Prevalence and proliferation of antibiotic resistance genes in two municipal wastewater treatment plants

The propagation of antibiotic resistance genes (ARGs) is an emerging health concern worldwide. Thus, it is important to understand and mitigate their occurrence in different systems. In this study, 30 ARGs that confer resistance to tetracyclines, sulfonamides, quinolones or macrolides were detected in two activated sludge wastewater treatment plants (WWTPs) in northern China. Bacteria harboring ARGs persisted through all treatment units, and survived disinfection by chlorination in greater percentages than total Bacteria (assessed by 16S rRNA genes). Although the absolute abundances of ARGs were reduced from the raw influent to the effluent by 89.0%-99.8%, considerable ARG levels [(1.0 ± 0.2) × 10(3) to (9.5 ± 1.8) × 10(5) copies/mL)] were found in WWTP effluent samples. ARGs were concentrated in the waste sludge (through settling of bacteria and sludge dewatering) at (1.5 ± 2.3) × 10(9) to (2.2 ± 2.8) × 10(11) copies/g dry weight. Twelve ARGs (tetA, tetB, tetE, tetG, tetH, tetS, tetT, tetX, sul1, sul2, qnrB, ermC) were discharged through the dewatered sludge and plant effluent at higher rates than influent values, indicating overall proliferation of resistant bacteria. Significant antibiotic concentrations (2%-50% of raw influent concentrations) remained throughout all treatment units. This apparently contributed selective pressure for ARG replication since the relative abundance of resistant bacteria (assessed by ARG/16S rRNA gene ratios) was significantly correlated to the corresponding effluent antibiotic concentrations. Similarly, the concentrations of various heavy metals (which induce a similar bacterial resistance mechanism as antibiotics - efflux pumps) were also correlated to the enrichment of some ARGs. Thus, curtailing the release of antibiotics and heavy metals to sewage systems (or enhancing their removal in pre-treatment units) may alleviate their selective pressure and mitigate ARG proliferation in WWTPs.

Persistence of extracellular DNA in river sediment facilitates antibiotic resistance gene propagation

The propagation of antibiotic resistance genes (ARGs) represents a global threat to both human health and food security. Assessment of ARG reservoirs and persistence is therefore critical for devising and evaluating strategies to mitigate ARG propagation. This study developed a novel, internal standard method to extract extracellular DNA (eDNA) and intracellular DNA (iDNA) from water and sediments, and applied it to determine the partitioning of ARGs in the Haihe River basin in China, which drains an area of intensive antibiotic use. The concentration of eDNA was higher than iDNA in sediment samples, likely due to the enhanced persistence of eDNA when associated with clay particles and organic matter. Concentrations of sul1, sul2, tetW, and tetT antibiotic resistance genes were significantly higher in sediment than in water, and were present at higher concentrations as eDNA than as iDNA in sediment. Whereas ARGs (frequently located on plasmid DNA) were detected for over 20 weeks, chromosomally encoded 16S rRNA genes were undetectable after 8 weeks, suggesting higher persistence of plasmid-borne ARGs in river sediment. Transformation of indigenous bacteria with added extracellular ARG (i.e., kanamycin resistance genes) was also observed. Therefore, this study shows that extracellular DNA in sediment is a major ARG reservoir that could facilitate antibiotic resistance propagation.

Occurrence and distribution of sulfonamides, tetracyclines, quinolones, macrolides, and nitrofurans in livestock manure and amended soils of Northern China

A feasible and rapid analysis for the simultaneous determination of sulfonamides (SAs), tetracyclines (TCs), fluoroquinolones (FQs), macrolides (MACs) and nitrofurans (NFs) in livestock manure and soils was established by solid-phase extraction (SPE)-ultra-performance liquid chromatography (UPLC)-tandem mass spectrometry (MS/MS). A total of 32 manure and 17 amended soil samples from the Liaoning and Tianjin areas in Northern China were collected for analysis. The largest detected frequencies and concentrations in manure samples were those of TCs (3326.6 ± 12,302.6 μg/kg), followed by FQs (411.3 ± 1453.4 μg/kg), SAs (170.6 ± 1060.2 μg/kg), NFs (85.1 ± 158.1 μg/kg), and MACs (1.4 ± 4.8 μg/kg). In general, veterinary antibiotics (VAs) were detected with higher concentrations in swine and chicken manure than in cattle manure, reflecting the heavy usage of VAs in swine and chicken husbandry in the studied area. Furthermore, higher residues of antibiotics were found in piglet and fattening swine manure than in sow manure. In addition, TCs were the most frequently (100%) detected antibiotics in amended soil with higher concentrations (up to 10,967.1 μg/kg) than any other VAs. The attenuation of SAs was more obvious than TCs in amended soil after fertilization, which can most likely be attributed to the stronger sorption of TCs than SAs to soil organic matter through cation exchange. This study illustrated the prevalence of TCs detected in both animal manure and fertilized agricultural soils in Northern China, which may increase the risk to human health through the food chain. Thus, TCs should be given more attention in the management of veterinary usage in livestock husbandry.

MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas

Temozolomide (TMZ) is an oral alkylating agent used for the treatment of glioblastoma and is now becoming a chemotherapeutic option in patients diagnosed with high-risk low-grade gliomas. The O-6-methylguanine-DNA methyltransferase (MGMT) is responsible for the direct repair of the main TMZ-induced toxic DNA adduct, the O6-Methylguanine lesion. MGMT promoter hypermethylation is currently the only known biomarker for TMZ response in glioblastoma patients. Here we show that a subset of recurrent gliomas carries MGMT genomic rearrangements that lead to MGMT overexpression, independently from changes in its promoter methylation. By leveraging the CRISPR/Cas9 technology we generated some of these MGMT rearrangements in glioma cells and demonstrated that the MGMT genomic rearrangements contribute to TMZ resistance both in vitro and in vivo. Lastly, we showed that such fusions can be detected in tumor-derived exosomes and could potentially represent an early detection marker of tumor recurrence in a subset of patients treated with TMZ.

Fate and proliferation of typical antibiotic resistance genes in five full-scale pharmaceutical wastewater treatment plants

This study investigated the characteristics of 10 subtypes of antibiotic resistance genes (ARGs) for sulfonamide, tetracycline, β-lactam and macrolide resistance and the class 1 integrase gene (intI1). In total, these genes were monitored in 24 samples across each stage of five full-scale pharmaceutical wastewater treatment plants (PWWTPs) using qualitative and real-time quantitative polymerase chain reactions (PCRs). The levels of typical ARG subtypes in the final effluents ranged from (2.08±0.16)×10(3) to (3.68±0.27)×10(6) copies/mL. The absolute abundance of ARGs in effluents accounted for only 0.6%-59.8% of influents of the five PWWTPs, while the majority of the ARGs were transported to the dewatered sludge with concentrations from (9.38±0.73)×10(7) to (4.30±0.81)×10(10) copies/g dryweight (dw). The total loads of ARGs discharged through dewatered sludge was 7-308 folds higher than that in the raw influents and 16-638 folds higher than that in the final effluents. The proliferation of ARGs mainly occurs in the biological treatment processes, such as conventional activated sludge, cyclic activated sludge system (CASS) and membrane bio-reactor (MBR), implying that significant replication of certain subtypes of ARGs may be attributable to microbial growth. High concentrations of antibiotic residues (ranging from 0.14 to 92.2 mg/L) were detected in the influents of selected wastewater treatment systems and they still remain high residues in the effluents. Partial correlation analysis showed significant correlations between the antibiotic concentrations and the associated relative abundance of ARG subtypes in the effluent. Although correlation does not prove causation, this study demonstrates that in addition to bacterial growth, the high antibiotic residues within the pharmaceutical WWTPs may influence the proliferation and fate of the associated ARG subtypes.

Occurrence of sulfonamide-, tetracycline-, plasmid-mediated quinolone- and macrolide-resistance genes in livestock feedlots in Northern China

