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The study was conducted to investigate the effects of Broussonetia papyrifera (BP) on growth performance, rumen fermentation, digestion and meat quality in Huanghuai white goats. Diets were developed with increasing doses of BP to replace maize silage [0% (control), 15% (BP15), 30% (BP30) and 45% (BP45)]. The design was completely randomized with 4 groups of 10 animals each, totalizing 40 animals (aged 150 ± 10 days and body weight of 25.32 ± 0.52 kg). Final body weight, average daily gain and average daily feed intake increased (linear and quadratic, P < 0.05) as BP increased in the diet. The highest body weight and average daily gain were seen in the BP30 group. Feed conversion ratio also improved significantly (linear and quadratic, P < 0.05) with the increasing level of BP. Although the concentration of microbial protein (MCP) in a linear (P = 0.0028) and quadratic (P = 0.0035) fashion with increasing level of BP, however, NH3-N in a quadratic (P = 0.0841) fashion with increasing level of BP. Crude protein was increased with increasing BP in the diets (linear and quadratic, P < 0.05). Nitrogen intake, urinary excretion nitrogen and nitrogen retention were significantly improved (linear and quadratic, P < 0.05) with dietary BP addition in goats. Dietary BP supplementation increased pH (linear and quadratic, P < 0.05) and tended to reduce L* (lightness) (linear and quadratic, P < 0.05). Additionally, the redness value of meat was significantly improved by BP addition (linear and quadratic, P < 0.05). The inclusion of BP in the goat diet promotes growth and increases the digestibility of crude protein in addition to improving the meat colour and rumen fermentation.

Corona Virus (CODID-19) was first reported in Wuhan in December 2019, then spread in different parts of China, and gradually became a global pandemic in March 2020. While the death toll is still increasing, the epicenter of casualty has shifted from Asia to Europe, and that of the affected people has shifted to USA. This paper analyzes the responses in East Asian countries, in China, Japan and South Korea, and provides some commonalities and lessons. While countries have different governance mechanism, it was found that a few governance decisions in respective countries made a difference, along with strong community solidarity and community behavior. Extensive use of emerging technologies is made along with medical/health care treatment to make the response more effective and reduce the risk of the spread of the disease. Although the pandemic was a global one, its responses were local, depending on the local governance, socio-economic and cultural context.

Abstract In order to investigate the association between the use of cardiomyopeptidin (CMP) and outcomes in critically ill patients with myocardial injury, we conducted a retrospective cohort study in Nanfang hospital, Southern Medical University. Clinical data of patients with myocardial injury were collected retrospectively and adjusted for possible confounders by propensity score weighting. The main outcome was the in-hospital mortality. Secondary outcomes included the major adverse cardiovascular events (MACE) occurring during the hospital, the individual components of MACEs, changes in high sensitive troponin T (hsTnT) levels, length of stay (LOS) in ICU and hospital. A Cox proportional hazards model was constructed to examine the association between the application of CMP and in-hospital mortality. Logistic regression and linear regression are used to analyze secondary outcomes. In total, 339 critically ill patients with myocardial injury were included in the analysis. After inverse probability of treatment weighting (IPTW), the use of CMP was associated with reduced in-hospital mortality (HR: 0.64, 95%CI: 0.43–0.96, P = 0.03). No significant differences were found in change of hsTnT, the occurrence of MACE and LOS in ICU as well as hospital after IPTW. The association was more significant in the subgroup with hsTnT > 3URL (HR: 0.41, 95%CI: 0.23–0.71, P

Maize, belonging to the Poaceae family and the Zea L. genus, stands as an excellent food crop. The plant type has a significant impact on crop growth, photosynthesis, lodging resistance, planting density, and final yield. In this study, 160 maize inbred lines were selected as experimental materials to conduct molecular markers research on maize plant type traits through the measurement of plant type-related traits, population structure, and genome-wide association analysis. The phenotypic data revealed differences in plant type-related traits among maize inbred lines grown in the Xinzhou and Jinzhong regions. The frequency distribution of plant height, ear height, spindle length of tassel, and first-order branch number of tassel traits in the 160 maize inbred lines previously studied generally conformed to a normal distribution. We identified 42,240 high-quality single nucleotide polymorphisms (SNPs) using the Affymetrix Axiom chip. The 160 maize inbred lines were categorized into six subgroups, each exhibiting an average gene diversity of 0.356 and an average polymorphism information content of 0.245. We identified 9, 23, 18, 8 and 32 loci that were significantly associated with first-order branch number of tassel, spindle length of tassel, ear height, plant height, and ear height/plant height ratio, respectively. At the same time, 6, 22, 14, 2, and 37 genes were identified as significantly associated with first-order branch number of tassel, spindle length of tassel, ear height, plant height, and ear height/plant height ratio, respectively. This study comprehensively delved into the genetic information of maize plant type-related traits, offering valuable genetic resources and a solid theoretical foundation for the breeding of novel maize varieties with optimized plant types.

