SCSMD: Single Cell Consistent Clustering based on Spectral Matrix Decomposition.

Cluster analysis, a pivotal step in single-cell sequencing data analysis, presents substantial opportunities to effectively unveil the molecular mechanisms underlying cellular heterogeneity and intercellular phenotypic variations. However, the inherent imperfections arise as different clustering algorithms yield diverse estimates of cluster numbers and cluster assignments. This study introduces Single Cell Consistent Clustering based on Spectral Matrix Decomposition (SCSMD), a comprehensive clustering approach that integrates the strengths of multiple methods to determine the optimal clustering scheme. Testing the performance of SCSMD across different distances and employing the bespoke evaluation metric, the methodological selection undergoes validation to ensure the optimal efficacy of the SCSMD. A consistent clustering test is conducted on 15 authentic scRNA-seq datasets. The application of SCSMD to human embryonic stem cell scRNA-seq data successfully identifies known cell types and delineates their developmental trajectories. Similarly, when applied to glioblastoma cells, SCSMD accurately detects pre-existing cell types and provides finer sub-division within one of the original clusters. The results affirm the robust performance of our SCSMD method in terms of both the number of clusters and cluster assignments. Moreover, we have broadened the application scope of SCSMD to encompass larger datasets, thereby furnishing additional evidence of its superiority. The findings suggest that SCSMD is poised for application to additional scRNA-seq datasets and for further downstream analyses.

City-scale distribution of airborne antibiotic resistance genes.

Concerns around urban air quality have been increasing worldwide due to large-scale urbanization. A large volume of work has been focused on the chemical pollutants in the air and their impacts on human health. However, the profile of airborne microbial contaminants, especially antibiotic resistance genes (ARGs), is largely understudied. Here, high-throughput quantitative PCR (HT-qPCR) was employed to explore the temporal and spatial distribution of airborne ARGs from 11 sites with various functional zones and different urbanization levels within Xiamen, China. A total of 104 unique ARGs and 23 mobile genetic elements (MGEs) were detected across all samples. Temporal shift was observed in the distribution of ARG profiles, with significantly higher relative abundance of ARGs detected in summer than that in spring. Temperature is the key predictor of the total relative abundance of ARGs and MGEs in summer, while PM2.5 and PM10 were the two most important factors affecting the abundance in spring. Our findings suggest that urban aerosols accommodate rich and dynamic ARGs and MGEs, and emphasize the role of temperature, air quality and anthropogenic activities in shaping the profile of ARGs.

Emerging photodynamic/sonodynamic therapies for urological cancers: progress and challenges.

Photodynamic therapy (PDT), and sonodynamic therapy (SDT) that developed from PDT, have been studied for decades to treat solid tumors. Compared with other deep tumors, the accessibility of urological tumors (e.g., bladder tumor and prostate tumor) makes them more suitable for PDT/SDT that requires exogenous stimulation. Due to the introduction of nanobiotechnology, emerging photo/sonosensitizers modified with different functional components and improved physicochemical properties have many outstanding advantages in cancer treatment compared with traditional photo/sonosensitizers, such as alleviating hypoxia to improve quantum yield, passive/active tumor targeting to increase drug accumulation, and combination with other therapeutic modalities (e.g., chemotherapy, immunotherapy and targeted therapy) to achieve synergistic therapy. As WST11 (TOOKAD® soluble) is currently clinically approved for the treatment of prostate cancer, emerging photo/sonosensitizers have great potential for clinical translation, which requires multidisciplinary participation and extensive clinical trials. Herein, the latest research advances of newly developed photo/sonosensitizers for the treatment of urological cancers, and the efficacy, as well as potential biological effects, are highlighted. In addition, the clinical status of PDT/SDT for urological cancers is presented, and the optimization of the photo/sonosensitizer development procedure for clinical translation is discussed.

Multiple fluorescence response behaviors towards antibiotics and bacteria based on a highly stable Cd-MOF.

