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Advances in DNA methylation and its role in cytoplasmic male sterility in higher plants

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Journal of Integrative Agriculture 2024年第1期23卷 1-19页

作者： Atiqur Rahman Hasan Sofiur Rahman Shakil Uddin Naima Sultana Shirin Akhter Ujjal Kumar Nath Shamsun Nahar Begum Mazadul Islam Afroz Naznin Nurul Amin Sharif Ahmed Akbar Hossain Department of Genetics and Plant Breeding Bangladesh Agricultural UniversityMymensingh 2202Bangladesh Plant Breeding Division Bangladesh Institute of Nuclear AgricultureMymensingh 2202Bangladesh Tuber Crop research Centre Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh Horticulture research Centre Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh Biotechnology Division Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh International Rice research institute Bangladesh OfficeDhaka 1213Bangladesh Division of Soil Science Bangladesh Wheat and Maize Research InstituteDinajpur 5200Bangladesh

The impact of epigenetic modifications like DNA methylation on plant phenotypes has expanded the possibilities for crop development.DNA methylation plays a part in the regulation of both the chromatin structure and gene expression,and the enzyme involved,DNA methyltransferase,executes the methylation process within the plant genome.By regulating crucial biological pathways,epigenetic changes actively contribute to the creation of the phenotype.Therefore,epigenome editing may assist in overcoming some of the drawbacks of genome editing,which can have minor off-target consequences and merely facilitate the loss of a gene’s function.These drawbacks include gene knockout,which can have such off-target effects.This review provides examples of several molecular characteristics of DNA methylation,as well as some plant physiological processes that are impacted by these epigenetic changes in the plants.We also discuss how DNA alterations might be used to improve crops and meet the demands of sustainable and environmentally-friendly farming.

关键词： DNA methylation epigenetics CMS male sterility chromatin architecture gene expression higher plants

Movement Trend Alterations in the Periaqueductal Gray(PAG)-Employed Ratbot Navigation Are Correlated with Stimulation Parameters

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Journal of Bionic Engineering 2024年第2期21卷 866-876页

作者： Sina Khajei Abed Khorasani Mohammad Reza Afarinesh Vahid Sheibani Neuroscience research Center Institute of NeuropharmacologyKerman University of Medical SciencesKerman***Iran Cognitive Neuroscience research Center Institute of NeuropharmacologyKerman University of Medical SciencesKerman***Iran

In previous studies,Periaqueductal Gray(PAG)stimulation was used to stop ratbots from moving.Due to the homology between the PAG and the intercollicular nucleus,which has been used for forward movement in birds,we investigated the possibility of PAG application to induce forward locomotion for the first time.Using a corridor maze,the traveled distances via PAG electrical stimulation were examined in nine Wistar male rats during three sessions.A custom-designed stimulator was developed to apply the stimulation.The results showed reductions in responses to stimulation over time.Accordingly,the traveled distances had negative slopes during the consecutive trials(in 8 out of the 9 rats),and the slope mean was significantly different from zero.There was a strong correlation between the stimulation parameters(electric Charge per Phase(CPP)and the Number of Pulses(NP))and the observed slopes.The negative Movement Slopes(MS)were highly correlated with the CPP and the NP,as the Pearson's linear correlation coefficients were−0.87 and−0.79,respectively.The MS-CPP coefficients of determination(R-squared)were also between 0.76 and 0.95.In addition,the MS-NP coefficients of determination were between 0.63 and 0.87.Thus,it is concluded that the electrical stimulation parameters influence the behavioral outcomes directly.Furthermore,the PAG area may be considered a suitable candidate for forward locomotion control in the future if the area is harnessed effectively to prevent undesirable chaotic behaviors.

关键词： Periaqueductal Gray(PAG) Navigation Ratbot Animal-robot Forward locomotion Movement slope

How variable progenitor clones construct a largely invariant neocortex

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National Science Review 2024年第1期11卷 129-144页

作者： Zhongfu Shen Jiajun Yang Qiangqiang Zhang Kuiyu Wang Xiaohui Lv Xiaolin Hu Jian Ma Song-Hai Shi New Cornerstone Science Laboratory IDG/McG overn Institute for Brain Research Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life Sciences Tsinghua University Department of Computer Sciences Tsinghua University College of Life Sciences Nankai University Chinese institute for Brain research

The neocortex contains a vast collection of diverse neurons organized into distinct layers. While nearly all neocortical neurons are generated by radial glial progenitors(RGPs), it remains largely unclear how a complex yet organized neocortex is constructed reliably and robustly. Here, we show that the division behavior and neuronal output of RGPs are highly constrained with patterned variabilities to support the reliable and robust construction of the mouse neocortex. The neurogenic process of RGPs can be well-approximated by a consistent Poisson-like process unfolding over time, producing deep to superficial layer neurons progressively. The exact neuronal outputs regarding layer occupation are variable; yet, this variability is constrained systematically to support all layer formation, largely reflecting the variable intermediate progenitor generation and RGP neurogenic entry and exit timing differences. Together, these results define the fundamental features of neocortical neurogenesis with a balanced reliability and variability for the construction of the complex neocortex.

