Transcriptomic and Molecular Docking Analysis Reveal Virulence Gene Regulation-Mediated Antibacterial Effects of Benzyl Isothiocyanate Against Staphylococcus aureus

Staphylococcus aureus (S. aureus) is a common pathogen that can cause many serious infections. Thus, efficient and practical techniques to fight S. aureus are required. In this study, transcriptomics was used to evaluate changes in S. aureus following treatment with benzyl isothiocyanate (BITC) to determine its antibacterial action. The results revealed that the BITC at subinhibitory concentrations (1/8th MIC) treated group had 94 differentially expressed genes compared to the control group, with 52 downregulated genes. Moreover, STRING analyses were used to reveal the protein interactions encoded by 36 genes. Then, we verified three significant virulence genes by qRT-PCR, including capsular polysaccharide synthesis enzyme (cp8F), capsular polysaccharide biosynthesis protein (cp5D), and thermonuclease (nuc). Furthermore, molecular docking analysis was performed to investigate the action site of BITC with the encoded proteins of cp8F, cp5D, and nuc. The results showed that the docking fraction of BITC with selected proteins ranged from - 6.00 to - 6.60 kcal/mol, predicting the stability of these complexes. BITC forms hydrophobic, hydrogen-bonded, π-π conjugated interactions with amino acids TRP (130), GLY (10), ILE (406), LYS (368), TYR (192), and ARG (114) of these proteins. These findings will aid future research into the antibacterial effects of BITC against S. aureus.

Blocking Ubiquitin-Specific Protease 7 Induces Ferroptosis in Gastric Cancer via Targeting Stearoyl-CoA Desaturase

Gastric cancer (GC) presents a formidable global health challenge, and conventional therapies face efficacy limitations. Ubiquitin-specific protease 7 (USP7) plays pivotal roles in GC development, immune response, and chemo-resistance, making it a promising target. Various USP7 inhibitors have shown selectivity and efficacy in preclinical studies. However, the mechanistic role of USP7 has not been fully elucidated, and currently, no USP7 inhibitors have been approved for clinical use. In this study, DHPO is identified as a potent USP7 inhibitor for GC treatment through in silico screening. DHPO demonstrates significant anti-tumor activity in vitro, inhibiting cell viability and clonogenic ability, and preventing tumor migration and invasion. In vivo studies using orthotopic gastric tumor mouse models validate DHPO's efficacy in suppressing tumor growth and metastasis without significant toxicity. Mechanistically, DHPO inhibition triggers ferroptosis, evidenced by mitochondrial alterations, lipid Reactive Oxygen Species (ROS), Malondialdehyde (MDA) accumulation, and iron overload. Further investigations unveil USP7's regulation of Stearoyl-CoA Desaturase (SCD) through deubiquitination, linking USP7 inhibition to SCD degradation and ferroptosis induction. Overall, this study identifies USP7 as a key player in ferroptosis of GC, elucidates DHPO's inhibitory mechanisms, and highlights its potential for GC treatment by inducing ferroptosis through SCD regulation.

Multi-kernel Learning Fusion Algorithm Based on RNN and GRU for ASD Diagnosis and Pathogenic Brain Region Extraction

Autism spectrum disorder (ASD) is a complex, severe disorder related to brain development. It impairs patient language communication and social behaviors. In recent years, ASD researches have focused on a single-modal neuroimaging data, neglecting the complementarity between multi-modal data. This omission may lead to poor classification. Therefore, it is important to study multi-modal data of ASD for revealing its pathogenesis. Furthermore, recurrent neural network (RNN) and gated recurrent unit (GRU) are effective for sequence data processing. In this paper, we introduce a novel framework for a Multi-Kernel Learning Fusion algorithm based on RNN and GRU (MKLF-RAG). The framework utilizes RNN and GRU to provide feature selection for data of different modalities. Then these features are fused by MKLF algorithm to detect the pathological mechanisms of ASD and extract the most relevant the Regions of Interest (ROIs) for the disease. The MKLF-RAG proposed in this paper has been tested in a variety of experiments with the Autism Brain Imaging Data Exchange (ABIDE) database. Experimental findings indicate that our framework notably enhances the classification accuracy for ASD. Compared with other methods, MKLF-RAG demonstrates superior efficacy across multiple evaluation metrics and could provide valuable insights into the early diagnosis of ASD.