The abuse of antibiotics has triggered the rise of drug-resistance bacteria, which has seriously threatened public health globally. As a result, carrying out efficient and accurate antibiotic and bacteria identification are quite significant but challenge. Herein, an unprecedented Cd-MOF-based sensor, [CdL]n [1, H2L = 4-(2-methyl-1H-benzo[d]imidazol-1-yl) isophthalic acid] with multiple fluorescence response behaviours towards antibiotics and bacteria was developed. Single-crystal X-ray diffraction revealed that 1 is a mesomeric 2D bilayer, which is comprised of two opposite chiral mono-layers, each assembled by left-handed or right-handed helixes. More interestingly, 1 represented multiplex detection capability towards antibiotics and bacteria through two detection behaviors: toward nitro-antibiotics and chlortetracycline (CTC) via fluorescent quenching, while toward Staphylococcus albus (S. albus) via fluorescent enhancement. Remarkably, 1 showed a low limit of detection (LOD, 47 CFU/mL) accompanied with specificity in the detection of S. albus compared to other bacteria, such as Staphylococcus aureus, Acinetobacter baumannii, Klebsiella pneumonia, Pseudomonas aeruginosa and Escherichia coli. In addition, the LOD could reach to ppm level for nitro-antibiotics and CTC. Moreover, the practical application of 1 was further reinforced through the detection of nitro-antibiotics and CTC, as well as S. albus in fetal calf serum and river water.

Earthworm gut: An overlooked niche for anaerobic ammonium oxidation in agricultural soil.

Soil fauna takes an active part in accelerating turnover of nutrients in terrestrial ecosystems. Anaerobic ammonium oxidation (anammox) has been widely characterized, however, whether anammox is active in earthworm gut and the effect of earthworm on anammox in soil remain unknown. In this study, the activity, abundance and community of anammox bacteria in earthworm guts and soils from microcosms were determined using a 15N-tracing technique, quantitative PCR, and anammox bacterial 16S rRNA gene amplicon sequencing. Results showed that anammox rates in guts ranged between 5.81 and 14.19 nmol N g-1 dw gut content h-1, which were significantly (P < 0.01) higher than that in their surrounding soils during 30 day incubation. On the contrary, abundances of hzsB genes encoding subunit B hydrazine synthase in guts were significantly (P < 0.05) lower than those in their surrounding soils. Anammox rates, denitrification N2 production rates and hzsB genes in soils with earthworms were significantly (P < 0.05) lower than those in control soils. Anammox bacterial compositions differed significantly (P < 0.05) between gut and soil, and earthworm altered anammox bacterial communities in soils. Brocadia, Kuenenia and abundant unclassified anammox bacteria were detected in collected soils and gut contents, in which Brocadia was only detected in guts. These results suggested that microbes in earthworm gut increase, but present of earthworm reduces anammox and denitrification associated N loss by altering the anammox bacterial community compositions in soils.

Nanomaterials-Based Urinary Extracellular Vesicles Isolation and Detection for Non-invasive Auxiliary Diagnosis of Prostate Cancer.

Extracellular vesicles (EVs) are natural nanoparticles secreted by cells in the body and released into the extracellular environment. They are associated with various physiological or pathological processes, and considered as carriers in intercellular information transmission, so that EVs can be used as an important marker of liquid biopsy for disease diagnosis and prognosis. EVs are widely present in various body fluids, among which, urine is easy to obtain in large amount through non-invasive methods and has a small dynamic range of proteins, so it is a good object for studying EVs. However, most of the current isolation and detection of EVs still use traditional methods, which are of low purity, time consuming, and poor efficiency; therefore, more efficient and highly selective techniques are urgently needed. Recently, inspired by the nanoscale of EVs, platforms based on nanomaterials have been innovatively explored for isolation and detection of EVs from body fluids. These newly developed nanotechnologies, with higher selectivity and sensitivity, greatly improve the precision of isolation target EVs from urine. This review focuses on the nanomaterials used in isolation and detection of urinary EVs, discusses the advantages and disadvantages between traditional methods and nanomaterials-based platforms, and presents urinary EV-derived biomarkers for prostate cancer (PCa) diagnosis. We aim to provide a reference for researchers who want to carry out studies about nanomaterial-based platforms to identify urinary EVs, and we hope to summarize the biomarkers in downstream analysis of urinary EVs for auxiliary diagnosis of PCa disease in detail.

