Bifidobacterium longum promotes postoperative liver function recovery in patients with hepatocellular carcinoma.

Timely liver function recovery (LFR) is crucial for postoperative hepatocellular carcinoma (HCC) patients. Here, we established the significance of LFR on patient long-term survival through retrospective and prospective cohorts and identified a key gut microbe, Bifidobacterium longum, depleted in patients with delayed recovery. Fecal microbiota transfer from HCC patients with delayed recovery to mice similarly impacted recovery time post hepatectomy. However, oral gavage of B. longum improved liver function and repair in these mice. In a clinical trial of HCC patients, orally administering a probiotic bacteria cocktail containing B. longum reduced the rates of delayed recovery, shortened hospital stays, and improved overall 1-year survival. These benefits, attributed to diminished liver inflammation, reduced liver fibrosis, and hepatocyte proliferation, were associated with changes in key metabolic pathways, including 5-hydroxytryptamine, secondary bile acids, and short-chain fatty acids. Our findings propose that gut microbiota modulation can enhance LFR, thereby improving postoperative outcomes for HCC patients.

Ultrasensitive therapeutic drug monitoring of methotrexate by a structure-switching aptamer with cascade primer exchange reaction.

As a folate antagonist, methotrexate (MTX) has been widely used in clinics with good effects on various tumors and inflammatory diseases. While the optimum dosage and total body clearance of MTX usually varies between individuals and even low-dose MTX has side effects, high-dose MTX may cause life-threatening side effects. Therefore, a convenient and simple method toward MTX sensing is highly demanded. Herein, we report a highly sensitive and selective method for therapeutic drug monitoring (TMD) of MTX by integrating a highly specific MTX-dependent structure-switching aptamer with a primer exchange reaction-based signal amplification technique. The detection limit is down to 1.7 nM with a linear range from 0.01 to 1 µM in buffer. More importantly, the sensing strategy can effectively detect MTX in a complex bio-environment with a linear response range from 0.05 to 2 µM and a LOD of 12.4 nM in 10% FBS and a range of 0.2 to 5 µM with a LOD of 63.73 nM in 10% whole blood. Considering the high sensitivity and selectivity and good performance in blood, the method reported herein paves a new avenue for the effective determination of MTX in clinics.

Aptamer-engineered extended-gate field-effect transistor device for point-of-care therapeutic drug monitoring.

Herein, we report a portable point-of-care testing (POCT) device based on an aptamer-engineered extended-gate field-effect transistor (EG-FET) for therapeutic monitoring of the drug methotrexate. This method was shown to be highly sensitive, efficient, and convenient to use, features contributing to its realizing a clinical detection of drugs in blood.

Cuticular lipids and associated gene expression analysis under NaCl stress in Thellungiella salsuginea.

Cuticular lipids, including wax and cutin, protect plants against external environmental stress. The relationship between the cuticle properties and salt tolerance is not clear. In this article, photosynthetic and physiological characteristics related to water use and cuticle permeability were assessed in the leaves of Thellungiella salsuginea under NaCl stress. The chemical composition of wax and cutin monomers, and the expression of cuticle-associated genes were also analyzed. The results showed that the net photosynthetic rate and stomatal conductance in the leaves of T. salsuginea decreased, and the water use efficiency increased with increasing NaCl concentration. Salt stress caused a significant increase in total wax, but total cutin monomers only increased under high salt. Transcriptome sequencing and lipid metabolism pathway analysis were performed on rosette leaves of T. salsuginea after 24 h of NaCl treatment. We analyzed the expression of 42 genes involved in cuticle lipid metabolism, and found that most of them exhibited higher expression levels at 0.15 mol L-1 NaCl, but lower expression levels at 0.3 mol L-1 NaCl. The expression of 12 of these genes was further detected by qRT-PCR after 1 week of NaCl treatment: most of them were upregulated both under low and high NaCl stress. Hence, we speculate that the cuticle acts as an adaptive trait in T. salsuginea in salty environments.

Selection of a Structure-Switching Aptamer for the Specific Methotrexate Detection.