Radiomics in cone-beam breast CT for the prediction of axillary lymph node metastasis in breast cancer: a multi-center multi-device study

OBJECTIVES

To develop a radiomics model in contrast-enhanced cone-beam breast CT (CE-CBBCT) for preoperative prediction of axillary lymph node (ALN) status and metastatic burden of breast cancer.

METHODS

Two hundred and seventy-four patients who underwent CE-CBBCT examination with two scanners between 2012 and 2021 from two institutions were enrolled. The primary tumor was annotated in each patient image, from which 1781 radiomics features were extracted with PyRadiomics. After feature selection, support vector machine models were developed to predict ALN status and metastatic burden. To avoid overfitting on a specific patient subset, 100 randomly stratified splits were made to assign the patients to either training/fine-tuning or test set. Area under the receiver operating characteristic curve (AUC) of these radiomics models was compared to those obtained when training the models only with clinical features and combined clinical-radiomics descriptors. Ground truth was established by histopathology.

RESULTS

One hundred and eighteen patients had ALN metastasis (N + (≥ 1)). Of these, 74 had low burden (N + (1~2)) and 44 high burden (N + (≥ 3)). The remaining 156 patients had none (N0). AUC values across the 100 test repeats in predicting ALN status (N0/N + (≥ 1)) were 0.75 ± 0.05 (0.67~0.93, radiomics model), 0.68 ± 0.07 (0.53~0.85, clinical model), and 0.74 ± 0.05 (0.67~0.88, combined model). For metastatic burden prediction (N + (1~2)/N + (≥ 3)), AUC values were 0.65 ± 0.10 (0.50~0.88, radiomics model), 0.55 ± 0.10 (0.40~0.80, clinical model), and 0.64 ± 0.09 (0.50~0.90, combined model), with all the ranges spanning 0.5. In both cases, the radiomics model was significantly better than the clinical model (both p < 0.01) and comparable with the combined model (p = 0.56 and 0.64).

CONCLUSIONS

Radiomics features of primary tumors could have potential in predicting ALN metastasis in CE-CBBCT imaging.

CLINICAL RELEVANCE STATEMENT

The findings support potential clinical use of radiomics for predicting axillary lymph node metastasis in breast cancer patients and addressing the limited axilla coverage of cone-beam breast CT.

KEY POINTS

• Contrast-enhanced cone-beam breast CT-based radiomics could have potential to predict N0 vs. N + (≥ 1) and, to a limited extent, N + (1~2) vs. N + (≥ 3) from primary tumor, and this could help address the limited axilla coverage, pending future verifications on larger cohorts. • The average AUC of radiomics and combined models was significantly higher than that of clinical models but showed no significant difference between themselves. • Radiomics features descriptive of tumor texture were found informative on axillary lymph node status, highlighting a higher heterogeneity for tumor with positive axillary lymph node.

A flexible mixed-optimization with H∞ control for coupled twin rotor MIMO system based on the method of inequality (MOI)- An experimental study

This article introduces a cutting-edge H∞ model-based control method for uncertain Multi Input Multi Output (MIMO) systems, specifically focusing on UAVs, through a flexible mixed-optimization framework using the Method of Inequality (MOI). The proposed approach adaptively addresses crucial challenges such as unmodeled dynamics, noise interference, and parameter variations. Central to the design is a two-step controller development process. The first step involves Nonlinear Dynamic Inversion (NDI) and system decoupling for simplification, while the second step integrates H∞ control with MOI for optimal response tuning. This strategy is distinguished by its adaptability and focus on balancing robust stability and performance, effectively managing the intricate cross-coupling dynamics in UAV systems. The effectiveness of the proposed approach is validated through simulations conducted in MATLAB/Simulink environment. Results demonstrated the efficiency of the proposed robust control approach as evidenced by reduced steady-state error, diminished overshoot, and faster system response times, thus significantly outperforming traditional control methods.