Antibiotic resistance genes (ARGs) in livestock feedlots deserve attention because they are prone to transfer to human pathogens and thus pose threats to human health. In this study, the occurrence of 21 ARGs, including tetracycline (tet)-, sulfonamide (sul)-, plasmid-mediated quinolone (PMQR)- and macrolide-resistance (erm) genes were investigated in feces and adjacent soils from chicken, swine, and cattle feedlots in Northern China. PMQR and sul ARGs were the most prevalent and account for over 90.0 % of the total ARGs in fecal samples. Specifically, PMQR genes were the most prevalent, accounting for 59.6 % of the total ARGs, followed by sul ARGs (34.2 %). The percentage of tet ARGs was 3.4 %, and erm ARGs accounted for only 1.9 %. Prevalence of PMQR and sul ARGs was also found in swine and cattle feces. The overall trend of ARG concentrations in feces of different feeding animals was chicken > swine > beef cattle in the studied area. In soils, sul ARGs had the highest concentration and account for 71.1 to 80.2 % of the total ARGs, which is possibly due to the widely distributed molecular carriers (i.e., class one integrons), facilitating sul ARG propagation. Overall, this study provides integrated profiles of various types of ARGs in livestock feedlots and thus provides a reference for the management of antibiotic use in livestock farming.

High-frequency repetitive transcranial magnetic stimulation over the left DLPFC for major depression: Session-dependent efficacy: A meta-analysis

Background

Depression is a major debilitating psychiatric disorder. Current antidepressant drugs are often associated with side effects or treatment resistance. The aim of this meta-analysis was to evaluate therapeutic effects of high-frequency repetitive transcranial magnetic stimulation (HF-rTMS) in major depression (MD).

Methods

The medical data bases of PubMed, Medline, Embase and Cochrane Central Register were searched for randomized controlled trials (RCTs) reporting the therapeutic effects of high-frequency rTMS for depression, which were published in English between January 1990 and June 2016. The index terms were “depress*”, “depression” and “transcranial magnetic stimulation”. Depression outcome data of different sessions (5, 10, 15, and 20 sessions of rTMS treatment) were extracted and synthesized by calculating standardized mean difference (SMD) with 95% confidence intervals (CI) by using a random-effect model. Within each session group, the subgroup analyses based on the number of pulses (≤ 1000, 1200–1500, 1600–1800, and 2000–3000) were also conducted.

Results

Thirty RCTs with a total of 1754 subjects including 1136 in the rTMS group and 618 in the sham group were included in this meta-analysis. rTMS had a significant overall therapeutic effect on depression severity scores (SMD = −0.73, P < 0.00001). The five, 10, 15, 20 sessions of rTMS treatments yielded the significant mean effect sizes of −0.43, −0.60, −1.13, and −2.74, respectively. In the four groups (5, 10, 15, 20 sessions), the maximal mean effect size was all obtained in the subgroup of 1200–1500 pulses per day (−0.97, −1.14, −1.91, −5.47; P < 0.05).

Conclusions

The increasing of HF-rTMS sessions is associated with the increased efficacy of HF-rTMS in reducing depressed patients’ symptom severity. A total number of pulses of 1200–1500 per day appear to deliver the best antidepressant effects of HF-rTMS.

Real-Time Imaging Revealed That Exoelectrogens from Wastewater Are Selected at the Center of a Gradient Electric Field

Exoelectrogens acclimated from the environment are the key to energy recovery from waste in bioelectrochemical systems. However, it is still unknown how these bacteria are selectively enriched on the electrode. Here we confirmed for the first time that the electric field (EF) intensity selects exoelectrogens from wastewater using an integrated electrovisual system with a gradient EF. Under the operating conditions ( I = 3 × 10^-3A), the EF intensity on the working electrode ranged from 6.00 V/cm at the center to 1.08 V/cm at the edge. A thick biofilm (88.9 μm) with spherical pink aggregates was observed at the center, while the color became gray at the edge (33.8 μm). The coverage of the biofilm also increased linearly with EF intensity from 0.42 at the edge (12 mm to the center) to 0.78 at the center. The biofilm at the center contained 76% Geobacter, which was 25% higher than that at the edge (60%). Geobacter anodireducens was the main species induced by the EF (50% at the center vs 24% at the edge). These results improve our fundamental knowledge of exoelectrogen acclimation and mixed electroactive biofilm formation, which has broader implications for energy recovery from waste and general understanding of microbial ecology.

