摘要：
Eukaryotic DNA is packaged into chromatin in the nucleus, restricting the binding of transcription factors (TFs) to their target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiate the opening of local chromatin for gene expression. However, the principles of FOXA1 recruitment and how it subsequently unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically forms submicron-sized condensates through its N- and C-terminal intrinsically disordered regions (IDRs). Notably, both IDRs enable FOXA1 to dissolve the condensed chromatin. In addition, the DNA-binding capacity of FOXA1 contributes to its ability to both form condensates and dissolve condensed chromatin. Further genome-wide investigation showed that IDRs enable FOXA1 to bind and unpack the condensed chromatin to regulate the proliferation and migration of breast cancer cells. This work provides a principle of how pioneer TFs function to initiate competent chromatin states using their IDRs.
摘要：
The intervention of nectar robbers in plant pollination systems will cause some pollinators to modify their foraging behavior to act as secondary robbers, consequently adopting a mixed foraging strategy. The influence of nectar robbing on pollinator behavior may be affected by spatio-temporal difference of robbing intensity, and consequently, may have different effects on the pollination of host plants. However, whether and how the nectar robbing might influence pollinators under different robbing intensity still needs further investigation. In this study, Symphytum officinale was used to detect the effect of nectar robbers on pollinators under different robbing intensity as well as their effects on plant reproductive success. Six robbing levels and three bumblebees with mixed foraging behaviors were used to evaluate the effect of different robbing intensity on pollinator behavior, visitation rate, flower longevity and pollen deposition. Our results indicated that the robbing rate increased gradually with the proportion of robbed flowers, but which did not affect the frequency of legitimate visits. The increase of robbing rate promoted the corolla abscission, and then enhanced the self-pollen deposition, but which had no significant effect on cross-pollen deposition. These results indicate that the overall fitness of S. officinale was improved by combined self and cross-pollination modes when visited by both pollinators and nectar robbers simultaneously. Although nectar robbing is not uncommon, its consequences for pollination in the interaction web have not been well studied. Our results emphasize the significance of indirect impacts in mediating the adaptive outcomes of species interactions.
摘要：
Ubiquitination is a fascinating post-translational modification that has received continuous attention since its discovery. In this review, we first provide a concise overview of the E3 ubiquitin ligases, delving into classification, characteristics and mechanisms of ubiquitination. We then specifically examine the ubiquitination pathways mediated by the N/C-degrons, discussing their unique features and substrate recognition mechanisms. Finally, we offer insights into the current state of development pertaining to inhibitors that target the N/C-degron pathways, as well as the promising advances in the field of PROTAC (PROteolysis TArgeting Chimeras). Overall, this review offers a comprehensive understanding of the rapidly-evolving field of ubiquitin biology.
摘要：
Significance Statement This study has revealed an important role of OsTIL1 in maintaining the cell membrane integrity by regulating the 18:3‐containing glycerolipids biosynthesis and reducing reactive oxygen species damage under cold stress in rice seedlings. SUMMARY Lipocalins constitute a conserved protein family that binds to and transports a variety of lipids while fatty acid desaturases (FADs) are required for maintaining the cell membrane fluidity under cold stress. Nevertheless, it remains unclear whether plant lipocalins promote FADs for the cell membrane integrity under cold stress. Here, we identified the role of OsTIL1 lipocalin in FADs‐mediated glycerolipid remodeling under cold stress. Overexpression and CRISPR/Cas9 mediated gene edition experiments demonstrated that OsTIL1 positively regulated cold stress tolerance by protecting the cell membrane integrity from reactive oxygen species damage and enhancing the activities of peroxidase and ascorbate peroxidase, which was confirmed by combined cold stress with a membrane rigidifier dimethyl sulfoxide or a H2O2 scavenger dimethyl thiourea. OsTIL1 overexpression induced higher 18:3 content, and higher 18:3/18:2 and (18:2 + 18:3)/18:1 ratios than the wild type under cold stress whereas the gene edition mutant showed the opposite. Furthermore, the lipidomic analysis showed that OsTIL1 overexpression led to higher contents of 18:3‐mediated glycerolipids, including galactolipids (monoglactosyldiacylglycerol and digalactosyldiacylglycerol) and phospholipids (phosphatidyl glycerol, phosphatidyl choline, phosphatidyl ethanolamine, phosphatidyl serine and phosphatidyl inositol) under cold stress. RNA‐seq and enzyme linked immunosorbent assay analyses indicated that OsTIL1 overexpression enhanced the transcription and enzyme abundance of four ω‐3 FADs (OsFAD3‐1/3‐2, 7, and 8) under cold stress. These results reveal an important role of OsTIL1 in maintaining the cell membrane integrity from oxidative damage under cold stress, providing a good candidate gene for improving cold tolerance in rice.
