Horizontal gene transfer and symbiotic microorganisms regulate the adaptive evolution of intertidal algae, Porphyra sense lato.

Intertidal algae may adapt to environmental challenges by acquiring genes from other organisms and relying on symbiotic microorganisms. Here, we obtained a symbiont-free and chromosome-level genome of Pyropia haitanensis (47.2 Mb), a type of intertidal algae, by using multiple symbiont screening methods. We identified 286 horizontal gene transfer (HGT) genes, 251 of which harbored transposable elements (TEs), reflecting the importance of TEs for facilitating the transfer of genes into P. haitanensis. Notably, the bulked segregant analysis revealed that two HGT genes, sirohydrochlorin ferrochelatase and peptide-methionine (R)-S-oxide reductase, play a significant role in the adaptation of P. haitanensis to heat stress. Besides, we found Pseudomonas, Actinobacteria, and Bacteroidetes are the major taxa among the symbiotic bacteria of P. haitanensis (nearly 50% of the HGT gene donors). Among of them, a heat-tolerant actinobacterial strain (Saccharothrix sp.) was isolated and revealed to be associated with the heat tolerance of P. haitanensis through its regulatory effects on the genes involved in proline synthesis (proC), redox homeostasis (ggt), and protein folding (HSP20). These findings contribute to our understanding of the adaptive evolution of intertidal algae, expanding our knowledge of the HGT genes and symbiotic microorganisms to enhance their resilience and survival in challenging intertidal environments.

AsmMix: an efficient haplotype-resolved hybrid de novo genome assembling pipeline.

Accurate haplotyping facilitates distinguishing allele-specific expression, identifying cis-regulatory elements, and characterizing genomic variations, which enables more precise investigations into the relationship between genotype and phenotype. Recent advances in third-generation single-molecule long read and synthetic co-barcoded read sequencing techniques have harnessed long-range information to simplify the assembly graph and improve assembly genomic sequence. However, it remains methodologically challenging to reconstruct the complete haplotypes due to high sequencing error rates of long reads and limited capturing efficiency of co-barcoded reads. We here present a pipeline, AsmMix, for generating both contiguous and accurate diploid genomes. It first assembles co-barcoded reads to generate accurate haplotype-resolved assemblies that may contain many gaps, while the long-read assembly is contiguous but susceptible to errors. Then two assembly sets are integrated into haplotype-resolved assemblies with reduced misassembles. Through extensive evaluation on multiple synthetic datasets, AsmMix consistently demonstrates high precision and recall rates for haplotyping across diverse sequencing platforms, coverage depths, read lengths, and read accuracies, significantly outperforming other existing tools in the field. Furthermore, we validate the effectiveness of our pipeline using a human whole genome dataset (HG002), and produce highly contiguous, accurate, and haplotype-resolved assemblies. These assemblies are evaluated using the GIAB benchmarks, confirming the accuracy of variant calling. Our results demonstrate that AsmMix offers a straightforward yet highly efficient approach that effectively leverages both long reads and co-barcoded reads for haplotype-resolved assembly.

Enhanced activation of peroxymonosulfate by ZIF-67/g-C3N4 S-scheme photocatalyst under visible light assistance for degradation of polyethylene terephthalate.

Photocatalyst-activated peroxymonosulfate (PMS) degradation of pollutants is already widely used for wastewater treatment under visible light. Polyethylene terephthalate (PET) is widely used in daily life, but waste plastics have an irreversible negative impact on the environment. In this paper, the ZIF-67/g-C3N4 S-scheme heterojunction catalyst was synthesized as a photocatalyst to achieve a good effect on PET degradation in coordination with PMS. The results indicated that PET could be degraded up to 60.63 ± 2.12 % under the combined effect of catalyst, PMS, and light. In this experiment, the influence of catalyst-to-plastic ratio, PMS concentration, aqueous pH, and inorganic anions on plastic degradation by the photocatalytic synergistic PMS system was discussed, and the excellent performance of this system for degrading PET was highlighted through a comparative test. Electron spin resonance (ESR) and free radical quenching experiments demonstrated that SO4•- contributes the largest amount to the PET degradation performance. Furthermore, results from gas chromatography and liquid chromatography-mass spectrometry (LC-MS) indicated that the plastic degradation products include CO, CH4, and organic small-molecule liquid fuels. Finally, a possible mechanism for the light/PMS system to degrade PET in water was suggested. This paper provides a feasible solution to treat waste microplastics in water.

