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Introduction The prevalence of obesity is rising, significantly impacting health and quality of life. Effective treatment is crucial, particularly for abdominal obesity (AO). Electroacupuncture (EA), which combines acupuncture and moxibustion with electric current, shows promise but lacks reliable clinical evidence for its efficacy and safety. Therefore, a meta-analysis is essential to assess the clinical effectiveness of EA in treating AO.Methods and analysis A systematic search of PubMed, Medline, Embase, the Cochrane Library, China National Knowledge Infrastructure, Wanfang and Allied and Alternative Medicine (AMED) databases will be conducted from database inception to 1 June 2024 to identify randomised controlled trials investigating the effectiveness and safety of EA in treating AO. Two authors will independently carry out data extraction and evaluate the risk of bias. RevMan software (V.5.4) will be used for data analysis, and publication bias will be assessed using funnel plots and Egger’s test. The quality of evidence will be evaluated according to Grades of Recommendation, Assessment, Development, and Evaluation, and trial sequence analysis will be used to calculate the final total sample size required for the meta-analysis. The primary outcome will be the measurement of waist circumference. Secondary outcomes will include the quality of life, hip circumference, waist-to-hip ratio, body mass index, body fat percentage, visceral fat thickness and serum markers such as triglycerides, total cholesterol, low-density lipoprotein and high-density lipoprotein cholesterol. The data will be pooled and analysed, with subgroup analyses conducted if needed.Ethics and dissemination This systematic review and meta-analysis does not require ethical approval because the data for this review will be extracted from already published journal articles. The protocol for this review has been registered in the International Prospective Register of Systematic Reviews (PROSPERO). This review and its findings will be published in a peer-reviewed journal or presented at scientific conferences.PROSPERO registration number CRD42024562984.

Protaetia brevitarsis larvae (PBL) are soil insects important for the soil organic carbon cycle, and PBL frass not only contains a large amount of humic acid but also affects the diversity, novelty, and potential functions of actinomycetes. Here, we characterized and assessed the actinomycete. The operational taxonomic unit (OTU) data showed that 90% of the actinomycetes cannot be annotated to species, and pure culture and genome analysis showed that 35% of the strains had the potential to be new species, indicating the novelty of PBL frass actinomycetes. Additionally, genome annotation showed that many gene clusters related to antifungal, antibacterial and insecticidal compound synthesis were identified, and confrontation culture confirmed the antifungal activities of the actinomycetes against soil-borne plant pathogenic fungi. The incubation experiment results showed that all isolates were able to thrive on media composed of straw powder and alkaline lignin. These results indicated that PBL hindgut-enriched actinomycetes could survive in soil by using the residual lignocellulose organic matter from plant residues, and the antibiotics produced not only give them a competitive advantage among soil microflora but also have a certain inhibitory effect on plant diseases and pests. This study suggests that the application of PBL frass can not only supplement soil humic acid but also potentially affect the soil microbiota of cultivated land, which is beneficial for the healthy growth of crops.

Abstract Background Major depressive disorder (MDD) has a high incidence and an unknown mechanism. There are no objective and sensitive indicators for clinical diagnosis. Objective This study explored specific electrophysiological indicators and their role in the clinical diagnosis of MDD using machine learning. Methods Forty first-episode and drug-naïve patients with MDD and forty healthy controls (HCs) were recruited. EEG data were collected from all subjects in the resting state with eyes closed for 10 min. The severity of MDD was assessed by the Hamilton Depression Rating Scale (HAMD-17). Machine learning analysis was used to identify the patients with MDD. Results Compared to the HC group, the relative power of the low delta and theta bands was significantly higher in the right occipital region, and the relative power of the alpha band in the entire posterior occipital region was significantly lower in the MDD group. In the MDD group, the alpha band scalp functional connectivity was overall lower, while the scalp functional connectivity in the gamma band was significantly higher than that in the HC group. In the feature set of the relative power of the ROI in each band, the highest accuracy of 88.2% was achieved using the KNN classifier while using PCA feature selection. In the explanatory model using SHAP values, the top-ranking influence feature is the relative power of the alpha band in the left parietal region. Conclusions Our findings reveal that the abnormal EEG neural oscillations may reflect an imbalance of excitation, inhibition and hyperactivity in the cerebral cortex in first-episode and drug-naïve patients with MDD. The relative power of the alpha band in the left parietal region is expected to be an objective electrophysiological indicator of MDD.