Access authentication via blockchain in space information network

Space Information Network (SIN) has significant benefits of providing communication anywhere at any time. This feature offers an innovative way for conventional wireless customers to access enhanced internet services by using SIN. However, SIN's characteristics, such as naked links and maximum signal latency, make it difficult to design efficient security and routing protocols, etc. Similarly, existing SIN authentication techniques can't satisfy all of the essentials for secure communication, such as privacy leaks or rising authentication latency. The article aims to develop a novel blockchain-based access authentication mechanism for SIN. The proposed scheme uses a blockchain application, which has offered anonymity to mobile users while considering the satellites' limited processing capacity. The proposed scheme uses a blockchain application, which offers anonymity to mobile users while considering the satellites' limited processing capacity. The SIN gains the likelihood of far greater computational capacity devices as technology evolves. Since authenticating in SIN, the technique comprises three entities: low Earth orbit, mobile user, and network control centre. The proposed mutual authentication mechanism avoids the requirement of a ground station, resulting in less latency and overhead during mobile user authentication. Finally, the new blockchain-based authentication approach is being evaluated with AVISPA, a formal security tool. The simulation and performance study results illustrate that the proposed technique delivers efficient security characteristics such as low authentication latency, minimal signal overhead and less computational cost with group authentication.

Pediococcus pentosaceus MIANGUAN Enhances the Immune Response to Vaccination in Mice

Increasing evidence shows that some probiotics can improve vaccine responses as adjuvants. This study aimed to evaluate the effect of Pediococcus pentosaceus MIANGUAN (PPM) on SARS-CoV-2 vaccine-elicited immune response in mice. Six-week-old female ICR mice were primed and boosted with SARS-CoV-2 vaccine intramuscularly at weeks 0 and 4, respectively. Mice were gavaged with PPM (5 × 109 CFU/mouse) or PBS (control) for 3 days immediately after boosting vaccination. Compared to the control, oral PPM administration resulted in significantly higher levels of RBD-specific IgG binding antibodies (> 2.3-fold) and RBD-specific IgG1 binding antibodies (> 4-fold) in the serum. Additionally, PPM-treated mice had higher titers of RBD-specific IgG binding antibodies (> 2.29-fold) and neutralization antibodies (> 1.6-fold) in the lung compared to the control mice. The transcriptional analyses showed that the B cell receptor (BCR) signaling pathway was upregulated in both splenocytes and BAL cells in the PPM group vs. the control group. In addition, the number of IFN-γ-producing splenocytes (mainly in CD4 + T cells as determined by flow cytometry) in response to restimulation of RBD peptides was significantly increased in the PPM group. RNA sequencing showed that the genes associated with T cell activation and maturation and MHC class II pathway (CD4, H2-DMa, H2-DMb1, H2-Oa, Ctss) were upregulated, suggesting that oral administration of PPM may enhance CD4 + T cell responses through MHC class II pathway. Furthermore, PPM administration could downregulate the expression level of proinflammatory genes. To conclude, oral administration of PPM could boost SARS-CoV-2 vaccine efficacy through enhancing the specific humoral and cellular immunity response and decrease the expression of inflammation pathways.