期刊：
Journal of Environmental Management,2024年351:119729 ISSN：0301-4797
通讯作者：
Yang, S
作者机构：
[Peng, Kaida; Yang, Shao; Yang, Hongyan; Xu, Min; Cheng, Hu; Liu, Yi; Yang, S; Liu, Pan; Liu, Xiaofeng] Cent China Normal Univ, Sch Life Sci, Wuhan 430079, Peoples R China.
通讯机构：
[Yang, S ] C;Cent China Normal Univ, Sch Life Sci, Wuhan 430079, Peoples R China.
关键词：
Anthropogenic activities;Bloom-forming cyanobacterial genera;Climate change;Driving factors;Sedimentary ancient DNA;Thresholds
摘要：
Cyanobacterial blooms pose a global environmental concern, with various genera contributing to their formation. The harmfulness of cyanobacterial blooms varies depending on the specific genus, yet the factors triggering their formation remain incompletely understood. This study conducted qPCR of sediment DNA in Lake Erhai to reconstruct the historical succession of three common bloom-forming cyanobacterial genera (i.e., Microcystis, Dolichospermum, and Aphanizomenon). The driving factors and their corresponding thresholds were identified, and human activities related to driving factors were evaluated. The results revealed two successions in the past century. The first succession transitioned from Aphanizomenon (1902-1978) to Microcystis and Dolichospermum (1978-1999), driven by TN:TP and TP. The second succession shifted from Microcystis and Dolichospermum (1978-1999) to Microcystis (1999-2010), driven by TP, TN:TP, and temperature. The thresholds of TP and TN:TP for the Microcystis bloom were 0.023mg/L and 17, respectively. TN:TP was significantly influenced by domestic pollution and crop farming in both successions, while TP was significantly impacted by domestic pollution in the first succession and by pollution from crop and dairy farming in the second succession. These results shed light on the underlying mechanism responsible for the blooms of various cyanobacterial genera and could serve as a valuable reference for effectively preventing and controlling nutrient input in the watershed.
作者机构：
[Wang, Dong; Wang, D; Cao, Dandan] Cent China Normal Univ, Sch Life Sci, Wuhan 430079, Hubei, Peoples R China.;[Yang, Yongqing] Chongqing Normal Univ, Coll Life Sci, Chongqing 401331, Peoples R China.;[Wang, Dong; Wang, D] Shaanxi Univ Technol, Bioresources Key Lab Shaanxi Prov, Hanzhong 723001, Shaanxi, Peoples R China.
通讯机构：
[Wang, D ] C;Cent China Normal Univ, Sch Life Sci, Wuhan 430079, Hubei, Peoples R China.;Shaanxi Univ Technol, Bioresources Key Lab Shaanxi Prov, Hanzhong 723001, Shaanxi, Peoples R China.
摘要：
Invasive plants have been shown to alter ecosystem functions. However, there is limited information available on the effect of the invasive species litter input on native litter decomposition and home-field advantage (HFA, increased decomposition at a home environment compared to a guest environment). To investigate this, we conducted a field experiment using leaves of native Trapa natans and Typha orientalis with and without invasive species Alternanthera philoxeroides and then incubated them at T. natans and T. orientalis habitats in a eutrophic lake for 50 days. In control and treatment, the decomposition and N release rate of T. natans were significantly higher than that in T. orientalis species litter at two habitats, indicating no HFA occurrence. A. philoxeroides litter input promoted the decomposition and N decay rate of T. orientalis, not T. natans. The mean decomposition rate of T. orientalis in control and treatment were 0.0138 and 0.0342 day-1; for T. natans, it was 0.0703 and 0.0754 day-1, respectively. The mean N decay rate of T. orientalis in control and treatment were 0.0235 and 0.0468 day-1; for T. natans, it was 0.0511 and 0.0544 day-1, respectively. Invasive species presence increased microbial respiration rate of T. orientalis, but not for T. natans species litter in two habitats. These results suggested that A. philoxeroides litter input accelerated low quality litter decomposition though increased microbial activity. However, it did not influence the HFA performance, which may be closely related to the lake eutrophication.
