Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives.

The extinction risk of the giant panda has been demoted from "endangered" to "vulnerable" on the International Union for Conservation of Nature Red List, but its habitat is more fragmented than ever before, resulting in 33 isolated giant panda populations according to the fourth national survey released by the Chinese government. Further comprehensive investigations of the genetic background and in-depth assessments of the conservation status of wild populations are still necessary and urgently needed. Here, we sequenced the genomes of 612 giant pandas with an average depth of ~26× and generated a high-resolution map of genomic variation with more than 20 million variants covering wild individuals from six mountain ranges and captive representatives in China. We identified distinct genetic clusters within the Minshan population by performing a fine-grained genetic structure. The estimation of inbreeding and genetic load associated with historical population dynamics suggested that future conservation efforts should pay special attention to the Qinling and Liangshan populations. Releasing captive individuals with a genetic background similar to the recipient population appears to be an advantageous genetic rescue strategy for recovering the wild giant panda populations, as this approach introduces fewer deleterious mutations into the wild population than mating with differentiated lineages. These findings emphasize the superiority of large-scale population genomics to provide precise guidelines for future conservation of the giant panda.

MACC1 enhances an oncogenic RNA splicing of IRAK1 through interacting with HNRNPH1 in lung adenocarcinoma.

Dysregulation of alternative pre-mRNA splicing plays a critical role in the progression of cancers, yet the underlying molecular mechanisms remain largely unknown. It is reported that metastasis-associated in colon cancer 1 (MACC1) is a novel prognostic and predictive marker in many types of cancers, including lung adenocarcinoma. Here, we reveal that the oncogene MACC1 specifically drives the progression of lung adenocarcinoma through its control over cancer-related splicing events. MACC1 depletion inhibits lung adenocarcinoma progression through triggering IRAK1 from its long isoform, IRAK1-L, to the shorter isoform, IRAK1-S. Mechanistically, MACC1 interacts with splicing factor HNRNPH1 to prevent the production of the short isoform of IRAK1 mRNA. Specifically, the interaction between MACC1 and HNRNPH1 relies on the involvement of MACC1's SH3 domain and HNRNPH1's GYR domain. Further, HNRNPH1 can interact with the pre-mRNA segment (comprising exon 11) of IRAK1, thereby bridging MACC1's regulation of IRAK1 splicing. Our research not only sheds light on the abnormal splicing regulation in cancer but also uncovers a hitherto unknown function of MACC1 in tumor progression, thereby presenting a novel potential therapeutic target for clinical treatment.

Genome-wide identification and analysis of abiotic stress responsiveness of the mitogen-activated protein kinase gene family in Medicago sativa L.

BACKGROUND: The mitogen-activated protein kinase (MAPK) cascade is crucial cell signal transduction mechanism that plays an important role in plant growth and development, metabolism, and stress responses. The MAPK cascade includes three protein kinases, MAPK, MAPKK, and MAPKKK. The three protein kinases mediate signaling to downstream response molecules by sequential phosphorylation. The MAPK gene family has been identified and analyzed in many plants, however it has not been investigated in alfalfa. RESULTS: In this study, Medicago sativa MAPK genes (referred to as MsMAPKs) were identified in the tetraploid alfalfa genome. Eighty MsMAPKs were divided into four groups, with eight in group A, 21 in group B, 21 in group C and 30 in group D. Analysis of the basic structures of the MsMAPKs revealed presence of a conserved TXY motif. Groups A, B and C contained a TEY motif, while group D contained a TDY motif. RNA-seq analysis revealed tissue-specificity of two MsMAPKs and tissue-wide expression of 35 MsMAPKs. Further analysis identified MsMAPK members responsive to drought, salt, and cold stress conditions. Two MsMAPKs (MsMAPK70 and MsMAPK75) responds to salt and cold stresses; two MsMAPKs (MsMAPK60 and MsMAPK73) responds to cold and drought stresses; four MsMAPKs (MsMAPK1, MsMAPK33, MsMAPK64 and MsMAPK71) responds to salt and drought stresses; and two MsMAPKs (MsMAPK5 and MsMAPK7) responded to all three stresses. CONCLUSION: This study comprehensively identified and analysed the alfalfa MAPK gene family. Candidate genes related to abiotic stresses were screened by analysing the RNA-seq data. The results provide key information for further analysis of alfalfa MAPK gene functions and improvement of stress tolerance.