Abstract The role of de novo evolved genes from non-coding sequences in regulating morphological differentiation between species/subspecies remains largely unknown. Here, we show that a rice de novo gene GSE9 contributes to grain shape difference between indica/xian and japonica/geng varieties. GSE9 evolves from a previous non-coding region of wild rice Oryza rufipogon through the acquisition of start codon. This gene is inherited by most japonica varieties, while the original sequence (absence of start codon, gse9) is present in majority of indica varieties. Knockout of GSE9 in japonica varieties leads to slender grains, whereas introgression to indica background results in round grains. Population evolutionary analyses reveal that gse9 and GSE9 are derived from wild rice Or-I and Or-III groups, respectively. Our findings uncover that the de novo GSE9 gene contributes to the genetic and morphological divergence between indica and japonica subspecies, and provide a target for precise manipulation of rice grain shape.

Abstract Herein, we synthesized Cr3+/Ln3+ (Er3+, Tm3+)‐codoped rare earth‐based Cs2NaScCl6 double perovskite, and the near‐infrared emission of Ln3+ can be excited by visible light through the energy transfer (ET) from Cr3+ to Ln3+. Moreover, there are two independent emission bands, which stems from 4T2 → 4A2 transition of Cr3+ (970 nm) and f‐f transition of Ln3+ (1542 nm for Er3+ and 1220 nm for Tm3+), respectively. Particularly, both compounds have ultra‐high photoluminescence quantum yield (PLQY) of 60% for 10%Cr3+/6%Er3+‐codoped Cs2NaScCl6 (Er3+ emission: ∼26%) and 68% for 10%Cr3+/4.5%Tm3+‐codoped Cs2NaScCl6 (Tm3+ emission: ∼56%), which can be attributed to the ultra‐high ET efficiency from Cr3+ to Ln3+ and the similar ionic activity of Sc3+ and Ln3+ allowing more dopants enter the host lattice. Considering the excellent stability of the samples, we demonstrated Cr3+/Tm3+‐codoped Cs2NaScCl6 in the applications of near‐infrared imaging and night vision. Finally, we reported 10%Cr3+/4.5%Tm3+/9%Er3+‐tridoped Cs2NaScCl6 and further applied it for optical thermometry.

Verticillium wilt, caused by Verticillium dahliae, poses a severe threat to cotton growth and yield as a soil-borne disease. The ABI five binding protein (AFP) family, characterized by alkaline leucine zip-like transcription factors, responds to ABA signals, and its expression is induced by ABA as well as various biological and abiotic stresses. In this study, we identified 23 members of the four cotton AFP families, revealing high conservation in both gene and protein structures. Collinearity analysis indicated a closer relationship between GhAFPs and AtAFPs than rice. Cis-element analysis of the cotton AFP promoters unveiled elements associated with plant hormones, abscisic acid, abiotic stress, and light response. To unravel the role of the cotton AFP family in verticillium wilt resistance, we pinpointed a highly expressed gene, GhAFP8, from a resistant variety by monitoring expression levels pre- and post-inoculation for each family gene. Subcellular localization confirmed nuclear localization for GhAFP8. Overexpression of GhAFP8 in tobacco demonstrated enhanced resistance to Verticillium dahliae compared to wild-type plants. Further functional exploration utilizing the VIGs system in cotton revealed that silencing the GhAFP8 gene compromised cotton's resistance to Verticillium dahliae. Transcriptome analysis 72 hours post-inoculation in TRV::00 plants and TRV::GhAFP8-silenced plants showed that GhAFP8 silencing primarily impacts the abscisic acid-activated signaling pathway, MAPK signaling pathway, plant hormone signal transduction, and the activation of plant-pathogen interaction pathway. Additionally, GhAFP8 exhibited responsiveness to signals from jasmonic acid (JA), abscisic acid (ABA), and salicylic acid (SA). In summary, we demonstrated the active role of the GhAFP8 gene in conferring resistance to Verticillium dahliae, positioning it as a promising candidate for cotton breeding against verticillium wilt.

