in West Sumbawa Regency. By relatively short period, this policy is considered superficial to discuss. Therefore, the urgency of this research was to focus on the extent of the impact of implementation the Pariri Cerdas Assistance, what factors has been supported and obstructed the implementation of the program, and what were the strategies for optimizing the program of Pariri Cerdas Assistance in West Sumbawa Regency. By applying a qualitative descriptive approach and Field Research, researcher attempted to examine facts in the field that related to the implementation of related policies to research objectivities. The data collection methods applied were observation, interviews and documentation, journal literature, articles and relevant sites to this study. There were 33 samples of informants from 3 zones in the West Sumbawa Regency (North, Central and South Zones). The analysis methods for this research were descriptive and SWOT. According to data analysis, it was concluded that: 1) It is important to identify some supporting and inhibiting factors as part of determining the effective strategy in optimizing Pariri Cerdas Assistance Program, 2) Implementation of Pariri Cerdas assistance is claimed to be quite effective and positive for several aspects, meant that there were still some points to be reinforced involved the factual process and target as evaluation for this program in the future, 3) Grand design strategy for optimizing the program of Pariri Cerdas included; the needs to develop Pariri Cerdas policies, Financing Analysis of Pariri Cerdas program, updating the DTKS as one of references for determining the addressees of Pariri Cerdas regularly, the need to strengthen Mechanism for the next implementation program of Pariri Cerdas, Monitoring and Evaluation of the Pariri Cerdas program, the need of forming such a Task Force Unit which is involving some private sectors and NGOs and supporting the Pariri Cerdas Program, Advocacy for Pariri Cerdas to some parties involved, Digital-Based Innovation in Education Financing Programs, Increasing partnerships to build Innovative breakthroughs in addressing education financing.

Realizing a high OER activity in new single-atom catalysts formed by introducing TMNx (x = 3 and 4) units into carbon nanotubes using high-throughput calculations.

Exploring highly efficient electrocatalysts for the oxygen evolution reaction (OER) is of great significance for hydrogen production through water splitting. By means of high-throughput density functional theory (DFT) calculations, we investigated the OER catalytic activity of a series of one-dimensional carbon nanotube (CNT)-based systems containing TMN4 or TMN3 functional units. Through the screening of 3d/4d/5d transition metals (TMs) from Group IVB to Group VIII, eight newly obtained TMNx@CNT (x = 3 and 4) systems were found to exhibit excellent OER activity, with very low overpotentials in the range 0.29-0.51 V, where the Co, Rh, Ir, Ti, Fe, and Ru atoms could be used as active sites. It was found that under the framework of TMN3@CNTs, the pre-adsorption of some species from water dissociation on the relevant TM sites (TM = Ti, Fe, and Ru) could lead to a high OER catalytic activity, which was different from the general situation where OER reactions directly occur on the clean surfaces of the remaining systems with Co/Rh/Ir metal centers. Moreover, the catalytic mechanisms were analyzed in detail. This work can be conducive to obtaining low-cost and high-performance OER single-atom electrocatalysts based on excellent CNT nanomaterials.

Theoretical Studies Regarding Corruption, Corruption Crimes, and Perspective Studies on Islamic Criminal Law Theory (Fiqh Jinayah)

The purpose of this discussion is to know and understand the theory of corruption, criminal acts of corruption, and the principles of jinayah fiqh related to corruption. The analytical method used is to use literature studies originating from various online reference books and journals as well as several credible and relevant internet sites. The resulting discussion is about the definition of corruption as outlined by several experts, criminal acts of corruption, the legal basis for criminal acts of corruption, forms of terms in Islamic law that are synonymous with corruption, and efforts made to eradicate corruption.

Computational unravelling of cathodic hydride formation on palladium surfaces

Palladium (Pd) is well-known for its role in catalyzing hydrogen-based reduction reactions, owing to its excellent catalytic activity and hydrogen storage ability. Its surface and subsurface structures under electrochemical conditions are vital in understanding the hydrogen evolution reaction (HER) mechanism at the Pd cathodes where the most active sites are located on ‘in situ’ formed Pd-hydride layers. In this work, we investigate the process of Pd-hydride formation as well as the step-by-step formation and stability of Pd-hydride/Pd interfaces under electrochemical conditions using first-principles calculations. Our results reveal that among the low-indexed surfaces (111), (110) and (100), the (111) surface is expected to be the most dominant surface in a Pd nanostructure in addition to being the most preferred surface for hydrogen adsorption. Based on calculated Pourbaix diagrams, we can identify the relevant regions close to the equilibrium electrode potential and pH for proton electroreduction and hydrogen evolution, where the Pd surfaces start to be covered by hydrogen adatoms, and when the electrode potential is decreased, there are clear thermodynamic indications for more and more subsurface hydride layers. Overall, the results provide insights into the stability and formation of hydrogen-containing Pd surfaces, forming PdH/Pd type interfaces. Our idealized model systems are a first step towards elucidation of relevant active sites on Pd.