Polysaccharide is one of the principal bioactive components found in medicinal mushrooms and has been proven to enhance host immunity. However, the possible mechanism of immunomodulatory activity of Cordyceps militaris polysaccharide is not fully understood. Hot water extraction and alcohol precipitation, DEAE-Sephadex A-25 chromatography, and Sephadex G-100 chromatography were used to isolate polysaccharide from C. militaris. A high-molecular-weight polysaccharide isolated from C. militaris was designated as HCMP, which had an Mw of 6.18 × 105 Da and was composed of arabinose, galactose, glucose, mannose, and xylose in a mole ratio of 2.00:8.01:72.54:15.98:1.02. The polysaccharide content of HCMP was 91.2% ± 0.16. The test in vitro showed that HCMP activated mouse macrophage RAW 264.7 cells by enhancing phagocytosis and NO production, and by regulating mRNA expressions of inflammation-related molecules in RAW 264.7 cells. Western blotting revealed that HCMP induced the phosphorylation of mitogen-activated protein kinases (MAPKs). Moreover, using inhibitors of MAPKs decreased the mRNA levels of inflammation-related molecules induced by HCMP. These data evidenced that the immunomodulatory effect of HCMP on RAW 264.7 macrophages was mediated via the MAPK signaling pathway. These findings suggested that HCMP could be developed as a potent immunomodulatory agent for use in functional foods and dietary supplements.

Abstract Comprehensive protein-protein interaction (PPI) maps are critical for understanding the functional organization of the proteome, but challenging to produce experimentally. Here, we developed a computational method for predicting PPIs based on protein docking. Evaluation of performance on benchmark sets demonstrated the ability of the docking-based method to accurately identify PPIs using predicted protein structures. By employing the docking-based method, we constructed a structurally resolved PPI network consisting of 24,653 interactions between 2,131 proteins, which greatly extends the current knowledge on the rice protein-protein interactome. Moreover, we mapped the trait-associated single nucleotide polymorphisms (SNPs) to the structural interactome, and computationally identified 14 SNPs that had significant consequences on PPI network. The protein structural interactome map provided a resource to facilitate functional investigation of PPI-perturbing alleles associated with agronomically important traits in rice.

For multi-level systems in hot atomic vapors the interplay between the Doppler shift due to atomic motion and the wavenumber mismatch between driving laser fields strongly influences transmission and absorption properties of the atomic medium. In a three-level atomic ladder-system, Doppler broadening limits the visibility of electromagnetically-induced transparency (EIT) when the probe and control fields are co-propagating, while EIT is recovered under the opposite condition of counter-propagating geometry and $k_\mathrm{p} \lt k_\mathrm{c}$ , with $k_\mathrm{p}$ and $k_\mathrm{c}$ being the wavenumbers of the probe and control fields, respectively. This effect has been studied and experimentally demonstrated as an efficient mechanism to realize non-reciprocal probe light transmission, which may enable applications as magnetic-field free optical isolators. Here, we describe the basics of this effect and discuss a simple picture for the underlying mechanism. We illustrate how the non-reciprocity scales with wavelength mismatch and show how to experimentally demonstrate the effect in a simple Rydberg-EIT system using thermal Rubidium atoms.

We develop a method based on the cross-spectrum of an intensity-modulated CW laser, which can extract a signal from an extremely noisy environment and image objects hidden in scattering media. We theoretically analyzed our scheme and performed the experiment by scanning the object placed in between two ground glass diffusers. The image of the object is retrieved by collecting the amplitudes at the modulation frequency of all the cross-spectra. Our method is non-invasive, easy-to-implement, and can work for both static and dynamic media.