Targeting ferroptosis in gastric cancer: Strategies and opportunities

Ferroptosis is a novel form of programmed cell death morphologically, genetically, and biochemically distinct from other cell death pathways and characterized by the accumulation of iron-dependent lipid peroxides and oxidative damage. It is now understood that ferroptosis plays an essential role in various biological processes, especially in the metabolism of iron, lipids, and amino acids. Gastric cancer (GC) is a prevalent malignant tumor worldwide with low early diagnosis rates and high metastasis rates, accounting for its relatively poor prognosis. Although chemotherapy is commonly used to treat GC, drug resistance often leads to poor therapeutic outcomes. In the last several years, extensive research on ferroptosis has highlighted its significant potential in GC therapy, providing a promising strategy to address drug resistance associated with standard cancer therapies. In this review, we offer an extensive summary of the key regulatory factors related to the mechanisms underlying ferroptosis. Various inducers and inhibitors specifically targeting ferroptosis are uncovered. Additionally, we explore the prospective applications and outcomes of these agents in the field of GC therapy, emphasizing their capacity to improve the outcomes of this patient population.

Research progress on antitumor mechanisms and molecular targets of Inula sesquiterpene lactones

The pharmacological effects of natural product therapy have received sigificant attention, among which terpenoids such as sesquiterpene lactones stand out due to their biological activity and pharmacological potential as anti-tumor drugs. Inula sesquiterpene lactones are a kind of sesquiterpene lactones extracted from Inula species. They have many pharmacological activities such as anti-inflammation, anti-asthma, anti-tumor, neuroprotective and anti-allergic. In recent years, more and more studies have proved that they are important candidate drugs for the treatment of a variety of cancers because of its good anti-tumor activity. In this paper, the structure, structure-activity relationship, antitumor activities, mechanisms and targets of Inula sesquiterpene lactones reported in recent years were reviewed in order to provide clues for the development of novel anticancer drugs.

Targeted Metabolomics Study on the Effect of Vinegar Processing on the Chemical Changes and Antioxidant Activity of Angelica sinensis

Angelica sinensis (Oliv.) Diels (A. sinensis) has a long processing history. In order to obtain a more valuable composition and higher antioxidant behavior, it is often processed by stir-frying and vinegar treatment. However, the underlying mechanism of chemical changes remains ambiguous. Using UPLC-QQQ-MS/MS alongside targeted metabolomics techniques, this study probed the variances between crude and processed A. sinensis. We identified 1046 chemical components in total, 123 differential components in stir-fried A. sinensis, and 167 in vinegar-treated ones were screened through multivariate statistical analysis. Moreover, 83 significant compounds, encompassing amino acids, phenolic acids, etc., were identified across both processing methods. The in vitro antioxidant activities of these A. sinensis forms were assessed, revealing a positive correlation between most of the unique components emerging after processing and the antioxidant capabilities. Notably, post-processing, the chemical composition undergoes significant alterations, enhancing the antioxidant activity. Specific compounds, including 4-hydroxybenzaldehyde, syringetin-3-O-glucoside, and salicylic acid, greatly influence antioxidant activity during processing.

An Evaluation of the Crop Preference and Phenotypic Characteristics of Ceracris kiangsu Tsai (Orthoptera: Arcypteridae) under Different Temperatures

The yellow-spined bamboo locust (YSBL), Ceracris kiangsu Tsai, has historically had a significant impact on different bamboo varieties in East Asia and Southeast Asia. Since 2014, there have been many outbreaks of YSBL populations in Laos, and YSBLs subsequently invaded Southwest China in 2020 and 2023. However, there was limited information about the damage to staple crops. Life table parameters and fitness parameters were assessed using wheat, rice, waxy maize, and sweet maize under three different temperatures (25 °C, 30 °C, and 35 °C) in the laboratory. The results indicated that the YSBLs feeding on wheat seedlings displayed a significantly higher survival rate, a shorter developmental time, and a higher adult emergence rate compared to YSBLs feeding on the other host species at 30 °C. The developmental durations of 1st and 3rd instar YSBLs on wheat (1st: 8.21 ± 0.35 d; 3rd: 6.32 ± 0.34 d) and rice (1st: 7.19 ± 0.23 d; 3rd: 9.00 ± 0.66 d) were significantly shorter than those of 1st and 3rd instar YSBLs on waxy maize (1st: 13.62 ± 1.22 d; 3rd: 13.67 ± 6.33 d) and sweet maize (1st: 16.00 ± 1.79 d; 3rd: 18.00 ± 3.49 d) at 30 °C. The body lengths of male and female YSBLs on wheat (male: 29.52 ± 0.40 mm, female: 34.97 ± 0.45 mm) and rice (male: 28.85 ± 0.68 mm, female: 34.66 ± 0.35 mm) were significantly longer than those observed when they were fed on sweet maize (male: 25.64 ± 1.60 mm, female: 21.93 ± 6.89 mm). There were only male adults obtained on waxy maize. The phenotypic characteristics of the YSBLs feeding on rice seedlings were very close to those of the YSBLs feeding on wheat seedlings. A relatively slower decline was observed in the survival rates of YSBL nymphs on wheat and rice compared to those on waxy maize and sweet maize at 25 °C, 30 °C, and 35 °C. In short, this study implied that YSBLs prefer wheat and rice. This study is the first report of direct damage caused by the YSBL to wheat in the laboratory, and its results could be useful in improving our understanding of the host preference of the YSBL and providing strategies for the management of this pest in field crops.