Deciphering Brain Complexity Using Single-cell Sequencing

The human brain contains billions of highly differentiated and interconnected cells that form intricate neural networks and collectively control the physical activities and high-level cognitive functions, such as memory, decision-making, and social behavior. Big data is required to decipher the complexity of cell types, as well as connectivity and functions of the brain. The newly developed single-cell sequencing technology, which provides a comprehensive landscape of brain cell type diversity by profiling the transcriptome, genome, and/or epigenome of individual cells, has contributed substantially to revealing the complexity and dynamics of the brain and providing new insights into brain development and brain-related disorders. In this review, we first introduce the progresses in both experimental and computational methods of single-cell sequencing technology. Applications of single-cell sequencing-based technologies in brain research, including cell type classification, brain development, and brain disease mechanisms, are then elucidated by representative studies. Lastly, we provided our perspectives into the challenges and future developments in the field of single-cell sequencing. In summary, this mini review aims to provide an overview of how big data generated from single-cell sequencing have empowered the advancements in neuroscience and shed light on the complex problems in understanding brain functions and diseases.

Long-Term Succession Shows Interspecies Competition of Geobacter in Exoelectrogenic Biofilms

Geobacter spp. are well-known exoelectrogenic microorganisms that often predominate acetate-fed biofilms in microbial fuel cells (MFCs) and other bioelectrochemical systems (BESs). By using an amplicon sequence variance analysis (at one nucleotide resolution), we observed a succession between two closely related species (98% similarity in 16S RNA), Geobacter sulfurreducens and Geobacter anodireducens, in the long-term studies (20 months) of MFC biofilms. Geobacter spp. predominated in the near-electrode portion of the biofilm, while the outer layer contained an abundance of aerobes, which may have helped to consume oxygen but reduced the relative abundance of Geobacter. Removal of the outer aerobes by norspermidine washing of biofilms revealed a transition from G. sulfurreducens to G. anodireducens. This succession was also found to occur rapidly in co-cultures in BES tests even in the absence of oxygen, suggesting that oxygen was not a critical factor. G. sulfurreducens likely dominated in early biofilms by its relatively larger cell size and production of extracellular polymeric substances (individual advantages), while G. anodireducens later predominated due to greater cell numbers (quantitative advantage). Our findings revealed the interspecies competition in the long-term evolution of Geobacter genus, providing microscopic insights into Geobacter's niche and competitiveness in complex electroactive microbial consortia.

scONE-seq: A single-cell multi-omics method enables simultaneous dissection of phenotype and genotype heterogeneity from frozen tumors

Single-cell multi-omics can provide a unique perspective on tumor cellular heterogeneity. Most previous single-cell whole-genome RNA sequencing (scWGS-RNA-seq) methods demonstrate utility with intact cells from fresh samples. Among them, many are not applicable to frozen samples that cannot produce intact single-cell suspensions. We have developed scONE-seq, a versatile scWGS-RNA-seq method that amplifies single-cell DNA and RNA without separating them from each other and hence is compatible with frozen biobanked samples. We benchmarked scONE-seq against existing methods using fresh and frozen samples to demonstrate its performance in various aspects. We identified a unique transcriptionally normal-like tumor clone by analyzing a 2-year frozen astrocytoma sample, demonstrating that performing single-cell multi-omics interrogation on biobanked tissue by scONE-seq could enable previously unidentified discoveries in tumor biology.

Binding of carbon nanotube to BMP receptor 2 enhances cell differentiation and inhibits apoptosis via regulating bHLH transcription factors

Biomaterials that can drive stem cells to an appropriate differentiation level and decrease apoptosis of transplanted cells are needed in regenerative medicine. Nanomaterials are promising novel materials for such applications. Here we reported that carboxylated multiwalled carbon nanotube (MWCNT 1) promotes myogenic differentiation of mouse myoblast cells and inhibits cell apoptosis under the differentiation conditions by regulating basic helix-loop-helix transcription factors. MWCNT 1 attenuates bone morphogenetic protein receptor (BMPR) signaling activity by binding to BMPR2 and attenuating the phosphorylation of BMPR1. This molecular understanding allowed us to tune stem cell differentiation to various levels by chemical modifications, demonstrating human control of biological activities of nanoparticles and opening an avenue for potential applications of nanomaterials in regenerative medicine.

