Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength.

The application of machine learning techniques in biological research, especially when dealing with limited data availability, poses significant challenges. In this study, we leveraged advancements in method development for predicting protein-protein binding strength to conduct a systematic investigation into the application of machine learning on limited data. The binding strength, quantitatively measured as binding affinity, is vital for understanding the processes of recognition, association, and dysfunction that occur within protein complexes. By incorporating transfer learning, integrating domain knowledge, and employing both deep learning and traditional machine learning algorithms, we mitigated the impact of data limitations and made significant advancements in predicting protein-protein binding affinity. In particular, we developed over 20 models, ultimately selecting three representative best-performing ones that belong to distinct categories. The first model is structure-based, consisting of a random forest regression and thirteen handcrafted features. The second model is sequence-based, employing an architecture that combines transferred embedding features with a multilayer perceptron. Finally, we created an ensemble model by averaging the predictions of the two aforementioned models. The comparison with other predictors on three independent datasets confirms the significant improvements achieved by our models in predicting protein-protein binding affinity. The programs for running these three models are available at https://github.com/minghuilab/BindPPI.

Assessing computational tools for predicting protein stability changes upon missense mutations using a new dataset.

Insight into how mutations affect protein stability is crucial for protein engineering, understanding genetic diseases, and exploring protein evolution. Numerous computational methods have been developed to predict the impact of amino acid substitutions on protein stability. Nevertheless, comparing these methods poses challenges due to variations in their training data. Moreover, it is observed that they tend to perform better at predicting destabilizing mutations than stabilizing ones. Here, we meticulously compiled a new dataset from three recently published databases: ThermoMutDB, FireProtDB, and ProThermDB. This dataset, which does not overlap with the well-established S2648 dataset, consists of 4038 single-point mutations, including over 1000 stabilizing mutations. We assessed these mutations using 27 computational methods, including the latest ones utilizing mega-scale stability datasets and transfer learning. We excluded entries with overlap or similarity to training datasets to ensure fairness. Pearson correlation coefficients for the tested tools ranged from 0.20 to 0.53 on unseen data, and none of the methods could accurately predict stabilizing mutations, even those performing well in anti-symmetric property analysis. While most methods present consistent trends for predicting destabilizing mutations across various properties such as solvent exposure and secondary conformation, stabilizing mutations do not exhibit a clear pattern. Our study also suggests that solely addressing training dataset bias may not significantly enhance accuracy of predicting stabilizing mutations. These findings emphasize the importance of developing precise predictive methods for stabilizing mutations.

Molecular imprinting-based ratiometric fluorescence sensors for environmental and food analysis.

Environmental protection and food safety are closely related to the healthy development of human society; there is an urgent need for relevant analytical methods to determine environmental pollutants and harmful substances in food. Molecular imprinting-based ratiometric fluorescence (MI-RFL) sensors, constructed by combining molecular imprinting recognition and ratiometric fluorescence detection, possess remarkable advantages such as high selectivity, anti-interference ability, high sensitivity, non-destruction and convenience, and have attracted increasing interest in the field of analytical determination. Herein, recent advances in MI-RFL sensors for environmental and food analysis are reviewed, aiming at new construction strategies and representative determination applications. Firstly, fluorescence sources and possible sensing principles are briefly outlined. Secondly, new imprinting techniques and dual/ternary-emission fluorescence types that improve sensing performances are highlighted. Thirdly, typical analytical applications of MI-RFL sensors in environmental and food samples are summarized. Lastly, the challenges and perspectives of the MI-RFL sensors are proposed, focusing on improving sensitivity/visualization and extending applications.

[Effects of Short-term Nitrogen Addition on Soil Organic Carbon Components in Robinia pseudoacacia L. Plantation].