LAFEM: A Scoring Model to Evaluate Functional Landscape of Lysine Acetylome

Protein lysine acetylation is a critical post-translational modification involved in a wide range of biological processes. To date, about 20,000 acetylation sites of Homo sapiens were identified through mass spectrometry–based proteomic technology, but more than 95% of them have unclear functional annotations because of the lack of existing prioritization strategy to assess the functional importance of the acetylation sites on large scale. Hence, we established a lysine acetylation functional evaluating model (LAFEM) by considering eight critical features surrounding lysine acetylation site to high-throughput estimate the functional importance of given acetylation sites. This was achieved by selecting one of the random forest models with the best performance in 10-fold cross-validation on undersampled training dataset. The global analysis demonstrated that the molecular environment of acetylation sites with high acetylation functional scores (AFSs) mainly had the features of larger solvent-accessible surface area, stronger hydrogen bonding–donating abilities, near motif and domain, higher homology, and disordered degree. Importantly, LAFEM performed well in validation dataset and acetylome, showing good accuracy to screen out fitness directly relevant acetylation sites and assisting to explain the core reason for the difference between biological models from the perspective of acetylome. We further used cellular experiments to confirm that, in nuclear casein kinase and cyclin-dependent kinase substrate 1, acetyl-K35 with higher AFS was more important than acetyl-K9 with lower AFS in the proliferation of A549 cells. LAFEM provides a prioritization strategy to large scale discover the fitness directly relevant acetylation sites, which constitutes an unprecedented resource for better understanding of functional acetylome.

Melatonin as a chronobiotic/cytoprotective agent in bone. Doses involved

AbstractBecause the chronobiotic and cytoprotective molecule melatonin diminishes with age, its involvement in postmenopausal and senescence pathology has been considered since long. One relevant melatonin target site in aging individuals is bone where melatonin chronobiotic effects mediated by MT1 and MT2 receptors are demonstrable. Precursors of bone cells located in bone marrow are exposed to high quantities of melatonin and the possibility arises that melatonin acts a cytoprotective compound via an autacoid effect. Proteins that are incorporated into the bone matrix, like procollagen type I c‐peptide, augment after melatonin exposure. Melatonin augments osteoprotegerin, an osteoblastic protein that inhibits the differentiation of osteoclasts. Osteoclasts are target cells for melatonin as they degrade bone partly by generating free radicals. Osteoclast activity and bone resorption are impaired via the free radical scavenger properties of melatonin. The administration of melatonin in chronobiotic doses (less than 10 mg daily) is commonly used in clinical studies on melatonin effect on bone. However, human equivalent doses allometrically derived from animal studies are in the 1–1.5 mg/kg/day range for a 75 kg human adult, a dose rarely used clinically. In view of the absence of toxicity of melatonin in phase 1 pharmacological studies with doses up to 100 mg in normal volunteers, further investigation is needed to determine whether high melatonin doses have higher therapeutic efficacy in preventing bone loss.

Abstract A142: Fragment based discovery of inhibitors of the eIF4E:eIF4G interaction

Abstract eIF4E is the rate limiting factor for cap-dependent protein translation, forming an essential part of the translation initiation complex, eIF4F and is a key signalling convergence point for the major oncogenic pathways MAPK and PI3K/AKT/MTOR. eIF4E has been shown to be overexpressed in cancer, which has been associated with poor prognosis and resistance to chemotherapeutics and targeted agents such as mTOR and MAPK inhibitors. eIF4E is therefore a promising target for cancer treatment but has so far been difficult to target with small molecules due to a lack of druggable pockets. Fragment based crystallographic screening is a powerful technique for probing the surface of proteins to identify potentially druggable binding sites. Here, we describe our fragment-based approach and hit optimisation campaign to generate potent compounds binding to eIF4E For the fragment screen, we generated an engineered form of eIF4E, where the N-terminal (residues 1-35) were removed and replaced a short, tethered peptide based on the canonical binding sequence of the eIF4E binding protein 4E-BP1, and screened 1400 fragments using a combination of Xray crystallography and NMR. Several low affinity (mM) fragment hits were identified, binding to both the mRNA cap- binding site and at an additional binding site of unknown functional relevance. Using a combination of biophysical and biochemical assays, subsequent rounds of iterative structure-based drug design of yielded potent lead molecules against both binding sites. For the cap-binding site, lead compounds of low nM potency were generated but due to the polar nature of the binding site, the molecules had very poor permeability properties and did not inhibit cell proliferation. For the non-canonical binding site, lead compounds with potency of 100nM alongside less potent enantiomers were generated which provided useful tools for probing the function of the binding site in vitro. We developed a MSD (Meso-scale discovery) assay to determine that the lead compound and not the inactive enantiomer could disrupt the eIF4E:eIF4G interaction in HeLa cell lysates with an IC50 of 1uM. Using a HeLa extract in vitro translation assay, we could also demonstrate that both the cap site and non-canonical site lead compounds could inhibit cap-dependent but not IRES driven protein translation. This work demonstrates the power of fragment screening to identify novel functional pockets on difficult to drug proteins such as eIF4E. Citation Format: Caroline J Richardson, Mladen Vincovic, Charlotte East, Nicola Wallis, George Ward, Andrew Woodhead. Fragment based discovery of inhibitors of the eIF4E:eIF4G interaction [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A142.