关键词： neocortex radial glial progenitor intermediate progenitor neurogenesis clonal variability layer formation

Impact of lifestyle interventions on pathogenesis of nonalcoholic fatty liver disease

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World Journal of gastroenterology 2024年第20期30卷 2633-2637页

作者： Wafaa Mohamed Ezzat Department of Internal Medicine Medical Research and Clinical Studies InstituteNational Research CenterGiza 12311Egypt

This editorial builds on the article titled“Establishment and validation of an adherence prediction system for lifestyle interventions in non-alcoholic fatty liver disease”by Zeng et al.We carried out a critical examination of nonalcoholic fatty liver disease(NAFLD)pathogenesis and how lifestyle interventions could facilitate disease resolution,particularly highlighting that non-alcoholic steatohepatitis(NASH)is a severe form of NAFLD.Our discussion details that weight loss is a pivotal factor in disease outcomes:A 3%-5%reduction is enough for resolution in 50%of non-obese individuals,while a 7%-10%reduction achieves similar benefits in obese individuals,as demonstrated by magnetic resonance spectroscopy.Additionally,the editorial underscores that such lifestyle changes are instrumental not only in resolving NAFLD but also in reversing hepatic steatosis and inflammation.These insights,derived from the research,emphasize the critical role of personalized lifestyle modifications in halting the progression of NAFLD to NASH and even reversing fibrosis,thus offering a template for effective patient management.

关键词： Nonalcoholic fatty liver disease Non-alcoholic steatohepatitis Diet Physical activity Life style

High-temperature corrosion of sintered RE_(2)Si_(2)O_(7)(RE=Yb and Ho)environmental barrier coating materials by volcanic ash

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International Journal of Minerals,Metallurgy and Materials 2024年第7期31卷 1628-1638页

作者： Ayahisa Okawa Son Thanh Nguyen Tadachika Nakayama Thi-Mai-Dung Do Hisayuki Suematsu Shu Yin Takuya Hasegawa Tsuneo Suzuki Takashi Goto Koichi Niihara institute of Multidisciplinary research for Advanced Materials Tohoku UniversitySendai 980-8577Japan Department of Creative Engineering National Institute of TechnologyKushiro 084-0916Japan Extreme Energy-Density research institute Nagaoka University of TechnologyNagaoka 940-2188Japan Advanced institute for Materials research(WPI-AIMR) Tohoku UniversitySendai 980-8577Japan

Rare-earth silicates are promising environmental barrier coatings(EBCs)that can protect SiC_(f)/Si C_(m)substrates in next-genera tion gas turbine blades.Notably,RE_(2)Si_(2)O_(7)(RE=Yb and Ho)shows potential as an EBC due to its coefficient of thermal expansion(CTE)compatible with substrates and high resistance to water vapor corrosion.The target operating temperature for next-generation tur bine blades is 1400°C.Corrosion is inevitable during adhesion to molten volcanic ash,and thus,understanding the corrosion behavior o the material is crucial to its reliability.This study investigates the high-temperature corrosion behavior of sintered RE_(2)Si_(2)O_(7)(RE=Yb and Ho).Samples were prepared using a solid-state reaction and hot-press method.They were then exposed to volcanic ash at 1400°C for 224,and 48 h.After 48 h of exposure,volcanic ash did not react with Yb_(2)Si_(2)O_(7)but penetrated its interior,causing damage.Meanwhile Ho_(2)Si_(2)O_(7)was partially dissolved in the molten volcanic ash,forming a reaction zone that prevented volcanic ash melts from penetrating the interior.With increasing heat treatment time,the reaction zone expanded,and the thickness of the acicular apatite grains increased The Ca:Si ratios in the residual volcanic ash were mostly unchanged for Yb_(2)Si_(2)O_(7)but decreased considerably over time for Ho_(2)Si_(2)O_(7).Th Ca in volcanic ash was consumed and formed apatite,indicating that RE^(3+)ions with large ionic radii(Ho>Yb)easily precipitated apatit from the volcanic ash.