Integrated Pristine van der Waals Homojunctions for Self-Powered Image Sensors.

Van der Waals junctions hold significant potentials for various applications in multifunctional and low-power electronics and optoelectronics. The multistep device fabrication process usually introduces lattice mismatch and defects at the junction interfaces, which deteriorate device performance. Here the layer engineering synthesis of van der Waals homojunctions consisting of 2H-MoTe2 with asymmetric thickness to eliminate heterogenous interfaces and thus obtain clean interfaces is reported. Experimental results confirm that the homostructure nature gives rise to the formation of pristine van der Waals junctions, avoiding chemical disorders and defects. The ability to tune the energy bands of 2H-MoTe2 continuously through layer engineering enables the creation of adjustable built-in electric field at the homojunction boundaries, which leads to the achievement of self-powered photodetection based on the obtained 2H-MoTe2 films. Furthermore, the successful integration of 2H-MoTe2 homojunctions into an image sensor with 10 × 10 pixels, brings about zero-power consumption and near-infrared imaging functions. The pristine van der Waals homojunctions and effective integration strategies shed new insights into the development of large-scale application for two-dimensional materials in advanced electronics and optoelectronics.

Poplar Bud (Populus) Extraction and Chinese Propolis Counteract Oxidative Stress in Caenorhabditis elegans via Insulin/IGF-1 Signaling Pathway.

Poplar buds are characterized by a high content of phenolic compounds, which exhibit a broad spectrum of biological activities. However, the relationship between Chinese propolis and poplar buds based on their antioxidant capacities and underlying mechanisms remains unclear. This study aimed to investigate the antioxidant properties of poplar bud (Populus) extract (PBE) and Chinese propolis (CP) and to elucidate the mechanisms behind their activity. High-performance liquid chromatography (HPLC) analysis revealed that both PBE and CP contain a significant amount of phenolic acids and flavonoids. 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and ferric-reducing antioxidant power (FRAP) assays demonstrated that PBE and CP possess excellent antioxidant activity. Furthermore, administration of PBE and CP improved the survival rate of C. elegans under oxidative stress. They also decreased the levels of reactive oxygen species (ROS) and malondialdehyde (MDA), while enhancing the activity of antioxidant enzymes (SOD, CAT). PBE and CP intervention upregulated the expression of key genes daf-16, sod-3, hsp-16.2, and skn-1 in nematodes. This suggests that the antioxidant activity of PBE and CP is dependent on daf-16 and skn-1 signaling pathways. In conclusion, poplar bud extracts ha have the potential to become a substitute for propolis and a potential therapeutic agent for treating diseases associated with oxidative damage.

The Chromosome-Scale Genome of Chitala ornata Illuminates the Evolution of Early Teleosts.

Teleosts are the most prolific vertebrates, occupying the vast majority of aquatic environments, and their pectoral fins have undergone remarkable physiological transformations throughout their evolution. Studying early teleost fishes, such as those belonging to the Osteoglossiformes order, could offer crucial insights into the adaptive evolution of pectoral fins within this group. In this study, we have assembled a chromosomal-level genome for the Clown featherback (Chitala ornata), achieving the highest quality genome assembly for Osteoglossiformes to date, with a contig N50 of 32.78 Mb and a scaffold N50 of 40.73 Mb. By combining phylogenetic analysis, we determined that the Clown featherback diverged approximately 202 to 203 million years ago (Ma), aligning with continental separation events. Our analysis revealed the intriguing discovery that a unique deletion of regulatory elements is adjacent to the Gli3 gene, specifically in teleosts. This deletion might be tied to the specialized adaptation of their pectoral fins. Furthermore, our findings indicate that specific contractions and expansions of transposable elements (TEs) in teleosts, including the Clown featherback, could be connected to their adaptive evolution. In essence, this study not only provides a high-quality genomic resource for Osteoglossiformes but also sheds light on the evolutionary trajectory of early teleosts.

Effect of oral tryptamines on the gut microbiome of rats-a preliminary study.

