(Plantaginaceae)

Plantago asiatica L. is a representative individual species of Plantaginaceae, whose high reputation is owed to its edible and medicinal values. However, the phylogeny and genes of the P. asiatica chloroplast have not yet been well described. Here we report the findings of a comprehensive analysis of the P. asiatica chloroplast genome. The P. asiatica chloroplast genome is 164,992 bp, circular, and has a GC content of 37.98%. The circular genome contains 141 genes, including 8 rRNAs, 38 tRNAs, and 95 protein-coding genes. Seventy-two simple sequence repeats are detected. Comparative chloroplast genome analysis of six related species suggests that a higher similarity exists in the coding region than the non-coding region, and differences in the degree of preservation is smaller between P. asiatica and Plantago depressa than among others. Our phylogenetic analysis illustrates P. asiatica has a relatively close relationship with P. depressa, which was also divided into different clades with Plantago ovata and Plantago lagopus in the genus Plantago. This analysis of the P. asiatica chloroplast genome contributes to an improved deeply understanding of the evolutionary relationships among Plantaginaceae.

Association of Circular RNAs levels in blood and Essential Hypertension with Carotid Plaque

BACKGROUND

As one of the essential hypertension (EH)-mediated target organ damage, carotid plaque is a crucial subclinical precursor for cardiovascular events. Therefore, it is vital to identify the risk factors and pathogenesis for EH with carotid plaque.

METHODS

Based on our previous microarray analysis, we selected four circRNAs as the candidate circRNAs and detected their expression levels in blood of 192 subjects (64 healthy controls, 64 EH patients, and 64 EH patients with carotid plaque) by qRT-PCR analysis. The regulatory mechanism of circRNAs involved in carotid plaque was predicted by bioinformatics analysis.

RESULTS

The level of hsa_circ_0124782 increased significantly and the levels of hsa_circ_0131618 and hsa_circ_0127342 decreased significantly in the EH group and EH with carotid plaque group compared with the control group (P < .05). Functional enrichment analysis showed that three circRNAs might be implicated in pathogenesis for carotid plaque.

CONCLUSION

Our study revealed the relationship between three circRNAs and carotid plaque, suggesting that they may serve as potential biomarkers for EH with carotid plaque.

The chromatin signatures of enhancers and their dynamic regulation

Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.

Copper coordination modulates prion conversion and infectivity in mammalian prion proteins

In mammals the cellular form of the prion protein (PrP^C) is a ubiquitous protein involved in many relevant functions in the central nervous system. In addition to its physiological functions PrP^C plays a central role in a group of invariably fatal neurodegenerative disorders collectively called prion diseases. In fact, the protein is a substrate in a process in which it converts into an infectious and pathological form denoted as prion. The protein has a unique primary structure where the unstructured N-terminal moiety possesses characteristic sequences wherein histidines are able to coordinate metal ions, in particular copper ions. These sequences are called octarepeats for their characteristic length. Moreover, a non-octarepeat fifth-copper binding site is present where copper coordination seems to control infectivity. In this review, I will argue that these sequences may play a significant role in modulating prion conversion and replication.

Through the lens of phase separation: intrinsically unstructured protein and chromatin looping

The establishment, maintenance and dynamic regulation of three-dimensional (3D) chromatin structures provide an important means for partitioning of genome into functionally distinctive domains, which helps to define specialized gene expression programs associated with developmental stages and cell types. Increasing evidence supports critical roles for intrinsically disordered regions (IDRs) harbored within transcription factors (TFs) and chromatin-modulatory proteins in inducing phase separation, a phenomenon of forming membrane-less condensates through partitioning of biomolecules. Such a process is also critically involved in the establishment of high-order chromatin structures and looping. IDR- and phase separation-driven 3D genome (re)organization often goes wrong in disease such as cancer. This review discusses about recent advances in understanding how phase separation of intrinsically disordered proteins (IDPs) modulates chromatin looping and gene expression.

Larval nutritional-stress and tolerance to extreme temperatures in the peach fruit fly, Bactrocera zonata (Diptera: Tephritidae)

Within the factors affecting insect tolerance to extreme environmental conditions, insect nutrition, particularly of immature stages, has received insufficient attention. In the present study, we address this gap by investigating the effects of larval nutrition on heat and cold tolerance of adult Bactrocera zonata - an invasive, polyphagous fruit fly pest. We manipulated the nutritional content in the larval diet by varying the amount of added yeast (2-10% by weight), while maintaining a constant sucrose content. Adults derived from the different larval diets were tested for their tolerance to extreme heat and cold stress. Restricting the amount of yeast reduced the efficacy of the larval diet (i.e. number of pupae produced per g of diet) as well as pupal and adult fresh weight, both being significantly lower for yeast-poor diets. Additionally, yeast restriction during the larval stage (2% yeast diet) significantly reduced the amount of protein but not lipid reserves of newly emerged males and females. Adults maintained after emergence on granulated sugar and water for 10 days were significantly more tolerant to extreme heat (i.e. knock-down time at 42 ^oC) when reared as larvae on yeast-rich diets (8% and 10% yeast) compared to counterparts developing on a diet containing 2% yeast. Nevertheless, the composition of the larval diet did not significantly affect adult survival following acute cold stress (exposure to -3°C for 2 hrs.). These results are corroborated by previous findings on Drosophilid flies. Possible mechanisms leading to nutrition-based heat-tolerance in flies are discussed.

