Function of mast cell and bile-cholangiocarcinoma interplay in cholangiocarcinoma microenvironment.

OBJECTIVE: The correlation between cholangiocarcinoma (CCA) progression and bile is rarely studied. Here, we aimed to identify differential metabolites in benign and malignant bile ducts and elucidate the generation, function and degradation of bile metabolites. DESIGN: Differential metabolites in the bile from CCA and benign biliary stenosis were identified by metabonomics. Biliary molecules able to induce mast cell (MC) degranulation were revealed by in vitro and in vivo experiments, including liquid chromatography-mass spectrometry (MS)/MS and bioluminescence resonance energy transfer assays. Histamine (HA) receptor expression in CCA was mapped using a single-cell mRNA sequence. HA receptor functions were elucidated by patient-derived xenografts (PDX) in humanised mice and orthotopic models in MC-deficient mice. Genes involved in HA-induced proliferation were screened by CRISPR/Cas9. RESULTS: Bile HA was elevated in CCA and indicated poorer prognoses. Cancer-associated fibroblasts (CAFs)-derived stem cell factor (SCF) recruited MCs, and bile N,N-dimethyl-1,4-phenylenediamine (DMPD) stimulated MCs to release HA through G protein-coupled receptor subtype 2 (MRGPRX2)-Gαq signalling. Bile-induced MCs released platelet-derived growth factor subunit B (PDGF-B) and angiopoietin 1/2 (ANGPT1/2), which enhanced CCA angiogenesis and lymphangiogenesis. Histamine receptor H1 (HRH1) and HRH2 were predominantly expressed in CCA cells and CAFs, respectively. HA promoted CCA cell proliferation by activating HRH1-Gαq signalling and hastened CAFs to secrete hepatocyte growth factor by stimulating HRH2-Gαs signalling. Solute carrier family 22 member 3 (SLC22A3) inhibited HA-induced CCA proliferation by importing bile HA into cells for degradation, and SLC22A3 deletion resulted in HA accumulation. CONCLUSION: Bile HA is released from MCs through DMPD stimulation and degraded via SLC22A3 import. Different HA receptors exhibit a distinct expression profile in CCA and produce different oncogenic effects. MCs promote CCA progression in a CCA-bile interplay pattern.

Polydopamine-assisted aptamer-carrying tetrahedral DNA microelectrode sensor for ultrasensitive electrochemical detection of exosomes.

BACKGROUND: Exosomes are nanoscale extracellular vesicles (30-160 nm) with endosome origin secreted by almost all types of cells, which are considered to be messengers of intercellular communication. Cancerous exosomes serve as a rich source of biomarkers for monitoring changes in cancer-related physiological status, because they carry a large number of biological macromolecules derived from parental tumors. The ultrasensitive quantification of trace amounts of cancerous exosomes is highly valuable for non-invasive early cancer diagnosis, yet it remains challenging. Herein, we developed an aptamer-carrying tetrahedral DNA (Apt-TDNA) microelectrode sensor, assisted by a polydopamine (PDA) coating with semiconducting properties, for the ultrasensitive electrochemical detection of cancer-derived exosomes. RESULTS: The stable rigid structure and orientation of Apt-TDNA ensured efficient capture of suspended exosomes. Without PDA coating signal amplification strategy, the sensor has a linear working range of 102-107 particles mL-1, with LOD of ~ 69 exosomes and ~ 42 exosomes for EIS and DPV, respectively. With PDA coating, the electrochemical signal of the microelectrode is further amplified, achieving single particle level sensitivity (~ 14 exosomes by EIS and ~ 6 exosomes by DPV). CONCLUSIONS: The proposed PDA-assisted Apt-TDNA microelectrode sensor, which integrates efficient exosome capture, sensitive electrochemical signal feedback with PDA coating signal amplification, provides a new avenue for the development of simple and sensitive electrochemical sensing techniques in non-invasive cancer diagnosis and monitoring treatment response.