The Draft Genome Sequence of Pseudomonas frederiksbergensis Strain 11-D3 Reveals Its Ability To Mobilize Phosphorus.

Pseudomonas frederiksbergensis strain 11-D3 is a Gram-negative, nonmotile, aerobic bacterium isolated from a managed maize field in North China. This strain displays high efficiency for solubilization of inorganic phosphorus (P). We present the draft genome sequence of strain 11-D3 with P cycling genes which indicate the presence of a probable mechanism for P mobilization.

Fate of Antibiotic Resistant Pseudomonas putida and Broad Host Range Plasmid in Natural Soil Microcosms.

Plasmid conjugation is one of the dominant mechanisms of horizontal gene transfer, playing a noticeable role in the rapid spread of antibiotic resistance genes (ARGs). Broad host range plasmids are known to transfer to diverse bacteria in extracted soil bacterial communities when evaluated by filter mating incubation. However, the persistence and dissemination of broad range plasmid in natural soil has not been well studied. In this study, Pseudomonas putida with a conjugative antibiotic resistance plasmid RP4 was inoculated into a soil microcosm, the fate and persistence of P. putida and RP4 were monitored by quantitative PCR. The concentrations of P. putida and RP4 both rapidly decreased within 15-day incubation. P. putida then decayed at a significantly lower rate during subsequent incubation, however, no further decay of RP4 was observed, resulting in an elevated RP4/P. putida ratio (up to 10) after 75-day incubation, which implied potential transfer of RP4 to soil microbiota. We further sorted RP4 recipient bacteria from the soil microcosms by fluorescence-activated cell sorting. Spread of RP4 increased during 75-day microcosm operation and was estimated at around 10-4 transconjugants per recipient at the end of incubation. Analysis of 16S rRNA gene sequences of transconjugants showed that host bacteria of RP4 were affiliated to more than 15 phyla, with increased diversity and shift in the composition of host bacteria. Proteobacteria was the most dominant phylum in the transconjugant pools. Transient transfer of RP4 to some host bacteria was observed. These results emphasize the prolonged persistence of P. putida and RP4 in natural soil microcosms, and highlight the potential risks of increased spread potential of plasmid and broader range of host bacteria in disseminating ARGs in soil.

UBE2T promotes hepatocellular carcinoma cell growth via ubiquitination of p53.

Deregulation of Ubiquitin-conjugating enzyme E2T (UBE2T) contributes to the progression of human cancers. However, its clinical significance and role in hepatocellular carcinoma (HCC) remain unclear. Here, we show that UBE2T is up-regulated in HCC and exerts oncogenic activities via ubiquitination of p53. High UBE2T expression was correlated with higher pathological grade, advanced TNM stage, tumor vascular invasion, and poor overall and disease-free survivals in two independent cohorts containing 827 patients with HCC. UBE2T was further identified as an independent factor for overall survival by multivariate analyses. Luciferase reporter assays confirmed that UBE2T was directly targeted by miR-543 which was down-regulated in HCC. In vitro experiments demonstrated that UBE2T overexpression promoted, whereas UBE2T knockdown inhibited HCC cell growth. Ectopic expression of UBE2T resulted in the decreases of p53, p21 and Noxa. Further studies revealed that UBE2T facilitated the degradation of p53 protein via enhancing its ubiquitination. Collectively, our findings suggest UBE2T serves as a promising prognostic factor for HCC and functions as an oncogene. The newly identified miR-543/UBE2T/p53 axis may represent a new potential therapeutic target for HCC intervention.