How do stretch rate, temperature, and solvent exchange affect elastic network rupture?

In this study, we investigate three different polymeric networks in terms of their tensile strength as a function of stretching rate, or temperature, or medium viscosity. Both an acrylate-based elastomer and a crosslinked poly(methyl acrylate) are stronger, more stretchable, and tougher at high rates. They are also much stronger at lower temperatures. Such phenomena systematically suggest that the kinetics of bond dissociation in backbones of those load-bearing strands dictate the rate and temperature dependencies. We apply Eyring's activation idea for chain scission to rationalize the influence of rate and temperature on rupture for both elastomers and hydrogels where hydrogels become much more stretchable and stronger when water is replaced by glycerol.

A convenient broad-host counterselectable system endowing rapid genetic manipulations of Kluyveromyces lactis and other yeast species.

Being generally regarded as safe, Kluyveromyces lactis has been widely taken for food, feed, and pharmaceutical applications, owing to its ability to achieve high levels of protein secretion and hence being suitable for industrial production of heterologous proteins. Production platform strains can be created through genetic engineering; while prototrophic cells without chromosomally accumulated antibiotics resistance genes have been generally preferred, arising the need for dominant counterselection. We report here the establishment of a convenient counterselection system based on a Frs2 variant, Frs2v, which is a mutant of the alpha-subunit of phenylalanyl-tRNA synthase capable of preferentially incorporating a toxic analog of phenylalanine, r-chloro-phenylalanine (4-CP), into proteins to bring about cell growth inhibition. We demonstrated that expression of Frs2v from an episomal plasmid in K. lactis could make the host cells sensitive to 2 mM 4-CP, and a Frs2v-expressing plasmid could be efficiently removed from the cells immediately after a single round of cell culturing in a 4-CP-contianing YPD medium. This Frs2v-based counterselection helped us attain scarless gene replacement in K. lactis without any prior engineering of the host cells. More importantly, counterselection with this system was proven to be functionally efficient also in Saccharomyces cerevisiae and Komagataella phaffii, suggestive of a broader application scope of the system in various yeast hosts. Collectively, this work has developed a strategy to enable rapid, convenient, and high-efficiency construction of prototrophic strains of K. lactis and possibly many other yeast species, and provided an important reference for establishing similar methods in other industrially important eukaryotic microbes.

High-nuclearity Luminescent Lanthanide Nanocages for Tumor Drug Delivery.

There is an unmet need for easy-to-visualize drug carriers that can deliver therapeutic cargoes deep into solid tumors. Herein, we report the preparation of ultrasmall luminescent imine-based lanthanide nanocages, Eu60 and Tb60 (collectively Ln60 ), designed to encapsulate anticancer chemotherapeutics for tumor therapy. The as-prepared nanocages possess large cavities suitable for the encapsulation of doxorubicin (DOX), yielding DOX@Ln60 nanocages with diameters around 5 nm. DOX@Ln60 are efficiently internalized by breast cancer cells, allowing the cells to be visualized via the intrinsic luminescent property of Ln(III). Once internalized, the acidic intracellular microenvironment promotes imine bond cleavage and the release of the loaded DOX. DOX@Ln60 inhibits DNA replication and triggers tumor cell apoptosis. In a murine triple negative breast cancer (TNBC) model, DOX@Ln60 was found to inhibit tumor growth with negligible side effects on normal tissues. It proved more effective than various controls, including DOX and Ln60 . The present nanocages thus point the way to the development of precise nanomedicines for tumor imaging and therapy.

Molecular Dynamics Simulation of Entangled Melts at High Rates: Identifying Entanglement Lockup Mechanism Leading to True Strain Hardening.

