Cohesin Loss Eliminates All Loop Domains.

The human genome folds to create thousands of intervals, called "contact domains," that exhibit enhanced contact frequency within themselves. "Loop domains" form because of tethering between two loci-almost always bound by CTCF and cohesin-lying on the same chromosome. "Compartment domains" form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.

Origin, evolution, and diversification of inositol 1,4,5-trisphosphate 3-kinases in plants and animals.

BACKGROUND: In Eukaryotes, inositol polyphosphates (InsPs) represent a large family of secondary messengers and play crucial roes in various cellular processes. InsPs are synthesized through a series of pohophorylation reactions catalyzed by various InsP kinases in a sequential manner. Inositol 1,4,5-trisphosphate 3-kinase (IP3 3-kinase/IP3K), one member of InsP kinase, plays important regulation roles in InsPs metabolism by specifically phosphorylating inositol 1,4,5-trisphosphate (IP3) to inositol 1,3,4,5-tetrakisphosphate (IP4) in animal cells. IP3Ks were widespread in fungi, plants and animals. However, its evolutionary history and patterns have not been examined systematically. RESULTS: A total of 104 and 31 IP3K orthologues were identified across 57 plant genomes and 13 animal genomes, respectively. Phylogenetic analyses indicate that IP3K originated in the common ancestor before the divergence of fungi, plants and animals. In most plants and animals, IP3K maintained low-copy numbers suggesting functional conservation during plant and animal evolution. In Brassicaceae and vertebrate, IP3K underwent one and two duplication events, respectively, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for IP3K duplications, and the IP3K duplicates have experienced functional divergence. Finally, a hypothetical evolutionary model for the IP3K proteins is proposed based on phylogenetic theory. CONCLUSION: Our study reveals the evolutionary history of IP3K proteins and guides the future functions of animal, plant, and fungal IP3K proteins.

Insights into the environmental factors shaping lateral root development.

Roots are important organs of plants. Plants rely on roots for water, nutrients, and organic salts. In the whole root system, lateral roots (LRs) account for a large proportion and are critical to the development of the plant. Many environmental factors affect LR development. Therefore, a systematic understanding of these factors can provide a theoretical basis for creating optimal growth conditions for plants. In this paper, the factors affecting LR development are systematically and comprehensively summarized, and the molecular mechanism and regulatory network of LR development are described. Changes in the external environment not only lead to hormone homeostasis in plants but also affect the composition and activity of rhizosphere microbial communities, which in turn affect plants' nitrogen and phosphorus uptake and growth dynamics. LR development is influenced by hormone levels and external environment. In particular, auxin and abscisic acid coordinate with each other to maintain normal LR development. Of course, changes in the external environment are also important for root development, and they affect the intrinsic hormone levels of plants by affecting the accumulation and transport of hormones. For example, nitrogen, phosphorus, reactive oxygen species, nitric oxide, water, drought, light, and rhizosphere microorganisms affect LR development and plant tolerance in a variety of ways, including regulating hormone levels. This review summarizes the factors affecting LR development and the regulatory network and points out the direction for future research.

Effect of boron supply on the uptake and translocation of cadmium in Capsicum annuum.

Large areas of soil in southern China are contaminated with cadmium (Cd) and are deficient in boron (B). Previously, we suggested that B supplementation could reduce Cd accumulation in hot peppers (Capsicum annuum L.); however, the physiological mechanisms underlying this reduction remain unclear. In this study, the uptake and translocation of Cd in hot pepper plants were investigated using hydroponic experiments with different B and Cd treatments. A pot experiment was performed to verify whether B decreased the Cd concentration in hot peppers by minimizing the Cd translocation rate. The results of the dose- and time-dependent experiments showed that B supplementation reduced root Cd uptake and root-to-shoot Cd translocation. Additionally, B supplementation increased the root length, diameter, volume, surface area, and number of root forks and tips, as well as improving the relative absorbance of carboxyl groups under Cd exposure, leading to enhanced Cd fixation in the cell walls of the roots. As a result, the fruit Cd concentration decreased because B inhibited Cd translocation from the roots. Overall, the results demonstrate that B supplementation can reduce Cd accumulation in hot peppers by promoting normal root growth and development and by limiting the uptake and translocation of Cd.