Lattice Strain Regulation Enables High-Performance Formamidinium Perovskite Photovoltaics

Formamidinium lead iodide (FAPbI3 ) perovskite possesses an ideal optical bandgap and is a potential material for fabricating the most efficient single-junction perovskite solar cells (PSCs). Nevertheless, large formamidinium (FA) cations result in residual lattice strain, which reduces the power conversion efficiency (PCE) and operational stability of PSCs. Herein, the modulation of lattice strain in FAPbI3 crystals via a π-conjugated organic amine, i.e., 4-pyrene oxy butylamine (PYBA), is proposed. PYBA pairs at the grain boundary serve as a template for the crystallization of FAPbI3 perovskite, thereby inducing a highly oriented crystal and a pure α-phase film. The PYBA pairs with strong π-π interactions provide a solid fulcrum for external compression strain, thus compensating for the inherent tension strain of FAPbI3 crystals. The strain release elevates the valence band of the perovskite crystals, thereby decreasing the bandgap and trap density. Consequently, the PYBA-regulated FAPbI3 PSC achieves an excellent PCE of 24.76%. Moreover, the resulting device exhibits improves operational stability and maintains over 80% of its initial PCE after 1500 h under maximum power point tracking conditions.

EAT-2 attenuates C. elegans development via metabolic remodeling in a chemically defined food environment

Dietary intake and nutrient composition regulate animal growth and development; however, the underlying mechanisms remain elusive. Our previous study has shown that either the mammalian deafness homolog gene tmc-1 or its downstream acetylcholine receptor gene eat-2 attenuates Caenorhabditis elegans development in a chemically defined food CeMM (C. elegans maintenance medium) environment, but the underpinning mechanisms are not well-understood. Here, we found that, in CeMM food environment, for both eat-2 and tmc-1 fast-growing mutants, several fatty acid synthesis and elongation genes were highly expressed, while many fatty acid β-oxidation genes were repressed. Accordingly, dietary supplementation of individual fatty acids, such as monomethyl branch chain fatty acid C17ISO, palmitic acid and stearic acid significantly promoted wild-type animal development on CeMM, and mutations in either C17ISO synthesis gene elo-5 or elo-6 slowed the rapid growth of eat-2 mutant. Tissue-specific rescue experiments showed that elo-6 promoted animal development mainly in the intestine. Furthermore, transcriptome and metabolome analyses revealed that elo-6/C17ISO regulation of C. elegans development may be correlated with up-regulating expression of cuticle synthetic and hedgehog signaling genes, as well as promoting biosynthesis of amino acids, amino acid derivatives and vitamins. Correspondingly, we found that amino acid derivative S-adenosylmethionine and its upstream metabolite methionine sulfoxide significantly promoted C. elegans development on CeMM. This study demonstrated that C17ISO, palmitic acid, stearic acid, S-adenosylmethionine and methionine sulfoxide inhibited or bypassed the TMC-1 and EAT-2-mediated attenuation of development via metabolic remodeling, and allowed the animals to adapt to the new nutritional niche.