Nitrogen (N) deposition in the context of human activities continuously affects the carbon cycle of ecosystems. The effect of N deposition on soil organic carbon is related to the differential responses of different carbon fractions. To investigate the changes in soil organic carbon fraction and its influencing factors in the context of short-term N deposition, four N addition gradients:0 (CK), 1.5 (N1), 3 (N2), and 6 (N3) g·(m2·a)-1 were set up in acacia plantations based on field N addition experiments, and the soil physicochemical properties, microbial biomass, and enzyme activities were measured in June and September. The results showed that:① exogenous N input reduced soil pH, promoted the increase in soluble organic carbon content, and increased soil nitrogen effectiveness. ② Short-term N addition significantly reduced soil organic carbon content, and the response of each component of organic carbon to N addition was different. Among them, the content of easily oxidized organic carbon was significantly reduced and reached the lowest value under the N2 treatment, with 54.4% and 48.2% reduction compared with that of the control, respectively, and the content of inert organic carbon increased, although the increase was not significant. Nitrogen addition reduced the soil carbon pool activity and improved the stability of the soil carbon pool. Soil carbon pool activity reached its lowest under the N3 and N2 treatments, with a decrease of 53.3% and 52.80%, respectively, compared to that of the control. ③Random forest modeling indicated that the soil microbial biomass stoichiometry ratio, microbial biomass carbon, and AP were the key factors driving the changes in soil organic carbon activity under short-term N addition, explaining 65.96% and 66.68% of the changes in oxidizable organic carbon and inert organic carbon, respectively. Structural equation modeling validated the results of the random forest modeling, and soil microbial biomass stoichiometric ratios significantly influenced carbon pool activity. Short-term nitrogen addition changed soil microbial biomass and its stoichiometric ratio in the acacia plantation forest mainly through two pathways, i.e., increasing soil nitrogen effectiveness and promoting soil acidification and inhibiting extracellular carbon hydrolase activity, thus changing the soil carbon fraction ratio and participating in the soil organic carbon cycling process.

Recent Advances in Molecularly Imprinted Polymers for Antibiotic Analysis.

The abuse and residues of antibiotics have a great impact on the environment and organisms, and their determination has become very important. Due to their low contents, varieties and complex matrices, effective recognition, separation and enrichment are usually required prior to determination. Molecularly imprinted polymers (MIPs), a kind of highly selective polymer prepared via molecular imprinting technology (MIT), are used widely in the analytical detection of antibiotics, as adsorbents of solid-phase extraction (SPE) and as recognition elements of sensors. Herein, recent advances in MIPs for antibiotic residue analysis are reviewed. Firstly, several new preparation techniques of MIPs for detecting antibiotics are briefly introduced, including surface imprinting, nanoimprinting, living/controlled radical polymerization, and multi-template imprinting, multi-functional monomer imprinting and dummy template imprinting. Secondly, several SPE modes based on MIPs are summarized, namely packed SPE, magnetic SPE, dispersive SPE, matrix solid-phase dispersive extraction, solid-phase microextraction, stir-bar sorptive extraction and pipette-tip SPE. Thirdly, the basic principles of MIP-based sensors and three sensing modes, including electrochemical sensing, optical sensing and mass sensing, are also outlined. Fourthly, the research progress on molecularly imprinted SPEs (MISPEs) and MIP-based electrochemical/optical/mass sensors for the detection of various antibiotic residues in environmental and food samples since 2018 are comprehensively reviewed, including sulfonamides, quinolones, ß-lactams and so on. Finally, the preparation and application prospects of MIPs for detecting antibiotics are outlined.

PfSET2 Is Involved in Genome Organization of Var Gene Family in Plasmodium falciparum.

The three-dimensional (3D) genome structure of human malaria parasite Plasmodium falciparum is highly organized and plays important roles in regulating coordinated expression patterns of specific genes such as virulence genes which are involved in antigenic variation and immune escape. However, the molecular mechanisms that control 3D genome of the parasite remain elusive. Here, by analyzing genome organization of P. falciparum, we identify high-interacting regions (HIRs) with strong chromatin interactions at telomeres and virulence genes loci. Specifically, HIRs are highly enriched with repressive histone marks (H3K36me3 and H3K9me3) and form the transcriptional repressive center. Deletion of PfSET2, which controls H3K36me3 level, results in marked reduction of both intrachromosomal and interchromosomal interactions for HIRs. Importantly, such chromatin reorganization coordinates with dynamic changes in epigenetic feature in HIRs and transcriptional activation of var genes. Additionally, different cluster of var genes based on the pattern of chromatin interactions show distinct transcriptional activation potential after deletion of PfSET2. Our results uncover a fundamental mechanism that the epigenetic factor PfSET2 controls the 3D organization of heterochromatin to regulate the transcription activities of var genes family in P. falciparum. IMPORTANCE PfSET2 has been reported to play key role in silencing var genes in Plasmodium falciparum, while the underlying molecular mechanisms remain unclear. Here, we provide evidence that PfSET2 is essential to maintain 3D genome organization of heterochromatin region to keep var genes in transcription repressive state. These findings can contribute better understanding of the regulation of high-order chromatin structure in P. falciparum.