Expression of FGF4 mRNA is mediated by mating behaviours in mice.

In mammals, breeding is preceded by species-specific mating behaviours. In this study, we investigated whether parthenogenetic embryo quality could be improved by mating behaviours in mice. To investigate this hypothesis, female mice were mated with vasectomized Kunming white male mice after superovulation. Oocytes were collected and counted at 16 h after superovulation. The oocytes were then artificially activated by medium containing 10 mM strontium chloride and 5 µg/ml cytochalasin B. Blastocysts were obtained by cultivating activated oocytes in vitro. Expression levels of reprogramming transcription factors (i.e. Oct4, Sox2, Klf4 and c-Myc) in oocytes, apoptosis-related genes (i.e. Bax, Bcl2 and c-Myc) in cumulus cells and pluripotency-related transcription factors (i.e. Oct4, Nanog and FGF4) in blastocysts were analysed in samples collected from mated and unmated mice. Additionally, developmental competence of parthenogenetic embryos was used to assess following fibroblast growth factor 4 (FGF4) treatment. The results showed that the formation rate of blastocysts in unmated mice was significantly higher than that in mated mice (p < 0.05). Embryo development was primarily blocked at the eight-cell stage in mated mice; however, the blastocyst formation rate did not differ significantly between groups after the addition of 25 ng/ml FGF4 to the medium at the four-cell stage (p > 0.05). Moreover, the expression of the reprogramming factor Sox2 was significantly different in oocytes collected from mated versus unmated mice. Taken together, our results demonstrated that mating behaviours influenced embryonic development in vitro by decreasing FGF4 expression.

Protective effect of rat pancreatic progenitors cells expressing Pdx1 and nestin on islets survival and function in vitro and in vivo

To maintain islets survival and function is critical in successful pancreatic transplantation. Pancreatic progenitors cells (PPCs) with lineage potentials, giving rise to exocrine, endocrine, and duct cells, reside in developing and adult pancreas. As tissue-specific stem cells, they can produce pancreatic tissue-specific matrix factors to promote islets survival and function. The aim of our research was to investigate the protective effect of rat pancreatic-duodenal homeobox 1 (Pdx1)+/nestin+ PPCs on islets. In vitro, co-culturing islets with Pdx1+/nestin+ PPCs prolonged the former survival from 7 to 14 days. Furthermore, with high glucose (300.8 mg/dl) stimuli, the yield of insulin in co-cultures was significantly higher than that in control group (single islets group). In vivo, co-transplanting islets and Pdx1+/nestin+ PPCs for 3 days, the blood glucose of diabetic rat was significantly decreased to normal level and sustained for 2 weeks. Without Pdx1+/nestin+ PPCs in islets transplantation, hyperglycemia was reversed at day 7 and recovered at day 15. Pathology analysis showed that islets had remnants in co-transplantation at day 21, as complete graft rejection in alone islets transplantation. Our study showed that Pdx1+/nestin+ PPCs displayed the ability of preserving islets viability and function in vitro and prolonging their survival in vivo (AU)

Protective effect of rat pancreatic progenitors cells expressing Pdx1 and nestin on islets survival and function in vitro and in vivo.