Eriocheir sinensis feminization-1c (Fem-1c) and Its Predicted miRNAs Involved in Sexual Development and Regulation

Feminization-1c (Fem-1c) is important for sex differentiation in the model organism Caenorhabditis elegans. In our previous study, the basic molecular characteristics of the Fem-1c gene (EsFem-1c) in Eriocheir sinensis (Henri Milne Edwards, 1854) were cloned to determine the relationship with sex differentiation. In this study, the genomic sequence of EsFem-1c contained five exons and four introns, with an exceptionally long 3'UTR sequence. The qRT-PCR results of EsFem-1c demonstrated lower tissue expression in the androgenic gland of the intersex crab than the normal male crab, implying that EsFem-1c plays a role in crab AG development. RNA interference experiments and morphological observations of juvenile and mature crabs indicated that EsFem-1c influences sexual development in E. sinensis. A dual-luciferase reporter assay disclosed that tcf-miR-315-5p effectively inhibits the translation of the EsFem-1c gene, influencing male development. An intriguing finding was that miRNA tcf-miR-307 could increase EsFem-1c expression by binding to the alternative splicing region with a length of 248 bp (ASR-248) in the 3'UTR sequence. The present research contributes to a better understanding of the molecular regulation mechanism of EsFem-1c and provides a resource for future studies of the miRNA-mediated regulation of sexual development and regulation in E. sinensis.

Disease progression based feature screening for ultrahigh-dimensional survival-associated biomarkers

The increased availability of ultrahigh-dimensional biomarker data and the high demand of identifying biomarkers importantly related to survival outcomes made feature screening methods commonplace in the analysis of cancer genome data. When survival outcomes include endpoints of overall survival (OS) and time-to-progression (TTP), a high concordance is typically found in both endpoints in cancer studies, namely, patients' OS would most likely be extended when tumour progression is delayed. Existing screening procedures are often performed on a single survival endpoint only and may result in biased selection of features for OS in ignorance of disease progression. We propose a novel feature screening method by incorporating information of TTP into the selection of important biomarker predictors for more accurate inference of OS subsequent to disease progression. The proposal is based on the rank of correlation between individual features and the conditional distribution of OS given observations of TTP. It is advantageous for its flexible model nature, which requires no marginal model assumption for each endpoint, and its minimal computational cost for implementation. Theoretical results show its ranking consistency, sure screening and false rate control properties. Simulation results demonstrate that the proposed screener leads to more accurate feature selection than the method without considering the prior observations of disease progression. An application to breast cancer genome data illustrates its practical utility and facilitates disease classification using selected biomarker predictors.

Identification of HQT gene family and their potential function in CGA synthesis and abiotic stresses tolerance in vegetable sweet potato

Hydroxycinnamate-CoA quinate hydroxycinnamoyl transferase (HQT) enzyme affect plant secondary metabolism and are crucial for growth and development. To date, limited research on the genome-wide analysis of HQT family genes and their regulatory roles in chlorogenic acid (CGA) accumulation in leafy vegetable sweet potato is available. Here, a total of 58 HQT family genes in the sweet potato genome (named IbHQT) were identified and analyzed. We studied the chromosomal distribution, phylogenetic relationship, motifs distribution, collinearity, and cis-acting element analysis of HQT family genes. This study used two sweet potato varieties, high CGA content Fushu 7-6-14-7 (HC), and low CGA content Fushu 7-6 (LC). Based on the phylogenetic analysis, clade A was unique among the identified four clades as it contained HQT genes from various species. The chromosomal location and collinearity analysis revealed that tandem gene duplication may promote the IbHQT gene expansion and expression. The expression patterns and profile analysis showed changes in gene expression levels at different developmental stages and under cold, drought, and salt stress conditions. The expression analysis verified by qRT-PCR revealed that IbHQT genes were highly expressed in the HC variety leaves than in the LC variety. Furthermore, cloning and gene function analysis unveiled that IbHQT family genes are involved in the biosynthesis and accumulation of CGA in sweet-potato. This study expands our understanding of the regulatory role of HQT genes in sweet-potato and lays a foundation for further functional characterization and genetic breeding by engineering targeted HQT candidate genes in various sweet-potato varieties and other species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01299-4.