Investigation of the effects of starvation stress in the midgut of the silkworm Bombyx mori

During their evolution, organisms have developed various mechanisms to adapt to changing nutritional conditions such as mobilization of storage molecules and activation of autophagy. In this study, the mechanism of adaptive responses in the midgut of the silkworm Bombyx mori L., 1758 (Lepidoptera: Bombycidae) larvae, which were starved for different days, was investigated. The study was carried out at the Insect Physiology Research Laboratory and Silkworm Culture Laboratory at Ege University between 2018 and 2020. For this purpose, the histological structure of the midgut was examined using hematoxylin&amp;eosin staining and its protein, sugar, glycogen, and lipid contents were determined. As autophagy markers, lysosomal enzyme activities were measured and expressions of autophagy-related genes (mTOR, ATG8, and ATG12) were analyzed by qRT-PCR. The results showed that, depending on the time of onset of starvation stress, autophagy plays no role as an adaptive response under starvation conditions or occurs at a much more moderate level than autophagy which happens as part of cell death during larval-pupal metamorphosis.

Expanding DdCBE-mediated targeting scope to aC motif preference in rat

An animal model harboring pathogenic mitochondrial DNA (mtDNA) mutations is important to understand the biological links between mtDNA variation and mitochondrial diseases. DdCBE, a DddA-derived cytosine base editor, has been utilized in zebrafish, mice, and rats for tC sequence-context targeting and human mitochondrial disease modeling. However, human pathogenic mtDNA mutations other than the tC context cannot be manipulated. Here, we screened the combination of different DdCBE pairs at pathogenic mtDNA mutation sites with nC (n for a, g, or c) context and identified that the left-G1333C (L1333C) + right G1333N (R1333N) pair could mediate C⋅G-to-T⋅A conversion effectively at aC sites in rat C6 cells. The editing efficiency at disease-associated mtDNA mutation sites within aC context was further confirmed to be up to 67.89% in vivo. Also, the installed disease-associated mtDNA mutations were germline transmittable. Moreover, the edited rats showed impaired cardiac function and mitochondrial function, resembling human mitochondrial disease symptoms. In summary, for the first time, we expanded the DdCBE targeting scope to an aC motif and installed the pathogenic mutation in rats to model human mitochondrial diseases.

Pheromone effect of estradiol regulates the conjugative transfer of pCF10 carrying antibiotic resistance genes

Horizontal gene transfer (HGT) mediated by conjugative plasmids greatly contributes to bacteria evolution and the transmission of antibiotic resistance genes (ARGs). In addition to the selective pressure imposed by extensive antibiotic use, environmental chemical pollutants facilitate the dissemination of antibiotic resistance, consequently posing a serious threat to the ecological environment. Presently, the majority of studies focus on the effects of environmental compounds on R plasmid-mediated conjugation transfer, and pheromone-inducible conjugation has largely been neglected. In this study, we explored the pheromone effect and potential molecular mechanisms of estradiol in promoting the conjugative transfer of pCF10 plasmid in Enterococcus faecalis. Environmentally relevant concentrations of estradiol significantly increased the conjugative transfer of pCF10 with a maximum frequency of 3.2 × 10^-2, up to 3.5-fold change compared to that of control. Exposure to estradiol induced the activation of pheromone signaling cascade by increasing the expression of ccfA. Furthermore, estradiol might directly bind to the pheromone receptor PrgZ and promote pCF10 induction and finally enhance the conjugative transfer of pCF10. These findings cast valuable insights on the roles of estradiol and its homolog in increasing antibiotic resistance and the potential ecological risk.

Interaction hub critical for telomerase recruitment and primer-template handling for catalysis

Telomerase processively adds telomeric DNA repeats to chromosome ends using catalytic protein subunit TERT and a template on its RNA subunit TR. Mammalian telomerase is recruited to telomeres by the TEL patch and NOB regions of shelterin component TPP1. Recent cryo-EM structures of human telomerase reveal that a composite TERT TEN-(IFD-TRAP) domain interacts with TPP1. Here, we generate TERT mutants to demonstrate that a three-way TEN-(IFD-TRAP)-TPP1 interaction is critical for telomerase recruitment to telomeres and processive telomere repeat addition. Single mutations of IFD-TRAP at its interface with TR or the DNA primer impair telomerase catalysis. We further reveal the importance of TERT motif 3N and TEN domain loop ⁹⁹FGF¹⁰¹ in telomerase action. Finally, we demonstrate that TPP1 TEL patch loop residue F172, which undergoes a structural rearrangement to bind telomerase, contributes to the human-mouse species specificity of the telomerase-TPP1 interaction. Our study provides insights into the multiple functions of TERT IFD-TRAP, reveals novel TERT and TPP1 elements critical for function, and helps explain how TPP1 binding licenses robust telomerase action at natural chromosome ends.

Temporal transitions in the postembryonic nervous system of the nematode Caenorhabditis elegans: Recent insights and open questions

After the generation, differentiation and integration into functional circuitry, post-mitotic neurons continue to change certain phenotypic properties throughout postnatal juvenile stages until an animal has reached a fully mature state in adulthood. We will discuss such changes in the context of the nervous system of the nematode C. elegans, focusing on recent descriptions of anatomical and molecular changes that accompany postembryonic maturation of neurons. We summarize the characterization of genetic timer mechanisms that control these temporal transitions or maturational changes, and discuss that many but not all of these transitions relate to sexual maturation of the animal. We describe how temporal, spatial and sex-determination pathways are intertwined to sculpt the emergence of cell-type specific maturation events. Finally, we lay out several unresolved questions that should be addressed to move the field forward, both in C. elegans and in vertebrates.

