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.

Sequential Separation of Linear, Mono-, and Di-Branched Hexane Isomers on a Robust Coordination Polymer with Nonbonding Flexibility.

Efficient separation of hexane isomers is a crucial process for upgrading gasoline. Herein, the sequential separation of linear, mono-, and di-branched hexane isomers by a robust stacked 1D coordination polymer termed as Mn-dhbq ([Mn(dhbq)(H2 O)2 ], H2 dhbq = 2,5-dihydroxy-1,4-benzoquinone) is reported. The interchain space of the activated polymer is of optimal aperture size (5.58 Å) that could exclude 2,3-dimethylbutane, while the chain structure can discriminate n-hexane with high capacity (1.53 mmol g-1 at 393 K, 6.67 kPa) by high-density open metal sites (5.18 mmol g-1 ). With the temperature- and adsorbate-dependent swelling of interchain spaces, the affinity between 3-methylpentane and Mn-dhbq can be deliberately controlled from sorption to exclusion, and thus a complete separation of ternary mixture can be achieved. Column breakthrough experiments confirm the excellent separation performance of Mn-dhbq. The ultrahigh stability and easy scalability further highlight the application prospect of Mn-dhbq for separation of hexane isomers.

Customizing Metal-Organic Frameworks by Lego-Brick Strategy for One-Step Purification of Ethylene from a Quaternary Gas Mixture.

One-step purification of ethylene (C2 H4 ) from a quaternary gas mixture of C2 H6 /C2 H4 /C2 H2 /CO2 by adsorption is a promising separation process, yet developing adsorbents that synergistically capture various gas impurities remains challenging. Herein, a Lego-brick strategy is proposed to customize pore chemistry in a unified framework material. The ethane-selective MOF platform is further modified with customized binding sites to specifically adsorb acetylene and carbon dioxide, thus one-step purification of C2 H4 with high productivity of polymer-grade product (134 mol kg-1 ) is achieved on the assembly of porous coordination polymer-2,5-furandicarboxylic acid (PCP-FDCA) and PCP-5-aminoisophthalic acid (IPA-NH2 ). Computational studies verify that the low-polarity surface of this MOFs-based platform provides a delicate environment for C2 H6 recognition, and the specific binding sites (FDCA and IPA-NH2 ) exhibit favorable trapping of C2 H2 and CO2 via CHδ+ ···Oδ- and Cδ+ ···Nδ- electrostatic interactions, respectively. The proposed Lego-brick strategy to customize binding sites within the MOFs structure provides new ideas for the design of adsorbents for compounded separation tasks.

Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios.

MOTIVATION: Achieving a near complete understanding of how the genome of an individual affects the phenotypes of that individual requires deciphering the order of variations along homologous chromosomes in species with diploid genomes. However, true diploid assembly of long-range haplotypes remains challenging. RESULTS: To address this, we have developed Haplotype-resolved Assembly for Synthetic long reads using a Trio-binning strategy, or HAST, which uses parental information to classify reads into maternal or paternal. Once sorted, these reads are used to independently de novo assemble the parent-specific haplotypes. We applied HAST to cobarcoded second-generation sequencing data from an Asian individual, resulting in a haplotype assembly covering 94.7% of the reference genome with a scaffold N50 longer than 11 Mb. The high haplotyping precision (∼99.7%) and recall (∼95.9%) represents a substantial improvement over the commonly used tool for assembling cobarcoded reads (Supernova), and is comparable to a trio-binning-based third generation long-read-based assembly method (TrioCanu) but with a significantly higher single-base accuracy [up to 99.99997% (Q65)]. This makes HAST a superior tool for accurate haplotyping and future haplotype-based studies. AVAILABILITY AND IMPLEMENTATION: The code of the analysis is available at https://github.com/BGI-Qingdao/HAST. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Shell-like Xenon Nano-Traps within Angular Anion-Pillared Layered Porous Materials for Boosting Xe/Kr Separation.

Adsorptive separation of xenon (Xe) and krypton (Kr) is a promising technique but remains a daunting challenge since they are atomic gases without dipole or quadruple moments. Herein we report a strategy for fabricating angular anion-pillared materials featuring shell-like Xe nano-traps, which provide a cooperative effect conferred by the pore confinement and multiple specific interactions. The perfect permanent pore channel (4-5 Å) of Ni(4-DPDS)2 MO4 (M=Cr, Mo, W) can host Xe atoms efficiently even at ultra-low concentration (400 ppm Xe), showing the second-highest selectivity of 30.2 in Ni(4-DPDS)2 WO4 and excellent Xe adsorption capacity in Ni(4-DPDS)2 CrO4 (15.0 mmol kg-1 ). Crystallography studies and DFT-D calculations revealed the energy favorable binding sites and angular anions enable the synergism between optimal pore size and polar porosity for boosting Xe affinity. Dynamic breakthrough experiments demonstrated three MOFs as efficient adsorbents for Xe/Kr separation.