Bridging Place-Based Astrobiology Education with Genomics, Including Descriptions of Three Novel Bacterial Species Isolated from Mars Analog Sites of Cultural Relevance.

Democratizing genomic data science, including bioinformatics, can diversify the STEM workforce and may, in turn, bring new perspectives into the space sciences. In this respect, the development of education and research programs that bridge genome science with "place" and world-views specific to a given region are valuable for Indigenous students and educators. Through a multi-institutional collaboration, we developed an ongoing education program and model that includes Illumina and Oxford Nanopore sequencing, free bioinformatic platforms, and teacher training workshops to address our research and education goals through a place-based science education lens. High school students and researchers cultivated, sequenced, assembled, and annotated the genomes of 13 bacteria from Mars analog sites with cultural relevance, 10 of which were novel species. Students, teachers, and community members assisted with the discovery of new, potentially chemolithotrophic bacteria relevant to astrobiology. This joint education-research program also led to the discovery of species from Mars analog sites capable of producing N-acyl homoserine lactones, which are quorum-sensing molecules used in bacterial communication. Whole genome sequencing was completed in high school classrooms, and connected students to funded space research, increased research output, and provided culturally relevant, place-based science education, with participants naming three novel species described here. Students at St. Andrew's School (Honolulu, Hawai'i) proposed the name Bradyrhizobium prioritasuperba for the type strain, BL16AT, of the new species (DSM 112479T = NCTC 14602T). The nonprofit organization Kauluakalana proposed the name Brenneria ulupoensis for the type strain, K61T, of the new species (DSM 116657T = LMG = 33184T), and Hawai'i Baptist Academy students proposed the name Paraflavitalea speifideiaquila for the type strain, BL16ET, of the new species (DSM 112478T = NCTC 14603T).

Sediment thickness map of United States Atlantic and Gulf Coastal Plain Strata, and their influence on earthquake ground motions

With the recent successful accounting of basin depth ground-motion adjustments in seismic hazard analyses for select areas of the western United States, we move toward implementing similar adjustments in the Atlantic and Gulf Coastal Plains by constructing a sediment thickness model and evaluating multiple relevant site amplification models for central and eastern United States seismic hazard analyses. We digitize and combine existing sediment thickness data sets into a composite surface that delineates the base of Cretaceous sediments under the Atlantic Coastal Plain and the base of Mesozoic sediments under the Gulf Coastal Plain. Amplification models dependent on sediment thickness, site natural period, and source-to-site path length are compared with data sets of observed ground motions to evaluate the ability of the new models to improve ground motion estimates. We find that the amplification models can account for observed trends in sediment-thickness and period-dependent residuals, but some tuning is required. For example, the model of Chapman and Guo requires a reference VS30, the time-averaged shear-wave velocity within 30 m of the Earth’s surface, for non-Coastal Plain sites, which we estimate to be between about 1 and 2 km/s. Along with our sediment thickness model, we estimate a velocity profile for application to the Harmon et al. site-natural-period-based model in order to best match the Chapman and Guo period dependence for a broad range of sediment thicknesses. The Next Generation of Attenuation models for the eastern United States Gulf Coast path-based adjustment models can also account for seismic attenuation in the Coastal Plain sediments and reduce the standard deviation of total residuals. If enacted in the U.S. Geological Survey National Seismic Hazard Model, these amplification models will reduce predicted short-period (<1 s) and increase predicted long-period (>1 s) ground motions in the Coastal Plains appreciably.