Abstract Background Cytoplasmic male sterility (CMS) is the basis of heterosis exploitation. CMS has been used to hybrid production in cotton, but its molecular mechanism remains unclear. CMS is associated with advanced or delayed tapetal programmed cell death (PCD), and reactive oxygen species (ROS) may mediate this process. In this study, we obtained Jin A and Yamian A, two CMS lines with different cytoplasmic sources. Results Compared with maintainer Jin B, Jin A anthers showed advanced tapetal PCD with DNA fragmentation, producing excessive ROS which accumulated around the cell membrane, intercellular space and mitochondrial membrane. The activities of peroxidase (POD) and catalase (CAT) enzymes which can scavenge ROS were significantly decreased. However, Yamian A tapetal PCD was delayed with lower ROS content, and the activities of superoxide dismutase (SOD) and POD were higher than its maintainer. These differences in ROS scavenging enzyme activities may be caused by isoenzyme gene expressions. In addition, we found the excess ROS generated in Jin A mitochondria and ROS overflow from complex III might be the source in parallel with the reduction of ATP content. Conclusion ROS accumulation or abrogation were mainly caused by the joint action of ROS generation and scavenging enzyme activities transformation, which led to the abnormal progression of tapetal PCD, affected the development of microspores, and eventually contributed to male sterility. In Jin A, tapetal PCD in advance might be caused by mitochondrial ROS overproduction, accompanied by energy deficiency. The above studies will provide new insights into the cotton CMS and guide the follow-up research ideas.

The most important goal in cotton breeding is to increase the fiber yield which can be increased by improving a key trait, lint percentage (LP). However, narrow genetic background of upland cotton resulting in stagnant yield. In order to effectively dissect the genetic mechanism and enrich the gene loci of LP in cotton, the genetic diversity and population structure and a genome-wide association study (GWAS) was conducted using 204 upland cotton accessions based on 191 pairs of polymorphic microsatellite markers. The results were as follows: (1) The agronomic traits of the materials especially LP varied widely. (2) The SSRs revealed relatively high degree level of genetic diversity at DNA level. (3) Similarity coefficient cluster analysis of SSR markers indicated the influence of male parent on female parents was different after cross, the variation sites of agronomic traits could be further excavate in F1. (4) The GWAS revealed that 3 SSR markers were associated with LP: BNL3649-2, GH0132-2, CIR0246-3. There were two genes, Gh_D02G0125 and Gh_D11G2610, near the three SSR loci. These results provided a theoretical basis for improving fiber yield.

BackgroundRelated studies have found that air pollution is an important factor affecting mental and behavioral disorders. Thus, we performed this time-series study to evaluate the relationship between short-term exposure to ambient air pollutants and visits to hospital by patients with mental and behavioral disorders in northeastern China.MethodsWe used quasi-Poisson regression models and generalized additive models to probe the links between air pollution and mental and behavioral disorders. The possible influences were also explored stratified by season, age and gender.ResultsWe found that sulfur dioxide (SO2) had a cumulative effect on mental and behavioral disorders at lag04–lag07 and had the greatest effect at lag07 [Relative risk (RR) = 1.068, 95%CI = 1.021–1.117]. Particulate matter of size 2.5 μm (PM2.5) and SO2 had a cumulative effect on depression and both had the largest effect at lag07 (RR = 1.021, 95%CI = 1.002–1.041; RR = 1.103, 95%CI = 1.032–1.178); SO2 also had a cumulative effect on anxiety disorders, with the largest effect at lag06 (RR = 1.058, 95%CI = 1.009–1.110). In the stratified analysis, people are more susceptible in the cold season compared to the warm season and females and the 18–60-year age group are more sensitive to air pollutants. It is suggested to strengthen management and preventive measures to decrease air pollution exposure.ConclusionThis study found an association between increased concentrations of air pollutants and increased outpatient visits for mental and behavioral disorders. We recommend that preventive and protective measures should be strengthened in an effort to reduce exposure to air pollution in order to maintain physical and mental health.

Cotton is one of the most important crops in the world. GDSL-type esterases/lipases (GELPs) are widely present in all kingdoms and play an essential role in regulating plant growth, development, and responses to abiotic and biotic stresses. However, the molecular mechanisms underlying this functional diversity remain unclear. Here, based on the identification of the GELP gene family, we applied genetic evolution and molecular simulation techniques to explore molecular mechanisms in cotton species. A total of 1502 GELP genes were identified in 10 cotton species. Segmental duplication and differences in evolutionary rates are the leading causes of the increase in the number and diversity of GELP genes during evolution for ecological adaptation. Structural analysis revealed that the GELP family has high structural diversity. Moreover, molecular simulation studies have demonstrated significant differences in the properties of the binding pockets among cotton GELPs. In the process of adapting to the environment, GELPs not only have segmental duplication but also have different evolutionary rates, resulting in gene diversity. This diversity leads to significant differences in the 3D structure and binding pocket properties and, finally, to functional diversity. These findings provide a reference for further functional analyses of plant GELPs.