Biological small-calibre tissue engineered blood vessels developed by electrospinning and in-body tissue architecture

There are no suitable methods to develop the small-calibre tissue-engineered blood vessels (TEBVs) that can be widely used in the clinic. In this study, we developed a new method that combines electrospinning and in-body tissue architecture(iBTA) to develop small-calibre TEBVs. Electrospinning imparted mechanical properties to the TEBVs, and the iBTA imparted biological properties to the TEBVs. The hybrid fibres of PLCL (poly(L-lactic-co-ε-caprolactone) and PU (Polyurethane) were obtained by electrospinning, and the fibre scaffolds were then implanted subcutaneously in the abdominal area of the rabbit (as an in vivo bioreactor). The biotubes were harvested after four weeks. The mechanical properties of the biotubes were most similar to those of the native rabbit aorta. Biotubes and the PLCL/PU vascular scaffolds were implanted into the rabbit carotid artery. The biotube exhibited a better patency rate and certain remodelling ability in the rabbit model, which indicated the potential use of this hybridization method to develop small-calibre TEBVs. Sketch map of developing the biotube. The vascular scaffolds were prepared by electrospinning (A). Silicone tube was used as the core, and the vascular scaffold was used as the shell (B). The vascular scaffold and silicone tube were implanted subcutaneously in the abdominal area of the rabbit (C). The biotube was extruded from the silicone tube after 4 weeks ofembedding (D). The biotube was implanted for the rabbit carotid artery (E).

Characterization of the Mitochondrial Genome of a Wheat AL-Type Male Sterility Line and the Candidate CMS Gene

Heterosis utilization is very important in hybrid seed production. An AL-type cytoplasmic male sterile (CMS) line has been used in wheat-hybrid seed production, but its sterility mechanism has not been explored. In the present study, we sequenced and verified the candidate CMS gene in the AL-type sterile line (AL18A) and its maintainer line (AL18B). In the late uni-nucleate stage, the tapetum cells of AL18A showed delayed programmed cell death (PCD) and termination of microspore at the bi-nucleate stage. As compared to AL18B, the AL18A line produced 100% aborted pollens. The mitochondrial genomes of AL18A and AL18B were sequenced using the next generation sequencing such as Hiseq and PacBio. It was found that the mitochondrial genome of AL18A had 99% similarity with that of Triticum timopheevii, AL18B was identical to that of Triticum aestivum cv. Chinese Yumai. Based on transmembrane structure prediction, 12 orfs were selected as candidate CMS genes, including a previously suggested orf256. Only the lines harboring orf279 showed sterility in the transgenic Arabidopsis system, indicating that orf279 is the CMS gene in the AL-type wheat CMS lines. These results provide a theoretical basis and data support to further analyze the mechanism of AL-type cytoplasmic male sterility in wheat.

Differential Profile of Plasma Circular RNAs in Type 1 Diabetes Mellitus

BACKGROUND

No currently available biomarkers or treatment regimens fully meet therapeutic needs of type 1 diabetes mellitus (T1DM). Circular RNA (circRNA) is a recently identified class of stable noncoding RNA that have been documented as potential biomarkers for various diseases. Our objective was to identify and analyze plasma circRNAs altered in T1DM.

METHODS

We used microarray to screen differentially expressed plasma circRNAs in patients with new onset T1DM (n=3) and age-/gender-matched healthy controls (n=3). Then, we selected six candidates with highest fold-change and validated them by quantitative real-time polymerase chain reaction in independent human cohort samples (n=12). Bioinformatic tools were adopted to predict putative microRNAs (miRNAs) sponged by these validated circRNAs and their downstream messenger RNAs (mRNAs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to gain further insights into T1DM pathogenesis.