Effect of potassium intake on cadmium transporters and root cell wall biosynthesis in sweet potato.

Large areas of farmland soil in southern China are deficient in potassium (K) and are contaminated with cadmium (Cd). Previously, we suggested that the K supplementation could reduce Cd accumulation in sweet potatoes (Ipomoea batatas (L.) Lam). In the present study, we investigated the underlying physiological and molecular mechanisms. A hydroponic experiment with different K and Cd treatments was performed to compare the transcriptome profile and the cell wall structure in the roots of sweet potato using RNA sequencing, Fourier transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM). The results showed that K supply inhibits the expressions of IRT1 and YSL3, which are responsible for root Cd uptake under Cd exposure. Furthermore, the expressions of COPT5 and Nramp3 were downregulated by K, which increased Cd retention in the root vacuoles. The upregulation of POD, CAD, INT1 and SUS by K contributed to lignin and cellulose biosynthesis and thickening of root xylem cell wall, which further reduced Cd translocation to the shoot. In addition, K affected the expressions of LHT, ACS, TPS and TPP associated with the production of ethylene and trehalose, which involved in plant resistance to Cd toxicity. In general, K application could decrease the uptake and translocation of Cd in sweet potatoes by regulating the expression of genes associated with Cd transporters and root cell wall components.

Amphibian-Derived Natural Anticancer Peptides and Proteins: Mechanism of Action, Application Strategies, and Prospects.

Cancer is one of the major diseases that seriously threaten human life. Traditional anticancer therapies have achieved remarkable efficacy but have also some unavoidable side effects. Therefore, more and more research focuses on highly effective and less-toxic anticancer substances of natural origin. Amphibian skin is rich in active substances such as biogenic amines, alkaloids, alcohols, esters, peptides, and proteins, which play a role in various aspects such as anti-inflammatory, immunomodulatory, and anticancer functions, and are one of the critical sources of anticancer substances. Currently, a range of natural anticancer substances are known from various amphibians. This paper aims to review the physicochemical properties, anticancer mechanisms, and potential applications of these peptides and proteins to advance the identification and therapeutic use of natural anticancer agents.

Promotion mechanism of self-transmissible degradative plasmid transfer in maize rhizosphere and its application in naphthalene degradation in soil.

Rhizospheres can promote self-transmissible plasmid transfer, however, the corresponding mechanism has not received much attention. Plant-microbe remediation is an effective way to promote pollutant biodegradation; however, some pollutants, such as naphthalene, are harmful to plants and result in inefficient plant-microbe remediation. In this study, transfer of a TOL-like plasmid, a self-transmissible plasmid loaded with genetic determinants for pollutant degradation, among different bacteria was examined in bulk and rhizosphere soils as well as addition of maize root exudate and its artificial root exudate (ARE). The results showed that the numbers of transconjugants and recipients as well as bacterial metabolic activities, such as xylE mRNA expression levels and catechol 2,3-dioxygenase (C23O) activities of bacteria, remained high in rhizosphere soils, when compared with bulk soils. The number of transconjugants and bacterial metabolic activities increased with the increasing exudate and ARE concentrations, whereas the populations of donor and recipient bacteria were substantially unaltered at all concentrations. All the experiments consistently showed that a certain number of bacteria is required for self-transmissible plasmid transfer, and that the increased plasmid transfer might predominantly be owing to bacterial metabolic activity stimulated by root exudates and ARE. Furthermore, ARE addition increased naphthalene degradation by transconjugants in both culture medium and soil. Thus, the combined action of a wide variety of components in ARE might contribute to the increased plasmid transfer and naphthalene degradation. These findings suggest that ARE could be an effectively alternative for plant-microbe remediation of pollutants in environments where plants cannot survive.

MicroRNA-27a-3p directly targets FosB to regulate cell proliferation, apoptosis, and inflammation responses in immunoglobulin a nephropathy.