Electrochemical studies of the mitochondrial ROMK2 potassium channel activity reconstituted into the free-standing and tethered bilayer lipid membranes

The renal-outer-medullary‑potassium (ROMK2) channel modulates potassium transport in the kidney. It has been postulated that the ROMK2 is the pore-forming subunit of the mitochondrial ATP-sensitive potassium channel as a mediator of cardioprotection. In this study, cell-free synthesis of the ROMK2 was performed in presence of membrane scaffold protein (MSP1D1) nanodiscs. Activity measurements were achieved after channel reconstitution into the planar lipid bilayer and tethered bilayer lipid membranes. Both methods allowed for monitoring of channel function, verified with channel blocking and activation/re-activation experiments. The primary function of the mitochondrial potassium channels is to regulate the potential of the mitochondrial membrane, which allows them to play an important role in cytoprotection. This work focuses on obtaining the ROMK2 using a cell-free expression system, followed by the incorporation of the channel protein into the lipid bilayer and studying the influence of voltage changes and molecular modulators on channel activity. Channel activity was measured after its reconstitution into two models of lipid bilayers - BLM (Bilayer Lipid Membrane) and tBLM (Tethered Bilayer Lipid Membrane) deposited on a solid gold electrode. These two model membranes and electrochemical measurements made it possible to measure the flux of K⁺ ions in the presence of channel modulators.

The role of PhoP/PhoQ system in regulating stress adaptation response in Escherichia coli O157:H7

The development of acid tolerance response (ATR) as a result of low pH in Escherichia coli O157:H7 (E. coli O157:H7) contaminating beef during processing is considered a major food safety concern. Thus, in order to explore the formation and molecular mechanisms of the tolerance response of E. coli O157:H7 in a simulated beef processing environment, the resistance of a wild-type (WT) strain and its corresponding ΔphoP mutant to acid, heat, and osmotic pressure was evaluated. Strains were pre-adapted under different conditions of pH (5.4 and 7.0), temperature (37 °C and 10 °C), and culture medium (meat extract and Luria-Bertani broth media). In addition, the expression of genes related to stress response and virulence was also investigated among WT and ΔphoP strains under the tested conditions. Pre-acid adaptation increased the resistance of E. coli O157:H7 to acid and heat treatment while resistance to osmotic pressure decreased. Moreover, acid adaptation in meat extract medium simulating slaughter environment increased ATR, whereas pre-adaptation at 10 °C reduced the ATR. Furthermore, it was shown that mildly acidic conditions (pH = 5.4) and the PhoP/PhoQ two-component system (TCS) acted synergistically to enhance acid and heat tolerance in E. coli O157:H7. Additionally, the expression of genes related to arginine and lysine metabolism, heat shock, and invasiveness was up-regulated, which revealed that the mechanism of acid resistance and cross-protection under mildly acidic conditions was mediated by the PhoP/PhoQ TCS. Both acid adaptation and phoP gene knockout reduced the relative expression of stx1 and stx2 genes which were considered as critical pathogenic factors. Collectively, the current findings indicated that ATR could occur in E. coli O157:H7 during beef processing. Thus, there is an increased food safety risk due to the persistence of tolerance response in the following processing conditions. The present study provides a more comprehensive basis for the effective application of hurdle technology in beef processing.

Self-organized collective cell behaviors as design principles for synthetic developmental biology

Over the past two decades, molecular cell biology has graduated from a mostly analytic science to one with substantial synthetic capability. This success is built on a deep understanding of the structure and function of biomolecules and molecular mechanisms. For synthetic biology to achieve similar success at the scale of tissues and organs, an equally deep understanding of the principles of development is required. Here, we review some of the central concepts and recent progress in tissue patterning, morphogenesis and collective cell migration and discuss their value for synthetic developmental biology, emphasizing in particular the power of (guided) self-organization and the role of theoretical advances in making developmental insights applicable in synthesis.

Automating the design-build-test-learn cycle towards next-generation bacterial cell factories

Automation is playing an increasingly significant role in synthetic biology. Groundbreaking technologies, developed over the past 20 years, have enormously accelerated the construction of efficient microbial cell factories. Integrating state-of-the-art tools (e.g. for genome engineering and analytical techniques) into the design-build-test-learn cycle (DBTLc) will shift the metabolic engineering paradigm from an almost artisanal labor towards a fully automated workflow. Here, we provide a perspective on how a fully automated DBTLc could be harnessed to construct the next-generation bacterial cell factories in a fast, high-throughput fashion. Innovative toolsets and approaches that pushed the boundaries in each segment of the cycle are reviewed to this end. We also present the most recent efforts on automation of the DBTLc, which heralds a fully autonomous pipeline for synthetic biology in the near future.

Bushen Wenyang Huayu Decoction inhibits autophagy by regulating the SIRT1-FoXO-1 pathway in endometriosis rats

ETHNOPHARMACOLOGICAL RELEVANCE

Bushen Wenyang Huayu Decoction (BWHD) is a traditional Chinese medicine for tonifying kidney and warming Yang, thereby resolving blood stasis and relieving pain. BWHD can significantly improve the clinical symptoms of patients with endometriosis (EMs), but its mechanism is still unclear.