摘要：
BACKGROUNDS AND AIMS: The hypothesis that plants evolve features that protect accessible pollen from consumption by flower visitors remains poorly understood. METHODS: To explore potential chemical defenses against pollen consumption, we examined the pollinator assemblage, foraging behaviour, visitation frequency and pollen transfer efficiency in Rhododendron molle, a highly toxic shrub containing Rhodojaponin III. Nutrient (protein and lipid) and toxic components in pollen and other tissues were measured. KEY RESULTS: Overall in the five populations, floral visits by butterflies and bumblebees were relatively more frequent than visits by honeybees. All foraged for nectar but not pollen. Butterflies did not differ from bumblebees in the amount of pollen removed per visit, but deposited more pollen per visit. Pollination experiments indicated that R. molle was self-compatible, but both fruit and seed production were pollen limited. Our analysis indicated that the pollen was not protein-poor and had a higher concentration of the toxic compound Rhodojaponin III than petals and leaves, which compound was undetectable in nectar. CONCLUSION: Pollen toxicity in Rhododendron flowers may discourage pollen robbers (bees) from taking the freely accessible pollen grains, while the toxin-free nectar rewards effective pollinators, promoting pollen transfer. This preliminary study supports the hypothesis that chemical defense in pollen would be likely to evolve in species without physical protection from pollinivores.
摘要：
During field work on mutualisms between oil bees and Cucurbitaceae in Yunnan, China, we discovered a new species of Thladiantha that we here describe and illustrate. It is overall similar to T. globicarpa A.M.Lu & Zhi Y.Zhang from Guangxi, but differs in the shape of its fruits. DNA sequences of the new species analyzed in the context of a densely sampled phylogeny of Thladiantha confirm its distinctness from all other species. The molecular data also revealed another collection of the new species made in Guangxi in 1937. Like all Thladiantha, the new species offers oil in glandular hairs on its petals and is pollinated by oil -collecting Ctenoplectra bees.
期刊：
International Journal of Biological Macromolecules,2024年267(Pt 1):131459 ISSN：0141-8130
通讯作者：
Liu, Leilei
作者机构：
[Liu, Leilei] Center of Applied Biotechnology, School of Life Sciences and Technology, Wuhan University of Bioengineering, Wuhan, Hubei, China. Electronic address: liulei@mails.ccnu.edu.cn;[Wang, Jintao; Xu, Peiwen; Wei, Wei; He, Wenfeng] Center of Applied Biotechnology, School of Life Sciences and Technology, Wuhan University of Bioengineering, Wuhan, Hubei, China;[Xu, Peiwen; He, Wenfeng] College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China;[Liu, Kaiyu] School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
通讯机构：
[Liu, Leilei] C;Center of Applied Biotechnology, School of Life Sciences and Technology, Wuhan University of Bioengineering, Wuhan, Hubei, China. Electronic address:
摘要：
Insect resistance evolution poses a significant threat to the advantages of biopesticides and transgenic crops utilizing insecticidal Cry-toxins from Bacillus thuringiensis (Bt). However, there is limited research on the relationship between transcriptional regulation of specific toxin receptors in lepidopteran insects and their resistance to Bt toxins. Here, we report the positive regulatory role of the SfGATAe transcription factor on the expression of the ABCC2 gene in Spodoptera frugiperda. DNA regions in the SfABCC2 promoter that are vital for regulation by SfGATAe, utilizing DAP-seq technology and promoter deletion mapping. Through yeast one-hybrid assays, DNA pull-down experiments, and site-directed mutagenesis, we confirmed that the transcription factor SfGATAe regulates the core control site PBS2 in the ABCC2 target gene. Tissue-specific expression analysis has revealed that SfGATAe is involved in the regulation and expression of midgut cells in the fall armyworm. Silencing SfGATAe in fall armyworm larvae resulted in reduced expression of SfABCC2 and decreased sensitivity to Cry1Ac toxin. Overall, this study elucidated the regulatory mechanism of the transcription factor SfGATAe on the expression of the toxin receptor gene SfABCC2 and this transcriptional control mechanism impacts the resistance of the fall armyworm to Bt toxins.