Immunoglobulin A nephropathy (IgAN) constitutes the most common primary glomerulonephritis worldwide; however, the exact pathogenesis of IgAN is unknown. Previous genome-wide analysis of microRNA (miRNA) expression in the kidney has confirmed that miRNAs are closely related to the pathological changes of IgAN. Accordingly, in this study we found that miR-27a-3p is upregulated in IgAN kidney tissues in addition to human podocytes and tubule epithelial HK2 but not mesangial cells. Methylthiazolyldiphenyl-tetrazolium bromide (MTT), flow cytometry, real-time polymerase chain reaction, western blot, and enzyme-linked immunosorbent assays were used to verify the regulatory effects of miR-27a-3p and its inhibition on cell proliferation, apoptosis, and release of inflammatory factors in podocytes and HK2 cells. The target genes of miR-27a-3p were predicted using bioinformatics software; the identity of FosB as a target gene of miR-27a-3p was confirmed by luciferase report assay and western blot. Overall, our findings demonstrated that miR-27a-3p regulates cell apoptosis, cell proliferation, and the release of inflammatory cytokines of human podocytes and HK2 cells by directly targeting FosB. Our results therefore suggested that miR-27a-3p might be associated with the pathophysiology of IgAN and may represent a potential target for further studies related to IgAN mechanism or therapeutics.

A self-centering and stiffness-controlled MEMS accelerometer.

This paper presents a high-performance MEMS accelerometer with a DC/AC electrostatic stiffness tuning capability based on double-sided parallel plates (DSPPs). DC and AC electrostatic tuning enable the adjustment of the effective stiffness and the calibration of the geometric offset of the proof mass, respectively. A dynamical model of the proposed accelerometer was developed considering both DC/AC electrostatic tuning and the temperature effect. Based on the dynamical model, a self-centering closed loop is proposed for pulling the reference position of the force-to-rebalance (FTR) to the geometric center of DSPP. The self-centering accelerometer operates at the optimal reference position by eliminating the temperature drift of the readout circuit and nulling the net electrostatic tuning forces. The stiffness closed-loop is also incorporated to prevent the pull-in instability of the tuned low-stiffness accelerometer under a dramatic temperature variation. Real-time adjustments of the reference position and the DC tuning voltage are utilized to compensate for the residue temperature drift of the proposed accelerometer. As a result, a novel controlling approach composed of a self-centering closed loop, stiffness-closed loop, and temperature drift compensation is achieved for the accelerometer, realizing a temperature drift coefficient (TDC) of approximately 7 µg/°C and an Allan bias instability of less than 1 µg.

Lateral root primordium: Formation, influencing factors and regulation.

Roots are the primary determinants of water and nutrient uptake by plants. The structure of roots is largely determined by the repeated formation of new lateral roots (LR). A new lateral root primordium (LRP) is formed between the beginning and appearance of LR, which defines the organization and function of LR. Therefore, proper LRP morphogenesis is a crucial process for lateral root formation. The development of LRP is regulated by multiple factors, including hormone and environmental signals. Roots integrate signals and regulate growth and development. At the molecular level, many genes regulate the growth and development of root organs to ensure stable development plans, while also being influenced by various environmental factors. To gain a better understanding of the LRP formation and its influencing factors, this study summarizes previous research. The cell cycle involved in LRP formation, as well as the roles of ROS, auxin, other auxin-related plant hormones, and genetic regulation, are discussed in detail. Additionally, the effects of gravity, mechanical stress, and cell death on LRP formation are explored. Throughout the text unanswered or poorly understood questions are identified to guide future research in this area.

Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae.

Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.

Exposure to Polybrominated Diphenyl Ethers and Risk of All-Cause and Cause-Specific Mortality.