Hydrogen-Bonded Metal-Nucleobase Frameworks for Efficient Separation of Xenon and Krypton.

Xe/Kr separation is an industrially important but challenging process owing to their inert properties and low concentrations in the air. Energy-effective adsorption-based separation is a promising technology. Herein, two isostructural hydrogen-bonded metal-nucleobase frameworks (HOF-ZJU-201 and HOF-ZJU-202) are capable of separating Xe/Kr under ambient conditions and strike an excellent balance between capacity and selectivity. The Xe capacity of HOF-ZJU-201a reaches 3.01 mmol g-1 at 298 K and 1.0 bar, while IAST selectivity and Henry's selectivity are 21.0 and 21.6, respectively. Direct breakthrough experiments confirmed the excellent separation performance, affording a Xe capacity of 25.8 mmol kg-1 from a Xe/Kr mixed-gas at dilute concentrations. Density functional theory calculations revealed that the selective binding arises from the enhanced polarization in the confined electric field produced by the electron-rich anions and the electron-deficient purine heterocyclic rings.

SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme.

BACKGROUND: Synthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone scaffolder with high efficiency is warranted for hybrid genome assembly. RESULTS: In this work, we developed a standalone scaffolding tool, SLR-superscaffolder, to link together contigs in draft assemblies using co-barcoding and paired-end read information. Our top-to-bottom scheme first builds a global scaffold graph based on Jaccard Similarity to determine the order and orientation of contigs, and then locally improves the scaffolds with the aid of paired-end information. We also exploited a screening algorithm to reduce the negative effect of misassembled contigs in the input assembly. We applied SLR-superscaffolder to a human single tube long fragment read sequencing dataset and increased the scaffold NG50 of its corresponding draft assembly 1349 fold. Moreover, benchmarking on different input contigs showed that this approach overall outperformed existing SLR scaffolders, providing longer contiguity and fewer misassemblies, especially for short contigs assembled by next-generation sequencing data. The open-source code of SLR-superscaffolder is available at https://github.com/BGI-Qingdao/SLR-superscaffolder . CONCLUSIONS: SLR-superscaffolder can dramatically improve the contiguity of a draft assembly by integrating a hybrid assembly strategy.

Deep Desulfurization with Record SO2 Adsorption on the Metal-Organic Frameworks.

Selective elimination of sulfur dioxide is significant in flue gas desulfurization and natural gas purification, yet developing adsorbents with high capture capacity especially at low partial pressure as well as excellent cycling stability remains a challenge. Herein, a family of isostructural gallate-based MOFs with abundant hydrogen bond donors decorating the pore channel was reported for selective recognition and dense packing of sulfur dioxide via multiple hydrogen bonding interactions. Multiple O···H-O hydrogen bonds and O···H-C hydrogen bonds guarantee SO2 molecules are firmly grasped within the framework, and appropriate pore apertures afford dense packing of SO2 with high uptake and density up to 1.86 g cm-3, which is evidenced by dispersion-corrected density functional theory calculations and X-ray diffraction resolution of a SO2-loaded single crystal. Ultrahigh adsorption uptake of SO2 at extremely low pressure (0.002 bar) was achieved on Co-gallate (6.13 mmol cm-3), outperforming all reported state-of-the-art MOFs. Record-high IAST selectivity of SO2/CO2 (325 for Mg-gallate) and ultrahigh selectivity of SO2/N2 (>1.0 × 104) and SO2/CH4 (>1.0 × 104) were also realized. Breakthrough experiments further demonstrate the excellent removal performance of trace amounts of SO2 in a deep desulfurization process. More importantly, M-gallate shows almost unchanged breakthrough performance after five cycles, indicating the robust cycling stability of these MOFs.

A Robust Squarate-Based Metal-Organic Framework Demonstrates Record-High Affinity and Selectivity for Xenon over Krypton.