Optical interfaces with subwavelength patterns make it possible to manipulate light waves beyond the typical capabilities of ordinary optical media. Subwavelength arrays of ultracold atoms enable such transformations at very low photon losses. Here, we show how the coupling of light to more than a single atomic array can expand these perspectives into the domain of quantum nonlinear optics. While a single array transmits and reflects light in a highly coherent but largely linear fashion, the combination of two arrays is found to induce strong photon-photon interactions that can convert an incoming classical beam into strongly correlated photonic states. Such quantum metasurfaces open up new possibilities for coherently generating and manipulating nonclassical light, and exploring quantum many-body phenomena in two-dimensional systems of strongly interacting photons.

Abstract Background Salmonella is a major bacterial pathogen associated with a large number of outbreaks of foodborne diseases. Many highly virulent serovars that cause human illness belong to Salmonella serogroup C1, and Salmonella ser. Choleraesuis is a prominent cause of invasive infections in Asia. Comparative genomic analysis in our previous study showed that two homologous genes, SC0368 and SC0595 in Salmonella ser. Choleraesuis were unique to serogroup C1. In this study, two single-deletion mutants (Δ0368 and Δ0595) and one double-deletion mutant (Δ0368Δ0595) were constructed based on the genome. All these mutants and the wild-type strain were subjected to RNA-Seq analysis to reveal functional relationships of the two serogroup C1-specific genes. Results Data from RNA-Seq indicated that deletion of SC0368 resulted in defects in motility through repression of σ28 in flagellar regulation Class 3. Consistent with RNA-Seq data, results from transmission electron microcopy (TEM) showed that flagella were not present in △0368 and △0368△0595 mutants resulting in both swimming and swarming defects. Interestingly, the growth rates of two non-motile mutants △0368 and △0368△0595 were significantly greater than the wild-type, which may be associated with up-regulation of genes encoding cytochromes, enhancing bacterial proliferation. Moreover, the △0595 mutant was significantly more invasive in Caco-2 cells as shown by bacterial enumeration assays, and the expression of lipopolysaccharide (LPS) core synthesis-related genes (rfaB, rfaI, rfaQ, rfaY, rfaK, rfaZ) was down-regulated only in the △0368△0595 mutant. In addition, this study also speculated that these two genes might be contributing to serotype conversion for Salmonella C1 serogroup based on their apparent roles in biosynthesis of LPS and the flagella. Conclusion A combination of biological and transcriptomic (RNA-Seq) analyses has shown that the SC0368 and SC0595 genes are involved in biosynthesis of flagella and complete LPS, as well as in bacterial growth and virulence. Such information will aid to revealing the role of these specific genes in bacterial physiology and evolution within the serogroup C1.

Abstract Background Antibiotic resistance genes (ARGs) can spread among pathogens via horizontal gene transfer, resulting in imparities in their distribution even within the same species. Therefore, a pan-genome approach to analyzing resistomes is necessary for thoroughly characterizing patterns of ARGs distribution within particular pathogen populations. Software tools are readily available for either ARGs identification or pan-genome analysis, but few exist to combine the two functions. Results We developed Pan Resistome Analysis Pipeline (PRAP) for the rapid identification of antibiotic resistance genes from various formats of whole genome sequences based on the CARD or ResFinder databases. Detailed annotations were used to analyze pan-resistome features and characterize distributions of ARGs. The contribution of different alleles to antibiotic resistance was predicted by a random forest classifier. Results of analysis were presented in browsable files along with a variety of visualization options. We demonstrated the performance of PRAP by analyzing the genomes of 26 Salmonella enterica isolates from Shanghai, China. Conclusions PRAP was effective for identifying ARGs and visualizing pan-resistome features, therefore facilitating pan-genomic investigation of ARGs. This tool has the ability to further excavate potential relationships between antibiotic resistance genes and their phenotypic traits.