In the present work, molecular dynamics simulations are carried out based on the bead-spring model to indicate how the entanglement lockup manifests in the late stage of fast Rouse-Weissnberg number (WiR >>1) uniaxial melt stretching of entangled polymer melts. At high strains, distinct features show up to reveal the emergence of an increasingly tightened entanglement network. Chain tension can build up, peaking at the middle of the chain, to a level for chain scission, through accumulated interchain interactions, as if there is a tug-of-war ongoing for each load-bearing chain. Thanks to the interchain uncrossability, network junctions form by the pairing of two or more hairpins. It is hypothesized that the interchain entanglement at junctions can lockup through prevailing twist-like interchain couplings as long as WiR > 9. In this limit, a significant fraction of chains act like cyclic chains to form a network held by interchain uncrossability, and appreciable chain tension emerges.

Nanoconfined Crystallization in Poly(lactic acid) (PLA) and Poly(ethylene terephthalate) (PET) Induced by Various Forms of Premelt-Deformation.

The processing-structure-property relationship using poly(lactic acid) (PLA) and poly(ethylene terephthalate) (PET) is explored. Specifically, both pre-extension and preshear of amorphous PLA and PET above their glass transition temperatures Tg , carried out in the affine deformation limit, can induce a specific type of cold crystallization during annealing, i.e., nanoconfined crystallization (NCC) where crystal sizes are limited to a nanoscopic scale in all dimensions so as to render the processed PLA and PET optically transparent. The new polymer structure after premelt deformation can show considerably enhanced mechanical properties. For example, premelt stretching produces geometric condensation of the chain network. This structural alternation can profoundly change the mechanical characteristics, e.g., turning brittle PLA ductile. In contrast, after preshear of amorphous PLA above Tg , the NCC containing PLA remains brittle, showing the importance to have geometric condensation from processing. Both AFM imaging and SAXS measurements are performed to verify that premelt deformation of PLA and PET indeed results in NCC from annealing that permits the strain-induced cold crystallization to take place on the length scale of the mesh size of the deformed chain network.

Steerable artificial magnetic bacteria with target delivery ability of calcium carbonate for soil improvement.

The microbial-induced carbonate precipitation (MICP) has acquired significant attention due to its immense potential in sustainable engineering applications, particularly in soil improvement. However, the precise control of microbial-induced calcium carbonate precipitation remains a formidable challenge in engineering practices, owing to the uncertain movement paths of bacteria and the nonuniform distribution of soil pores. Taking inspiration from targeted therapy in medicine, this paper presents novel research on the development and validation of magnetically responsive bacteria. These bacteria demonstrate the ability to target calcium carbonate precipitation in a microfluidic chip, thereby promoting an environmentally friendly and ecologically sustainable biomineralization paradigm. The study focuses on investigating the migration of magnetite nanoparticles (MNPs) in aqueous solutions and enhancing the stability of MNP culture liquids. A specially designed microfluidic chip is utilized to simulate natural sand particles and their pores, while an external magnetic field is applied to precisely control the movement path of the artificial magnetic bacteria, enabling targeted precipitation of calcium carbonate at the micron-scale. Verification of the engineered artificial magnetic bacteria and their ability to induce calcium carbonate precipitation is conducted through SEM-EDS analysis, microfluidic chip observations, and the application of the K-means algorithm and ImageJ software to analyze calcium carbonate formation. The influence of the concentration of magnetic nanoparticles on the calcium carbonate production rate was also studied. The results confirm the potential of the artificial magnetic bacteria for future engineering applications. KEY POINTS: • Sporosarcina pasteurii is first time successfully engineered into artificial magnetic bacteria. • The artificial magnetic bacteria show excellent performance of targeted transportation and directional deposition of CaCO3 in microfluidic chip. • The emergence of artificial magnetic bacteria promotes paradigm shift of next generation environmentally friendly biomineralization.

SiamPKHT: Hyperspectral Siamese Tracking Based on Pyramid Shuffle Attention and Knowledge Distillation.

