Anti-Tumor Effects and Toxicity Reduction Mechanisms of Prunella vulgaris: A Comprehensive Review

PURPOSE

To investigate and systematically describe the mechanism of action of Prunella vulgaris (P. vulgaris) against digestive system tumors and related toxicity reduction.

METHODS

This study briefly describes the history of medicinal food and the pharmacological effects of P. vulgaris, focusing on the review of the anti-digestive tumor effects of the active ingredients of P. vulgaris and the mechanism of its toxicity reduction.

RESULTS

The active ingredients of P. vulgaris may exert anti-tumor effects by inducing the apoptosis of cancer cells, inhibiting angiogenesis, inhibiting the migration and invasion of tumor cells, and inhibiting autophagy. In addition, P. vulgaris active ingredients inhibit the release of inflammatory factors and macrophages and increase the level of indicators of oxidative stress through the modulation of target genes in the pathway to achieve the effect of toxicity reduction.

CONCLUSION

The active ingredients in the medicine food homology plant P. vulgaris not only treat digestive system tumors through different mechanisms but also reduce the toxic effects. P. vulgaris is worthy of being explored more deeply.

Exploring anti-inflammatory and antioxidant-related quality markers of Artemisia absinthium L. based on spectrum-effect relationship

INTRODUCTION

Artemisia absinthium L. is a well-known medicinal, aromatic, and edible plant with important medicinal and economic properties and a long history of use in treating liver inflammation and other diseases; however, there has been insufficient progress in quality control.

OBJECTIVE

This study aimed to investigate the quality markers for the anti-inflammatory and antioxidant activities of A. absinthium based on spectrum-effect relationship analysis.

MATERIALS AND METHODS

Eighteen batches of A. absinthium from different origins were used. Chemical fingerprints were obtained by ultra-performance liquid chromatography (UPLC). The chemical compositions were identified by quadrupole-Orbitrap high-resolution mass spectrometry. Anti-inflammatory activity was assessed by inhibition of cyclooxygenase-2 and 15-lipoxygenase in vitro and inhibition of nitric oxide release in lipopolysaccharide-induced BV-2 cells. Antioxidant activity was assessed by DPPH and ABTS radical scavenging assays. The relationship between bioactivity and chemical fingerprints was then analyzed using chemometrics including gray relational analysis, bivariate correlation analysis, and orthogonal partial least squares analysis.

RESULTS

Different batches of A. absinthium extracts possessed significant anti-inflammatory and antioxidant activities to varying degrees. Eighty compounds were identified from A. absinthium, and 12 main common peaks were obtained from the UPLC fingerprints. P3 (chlorogenic acid), P5 (isochlorogenic acid A), and P6 (isochlorogenic acid C) were screened as the most promising active compounds by correlation analysis and further validated for their remarkable anti-inflammatory effects.

CONCLUSION

This is the first study to screen the quality markers of A. absinthium by establishing the spectrum-effect relationship, which can provide a reference for the development of quality standards and further research on A. absinthium.

Methylation entropy landscape of Chinese long-lived individuals reveals lower epigenetic noise related to human healthy aging

The transition from ordered to noisy is a significant epigenetic signature of aging and age-related disease. As a paradigm of healthy human aging and longevity, long-lived individuals (LLI, >90 years old) may possess characteristic strategies in coping with the disordered epigenetic regulation. In this study, we constructed high-resolution blood epigenetic noise landscapes for this cohort by a methylation entropy (ME) method using whole genome bisulfite sequencing (WGBS). Although a universal increase in global ME occurred with chronological age in general control samples, this trend was suppressed in LLIs. Importantly, we identified 38,923 genomic regions with LLI-specific lower ME (LLI-specific lower entropy regions, for short, LLI-specific LERs). These regions were overrepresented in promoters, which likely function in transcriptional noise suppression. Genes associated with LLI-specific LERs have a considerable impact on SNP-based heritability of some aging-related disorders (e.g., asthma and stroke). Furthermore, neutrophil was identified as the primary cell type sustaining LLI-specific LERs. Our results highlight the stability of epigenetic order in promoters of genes involved with aging and age-related disorders within LLI epigenomes. This unique epigenetic feature reveals a previously unknown role of epigenetic order maintenance in specific genomic regions of LLIs, which helps open a new avenue on the epigenetic regulation mechanism in human healthy aging and longevity.

Primary study of the relative and compound biological effectiveness model for boron neutron capture therapy based on nanodosimetry

BACKGROUND

The current radiobiological model employed for boron neutron capture therapy (BNCT) treatment planning, which relies on microdosimetry, fails to provide an accurate representation the biological effects of BNCT. The precision in calculating the relative biological effectiveness (RBE) and compound biological effectiveness (CBE) plays a pivotal role in determining the therapeutic efficacy of BNCT. Therefore, this study focuses on how to improve the accuracy of the biological effects of BNCT.

PURPOSE

The purpose of this study is to propose new radiation biology models based on nanodosimetry to accurately assess RBE and CBE for BNCT.

METHODS

Nanodosimetry, rooted in ionization cluster size distributions (ICSD), introduces a novel approach to characterize radiation quality by effectively delineating RBE through the ion track structure at the nanoscale. In the context of prior research, this study presents a computational model for the nanoscale assessment of RBE and CBE. We establish a simplified model of DNA chromatin fiber using the Monte Carlo code TOPAS-nBio to evaluate the applicability of ICSD to BNCT and compute nanodosimetric parameters.

RESULTS

Our investigation reveals that both homogeneous and heterogeneous nanodosimetric parameters, as well as the corresponding biological model coefficients α and β, along with RBE values, exhibit variations in response to varying intracellular 10B concentrations. Notably, the nanodosimetric parameterM 1 C 2 $M_1^{{{\mathrm{C}}}_2}$ effectively captures the fluctuations in model coefficients α and RBE.

CONCLUSION

Our model facilitates a nanoscale analysis of BNCT, enabling predictions of nanodosimetric quantities for secondary ions as well as RBE, CBE, and other essential biological metrics related to the distribution of boron. This contribution significantly enhances the precision of RBE calculations and holds substantial promise for future applications in treatment planning.

Characterisation and identification of chemical constituents in aqueous extract of Fomes officinalis Ames based on ultrahigh-performance liquid chromatography tandem quadrupole-Orbitrap high-resolution mass spectrometry

INTRODUCTION

Fungal species are an attractive resource for physiologically functional food and drug precursor. Fomes officinalis Ames, a medicinal fungus, is traditionally used as a folk medicine in traditional Chinese medicine prescription for the therapy of cough and asthma. The water-soluble substances in Chinese herbal medicines are likely to play an important physiological function. However, information on probing and identifying chemical components of the aqueous extract of Fomes officinalis Ames (AFO) remains unknown.

OBJECTIVE

This study was conducted to screen and characterise the chemical components of AFO.

MATERIAL AND METHODS

An effective and sensitive ultrahigh-performance liquid chromatography tandem quadrupole-Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap-HRMS) method with the Full MS/PIL/dd-MS2 acquisition approach was applied for the profiling of chemical components in AFO. An HSS T3 column was used for component separation, and a strategy of simultaneous targeted and untargeted multicomponent characterisation was implemented. Multiple identification approaches were used, including accurate molecular mass and elemental composition matching, literature and database searching, and fragmentation rules elucidation.

RESULTS

A total of 115 components, including 20 amino acids and derivatives, six nucleobases, nine nucleosides, 75 dipeptides, two tripeptides, and three other components, were tentatively identified. Among them, the targeted exploring method screened six nucleobases and nine nucleosides including modified nucleosides. To our best knowledge, this is the first time a report has been done on the presence of the 115 compounds in AFO.