Apoptosis, as a very important biological process, is a response to developmental cues or cellular stress. Impaired apoptosis plays a central role in the development of cancer and also reduces the efficacy of traditional cytotoxic therapies. Members of the B-cell lymphoma 2 (BCL-2) protein family have pro- or anti-apoptotic activities and have been studied intensively over the past decade for their importance in regulating apoptosis, tumorigenesis, and cellular responses to anticancer therapy. Since the inflammatory response induced by apoptosis-induced cell death is very small, at present, the development of anticancer drugs targeting apoptosis has attracted more and more attention. Consequently, the focus of this review is to summarize the current research on the role of BCL-2 family proteins in regulating apoptosis and the development of drugs targeting BCL-2 anti-apoptotic proteins. Additionally, the mechanism of BCL-2 family proteins in regulating apoptosis was also explored. All the findings indicate the potential of BCL-2 family proteins in the therapy of cancer.

Class III peroxidase (PRX) genes play essential roles in various processes, such as auxin catabolism, removal of H2O2, crosslinking cell wall components, and response to biotic and abiotic stresses. In this study, we identified 166, 78 and 89 PRX genes from G. hirsutum, G. arboretum and G. raimondii, respectively. These PRX genes were classified into seven subfamilies based on phylogenetic tree analysis and the classification of PRX genes in Arabidopsis. Segmental duplication and purifying selection were the major factors driving the evolution of GhPRXs. GO and KEGG enrichment analysis revealed that GhPRX genes were mainly associated with responding to oxidative stresses, peroxidase activities and phenylpropanoid biosynthesis pathways. Transcriptome data analysis showed that GhPRX genes expression were significantly different in microspore development between the sterility line-JinA and the maintainer line MB177. We confirmed the up-regulation of GhPRX107 and down-regulation of GhPRX128 in the sterile line compared to its maintainer line using qRT-PCR, suggesting their roles in pollen fertility. In addition, silencing GhPRX107 in cotton showed a significant decrease of the reactive oxygen species (ROS) levels of microsporocyte stage anthers compared to control. Overexpressing GhPRX107 in Arabidopsis significantly increased the ROS levels of anthers compared to wild type. In conclusion, we identified GhPRX107 as a determinant of ROS levels in anther. This work sets a foundation for PRX studies in pollen development.

Abstract Background Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge, no studies have investigated CMS Yamian A in cotton with the genetic background of Australian wild Gossypium bickii. Conjoint transcriptomic and proteomic analysis was first performed between Yamian A and its maintainer Yamian B. Results We detected 550 differentially expressed transcript-derived fragments (TDFs) and at least 1013 proteins in anthers at various developmental stages. Forty-two TDFs and 11 differentially expressed proteins (DEPs) were annotated by analysis in the genomic databases of G. austral, G. arboreum and G. hirsutum. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to better understand the functions of these TDFs and DEPs. Transcriptomic and proteomic results showed that UDP-glucuronosyl/UDP-glucosyltransferase, 60S ribosomal protein L13a-4-like, and glutathione S-transferase were upregulated; while heat shock protein Hsp20, ATPase, F0 complex, and subunit D were downregulated at the microspore abortion stage of Yamian A. In addition, several TDFs from the transcriptome and several DEPs from the proteome were detected and confirmed by quantitative real-time PCR as being expressed in the buds of seven different periods of development. We established the databases of differentially expressed genes and proteins between Yamian A and its maintainer Yamian B in the anthers at various developmental stages and constructed an interaction network based on the databases for a comprehensive understanding of the mechanism underlying CMS with a wild cotton genetic background. Conclusion We first analyzed the molecular mechanism of CMS Yamian A from the perspective of omics, thereby providing an experimental basis and theoretical foundation for future research attempting to analyze the abortion mechanism of new CMS with a wild Gossypium bickii background and to realize three-line matching.

Plant evolution is intimately associated with fungal partners. Here the authors provide evidence that Physcomitrella patens MACRO2, a gene likely derived from early mycorrhizae-like fungi, was transferred to early land plants and plays an important role in regulating stem cell growth and gametophore development in moss.