Hyperspectral images provide a wealth of spectral and spatial information, offering significant advantages for the purpose of tracking objects. However, Siamese trackers are unable to fully exploit spectral features due to the limited number of hyperspectral videos. The high-dimensional nature of hyperspectral images complicates the model training process. In order to address the aforementioned issues, this article proposes a hyperspectral object tracking (HOT) algorithm callled SiamPKHT, which leverages the SiamCAR model by incorporating pyramid shuffle attention (PSA) and knowledge distillation (KD). First, the PSA module employs pyramid convolutions to extract multiscale features. In addition, shuffle attention is adopted to capture relationships between different channels and spatial positions, thereby obtaining good features with a stronger classification performance. Second, KD is introduced under the guidance of a pre-trained RGB tracking model, which deals with the problem of overfitting in HOT. Experiments using HOT2022 data indicate that the designed SiamPKHT achieves better performance compared to the baseline method (SiamCAR) and other state-of-the-art HOT algorithms. It also achieves real-time requirements at 43 frames per second.

Characterization of the Heat Shock Transcription Factor Family in Medicago sativa L. and Its Potential Roles in Response to Abiotic Stresses.

Heat shock transcription factors (HSFs) are important regulatory factors in plant stress responses to various biotic and abiotic stresses and play important roles in growth and development. The HSF gene family has been systematically identified and analyzed in many plants but it is not in the tetraploid alfalfa genome. We detected 104 HSF genes (MsHSFs) in the tetraploid alfalfa genome ("Xinjiangdaye" reference genome) and classified them into three subgroups: 68 in HSFA, 35 in HSFB and 1 in HSFC subgroups. Basic bioinformatics analysis, including genome location, protein sequence length, protein molecular weight and conserved motif identification, was conducted. Gene expression analysis revealed tissue-specific expression for 13 MsHSFs and tissue-wide expression for 28 MsHSFs. Based on transcriptomic data analysis, 21, 11 and 27 MsHSFs responded to drought stress, cold stress and salt stress, respectively, with seven responding to all three. According to RT-PCR, MsHSF27/33 expression gradually increased with cold, salt and drought stress condition duration; MsHSF6 expression increased over time under salt and drought stress conditions but decreased under cold stress. Our results provide key information for further functional analysis of MsHSFs and for genetic improvement of stress resistance in alfalfa.

Coordination Polymers with 2,2':6',2″-Terpyridine Earth-Abundant Metal Complex Units for Selective CO2 Photoreduction.

Combining molecular metal complexes into coordination polymers (CPs) is an effective strategy for developing photocatalysts for CO2 reduction; however, most such reported catalysts are noble metal-containing CPs. Herein, two novel Zr-containing bimetallic CPs, Co-Zr and Ni-Zr, were designed and successfully synthesized by connecting 2,2':6',2″-terpyridine-based molecular earth-abundant metal (Co or Ni) complexes with ZrO8 nodes. Both CPs were applied as catalysts for CO2 photoreduction to selectively produce CO. The catalytic performance of Co-Zr is better than that of Ni-Zr with a yield of 3654 µmol (g of catalyst)-1 for CO in 6 h (TON = 18.2). The difference between these two catalysts was analyzed with respect to band structure and charge migration ability. This work provides an effective way to introduce molecular earth-abundant metal complexes into coordination polymers for the construction of efficient noble metal-free CO2 photocatalysts.

Crystal transformation and self-assembly theory of microbially induced calcium carbonate precipitation.

Microbially induced calcium carbonate precipitation (MICP) is ubiquitous in the earth's lithosphere and brings the inspiration of bionic cementation technology. Over recent years, MICP has been proposed as a potential solution to address many environmental and engineering issues. However, the stability of cemented precipitations generated via MICP technology, especially the characteristics and change mechanism of crystal forms, is still unclear, which substantially hindered the understanding of biomineralization and prohibited the application and upscaling of MICP technology. Here, Sporosarcina pasteurii was selected as a model microbe to induce calcium carbonate mineralization in a series of standard nutrient solutions. The authors studied the process of precipitation from amorphous calcium carbonate to calcite crystal form and revealed the assembly behavior and mechanism of precipitations by FTIR, SEM, TEM and EDS. In the two crystal forms of induced calcium carbonate, the relative position and content of C, O, N, P and Ca elements were only slightly different. The molecular attachment and structural match of organic matrix made the crystals form change. Finally, a self-assembly theory was proposed to MICP, and it provided a solid theoretical basis for the technical specification of MICP technology in engineering application. KEY POINTS: • Organic matrix is intensively involved in MICP by forming functional groups. • Molecular attachment and structural match cause calcite crystal evolution. • A self-assembly theory is proposed for MICP.