摘要：
Upland cotton, the mainly cultivated cotton species in the world, provides over 90% of natural raw materials (fibers) for the textile industry. The development of cotton fibers that are unicellular and highly elongated trichomes on seeds is a delicate and complex process. However, the regulatory mechanism of fiber development is still largely unclear in detail. In this study, we report that a homeodomain-leucine zipper (HD-ZIP) IV transcription factor, GhHOX4, plays an important role in fiber elongation. Overexpression of GhHOX4 in cotton resulted in longer fibers, while GhHOX4-silenced transgenic cotton displayed a "shorter fiber" phenotype compared with wild type. GhHOX4 directly activates two target genes, GhEXLB1D and GhXTH2D, for promoting fiber elongation. On the other hand, phosphatidic acid (PA), which is associated with cell signaling and metabolism, interacts with GhHOX4 to hinder fiber elongation. The basic amino acids KR-R-R in START domain of GhHOX4 protein are essential for its binding to PA that could alter the nuclear localization of GhHOX4 protein, thereby suppressing the transcriptional regulation of GhHOX4 to downstream genes in the transition from fiber elongation to secondary cell wall (SCW) thickening during fiber development. Thus, our data revealed that GhHOX4 positively regulates fiber elongation, while PA may function in the phase transition from fiber elongation to SCW formation by negatively modulating GhHOX4 in cotton.
期刊：
Science of The Total Environment,2024年922:171299 ISSN：0048-9697
通讯作者：
Mingqing Chen
作者机构：
[Xu, Ke; Jiang, Mengling; Wang, Shuxin; Han, Qi; Gao, Xiao; Du, Wanting; Wang, Yunyi] Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China;[Chen, Mingqing] Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China. Electronic address: chenmq@mail.ccnu.edu.cn
通讯机构：
[Mingqing Chen] H;Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, Hubei, China
摘要：
After aging in the environment, some nanoplastics will carry different charges and functional groups, thereby altering their toxicological effects. To evaluate the potential impact of aging of nanoplastics on the mammalian reproductive system, we exposed C57BL/6 male mice to a dose of 5mg/kg/d polystyrene nanoparticles (PS-NPs) with different functional groups (unmodified, carboxyl functionalized and amino functionalized) for 45days for this study. The results suggest that PS-NPs with different functional groups triggered oxidative stress, a decreased in the testis index, disruption of the outer wall of the seminiferous tubules, reduction in the number of spermatogonia cells and sperm counts, and an increased in sperm malformations. We performed GO and KEGG enrichment analysis on the differentially expressed proteins, and found they were mainly enriched in protein transport, RNA splicing and mTOR signaling. We confirmed that the PI3K-AKT-mTOR pathway is over activated, which may lead to reduction of spermatogonia stem cells by over differentiation. Strikingly, PS-NPs with functional group modifications are more toxic than those of unmodified polystyrene, and that PS-NPs with positively charged amino modifications are the most toxic. This study provides a new understanding for correctly evaluating the toxicological effects of plastic aging, and of the mechanism responsible for the reproductive toxicity caused by nanoplastics.
期刊：
Trends in Pharmacological Sciences,2024年45(3):193-196 ISSN：0165-6147
通讯作者：
Jinrong Min
作者机构：
[Li, Yanxi; Huang, Yunyuan] Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China;[Min, Jinrong] Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China. Electronic address: minjinrong@ccnu.edu.cn
通讯机构：
[Jinrong Min] H;Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
摘要：
The PWWP domain binds to both histone and DNA of a nucleosome in a bivalent way. PWWP domain-containing proteins are involved in different biological processes, and their aberrant expression is implicated in various human diseases. Here, we discuss the recent developments and challenges in targeting the PWWP domain for therapeutic intervention.