Calcitonin driven v-Ha-ras induces multilineage pulmonary epithelial hyperplasias and neoplasms

We initiated a transgenic model for primary pulmonary neuroendocrine cell (PNEC) hyperplasia/neoplasia using v-Ha-ras driven by the neural/neuroendocrine (NE)-specific calcitonin promoter (rascal). Previously, we showed that nitrosamine treated rodents develop PNEC hyperplasia but non-NE lung tumors, with variable outcomes presumably reflecting ras activation in multiple cell lineages. Interestingly, all rascal transgenic mouse lineages develop hyperplasias of NE and non-NE cells but mostly non-NE lung carcinomas, with rascal mRNA in differentiated PNECs and tumor cells. Analyses of embryonic lung demonstrate rascal mRNA in undifferentiated epithelium, consistent with expression in a common pluripotent precursor cell. These unexpected observations indicate that v-Ha-ras can lead to both NE and non-NE hyperplasia/neoplasia in vivo, opening new avenues for studies of lung carcinogenesis.

Calpain-activated mTORC2/Akt pathway mediates airway smooth muscle remodelling in asthma

BACKGROUND

Allergic asthma is characterized by inflammation and airway remodelling. Airway remodelling with excessive deposition of extracellular matrix (ECM) and larger smooth muscle mass are correlated with increased airway responsiveness and asthma severity. Calpain is a family of calcium-dependent endopeptidases, which plays an important role in ECM remodelling. However, the role of calpain in airway smooth muscle remodelling remains unknown.

OBJECTIVE

To investigate the role of calpain in asthmatic airway remodelling as well as the underlying mechanism.

METHODS

The mouse asthma model was made by ovalbumin sensitization and challenge. Calpain conditional knockout mice were studied in the model. Airway smooth muscle cells (ASMCs) were isolated from smooth muscle bundles in airway of rats. Cytokines IL-4, IL-5, TNF-α, and TGF-β1, and serum from patients with asthma were selected to treated ASMCs. Collagen-I synthesis, cell proliferation, and phosphorylation of Akt in ASMCs were analysed.

RESULTS

Inhibition of calpain using calpain knockout mice attenuated airway smooth muscle remodelling in mouse asthma models. Cytokines IL-4, IL-5, TNF-α, and TGF-β1, and serum from patients with asthma increased collagen-I synthesis, cell proliferation, and phosphorylation of Akt in ASMCs, which were blocked by the calpain inhibitor MDL28170. Moreover, MDL28170 reduced cytokine-induced increases in Rictor protein, which is the most important component of mammalian target of rapamycin complex 2 (mTORC2). Blockage of the mTORC2 signal pathway prevented cytokine-induced phosphorylation of Akt, collagen-I synthesis, and cell proliferation of ASMCs and attenuated airway smooth muscle remodelling in mouse asthma models.

CONCLUSIONS AND CLINICAL RELEVANCE

Our results indicate that calpain mediates cytokine-induced collagen-I synthesis and proliferation of ASMCs via the mTORC2/Akt signalling pathway, thereby regulating airway smooth muscle remodelling in asthma.

Bombesin-like peptides and receptors in normal fetal baboon lung: roles in lung growth and maturation

Previously, we have shown that bombesin-like peptide (BLP) promotes fetal lung development in rodents and humans but mediates postnatal lung injury in hyperoxic baboons. The present study analyzed the normal ontogeny of BLP and BLP receptors as well as the effects of BLP on cultured normal fetal baboon lungs. Transcripts encoding gastrin-releasing peptide (GRP), a pulmonary BLP, were detectable on gestational day 60 (ED60), peaked on approximately ED90, and then declined before term (ED180). Numbers of BLP-immunopositive neuroendocrine cells peaked from ED80 to ED125 and declined by ED160, preceding GRP-receptor mRNAs detected from ED125 until birth. BLP (0.1-10 nM) stimulated type II cell differentiation in organ cultures as assessed by [(3)H]choline incorporation into surfactant phospholipids, electron microscopy, and increased surfactant protein (SP) A- and/or SP-C-immunopositive cells and SP-A mRNA. BLP also induced neuroendocrine differentiation on ED60. Cell proliferation was induced by GRP, peaking on ED90. Similarly, blocking BLP degradation stimulated lung growth and maturation, which was completely reversed by a BLP-specific antagonist. The dissociation between GRP and GRP-receptor gene expression during ontogeny suggests that novel BLP receptors and/or peptides might be implicated in these responses.