To create novel tomato (Solanum lycopersicum) germplasm, a wild tomato relative, S. pimpinellifolium (a red-fruited LA1585 accession), was used as the male parent to cross with the yellow-fruited tomato mutant, e9292 (S. lycopersicum). Forty-four morphological characteristics were examined in the present study; 22 S. pimpinellifolium (LA1585) traits and six S. lycopersicum (e9292) traits were dominant in the hybrids (first generation, F1); 10 were intermediate types, and the remaining six resulted in a nonmorphological difference. Ten representative lines were chosen from 1338 line of the second generation of the hybrid (e9292 × LA1585). The ascorbic acid content was higher in three F2 hybrids than in LA1585, which had higher parental levels, as well as the lycopene content in two of the hybrid lines. The fructose and glucose contents were higher in five F2 hybrids compared to e9292, and the sugar/acid value was higher in three hybrid lines. The broad-sense heritability values ranged from 75.06% for total soluble solids to 99.92% for ascorbic acid, and the average value was 92.66% for 15 quality traits. When seedlings were exposed to NaCl and mannitol, the tolerance of high salt concentrations and drought was enhanced in two hybrid lines (F2-266 and F2-299) compared with else tomatoes (e9292, LA1585, F1 hybrids, and F2-332). We created novel tomato germplasm resources with horticulturally desirable quality traits and abiotic stress tolerance, thus offering a methodology for novel tomato germplasm creation and evaluation.

Rice blast, caused by the fungus Magnaporthe oryzae, is the most devastating disease affecting rice production. Identification of protein–protein interactions (PPIs) is a critical step toward understanding the molecular mechanisms underlying resistance to blast fungus in rice. In this study, we presented a computational framework for predicting plant–pathogen PPIs based on structural information. Compared with the sequence-based methods, the structure-based approach showed to be more powerful in discovering new PPIs between plants and pathogens. Using the structure-based method, we generated a global PPI network consisted of 2,018 interacting protein pairs involving 1,344 rice proteins and 418 blast fungus proteins. The network analysis showed that blast resistance genes were enriched in the PPI network. The network-based prediction enabled systematic discovery of new blast resistance genes in rice. The network provided a global map to help accelerate the identification of blast resistance genes and advance our understanding of plant–pathogen interactions.

We investigate the interaction of weak light fields with two-dimensional lattices of atoms with high lying atomic Rydberg states. This system features different interactions that act on disparate length scales, from zero-range defect scattering of atomic excitations and finite-range dipole exchange processes to long-range Rydberg-state interactions, which span the entire array and can block multiple Rydberg excitations. Analyzing their interplay, we identify conditions that yield a nonlinear quantum mirror which coherently splits incident fields into correlated photon-pairs in a single transverse mode, while transmitting single photons unaffected. In particular, we find strong anti-bunching of the transmitted light with equal-time pair correlations that decrease exponentially with an increasing range of the Rydberg blockade. Such strong photon-photon interactions in the absence of photon losses open up promising avenues for the generation and manipulation of quantum light, and the exploration of many-body phenomena with interacting photons.

Abstract Drought is one of the most severe abiotic factors restricting plant growth and yield. Numerous genes functioning in drought response are regulated by abscisic acid (ABA) dependent and independent pathways, but knowledge of interplay between the two pathways is still limited. Here, we integrated transcriptome sequencing and network analyses to explore interplays between ABA-dependent and ABA-independent pathways responding to drought stress in Arabidopsis thaliana. We identified 211 ABA-dependent differentially expressed genes (DEGs) and 1,118 ABA-independent DEGs under drought stress. Functional analysis showed that ABA-dependent DEGs were significantly enriched in expected biological processes in response to water deprivation and ABA stimulus, while ABA-independent DEGs were preferentially enriched in response to jasmonic acid (JA), salicylic acid (SA) and gibberellin (GA) stimuli. We found significantly enriched interactions between ABA-dependent and ABA-independent pathways with 94 genes acting as core interacting components by combining network analyses. A link between ABA and JA signaling mediated through a direct interaction of the ABA responsive elements-binding factor ABF3 with the basic helix-loop-helix transcription factor MYC2 was validated by yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Our study provides a systematic view of the interplay between ABA-dependent and ABA-independent pathways in response to drought stress.