CONCLUSION

Profiling and characterisation compounds of AFO enriched its material basis, which would lay the foundation for improving potential medicinal and nutritional values and effecting comprehensive quality control of Fomes officinalis Ames.

Scalable Superhydrophilic Solar Evaporators for Long-Term Stable Desalination, Fresh Water Collection and Salt Collection by Vertical Salt Deposition

Solar-driven interfacial evaporation (SIE) is very promising to solve the issue of fresh water shortage, however, poor salt resistance severely hinders long-term stable SIE and fresh water collection. Here, we report design of superhydrophilic solar evaporators for long-term stable desalination, fresh water collection and salt collection by vertical salt deposition. The evaporators are prepared by sequentially deposition of silicone nanofilaments, polypyrrole and Au nanoparticles on a polyester fabric composed of microfibers. The evaporators feature excellent photothermal effect and ultrafast water transport, due to their unique micro-/nanostructure and superhydrophilicity. As a result, during SIE the salt gradually deposits vertically rather than occupies larger area on the evaporators. Consequently, long-term stable SIE with high evaporation rates of 2.4-2.1 kg m-2 h-1 for 3.5-20 wt % brine in continuous 10 h is achieved under 1 sun illumination. Meanwhile, the loosely deposited salt can be easily collected, realizing zero brine discharge. Moreover, scalable preparation of the evaporator is achieved, which exhibits efficient collection of high quality fresh water (10.08 kg m-2 in 8 h) via SIE desalination under weak natural sunlight (0.46~0.66 sun). This strategy sheds a new light on the design of high-performance solar evaporators and their real-world fresh water collection.

In vivo pharmacokinetic study of vanillic acid in monocrotaline-induced pulmonary arterial hypertension rats and its tissue distribution

Vanillic acid (VA) is a bioactive chemical present in many food plants and fruits. It has been shown to have a protective effect on pulmonary tissues in monocrotaline-induced pulmonary arterial hypertension, as well as an intervention effect on right ventricular remodeling. The purpose of this study was to develop and test a reliable method for assessing VA utilizing ultra-performance liquid chromatography-high resolution mass spectrometry using caffeic acid as the internal standard. Across diverse substrates, the correlation coefficient for VA ranged from 0.9992 to 0.9995. The method's intraday precision was <13.53% (RSD), and its accuracy (RE) ranged from -9.88 to 4.35%. The precision across days was <13.69% (RSD), while the accuracy ranged from 2.16 to 10.94% (RE). The extraction recoveries ranged from 80.30 to 118.81%, with a lower limit of quantification of 20 ng/mL. The approach was successfully applied to pharmacokinetic and tissue distribution studies of VA in rat plasma after gavage administration, and the pharmacokinetic parameters of VA in the plasma of the monocrotaline-induced pulmonary arterial hypertension were significantly different from those of the control group.

Primary cilium participates in radiation-induced bystander effects through TGF-β1 signaling

Many studies have indicated that tumor growth factor-beta (TGF-β) signaling mediates radiation-induced bystander effects (RIBEs). The primary cilium (PC) coordinates several signaling pathways including TGF-β signaling to regulate diverse cellular processes. But whether the PC participates in TGF-β induced RIBEs remains unclear. The cellular levels of TGF-β1 were detected by western blot analysis and the secretion of TGF-β1 was measured by ELISA kit. The ciliogenesis was altered by CytoD treatment, STIL siRNA transfection, IFT88 siRNA transfection, or KIF3a siRNA transfection, separately, and was detected by western blot analysis and immunofluorescence staining. G0 /G1 phase cells were arrested by serum starvation and S phase cells were induced by double thymidine block. The TGF-β1 signaling was interfered by LY2109761, a TGF-β receptor 1 (TβR1) inhibitor, or TGF-β1 neutral antibody. The DNA damages were induced by TGF-β1 or radiated conditional medium (RCM) from irradiated cells and were reflected by p21 expression, 53BP1 foci, and γH2AX foci. Compared with unirradiated control, both A549 and Beas-2B cells expressed and secreted more TGF-β1 after carbon ion beam or X-ray irradiation. RCM collected from irradiated cells or TGF-β1 treatment caused an increase of DNA damage in cocultured unirradiated Beas-2B cells while blockage of TGF-β signaling by TβR1 inhibitor or TGF-β1 neutral antibody alleviates this phenomenon. IFT88 siRNA or KIF3a siRNA impaired PC formation resulted in an aggravated DNA damage in bystander cells, while elevated PC formation by CytoD or STIL siRNA resulted in a decrease of DNA damage. Furthermore, TGF-β1 induced more DNA damages in S phases cells which showed lower PC formation rate and less DNA damages in G0 /G1 phase cells which showed higher PC formation rate. This study demonstrates the particular role of primary cilia during RCM induced DNA damages through TGF-β1 signaling restriction and thereby provides a functional link between primary cilia and RIBEs.

Scrutiny of genome-wide somatic mutation profiles in centenarians identifies the key genomic regions for human longevity

Somatic mutations accumulate with age and are associated closely with human health, their characterization in longevity cohorts remains largely unknown. Here, by analyzing whole genome somatic mutation profiles in 73 centenarians and 51 younger controls in China, we found that centenarian genomes are characterized by a markedly skewed distribution of somatic mutations, with many genomic regions being specifically conserved but displaying a high function potential. This, together with the observed more efficient DNA repair ability in the long-lived individuals, supports the existence of key genomic regions for human survival during aging, with their integrity being of essential to human longevity.

Sodium Butyrate Induces Mitophagy and Apoptosis of Bovine Skeletal Muscle Satellite Cells through the Mammalian Target of Rapamycin Signaling Pathway

Sodium butyrate (NaB) is one of the short-chain fatty acids and is notably produced in large amounts from dietary fiber in the gut. Recent evidence suggests that NaB induces cell proliferation and apoptosis. Skeletal muscle is rich in plenty of mitochondrial. However, it is unclear how NaB acts on host muscle cells and whether it is involved in mitochondria-related functions in myocytes. The present study aimed to investigate the role of NaB treatment on the proliferation, apoptosis, and mitophagy of bovine skeletal muscle satellite cells (BSCs). The results showed that NaB inhibited proliferation, promoted apoptosis of BSCs, and promoted mitophagy in a time- and dose-dependent manner in BSCs. In addition, 1 mM NaB increased the mitochondrial ROS level, decreased the mitochondrial membrane potential (MMP), increased the number of autophagic vesicles in mitochondria, and increased the mitochondrial DNA (mtDNA) and ATP level. The effects of the mTOR pathway on BSCs were investigated. The results showed that 1 mM NaB inhibited the mRNA and protein expression of mTOR and genes AKT1, FOXO1, and EIF4EBP1 in the mTOR signaling pathway. In contrast, the addition of PP242, an inhibitor of the mTOR signaling pathway also inhibited mRNA and protein expression levels of mTOR, AKT1, FOXO1, and EIF4EBP1 and promoted mitophagy and apoptosis, which were consistent with the effect of NaB treatment. NaB might promote mitophagy and apoptosis in BSCs by inhibiting the mTOR signaling pathway. Our results would expand the knowledge of sodium butyrate on bovine skeletal muscle cell state and mitochondrial function.