Kinome-Wide Virtual Screening by Multi-Task Deep Learning.

Deep learning is a machine learning technique to model high-level abstractions in data by utilizing a graph composed of multiple processing layers that experience various linear and non-linear transformations. This technique has been shown to perform well for applications in drug discovery, utilizing structural features of small molecules to predict activity. Here, we report a large-scale study to predict the activity of small molecules across the human kinome-a major family of drug targets, particularly in anti-cancer agents. While small-molecule kinase inhibitors exhibit impressive clinical efficacy in several different diseases, resistance often arises through adaptive kinome reprogramming or subpopulation diversity. Polypharmacology and combination therapies offer potential therapeutic strategies for patients with resistant diseases. Their development would benefit from a more comprehensive and dense knowledge of small-molecule inhibition across the human kinome. Leveraging over 650,000 bioactivity annotations for more than 300,000 small molecules, we evaluated multiple machine learning methods to predict the small-molecule inhibition of 342 kinases across the human kinome. Our results demonstrated that multi-task deep neural networks outperformed classical single-task methods, offering the potential for conducting large-scale virtual screening, predicting activity profiles, and bridging the gaps in the available data.

Higher clearance rates of multiple HPV infections may explain their lower risk of HSIL: A retrospective study in Wenzhou, China.

Persistent human papilloma virus (HPV) infection is known to be associated with cervical lesions. The chief object of the study is to investigate if the pathogenicity of multiple HPV infections is different from a single infection. Furthermore, we would like to corroborate the discrepancy with clearance rates. Between August 1, 2020, and September 31, 2021, 5089 women underwent a colposcopy-directed biopsy in our hospital. We divided the 2999 patients who met the criteria into multiple and single HPV infection groups. The HPV genotypes were identified using the flow cytometry fluorescence hybridization technology. Binary logistic regression and survival analysis were used to perform statistics. Among HPV-positive individuals, 34.78% (1043/2999) were positive for 2 or more HPV types. After adjusting for the main factors, compared with single infection, multiple infections were associated with a significantly decreased risk of high squamous intraepithelial lesions (HSIL) (odds ratio [OR]: 0.570; 95% confidence interval [CI]: 0.468-0.694). In the mean time, the clearance rates of multiple infections were significantly higher (OR: 2.240; 95% CI: 1.919-2.614). When analyzing specific types covered by the 9-valent HPV vaccine, consistency between the lower risk of HSIL and the higher clearance rate was found in the most groups. Compared with a single infection, multiple HPV infections have a lower risk of HSIL, which may be related to its higher clearance rate. It suggests that aggressive treatment of multiple HPV infections early in their detection may be beneficial.

A genetic glimpse of the Chinese straight-tusked elephants.

Straight-tusked elephants (genus: Palaeoloxodon) including their island dwarf forms are extinct enigmatic members of the Pleistocene megafauna and the most common Pleistocene elephants after the mammoths. Their taxonomic placement has been revised several times. Using palaeogenomic evidence, previous studies suggested that the European P. antiquus has a hybrid origin, but no molecular data have been retrieved from their Asian counterparts, leaving a gap in our knowledge of the global phylogeography and population dynamics of Palaeoloxodon. Here, we captured a high-quality complete mitogenome from a Pleistocene Elephantidae molar (CADG841) from Northern China, which was previously morphologically assigned to the genus Elephas (Asian elephant), and partial mitochondrial sequences (838 bp) of another Palaeoloxodon sp. specimen (CADG1074) from Northeastern China. We found that both Chinese specimens cluster with a 244 000-year-old P. antiquus (specimen name: WE) from Western Europe, suggesting that this clade may represent a population with a large spatial span across Eurasia. Based on the fossil record and the molecular dating of both the divergences of different Palaeoloxodon mitochondrial clades and previously determined hybridization events, we propose that this Eurasian-wide WE clade provides evidence for an earlier migration and/or another hybridization event that happened in the evolutionary history of straight-tusked elephants.