Abstract Background Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD1), G. barbadense (AD2), G. raimondii (D5) and G. arboreum (A2), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium. Results Six Gossypium mitochondrial genomes, including three diploid species from D and three allotetraploid species from AD genome groups (G. thurberi D1, G. davidsonii D3-d and G. trilobum D8; G. tomentosum AD3, G. mustelinum AD4 and G. darwinii AD5), were assembled as the single circular molecules of lengths about 644 kb in diploid species and 677 kb in allotetraploid species, respectively. The genomic structures of mitochondrial in D group species were identical but differed from the mitogenome of G. arboreum (A2), as well as from the mitogenomes of five species of the AD group. There mainly existed four or six large repeats in the mitogenomes of the A + AD or D group species, respectively. These variations in repeat sequences caused the major inversions and translocations within the mitochondrial genome. The mitochondrial genome complexity in Gossypium presented eight unique segments in D group species, three specific fragments in A + AD group species and a large segment (more than 11 kb) in diploid species. These insertions or deletions were most probably generated from crossovers between repetitive or homologous regions. Unlike the highly variable genome structure, evolutionary distance of mitochondrial genes was 1/6th the frequency of that in chloroplast genes of Gossypium. RNA editing events were conserved in cotton mitochondrial genes. We confirmed two near full length of the integration of the mitochondrial genome into chromosome 1 of G. raimondii and chromosome A03 of G. hirsutum, respectively, with insertion time less than 1.03 MYA. Conclusion Ten Gossypium mitochondrial sequences highlight the insights to the evolution of cotton mitogenomes.

Protein-protein interactions (PPIs) play fundamental roles in various cellular processes. Here, we present a new version of computational interactome that contains more than 345,000 predicted PPIs involving about 51.2% of the Arabidopsis proteins. Compared to the earlier version, the updated AraPPINet displays a higher accuracy in predicting protein interactions through performance evaluation with independent datasets. In addition to the experimental verifications of the previous version, the new version has been subjected to further validation test that demonstrates its ability to discover novel PPIs involved in hormone signaling pathways. Moreover, network analysis shows that many overlapping proteins are significantly involved in the interactions which mediated the crosstalk among plant hormones. The new version of AraPPINet provides a more reliable interactome which would facilitate the understanding of crosstalk among hormone signaling pathways in plants.

Ralstonia solanacearum is an important soil-borne bacterial plant pathogen. In this study, an actinomycete strain named NEAU-HV9 that showed strong antibacterial activity against Ralstonia solanacearum was isolated from soil using an in vitro screening technique. Based on physiological and morphological characteristics and 98.90% of 16S rRNA gene sequence similarity with Streptomyces panaciradicis 1MR-8T, the strain was identified as a member of the genus Streptomyces. Tomato seedling and pot culture experiments showed that after pre-inoculation with the strain NEAU-HV9, the disease occurrence of tomato seedlings was effectively prevented for R. solanacearum. Then, a bioactivity-guided approach was employed to isolate and determine the chemical identity of bioactive constituents with antibacterial activity from strain NEAU-HV9. The structure of the antibacterial metabolite was determined as actinomycin D on the basis of extensive spectroscopic analysis. To our knowledge, this is the first report that actinomycin D has strong antibacterial activity against R. solanacearum with a MIC (minimum inhibitory concentration) of 0.6 mg L−1 (0.48 μmol L−1). The in vivo antibacterial activity experiment showed that actinomycin D possessed significant preventive efficacy against R. solanacearum in tomato seedlings. Thus, strain NEAU-HV9 could be used as BCA (biological control agent) against R. solanacearum, and actinomycin D might be a promising candidate for a new antibacterial agent against R. solanacearum.

Salmonellaenterica serovar Enteritidis (Salmonella Enteritidis) is a globally important foodborne pathogen, and the contaminated chicken eggs are the major source of salmonellosis in humans. Salmonella Enteritidis strains are differentially susceptible to the hostile environment of egg whites. Strains with superior survival ability in egg whites are more likely to contaminate eggs and consequently infect humans. However, the genetic basis for this phenotype is unclear. We characterized two Salmonella Enteritidis strains isolated from chicken meat that had similar genetic backgrounds but large differences in survival ability in egg whites. Although genome comparisons indicated that the gene content and genomic synteny were highly conserved, variations including six insertions or deletions (INDELs) and 70 single nucleotide polymorphisms (SNPs) were observed between the two genomes. Of these, 38 variations including four INDELs and 34 non-synonymous SNPs (nsSNP) were annotated to result in amino acid substitutions or INDELs in coding proteins. These variations were located in 38 genes involved in lysozyme inhibition, vitamin biosynthesis, cell division and DNA damage response, osmotic and oxidative protection, iron-related functions, cell envelope maintenance, amino acid and carbohydrate metabolism, antimicrobial resistance, and type III secretion system. We carried out allelic replacements for two nsSNPs in bioC (biotin synthesis) and pliC (lysozyme inhibition), and two INDELs in ftsK and yqiJ (DNA damage response) by homologous recombination, and these replacements did not alter the bacterial survival ability in egg whites. However, the bacterial survival ability in egg whites was reduced when deletion mutation of the genes bioC and pliC occurred. This study provides initial correlations between observed genotypes and phenotypes and serves as an important caveat for further functional studies.