AIM OF THE STUDY

We evaluated the expression and role of the SIRT1-FoxO-1 pathway and autophagy levels in EMs rats. The therapeutic effects and potential therapeutic mechanisms of BWHD were also investigated.

METHODS

Twenty rats were randomized into the sham group and eighty rats were used for model establishment by autologous transplantation. After successful modeling, they were randomized into the model, BWHD, EX527+BWHD and EX527 groups, with 20 rats in each group. All rats were intragastrically administered with for 3 weeks. Localization of Sirtuin 1 (SIRT1), Forkhead boxO-1 (FoXO-1), Beclin-1, autophagy-related 5 (Atg5) and autophagy-related 7 (Atg7) was determined by immunohistochemical staining. The expression of the above proteins was determined by Western blot and their messenger RNA (mRNA) levels were detected by Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR).

RESULTS

The protein and mRNA expressions of FoXO-1, Beclin-1, Atg5 and Atg7 in the model group were markedly increased, while that of SIRT1 was markedly decreased relative to the sham group (p < 0.05 and p<0.01, respectively). Results showed that the protein and mRNA expressions of FoXO-1, Beclin-1, Atg5 and Atg7 in eutopic and ectopic endometrium of BWHD group were lower, while SIRT1 expression was higher than in the model group (p < 0.05 and p<0.01, respectively). Furthermore, protein and mRNA expression levels of FoXO-1, Beclin-1, Atg5 and Atg7 in eutopic and ectopic endometrium of EX527 group were higher, while SIRT1 level was significantly lower than in the model group (p < 0.05 and p < 0.01, respectively). The EX527-induced changes in protein and mRNA expressions were reversed in the EX527+BWHD group (p < 0.05 and p < 0.01, respectively).

CONCLUSIONS

BWHD inhibits autophagy by up-regulating SIRT1 and down-regulating FoXO-1 expression in EMs via the SIRT1-FoXO-1 signaling pathway. Therefore, it is a potential treatment for EMs.

Influence of substitution model selection on protein phylogenetic tree reconstruction

Probabilistic phylogenetic tree reconstruction is traditionally performed under a best-fitting substitution model of molecular evolution previously selected according to diverse statistical criteria. Interestingly, some recent studies proposed that this procedure is unnecessary for phylogenetic tree reconstruction leading to a debate in the field. In contrast to DNA sequences, phylogenetic tree reconstruction from protein sequences is traditionally based on empirical exchangeability matrices that can differ among taxonomic groups and protein families. Considering this aspect, here we investigated the influence of selecting a substitution model of protein evolution on phylogenetic tree reconstruction by the analyses of real and simulated data. We found that phylogenetic tree reconstructions based on a selected best-fitting substitution model of protein evolution are the most accurate, in terms of topology and branch lengths, compared with those derived from substitution models with amino acid replacement matrices far from the selected best-fitting model, especially when the data has large genetic diversity. Indeed, we found that substitution models with similar amino acid replacement matrices produce similar reconstructed phylogenetic trees, suggesting the use of substitution models as similar as possible to a selected best-fitting model when the latter cannot be used. Therefore, we recommend the use of the traditional protocol of selection among substitution models of evolution for protein phylogenetic tree reconstruction.

Environmental stress stimulates microbial activities as indicated by cyclopropane fatty acid enhancement

Soil microbial responses to environmental stress remain a critical question in microbial ecology. The content of cyclopropane fatty acid (CFA) in cytomembrane has been widely used to evaluate environmental stress on microorganisms. Here, we used CFA to investigate the ecological suitability of microbial communities and found a stimulating impact of CFA on microbial activities during wetland reclamation in Sanjiang Plain, Northeastern China. The seasonality of environmental stress resulted in the fluctuation of CFA content in the soil, which suppressed microbial activities due to nutrient loss upon wetland reclamation. After land conversion, the aggravation of temperature stress to microbes increased the CFA content by 5 % (autumn) to 163 % (winter), which led to the suppression of microbial activities by 7 %-47 %. By contrast, the warmer soil temperature and permeability decreased the CFA content by 3 % to 41 % and consequently aggravated the microbial reduction by 15 %-72 % in spring and summer. Complex microbial communities of 1300 CFA-produced species were identified using a sequencing approach, suggesting that soil nutrients dominated the differentiation in these microbial community structures. Further analysis with structural equation modeling highlighted the important function of CFA content to environmental stress and the stimulating influence of CFA induced by environmental stress on microbial activities. Our study shows the biological mechanisms of seasonal CFA content for microbial adaption to environmental stress under wetland reclamation. It advances our knowledge of microbial physiology affecting soil element cycling caused by anthropogenic activities.

Qidan Tiaozhi capsule attenuates metabolic syndrome via activating AMPK/PINK1-Parkin-mediated mitophagy

ETHNOPHARMACOLOGICAL RELEVANCE

Qidan Tiaozhi capsule (QD), a traditional Chinese medicine, has been used to treat metabolic syndrome for over a decade. However, the mechanism of QD in the treatment of metabolic syndrome is still unknown.

AIM OF THE STUDY

Growing studies demonstrate that impaired mitophagy is one of the important causes of metabolic syndrome. Thus, this research aims to investigate the mechanism of mitophagy in the QD treatment of metabolic syndrome.