Methotrexate (MTX), a folate antagonist drug, has been widely used for treating various cancers. Since high-dose MTX treatment can cause unwanted serious side effects, tracking the blood concentration of MTX is essential for safe medication. However, available methods are often complex, time-consuming, and expensive. In this study, a highly selective DNA aptamer was selected for recognizing MTX based on a capture-systematic evolution of ligands by an exponential enrichment (C-SELEX) approach. Taking advantage of our selected MTX aptamer, we further unveil a novel structure-switching fluorescent sensor for the specific and rapid monitoring of MTX with good analytical performances (i.e., a linear detection range of 0.1-2 µM with a low detection limit (LOD) of 0.03 µM in buffer and a linear detection range of 0.5-10 µM with an LOD of 0.18 µM in 50% serum). Compared with conventional methods, this assay has great potential for detecting the blood concentration of MTX in clinical use. By coupling with other sensory techniques, our presented aptamer will potentially inspire the development of various sensors toward the monitoring of MTX.

Dual-emission fluorescence biosensing of vancomycin based on AIEgen-peptide conjugates and aptamer-modified Au nanoclusters.

Precise doses of antibiotics are necessary to prevent bacterial drug resistance. Although fluorescent sensors are promising for quantitative analyses of antibiotics, improvements in feasibility, selectivity, and sensitivity are needed. In this study, a dual-emission fluorescence biosensor platform was developed for simple, selective, and sensitive determination of vancomycin (Van) based on a peptide conjugated with blue-emitting aggregation-induced emission luminogens (AIEgen) and aptamer-modified red-emitting gold nanoclusters (AuNCs-apt). The peptide and aptamer together recognized Van with high affinity, thus changing the fluorescence intensity at 470 nm and 650 nm, respectively. This platform displayed excellent linear correlation between the fluorescence response and a Van concentration ranging 0.01-100 µg mL-1, and the limit of detection (LOD) was 2.79 ng mL-1. In addition to the ability to accurately distinguish Van from glycopeptide antibiotics, the newly developed biosensor allowed for naked-eye detection of 1 µg mL-1 Van. These results and those of serum samples and microdialysate samples support the application of this newly developed method for Van monitoring and clinical diagnosis.

Chemical and Transcriptomic Analysis of Cuticle Lipids under Cold Stress in Thellungiella salsuginea.

Plant cuticle lipids form outer protective layers to resist environmental stresses; however, the relationship between cuticle properties and cold tolerance is unclear. Here, the extremophyte Thellungiella salsuginea was stressed under cold conditions (4 °C) and the cuticle of rosette leaves was examined in terms of epicuticular wax crystal morphology, chemical composition, and cuticle-associated gene expression. The results show that cold induced formation of distinct lamellas within the cuticle ultrastructure. Cold stress caused 14.58% and 12.04% increases in the amount of total waxes and cutin monomer per unit of leaf area, respectively, probably associated with the increase in total fatty acids. The transcriptomic analysis was performed on rosette leaves of Thellungiella exposed to cold for 24 h. We analyzed the expression of 72 genes putatively involved in cuticle lipid metabolism, some of which were validated by qRT-PCR (quantitative reverse transcription PCR) after both 24 h and one week of cold exposure. Most cuticle-associated genes exhibited higher expression levels under cold conditions, and some key genes increased more dramatically over the one week than after just 24 h, which could be associated with increased amounts of some cuticle components. These results demonstrate that the cuticle provides some aspects of cold adaptation in T. salsuginea.

The relationship between cuticular lipids and associated gene expression in above ground organs of Thellungiella salsugineum (Pall.) Al-Shehbaz & Warwick.

The cuticle plays a critical role as barrier between plant and environment. Here, cuticular wax morphology, cuticular wax and cutin monomer composition, and expression of associated genes in five above ground organs were examined in model extremophyte Thellungiella salsugineum. Alkanes, ketones, and 2-alcohols were the predominant wax constitutes in rosette leaves, inflorescence stem leaves, stems, and siliques, whereas alkanes and acids were the predominant cuticular lipids in whole flowers. Unsubstituted acids were the most abundant cutin monomers in vegetative organs, especially C18:2 dioic acids, which reached the highest levels in stems. Hydroxy fatty acids were the predominant cutin monomers in flowers, especially 16-OH C16:0 and diOH C16:0. High-throughput RNA-Seq analysis using the Hiseq4000 platform was performed on these five above organs of T. salsugineum, and the differentially expressed lipid-associated genes and their associated metabolic pathways were identified. Expression of genes associated in previous reports to cuticle production, including those having roles in cuticle lipid biosynthesis, transport, and regulation were examined. The association of cuticle lipid composition and gene expression within different organs of T. salsugineum, and potential relationships between T. salsugineum's extreme cuticle and its adaptation to extreme environments is discussed.

The Mechanism of the Selective Antiproliferation Effect of Guanine-Based Biomolecules and Its Compensation.