Interphasial Pre-lithiation and Reinforcement of Micro-Si Anode through Fluorine-free Electrolytes.

Micro-sized silicon (mSi) anodes offer advantages in cost and tap density over nanosized counterparts. However, its practical application still suffers from poor cyclability and low initial and later-cycle coulombic efficiency (CE), caused by the unstable solid electrolyte interphase (SEI) and irreversible lithiation of the surface oxide layer. Herein, a bifunctional fluorine (F)-free electrolyte was designed for the mSi anode to stabilize the interphase and improve the CE. A combined analysis revealed that this electrolyte can chemically pre-lithiate the native oxide layer by the reductive LiBH4 , and relieve SEI formation and accumulation to preserve the internal conductive network. The significance of this F-free electrolyte brings unprecedented F-free interphase that also enables the high-performance mSi electrode (80 wt % mSi), including high specific capacity of 2900 mAh/g, high initial CE of 94.7 % and excellent cyclability capacity retention of 94.3 % after 100 cycles at 0.2 C. This work confirms the feasibility of F-free interphase, thus opening up a new avenue toward cost-advantaged and environmentally friendly electrolytes for more emerging battery systems.

Chloride Oxidation by One- or Two-Photon Excitation of N-Phenylphenothiazine.

Chloride oxidation has tremendous utility in the burgeoning field of chlorine-mediated C-H activation, yet it remains a challenging process to initiate with light because of the exceedingly positive one-electron reduction potential, E° (Cl•/-), beyond most common transition-metal photooxidants. Herein, two photocatalytic chloride oxidation pathways that involve either one- or consecutive two-photon excitation of N-phenylphenothiazine (PTH) are presented. The one-photon pathway generates PTH•+ by oxidative quenching that subsequently disproportionates to yield PTH2+ that oxidizes chloride; this pathway is also accessed by the electrochemical oxidation of PTH. The two-photon pathway, which proceeded through the radical cation excited state, 2PTH•+*, was of particular interest as this super-photooxidant was capable of directly oxidizing chloride to chlorine atoms. Laser flash photolysis revealed that the photooxidation by the doublet excited state proceeded on a subnanosecond timescale through a static quenching mechanism with an ion-pairing equilibrium constant of 0.36 M-1. The PTH photoredox chemistry was quantified spectroscopically on nanosecond and longer time scales, and chloride oxidation chemistry was revealed by reactivity studies with model organic substrates. One- and two-photon excitation of PTH enabled chlorination of unactivated C(sp3)-H bonds of organic compounds such as cyclohexane with substantial yield enhancement observed from inclusion of the second excitation wavelength. This study provides new mechanistic insights into chloride oxidation catalyzed by an inexpensive and commercially available organic photooxidant.

Living Cell Nanoporation and Exosomal RNA Analysis Platform for Real-Time Assessment of Cellular Therapies.

Efficient transfection of therapeutic agents and timely potency testing are two key factors hindering the development of cellular therapy. Here we present a cellular-nanoporation and exosome assessment device, a quantitative platform for nanochannel-based cell electroporation and exosome-based in situ RNA expression analysis. In its application to transfection of anti-miRNAs and/or chemotherapeutics into cells, we have systematically described the differences in RNA expression in secreted exosomes and assessed cellular therapies in real time.

An extinct and deeply divergent tiger lineage from northeastern China recognized through palaeogenomics.

Tigers (Panthera tigris) are flagship big cats and attract extensive public attention due to their charismatic features and endangered status. Despite this, little is known about their prehistoric lineages and detailed evolutionary histories. Through palaeogenomic analyses, we identified a Pleistocene tiger from northeastern China, dated to beyond the limits of radiocarbon dating (greater than 43 500 years ago). We used a simulated dataset and different reads processing pipelines to test the validity of our results and confirmed that, in both mitochondrial and nuclear phylogenies, this ancient individual belongs to a previously unknown lineage that diverged prior to modern tiger diversification. Based on the mitochondrial genome, the divergence time of this ancient lineage was estimated to be approximately 268 ka (95% CI: 187-353 ka), doubling the known age of tigers' maternal ancestor to around 125 ka (95% CI: 88-168 ka). Furthermore, by combining our findings with putative mechanisms underlying the discordant mito-nuclear phylogenetic placement for the South China tigers, we proposed a more complex scenario of tiger evolution that would otherwise be missed using data from modern tigers only. Our study provides the first glimpses of the genetic antiquity of tigers and demonstrates the utility of aDNA-based investigation for further understanding tiger evolution.