MATERIALS AND METHODS

Network pharmacology and molecular docking were used to probe the mechanism of QD treatment of metabolic syndrome. In an oleic acid-induced cell model, glucose consumption and uptake capacity, triglyceride (TG), total cholesterol (TC), malonaldehyde (MDA), superoxide dismutase (SOD) and ROS levels, and mitochondrial membrane potential (MMP) were examined. mRFP-GFP-LC3 adenovirus and GFP-LC3 lentivirus were used to examine the effect of QD on mitophagy. The IRS2-PI3K and AMPK/PINK1-Parkin signal pathways were also determined. What's more, the PINK1 gene was silenced to verify the above findings. In a high-fat diet-fed mouse model, body weight, organ indexes, OGTT, ITT, HOMA-IR, insulin sensitivity, serum MDA, SOD, TC, TG, LDL-C and HDL-C, hepatic TC, TG, LDL-C and HDL-C levels, hepatic steatosis, and IRS2-PI3K and AMPK/PINK1-Parkin signal pathways were investigated.

RESULTS

Results from network pharmacology and molecular docking suggested that QD might suppress oxidative stress to improve metabolic syndrome. In an oleic acid-induced cell model, compared with the model group, enhanced glucose consumption and uptake ability, inhibited intracellular lipid accumulation, TC, TG, MDA and ROS levels, and increased SOD level and MMP were found in QD groups. And mitophagy levels, IRS2-PI3K and AMPK/PINK1-Parkin signal pathways were promoted. Interestingly, PINK1 silencing reversed the therapeutic action of QD on oleic acid-induced cells. In high-fat diet-fed mice, inhibited body weight, abdominal fat indexes, liver indexes, HOMA-IR, serum and hepatic TC, TG and LDL-C, serum MDA and hepatic steatosis, and increased insulin sensitivity, serum and hepatic HDL-C, serum SOD, and activated IRS2-PI3K and AMPK/PINK1-Parkin signal pathways were found in QD groups.

CONCLUSION

QD activates AMPK/PINK1-Parkin-mediated mitophagy to suppress oxidative stress to treat metabolic syndrome.

Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India

Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequencing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p < 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic assessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.

The early rise and spread of evolutionary game theory: perspectives based on recollections of early workers

Though the first attempts to introduce game theory into evolutionary biology failed, new formalism by Maynard Smith and Price in 1973 had almost instant success. We use information supplied by early workers to analyse how and why evolutionary game theory (EGT) spread so rapidly in its earliest years. EGT was a major tool for the rapidly expanding discipline of behavioural ecology in the 1970s; each catalysed the other. The first models were applied to animal contests, and early workers sought to improve their biological reality to compare predictions with observations. Furthermore, it was quickly realized that EGT provided a general evolutionary modelling method; not only was it swiftly applied to diverse phenotypic adaptations in evolutionary biology, it also attracted researchers from other disciplines such as mathematics and economics, for which game theory was first devised. Lastly, we pay attention to exchanges with population geneticists, considering tensions between the two modelling methods, as well as efforts to bring them closer. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Rate accelerations in plastid and mitochondrial genomes of Cyperaceae occur in the same clades

Cyperaceae, the second largest family in the monocot order Poales, comprises >5500 species and includes the genus Eleocharis with ∼ 250 species. A previous study of complete plastomes of two Eleocharis species documented extensive structural heteroplasmy, gene order changes, high frequency of dispersed repeats along with gene losses and duplications. To better understand the phylogenetic distribution of gene and intron content as well as rates and patterns of sequence evolution within and between mitochondrial and plastid genomes of Eleocharis and Cyperaceae, an additional 29 Eleocharis organelle genomes were sequenced and analyzed. Eleocharis experienced extensive gene loss in both genomes while loss of introns was mitochondria-specific. Eleocharis has higher rates of synonymous (dS) and nonsynonymous (dN) substitutions in the plastid and mitochondrion than most sampled angiosperms, and the pattern was distinct from other eudicot lineages with accelerated rates. Several clades showed higher dS and dN in mitochondrial genes than in plastid genes. Furthermore, nucleotide substitution rates of mitochondrial genes were significantly accelerated on the branch leading to Cyperaceae compared to most angiosperms. Mitochondrial genes of Cyperaceae exhibited dramatic loss of RNA editing sites and a negative correlation between RNA editing and dS values was detected among angiosperms. Mutagenic retroprocessing and dysfunction of DNA replication, repair and recombination genes are the most likely cause of striking rate accelerations and loss of edit sites and introns in Eleocharis and Cyperaceae organelle genomes.

A protocol for single nucleus RNA-seq from frozen skeletal muscle

Single-cell technologies are a method of choice to obtain vast amounts of cell-specific transcriptional information under physiological and diseased states. Myogenic cells are resistant to single-cell RNA sequencing because of their large, multinucleated nature. Here, we report a novel, reliable, and cost-effective method to analyze frozen human skeletal muscle by single-nucleus RNA sequencing. This method yields all expected cell types for human skeletal muscle and works on tissue frozen for long periods of time and with significant pathological changes. Our method is ideal for studying banked samples with the intention of studying human muscle disease.