Objective To investigate the contamination situation of Salmonella at different times, slaughtering and processing sites in a broiler slaughter factory to acquire the key contamination point. Methods Chicken anal swabs, carcasses and broiler samples in different slaughtering stages were timely collected in a broiler slaughterhouse in Shaanxi Province from November 2016 to November 2017, Salmonella concentration was quantitatively detected by most probable number (MPN) method, Salmonella isolate recovered from positive samples were identified by polymerase chain reaction (PCR) combined with serum agglutination techniques. Results Among the 284 samples, 67 (23.6%) were positive to Salmonella, the average MPN value was 0.051 6 MPN/g. During sampling period, samples in July was the most frequently contaminated with the positive rate of 37.8% (14/37) and average MPN value of 0.064 7 MPN/g. the lowest Salmonella contamination rate was detected in November 2016 (13.9%, 5/36) with average MPN value of 0.043 6 MPN/g. Among different processing stages, the highest positive rate was detected after scalding and fading (43.3%, 26/60), the average MPN value of which was 0.060 5 MPN/g. The positive rate of chicken breast before freezing was the lowest (18.3%, 11/60), and the average MPN value was 0.036 8 MPN/g, which was slightly higher than that of the whole chicken carcass/chicken breast collected from distribution and storage processes (0.035 8 MPN/g). Conclusion The result showed detection rate and MPN values of Salmonella positive samples in broiler slaughtering process had a strong seasonality, detection of Salmonella in different slaughtering stages indicated that vertical and cross-contamination might happen during the whole process. It was necessary to strengthen the regulation of broilers processing as well as the critical control points.

Callose deposition occurs during plant growth and development, as well as when plants are under biotic and abiotic stress. Callose synthase is a key enzyme for the synthesis of callose. In this study, 27, 28, 16, and 15 callose synthase family members were identified in Gossypium hirsutum, Gossypium barbadense, Gossypium raimondii, and Gossypium arboreum using the sequence of Arabidopsis callose synthase. The CalSs were divided into five groups by phylogenetic, gene structure, and conservative motif analysis. The conserved motifs and gene structures of CalSs in each group were highly similar. Based on the analysis of cis-acting elements, it is inferred that GhCalSs were regulated by abiotic stress. WGD/Segmental duplication promoted the amplification of the CalS gene in cotton, and purification selection had an important function in the CalS family. The transcriptome data and qRT-PCR under cold, heat, salt, and PEG treatments showed that GhCalSs were involved in abiotic stress. The expression patterns of GhCalSs were different in various tissues. We predicted that GhCalS4, which was highly expressed in fibers, had an important effect on fiber elongation. Hence, these results help us understand the role of GhCalSs in fiber development and stress response.

Rheumatoid arthritis (RA) is a chronic autoimmune disease of unknown etiology, mainly manifested by persistent abnormal proliferation of fibroblast-like synoviocytes (FLSs), inflammation, synovial hyperplasia and cartilage erosion, accompanied by joint swelling and joint destruction. Abnormal expression or function of long noncoding RNAs (lncRNAs) are closely related to human diseases, including cancers, mental diseases, autoimmune diseases and others. The abnormal sequence and spatial structure of lncRNAs, the disorder expression and the abnormal interaction with the binding protein will lead to the change of gene expression in the way of epigenetic modification. Increasing evidence demonstrated that lncRNAs were involved in the activation of FLSs, which played a key role in the pathogenesis of RA. In this review, the research progress of lncRNAs in the pathogenesis of RA was systematically summarized, including the role of lncRNAs in the diagnosis of RA, the regulatory mechanism of lncRNAs in the pathogenesis of RA, and the intervention role of lncRNAs in the treatment of RA. Furthermore, the activated signal pathways, the role of DNA methylation and other mechanism have also been overview in this review.

Ligustilide (LIG), a main lipophilic component isolated from Cnidii Rhizoma (Cnidium officinale, rhizome) and Angelicae Gigantis Radix (Angelica gigas Nakai, root), has been shown to alleviate cerebral ischemia injury and paly a neuroprotective role. We investigated mechanisms underlying the antiapoptotic effects of LIG in vitro and in vivo, respectively, using cultured primary hippocampal neurons under oxygen-glucose deprivation/reperfusion (OGD/R) and rats under cerebral ischemia reperfusion(I/R) conditions. In vitro studies revealed that the suppressed apoptosis in hippocampal neurons upon LIG treatment was associated with reduced calcium influx and generation of reactive oxygen species. The LIG-treated hippocampal neurons exhibited decreased the ratio of Bax/Bcl-2, and the release of CytC from mitochondria as well as the expression of cleaved caspase-3, which were accompanied with enhanced the phosphorylation of Akt protein, in a PI3K-dependent manner. In vivo studies demonstrated a neuroprotective role of LIG in attenuating cerebral infarction volume, neurological injury and hippocampal neuron injury, suggesting that LIG could reverse ischemia reperfusion(I/R)-induced apoptosis of hippocampal neurons. These results together suggest that LIG may be considered as a neuroprotectant in the treatment of ischemia stroke.