To maintain islets survival and function is critical in successful pancreatic transplantation. Pancreatic progenitors cells (PPCs) with lineage potentials, giving rise to exocrine, endocrine, and duct cells, reside in developing and adult pancreas. As tissue-specific stem cells, they can produce pancreatic tissue-specific matrix factors to promote islets survival and function. The aim of our research was to investigate the protective effect of rat pancreatic-duodenal homeobox 1 (Pdx1)(+)/nestin(+) PPCs on islets. In vitro, co-culturing islets with Pdx1(+)/nestin(+) PPCs prolonged the former survival from 7 to 14 days. Furthermore, with high glucose (300.8 mg/dl) stimuli, the yield of insulin in co-cultures was significantly higher than that in control group (single islets group). In vivo, co-transplanting islets and Pdx1(+)/nestin(+) PPCs for 3 days, the blood glucose of diabetic rat was significantly decreased to normal level and sustained for 2 weeks. Without Pdx1(+)/nestin(+) PPCs in islets transplantation, hyperglycemia was reversed at day 7 and recovered at day 15. Pathology analysis showed that islets had remnants in co-transplantation at day 21, as complete graft rejection in alone islets transplantation. Our study showed that Pdx1(+)/nestin(+) PPCs displayed the ability of preserving islets viability and function in vitro and prolonging their survival in vivo.

Predicting the classification of transcription factors by incorporating their binding site properties into a novel mode of Chou's pseudo amino acid composition.

Transcription factors (TF) are proteins that control the first step of gene expression, the transcription of DNA into RNA sequences. The mechanism of transcriptional regulatory can be much better understood if the category of transcription factors is known. We developed a new method for predicting the classification of transcription factors by incorporating their binding site properties into a novel mode of Chou's pseudo amino acid composition. The properties include the length of TFBSs for a TF, a new_PWM value, the proportion of not conservative TFBSs, the proportion of nonucleosome of TFBSs, the proportion of conserved-nucleosome of TFBSs, and the GC content of TFBSs. We construct a vector with these properties to represent a TF. Then the vectors which stand for TFs were classified with SVMs. The high accuracy obtained shows that these properties are of great significance for a TF.

[Randomized controlled clinical trails for treatment of knee osteoarthritis by warm acupuncture combined with intra-articular injection of sodium hyaluronate].

OBJECTIVE: To observe the synergism of warm acupuncture combined with intra-articular injection of sodium hyaluronate on knee osteoarthritis (KOA). METHODS: A total of 179 KOA outpatients were randomized into warm acupuncture group (n=90) and control group (n=89) according to a randomized numeral table. Warm acupuncture (needle warmed by moxibustion) was applied to Zusanli (ST 36), Xuehai (SP 10), Yinlingquan (SP 9), Nèixiyan(EX-LE4), etc. from the second day on after intra-articular Injection of sodium hyaluronate (2 mL, once a week for 5 weeks). Sodium hyaluronate intra-articular injection was given to the patients alone in the control group. Knee joint motor function was scaled before, 2 weeks (W) and 5 W after the therapy. The patients' quality of life was determined by using "Arthritis Impact Measurement Scale" before and 5 W after the therapy. RESULTS: In comparison with pre-therapy, the knee-joint motor function scores of both control group and acupuncture group were increased progressively and significantly 2 W and 5 W after the therapy. Both the knee-joint motor function score and the therapeutic effective rate of the acupuncture group were significantly higher than those of the control group (P<0.001, P<0.05). After the therapy, the scores of the Arthritis Impact Measurement Scale were significantly improved in both groups (P<0.01), and that of the acupuncture group was obviously lower than that of the control group (P<0.01). CONCLUSION: Warm acupuncture combined with intra-articular injection of sodium hyaluronate is an effective therapy for knee osteoarthritis.

[Current application of confocal laser scanning microscope (CLSM) in stomatology].

Confocal laser scanning microscopy is one kind of modern Hi-tech on the basis of confocal imaging which is characterized by depth discrimination capability. It has been widely used in the field of stomatology due to its great advantages of non-destructive and non-invasive optical sectioning and three-dimensional reconstruction of the vital objects, in situ and dynamic real-time observation of the tissues and cells can be performed at high resolution. This paper reviews the fundamentals of confocal imaging and the application of CLSM in the fields of dental material, caries, dentin bonding interface and other basic researches in stomatology in recent years.