Importance: Polybrominated diphenyl ethers (PBDEs) are an important group of persistent organic pollutants with endocrine-disrupting properties. However, prospective cohort studies regarding the association of PBDE exposure with long-term health outcomes, particularly mortality, are lacking. Objective: To examine the association of environmental exposure to PBDEs with risk of all-cause and cause-specific mortality. Design, Setting, and Participants: This nationally representative cohort study used data from the National Health and Nutrition Examination Survey 2003 to 2004 and linked mortality information through December 31, 2019. Adults aged 20 years or older with available data on PBDE measurements and mortality were included. Statistical analysis was performed from February 2022 to April 2023. Exposures: PBDE analytes in serum samples were measured using solid phase extraction and isotope dilution gas chromatography high-resolution mass spectrometry. Main Outcomes and Measures: All-cause mortality, cancer mortality, and cardiovascular mortality. Results: This study included 1100 participants (mean [SE] age, 42.9 [0.6] years; proportion [SE] female, 51.8% [1.6%]; proportion [SE] Hispanic, 12.9% [2.7%]; proportion [SE] non-Hispanic Black, 10.5% [1.6%]; proportion [SE] non-Hispanic White, 70.8% [3.7%]; proportion [SE] other race and ethnicity, 5.8% [1.1%]). During 16 162 person-years of follow-up (median [IQR] follow-up, 15.8 [15.2-16.3] years; maximum follow-up, 17 years), 199 deaths occurred. Participants with higher serum PBDE levels were at higher risk for death. After adjustment for age, sex, and race and ethnicity, lifestyle and socioeconomic factors, and body mass index, participants with the highest tertile of serum PBDE levels had an approximately 300% increased risk of cancer mortality (HR, 4.09 [95% CI, 1.71-9.79]) compared with those with the lowest tertile of serum PBDE levels. No significant association of PBDE exposure with all-cause mortality (HR, 1.43 [95% CI, 0.98-2.07]) or cardiovascular mortality (HR, 0.92 [95% CI, 0.41-2.08]) was observed. Conclusions and Relevance: In this nationally representative cohort study, PBDE exposure was significantly associated with an increased risk of cancer mortality. Further studies are needed to replicate the findings and determine the underlying mechanisms.

Decipher the molecular evolution and expression patterns of Cupin family genes in oilseed rape.

Cupin proteins are involved in plant growth and development as well as in response to various stresses. Here, a total of 173 Cupin genes were identified in Brassica napus, and their molecular evolution and expression patterns were analyzed. These genes were classified into ten groups. Motif and exon-intron structure indicated a high degree of conservation within each group during evolution. BnaCupins were distributed on 19 chromosomes and their expansion is mainly contributed by whole-genome duplication (WGD) and segmental duplication events. BnaCupins have undergone severe purifying selection during a long evolutionary process. Meanwhile, some positive selection sites were identified. Expression patterns and cis-element analysis indicated that BnaCupins play significant roles in plant growth and stress responses. In addition, the expression levels of some BnCupins were significantly altered when treated with different conditions (cold, salt, drought, IAA, ABA, and 6-BA). Some BnaCupin interacting proteins, such as glycosyl hydrolase5 (GHs5), carbohydrate kinase (CHKs), ATP-dependent 6-phosphofructokinase (ATP-PFK), S-adenosylmethionine synthase (S-MAT), and aldolase class II (ALD II), were identified by the protein-protein interaction network. It will contribute to enriching our knowledge of the Cupin gene family in B. napus and provide a basis for further studies of their functions.

The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions.

Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.

Identification and molecular evolution of the La and LARP genes in 16 plant species: A focus on the Gossypium hirsutum.

La and La-related proteins (LARPs) are RNA-binding proteins regulating gene expression. Here, identification and molecular evolution of La and LARP gene family were performed in 16 plant species. Firstly, 188 La and LARP genes were identified. Based on phylogenetic tree and gene structure, they can be divided into three categories: La, LARP1 and LARP6. LARP1 can be further divided into LARP1-L and LARP1-S sub-categories. Compared with the LARP1-S, one additional DM15 domain was found in the C-terminal of LARP1-L. La and LARP genes are mainly distributed at both ends of chromosomes with a relatively consistent distribution position in A and D genomes of Gossypium hirsutum. Las and LARPs of G. hirsutum probably came from cruciferae, and gene recombination and chromosome structure variation occurred in G. hirsutum during evolution. The expression patterns and the distribution of cis-acting elements were also analyzed. The results showed that Las and LARPs respond to some abiotic stresses and hormone stimulation. The protein interaction network indicated that La and LARP proteins may be involved in meristem differentiation, hormone signal transduction, and post-translational modification. This study will provide a basis for the further functional and evolutional study of this gene family.

Divergent structures and functions of the Cupin proteins in plants.

Cupin superfamily proteins have extensive functions. Their members are not only involved in the development of plants but also responded to various stresses. Whereas, the research on the Cupin members has not attracted enough attention. In this article, we summarized the research progress on these family genes in recent years and explored their evolution, structural characteristics, and biological functions. The significance of members of the Cupin family in the development of plant cell walls, roots, leaves, flowers, fruits, and seeds and their role in stress response are highlighted. Simultaneously, the prospective application of Cupin protein in crop enhancement was introduced. Some members can enhance plant growth, development, and resistance to adversity, thereby increasing crop yield. It will be as a foundation for future effective crop research and breeding.