The efficient separation of xenon (Xe) and krypton (Kr) is one of the industrially important processes. While adsorptive separation of these two species is considered to be an energy efficient process, developing highly selective adsorbent remains challenging. Herein, a rigid squarate-based metal-organic framework (MOF), having a perfect pore size (4.1 Å × 4.3 Å) comparable with the kinetic diameter of Xe (4.047 Å) as well as pore surface decorated with very polar hydroxyl groups, is able to effectively discriminate Xe atoms, affording a record-high Xe/Kr selectivity. An exceptionally high Xe uptake capacity of 58.4 cm3/cm3 and selectivity of 60.6 at low pressure (0.2 bar) are achieved at ambient temperature. The MOF exhibits the highest Xe Henry coefficient (192.1 mmol/g/bar) and Xe/Kr Henry selectivity (54.1) among all state-of-the-art adsorbents reported so far. Direct breakthrough experiments further confirm the excellent separation performance. The density functional theory calculations reveal that the strong interaction between Xe and the framework is a result of the synergy between optimal pore size and polar porosity.

Adsorptive Separation of Acetylene from Ethylene in Isostructural Gallate-Based Metal-Organic Frameworks.

The separation of acetylene from ethylene is of paramount importance in the purification of chemical feedstocks for industrial manufacturing. Herein, an isostructural series of gallate-based metal-organic frameworks (MOFs), M-gallate (M=Ni, Mg, Co), featuring three-dimensionally interconnected zigzag channels, the aperture size of which can be finely tuned within 0.3 Šby metal replacement. Controlling the aperture size of M-gallate materials slightly from 3.69 down to 3.47 Šcould result in a dramatic enhancement of C2 H2 /C2 H4 separation performance. As the smallest radius among the studied metal ions, Ni-gallate exhibits the best C2 H2 /C2 H4 adsorption separation performance owing to the strongest confinement effect, ranking after the state-of-the-art UTSA-200a with a C2 H4 productivity of 85.6 mol L-1 from 1:99 C2 H2 /C2 H4 mixture. The isostructural gallate-based MOFs, readily synthesized from inexpensive gallic acid, are demonstrated to be a new top-performing porous material for highly efficient adsorption of C2 H2 from C2 H4 .

In vitro assessment of the multifunctional bioactive potential of Alaska pollock skin collagen following simulated gastrointestinal digestion.

BACKGROUND: Dietary mineral deficiency, hypertension and diabetes have become serious human health problems. Dietary approaches are increasingly being investigated to address these issues. Identification of food-derived biological peptides has become an important approach to control such diseases. Peptides generated from aquatic byproducts have been shown to possess biological activities. RESULTS: Significantly higher copper-chelating activity was observed on simulated hydrolysis of intact collagen. The collagen hydrolysate generated in the gastric stage exhibited moderate angiotensin-converting enzyme (ACE)-inhibitory activity with an IC50 value of 2.92 ± 0.22 mg mL(-1), which significantly decreased to 0.49 ± 0.02 mg mL(-1) after intestinal digestion. The dipeptidyl peptidase (DPP) IV-inhibitory potency of the collagen hydrolysate generated directly following simulated gastrointestinal digestion (SGID) (IC50 2.59 ± 0.04 mg mL(-1)) was significantly lower than that of the collagen tryptic hydrolysate (CTH) (IC50 1.53 ± 0.01 mg mL(-1)). The antioxidant activities of collagen and CTH using the ferric-reducing antioxidant power (FRAP) assay were 0.87 ± 0.10 and 1.27 ± 0.03 µmol Trolox equivalent (TE) g(-1) respectively after SGID. CONCLUSION: This study identifies collagen as a good and inexpensive substrate for the generation of biologically active peptides with potential applications as functional ingredients in the management of chronic illness and mineral deficiency problems.

Insight into oil-water interfacial adsorption of protein particles towards regulating Pickering emulsions: A review.

Over the past decade, Pickering emulsions (PEs) stabilized by protein particles have been the focus of researches. The characteristics of protein particles at the oil-water interface are crucial for stabilizing PEs. The unique adsorption behaviors of protein particles and various modification methods enable oil-water interface to exhibit controllable regulation strategies. However, from the perspective of the interface, studies on the regulation of PEs by the adsorption behaviors of protein particles at oil-water interface are limited. Therefore, this review provides an in-depth study on oil-water interfacial adsorption of protein particles and their regulation on PEs. Specifically, the formation of interfacial layer and effects of their interfacial characteristics on PEs stabilized by protein particles are elaborated. Particularly, complicated behaviors, including adsorption, arrangement and deformation of protein particles at the oil-water interface are the premise of affecting the formation of interfacial layer. Moreover, the particle size, surface charge, shape and wettability greatly affect interfacial adsorption behaviors of protein particles. Importantly, stabilities of protein particles-based PEs also depend on properties of interfacial layers, including interfacial layer thickness and interfacial rheology. This review provides useful insights for the development of PEs stabilized by protein particles based on interfacial design.