A core epiphytic bacterial consortia synergistically protect citrus from postharvest disease

Biological antagonists are a series of microbes that can control pathogens to reduce the incidence of disease or reduce symptoms. Herein, four varieties of citrus fruit were selected to perform an amplicon sequencing on their epiphytic microbiota to get a systematic understanding of them. Co-occurrence network, Venn, and LefSe analysis were performed to filter to 24 genera which represent the universality, specificity, and correlation among samples. Functional analysis hinted that the genes related to chitinase, which most of these 24 bacteria carry, might lead to a disease-suppressive phenotype. 115 strains of epiphytic bacteria were isolated, and the bacterial synthetic community was constructed by 8 strains. The in vivo test results indicated they were able to reduce pathogen development for a longer time than separate inoculation. Collectively, this study showed the disease control potential provided by native epiphytic bacteria of fruit and give a new strategy to sustainable agriculture.

Effect of HSPA8 gene on the proliferation, apoptosis and immune function of HD11 cells

HSPA8 (Heat shock 70 kDa protein 8) is a molecular chaperone involved in a variety of cellular processes. This gene may affect the proliferation, apoptosis and immune function of chicken macrophages, but the specific mechanism remains unclear. The purpose of this study was to explore the effect of the HSPA8 gene on the proliferation, apoptosis and immune function of chicken macrophages. In this study, a chicken HSPA8 overexpression plasmid, interference fragment and corresponding controls were transfected into HD11 cells, and then the expression of the HSPA8 gene, cell proliferation, cell cycle, apoptosis rate and immune function of each group were detected. The results showed that transfection of the HSPA8 overexpression plasmid significantly upregulated the level of HSPA8 expression in HD11 cells compared with the control; significantly promoted the proliferation of HD11 cells and the expression of PCNA, CCND1 and CCNB3; decreased the number of cells in the G1 phase and increased the number of cells in the S phase; decreased the rate of apoptosis and upregulated the expression of Bcl-2; and promoted the expression of the LPS-induced cytokines IL-1β, IL-6 and TNF-α. Transfection of the HSPA8 interference fragment significantly downregulated the level of HSPA8 expression in HD11 cells; significantly inhibited the proliferation of HD11 cells and the expression of PCNA, CCND1 and CDK1; increased the number of cells in the G1 phase and decreased the number of cells in the S phase; increased the rate of apoptosis, downregulated the expression of Bcl-2 and upregulated the expression levels of Fas and FasL; and inhibited the expression of the LPS-induced cytokines IL-1β and NF-κB. The results suggested that HSPA8 promotes the proliferation of and inhibits the apoptosis of HD11 cells and has a proinflammatory effect.

Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia

Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.

Histone demethylase MaJMJ15 is involved in the regulation of postharvest banana fruit ripening

Histone methylation plays important roles in plant development. However, the role of histone methylation in fruit ripening remains unclear. Here, a total of 16 Jumonji domain-containing proteins (JMJs) were identified from banana genome. During fruit ripening, expression of MaJMJ15 was significantly upregulated. Exogenous ethylene accelerated the upregulation whereas 1-methylcyclopropene delayed the process, suggesting that MaJMJ15 positively regulates banana fruit ripening. MaJMJ15 is an H3K27me3 site-specific demethylase. Transient overexpression of MaJMJ15 promoted banana fruit ripening. Moreover, the global H3K27me3 was decreased by MaJMJ15. Furthermore, MaJMJ15 directly targeted several key ripening-related genes (RRGs) in banana including NAC transcription factor 1/2 (MaNAC1/2), 1-aminocyclopropane-1-carboxylate synthase 1 (MaACS1), 1-aminocyclopropane-1-carboxylate oxidase 1 (MaACO1) and expansin 2 (MaEXP2), removed H3K27me3 from their chromatin, and activated their expression. Our data suggest that MaJMJ15 is an H3K27me3 demethylase, which is involved in the regulation of banana fruit ripening by activating expression of key RRGs via removal of H3K27me3.

Astaxanthin delays brain aging in senescence-accelerated mouse prone 10: inducing autophagy as a potential mechanism

Brain aging is a complex biological process often associated with a decline in cognitive functions and motility. Astaxanthin (AST) is a strong antioxidant capable of crossing the blood-brain barrier. The effect of AST on brain aging and its physiological and molecular mechanism are still unclear. The study aimed to investigate whether AST from AstaReal A1010 improved brain aging by inducing autophagy in SAMP10 mice. Different concentrations of AstaReal A1010 were intragastrically administered to 6-month-old SAMP10 mice for 3 months. The results demonstrated that AST delayed age-related cognitive decline, motor ability and neurodegeneration, upregulated the expression levels of autophagy-related genes beclin-1 and LC3 in the brain. It may induce autophagy by regulating IGF-1/Akt/mTOR and IGF-1/Akt/FoxO3a signaling. Treatment with autophagy inhibitor 3-methyladenine (3MA) partly reversed the anti-aging effect of AST. In conclusion, our findings suggest that AST may induce autophagy by regulating IGF-1/Akt/mTOR and IGF-1/Akt/FoxO3a signaling, thereby delaying age-related neurodegeneration and cognitive decline in SAMP10 mice.