PremPLI: a machine learning model for predicting the effects of missense mutations on protein-ligand interactions.

Resistance to small-molecule drugs is the main cause of the failure of therapeutic drugs in clinical practice. Missense mutations altering the binding of ligands to proteins are one of the critical mechanisms that result in genetic disease and drug resistance. Computational methods have made a lot of progress for predicting binding affinity changes and identifying resistance mutations, but their prediction accuracy and speed are still not satisfied and need to be further improved. To address these issues, we introduce a structure-based machine learning method for quantitatively estimating the effects of single mutations on ligand binding affinity changes (named as PremPLI). A comprehensive comparison of the predictive performance of PremPLI with other available methods on two benchmark datasets confirms that our approach performs robustly and presents similar or even higher predictive accuracy than the approaches relying on first-principle statistical mechanics and mixed physics- and knowledge-based potentials while requires much less computational resources. PremPLI can be used for guiding the design of ligand-binding proteins, identifying and understanding disease driver mutations, and finding potential resistance mutations for different drugs. PremPLI is freely available at https://lilab.jysw.suda.edu.cn/research/PremPLI/ and allows to do large-scale mutational scanning.

Design, Synthesis, and Evaluation of Chalcone Derivatives as Multifunctional Agents against Alzheimer's Disease.

Fifteen chalcone derivatives 3a-3o were synthesized, and evaluated as multifunctional agents against Alzheimer's disease. In vitro studies revealed that these compounds inhibited self-induced Aß1-42 aggregation effectively ranged from 45.9-94.5 % at 20 µM, and acted as potential antioxidants. Their structure-activity relationships were summarized. In particular, (2E)-3-[4-(dimethylamino)phenyl]-1-(pyridin-2-yl)prop-2-en-1-one (3g) exhibited an excellent inhibitory activity of 94.5 % at 20 µM, and it could disassemble the self-induced Aß1-42 aggregation fibrils with ratio of 57.1 % at 20 µM concentration. In addition, compound 3g displayed good chelating ability for Cu2+ , and could effectively inhibit and disaggregate Cu2+ -induced Aß aggregation. Moreover, compound 3g exerted low cytotoxicity, significantly reversed Aß1-42 -induced SH-SY5Y cell damage. More importantly, compound 3g remarkably ameliorated scopolamine-induced memory impairment in mice. In summary, all the results revealed compound 3g was a potential multifunctional agent for AD therapy.

Mild synthesis of superadhesive hydrogel electrolyte with low interfacial resistance and enhanced ionic conductivity for flexible zinc ion battery.

Flexible aqueous battery is considered to be one of the most promising energy storage devices for powering flexible electronics. However, inferior interfacial compatibility in electrode-electrolyte interfaces and inefficient ionic channel of electrolytes usually result in potential troubles when applied in practical applications. Herein, we report a mild synthetic route to a sodium lignosulfonate-polyacrylamide hydrogel electrolyte with a high adhesiveness to achieve low electrode-electrolyte interfacial resistance and fast ionic conduction. Comprehensive experiments show that the catechol groups from sodium lignosulfonate demonstrate strong interactions with both cathode and anode materials, and thus greatly reduce the contact resistances across the electrodes. Meanwhile, the existence of sulfonate groups significantly enhances the ionic conductivity of the hydrogel electrolyte. Benefiting from this design, a low ohmic resistance of 3.8 Ω (i.e., 11.4 Ω cm2 ), a low charge transfer resistance of 22.5 Ω (i.e., 67.5 Ω cm2 ), a high ionic conductivity of 31.1 mS cm-1 as well as a 100% capacity retention upon harsh bending deformation can be realized in the flexible zinc ion battery, which are significantly superior to those in the traditional candidates. The present investigation provides new insight into addressing the interfacial issue plaguing flexible energy storage devices.