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.

Supramolecular Assembly of One-Dimensional Coordination Polymers for Efficient Separation of Xenon and Krypton.

Efficient separation and purification of xenon (Xe) from krypton (Kr) represent an industrially crucial but challenging process. While the adsorption-based separation of these atomic gases represents an energy-efficient process, achieving highly selective adsorbents remains a difficult task. Here, we demonstrate a supramolecular assembly of coordination polymers, termed as M(II)-dhbq (M = Mg, Mn, Co, and Zn; dhbq = 2,5-dihydroxy-1,4-benzoquinone), with high-density open metal sites (5.3 nm-3) and optimal pore size (5.5 Å), which are able to selectively capture Xe among other chemically inert gases including Kr, Ar, N2, and O2. Among M(II)-dhbq materials, Mn-dhbq exhibits the highest Xe uptake capacity of 3.1 mmol/g and a Xe/Kr selectivity of 11.2 at 298 K and 1.0 bar, outperforming many state-of-the-art adsorbents reported so far. Remarkably, the adsorption selectivity of Mn-dhbq for Xe/O2, Xe/N2, and Xe/Ar at ambient conditions reaches as high as 70.0, 139.3, and 64.0, respectively. Direct breakthrough experiments further confirm that all M(II)-dhbq materials can efficiently discriminate Xe atoms from other inert gases. It is revealed from the density functional theory calculations that the strong affinity between Xe and the coordination polymer is mainly attributed to the polarization by open metal sites.

VT3D: a visualization toolbox for 3D transcriptomic data.

Data visualization empowers researchers to communicate their results that support scientific reasoning in an intuitive way. Three-dimension (3D) spatially resolved transcriptomic atlases constructed from multi-view and high-dimensional data have rapidly emerged as a powerful tool to unravel spatial gene expression patterns and cell type distribution in biological samples, revolutionizing the understanding of gene regulatory interactions and cell niches. However, limited accessible tools for data visualization impede the potential impact and application of this technology. Here we introduce VT3D, a visualization toolbox that allows users to explore 3D transcriptomic data, enabling gene expression projection to any 2D plane of interest, 2D virtual slice creation and visualization, and interactive 3D data browsing with surface model plots. In addition, it can either work on personal devices in standalone mode or be hosted as a web-based server. We apply VT3D to multiple datasets produced by the most popular techniques, including both sequencing-based approaches (Stereo-seq, spatial transcriptomics, and Slide-seq) and imaging-based approaches (MERFISH and STARMap), and successfully build a 3D atlas database that allows interactive data browsing. We demonstrate that VT3D bridges the gap between researchers and spatially resolved transcriptomics, thus accelerating related studies such as embryogenesis and organogenesis processes. The source code of VT3D is available at https://github.com/BGI-Qingdao/VT3D, and the modeled atlas database is available at http://www.bgiocean.com/vt3d_example.

Visible-Light-Induced Phenoxyl Radical-based Metal-Organic Framework for Selective Photooxidation of Sulfides.

Phenoxyl radicals originating from phenols through oxidation or photoinduction are relatively stable and exhibit mild oxidative activity, which endows them with the potential for photocatalysis. Herein, a stable and recyclable metal-organic framework Zr-MOF-OH constructed of a binaphthol derivative ligand has been synthesized and functions as an efficient heterogeneous photocatalyst. Zr-MOF-OH shows fairly good catalytic activity and substrate compatibility toward the selective oxidation of sulfides to sulfoxides under visible light irradiation. Such irradiation of Zr-MOF-OH converts the phenolic hydroxyl groups of the binaphthol derivative ligand to phenoxyl radicals through excited state intramolecular proton transfer, and the excited state photocatalyst triggers the single-electron oxidation of the sulfide. No reactive oxygen species are produced in the photocatalytic process, and triplet O2 directly participates in the reaction, endowing Zr-MOF-OH with wide substrate compatibility and high selectivity, which also proposes a promising pathway for the direct activation of substrates via phenoxyl radicals.

The complete and fully-phased diploid genome of a male Han Chinese.