Nickel-Catalyzed Radical Ring-Opening Phosphorylation of Cycloalkyl Hydroperoxides Leading to Distal Acylphosphine Oxides.

A facile and efficient nickel-catalyzed C-C bond cleavage/phosphorylation of various cycloalkyl hydroperoxides was developed. This radical ring-opening strategy provided practical access to structurally diverse distal ketophosphine oxides in one pot through concurrent C═O/C-P bond formation with high atom economy under mild room temperature and base-free conditions.

Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species.

The plant-specific SHORT INTERNODES/STYLISH (SHI/STY) proteins belong to a family of transcription factors that are involved in the formation and development of early lateral roots. However, the molecular evolution of this family is rarely reported. Here, a total of 195 SHI/STY genes were identified in 21 terrestrial plants, and the Brassica species is the focus of our research. Their physicochemical properties, chromosome location and duplication, motif distribution, exon-intron structures, genetic evolution, and expression patterns were systematically analyzed. These genes are divided into four clades (Clade 1/2/3/4) based on phylogenetic analysis. Motif distribution and gene structure are similar in each clade. SHI/STY proteins are localized in the nucleus by the prediction of subcellular localization. Collinearity analysis indicates that the SHI/STYs are relatively conserved in evolution. Whole-genome duplication is the main factor for their expansion. SHI/STYs have undergone intense purifying selection, but several positive selection sites are also identified. Most promoters of SHI/STY genes contain different types of cis-elements, such as light, stress, and hormone-responsive elements, suggesting that they may be involved in many biological processes. Protein-protein interaction predicted some important SHI/STY interacting proteins, such as LPAT4, MBOATs, PPR, and UBQ3. In addition, the RNA-seq and qRT-PCR analysis were studied in detail in rape. As a result, SHI/STYs are highly expressed in root and bud, and can be affected by Sclerotinia sclerotiorum, drought, cold, and heat stresses. Moreover, quantitative real-time PCR (qRT-PCR) analyses indicates that expression levels of BnSHI/STYs are significantly altered in different treatments (cold, salt, drought, IAA, auxin; ABA, abscisic acid; 6-BA, cytokinin). It provides a new understanding of the evolution and expansion of the SHI/STY family in land plants and lays a foundation for further research on their functions.

Applications and influencing factors of the biochar-persulfate based advanced oxidation processes for the remediation of groundwater and soil contaminated with organic compounds.

Biochar (BC) is a low-cost material rich in carbon, which is being used increasingly as a catalyst in persulfate-based advanced oxidation processes (PS-AOPs) for the remediation of groundwater and soil contaminated with organic compounds. In this work, a general summary of preparation methods and applications of various BC (i.e., pristine BC, magnetic BC, and chemically modified BC) in PS-AOPs is presented. Different influence factors (e.g., pH, anions, natural organic matter) for the degradation of organic compounds are discussed. Meanwhile, the influence of external energy (e.g., solar irradiation, UV-Vis, ultrasonic) is also mentioned. Furthermore, the advantage of different BC in PS-AOPs are compared. Finally, potential problems, challenges, and prospects in the application of biochar-persulfate based advanced oxidation processes (BCPS-AOPs) are discussed in the conclusion and perspective.

Liquid Biopsy of Methylation Biomarkers in Cell-Free DNA.

Liquid biopsies, in particular, analysis of cell-free DNA (cfDNA), have emerged as a promising noninvasive diagnostic approach in oncology. Abnormal distribution of DNA methylation is one of the hallmarks of many cancers and methylation changes occur early during carcinogenesis. Systemic analysis of cfDNA methylation profiles is being developed for cancer early detection, monitoring for minimal residual disease (MRD), predicting treatment response and prognosis, and tracing the tissue origin. This review highlights the advantages and disadvantages of ctDNA profiling for noninvasive diagnosis of early-stage cancers and explores recent advances in the clinical application of ctDNA methylation assays. We also summarize the technologies for ctDNA methylation analysis and provide a brief overview of the bioinformatic approaches for analyzing DNA methylation sequencing data.