As one of the three key components of photodynamic therapy (PDT), photosensitizers (PSs) greatly influence the photodynamic efficiency in the treatment of tumors. Photosensitizers with tetrapyrrole structure, such as porphyrins, chlorins and phthalocyanines, have been extensively investigated for PDT and some of them have already received clinical approval. However, only a few of porphyrin-based photosensitizers are available for clinical applications, and PDT has not received wide recognition in clinical practice. In this regard, PSs remain a limiting factor. Our research focuses on the rational design of new PSs. Photocyanine, a Zinc (II) phthalocyanine (ZnPc) type photosensitizer with low dark toxicity and high single oxygen quantum yield, is one of the promising PSs candidates and currently being tested in clinical trials. Here, we present an overview on the development of Photocyanine, including its design, synthesis, purification, characterization and preclinical studies, wishing to contribute to the research of more promising PSs.

The emergence of antibiotic-resistant Salmonella through mutations led to mismatch repair (MMR) deficiency that represents a potential hazard to public health. Here, four representative MMR-deficient Salmonella hypermutator strains and Salmonella Typhimurium LT2 were used to comprehensively reveal the influence of MMR deficiency on antibiotic resistance among Salmonella. Our results indicated that the mutation frequency ranged from 3.39 × 10–4 to 5.46 × 10–2 in the hypermutator. Mutation sites in MutS, MutL, MutT, and UvrD of the four hypermutators were all located in the essential and core functional regions. Mutation frequency of the hypermutator was most highly correlated with the extent of mutation in MutS. Mutations in MMR genes (mutS, mutT, mutL, and uvrD) were correlated with increased mutation in antibiotic resistance genes, and the extent of antibiotic resistance was significantly correlated with the number of mutation sites in MutL and in ParC. The number of mutation sites in MMR genes and antibiotic resistance genes exhibited a significant positive correlation with the number of antibiotics resisted and with expression levels of mutS, mutT, and mutL. Compared to Salmonella Typhimurium LT2, a total of 137 differentially expressed and 110 specifically expressed proteins were identified in the four hypermutators. Functional enrichment analysis indicated that the proteins significantly overexpressed in the hypermutators primarily associated with translation and stress response. Interaction network analysis revealed that the ribosome pathway might be a critical factor for high mutation frequency and multidrug resistance in MMR-deficient Salmonella hypermutators. These results help elucidate the mutational dynamics that lead to hypermutation, antibiotic resistance, and activation of stress response pathways in Salmonella.

Summary: Kingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionarily long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) of K. uniflora and found significant overrepresentation in gene families associated with DNA repair, underrepresentation in gene families associated with stress response, and loss of most plastid ndh genes. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexual K. uniflora reduce the accumulation of deleterious mutations, while reducing genetic diversity, which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss of ndh genes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.

The aim of this study was to develop homogeneous and stable plasmid DNA reference materials for detecting the mechanisms of resistance to quinolones and fluoroquinolones in foodborne pathogens. The DNA fragments of 11 target genes associated with quinolone and fluoroquinolone resistance were artificially synthesized, inserted into plasmid vectors, and transferred into recipient cells. PCR and sequencing of DNA were performed to assess the genetic stability of the target DNA in recombinant Escherichia coli DH5α cells during subculturing for 15 generations. The limit of detection (LOD) of the target DNA was determined using PCR and real-time qualitative PCR (qPCR). The homogeneity and storage stability of plasmid DNA reference materials were evaluated in terms of plasmid DNA quantity, PCR-measured gene expression, and qPCR threshold cycle. All 11 target DNAs were successfully synthesized and inserted into vectors to obtain recombinant plasmids. No nucleotide mutations were identified in the target DNA being stably inherited and detectable in the corresponding plasmids during subculturing of recombinant strains. When the target DNA was assessed using PCR and qPCR, the LOD was ≤1.77 × 105 and 3.26 × 104 copies/μL, respectively. Further, when the reference materials were stored at 37 °C for 13 days, 4 °C for 90 days, and −20 °C for 300 days, each target DNA was detectable by PCR, and no mutations were found. Although the threshold cycle values of qPCR varied with storage time, they were above the LOD, and no significant differences were found in the quantity of each plasmid DNA at different timepoints. Further, the homogeneity and stability of the materials were highly consistent with the requirements of standard reference materials. To summarize, considering that our plasmid DNA reference materials conformed to standard requirements, they can be used to detect the mechanisms of quinolone and fluoroquinolone resistance in foodborne pathogens.

Extant representatives of the earliest land plant lineages adapt to various terrestrial habitats with structural and physiological innovations. Here the authors show a dual-coding gene in the moss Physcomitrella patens evolved from a hemerythrin gene, with effects on oil body biogenesis and dehydration resistance.