Background: Psilocybin and related tryptamines have come into the spotlight in recent years as potential therapeutics for depression. Research on the mechanisms of these effects has historically focused on the direct effects of these drugs on neural processes. However, in addition to such neural effects, alterations in peripheral physiology may also contribute to their therapeutic effects. In particular, substantial support exists for a gut microbiome-mediated pathway for the antidepressant efficacy of other drug classes, but no prior studies have determined the effects of tryptamines on microbiota. Methods: To address this gap, in this preliminary study, male Long Evans rats were treated with varying dosages of oral psilocybin (0.2 or 2 mg/kg), norbaeocystin (0.25 or 2.52 mg/kg), or vehicle and their fecal samples were collected 1 week and 3 weeks after exposure for microbiome analysis using integrated 16S ribosomal DNA sequencing to determine gut microbiome composition. Results: We found that although treatment with neither psilocybin nor norbaeocystin significantly affected overall microbiome diversity, it did cause significant dose- and time-dependent changes in bacterial abundance at the phylum level, including increases in Verrucomicrobia and Actinobacteria, and decreases in Proteobacteria. Conclusion and Implications: These preliminary findings support the idea that psilocybin and other tryptamines may act on the gut microbiome in a dose- and time-dependent manner, potentially identifying a novel peripheral mechanism for their antidepressant activity. The results from this preliminary study also suggest that norbaeocystin may warrant further investigation as a potential antidepressant, given the similarity of its effects to psilocybin.

Facile synthesis of MOF-808/RGO-based 3D macroscopic aerogel for enhanced photoreduction CO2.

Three-dimensional (3D) macroscopic aerogels have emerged as a critical component in the realm of photocatalysis. Maximizing the integration of materials can result in enhanced efficiency and selectivity in photocatalytic processes. In this investigation, we fabricated MOF-808/reduced graphene oxide (RGO) 3D macroscopic aerogel composite materials employing the techniques of hydrothermal synthesis and freeze-drying. The results revealed that the macroscopic aerogel material exhibited the highest performance in CO2 reduction to CO, particularly when the concentration of RGO was maintained at 5 mg mL-1. In addition, we synthesized powder materials of MR-5 composite photocatalysts and conducted a comparative analysis in terms of photocatalytic CO2 reduction performance and electron transfer efficiency. The results showthat the macroscopic aerogel material boasts a high specific surface area, an abundant internal pore structure, and increased active sites. These attributes collectively enhance light energy utilization, and electron transfer rates, thereby, improving photothermal and photoelectric conversion efficiencies. Furthermore, we conducted in-situ FT-IR measurements and found that the M/R-5 aerogel exhibited the best CO2 adsorption capacity under a CO2 flow rate of 10 mL min-1. The density functional theory results demonstrate the correlation between the formation pathway of the product and the charge transfer pathway. This study provides useful ideas for realizing photocatalytic CO2 reduction of macroscopic aerogel materials in gas-solid reaction mode.

Designing efficient randstrobes for sequence similarity analyses.

MOTIVATION: Substrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis. However, k-mers are limited to exact matches between sequences leading to alternative constructs. We recently introduced a class of new constructs, strobemers, that can match across substitutions and smaller insertions and deletions. Randstrobes, the most sensitive strobemer proposed in Sahlin (Effective sequence similarity detection with strobemers. Genome Res 2021a;31:2080-94. https://doi.org/10.1101/gr.275648.121), has been used in several bioinformatics applications such as read classification, short-read mapping, and read overlap detection. Recently, we showed that the more pseudo-random the behavior of the construction (measured in entropy), the more efficient the seeds for sequence similarity analysis. The level of pseudo-randomness depends on the construction operators, but no study has investigated the efficacy. RESULTS: In this study, we introduce novel construction methods, including a Binary Search Tree-based approach that improves time complexity over previous methods. To our knowledge, we are also the first to address biases in construction and design three metrics for measuring bias. Our evaluation shows that our methods have favorable speed and sampling uniformity compared to existing approaches. Lastly, guided by our results, we change the seed construction in strobealign, a short-read mapper, and find that the results change substantially. We suggest combining the two results to improve strobealign's accuracy for the shortest reads in our evaluated datasets. Our evaluation highlights sampling biases that can occur and provides guidance on which operators to use when implementing randstrobes. AVAILABILITY AND IMPLEMENTATION: All methods and evaluation benchmarks are available in a public Github repository at https://github.com/Moein-Karami/RandStrobes. The scripts for running the strobealign analysis are found at https://github.com/NBISweden/strobealign-evaluation.