H4K20me1 plays a dual role in transcriptional regulation of regeneration and axis patterning in Hydra

The evolution of the first body axis in the animal kingdom and its extensive ability to regenerate makes Hydra, a Cnidarian, an excellent model system for understanding the underlying epigenetic mechanisms. We identify that monomethyltransferase SETD8 is critical for regeneration in Hydra because of its conserved interaction with β-catenin to fine-tune the associated gene regulatory network. Inhibition of SETD8 activity abolishes head and foot regeneration in Hydra Furthermore, we show that H4K20me1, the histone mark imparted by SETD8, colocalizes with the transcriptional activation machinery locally at the β-catenin-bound TCF/LEF-binding sites on the promoters of head-associated genes, marking an epigenetic activation mode. In contrast, genome-wide analysis of the H4K20me1 occupancy revealed a negative correlation with transcriptional activation. We propose that H4K20me1 acts as a general repressive histone mark in Cnidaria and describe its dichotomous role in transcriptional regulation in Hydra.

The triticale mature pollen and stigma proteomes - assembling the proteins for a productive encounter

Triticeae crops are major contributors to global food production and ensuring their capacity to reproduce and generate seeds is critical. However, despite their importance our knowledge of the proteins underlying Triticeae reproduction is severely lacking and this is not only true of pollen and stigma development, but also of their pivotal interaction. When the pollen grain and stigma are brought together they have each accumulated the proteins required for their intended meeting and accordingly studying their mature proteomes is bound to reveal proteins involved in their diverse and complex interactions. Using triticale as a Triticeae representative, gel-free shotgun proteomics was used to identify 11,533 and 2977 mature stigma and pollen proteins respectively. These datasets, by far the largest to date, provide unprecedented insights into the proteins participating in Triticeae pollen and stigma development and interactions. The study of the Triticeae stigma has been particularly neglected. To begin filling this knowledge gap, a developmental iTRAQ analysis was performed revealing 647 proteins displaying differential abundance as the stigma matures in preparation for pollination. An in-depth comparison to an equivalent Brassicaceae analysis divulged both conservation and diversification in the makeup and function of proteins involved in the pollen and stigma encounter. SIGNIFICANCE: Successful pollination brings together the mature pollen and stigma thus initiating an intricate series of molecular processes vital to crop reproduction. In the Triticeae crops (e.g. wheat, barley, rye, triticale) there persists a vast deficit in our knowledge of the proteins involved which needs to be addressed if we are to face the many upcoming challenges to crop production such as those associated with climate change. At maturity, both the pollen and stigma have acquired the protein complement necessary for their forthcoming encounter and investigating their proteomes will inevitably provide unprecedented insights into the proteins enabling their interactions. By combining the analysis of the most comprehensive Triticeae pollen and stigma global proteome datasets to date with developmental iTRAQ investigations, proteins implicated in the different phases of pollen-stigma interaction enabling pollen adhesion, recognition, hydration, germination and tube growth, as well as those underlying stigma development were revealed. Extensive comparisons between equivalent Triticeae and Brassiceae datasets highlighted both the conservation of biological processes in line with the shared goal of activating the pollen grain and promoting pollen tube invasion of the pistil to effect fertilization, as well as the significant distinctions in their proteomes consistent with the considerable differences in their biochemistry, physiology and morphology.

Genome-wide identification and skin expression of immunoglobulin superfamily in discus fish (Symphysodon aequifasciatus) reveal common genes associated with vertebrate lactation

Discus Symphysodon spp. employs an unusual parental care behavior where fry feed on parental skin mucus after hatching. Studies on discus immunoglobulin superfamily (IgSF) especially during parental care are scarce. Here, a total of 518 IgSF members were identified based on discus genome and clustered into 12 groups, unevenly distributing on 30 linkage groups. A total of 92 pairs of tandem duplication and 40 pairs of segmental duplication that underwent purifying selection were identified. IgSF genes expressed differentially in discus skin during different care stages and between male and female parents. Specifically, the transcription of btn1a1, similar with mammalian lactation, increased after spawning, reached a peak when fry started biting on parents' skin mucus, and then decreased. The expression of btn2a1 and other immune members, e.g., nect4, fcl5 and cd22, were up-regulated when fry stopped biting on mucus. These results suggest the expression differentiation of IgSF genes in skin of discus fish during parental care.

A comparison of algorithms for identifying copy number variants in family-based whole-exome sequencing data and its implications in inheritance pattern analysis

There remain challenges in accurately identifying constitutional or germline copy number variants (gCNVs) based on whole-exome sequencing data that have implications for genetic diagnosis for 'rare undiagnosed disease' in the clinical setting. Although multiple algorithms have been proposed, a systematic comparison of these algorithms for calling gCNVs and analyzing inherited pattern have yet to be fully conducted. Therefore, we empirically compared seven exome-based algorithms, including XHMM, CLAMMS, CODEX2, ExomeDepth, DECoN, CN.MOPS, and GATK gCNV, for calling gCNVs in 151 individuals from 44 pedigrees, together with the gold standard of genotyping-derived gCNVs in the same cohort for the performance assessment. These algorithms demonstrated varied powers in identifying gCNVs, although the distribution of gCNVs size was similar. The number of shared gCNVs across these algorithms was limited (e.g., only four gCNVs shared among seven algorithms); however, several algorithms showed varying degrees of consistency (e.g., 1,843 gCNVs shared between DECoN and ExomeDepth). CLAMMS and CODEX2 outperformed the remaining algorithms according to a relatively higher F-score (i.e., 0.145 and 0.152, respectively). In addition, these algorithms exhibited different Mendelian inconsistencies of gCNVs and significant challenges remained in inheritance pattern analysis. In conclusion, selecting good algorithms may have important implications in gCNVs-based inheritance pattern analysis for family-based studies.