As endogenous biomolecules, guanine, guanine-based nucleosides, and nucleotides are essential for cellular DNA/RNA synthesis, energy metabolism, and signal transduction. However, these biomolecules have been found to have a cell-specific antiproliferation effect at higher concentrations, and the mechanism is unclear. In this study, we demonstrate that guanine deaminase (GDA) is a major factor in determining the cell-type selectivity to the antiproliferation effect of guanine-based biomolecules. GDA catalyzes the deamination of guanine to xanthine, which is an essential part of the guanine degradation pathway. GDA deficient cells could not efficiently remove the excess guanine-based biomolecules. These excess molecules disturb the metabolism of adenine-, cytosine-, and thymine-based nucleotides; subsequently inhibit the DNA synthesis and cell growth; and eventually result in the apoptosis/death of GDA deficient cells. The inhibition of DNA synthesis could be relieved by simultaneous addition of adenine- and cytosine-based nucleosides, and the inhibited DNA synthesis could be restarted by post addition of them, which subsequently reduces the antiproliferation effect of guanine-based biomolecules or even totally restores the cell proliferation. These results provide important information for the development of guanine-based drugs or guanine-rich oligonucleotide drugs, as well as for the safety evaluation of food with a high level of guanine-based compounds.

Applying deep matching networks to Chinese medical question answering: a study and a dataset.

BACKGROUND: Medical and clinical question answering (QA) is highly concerned by researchers recently. Though there are remarkable advances in this field, the development in Chinese medical domain is relatively backward. It can be attributed to the difficulty of Chinese text processing and the lack of large-scale datasets. To bridge the gap, this paper introduces a Chinese medical QA dataset and proposes effective methods for the task. METHODS: We first construct a large scale Chinese medical QA dataset. Then we leverage deep matching neural networks to capture semantic interaction between words in questions and answers. Considering that Chinese Word Segmentation (CWS) tools may fail to identify clinical terms, we design a module to merge the word segments and produce a new representation. It learns the common compositions of words or segments by using convolutional kernels and selects the strongest signals by windowed pooling. RESULTS: The best performer among popular CWS tools on our dataset is found. In our experiments, deep matching models substantially outperform existing methods. Results also show that our proposed semantic clustered representation module improves the performance of models by up to 5.5% Precision at 1 and 4.9% Mean Average Precision. CONCLUSIONS: In this paper, we introduce a large scale Chinese medical QA dataset and cast the task into a semantic matching problem. We also compare different CWS tools and input units. Among the two state-of-the-art deep matching neural networks, MatchPyramid performs better. Results also show the effectiveness of the proposed semantic clustered representation module.

In vitro selection of DNA aptamers recognizing drug-resistant ovarian cancer by cell-SELEX.

Ovarian cancer is regarded as the most lethal gynecologic malignancy with poor prognosis and high mortality rate. Drug-resistance was thought to be the main obstacle to improving overall survival rate of ovarian cancer. New ligands for drug-resistant ovarian cancer cells have potential for the development of diagnosis and therapy of ovarian cancer. In present work, we reported two aptamers, HF3-58 and HA5-68 generated by cell-SELEX, against a paclitaxel-resistant ovarian cancer cell line (A2780T). Both two aptamers exhibited high selectivity and strong affinity to target cells with low nanomolar dissociation constants. The binding of aptamers to target cells was independent of divalent ions, and was tolerant of incubation temperature and nucleases in serum. Molecular targets of the two aptamers were preliminarily demonstrated to be two different glycoproteins on cell surface of A2780T cells. Owing to the structure stability and high resistance to nuclease, these two aptamers had good performance in the detection of drug-resistant ovarian cancer cells in human serum.

Compositional and transcriptomic analysis associated with cuticle lipid production on rosette and inflorescence stem leaves in the extremophyte Thellungiella salsuginea.