Heritability and recursive influence of host genetics on the rumen microbiota drive body weight variance in male Hu sheep lambs

BACKGROUND

Heritable rumen microbiota is an important modulator of ruminant growth performance. However, no information exists to date on host genetics-rumen microbiota interactions and their association with phenotype in sheep. To solve this, we curated and analyzed whole-genome resequencing genotypes, 16S rumen-microbiota data, and longitudinal body weight (BW) phenotypes from 1150 sheep.

RESULTS

A variance component model indicated significant heritability of rumen microbial community diversity. Genome-wide association studies (GWAS) using microbial features as traits identified 411 loci-taxon significant associations (P < 10-8). We found a heritability of 39% for 180-day-old BW, while also the rumen microbiota likely played a significant role, explaining that 20% of the phenotypic variation. Microbiota-wide association studies (MWAS) and GWAS identified four marker genera (Bonferroni corrected P < 0.05) and five novel genetic variants (P < 10-8) that were significantly associated with BW. Integrative analysis identified the mediating role of marker genera in genotype influencing phenotype and unravelled that the same genetic markers have direct and indirect effects on sheep weight.

CONCLUSIONS

This study reveals a reciprocal interplay among host genetic variations, the rumen microbiota and the body weight traits of sheep. The information obtained provide insights into the diverse microbiota characteristics of rumen and may help in designing precision microbiota management strategies for controlling and manipulating sheep rumen microbiota to increase productivity. Video Abstract.

Ruta graveolens: Boost Melanogenic Effects and Protection against Oxidative Damage in Melanocytes

Vitiligo, an acquired depigmentation disorder, is characterized by the loss of functional melanocytes and epidermal melanin. In recent years, research has focused on promoting melanin biosynthesis and protecting melanocytes to reduce stress-related damage for the purpose of applying it to vitiligo treatment. Ruta graveolens L. has been utilized as a medicinal herb in diverse traditional medicine systems to address conditions like vitiligo. In this investigation, we isolated and purified 16 unique alkaloid compounds from the chloroform extracts of R. graveolens, encompassing a new quinoline alkaloid and several recognized compounds. Bioactivity analysis showed that compound 13, an alkaloid derived from R. graveolens, promotes melanin production while protecting PIG3V melanocytes against 4-tert-butylphenol (4-TBP)-induced oxidative damage by downregulating endoplasmic reticulum (ER) stress and pro-inflammatory cytokines through interleukin-6 (IL-6) regulation. Additionally, the compound suppressed the expression of Bip, IRE1, p-IRE1, and XBP-1 proteins, suggesting a potential antioxidant function. These findings suggest that compound 13 isolated from R. graveolens can augment melanogenesis in melanocytes, reduce endoplasmic reticulum (ER) stress, and ameliorate vitiligo exacerbation. The melanogenic activity observed in the chloroform fraction emphasizes R. graveolens's potential as a novel therapeutic target for vitiligo treatment, warranting further exploration in future studies.

Comparison of Gas-Particle Partitioning of Glyoxal and Methylglyoxal in the Summertime Atmosphere at the Foot and Top of Mount Hua

Glyoxal and methylglyoxal are important volatile organic compounds in the atmosphere. The gas-particle partitioning of these carbonyl compounds makes significant contributions to O₃ formation. In this study, both the gas- and particle-phase glyoxal and methylglyoxal concentrations at the foot and top of Mount Hua were determined simultaneously. The results showed that the gaseous-phase glyoxal and methylglyoxal concentrations at the top were higher than those at the foot of the mountain. However, the concentrations for the particle phase showed the opposite trend. The average theoretical values of the gas-particle partitioning coefficients of the glyoxal and methylglyoxal concentrations (4.57 × 10^-10 and 9.63 × 10^-10 m³ μg^-1, respectively) were lower than the observed values (3.79 × 10^-3 and 6.79 × 10^-3 m³ μg^-1, respectively). The effective Henry's law constants (eff.K_H) of the glyoxal and methylglyoxal were in the order of 10⁸ to 10⁹ mol/kgH2O/atm, and they were lower at the foot than they were at the top. The particle/gas ratios (P/G ratios) of the glyoxal and methylglyoxal were 0.039 and 0.055, respectively, indicating more glyoxal and methylglyoxal existed in the gas phase. The factors influencing the partitioning coefficients of the glyoxal and methylglyoxal were positively correlated with the relative humidity (RH) and negatively correlated with the PM_2.5 value. Moreover, the partitioning coefficient of the glyoxal and methylglyoxal was more significant at the top than at the foot of Mount Hua.

Impacts of future climate on the distribution of 4 bumblebee species in the Qinghai-Tibet Plateau

Climate warming threatens dozens of bumblebee species across the world, including alpine areas. In plateaus with vast and continuous high-altitude areas, bumblebees' response to climate warming may be relatively optimistic. To study the species' responses to future climate in the Qinghai-Tibet Plateau, we quantified the suitable areas for 4 local bumblebee indicator species under current and future climate scenarios (Shared Socio-economic Pathway 126, 245, 370, and 585 in 2,100) using MaxEnt models. Suitable areas of indicator species were stacked to obtain the species richness layer. According to the acreage and connectivity of suitable areas and the acreage of the high richness area, a warmed climate will be more suitable for bumblebees' distribution compared to the current climate. The SSP 126 and SSP 245 scenario will be the 2 most suitable. Meanwhile, with climate warming, suitable areas and the high richness areas will move to high altitudes and their altitude range will decrease. The greater suitability in warmed climates may be caused by the topography of plateaus, which provides an opportunity for bumblebees to migrate to cooler areas. However, mitigation of warming is still necessary because an excessively warm climate will decrease bumblebees' habitat suitability. In plateaus, species in lower altitudes will migrate to higher altitudes, conservation in high altitudes should pay attention to not only original species, but also immigrated species. In lower altitudes, many species will migrate to higher altitudes, then local bumblebee diversity will decrease. Local conservation should be focused on these lower altitude areas.

GKLOMLI: a link prediction model for inferring miRNA-lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm

BACKGROUND

The limited knowledge of miRNA-lncRNA interactions is considered as an obstruction of revealing the regulatory mechanism. Accumulating evidence on Human diseases indicates that the modulation of gene expression has a great relationship with the interactions between miRNAs and lncRNAs. However, such interaction validation via crosslinking-immunoprecipitation and high-throughput sequencing (CLIP-seq) experiments that inevitably costs too much money and time but with unsatisfactory results. Therefore, more and more computational prediction tools have been developed to offer many reliable candidates for a better design of further bio-experiments.

METHODS

In this work, we proposed a novel link prediction model based on Gaussian kernel-based method and linear optimization algorithm for inferring miRNA-lncRNA interactions (GKLOMLI). Given an observed miRNA-lncRNA interaction network, the Gaussian kernel-based method was employed to output two similarity matrixes of miRNAs and lncRNAs. Based on the integrated matrix combined with similarity matrixes and the observed interaction network, a linear optimization-based link prediction model was trained for inferring miRNA-lncRNA interactions.

RESULTS

To evaluate the performance of our proposed method, k-fold cross-validation (CV) and leave-one-out CV were implemented, in which each CV experiment was carried out 100 times on a training set generated randomly. The high area under the curves (AUCs) at 0.8623 ± 0.0027 (2-fold CV), 0.9053 ± 0.0017 (5-fold CV), 0.9151 ± 0.0013 (10-fold CV), and 0.9236 (LOO-CV), illustrated the precision and reliability of our proposed method.

CONCLUSION

GKLOMLI with high performance is anticipated to be used to reveal underlying interactions between miRNA and their target lncRNAs, and deciphers the potential mechanisms of the complex diseases.