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS,2024年1867(2):195028 ISSN：1874-9399
通讯作者：
Tong, Jingjing
作者机构：
[Zhong, Shu] Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China;[Tong, Jingjing] Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China. Electronic address: tongjj@mail.ccnu.edu.cn
通讯机构：
[Tong, Jingjing] H;Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China. Electronic address:
摘要：
Immunotherapy is a promising and long-lasting tumor treatment method, but it is challenged by the complex metabolism of tumors. To optimize immunotherapy, it is essential to further investigate the key proteins that regulate tumor metabolism and immune response. STAT3 plays a crucial role in regulating tumor dynamic metabolism and affecting immune cell function by responding to various cytokines and growth factors, which can be used as a potential target for immunotherapy. This review focuses on the crosstalk between STAT3 and tumor metabolism (including glucose, lipid, and amino acid metabolism) and its impact on the differentiation and function of immune cells such as T cells, tumor-associated macrophages (TAMs), and myeloid-derived suppressor cells (MDSCs), and reveals potential treatment strategies.
期刊：
Journal of Biological Education,2024年 ISSN：0021-9266
通讯作者：
Kong, Y
作者机构：
[Kong, Yi; Kong, Y] Cent China Normal Univ, Sch Life Sci, Wuhan, Hubei, Peoples R China.;[Olimpo, Jeffrey T.] Univ Texas El Paso, Dept Biol Sci, El Paso, TX USA.
通讯机构：
[Kong, Y ] C;Cent China Normal Univ, Sch Life Sci, Wuhan, Hubei, Peoples R China.
摘要：
Tree-thinking ability is essential in the learning of biological evolution. Spatial ability as a potential factor which might impact students' tree-thinking ability remains unknown. To explore the influence of spatial ability and spatial-related interventions on students' tree-thinking ability, 312 undergraduate students participated in this study. Students' spatial ability was evaluated using the Mental Rotation Test (MRT). A pre-test-post-test design was adopted to assess students' tree-thinking ability by using the Model of the Use of Evolutionary Trees (MUET) survey. Multiple linear regression analyses were conducted to explore the factors that influenced students' tree-thinking ability. Pearson product-moment correlation coefficients were calculated when positive or negative predictors of student' tree-thinking ability were identified. Results shown that students' MRT scores and previous tree-learning experience were the sole factors that positively predicted students' pre-MUET survey scores, explaining 2.5% and 4.1% of the observed variance, respectively. Pre-MUET survey scores and the type of tree-thinking-related instructional intervention were found to be the only unique predictors of students' post-MUET survey scores, explaining 22.2% and 6.5% of the observed variance, respectively. Results suggest that the tree-thinking-related instructional intervention has the potential to modulate the relationship between individuals' spatial ability and tree-thinking ability.
期刊：
BRIEFINGS IN BIOINFORMATICS,2024年25(3) ISSN：1467-5463
通讯作者：
Xingpeng Jiang<&wdkj&>Cuihong Wan
作者机构：
[Wan, Cuihong; Peng, Zhao] School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, People's Republic of China;[Li, Jiaqiang; Jiang, Xingpeng] School of Computer Science, and Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University, Wuhan 430079, Hubei, People's Republic of China
通讯机构：
[Xingpeng Jiang; Cuihong Wan] S;School of Computer Science , and Hubei Provincial Key Laboratory of Artificial Intelligence and Smart Learning, Central China Normal University , Wuhan 430079, Hubei , People’s Republic of China<&wdkj&>School of Life Sciences , and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University , Wuhan 430079, Hubei , People’s Republic of China
摘要：
Small open reading frames (smORFs) have been acknowledged to play various roles on essential biological pathways and affect human beings from diabetes to tumorigenesis. Predicting smORFs in silico is quite a prerequisite for processing the omics data. Here, we proposed the smORF-coding-potential-predicting framework, sOCP, which provides functions to construct a model for predicting novel smORFs in some species. The sOCP model constructed in human was based on in-frame features and the nucleotide bias around the start codon, and the small feature subset was proved to be competent enough and avoid overfitting problems for complicated models. It showed more advanced prediction metrics than previous methods and could correlate closely with experimental evidence in a heterogeneous dataset. The model was applied to Rattus norvegicus and exhibited satisfactory performance. We then scanned smORFs with ATG and non-ATG start codons from the human genome and generated a database containing about a million novel smORFs with coding potential. Around 72000 smORFs are located on the lncRNA regions of the genome. The smORF-encoded peptides may be involved in biological pathways rare for canonical proteins, including glucocorticoid catabolic process and the prokaryotic defense system. Our work provides a model and database for human smORF investigation and a convenient tool for further smORF prediction in other species.