As high-strength cotton fibers are critical components of high quality cotton, developing cotton cultivars with high-strength fibers as well as high yield is a top priority for cotton development. Recently, chromosome segment substitution lines (CSSLs) have been developed from high-yield Upland cotton (Gossypium hirsutum) crossed with high-quality Sea Island cotton (G. barbadense). Here, we constructed a CSSL population by crossing CCRI45, a high-yield Upland cotton cultivar, with Hai1, a Sea Island cotton cultivar with superior fiber quality. We then selected two CSSLs with significantly higher fiber strength than CCRI45 (MBI7747 and MBI7561), and one CSSL with lower fiber strength than CCRI45 (MBI7285), for further analysis. We sequenced all four transcriptomes at four different time points postanthesis, and clustered the 44,678 identified genes by function. We identified 2200 common differentially-expressed genes (DEGs): those that were found in both high quality CSSLs (MBI7747 and MBI7561), but not in the low quality CSSL (MBI7285). Many of these genes were associated with various metabolic pathways that affect fiber strength. Upregulated DEGs were associated with polysaccharide metabolic regulation, single-organism localization, cell wall organization, and biogenesis, while the downregulated DEGs were associated with microtubule regulation, the cellular response to stress, and the cell cycle. Further analyses indicated that three genes, XLOC_036333 [mannosyl-oligosaccharide-α-mannosidase (MNS1)], XLOC_029945 (FLA8), and XLOC_075372 (snakin-1), were potentially important for the regulation of cotton fiber strength. Our results suggest that these genes may be good candidates for future investigation of the molecular mechanisms of fiber strength formation and for the improvement of cotton fiber quality through molecular breeding.

Salinity levels and drought status of coastal wetlands may be strongly affected by climate change, and changes in the nitrogen cycle of mangrove wetlands may also be affected. We established combinations of three salinity and water levels with applied stable isotope 15N to study the δ15N distributions in the sediment and plants of a greenhouse-based simulated mangrove Aegiceras corniculatum wetland system. The stable isotope 13C and 15N, C and N contents and the C:N ratio were determined. Results showed that increasing in salinity significantly increased the δ13C value in plant organs. The δ15N value of plant organs increased with increasing water level in low salinity (10‰) and medium salinity (20‰) treatment groups but not in the high salinity (30‰) treatment group. This may attributed to A. corniculatum adjusting the δ15N distribution in different organs in response to high salinity stress. Compared to the δ13C, the δ15N values of plant were strongly affected by salinity and water level treatments, indicating that the behavior of N cycle was somewhat different than the C cycle, and affected by the combined effects of both salinity and water level. Most of 15N absorbed by plant tissues were in leaves except for the highest salinity and high water level treatment, showing at increasing water level, the proportion of 15N increased in root. Overall, the measured indicators exhibited different responses to salinity level and water level, suggesting that the changes in salinity and water levels have an impact on N cycling processes of wetland systems.

Pickled ready-to-eat meat (PRTEM) is a meat product that is treated with various seasonings and then cooked. PRTEM is a popular food consumed mostly in China and some Asian countries. Since this food is considered ‘ready to eat’, once it is contaminated by foodborne pathogens such as Salmonella, the prospect for significant morbidity, mortality, and immeasurable economic losses can occur. Here we investigated the prevalence and concentration of Salmonella in 107 PRTEM samples collected from Shaanxi, China during 2015–2016. Furthermore, we analyzed the serotype, antibiotic susceptibility, and presence of antibiotic resistance genes and amino acid mutations in 219 Salmonella isolates, followed by subtyping of 115 representative isolates. The average detection rate of Salmonella-positive PRTEM was 58.9%, and the average most probable number (MPN) of Salmonella in positive samples was 2.27 logMPN per gram of sample (range: 2.10–2.43). Ten serotypes were identified from the 219 Salmonella isolates, with S. Thompson (37.9%) and S. Indiana (20.5%) being predominant. The remaining serotypes were S. Typhi (7.8%), S. Typhimurium (7.3%), S. Mbandaka (6.9%), S. Albany (6.4%), S. Blockley (5.5%), S. Infantis (4.1%), S. Escanaba (3.2%), and S. Dusseldorf (0.5%). All isolates were resistant to ceftiofur (100%), while most of them were resistant to ciprofloxacin (99.1%), amoxicillin-clavulanic acid (97.7%), trimethoprim-sulfamethoxazole (96.4%), ampicillin (92.3%), sulfisoxazole (92.2%), tetracyclines (90.4%), and nalidixic acid (90.4%), respectively. A single mutation of Ser83Phe (27.1%) and double mutations of Ser83Phe-Asp87Gly (25.9%) in GyrA were detected in 85 isolates, whereas mutations of Thr57Ser (63.9%) and Ser80Arg (36.1%) in ParC were detected in 122 isolates. qnrB, oqxAB, aac(6′)-Ib, and qnrA were present in 50 (22.8%), 48 (21.9%), 26 (11.9%), and 1 (0.5%) isolate(s), respectively. Pulse field gel electrophoresis results revealed that those isolates recovered from the same type of PRTEM or the same sampling place shared identical or similar DNA profiles, antibiotic resistance phenotypes, and even plasmid-mediated quinolone resistance encoding genes. The findings indicate that Salmonella is commonly prevalent in PRTEMs at high concentrations in Shaanxi, China. More attention should be paid to the processing and storage of this ready-to-eat food to prevent bacterial contamination and foodborne outbreaks.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Arbuscular mycorrhizal fungi (AMF) belong to Glomeromycotina, and are mutualistic symbionts of many land plants. Associated bacteria accompany AMF during their lifecycle to establish a robust tripartite association consisting of fungi, plants and bacteria. Physical association among this trinity provides possibilities for the exchange of genetic materials. However, very few horizontal gene transfer (HGT) from bacteria or plants to AMF has been reported yet. In this study, we complement existing algorithms by developing a new pipeline, Blast2hgt, to efficiently screen for putative horizontally derived genes from a whole genome. Genome analyses of the glomeromycete Rhizophagus irregularis identified 19 fungal genes that had been transferred between fungi and bacteria/plants, of which seven were obtained from bacteria. Another 18 R. irregularis genes were found to be recently acquired from either plants or bacteria. In the R. irregularis genome, gene duplication has contributed to the expansion of three foreign genes. Importantly, more than half of the R. irregularis foreign genes were expressed in various transcriptomic experiments, suggesting that these genes are functional in R. irregularis. Functional annotation and available evidence showed that these acquired genes may participate in diverse but fundamental biological processes such as regulation of gene expression, mitosis and signal transduction. Our study suggests that horizontal gene influx through endosymbiosis is a source of new functions for R. irregularis, and HGT might have played a role in the evolution and symbiotic adaptation of this arbuscular mycorrhizal fungus.