Ionic Liquid Enriches the Antibiotic Resistome, Especially Efflux Pump Genes, Before Significantly Affecting Microbial Community Structure

An expanding list of chemicals may permeabilize bacterial cells and facilitate horizontal gene transfer (HGT), which enhances propagation of antibiotic resistance genes (ARGs) in the environment. Previous studies showed that 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]), an ionic liquid, can facilitate HGT of some ARGs among bacteria. However, the dynamic response of a wider range of ARGs and associated mobile genetic elements (MGEs) in different environments is unknown. Here, we used metagenomic tools to study shifts of the resistome and microbiome in both sediments and freshwater microcosms exposed to [BMIm][PF6]. Exposure for 16 h to 0.1 or 1.0 g/L significantly enriched more than 207 ARG subtypes primarily encoding efflux pumps in freshwater microcosms as well as cultivable antibiotic-resistant bacteria. This resistome enrichment was attributed to HGT facilitated by MGEs (428 plasmids, 61 integron-integrase genes, and 45 gene cassettes were enriched) as well as to HGT-related functional genes. Interestingly, resistome enrichment occurred fast (within 16 h) after [BMIm][PF6] exposure, before any significant changes in bacterial community structure. Similar ARG enrichment occurred in sediment microcosms exposed to [BMIm][PF6] for 28 d, and this longer exposure affected the microbial community structure (e.g., Proteobacteria abundance increased significantly). Overall, this study suggests that [BMIm][PF6] releases could rapidly enrich the antibiotic resistome in receiving environments by increasing HGT and fortuitously selecting for efflux pump genes, thus contributing to ARG propagation.

Machine learning of genomic features in organotropic metastases stratifies progression risk of primary tumors

Metastatic cancer is associated with poor patient prognosis but its spatiotemporal behavior remains unpredictable at early stage. Here we develop MetaNet, a computational framework that integrates clinical and sequencing data from 32,176 primary and metastatic cancer cases, to assess metastatic risks of primary tumors. MetaNet achieves high accuracy in distinguishing the metastasis from the primary in breast and prostate cancers. From the prediction, we identify Metastasis-Featuring Primary (MFP) tumors, a subset of primary tumors with genomic features enriched in metastasis and demonstrate their higher metastatic risk and shorter disease-free survival. In addition, we identify genomic alterations associated with organ-specific metastases and employ them to stratify patients into various risk groups with propensities toward different metastatic organs. This organotropic stratification method achieves better prognostic value than the standard histological grading system in prostate cancer, especially in the identification of Bone-MFP and Liver-MFP subtypes, with potential in informing organ-specific examinations in follow-ups.

Enhanced horizontal transfer of antibiotic resistance genes in freshwater microcosms induced by an ionic liquid

The spread and propagation of antibiotic resistance genes (ARGs) is a worldwide public health concern. Ionic liquids (ILs), considered as "environmentally friendly" replacements for industrial organic solvents, have been widely applied in modern industry. However, few data have been collected regarding the potential ecological and environmental risks of ILs, which are important for preparing for their potential discharge into the environment. In this paper, the IL 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]) (0.001-5.0 g/L) was tested for its effects on facilitating ARGs horizontal transfer mediated by plasmid RP4 in freshwater microcosms. In the horizontal transfer microcosms, the transfer frequency of plasmid RP4 was significantly enhanced (60-fold higher than untreated groups) by the IL [BMIm][PF6] (1.0 g/L). Meanwhile, two strains of opportunistic pathogen Acinetobacter spp. and Salmonella spp. were isolated among the transconjugants, illustrating plasmid RP4 mediated horizontal transfer of ARGs occurred in pathogen. This could increase the risk of ARGs dissemination to human pathogens and pose great threat to public health. The cause that [BMIm[PF6] enhanced the transfer frequency of plasmid RP4 was proposed by suppressed cell membrane barrier and enhanced cell membrane permeability, which was evidenced by flow cytometry (FCM). This is the first report that some ILs facilitate horizontal transfer of plasmid RP4 which is widely distributed in the environment and thus add the adverse effects of the environmental risk of ILs.