Multiomics analysis reveals the presence of a microbiome in the gut of fetal lambs.

OBJECTIVE: Microbial exposure is critical to neonatal and infant development, growth and immunity. However, whether a microbiome is present in the fetal gut prior to birth remains debated. In this study, lambs delivered by aseptic hysterectomy at full term were used as an animal model to investigate the presence of a microbiome in the prenatal gut using a multiomics approach. DESIGN: Lambs were euthanised immediately after aseptic caesarean section and their cecal content and umbilical cord blood samples were aseptically acquired. Cecal content samples were assessed using metagenomic and metatranscriptomic sequencing to characterise any existing microbiome. Both sample types were analysed using metabolomics in order to detect microbial metabolites. RESULTS: We detected a low-diversity and low-biomass microbiome in the prenatal fetal gut, which was mainly composed of bacteria belonging to the phyla Proteobacteria, Actinobacteria and Firmicutes. Escherichia coli was the most abundant species in the prenatal fetal gut. We also detected multiple microbial metabolites including short chain fatty acids, deoxynojirimycin, mitomycin and tobramycin, further indicating the presence of metabolically active microbiota. Additionally, bacteriophage phiX174 and Orf virus, as well as antibiotic resistance genes, were detected in the fetal gut, suggesting that bacteriophage, viruses and bacteria carrying antibiotic resistance genes can be transmitted from the mother to the fetus during the gestation period. CONCLUSIONS: This study provides strong evidence that the prenatal gut harbours a microbiome and that microbial colonisation of the fetal gut commences in utero.

Inducing nano-confined crystallization in PLLA and PET by elastic melt stretching.

Based on the widely studied poly(l-lactic acid) (PLLA) and polyethylene terephthalate (PET) that are brittle in their fully crystalline form, this Letter shows that they can be made to be super ductile, heat resistant and optically clear by creating nano-sized crystals while preserving the entanglement network. Atomic force microscopic images confirm the perceived nano-confined crystallization. Time-resolved X-ray scattering/diffraction measurements reveal the emergence of cold crystallization during either stress relaxation from large stepwise melt-stretching or annealing of pre-melt-stretched PLLA and PET above Tg. Mechanical tests show that these polymers in such a new state are rigid even well above Tg, e.g., at 100 °C.

Uncommon nonlinear rheological phenomenology in uniaxial extension of polystyrene solutions and melts.

This study examines nonlinear rheological responses to uniaxial extension of two entangled polystyrene (PS) solutions and two PS melts. Several unusual characteristics are revealed. The pair of the PS solutions have the same number of entanglements per chain (because of the same concentration) but well separated effective glass transition temperatures Tg. When examined at a common effective rate of extension (e.g., the same Rouse-Weissenberg number WiR) and at a comparable distance from their respective Tg, the solution A with lower Tg, examined at a lower temperature, shows stronger stress responses when WiR > 1. At the same test temperature and a common WiR, the solution A is still found to display a stronger stress response than the solution B that is made of the same fraction of parent PS in a second solvent also made of oligomeric PS of higher molecular weight. Finally, there are two features intrinsic to each of the four PS samples. First, at the same WiR they show reduced stress level at a lower temperature. Second, at sufficiently high applied Hencky rates, they show limiting rate behavior, i.e., undergoing the same melt rupture independent of the applied rate. These remarkable rheological responses indicate major theoretical difficulties facing the subject of nonlinear extensional rheology of entangled polymers.

Association of sleep duration with stroke, myocardial infarction, and tumors in a Chinese population with metabolic syndrome: a retrospective study.