作者：
Meng Zhang;Li-Bing Jia;Susanne S Renner;Zhi-Xi Tian;Xiao-An Wang;...
期刊：
国家科学评论(英文),2024年 ISSN：2095-5138
通讯作者：
Susanne S Renner<&wdkj&>Huan-Li Xu<&wdkj&>Shuang-Quan Huang
作者机构：
[Meng Zhang; Li-Bing Jia; Zhi-Xi Tian; Xiao-An Wang; Shuang-Quan Huang] Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University , Wuhan 430079 , China;[Jiang-Yun Gao] State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University , Kunming 650091 , China;[Yi- Bo Luo] State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 , China;[Antonio J C Aguiar] Department of Zoology, University of Brasília , Distrito Federal 70910 900 , Brazil;[Susanne S Renner] Department of Biology, Washington University , St. Louis , MO 63130 , USA
通讯机构：
[Susanne S Renner; Huan-Li Xu] D;[Shuang-Quan Huang] I;Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University , Wuhan 430079 , China<&wdkj&>Department of Biology, Washington University , St. Louis , MO 63130 , USA<&wdkj&>Department of Entomology, College of Plant Protection, China Agricultural University , Beijing 100193 , China
摘要：
Meng Zhang, Li-Bing Jia, Susanne S Renner, Zhi-Xi Tian, Xiao-An Wang, Jiang-Yun Gao, Yi- Bo Luo, Antonio J C Aguiar, Huan-Li Xu, Shuang-Quan Huang; Multipa
作者机构：
School of Life Sciences, Central China Normal University, Wuhan 430079, China;[Wensheng Liang; Chang Liu] School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi’an 710021, China;Author to whom correspondence should be addressed.;[Xiang Gao] School of Life Sciences, Central China Normal University, Wuhan 430079, China<&wdkj&>School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi’an 710021, China<&wdkj&>Author to whom correspondence should be addressed.
通讯机构：
[Xiang Gao] S;School of Life Sciences, Central China Normal University, Wuhan 430079, China<&wdkj&>School of Food and Biological Engineering, Shaanxi University of Science & Technology, Xi’an 710021, China<&wdkj&>Author to whom correspondence should be addressed.
摘要：
Heterocyst-forming cyanobacteria that colonize the drylands contribute to carbon and nitrogen supplies in nutrient-poor soils. As one of the representative cyanobacteria, Nostoc flagelliforme adapts well to the arid environment in the form of filamentous colonies (or filaments). To date, the adaptive changes, either genetic or micromorphological, that occur within single colonies of dryland cyanobacteria remain largely unclear. In this study, unusual long chains or trichomes of vegetative cells (not containing heterocysts) were observed within N. flagelliforme filaments. And the overall heterocyst frequency in the trichomes was counted to be 1.3–2.7%, different from the usually observed 5–10% heterocyst frequency in model Nostoc strains when grown in nitrogen-deprived medium. Thus, these phenomena seem contradictory to our usual recognition of Nostoc strains. Related transcriptional and heterocyst frequency analyses suggested no genetically significant alteration in heterocyst formation and nitrogen fixation in this strain. Also, the amounts of nitrogen sources in the extracellular polysaccharide (EPS) matrix released by N. flagelliforme cells that may cause the low heterocyst frequency were assessed to be equivalent to 0.28–1.10 mM NaNO3. When combining these findings with the habitat characters, it can be envisaged that the released nitrogen sources from cells are confined, accumulated, and re-utilized in the EPS matrix, thereby leading to the formation of reduced heterocyst frequency and long-chained vegetative cells. This study will contribute to our understanding of the distinctive adaptation properties of colonial cyanobacteria in dryland areas.