Historic evolution of population exposure to heatwaves in Xinjiang Uygur Autonomous Region, China

Heatwaves have pronounced impacts on human health and the environment on a global scale. Although the characteristics of heatwaves has been well documented, there still remains a lack of dynamic studies of population exposure to heatwaves (PEH), particularly in the arid regions. In this study, we analyzed the spatio-temporal evolution characteristics of heatwaves and PEH in Xinjiang using the daily maximum temperature (T_max), relative humidity (RH), and high-resolution gridded population datasets. The results revealed that the heatwaves in Xinjiang occur more continually and intensely from 1961 to 2020. Furthermore, there is substantial spatial heterogeneity of heatwaves with eastern part of the Tarim Basin, Turpan, and Hami been the most prone areas. The PEH in Xinjiang showed an increasing trend with high areas mainly in Kashgar, Aksu, Turpan, and Hotan. The increase in PEH is mainly contributed from population growth, climate change and their interaction. From 2001 to 2020, the climate effect contribution decreased by 8.5%, the contribution rate of population and interaction effects increased by 3.3% and 5.2%, respectively. This work provides a scientific basis for the development of policies to improve the resilience against hazards in arid regions.

High carbon emissions from thermokarst lakes and their determinants in the Tibet Plateau

Thermokarst lakes are potentially important sources of methane (CH₄ ) and carbon dioxide (CO₂ ). However, considerable uncertainty exists regarding carbon emissions from thermokarst lakes owing to a limited understanding of their patterns and motivators. In this study, we measured CH₄ and CO₂ diffusive fluxes in 163 thermokarst lakes in the Qinghai-Tibet Plateau (QTP) over 3 years from May to October. The median carbon emissions from the QTP thermokarst lakes were 1440 mg CO₂ m^-2 day^-1 and 60 mg CH₄ m^-2 day^-1 , respectively. The diffusive rates of CO₂ and CH₄ are related to the catchment land cover type. Sediment microbial abundance and hydrochemistry explain 51.9% and 38.3% of the total variance in CH₄ diffusive emissions, respectively, while CO₂ emissions show no significant relationship with environmental factors. When upscaling carbon emissions from the QTP thermokarst lakes, the annual average CH₄ release per lake area is equal to that of the pan-Arctic region. Our findings highlight the importance of incorporating in situ observation data with different emission pathways for different land cover types in predicting carbon emissions from thermokarst lakes in the future.

rcCAE: a convolutional autoencoder method for detecting intra-tumor heterogeneity and single-cell copy number alterations

Intra-tumor heterogeneity (ITH) is one of the major confounding factors that result in cancer relapse, and deciphering ITH is essential for personalized therapy. Single-cell DNA sequencing (scDNA-seq) now enables profiling of single-cell copy number alterations (CNAs) and thus aids in high-resolution inference of ITH. Here, we introduce an integrated framework called rcCAE to accurately infer cell subpopulations and single-cell CNAs from scDNA-seq data. A convolutional autoencoder (CAE) is employed in rcCAE to learn latent representation of the cells as well as distill copy number information from noisy read counts data. This unsupervised representation learning via the CAE model makes it convenient to accurately cluster cells over the low-dimensional latent space, and detect single-cell CNAs from enhanced read counts data. Extensive performance evaluations on simulated datasets show that rcCAE outperforms the existing CNA calling methods, and is highly effective in inferring clonal architecture. Furthermore, evaluations of rcCAE on two real datasets demonstrate that it is able to provide a more refined clonal structure, of which some details are lost in clonal inference based on integer copy numbers.

Development and Determinants of Topsoil Bacterial and Fungal Communities of Afforestation by Aerial Sowing in Tengger Desert, China

It was previously reported that afforestation in the desert can help improve soil texture, carbon accumulation, and nutrient status. However, the effects of afforestation on soil microbial composition, diversity, and microbial interactions with soil physicochemical properties have been rarely evaluated quantitatively. Using the method of space-for-time substitutions, we assessed the development and determinants of topsoil bacterial and fungal communities over nearly 40 years of successive afforestation by aerial sowing in Tengger Desert, China. The results showed that afforestation by aerial sowing comprised a considerable proportion of Chloroflexi and Acidobacteria in the bacterial community in addition to the ubiquitous phyla found in desert but had fewer effects on the dominant phyla of the fungal community. At the phylum level, the bacterial community was clearly clustered into two groups. However, it was difficult to differentiate the constituents of the fungal community based on principal coordinate analysis. The richness of the bacterial and fungal communities was significantly higher after five years than at zero years and three years. Additionally, the bacterial community varied parabolically and reached its largest size at twenty years, while the fungal community increased exponentially. Soil physicochemical properties were found to have divergent effects on the abundance and diversity of bacterial and fungal communities, among which salt- and carbon-associated properties (e.g., electrical conductivity, calcium, magnesium, total carbon, and organic carbon) were closely related with the abundance of bacterial-dominant phyla and the diversity of bacteria and fungi, but nutrient-associated properties (e.g., total phosphorus and available phosphorus) were not. The results indicate that afforestation through the salt secretions of plants leaves and carbon inputs from litter promote the development of topsoil bacterial and fungal communities in the desert.

Separation and Qualitative Study of Mentha asiatica Boriss. Essential Oil Components by prep-GC, GC-QTOF-MS, NMR and Prediction of Bioactive Compounds

In order to understand the material basis of wild Mentha asiatica Boris. in Xinjiang, the chemical constituents of essential oil extracted from aerial parts of this plant were studied. A total 52 components were detected and 45 compounds were identified. First of all, the essential oil was separated by silica gel column chromatography, and divided into several parts according to the results of thin layer chromatography. Eight fractions were obtained, and then each fragment was preliminarily screened for antibacterial activity. It was found that all eight fragments had certain antibacterial activity in different level. Then the fractions were subjected to preparative gas chromatography (prep-GC) for further isolation. Ten compounds were identified by ¹³ C-NMR, ¹ H-NMR and gas chromatography-quadrupole time of flight-Mass spectrometry (GC-QTOF-MS). They are sabinene, limonene and β-caryophyllene, (1R*,3S*,5R*)-sabinyl acetate, piperitone oxide, rotundifolone, thymol, piperitone, 4-hydroxypiperiditone, cedrol. After screened by bioautography, 4-hydroxypiperone and thymol were showed best antibacterial activity. The inhibitory effects of the two isolated compounds on Candida albicans and their related mechanisms were studied. The results showed that, 4-hydroxypiperone and thymol significantly reduced ergosterol content on the surface of Candida albicans cell membrane in a dose-dependent manner. This work has accumulated experience for the development and utilization of Xinjiang characteristic medicinal plant resources and new drug research and development, and provided scientific basis and support for the later research and development of Mentha asiatica Boris.

Facile Synthesis of Benzimidazoles via N-Arylamidoxime Cyclization

A facile synthesis of benzimidazoles was described by a one-pot process containing acylation-cyclization of N-arylamidoxime. This method provided an alternative synthesis of benzimidazoles with a certain diversity of substituted groups in acceptable yields (up to 96%). More importantly, the construction of bis-benzimidazole (8), the key intermediate for making telmisartan, was achieved by adopting this method that enabled avoiding the undesired nitration with nitric/sulfuric acid and the cyclization in polyphosphoric acid in the existing operations.