A novel multistage antiplasmodial inhibitor targeting Plasmodium falciparum histone deacetylase 1.

Although artemisinin combination therapies have succeeded in reducing the global burden of malaria, multidrug resistance of the deadliest malaria parasite, Plasmodium falciparum, is emerging worldwide. Innovative antimalarial drugs that kill all life-cycle stages of malaria parasites are urgently needed. Here, we report the discovery of the compound JX21108 with broad antiplasmodial activity against multiple life-cycle stages of malaria parasites. JX21108 was developed from chemical optimization of quisinostat, a histone deacetylase inhibitor. We identified P. falciparum histone deacetylase 1 (PfHDAC1), an epigenetic regulator essential for parasite growth and invasion, as a molecular target of JX21108. PfHDAC1 knockdown leads to the downregulation of essential parasite genes, which is highly consistent with the transcriptomic changes induced by JX21108 treatment. Collectively, our data support that PfHDAC1 is a potential drug target for overcoming multidrug resistance and that JX21108 treats malaria and blocks parasite transmission simultaneously.

The cryptic unstable transcripts are associated with developmentally regulated gene expression in blood-stage Plasmodium falciparum.

The tight gene expression regulation controls the development and pathogenesis of human malaria parasite Plasmodium falciparum throughout the complex life cycle. Recent studies have revealed the pervasive nascent transcripts in the genome of P. falciparum, suggesting the existence of a hidden transcriptome involved in the dynamic gene expression. However, the landscape and related biological functions of nascent non-coding RNAs (ns-ncRNAs) are still poorly explored. Here we profiled the transcription dynamics of nascent RNAs by rRNA-depleted and stranded RNA sequencing over the course of 48-h intraerythrocytic developmental cycle (IDC). We identified the genome-wide sources of a total of 2252 ns-ncRNAs, mostly originating from intergenic and untranslated regions of annotated genes. By integrating the nascent RNA abundances with ATAC-seq and ChIP-seq analysis, we uncovered the euchromatic microenvironment surrounding the ns-ncRNA loci, and revealed a positive correlation between ns-ncRNAs and corresponding mRNA abundances. Finally, by gene knock-down strategy, we showed that the cooperation of RNA exosome catalytic subunit PfDis3 and PfMtr4 cofactor played a major role in ns-ncRNAs degradation. Collectively, this study contributes to understanding of the potential roles of short-lived nascent ncRNAs in regulating gene expression in malaria parasites.

PfAP2-G2 Is Associated to Production and Maturation of Gametocytes in Plasmodium falciparum via Regulating the Expression of PfMDV-1.

Gametocyte is the sole form of the Plasmodium falciparum which is transmissible to the mosquito vector. Here, we report that an Apicomplexan Apetala2 (ApiAP2) family transcription factor, PfAP2-G2 (Pf3D7_1408200), plays a role in the development of gametocytes in P. falciparum by regulating the expression of PfMDV-1 (Pf3D7_1216500). Reverse transcriptase-quantitative PCR (RT-qPCR) analysis showed that PfAP2-G2 was highly expressed in the ring stage. Indirect immunofluorescence assay showed nuclear localization of PfAP2-G2 in asexual stages. The knockout of PfAP2-G2 led to a ~95% decrease in the number of mature gametocytes with a more substantial influence on the production and maturation of the male gametocytes, resulting in a higher female/male gametocyte ratio. To test the mechanism of this phenotype, RNA-seq and RT-qPCR showed that disruption of PfAP2-G2 led to the down-regulation of male development gene-1 (PfMDV-1) in asexual stages. We further found that PfAP2-G2 was enriched at the transcriptional start site (TSS) of PfMDV-1 by chromatin immunoprecipitation and qPCR assay in both ring stage and schizont stage, which demonstrated that PfMDV-1 is one of the targets of PfAP2-G2. In addition, RT-qPCR also showed that PfAP2-G (Pf3D7_1222600), the master regulator for sexual commitment, was also down-regulated in the PfAP2-G2 knockout parasites in the schizont stage, but no change in the ring stage. This phenomenon suggested that PfAP2-G2 played a role at the asexual stage for the development of parasite gametocytes and warrants further investigations in regulatory pathways of PfAP2-G2.