Salmonella is one of the primary causes of foodborne disease, especially Salmonella enterica subsp. enterica (I) which has caused ~99% of clinical salmonellosis cases for humans and domestic mammals. The flagella genes, fliC and fljB, which encode the Salmonella phase 1 and phase 2 antigens respectively, are considered as the Salmonella serotype determinant genes, and contribute to the virulence of Salmonella. However, the evolution of the two flagellin genes is still not well-understood. In this study, the fliC and fljB gene clusters were analyzed among 205 S. enterica subspecies I genomes. The dataset covered 87 different serovars of S. enterica subsp. enterica and included 9 genomes (six serovars) of four other Salmonella subspecies. Based on a pan-genome definition and flanked gene linkages, the fliC and fljB gene clusters were identified in 207 (91 serovars) and 138 (61 serovars) genomes, respectively. A phylogenetic tree constructed based on SNPs (Single Nucleotide Polymorphisms) of core genes were used to reflect the essential evolutionary relationships among various serovars. Congruence analysis was performed among the core genome and each gene of fliC and fljB gene clusters, with only fliA and fliS showing congruence to Salmonella core genome. Congruence was also observed among fliB, fliC/fljB, and fliD genes, and their phylogeny revealed a division into two major groups, which strongly corresponded to monophasic and biphasic serovars. Besides, homologous recombination events referring fliB, fliC, and fliD were found to have mainly occurred within each group. These results suggested two distinct evolutionary patterns of Salmonella flagellin gene clusters. Further insight on the evolutionary implication of the two patterns and a framework for phase variation mechanism are needed to be further processed.

Silique shattering resistance is one of the most important agricultural traits in oil crop breeding. Seed shedding from siliques prior to and during harvest causes devastating losses in oilseed yield. Lignin biosynthesis in the silique walls is thought to affect silique-shattering resistance in oil crops. Here, we identified and characterized B. napus LATE FLOWERING (BnLATE), which encodes a Cys2/His2-type zinc-finger protein. Heterologous expression of BnLATE under the double enhanced CaMV 35S promoter (D35S) in wild-type Arabidopsis plants resulted in a marked decrease in lignification in the replum, valve layer (carpel) and dehiscence zone. pBnLATE::GUS activity was strong in the yellowing silique walls of transgenic lines. Furthermore, the expression pattern of BnLATE and the lignin content gradient in the silique walls at 48 days after pollination (DAP) of 73290, a B. napus silique shattering-resistant line, are similar to those in transgenic Arabidopsis lines expressing BnLATE. Transcriptome sequencing of the silique walls revealed that genes encoding peroxidases, which polymerize monolignols and lignin in the phenylpropanoid pathway, were down-regulated at least two-fold change in the D35S::BnLATE transgenic lines. pBnLATE::BnLATE transgenic lines were further used to identify the function of BnLATE, and the results showed that lignification in the carpel and dehiscence zone of yellowing silique also remarkably decreased compared with the wild-type control, the silique shattering-resistance and expression pattern of peroxidase genes are very similar to results with D35S::BnLATE. These results suggest that BnLATE is a negative regulator of lignin biosynthesis in the yellowing silique walls, and promotes silique-shattering resistance in B. napus through restraining the polymerization of monolignols and lignin.