Exploring Short-Wavelength Phase-Matching Nonlinear Optical Crystals by Employing KBe2BO3F2 as the Template

Exploration of nonlinear optical (NLO) crystals that are competent in generating short-wavelength ultraviolet (UV, λ ≤ 266 nm, and even deep-UV, λ ≤ 200 nm) coherent light output by direct second harmonic generation (SHG) remains a formidable challenge. Herein, four UV/deep-UV NLO crystals, M₂B₄SO₁₀ (M = K, Rb, and Cs) and Rb₃B₁₁PO₁₉F₃, were successfully synthesized by evolving the KBe₂BO₃F₂ (KBBF) structure into mixed-anionic borosulfate and fluoroborophosphate systems. They display functional [B₄SO₁₀]_∞ or [B₁₁PO₁₉F₃]_∞ KBBF-type layers that are composed of [BO₃], [BO₄], and [SO₄] groups or [BO₃], [BO₄], [BO₃F], and [PO₄] groups, respectively. Experimental characterization and numerical computation results indicate that these crystals possess exceptional NLO performance, including large SHG responses (0.9-1.7 × KDP at 1064 nm and 0.1-0.3 × β-BBO at 532 nm) and adequate birefringence to fulfill the SHG phase-matching (PM) condition at 266 nm. In particular, the shortest type-I PM wavelength (λ_PM) of Rb₃B₁₁PO₁₉F₃ reaches 180 nm, which implies that Rb₃B₁₁PO₁₉F₃ can become a prospective deep-UV NLO crystal. In addition, single crystals of K₂B₄SO₁₀, Rb₂B₄SO₁₀, and Cs₂B₄SO₁₀ are easily obtained by the high-temperature solution approach. This work will facilitate the discovery of short-wavelength PM NLO crystals by using the KBBF structure as the template.

Association between rumen microbiota and marbling grade in Hu sheep

The marbling fat regulates the flavor of mutton and measures the fat density in the loin eye and is the most important parameter of carcass grading. The objective of this study was to explore the relationship of rumen microbiota and mutton marbling grade. One hundred and eighty-seven feedlot-finished Hu male lambs (Age: 180 day; Final BW: 46.32 ± 6.03 kg) were slaughtered, and ruminal contents and marbling grade were collected. Ruminal microbial DNA extraction and 16S rRNA gene sequencing was performed to investigate microbial composition and to predict microbial metabolic pathways. The animal cohort was then grouped based on marbling grades [low marbling (LM), marbling grade ≤ 1; Medium marbling (MM), 1 < marbling grade ≤ 3; High Marbling (HM), 3 < marbling grade ≤ 5] and intramuscular fat-associated microorganisms were pinpointed using LEfSe and random forest classification model. Intramuscular fat content had significantly differences among the three groups (P < 0.05), and was significantly correlated with VFAs profiling. HM sheep showed a higher abundance of one bacterial taxon (Kandleria), and two taxa were overrepresented in the MM sheep (Pseudobutyrivibrio and Monoglobus), respectively. In addition, the main intramuscular fat deposition pathway was found to involve peroxisome proliferator-activated receptor (PPAR) fatty acid synthesis. By studying the effect of the ruminal microbiome on the marbling of sheep, the present study provides insights into the production of high-quality mutton.

Comparative chloroplast genome analysis of Ficus (Moraceae): Insight into adaptive evolution and mutational hotspot regions

As the largest genus in Moraceae, Ficus is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in Ficus remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of Ficus, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (Ficus langkokensis) to 160,657 bp (Ficus religiosa). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (infA). The number of simple sequence repeats (SSRs) ranged from 67 (Ficus sagittata) to 89 (Ficus microdictya) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the clpP, rbcL, and ccsA genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of Ficus were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that Ficus species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of Ficus.

Iron-Modified Biochar Strengthens Simazine Adsorption and Decreases Simazine Decomposition in the Soil

Currently, modified biochar has been successfully used in the remediation of soil polluted with heavy metals. However, the effects of the modified biochar on pesticides (such as simazine) are still unclear. Herein, the environmental fate of simazine, such as decomposition, leaching, and adsorption in unamended soil, in the soil amended with unmodified and modified biochar (biochar + FeCl₃, biochar + FeOS, biochar + Fe) were evaluated. In addition, an incubation experiment was also performed to observe the influence of modified biochar on the microbial community and diversity in the soil. The results showed that modified biochar significantly decreased the decomposition of simazine in the soil compared to its counterpart. Modified biochar also reduced the concentration of simazine in the leachate. Compared with the control, soil microbial biomass in the soil amended with unmodified biochar, biochar + FeCl₃, biochar + Fe, and biochar + FeOS was decreased by 5.3%, 18.8%, 8.7%, and 18.1%, respectively. Furthermore, modified biochar changed the structure of the microbial community. This shows that modified biochar could increase the soil adsorption capacity for simazine and change the amount and microbial community that regulates the fate of simazine in the soil. This study concludes that iron-modified biochar has positive and negative effects on the soil. Therefore, its advantages and side effects should be considered before applying it to the soil.

Towards the plastome evolution and phylogeny of Cycas L. (Cycadaceae): molecular-morphology discordance and gene tree space analysis

BACKGROUND

Plastid genomes (plastomes) present great potential in resolving multiscale phylogenetic relationship but few studies have focused on the influence of genetic characteristics of plastid genes, such as genetic variation and phylogenetic discordance, in resolving the phylogeny within a lineage. Here we examine plastome characteristics of Cycas L., the most diverse genus among extant cycads, and investigate the deep phylogenetic relationships within Cycas by sampling 47 plastomes representing all major clades from six sections.

RESULTS

All Cycas plastomes shared consistent gene content and structure with only one gene loss detected in Philippine species C. wadei. Three novel plastome regions (psbA-matK, trnN-ndhF, chlL-trnN) were identified as containing the highest nucleotide variability. Molecular evolutionary analysis showed most of the plastid protein-coding genes have been under purifying selection except ndhB. Phylogenomic analyses that alternatively included concatenated and coalescent methods, both identified four clades but with conflicting topologies at shallow nodes. Specifically, we found three species-rich Cycas sections, namely Stangerioides, Indosinenses and Cycas, were not or only weakly supported as monophyly based on plastomic phylogeny. Tree space analyses based on different tree-inference methods both revealed three gene clusters, of which the cluster with moderate genetic properties showed the best congruence with the favored phylogeny.

CONCLUSIONS

Our exploration in plastomic data for Cycas supports the idea that plastid protein-coding genes may exhibit discordance in phylogenetic signals. The incongruence between molecular phylogeny and morphological classification reported here may largely be attributed to the uniparental attribute of plastid, which cannot offer sufficient information to resolve the phylogeny. Contrasting to a previous consensus that genes with longer sequences and a higher proportion of variances are superior for phylogeny reconstruction, our result implies that the most effective phylogenetic signals could come from loci that own moderate variation, GC content, sequence length, and underwent modest selection.

Not that young: combining plastid phylogenomic, plate tectonic and fossil evidence indicates a Palaeogene diversification of Cycadaceae

BACKGROUND AND AIMS

Previous molecular dating studies revealed historical mass extinctions and recent radiations of extant cycads, but debates still exist between palaeobotanists and evolutionary biologists regarding the origin and evolution of Cycadaceae.

METHODS

Using whole plastomic data, we revisited the phylogeny of this family and found the Palawan endemic Cycas clade was strongly related to all lineages from Southeast Eurasia, coinciding with a plate drift event occurring in the Early Oligocene. By integrating fossil and biogeographical calibrations as well as molecular data from protein-coding genes, we established different calibration schemes and tested competing evolutionary timelines of Cycadaceae.