Design, synthesis, fungicidal activity and molecular docking studies of novel 2-((2-hydroxyphenyl)methylamino)acetamide derivatives.

A series of novel 2-hydroxyphenyl substituted aminoacetamides was designed by molecular hybridization of the aminoacetamide scaffold and 2-hydroxyphenyl motif. The target compounds were synthesized and their fungicidal activities were evaluated. Some of the target compounds showed excellent antifungal activities against S. sclerotiorum and P. capsici. Significantly, compounds 5e displayed the most potent activity against S. sclerotiorum with EC50 = 2.89 µg/mL, which was lower than that of commercial chlorothalonil. The systematic studies provided strong confidence that the hydroxyl group and the carbonyl group are crucial for the fungicidal activity. Molecular docking studies suggest that SDH enzyme could be one of the potential action targets of our compounds.

Epigenetic editing by CRISPR/dCas9 in Plasmodium falciparum.

Genetic manipulation remains a major obstacle for understanding the functional genomics of the deadliest malaria parasite Plasmodium falciparum Although the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9) system has been successfully applied to introduce permanent changes in the parasite genome, its use is still limited. Here we show that fusing different epigenetic effector domains to a Cas9 null mutant efficiently and specifically reprograms the expression of target genes in P. falciparum By precisely writing and erasing histone acetylation at the transcription start site regions of the invasion-related genes reticulocyte binding protein homolog 4 (rh4) and erythrocyte binding protein 175 (eba-175), respectively, we achieved significant activation of rh4 and repression of eba-175, leading to the switch of the parasite invasion pathways into human erythrocytes. By using the epigenetic knockdown system, we have also characterized the effects of PfSET1, previously identified as an essential gene, on expression of mainly trophozoite- and schizont-specific genes, and therefore regulation of the growth of the mature forms of P. falciparum This epigenetic CRISPR/dCas9 system provides a powerful approach for regulating gene expression at the transcriptional level in P. falciparum.

QAGView: Interactively Summarizing High-Valued Aggregate Query Answers.

Methods for summarizing and diversifying query results have drawn significant attention recently, because they help present query results with lots of tuples to users in more informative ways. We present QAGView (Quick AGgregate View), which provides a holistic overview of high-valued aggregate query answers to the user in the form of summaries (showing high-level properties that emerge from subsets of answers) with coverage guarantee (for a user-specified number of top-valued answers) that is both diverse (avoiding overlapping or similar summaries) and relevant (focusing on high-valued aggregate answers). QAGView allows users to view the high-level summaries as clusters, and to expand individual clusters for their constituent result tuples. Users can fine-tune the behavior of QAGView by specifying a number of parameters according their preference. To help users choose appropriate parameters interactively, QAGView employ a suite of optimizations that enable quick preview of how the quality of the summaries changes over wide ranges of parameter settings, as well as real-time visualization of how the summaries evolve in response to parameter updates.

Interactive Summarization and Exploration of Top Aggregate Query Answers.

We present a system for summarization and interactive exploration of high-valued aggregate query answers to make a large set of possible answers more informative to the user. Our system outputs a set of clusters on the high-valued query answers showing their common properties such that the clusters are diverse as much as possible to avoid repeating information, and cover a certain number of top original answers as indicated by the user. Further, the system facilitates interactive exploration of the query answers by helping the user (i) choose combinations of parameters for clustering, (ii) inspect the clusters as well as the elements they contain, and (iii) visualize how changes in parameters affect clustering. We define optimization problems, study their complexity, explore properties of the solutions investigating the semi-lattice structure on the clusters, and propose efficient algorithms and optimizations to achieve these goals. We evaluate our techniques experimentally and discuss our prototype with a graphical user interface that facilitates this interactive exploration. A user study is conducted to evaluate the usability of our approach.