The spread of photosynthesis is one of the most important but constantly debated topics in eukaryotic evolution. Various hypotheses have been proposed to explain the plastid distribution in extant eukaryotes. Notably, the chromalveolate hypothesis suggested that multiple eukaryotic lineages were derived from a photosynthetic ancestor that had a red algal endosymbiont. As such, genes of plastid/algal origin in aplastidic chromalveolates, such as oomycetes, were considered to be important supporting evidence. Although the chromalveolate hypothesis has been seriously challenged, some of its supporting evidence has not been carefully investigated. In this study, we re-evaluate the “algal” genes from oomycetes with a larger sampling and careful phylogenetic analyses. Our data provide no conclusive support for a common photosynthetic ancestry of stramenopiles, but show that the initial estimate of “algal” genes in oomycetes was drastically inflated due to limited genome data available then for certain eukaryotic lineages. These findings also suggest that the evolutionary histories of these “algal” genes might be attributed to complex scenarios such as differential gene loss, serial endosymbioses, or horizontal gene transfer.

Growth arrest special 5 (GAS5) is a long non-coding RNA reported to function as an inhibitor in various tumors including cervical cancer. However, the molecular mechanism of GAS5 involved in cervical cancer progression remains far from being elucidated. The expression of GAS5, forkhead box protein O1 and phosphatase and tensin homolog was examined by quantitative reverse transcription polymerase chain reaction qRT-PCR. cell growth, invasion, and apoptosis were assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, colony formation assay, transwell invasion assay, and flow cytometry analysis, respectively. The interaction between GAS5 and miR-196a or miR-205 was confirmed by luciferase reporter assay, RNA immunoprecipitation assay, and qRT-PCR. Xenograft tumor experiments were performed to validate the biological role of GAS5 and its molecular mechanism in cervical cancer in vivo. GAS5 expression was decreased in cervical cancer tissues and cells. GAS5 overexpression suppressed cervical cancer cell proliferation, invasion, and apoptosis. GAS5 was able to directly bind to miR-196a and miR-205 to downregulate their expression. Moreover, GAS5 induced forkhead box protein O1 and phosphatase and tensin homolog expression by repressing miR-196a and miR-205, respectively. Exogenous expression of GAS5 hindered tumor growth in vivo by downregulating miR-196a and miR-205. Upregulation of GAS5 suppressed cell proliferation, invasion, and apoptosis of cervical cancer cells by downregulating miR-196a and miR-205, contributing to our understanding the pathogenesis of cervical cancer and development of long non-coding RNA–mediated clinical therapy against this disease.

Recent studies suggest that horizontal gene transfer (HGT) played a significant role in the evolution of eukaryotic lineages. We here review the mechanisms of HGT in plants and the importance of HGT in land plant evolution. In particular, we discuss the role of HGT in plant colonization of land, phototropic response, C4 photosynthesis, and mitochondrial genome evolution.