Correction: Metal-free oxidative synthesis of benzimidazole compounds by dehydrogenative coupling of diamines and alcohols.

Correction for 'Metal-free oxidative synthesis of benzimidazole compounds by dehydrogenative coupling of diamines and alcohols' by Jiaming Hu et al., Org. Biomol. Chem., 2022, DOI: 10.1039/d2ob00165a.

Metal-free oxidative synthesis of benzimidazole compounds by dehydrogenative coupling of diamines and alcohols.

We report a novel metal-free synthesis of benzimidazole compounds by dehydrogenative coupling of diamines and alcohols. Using NHPI as a nonmetallic catalyst combined with molecular oxygen or air as the oxidant, this transformation represents a widely applicable protocol to N-heterocycles, such as benzimidazoles, benzothiophenes, benzooxazoles and quinazolines. Flow microreactors operating under optimized conditions enabled this reaction with higher efficiency, and the total residence time was 30 min compared with the batch bubbling reactor (10 h). Moreover, a possible reaction mechanism is proposed according to the control experiments.

Multiple Visuotopically Organized Subdivisions of the Lateral Pulvinar/Central Lateral Inferior Pulvinar Project into Thin and Thick Stripe Compartments of V2 in Macaques.

The lateral and central lateral inferior pulvinar (PL/PIcl) of primates has been implicated in playing an important role in visual processing, but its physiological and anatomical characteristics remain to be elucidated. It has been suggested that there are two complete visuotopic maps in the PL/PIcl, each of which sends afferents into V2 and V4 in primates. Given that functionally distinct thin and thick stripes of V2 both receive inputs from the PL/PIcl, this raises the possibility of a presence of parallel segregated pathways within the PL/PIcl. To address this question, we selectively injected three types of retrograde tracers (CTB-488, CTB-555, and BDA) into thin or thick stripes in V2 and examined labeling in the PL/PIcl in macaques. As a result, we found that every cluster of retrograde labeling in the PL/PIcl included all three types of signals next to each other, suggesting that thin stripe- and thick stripe-projecting compartments are not segregated into domains. Unexpectedly, we found at least five topographically organized retrograde labeling clusters in the PL/PIcl, indicating the presence of more than two V2-projecting maps. Our results suggest that the PL/PIcl exhibits greater compartmentalization than previously thought. They may be functionally similar but participate in multiple cortico-pulvinar-cortical loops.

Single Living Cell Analysis Nanoplatform for High-Throughput Interrogation of Gene Mutation and Cellular Behavior.

The genetic heterogeneities in cancer cells pose challenges to achieving precise drug treatment in a widely applicable manner. Most single-cell gene analysis methods rely on cell lysis for gene extraction and identification, showing limited capacity to provide the correlation of genetic properties and real-time cellular behaviors. Here, we report a single living cell analysis nanoplatform that enables interrogating gene properties and drug resistance in millions of single cells. We designed a Domino-probe to identify intracellular target RNAs while releasing 10-fold amplified fluorescence signals. An on-chip addressable microwell-nanopore array was developed for enhanced electro-delivery of the Domino-probe and in situ observation of cell behaviors. The proof-of-concept of the system was validated in primary lung cancer cell samples, revealing the positive-correlation of the ratio of EGFR mutant cells with their drug susceptibilities. This platform provides a high-throughput yet precise tool for exploring the relationship between intracellular genes and cell behaviors at the single-cell level.