KEY RESULTS

We found recent dispersal cannot explain the distribution of Palawan Cycas, yet the scenario including the tectonic calibration yielded a mean crown age of extant Cycadaceae of ~69-43 million years ago by different tree priors, consistent with multiple Palaeogene fossils assigned to this family. Biogeographical analyses incorporating fossil distributions revealed East Asia as the ancestral area of Cycadaceae.

CONCLUSIONS

Our findings challenge the previously proposed Middle-Late Miocene diversification of cycads and an Indochina origin for Cycadaceae and highlight the importance of combining phylogenetic clades, tectonic events and fossils for rebuilding the evolutionary history of lineages that have undergone massive extinctions.

Genome-Wide Survey of Leucine-Rich Repeat Receptor-Like Protein Kinase Genes and CRISPR/Cas9-Targeted Mutagenesis BnBRI1 in Brassica napus

The leucine-rich repeat receptor-like protein kinase (LRR-RLK) family represents the largest group of RLKs in plants and plays vital roles in plant growth, development and the responses to environmental stress. Although LRR-RLK families have been identified in many species, they have not yet been reported in B. napus. In this study, a total of 444 BnLRR-RLK genes were identified in the genome of Brassica napus cultivar "Zhongshuang 11" (ZS11), and classified into 22 subfamilies based on phylogenetic relationships and genome-wide analyses. Conserved motifs and gene structures were shared within but not between subfamilies. The 444 BnLRR-RLK genes were asymmetrically distributed on 19 chromosomes and exhibited specific expression profiles in different tissues and in response to stress. We identified six BnBRI1 homologs and obtained partial knockouts via CRISPR/Cas9 technology, generating semi-dwarf lines without decreased yield compared with controls. This study provides comprehensive insight of the LRR-RLK family in B. napus. Additionally, the semi-dwarf lines expand the "ideotype" germplasm resources and accelerate the breeding process for B. napus.

Combined transcriptomic, proteomic and biochemical approaches to identify the cadmium hyper-tolerance mechanism of turnip seedling leaves

Cadmium (Cd) pollution is a prominent environment problem, and great interests have been developed towards the molecular mechanism of Cd accumulation in plants. In this study, we conducted combined transcriptomic, proteomic and biochemical approaches to explore the detoxification of a Cd-hyperaccumulating turnip landrace exposed to 5 μM (T5) and 25 μM (T25) Cd treatments. A total of 1090 and 2111 differentially expressed genes (DEGs) and 161 and 303 differentially expressed proteins (DEPs) were identified in turnips under T5 and T25, respectively. However, poor correlations were observed in expression changes between mRNA and protein levels. The enriched KEGG pathways of DEGs with a high proportion (> 80%) of upregulated genes were focused on the flavonoid biosynthesis, sulphur metabolism and glucosinolate biosynthesis pathways, whereas those of DEPs were enriched on the glutathione metabolism pathway. This result suggests that these pathways contribute to Cd detoxification in turnips. Furthermore, induced antioxidant enzymes, heat stock proteins and stimulated protein acetylation modification seemed to play important roles in Cd tolerance in turnips. In addition, several metal transporters were found responsible for the Cd accumulation capacity of turnips. This study may serve as a basis for breeding low-Cd-accumulating vegetables for foodstuff or high-Cd-abstracting plants for phytoremediation.

Cohesin promotes HSV-1 lytic transcription by facilitating the binding of RNA Pol II on viral genes

BACKGROUND

Herpes Simplex Virus type I (HSV-1) is a large double-stranded DNA virus that enters productive infection in epithelial cells and reorganizes the host nucleus. Cohesin, a major constituent of interphase and mitotic chromosomes comprised of SMC1, SMC3, and SCC1 (Mcd1/Rad21), SCC3 (SA1/SA2), have diverse functions, including sister chromatid cohesion, DNA double-stranded breaks repair, and transcriptional control. Little is known about the role of cohesin in HSV-1 lytic infection.

METHODS

We measured the effect on HSV-1 transcription, genome copy number, and viral titer by depleting cohesin components SMC1 or Rad21 using RNAi, followed by immunofluorescence, qPCR, and ChIP experiments to gain insight into cohesin's function in HSV-1 transcription and replication.

RESULTS

Here, we report that cohesion subunits SMC1 and Rad21 are recruited to the lytic HSV-1 replication compartment. The knockdown results in decreased viral transcription, protein expression, and maturation of viral replication compartments. SMC1 and Rad21 knockdown leads to the reduced overall RNA pol II occupancy level but increased RNA pol II ser5 phosphorylation binding on viral genes. Consistent with this, the knockdown increased H3K27me3 modification on these genes.

CONCLUSIONS

These results suggest that cohesin facilitates HSV-1 lytic transcription by promoting RNA Pol II transcription activity and preventing chromatin's silencing on the viral genome.

Arthrinins E-G, Three Botryane Sesquiterpenoids from the Plant Endophytic Fungus Arthrinium sp. HS66

Arthrinins E-G (1-3), three new sesquiterpenoids possessing non-isoprenoid botryane skeleton, were isolated from the fermentation of an endophytic fungus named Arthrinium sp. HS66 which colonized in the stems of Isodon xerophilus. Their structures were determined by extensive spectroscopic methods. Furthermore, the structure of 1 was unambiguously confirmed by X-ray diffraction, while those of 2 and 3 were verified through quantum chemical calculation of NMR data and ECD spectra.

Uncovering the role of a positive selection site of wax ester synthase/diacylglycerol acyltransferase in two closely related Stipa species in wax ester synthesis under drought stress

Natural selection drives local adaptations of species to biotic or abiotic environmental stresses. As a result, adaptive phenotypic divergence can evolve among related species living in different habitats. However, the genetic foundation of this divergence process remains largely unknown. Two closely related alpine grass species, Stipa capillacea and Stipa purpurea, are distributed in different rainfall regions of northern Tibet. Here, we analyzed the drought tolerance of these two closely related Stipa species, and found that S. purpurea was more resistance to drought stress than S. capillacea. To further understand the genetic diversity behind their adaptation to drought environments, a comprehensive gene repertoire was generated using PacBio isoform and Illumina RNA sequencing technologies. Bioinformatics analyses revealed that differential transcripts were mainly enriched in the wax synthetic pathway, and a threonine residue at position 239 of WSD1 was identified as having undergone positive selection in S. purpurea. Using heterologous expression in the Saccharomyces cerevisiae mutant H1246, site-directed mutagenesis studies demonstrated that a positive selection site results in changes to the wax esters profile. This difference may play an important role in S. purpurea in response to drought conditions, indicating that S. purpurea has evolved specific strategies involving its wax biosynthetic pathway as part of its long-term adaptation to the Qinghai-Tibet Plateau.

Functional MYB transcription factor gene HtMYB2 is associated with anthocyanin biosynthesis in Helianthus tuberosus L

BACKGROUND

Tuber color is an important trait for Helianthus tuberosus L. (Jerusalem artichoke). Usually, purple tubers with high anthocyanin content are more nutritious than white tuber. But, the molecular mechanism underlying it is unknown.