RNA Exosome Complex-Mediated Control of Redox Status in Pluripotent Stem Cells

The RNA exosome complex targets AU-rich element (ARE)-containing mRNAs in eukaryotic cells. We identified a transcription factor, ZSCAN10, which binds to the promoters of multiple RNA exosome complex subunits in pluripotent stem cells to maintain subunit gene expression. We discovered that induced pluripotent stem cell clones generated from aged tissue donors (A-iPSC) show poor expression of ZSCAN10, leading to poor RNA exosome complex expression, and a subsequent elevation in ARE-containing RNAs, including glutathione peroxidase 2 (Gpx2). Excess GPX2 leads to excess glutathione-mediated reactive oxygen species scavenging activity that blunts the DNA damage response and apoptosis. Expression of ZSCAN10 in A-iPSC recovers RNA exosome gene expression, the DNA damage response, and apoptosis. These findings reveal the central role of ZSCAN10 and the RNA exosome complex in maintaining pluripotent stem cell redox status to support a normal DNA damage response.

CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression

Detection of DNA copy number alteration in cancer cells is critical to understanding cancer initiation and progression. Widely used methods, such as DNA arrays and genomic DNA sequencing, are relatively expensive and require DNA samples at a microgram level, which are not avaiblable in certain situations like clinical biopsies or single-cell genomes. Here, we developed an alternative method-CNAPE to computationally infer copy number alterations from gene expression data. A prior knowledge-aided machine learning model was proposed, trained and tested on 9,740 cancer samples from The Cancer Genome Atlas. We then applied CNAPE to study gliomas, the most common and aggressive brain cancer in adult. Particularly, using RNA sequencing data, CNAPE respectively predicted DNA copy number of chromosomes, chromosomal arms, and 12 commonly altered genes, and achieved over 80 percent accuracy in almost all broad regions and some focal regions. CNAPE was developed as an easy-to-use tool at https://github.com/WangLabHKUST/CNAPE.

Metagenomic and bioanalytical insights into quorum sensing of methanogens in anaerobic digestion systems with or without the addition of conductive filter

Understanding microbial interactions in the methanogenesis system through quorum sensing (QS) is very important for system optimization. Known QS genes were collected and classified into seven groups based on the signal molecules, which were used for constructing a hierarchical quorum sensing database (QSDB). QSDB containing 39,981 QS genes of seven QS groups was constructed and QS genes were analyzed with QSDB. Methanogen genomes were aligned with QSDB and acyl-homoserine lactones (AHLs) system was predicted as the most probable QS system. This database was further applied to analyze QS in methanogens from two upflow anaerobic sludge blanket-anaerobic filter hybrid reactors with conductive filter (CFB) and nonconductive filter (SEP), and a control without filter (CON). The maximum COD degradation rates in CFB (722.2 ± 10.1 mg/L·h) was elevated by 42.9% compared to CON (505.4 ± 5.98 mg/L·h). Metagenomic sequencing revealed Methanosaeta, Methanobacterium, and Methanosarcina were dominant, and the abundances was 4.3 times higher in the sludge of CFB compared to CON. The overall abundance of QS genes was CFB > SEP > CON, and AHLs were the most abundant group of QS genes. The filI/filR system, a luxI/luxR homolog, was firstly detected in methanogens, showing a high abundance in the CFB (0.085%) compared to in the CON (0.058%). The concentration of AHL molecules in CFB biofilms (0.04%) was about four times that in the CON (0.01%). Syntrophobacter and Smithella were the two major syntrophic bacteria of methanogens, and their abundances were positively correlated with methanogens. In addition, Syntrophobacter and Smithella harbored QS RpfB (component of the diffusible signal factor system) and PDE (component of cyclic di-GMP system). This study provides useful guidance for deeply understanding of QS in anaerobic digestion systems.

Pharmacogenomic profiling reveals molecular features of chemotherapy resistance in IDH wild-type primary glioblastoma

BACKGROUND

Although temozolomide (TMZ) has been used as a standard adjuvant chemotherapeutic agent for primary glioblastoma (GBM), treating isocitrate dehydrogenase wild-type (IDH-wt) cases remains challenging due to intrinsic and acquired drug resistance. Therefore, elucidation of the molecular mechanisms of TMZ resistance is critical for its precision application.

METHODS

We stratified 69 primary IDH-wt GBM patients into TMZ-resistant (n = 29) and sensitive (n = 40) groups, using TMZ screening of the corresponding patient-derived glioma stem-like cells (GSCs). Genomic and transcriptomic features were then examined to identify TMZ-associated molecular alterations. Subsequently, we developed a machine learning (ML) model to predict TMZ response from combined signatures. Moreover, TMZ response in multisector samples (52 tumor sectors from 18 cases) was evaluated to validate findings and investigate the impact of intra-tumoral heterogeneity on TMZ efficacy.