The molecular mechanisms of apoptosis accompanied with the epigenetic regulation of the NY-ESO-1 antigen in non-small lung cancer cells treated with decitabine (5-aza-CdR)

Dysregulated epigenetic modifications are common in lung cancer but have been reversed using demethylating agent like 5-Aza-CdR. 5-Aza-CdR induces/upregulates the NY-ESO-1 antigen in lung cancer. Therefore, we investigated the molecular mechanisms accompanied with the epigenetic regulation of NY-ESO-1 in 5-Aza-CdR-treated NCI-H1975 cell line. We showed significant induction of the NY-ESO-1 protein (**p < 0.0097) using Cellular ELISA. Bisulfite-sequencing demonstrated 45.6% demethylation efficiency at the NY-ESO-1 gene promoter region and RT-qPCR analysis confirmed the significant induction of NY-ESO-1 at mRNA level (128-fold increase, *p < 0.050). We then investigated the mechanism by which 5-Aza-CdR inhibits cell proliferation in the NCI-H1975 cell line. Upregulation of the death receptors TRAIL (2.04-fold *p < 0.011) and FAS (2.1-fold *p < 0.011) indicate activation of the extrinsic apoptotic pathway. The upregulation of Voltage-dependent anion-selective channel protein 1 (1.9-fold), Major vault protein (1.8-fold), Bax (1.16-fold), and Cytochrome C (1.39-fold) indicate the activation of the intrinsic pathway. We also observed the differential expression of protein Complement C3 (3.3-fold), Destrin (-5.1-fold), Vimentin (-1.7-fold), Peroxiredoxin 4 (-1.6-fold), Fascin (-1.8-fold), Heme oxygenase-2 (-0.67-fold**p < 0.0055), Hsp27 (-0.57-fold**p < 0.004), and Hsp70 (-0.39-fold **p < 0.001), indicating reduced cell growth, cell migration, and metastasis. The upregulation of 40S ribosomal protein S9 (3-fold), 40S ribosomal protein S15 (4.2-fold), 40S ribosomal protein S18 (2.5-fold), and 60S ribosomal protein L22 (4.4-fold) implied the induction of translation machinery. These results reiterate the decisive role of 5-Aza-CdR in lung cancer treatment since it induces the epigenetic regulation of NY-ESO-1 antigen, inhibits cell proliferation, increases apoptosis, and decreases invasiveness.

Molecular patterns and processes in evolving sociality: lessons from insects

Social insects have provided some of the clearest insights into the origins and evolution of collective behaviour. Over 20 years ago, Maynard Smith and Szathmáry defined the most complex form of insect social behaviour-superorganismality-among the eight major transitions in evolution that explain the emergence of biological complexity. However, the mechanistic processes underlying the transition from solitary life to superorganismal living in insects remain rather elusive. An overlooked question is whether this major transition arose via incremental or step-wise modes of evolution. We suggest that examination of the molecular processes underpinning different levels of social complexity represented across the major transition from solitary to complex sociality can help address this question. We present a framework for using molecular data to assess to what extent the mechanistic processes that take place in the major transition to complex sociality and superorganismality involve nonlinear (implying step-wise evolution) or linear (implying incremental evolution) changes in the underlying molecular mechanisms. We assess the evidence for these two modes using data from social insects and discuss how this framework can be used to test the generality of molecular patterns and processes across other major transitions. This article is part of a discussion meeting issue 'Collective behaviour through time'.

Evolution of codon and amino acid usage in bacterial protein toxins

Toxin proteins are secreted by most pathogens as an integral part of pathogenic mechanism(s). The toxins act by either damaging the host cell membrane (for example, pore-forming toxins and RTX toxins) or by modulation of important cellular pathways (for example, inhibition of protein translation by ribosome-inactivating proteins). The mechanism of action of these toxins provides the pathogen with strategies for adaptation in the unfavorable host environment. Though, secreted by different pathogenic species, the protein toxins seem to share common features that allow the protein to bind to specific molecules and enter the host cell. Earlier studies have suggested role of several events like horizontal gene transfer and insertion-deletion mutations in evolution of protein toxins. The present study involving 125 bacterial protein toxins secreted by 49 pathogenic bacteria focuses on the role and constraints of the bacterial genome on evolution of codon and amino acid usage in respective bacterial protein toxins. We compare the nucleotide composition, codon and dinucleotide usage trends between different classes of bacterial protein toxins and between individual toxins and the parent bacterial genome expressing the toxin(s).

Structural basis for H2A-H2B recognitions by human Spt16

The human facilitates chromatin transcription (FACT) complex, consisting of Spt16 and SSRP1, is a versatile histone chaperone that can engage free H2A-H2B dimer and H3-H4 tetramer (or dimer), and partially unraveled nucleosome. The C-terminal domain of human Spt16 (hSpt16-CTD) is the decisive element for engaging H2A-H2B dimer and partially unraveled nucleosome. The molecular basis of the H2A-H2B dimer recognitions by hSpt16-CTD is not fully comprehended. Here, we present a high-resolution snapshot of the recognitions of the H2A-H2B dimer by hSpt16-CTD via an acidic intrinsically disordered (AID) segment, and reveal some distinct structural features of hSpt16-CTD as compared to the budding yeast Spt16-CTD.