Proteomic and Transcriptomic Analyses Provide New Insights into the Mechanism Underlying Lipid Deterioration in Pecan Kernels during Storage.

Pecan nuts are rich in lipids that tend to deteriorate during storage. Tandem mass-tag-based quantitative proteomics and transcriptomics were used to investigate the changes in the protein and gene profiles of stored pecan kernels for the first time. Our previous lipidomic data were jointly analyzed to elucidate the coordinated changes in lipid molecules and related proteins/genes. The mechanism underlying lipid deterioration in pecan kernels during storage was revealed by multiomics analyses. Lipid metabolism-related pathways were activated during pecan storage. Phospholipases, triacylglycerol lipases, lipoxygenases, and oil body-related proteins/genes were highly expressed during storage, revealing their involvement in lipid deterioration. These data provide rich information and will be valuable for future genetic or chemical research to alleviate lipid deterioration in pecans.

Deciphering spatial domains from spatially resolved transcriptomics with Siamese graph autoencoder.

BACKGROUND: Cell clustering is a pivotal aspect of spatial transcriptomics (ST) data analysis as it forms the foundation for subsequent data mining. Recent advances in spatial domain identification have leveraged graph neural network (GNN) approaches in conjunction with spatial transcriptomics data. However, such GNN-based methods suffer from representation collapse, wherein all spatial spots are projected onto a singular representation. Consequently, the discriminative capability of individual representation feature is limited, leading to suboptimal clustering performance. RESULTS: To address this issue, we proposed SGAE, a novel framework for spatial domain identification, incorporating the power of the Siamese graph autoencoder. SGAE mitigates the information correlation at both sample and feature levels, thus improving the representation discrimination. We adapted this framework to ST analysis by constructing a graph based on both gene expression and spatial information. SGAE outperformed alternative methods by its effectiveness in capturing spatial patterns and generating high-quality clusters, as evaluated by the Adjusted Rand Index, Normalized Mutual Information, and Fowlkes-Mallows Index. Moreover, the clustering results derived from SGAE can be further utilized in the identification of 3-dimensional (3D) Drosophila embryonic structure with enhanced accuracy. CONCLUSIONS: Benchmarking results from various ST datasets generated by diverse platforms demonstrate compelling evidence for the effectiveness of SGAE against other ST clustering methods. Specifically, SGAE exhibits potential for extension and application on multislice 3D reconstruction and tissue structure investigation. The source code and a collection of spatial clustering results can be accessed at https://github.com/STOmics/SGAE/.

MetaTrass: A high-quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads.

Metagenomic evidence of great genetic diversity within the nonconserved regions of the human gut microbial genomes appeals for new methods to elucidate the species-level variability at high resolution. However, current approaches cannot satisfy this methodologically challenge. In this study, we proposed an efficient binning-first-and-assembly-later strategy, named MetaTrass, to recover high-quality species-resolved genomes based on public reference genomes and the single-tube long fragment read (stLFR) technology, which enables cobarcoding. MetaTrass can generate genomes with longer contiguity, higher completeness, and lower contamination than those produced by conventional assembly-first-and-binning-later strategies. From a simulation study on a mock microbial community, MetaTrass showed the potential to improve the contiguity of assembly from kb to Mb without accuracy loss, as compared to other methods based on the next-generation sequencing technology. From four human fecal samples, MetaTrass successfully retrieved 178 high-quality genomes, whereas only 58 ones were provided by the optimal performance of other conventional strategies. Most importantly, these high-quality genomes confirmed the high level of genetic diversity among different samples and unveiled much more. MetaTrass was designed to work with metagenomic reads sequenced by stLFR technology, but is also applicable to other types of cobarcoding libraries. With the high capability of assembling high-quality genomes of metagenomic data sets, MetaTrass seeks to facilitate the study of spatial characters and dynamics of complex microbial communities at enhanced resolution. The open-source code of MetaTrass is available at https://github.com/BGI-Qingdao/MetaTrass.