RESULTS

In the current study, high-throughput RNA-sequencing was used to compare the transcriptomes between plants with tubers with red or white epidermis. Compared with the white-skinned tubers of cultivar QY3, anthocyanin biosynthesis structural genes had greater expression in the red-skinned tubers of cultivar QY1, indicating that the anthocyanin biosynthesis pathway was activated in 'QY1'; quantitative PCR confirmed this difference in expression. HtMYB2 (Unigene44371_All) was the only MYB transcription factor, homologous to the MYB transcription factor regulating anthocyanin biosynthesis, expressed in the red tuber epidermis of 'QY1'. The anthocyanin concentration in the root, stem, leaf, flower, and tuber epidermis of 'QY1' was higher than in 'QY3', especially tuber epidermis. Correspondingly, HtMYB2 had greater expression in these tissues of 'QY1' than in 'QY3'. The expression of HtMYB2 was associated with anthocyanin accumulation in the different tissues. Overexpression of HtMYB2 activated the anthocyanin biosynthesis pathway, accumulating the pigment in leaves of transgenic tobacco, supporting the model that HtMYB2 regulated anthocyanin biosynthesis. Further experiments found that HtMYB2 had the same coding sequence and genomic sequence in 'QY1' and 'QY3', but that there were several single nucleotide polymorphisms and one insertion-deletion (indel) mutation of 21 nucleotides in the promoter region between the two alleles. The deletion of three nucleotides "AAA" made the promoter of 'QY1' predicted to contain one more possible promoter region. A specific primer, based on the indel, could differentiate between cultivars with red or white tuber epidermis. The genetic variation in HtMYB2 was associated with the tuber skin color in a natural population.

CONCLUSIONS

RNA-seq can successfully isolate the candidate gene (HTMYB2) controlling anthocyanin biosynthesis in purple epidermis of Jerusalem artichoke tuber. HTMYB2 can regulate anthocyanin biosynthesis in plants and is closely related to the formation of purple phenotype in tubers. This study should be useful in understanding the genetic mechanism underlying different tuber skin colors and in breeding new H. tuberosus cultivars with different tuber skin colors.

GCNCDA: A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm

Numerous evidences indicate that Circular RNAs (circRNAs) are widely involved in the occurrence and development of diseases. Identifying the association between circRNAs and diseases plays a crucial role in exploring the pathogenesis of complex diseases and improving the diagnosis and treatment of diseases. However, due to the complex mechanisms between circRNAs and diseases, it is expensive and time-consuming to discover the new circRNA-disease associations by biological experiment. Therefore, there is increasingly urgent need for utilizing the computational methods to predict novel circRNA-disease associations. In this study, we propose a computational method called GCNCDA based on the deep learning Fast learning with Graph Convolutional Networks (FastGCN) algorithm to predict the potential disease-associated circRNAs. Specifically, the method first forms the unified descriptor by fusing disease semantic similarity information, disease and circRNA Gaussian Interaction Profile (GIP) kernel similarity information based on known circRNA-disease associations. The FastGCN algorithm is then used to objectively extract the high-level features contained in the fusion descriptor. Finally, the new circRNA-disease associations are accurately predicted by the Forest by Penalizing Attributes (Forest PA) classifier. The 5-fold cross-validation experiment of GCNCDA achieved 91.2% accuracy with 92.78% sensitivity at the AUC of 90.90% on circR2Disease benchmark dataset. In comparison with different classifier models, feature extraction models and other state-of-the-art methods, GCNCDA shows strong competitiveness. Furthermore, we conducted case study experiments on diseases including breast cancer, glioma and colorectal cancer. The results showed that 16, 15 and 17 of the top 20 candidate circRNAs with the highest prediction scores were respectively confirmed by relevant literature and databases. These results suggest that GCNCDA can effectively predict potential circRNA-disease associations and provide highly credible candidates for biological experiments.

The recognition of circRNA-disease association is the key of disease diagnosis and treatment, and it is of great significance for exploring the pathogenesis of complex diseases. Computational methods can predict the potential disease-related circRNAs quickly and accurately. Based on the hypothesis that circRNA with similar function tends to associate with similar disease, GCNCDA model is proposed to effectively predict the potential association between circRNAs and diseases by combining FastGCN algorithm. The performance of the model was verified by cross-validation experiments, different feature extraction algorithm and classifier models comparison experiments. Furthermore, 16, 15 and 17 of the top 20 candidate circRNAs with the highest prediction scores in disease including breast cancer, glioma and colorectal cancer were respectively confirmed by relevant literature and databases. It is anticipated that GCNCDA model can give priority to the most promising circRNA-disease associations on a large scale to provide reliable candidates for further biological experiments.

iCDA-CGR: Identification of circRNA-disease associations based on Chaos Game Representation

Found in recent research, tumor cell invasion, proliferation, or other biological processes are controlled by circular RNA. Understanding the association between circRNAs and diseases is an important way to explore the pathogenesis of complex diseases and promote disease-targeted therapy. Most methods, such as k-mer and PSSM, based on the analysis of high-throughput expression data have the tendency to think functionally similar nucleic acid lack direct linear homology regardless of positional information and only quantify nonlinear sequence relationships. However, in many complex diseases, the sequence nonlinear relationship between the pathogenic nucleic acid and ordinary nucleic acid is not much different. Therefore, the analysis of positional information expression can help to predict the complex associations between circRNA and disease. To fill up this gap, we propose a new method, named iCDA-CGR, to predict the circRNA-disease associations. In particular, we introduce circRNA sequence information and quantifies the sequence nonlinear relationship of circRNA by Chaos Game Representation (CGR) technology based on the biological sequence position information for the first time in the circRNA-disease prediction model. In the cross-validation experiment, our method achieved 0.8533 AUC, which was significantly higher than other existing methods. In the validation of independent data sets including circ2Disease, circRNADisease and CRDD, the prediction accuracy of iCDA-CGR reached 95.18%, 90.64% and 95.89%. Moreover, in the case studies, 19 of the top 30 circRNA-disease associations predicted by iCDA-CGR on circRDisease dataset were confirmed by newly published literature. These results demonstrated that iCDA-CGR has outstanding robustness and stability, and can provide highly credible candidates for biological experiments.

Understanding the association between circRNAs and diseases is an important step to explore the pathogenesis of complex diseases and promote disease-targeted therapy. Computational methods contribute to discovering the potential disease-related circRNAs. Based on the analysis of the location information expression of biological sequences, the model of iCDA-CGR is proposed to predict the circRNA-disease associations by integrates multi-source information, including circRNA sequence information, gene-circRNA associations information, circRNA-disease associations information and the disease semantic information. In particular, the location information of circRNA sequences was first introduced into the circRNA-disease associations prediction model. The promising results on cross-validation and independent data sets demonstrated the effectiveness of the proposed model. We further implemented case studies, and 19 of the top 30 predicted scores of the proposed model were confirmed by recent experimental reports. The results show that iCDA-CGR model can effectively predict the potential circRNA-disease associations and provide highly reliable candidates for biological experiments, thus helping to further understand the complex disease mechanism.

A fructan: the fructan 1-fructosyl-transferase gene from Helianthus tuberosus increased the PEG-simulated drought stress tolerance of tobacco

BACKGROUND

Jerusalem artichoke (Helianthus tuberosus) is a fructan-accumulating plant, and an industrial source of raw material for fructan production, but the crucial enzymes involved in fructan biosynthesis remain poorly understood in this plant.

RESULTS

In this study, a fructan: fructan 1-fructosyl-transferase (1-FFT) gene, Ht1-FFT, was isolated from Jerusalem artichoke. The coding sequence of Ht1-FFT was 2025 bp in length, encoding 641 amino acids. Ht1-FFT had the type domain of the 1-FFT protein family, to which it belonged, according to phylogenetic tree analysis, which implied that Ht1-FFT had the function of catalyzing the formation and extension of beta-(2,1)-linked fructans. Overexpression of Ht1-FFT in the leaves of transgenic tobacco increased fructan concentration. Moreover, the soluble sugar and proline concentrations increased, and the malondialdehyde (MDA) concentration was reduced in the transgenic lines. The changes in these parameters were associated with increased stress tolerance exhibited by the transgenic tobacco plants. A PEG-simulated drought stress experiment confirmed that the transgenic lines exhibited increased PEG-simulated drought stress tolerance.