Vast amounts of allergen sequence data have been accumulated, thus complicating the identification of specific allergenic proteins when performing diagnostic allergy tests and immunotherapy. This study aims to rank the importance/potency of the allergens so as to logically reduce the number of allergens and/or allergenic sources. Meta-analysis of 62 allergenic sources used for intradermal testing on 3,335 allergic patients demonstrated that in southern China, mite, sesame, spiny amaranth, Pseudomonas aeruginosa, and house dust account for 88.0% to 100% of the observed positive reactions to the 62 types of allergenic sources tested. The Kolmogorov-Smironov Test results of the website-obtained allergen data and allergen family featured peptides suggested that allergen research in laboratories worldwide has been conducted in parallel on many of the same species. The major allergens were reduced to 21 representative allergens, which were further divided into seven structural classes, each of which contains similar structural components. This study therefore has condensed numerous allergenic sources and major allergens into fewer major representative ones, thus allowing for the use of a smaller number of allergens when conducting comprehensive allergen testing and immunotherapy treatments.

The effect of the number of pods on the main inflorescence (NPMI) on seed yield in Brassica napus plants grown at high density is a topic of great economic and scientific interest. Here, we sought to identify patterns of gene expression that determine the NPMI during inflorescence differentiation. We monitored gene expression profiles in the main inflorescence of two B. napus F6 RIL pools, each composed of nine lines with a low or high NPMI, and their parental lines, Zhongshuang 11 (ZS11) and 73290, using a Brassica 90K elements oligonucleotide array. We identified 4,805 genes that were differentially expressed (≥1.5 fold-change) between the low- and high-NPMI samples. Of these, 82.8% had been annotated and 17.2% shared no significant homology with any known genes. About 31 enriched GO clusters were identified amongst the differentially expressed genes (DEGs), including those involved in hormone responses, development regulation, carbohydrate metabolism, signal transduction, and transcription regulation. Furthermore, 92.8% of the DEGs mapped to chromosomes that originated from B. rapa and B. oleracea, and 1.6% of the DEGs co-localized with two QTL intervals (PMI10 and PMI11) known to be associated with the NPMI. Overexpression of BnTPI, which co-localized with PMI10, in Arabidopsis suggested that this gene increases the NPMI. This study provides insight into the molecular factors underlying inflorescence architecture, NPMI determination and, consequently, seed yield in B. napus.

Annexins are assumed to be involved in regulating cotton fiber elongation, but direct evidence remains to be presented. Here we cloned six Annexin genes (AnxGb) abundantly expressed in fiber from sea-island cotton (G. barbadense). qRT-PCR results indicated that all six G. barbadense annexin genes were expressed in elongating cotton fibers, while only the expression of AnxGb6 was cotton fiber-specific. Yeast two hybridization and BiFC analysis revealed that AnxGb6 homodimer interacted with a cotton fiber specific actin GbAct1. Ectopic-expressed AnxGb6 in Arabidopsis enhanced its root elongation without increasing the root cell number. Ectopic AnxGb6 expression resulted in more F-actin accumulation in the basal part of the root cell elongation zone. Analysis of AnxGb6 expression in three cotton genotypes with different fiber length confirmed that AnxGb6 expression was correlated to cotton fiber length, especially fiber elongation rate. Our results demonstrated that AnxGb6 was important for fiber elongation by potentially providing a domain for F-actin organization.

Understanding the molecular mechanisms that underlie plant responses to drought stress is challenging due to the complex interplay of numerous different genes. Here, we used network-based gene clustering to uncover the relationships between drought-responsive genes from large microarray datasets. We identified 2,607 rice genes that showed significant changes in gene expression under drought stress; 1,392 genes were highly intercorrelated to form 15 gene modules. These drought-responsive gene modules are biologically plausible, with enrichments for genes in common functional categories, stress response changes, tissue-specific expression and transcription factor binding sites. We observed that a gene module (referred to as module 4) consisting of 134 genes was significantly associated with drought response in both drought-tolerant and drought-sensitive rice varieties. This module is enriched for genes involved in controlling the response of the plant to water and embryonic development, including a heat shock transcription factor as the key regulator in the expression of ABRE-containing genes. These results suggest that module 4 is highly conserved in the ABA-mediated drought response pathway in different rice varieties. Moreover, our study showed that many hub genes clustered in rice chromosomes had significant associations with QTLs for drought stress tolerance. The relationship between hub gene clusters and drought tolerance QTLs may provide a key to understand the genetic basis of drought tolerance in rice.