RESULTS

We identified 68 differentially expressed circRNAs, with 61 and seven being up- and downregulated respectively. Four of the six selected candidates were successfully validated. Curations of their predicted interacting miRNAs revealed critical roles in inflammation and pathogenesis of autoimmune disorders. Functional relations were visualized by a circRNA-miRNA-mRNA network. GO and KEGG analyses identified multiple inflammation-related processes that could be potentially associated with T1DM pathogenesis, including cytokine-cytokine receptor interaction, inflammatory mediator regulation of transient receptor potential channels and leukocyte activation involved in immune response.

CONCLUSION

Our study report, for the first time, a profile of differentially expressed plasma circRNAs in new onset T1DM. Further in silico annotations and bioinformatics analyses supported future application of circRNAs as novel biomarkers of T1DM.

QTL mapping for aluminum tolerance in RIL population of soybean (Glycine max L.) by RAD sequencing

Aluminum (Al3+) toxicity is a typical abiotic stress that severely limits crop production in acidic soils. In this study, an RIL (recombinant inbred line, F12) population derived from the cross of Zhonghuang 24 (ZH 24) and Huaxia 3 (HX 3) (160 lines) was tested using hydroponic cultivation. Relative root elongation (RRE) and apical Al3+ content (AAC) were evaluated for each line, and a significant negative correlation was detected between the two indicators. Based on a high-density genetic linkage map, the phenotypic data were used to identify quantitative trait loci (QTLs) associated with these traits. With composite interval mapping (CIM) of the linkage map, five QTLs that explained 39.65% of RRE and AAC variation were detected on chromosomes (Chrs) Gm04, Gm16, Gm17 and Gm19. Two new QTLs, qRRE_04 and qAAC_04, were located on the same region of bin93-bin94 on Chr Gm04, which explained 7.09% and 8.98% phenotypic variation, respectively. Furthermore, the results of the expression analysis of candidate genes in the five genetic regions of the QTLs showed that six genes (Glyma.04g218700, Glyma.04g212800, Glyma.04g213300, Glyma.04g217400, Glyma.04g216100 and Glyma.04g220600) exhibited significant differential expression between the Al3+ treatment and the control of two parents. The results of qRT-PCR analysis indicated that Glyma.04g218700 was upregulated by Al3+ treatment with the hundreds-fold increased expression level and may be a candidate gene with potential roles in the response to aluminum stress. Therefore, our efforts will enable future functional analysis of candidate genes and will contribute to the strategies for improvement of aluminum tolerance in soybean.

Screening of seaweeds in the East China Sea as potential bio-monitors of heavy metals

Seaweeds are good bio-monitors of heavy metal pollution and have been included in European coastal monitoring programs. However, data for seaweed species in China are scarce or missing. In this study, we explored the potential of seaweeds as bio-monitor by screening the natural occurring seaweeds in the "Kingdom of seaweed and shellfish" at Dongtou Islands, the East China Sea. Totally, 12 seaweed species were collected from six sites, with richness following the sequence of Rhodophyta > Phaeophyta > Chlorophyta. The concentration of heavy metals (Cu, Cr, Ni, Zn, Pb, Cd, As) in the seaweeds was determined, and the bioaccumulation coefficient was calculated. A combination of four seaweeds, Pachydictyon coriaceum, Gelidium divaricatum, Sargassum thunbergii, and Pterocladiella capillacea, were proposed as bio-monitors due to their high bioaccumulation capabilities of specific heavy metals in the East China Sea and hence hinted the importance of using seaweed community for monitoring of pollution rather than single species. Our results provide first-hand data for the selection of bio-monitor species for heavy metals in the East China Sea and contribute to selection of cosmopolitan bio-monitor communities over geographical large area, which will benefit the establishment of monitoring programs for coastal heavy metal contamination.