Since the release of the complete human genome, the priority of human genomic study has now been shifting towards closing gaps in ethnic diversity. Here, we present a fully phased and well-annotated diploid human genome from a Han Chinese male individual (CN1), in which the assemblies of both haploids achieve the telomere-to-telomere (T2T) level. Comparison of this diploid genome with the CHM13 haploid T2T genome revealed significant variations in the centromere. Outside the centromere, we discovered 11,413 structural variations, including numerous novel ones. We also detected thousands of CN1 alleles that have accumulated high substitution rates and a few that have been under positive selection in the East Asian population. Further, we found that CN1 outperforms CHM13 as a reference genome in mapping and variant calling for the East Asian population owing to the distinct structural variants of the two references. Comparison of SNP calling for a large cohort of 8869 Chinese genomes using CN1 and CHM13 as reference respectively showed that the reference bias profoundly impacts rare SNP calling, with nearly 2 million rare SNPs miss-called with different reference genomes. Finally, applying the CN1 as a reference, we discovered 5.80 Mb and 4.21 Mb putative introgression sequences from Neanderthal and Denisovan, respectively, including many East Asian specific ones undetected using CHM13 as the reference. Our analyses reveal the advances of using CN1 as a reference for population genomic studies and paleo-genomic studies. This complete genome will serve as an alternative reference for future genomic studies on the East Asian population.

New insights into immunomodulatory properties of lactic acid bacteria fermented herbal medicines.

The COVID-19 pandemic has brought more attention to the immune system, the body's defense against infectious diseases. The immunomodulatory ability of traditional herbal medicine has been confirmed through clinical trial research, and has obvious advantages over prescription drugs due to its high number of potential targets and low toxicity. The active compounds of herbal drugs primarily include polysaccharides, saponins, flavonoids, and phenolics and can be modified to produce new active compounds after lactic acid bacteria (LAB) fermentation. LAB, primary source of probiotics, can produce additional immunomodulatory metabolites such as exopolysaccharides, short-chain fatty acids, and bacteriocins. Moreover, several compounds from herbal medicines can promote the growth and production of LAB-based immune active metabolites. Thus, LAB-mediated fermentation of herbal medicines has become a novel strategy for regulating human immune responses. The current review discusses the immunomodulatory properties and active compounds of LAB fermented herbal drugs, the interaction between LAB and herbal medicines, and changes in immunoregulatory components that occur during fermentation. This study also discusses the mechanisms by which LAB-fermented herbal medicines regulate the immune response, including activation of the innate or adaptive immune system and the maintenance of intestinal immune homeostasis.

Integrating Metabolomics and Network Pharmacology to Explore the Protective Effect of Ginsenoside Re against Radiotherapy Injury in Mice.

Ionizing radiation (IR) can cause radiation damage, mutagenesis, or carcinogenesis in the irradiated subject. It is manifested as metabolic disorders of the body and damage to the immune system, nervous system, and endocrine system, which can lead to physiological and pathological changes and endogenous metabolic disorders. Ginsenoside Re (G-Re), a single component of traditional Chinese medicine, has a certain ameliorating effect on radiation damage. However, its mechanism of action in the treatment of radiotherapy injury remains unclear. With this purpose, the hematopoietic function of mice damaged by X-ray radiation was studied, and the protective effect of G-Re on mice damaged by radiation was preliminarily evaluated. Network pharmacology and metabolomics analysis are used to further reveal the mechanism of G-Re to improve radiation damage through metabolomics research. Results of metabolomics analysis showed that 16 potential biomarkers were identified as participating in the therapeutic effect of G-Re on IR. Most of these metabolites are adjusted to recover after G-Re treatment. The pathways involved included glycerophospholipid metabolism, sphingolipid metabolism, and linoleic acid metabolism. According to network pharmacology analysis, we found 10 hub genes, which is partly consistent with the findings of metabolomics. Further comprehensive analysis focused on 4 key targets, including SRC, EGFR, AKT1, and MAPK8, and their related core metabolites and pathways. This study combines metabolomics and network pharmacology analysis to explore the key targets and mechanisms of G-Re in the treatment of IR, in order to provide new strategies for clinical treatment of radiotherapy injury.

Discrimination of xylene isomers in a stacked coordination polymer.

The separation and purification of xylene isomers is an industrially important but challenging process. Developing highly efficient adsorbents is crucial for the implementation of simulated moving bed technology for industrial separation of these isomers. Herein, we report a stacked one-dimensional coordination polymer {[Mn(dhbq)(H2O)2], H2dhbq = 2,5-dihydroxy-1,4-benzoquinone} that exhibits an ideal molecular recognition and sieving of xylene isomers. Its distinct temperature-adsorbate-dependent adsorption behavior enables full separation of p-, m-, and o-xylene isomers in both vapor and liquid phases. The delicate stimuli-responsive swelling of the structure imparts this porous material with exceptionally high flexibility and stability, well-balanced adsorption capacity, high selectivity, and fast kinetics at conditions mimicking industrial settings. This study may offer an alternative approach for energy-efficient and adsorption-based industrial xylene separation and purification processes.