Expression of Foreign Genes Demonstrates the Effectiveness of Pollen-Mediated Transformation in Zea mays

Plant genetic transformation has arguably been the core of plant improvement in recent decades. Efforts have been made to develop in planta transformation systems due to the limitations present in the tissue-culture-based methods. Herein, we report an improved in planta transformation system, and provide the evidence of reporter gene expression in pollen tube, embryos and stable transgenicity of the plants following pollen-mediated plant transformation with optimized sonication treatment of pollen. The results showed that the aeration at 4°C treatment of pollen grains in sucrose prior to sonication significantly improved the pollen viability leading to improved kernel set and transformation efficiency. Scanning electron microscopy observation revealed that the removal of operculum covering pollen pore by ultrasonication might be one of the reasons for the pollen grains to become competent for transformation. Evidences have shown that the eGfp gene was expressed in the pollen tube and embryos, and the Cry1Ac gene was detected in the subsequent T(1) and T(2) progenies, suggesting the successful transfer of the foreign genes to the recipient plants. The Southern blot analysis of Cry1Ac gene in T(2) progenies and PCR-identified Apr gene segregation in T(2) seedlings confirmed the stable inheritance of the transgene. The outcome illustrated that the pollen-mediated genetic transformation system can be widely applied in the plant improvement programs with apparent advantages over tissue-culture-based transformation methods

Classification of protein quaternary structure by functional domain composition

BACKGROUND: The number and the arrangement of subunits that form a protein are referred to as quaternary structure. Quaternary structure is an important protein attribute that is closely related to its function. Proteins with quaternary structure are called oligomeric proteins. Oligomeric proteins are involved in various biological processes, such as metabolism, signal transduction, and chromosome replication. Thus, it is highly desirable to develop some computational methods to automatically classify the quaternary structure of proteins from their sequences. RESULTS: To explore this problem, we adopted an approach based on the functional domain composition of proteins. Every protein was represented by a vector calculated from the domains in the PFAM database. The nearest neighbor algorithm (NNA) was used for classifying the quaternary structure of proteins from this information. The jackknife cross-validation test was performed on the non-redundant protein dataset in which the sequence identity was less than 25%. The overall success rate obtained is 75.17%. Additionally, to demonstrate the effectiveness of this method, we predicted the proteins in an independent dataset and achieved an overall success rate of 84.11% CONCLUSION: Compared with the amino acid composition method and Blast, the results indicate that the domain composition approach may be a more effective and promising high-throughput method in dealing with this complicated problem in bioinformatics

Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study

Background: Metabolomics helps to identify links between environmental exposures and intermediate biomarkers of disturbed pathways. We previously reported variations in phosphatidylcholines in male smokers compared with non-smokers in a cross-sectional pilot study with a small sample size, but knowledge of the reversibility of smoking effects on metabolite profiles is limited. Here, we extend our metabolomics study with a large prospective study including female smokers and quitters. Methods: Using targeted metabolomics approach, we quantified 140 metabolite concentrations for 1,241 fasting serum samples in the population-based Cooperative Health Research in the Region of Augsburg (KORA) human cohort at two time points: baseline survey conducted between 1999 and 2001 and follow-up after seven years. Metabolite profiles were compared among groups of current smokers, former smokers and never smokers, and were further assessed for their reversibility after smoking cessation. Changes in metabolite concentrations from baseline to the follow-up were investigated in a longitudinal analysis comparing current smokers, never smokers and smoking quitters, who were current smokers at baseline but former smokers by the time of follow-up. In addition, we constructed protein-metabolite networks with smoking-related genes and metabolites. Results: We identified 21 smoking-related metabolites in the baseline investigation (18 in men and six in women, with three overlaps) enriched in amino acid and lipid pathways, which were significantly different between current smokers and never smokers. Moreover, 19 out of the 21 metabolites were found to be reversible in former smokers. In the follow-up study, 13 reversible metabolites in men were measured, of which 10 were confirmed to be reversible in male quitters. Protein-metabolite networks are proposed to explain the consistent reversibility of smoking effects on metabolites. Conclusions: We showed that smoking-related changes in human serum metabolites are reversible after smoking cessation, consistent with the known cardiovascular risk reduction. The metabolites identified may serve as potential biomarkers to evaluate the status of smoking cessation and characterize smoking-related diseases