Flower-Like Interlayer-Expanded MoS2- x Nanosheets Confined in Hollow Carbon Spheres with High-Efficiency Electrocatalysis Sites for Advanced Sodium-Sulfur Battery.

The room-temperature sodium-sulfur (RT-Na/S) battery is one of the most promising technologies for low-cost energy storage. However, application of RT-Na/S batteries is currently impeded by severe shuttle effects and volume expansion that limits both energy density and cycling stability. Herein, first, the first-principal calculation is used to find that the introduction of sulfur vacancies in MoS2 can effectively enhance polysulfide adsorption and catalytic ability as well as both the ion and electron conductivities. Then, unique MoS2- x /C composite spheres are further designed and synthesized with flower-like few-layer and interlayer-enlarged MoS2- x nanosheets space-confined in hollow carbon nanospheres by a "ship-in-a-bottle" strategy. With this novel design, the mass loading of S in the MoS2- x /C composite can be reached to as high as 75 wt%. Owing to the synergetic effect of interlayer-expanded and few-layer MoS2- x nanosheets and hollow carbon spheres matrix with high electronic/Na+ conductivity, the RT-Na/S batteries deliver highly stable cycle durability (capacity retention of 85.2% after 100 cycles at 0.1 A g-1 ) and remarkable rate capability (415.7 mAh g-1 at 2 A g-1 ) along with high energy density. This design strategy of defect- and interlayer-engineering may find wide applications in synthesizing electrode materials for high-performance RT-Na/S batteries.

Ancient mitochondrial genomes from Chinese cave hyenas provide insights into the evolutionary history of the genus Crocuta.

Cave hyenas (genus Crocuta) are extinct bone-cracking carnivores from the family Hyaenidae and are generally split into two taxa that correspond to a European/Eurasian and an (East) Asian lineage. They are close relatives of the extant African spotted hyenas, the only extant member of the genus Crocuta. Cave hyenas inhabited a wide range across Eurasia during the Pleistocene, but became extinct at the end of the Late Pleistocene. Using genetic and genomic datasets, previous studies have proposed different scenarios about the evolutionary history of Crocuta. However, causes of the extinction of cave hyenas are widely speculative and samples from China are severely understudied. In this study, we assembled near-complete mitochondrial genomes from two cave hyenas from northeastern China dating to 20 240 and 20 253 calBP, representing the youngest directly dated fossils of Crocuta in Asia. Phylogenetic analyses suggest a monophyletic clade of these two samples within a deeply diverging mitochondrial haplogroup of Crocuta. Bayesian analyses suggest that the split of this Asian cave hyena mitochondrial lineage from their European and African relatives occurred approximately 1.85 Ma (95% CI 1.62-2.09 Ma), which is broadly concordant with the earliest Eurasian Crocuta fossil dating to approximately 2 Ma. Comparisons of mean genetic distance indicate that cave hyenas harboured higher genetic diversity than extant spotted hyenas, brown hyenas and aardwolves, but this is probably at least partially due to the fact that their mitochondrial lineages do not represent a monophyletic group, although this is also true for extant spotted hyenas. Moreover, the joint female effective population size of Crocuta (both cave hyenas and extant spotted hyenas) has sustained two declines during the Late Pleistocene. Combining this mitochondrial phylogeny, previous nuclear findings and fossil records, we discuss the possible relationship of fossil Crocuta in China and the extinction of cave hyenas.

Ancient DNA of northern China Hystricidae sub-fossils reveals the evolutionary history of old world porcupines in the Late Pleistocene.