BACKGROUND: Previous studies have suggested that abnormal sleep duration is associated with increased risk of metabolic syndrome (MetS). However, evidence on the association of sleep duration with stroke, myocardial infarction (MI) and tumors in populations with MetS is limited. METHODS: A total of 8968 participants (2754 with MetS at baseline) were recruited in this retrospective study between March 2012 and December 2012. The baseline characteristics and information on sleep duration were collected by self-reported questionnaires. In addition, physical examination and blood test were also performed. The outcome events in this study were new onset of stroke, MI and tumors during subsequent follow-up. Multivariate logistic regressions were adopted to investigate the relationships between sleep duration and outcome events among different sleep duration groups (< 6 h, 6-7 h, 7-8 h [reference], 8-9 h, and > 9 h per day) in participants with MetS. RESULTS: The mean self-reported total sleep duration was 7.8 ± 1.2 h. Compared with participants with MetS slept for 7-8 h per day, the adjusted odds ratios (ORs) for those slept for > 9 h in stroke, MI and tumors were 2.014 (95% confidence interval [CI]: 1.184-3.426, P = 0.010), 1.731 (95% CI: 0.896-3.344, P = 0.102) and 2.159 (95% CI: 0.991-4.704, P = 0.053), respectively, whereas the adjusted ORs for those slept for < 6 h in stroke, MI and tumors were 2.249 (95% CI: 0.973-5.195, P = 0.058), 1.213 (95% CI, 0.358-4.104, P = 0.756) and 1.743 (95% CI, 0.396-7.668, P = 0.462), respectively. CONCLUSIONS: Long sleep duration (> 9 h) significantly increased the risk of stroke but not MI and tumors in individuals with MetS compared with 7-8 h of sleep duration. Short sleep duration (< 6 h) was not associated with the increased risk of stroke, MI and tumors in individuals with MetS.

Characterizing effects of fast melt deformation on entangled polymers in their glassy state.

Fast deformation of entangled melts is known to cause chain stretching due to affinelike straining of the entanglement network. Since the chain deformation may also result in perturbations of covalent bond angles and bond length, there are always possible enthalpic effects. In this study, we first subject polystyrene and PMMA of different molecular weights to either uniaxial melt extension or planar extension and subsequently impose rapid thermal quenching to preserve the chain deformation. Then, such pre-melt-deformed samples are annealed at various temperatures below the glass transition temperature Tg. During annealing, these samples can undergo appreciable contraction on a time scale much shorter than the alpha relaxation time. Significant retractive stress is observed when such contracting samples are held fixed during the annealing. The stress level can be nearly as high as the Cauchy stress produced during melt stretching. These observations not only allowed us to investigate glassy chain dynamics as well as the molecular nature of mechanical stress but may also suggest that pre-melt-stretched polymers can cause segmental mobilization in the glassy state. The available evidence indicates that the retractive stress is enthalpic in origin, associated with the conformational distortion at the bond level produced by melt stretching.

Inability to activate Rac1-dependent forgetting contributes to behavioral inflexibility in mutants of multiple autism-risk genes.

The etiology of autism is so complicated because it involves the effects of variants of several hundred risk genes along with the contribution of environmental factors. Therefore, it has been challenging to identify the causal paths that lead to the core autistic symptoms such as social deficit, repetitive behaviors, and behavioral inflexibility. As an alternative approach, extensive efforts have been devoted to identifying the convergence of the targets and functions of the autism-risk genes to facilitate mapping out causal paths. In this study, we used a reversal-learning task to measure behavioral flexibility in Drosophila and determined the effects of loss-of-function mutations in multiple autism-risk gene homologs in flies. Mutations of five autism-risk genes with diversified molecular functions all led to a similar phenotype of behavioral inflexibility indicated by impaired reversal-learning. These reversal-learning defects resulted from the inability to forget or rather, specifically, to activate Rac1 (Ras-related C3 botulinum toxin substrate 1)-dependent forgetting. Thus, behavior-evoked activation of Rac1-dependent forgetting has a converging function for autism-risk genes.

Illustrating the Molecular Origin of Mechanical Stress in Ductile Deformation of Polymer Glasses.

New experiments show that tensile stress vanishes shortly after preyield deformation of polymer glasses while tensile stress after postyield deformation stays high and relaxes on much longer time scales, thus hinting at a specific molecular origin of stress in ductile cold drawing: chain tension rather than intersegmental interactions. Molecular dynamics simulation based on a coarse-grained model for polystyrene confirms the conclusion that the chain network plays an essential role, causing the glassy state to yield and to respond with a high level of intrachain retractive stress. This identification sheds light on the future development regarding an improved theoretical account for molecular mechanics of polymer glasses and the molecular design of stronger polymeric materials to enhance their mechanical performance.