CHSMiner: a GUI tool to identify chromosomal homologous segments

<p>Abstract</p> <p>Background</p> <p>The identification of chromosomal homologous segments (CHS) within and between genomes is essential for comparative genomics. Various processes including insertion/deletion and inversion could cause the degeneration of CHSs.</p> <p>Results</p> <p>Here we present a Java software CHSMiner that detects CHSs based on shared gene content alone. It implements fast greedy search algorithm and rigorous statistical validation, and its friendly graphical interface allows interactive visualization of the results. We tested the software on both simulated and biological realistic data and compared its performance with similar existing software and data source.</p> <p>Conclusion</p> <p>CHSMiner is characterized by its integrated workflow, fast speed and convenient usage. It will be useful for both experimentalists and bioinformaticians interested in the structure and evolution of genomes.</p

Water quality and pollution source apportionment responses to rainfall in steppe lake estuaries: A case study of Hulun Lake in northern China

Hulun Lake, the largest inland steppe lake in China, is encountering severe water quality degradation. Estuaries play important roles in material and energetic exchange between rivers and lakes. The water quality at the estuaries of Hulun Lake directly reflects the impact of both human activities and natural factors on the lake’s overall water quality, especially during rainfall events. From July 28, 2021, to August 4, 2021, water samples from 62 sites were collected in the three estuaries of Hulun Lake before and after a moderate rainfall event. 13 water parameters, including dissolved oxygen (DO), Turbidity (Tur), Total Nitrogen (TN), Total Phosphorus (TP), Total Organic Nitrogen (TON), and Total Organic Phosphorus (TOP) were measured. The spatio-temporal distribution of water quality in the estuaries was assessed based on water quality index (WQI). Besides, an improved approach integrating stepwise linear regression (SLR) and principal component analysis (PCA) was utilized to construct a WQImin model for an effective assessment of water quality in these estuaries. Furthermore, the absolute principal component scores-multiple linear regression (APCS-MLR) model was employed to identify and quantify the environmental drivers underlying the water quality in the estuaries. The results of WQI indicated that the water quality of the sites in the estuaries of Hulun Lake was “medium” or “poor”, both before and after the rainfall, with a general deterioration in water quality in response to the rainfall. The simplified WQImin model consisted of 5 crucial parameters (i.e., TN, TP, ammonium (NH4+-N), Tur, and permanganate index (CODMn)), and it performed well without parameter weights. Spatial differences in some water parameters among the estuaries were detected, which were attributed to the natural factors and human activities upstream. The principal environmental factors affecting the water quality in the estuaries consisted of hydrodynamic processes, internal phosphorus release, external phosphorus input, external nitrogen input, nitrification in the estuaries, and external organic input and internal organic release. Therefore, we propose basin management strategies such as limiting grazing pressure, adopting enclosed pasture, wetland restoration, optimizing water renewal cycle in Hulun Lake, and transboundary water quality management to tackle water contamination in Hulun Lake.publishedVersio

Multimodal Physiological Signals Representation Learning via Multiscale Contrasting for Depression Recognition

Depression recognition based on physiological signals such as functional near-infrared spectroscopy (fNIRS) and electroencephalogram (EEG) has made considerable progress. However, most existing studies ignore the complementarity and semantic consistency of multimodal physiological signals under the same stimulation task in complex spatio-temporal patterns. In this paper, we introduce a multimodal physiological signals representation learning framework using Siamese architecture via multiscale contrasting for depression recognition (MRLMC). First, fNIRS and EEG are transformed into different but correlated data based on a time-domain data augmentation strategy. Then, we design a spatio-temporal contrasting module to learn the representation of fNIRS and EEG through weight-sharing multiscale spatio-temporal convolution. Furthermore, to enhance the learning of semantic representation associated with stimulation tasks, a semantic consistency contrast module is proposed, aiming to maximize the semantic similarity of fNIRS and EEG. Extensive experiments on publicly available and self-collected multimodal physiological signals datasets indicate that MRLMC outperforms the state-of-the-art models. Moreover, our proposed framework is capable of transferring to multimodal time series downstream tasks