BACKGROUND: Old World porcupines (Family: Hystricidae) are the third-largest rodents and inhabit southern Europe, Asia, and most regions of Africa. They are a typical indicator of warm climate and their distribution is restricted to tropical and subtropical zones. In China, porcupines are widely distributed in southern areas of the Yangtze River. However, fossil remains have been identified in a few sites in northern China, among which Tianyuan Cave-near Zhoukoudian site-represents the latest known porcupine fossil record. So far, studies have focused mainly on porcupines' husbandry and domestication but little is known about their intrafamilial phylogenetic relationships and evolutionary history. RESULTS: In this study, we sequence partial mitochondrial 12S rRNA and cyt b genes for seven Late Pleistocene porcupine individuals from Northern, Southern and Central China. Phylogenetic analyses show that the Tianyuan Cave porcupines, which had been morphologically identified as Hystrix subcristata, have a closer relationship to Hystrix brachyura. CONCLUSION: Together with morphological adaptation characteristics, associated fauna, and climate change evidence, the molecular results reveal that a Late Quaternary extirpation has occurred during the evolutionary history of porcupines.

An Orientation Map for Disparity-Defined Edges in Area V4.

Binocular disparity information is an important source of 3D perception. Neurons sensitive to binocular disparity are found in almost all major visual areas in nonhuman primates. In area V4, disparity processes are suggested for the purposes of 3D-shape representation and fine disparity perception. However, whether neurons in V4 are sensitive to disparity-defined edges used in shape representation is not clear. Additionally, a functional organization for disparity edges has not been demonstrated so far. With intrinsic signal optical imaging, we studied functional organization for disparity edges in the monkey visual areas V1, V2, and V4. We found that there is an orientation map in V4 activated by edges purely defined by binocular disparity. This map is consistent with the orientation map obtained with regular luminance-defined edges, indicating a cue-invariant edge representation in this area. In contrast, such a map is much weaker in V2 and totally absent in V1. These findings reveal a hierarchical processing of 3D shape along the ventral pathway and the important role that V4 plays in shape-from-disparity detection.

Rivalry-Like Neural Activity in Primary Visual Cortex in Anesthetized Monkeys.

Two incongruent images viewed by the two eyes cause binocular rivalry, during which observers perceive continuous alternations between these two visual images. Previous studies in both humans and monkeys have shown that the primary visual cortex (V1) plays a critical role in the rivalry perception. However, it is unclear whether the rivalry activity observed in V1 relies on conscious influences. Here, we examine the responses of V1 in monkeys under general anesthesia. With intrinsic signal optical imaging and single-trial analysis, alternating activation of ocular dominance columns in V1 was observed during binocularly incongruent stimulation. Left- and right-eye columns exhibited counterphase activation, which were modulated by stimulus features in ways similar to those found in conscious human observers. These observations indicated that binocular rivalry occurs in V1 without consciousness, suggesting that the low-level automatic mechanisms play a more important role than previously believed in handling visual ambiguities. SIGNIFICANCE STATEMENT: When visual input is ambiguous, for example, in viewing bistable images, human subjects normally perceive one of the interpretations at a particular moment. Previous studies have shown that both low-level visual processing and high-level attention contribute to the establishment of the final visual perception. However, it is not clear whether attention is indispensable in such a process. Here we show that rivalry-like neural activity persisted in monkey V1 when the monkeys were anesthetized and viewed binocularly incongruent stimuli. Such activity has many key features similar to those observed in conscious human subjects. These findings indicate that low-level visual processes play a critical role in solving visual ambiguity such as binocular rivalry.

An Orientation Map for Motion Boundaries in Macaque V2.

The ability to extract the shape of moving objects is fundamental to visual perception. However, where such computations are processed in the visual system is unknown. To address this question, we used intrinsic signal optical imaging in awake monkeys to examine cortical response to perceptual contours defined by motion contrast (motion boundaries, MBs). We found that MB stimuli elicit a robust orientation response in area V2. Orientation maps derived from subtraction of orthogonal MB stimuli aligned well with the orientation maps obtained with luminance gratings (LGs). In contrast, area V1 responded well to LGs, but exhibited a much weaker orientation response to MBs. We further show that V2 direction domains respond to motion contrast, which is required in the detection of MB in V2. These results suggest that V2 represents MB information, an important prerequisite for shape recognition and figure-ground segregation.