CONCLUSIONS

The 1-FFT gene from Helianthus tuberosus was a functional fructan: fructan 1-fructosyl-transferase and played a positive role in PEG-simulated drought stress tolerance. This transgene could be used to increase fructan concentration and PEG-simulated drought stress tolerance in plants by genetic transformation.

Preparation and Modification of Biomass-Based Functional Rubbers for Removing Mercury(II) from Aqueous Solution

Biomass-based functional rubber adsorbents were designed and prepared via inverse vulcanization and post-modification. The plant rubber was synthesized with sulfur and renewable cottonseed oil as well as various micromolecular modifiers with nitrogen-containing functional groups. Results showed that types of nitrogen-containing functional groups and dosages of modifiers had a significant impact on the adsorption capacities of the resulting polymers for Hg2+. Notably, when the mass ratio of 2-aminoethyl methacrylate (AEMA) to sulfur was 0.05, the resulting polymer polysulfide-co-cottonseed oil modified by AEMA (SCOA2) showed the highest adsorption capacity (343.3 mg g-1) among all the prepared samples. Furthermore, the Hg2+ removal efficiency of SCOA2 remained over 80% of its original value after five adsorption-desorption cycles. It demonstrated a promising case for utilizing cheap industrial by-products (sulfur) and renewable materials (cottonseed oil). The prepared functional rubber provides alternative approach for mercury removal in waste utilization and sustainable chemistry.

An efficient in vitro regeneration system from different wild apple (Malus sieversii) explants

BACKGROUND

Wild apple, Malus sieversii, is an endangered species and a valuable genetic resource that requires a variety of conservation techniques. This study aimed to investigate the influence of different concentrations of hormones on wild apple regeneration from leaf and stem explants to establish an optimal regeneration system.

RESULTS

Leaves and stems derived from seedlings were cultured on several media supplemented with various concentrations of thidiazuron (TDZ) or 6-benzylaminopurine (BA) in different combinations with 1-naphthaleneacetic acid (NAA). The results showed that the most efficient shoot formation media (35% and 90%) were MS medium containing 4.0 mg L^-1 TDZ and 1.0 mg L^-1 NAA for leaf explants and MS medium containing 1.0 mg L^-1 BA without NAA for stem explant. MS medium supplemented with 0.4 mg L^-1 BA and 0.1 mg L^-1 NAA (for shoot multiplication) and 1/2 MS + 0.1 mg L^-1 NAA + 1.5% sucrose (for rooting) were effective media. Shoot regeneration from leaf explants was the most effective when the explants were placed abaxial side down onto the medium and were subjected to a pre-treatment of 3 weeks in darkness.

CONCLUSIONS

An optimized regeneration system for M. sieversii that allowed regeneration within 2-3 months developed. The protocol developed herein can be used in large-scale clonal propagation for the conservation of wild apple, M. sieversii.

Phylogenetic approaches resolve taxonomical confusion in Pedicularis (Orobanchaceae): Reinstatement of Pedicularis delavayi and discovering a new species Pedicularis milliana

Morphological identification of Pedicularis depends on floral characters. However, some important characters may be lost during the process of pressing the specimen. Pedicularis delavayi was described from northwestern Yunnan, and widely adopted as a variety of P. siphonantha. Unfortunately, the name "P. siphonantha var. delavayi' incorrectly referred to P. milliana (a new species described in this study) or P. tenuituba in some herbarium specimens and publications. Moreover, phylogenetic relationships among P. delavayi, P. siphonantha and its allies (P. milliana and P. tenuituba) were not fully resolved. In this study, we sampled 76 individuals representing 56 taxa. Of them, 10 taxa were from P. siphonantha lineage, and 11 individuals of P. delavayi represented 9 populations. These species were named as P. siphonantha group on the basis of morphological similarity. Nuclear ribosomal internal transcribed spacer (nrITS) and four chloroplast genes/regions were used for phylogenetic analyses. Phylogenetic analyses showed that the P. siphonantha group was polyphyletic: P. delavayi was sister to P. obliquigaleata in clade A; and the remaining species of P. siphonantha group were monophyletic in clade B, named as P. siphonantha lineage. In the P. siphonantha lineage, P. milliana, P. siphonantha, and P. tenuituba were well supported as monophyletic, and P. dolichosiphon was sister to P. leptosiphon. Morphologically, P. delavayi differs from species of the P. siphonantha lineage in having a long petiole (~ 50 mm) and pedicel (~ 40 mm), a ridged corolla tube, and a folded lower-lip of the corolla. Therefore, both morphological characters and phylogenetic evidence strongly supported to reinstate P. delavayi as an independent species and describe P. milliana as new species. In addition, P. neolatituba was proposed to reduce as a new synonymy of P. delavayi.

Fine structure of mouthparts and feeding performance of Pyrrhocoris sibiricus Kuschakevich with remarks on the specialization of sensilla and stylets for seed feeding

Mouthpart structure and feeding behavior in the temperate firebug, Pyrrhocoris sibiricus Kuschakevich, an important pest that feeds on seeds of leguminous and gramineous plants, are described for the first time. Mouthparts were observed using scanning electron microscopy to examine the external morphology, distribution and abundance of sensilla on mouthparts. Feeding performance by adults on both seeds and shoots were observed using a binocular microscope. The four-segmented labium contains 3 types of sensilla trichodea, 3 types of sensilla basiconica, 1 type of sensilla placodea and 1 type of sensilla campaniformia. Among them, sensilla trichodea are most abundant. The tripartite apex of the labium consists of two lateral lobes and an apical plate. Each lateral lobe possesses a field of 12 thick-walled uniporous peg sensilla and long non-porous hair sensilla. The mandibular stylet tips have three central teeth and two pairs of lateral teeth, which may help in penetrating hard seed coats. A series of scale-like projections are present on the inner surface of the mandibular stylets. The externally smooth maxillary stylets interlock to form a larger food canal and a smaller salivary canal, and there are five tubercles near the tip of the right stylet. Cross-sections of the stylet fascicle show that each mandibular stylet has a dendritic canal. The adult feeding process involves several steps, including exploring and puncturing of the host epidermis, a probing phase, an engorgement phase, and removal of the mouthparts from the host tissue. The structure and function of the mouthparts are adapted for the seed feeding habits.

Onymity promotes cooperation in social dilemma experiments

One of the most elusive scientific challenges for over 150 years has been to explain why cooperation survives despite being a seemingly inferior strategy from an evolutionary point of view. Over the years, various theoretical scenarios aimed at solving the evolutionary puzzle of cooperation have been proposed, eventually identifying several cooperation-promoting mechanisms: kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection. We report the results of repeated Prisoner's Dilemma experiments with anonymous and onymous pairwise interactions among individuals. We find that onymity significantly increases the frequency of cooperation and the median payoff per round relative to anonymity. Furthermore, we also show that the correlation between players' ranks and the usage of strategies (cooperation, defection, or punishment) underwent a fundamental shift, whereby more prosocial actions are rewarded with a better ranking under onymity. Our findings prove that reducing anonymity is a valid promoter of cooperation, leading to higher payoffs for cooperators and thus suppressing an incentive-anonymity-that would ultimately favor defection.