CompreTAP: Feasibility and reliability of a new language comprehension mapping task via preoperative navigated transcranial magnetic stimulation

ObjectiveStimulation-based language mapping approaches that are used pre- and intraoperatively employ predominantly overt language tasks requiring sufficient language production abilities. Yet, these production-based setups are often not feasible in brain tumor patients with severe expressive aphasia. This pilot study evaluated the feasibility and reliability of a newly developed language comprehension task with preoperative navigated transcranial magnetic stimulation (nTMS). MethodsFifteen healthy subjects and six brain tumor patients with severe expressive aphasia unable to perform classic overt naming tasks underwent preoperative nTMS language mapping based on an auditory single-word Comprehension TAsk for Perioperative mapping (CompreTAP). Comprehension was probed by button-press responses to auditory stimuli, hence not requiring overt language responses. Positive comprehension areas were identified when stimulation elicited an incorrect or delayed button press. Error categories, case-wise cortical error rate distribution and inter-rater reliability between two experienced specialists were examined. ResultsOverall, the new setup showed to be feasible. Comprehension-disruptions induced by nTMS manifested in no responses, delayed or hesitant responses, searching behavior or selection of wrong target items across all patients and controls and could be performed even in patients with severe expressive aphasia. The analysis agreement between both specialists was substantial for classifying comprehension-positive and -negative sites. Extensive left-hemispheric individual cortical comprehension sites were identified for all patients. Apart from one case presenting with transient worsening of aphasic symptoms, pre-existing language deficits did not aggravate if results were used for subsequent surgical planning. ConclusionEmploying this new comprehension-based nTMS setup allowed to identify language relevant cortical sites in all healthy subjects and severely aphasic patients who were thus far precluded from classic production-based mapping. This pilot study, moreover, provides first indications that the CompreTAP mapping results may support the preservation of residual language function if used for subsequent surgical planning.

Optimizing cleaning strategies for biofouling in reverse osmosis membrane systems: A comparative study using a self-formed instrument

Membrane biofouling poses a serious challenge in reverse osmosis (RO) plants used for water recovery, which cannot be addressed by traditional chlorine-based cleaning agents. To accommodate this problem and enhance membrane performance while maintaining high-quality water production, various cleaning strategies have been applied. It remains however challenging to identify optimal cleaning agents, as tests require discontinuation of production to evaluate the effect. This study introduces a self-formed instrument that mimics industrial RO plants on a small scale to compare the cleaning agents in a fast, affordable and feasible approach. The setup was demonstrated using three cells operating in parallel and a thorough comparison of these. Specifically, the online cleaning efficiency of a typical biofouling cleaner, a solution of NaOH/sodium dodecyl sulfate (SDS), and the commonly used non-oxidizing biocide, 2,2-dibromo-3-nitrilopropionamide, were compared to validate the system performance when fed with membrane bioreactor effluent. The effectiveness of the cleaning process was evaluated using a combination of hydrodynamic operation and membrane autopsy to estimate the biofoulant amount and composition. During a 7-day operating period, it was observed that treated membranes demonstrated higher flux rates compared to untreated membranes. The normalized flux increased more than double in the membrane after it had been cleaned with NaOH/SDS solution. CLSM analysis clearly showed the distinct effects of the two cleaning solutions on the amount and spatial structure of the biofilm layer. Cleaning with DBNPA was able to reduce the load of living bacteria, but not necessarily remove the biofilm components completely. Comparative analyses of membranes revealed that NaOH/SDS exhibited the highest cleaning efficiency during the online cleaning operation mode. This benchmark highlights the versatility of the system, which can be assembled at relevant sites and assist in the identification of efficient and eco-friendly agents that promote the lifespan of membranes. With the distribution of this instrument, it will be possible to accelerate the investigation of multiple cleaning strategies and also analyze interactions among cleaning agents in an attempt to reduce water shortage.

A comparative study of pyridine and pyrimidine derivatives based formamidine for copper corrosion inhibition in nitric acid: Experimental and computational exploration

This paper investigates the performances of two synthesized formamidine derivatives, namely: N,N-dimethyl-N’-(pyridin-2-yl) formamidine (A) and N,N-dimethyl-N’-(pyrimidin-2-yl) formamidine (B) to inhibit the corrosion of copper in 1.0 M HNO3 solution at fixed temperatures. Different tools, viz. electrochemical, chemical, and microscopic techniques were utilized in this paper. The evaluated inhibition efficiencies (% IEs) of the tested formamidine derivatives increased with their concentrations. Results indicated that the tested compounds acted as mixed-kind inhibitors with anodic seniority. The acquired great% IEs of such compounds were mainly attributed to the strong adsorption of the compounds’ molecules on the copper surface. The mode of adsorption was agreed with Langmuir isotherm. The results acquired from all utilized tools agreed with each other which disclosed that the %IE values of inhibitor A were somewhat lesser than those of inhibitor B under analogous circumstances. The influence of temperature was investigated and revealed that the %IE values decreased with rising temperature. Also, thermodynamic parameters were evaluated and discussed herein. The kinetics and mechanisms of the copper corrosion and its inhibition by the tested compounds were investigated. Molecular modeling provided strong evidence for the preference of the molecules A and B for their adsorption on the copper surface, while DFT investigations underlined the importance of N heteroatom as a relevant local site for molecular adsorption.