The plant cuticle is a complex structure composed primarily of wax and cutin, but also contains cutan, glycerolipids, phenolics, polysaccharides and proteins. The cuticle plays an important protective role as barrier between plants and their environment. In this paper, 4-week-old leaves produced either on the rosette or on the inflorescence stem of the model extremophyte Thellungiella salsuginea were examined using scanning electron microscopy, cuticle permeability assays and chemical composition analysis. Results showed that stem leaves (SL) had more abundant cuticle lipids and lower cuticle permeability than rosette leaves (RL). SL were dominated by alkanes, especially the C29 and C31 homologs, whereas in RL the most abundant wax class was free very long-chain acids. The major cutin monomers for both leaf types were C18:2 dioic acids and 18-OH C18:2 acids. We performed Illumina high-throughput sequencing for SL and RL, and 3577 differentially expressed genes were identified. Sixty-five genes possibly involved in cuticular lipid biosynthesis, transport, or regulation was selected for further analysis. Many cuticle-associated genes exhibited differential expression levels that could be associated with compositional differences between these two leaf types. Furthermore, transcription factors and other regulatory proteins previously associated with cuticle production were expressed at higher levels in SL than in RL. The associations between gene expression and characteristics of this extremophile's leaf cuticles sheds new light on cuticle as an adaptive trait in extreme environments, and contributes new information that may guide efforts to modify crop cuticles for improved stress tolerance.

Development of squaraine based G-quadruplex ligands using click chemistry.

The G-quadruplex (G4) structures of nucleic acids are considered to play an intrinsic role in gene expression. To this end, the development of new G4 ligands has attracted extensive research interests towards potential applications as G4-targeted drugs and molecular probes. To date, the majority of G4 ligands have been composed of an extended planar aromatic scaffold that interacts with the terminal G-tetrad plane via π-π interactions, and various side chains that interact with the sugar-phosphate backbone, loops or grooves of the G4 structures. The side chains act to modulate the affinity and selectivity of the G4 ligands, alongside influencing their biodistribution. Here, we present a click chemistry methodology to generate a series of squaraine-based G4 ligand derivatives based on our previously reported G4 probe (named CSTS) but with varing side chains. We find that importantly these new G4 ligand derivatives retain the G4 selectivity, optical properties and low cytotoxicity of CSTS, but exhibit different binding behaviors to G4 structures, and distinct cellular uptake efficiencies. Indeed, of these new complexes, several exhibit much higher affinity and cellular uptake than CSTS. Overall, this novel, facile and highly effective strategy has significant future potential for the high-throughput screening of G4 ligands or probes targeted towards in vivo applications.

Gain of glucose-independent growth upon metastasis of breast cancer cells to the brain.

Breast cancer brain metastasis is resistant to therapy and a particularly poor prognostic feature in patient survival. Altered metabolism is a common feature of cancer cells, but little is known as to what metabolic changes benefit breast cancer brain metastases. We found that brain metastatic breast cancer cells evolved the ability to survive and proliferate independent of glucose due to enhanced gluconeogenesis and oxidations of glutamine and branched chain amino acids, which together sustain the nonoxidative pentose pathway for purine synthesis. Silencing expression of fructose-1,6-bisphosphatases (FBP) in brain metastatic cells reduced their viability and improved the survival of metastasis-bearing immunocompetent hosts. Clinically, we showed that brain metastases from human breast cancer patients expressed higher levels of FBP and glycogen than the corresponding primary tumors. Together, our findings identify a critical metabolic condition required to sustain brain metastasis and suggest that targeting gluconeogenesis may help eradicate this deadly feature in advanced breast cancer patients.

Active specific immunotherapy against occult brain metastasis.

We determined whether lyophilized High Five (H5) insect cells engineered to produce IFN-beta (H5BVIFN-beta) could induce systemic immunity against occult brain metastases. C3H/HeN mice were injected s.c. with syngeneic UV-2237M fibrosarcoma or K-1735M2 melanoma cells. Intralesional injection of 2 x 10(6) lyophilized H5BVIFN-beta cells produced complete regression of the s.c. tumors. Six weeks later, UV-2237M fibrosarcoma cells or K-1735M2 melanoma cells were injected into the internal carotid artery of naive or treated mice. UV-2237M brain metastases developed in naive mice or mice cured of K-1735M2 tumors but not in mice cured of UV-2237M tumors. Similarly, K-1735M2 brain metastases developed in naive mice or mice cured of UV-2237M fibrosarcomas but not in mice cured of K-1735M2 melanoma. In the next set of studies, mice were injected s.c. with UV-2237M fibrosarcoma cells. On day 7, UV-2237M fibrosarcoma cells or K-1735M2 cells were implanted into the internal carotid artery, and on day 10, the s.c. tumors were injected with lyophilized H5BVIFN-beta. Both the s.c. tumors and the occult brain metastases produced from carotid injections were eradicated in a tumor-specific manner. The regression of the brain metastases was abrogated by depletion of CD4(+) or CD8(+) cells from immunized mice. These results demonstrate that specific systemic immunity can be induced by lyophilized H5BVIFN-beta and that the resultant immune response can eliminate established brain metastasis.