摘要：
This study developed a prediction method to determine the distribution of phthalate esters (PAEs) in indoor dust. A gradient boosting decision tree model (GBRT) was trained by using 267 samples in Shanghai, including PAEs concentrations in indoor dust and data obtained from continuous monitoring, as well as the survey of indoor environment. Environmental exposure, residents' lifestyle, and building characteristics data were collected from 8 cities in China. Based on this, the well -trained GBRT model accurately predicted PAEs concentrations, with goodness of fit (R-2) > 0.94, mean absolute error (MAE) approaching 0, and mean squared error (MSE) approaching 0. This study identified key relationships between input parameters and PAEs concentrations. The average increment of PAEs concentration was greater than 50 % when using more than 2 electronic devices in bedroom. Diisobutyl phthalate (DiBP) concentration increased by approximately 200 % when cleaning frequency was less than once every fortnight. Bis (2-ethylhexyl) phthalate (DEHP) concentration increased by over 43 % when dampness -related exposure indicators exceeding 3, and by up to 74 % with extensive usage of polyvinyl chloride (PVC) floorings. Furthermore, the study found higher PAEs concentrations in southern China compared to northern cities.
期刊：
BRIEFINGS IN BIOINFORMATICS,2024年25(2) ISSN：1467-5463
通讯作者：
Peng, YH
作者机构：
[Xu, Wang; Peng, Yunhui; Zhang, Houfang; Peng, YH; Zhao, Yunjie] Cent China Normal Univ, Inst Biophys, Wuhan, Peoples R China.;[Xu, Wang; Peng, Yunhui; Zhang, Houfang; Peng, YH; Zhao, Yunjie] Cent China Normal Univ, Dept Phys, Wuhan, Peoples R China.;[Guo, Wenhan] Univ Texas El Paso, Computat Sci Program, El Paso, TX USA.;[Jiang, Lijun] Cent China Normal Univ, Sch Life Sci, Wuhan, Peoples R China.
通讯机构：
[Peng, YH ] C;Cent China Normal Univ, Inst Biophys, Wuhan, Peoples R China.;Cent China Normal Univ, Dept Phys, Wuhan, Peoples R China.
关键词：
histone/nucleosome interaction;interaction network;histone cancer mutation;nucleosome binding mode;epigenetic regulation
摘要：
Nucleosomes represent hubs in chromatin organization and gene regulation and interact with a plethora of chromatin factors through different modes. In addition, alterations in histone proteins such as cancer mutations and post-translational modifications have profound effects on histone/nucleosome interactions. To elucidate the principles of histone interactions and the effects of those alterations, we developed histone interactomes for comprehensive mapping of histone-histone interactions (HHIs), histone-DNA interactions (HDIs), histone-partner interactions (HPIs) and DNA-partner interactions (DPIs) of 37 organisms, which contains a total of 3808 HPIs from 2544 binding proteins and 339 HHIs, 100 HDIs and 142 DPIs across 110 histone variants. With the developed networks, we explored histone interactions at different levels of granularities (protein-, domain- and residue-level) and performed systematic analysis on histone interactions at a large scale. Our analyses have characterized the preferred binding hotspots on both nucleosomal/linker DNA and histone octamer and unraveled diverse binding modes between nucleosome and different classes of binding partners. Last, to understand the impact of histone cancer-associated mutations on histone/nucleosome interactions, we complied one comprehensive cancer mutation dataset including 7940 cancer-associated histone mutations and further mapped those mutations onto 419,125 histone interactions at the residue level. Our quantitative analyses point to histone cancer-associated mutations' strongly disruptive effects on HHIs, HDIs and HPIs. We have further predicted 57 recurrent histone cancer mutations that have large effects on histone/nucleosome interactions and may have driver status in oncogenesis.