RESULTS

In vitro TMZ sensitivity of patient-derived GSCs classified patients into groups with different survival outcomes (P = 1.12e-4 for progression-free survival (PFS) and 3.63e-4 for overall survival (OS)). Moreover, we found that elevated gene expression of EGR4, PAPPA, LRRC3, and ANXA3 was associated to intrinsic TMZ resistance. In addition, other features such as 5-aminolevulinic acid negative, mesenchymal/proneural expression subtypes, and hypermutation phenomena were prone to promote TMZ resistance. In contrast, concurrent copy-number-alteration in PTEN, EGFR, and CDKN2A/B was more frequent in TMZ-sensitive samples (Fisher's exact P = 0.0102), subsequently consolidated by multi-sector sequencing analyses. Integrating all features, we trained a ML tool to segregate TMZ-resistant and sensitive groups. Notably, our method segregated IDH-wt GBM patients from The Cancer Genome Atlas (TCGA) into two groups with divergent survival outcomes (P = 4.58e-4 for PFS and 3.66e-4 for OS). Furthermore, we showed a highly heterogeneous TMZ-response pattern within each GBM patient using in vitro TMZ screening and genomic characterization of multisector GSCs. Lastly, the prediction model that evaluates the TMZ efficacy for primary IDH-wt GBMs was developed into a webserver for public usage ( http://www.wang-lab-hkust.com:3838/TMZEP ).

CONCLUSIONS

We identified molecular characteristics associated to TMZ sensitivity, and illustrate the potential clinical value of a ML model trained from pharmacogenomic profiling of patient-derived GSC against IDH-wt GBMs.

A new strategy employed for identification of sweet orange cultivars with RAPD markers

We optimized RAPD techniques by increasing the length of RAPD primers and performing a strict screening of PCR annealing temperature to distinguish 60 sweet orange cultivars from the Research Institute of Pomology at the Chinese Academy of Agricultural Sciences. A new approach called cultivar identification diagram (CID) was used to improve the efficiency of RAPD markers for cultivar identification. Thirteen effective primers were first screened from 54 RAPD arbitrary 11-mer primers based on their amplification products and amplified polymorphic bands; they were then used for PCR amplification of all 60 cultivars. All cultivars were manually and completely separated by the polymorphic bands appearing in DNA fingerprints from 13 primers; a CID of the 60 sweet orange cultivars was then constructed. This CID separated all the cultivars from each other, based on the polymorphic bands; the corresponding primers were marked in the correct positions on the sweet orange CID. The CID strategy facilitates the identification of fruit cultivars with DNA markers. This CID of sweet orange cultivars will be very useful for the protection of cultivar rights and for early identification of seedlings in the nursery industry.

Orthogonal design in the optimization of a start codon targeted (SCoT) PCR system in Roegneria kamoji Ohwi

Roegneria kamoji Ohwi is an excellent forage grass due to its high feeding value and high resistance to some biotic and abiotic stresses. However, the start codon targeted (SCoT) polymorphism has not been conducted on R. kamoji. In this study, an orthogonal L₁₆ (4⁵) design was employed to investigate the effects of five factors (Mg²⁺, dNTPs, Taq DNA polymerase, primer, and template DNA) on the polymerase chain reaction (PCR) to determine the optimal SCoT-PCR system for R. kamoji. The results showed that the most suitable conditions for SCoT-PCR in R. kamoji included 1.5 mM Mg²⁺, 0.15 mM dNTPs, 1.0 U Taq DNA polymerase, 0.4 pM primer, and 40 ng template DNA. SCoT primers 39 and 41 were used to verify the stability of the optimal reaction system, and amplification bands obtained from diverse samples were found to be clear, rich, and stable in polymorphisms, indicating that this reaction system can be used for SCoT-PCR analysis of R. kamoji. We have developed a simple and rapid way to study the mutual effects of factors and to obtain positive results through the use of an orthogonal design L₁₆ (4⁵) to optimize the SCoT-PCR system. This method may provide basic information for molecular marker-assisted breeding and analyses of genetic diversity in R. kamoji.