关键词： environmental barrier coating volcanic ash rare-earth disilicate corrosion

A reweighted damped singular spectrum analysis method for robust seismic noise suppression

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Petroleum Science 2024年第3期21卷 1671-1682页

作者： Wei-Lin Huang Yan-Xin Zhou Yang Zhou Wei-Jie Liu Ji-Dong Li State Key Laboratory of Petroleum Resources and Engineering China University of Petroleum (Beijing) SINOPEC Petroleum Exploration and Production research institute SINOPEC Geophysical research institute

(Multichannel) Singular spectrum analysis is considered as one of the most effective methods for seismic incoherent noise suppression. It utilizes the low-rank feature of seismic signal and regards the noise suppression as a low-rank reconstruction problem. However, in some cases the seismic geophones receive some erratic disturbances and the amplitudes are dramatically larger than other receivers. The presence of this kind of noise, called erratic noise, makes singular spectrum analysis(SSA) reconstruction unstable and has undesirable effects on the final results. We robustify the low-rank reconstruction of seismic data by a reweighted damped SSA(RD-SSA) method. It incorporates the damped SSA, an improved version of SSA, into a reweighted framework. The damping operator is used to weaken the artificial disturbance introduced by the low-rank projection of both erratic and random noise. The central idea of the RD-SSA method is to iteratively approximate the observed data with the quadratic norm for the first iteration and the Tukeys bisquare norm for the rest iterations. The RD-SSA method can suppress seismic incoherent noise and keep the reconstruction process robust to the erratic disturbance. The feasibility of RD-SSA is validated via both synthetic and field data examples.

关键词： Singular spectrum analysis Damping operator Seismic erratic noise Seismic signal processing Robust low-rank reconstruction

Induced pluripotent stem cells(iPSCs):molecular mechanisms of induction and applications

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Signal Transduction and Targeted Therapy 2024年第5期9卷 2065-2090页

作者： Jonas Cerneckis Hongxia Cai Yanhong Shi Department of Neurodegenerative Diseases Beckman Research Institute of City of HopeDuarteCA 91010USA Irell&Manella Graduate School of Biological Sciences Beckman Research Institute of City of HopeDuarteCA 91010USA

The induced pluripotent stem cell(iPSC)technology has transformed in vitro research and holds great promise to advance regenerative medicine.iPSCs have the capacity for an almost unlimited expansion,are amenable to genetic engineering,and can be differentiated into most somatic cell types.iPSCs have been widely applied to model human development and diseases,perform drug screening,and develop cell therapies.In this review,we outline key developments in the iPSC field and highlight the immense versatility of the iPSC technology for in vitro modeling and therapeutic applications.We begin by discussing the pivotal discoveries that revealed the potential of a somatic cell nucleus for reprogramming and led to successful generation of iPSCs.We consider the molecular mechanisms and dynamics of somatic cell reprogramming as well as the numerous methods available to induce pluripotency.Subsequently,we discuss various iPSC-based cellular models,from mono-cultures of a single cell type to complex three-dimensional organoids,and how these models can be applied to elucidate the mechanisms of human development and diseases.We use examples of neurological disorders,coronavirus disease 2019(COVID-19),and cancer to highlight the diversity of disease-specific phenotypes that can be modeled using iPSC-derived cells.We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies.Finally,we discuss the process of developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases.

关键词： mechanisms programming holds

Global analysis of basic leucine zipper transcription factors in trifoliate orange and the function identification of PtbZIP49 in salt tolerance

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Horticultural Plant Journal 2024年第1期10卷 115-130页

作者： Yuanyuan Xu Qiuling Hui Meng Li Hongxian Peng Yizhong He Changpin Chun Liangzhi Peng Xingzheng Fu National Citrus Engineering research Center Citrus Research InstituteSouthwest UniversityChongqing 400712China

As one of the most widely distributed and highly conserved transcription factors in eukaryotes,basic leucine zipper proteins(bZIPs)are involved in a variety of biological processes in plants,but they are largely unknown in citrus.In this study,56 bZIP family members were identified genome-wide from an important citrus rootstock,namely trifoliate orange(Poncirus trifoliata L.Raf.),and these putative bZIPs were named PtbZIP1—PtbZIP56.All PtbZIPs were classified into 13 subgroups by phylogenetic comparison with Arabidopsis thaliana bZIPs(AtbZIPs),and they were randomly distributed on nine known(50 genes)chromosomes and one unknown(6 genes)chromosome.Sequence analysis revealed the detailed characteristics of PtPZIPs,including their amino acid length,isoelectric point(pI),molecular weight(MW),predicted subcellular localization,gene structure,and conserved motifs.Prediction of promoter elements suggested the presence of drought,low-temperature,wound,and defense and stress responsive elements,as well as multiple hormone-responsive cis-acting elements.Spatiotemporal expression analysis showed the transcriptional patterns of PtbZIPs in different tissues and under dehydration,high salt,ABA,and IAA treatments.In addition,21 PtbZIPs were predicted to have direct or indirect protein—protein interactions.Among these,PtbZIP49 was experimentally proven to interact with PtbZIP1 or PtbZIP11 by using a yeast two-hybrid assay and bimolecular fluorescence complementation(BiFC).Subcellular localization analysis further revealed that PtbZIP1,PtbZIP11,and PtbZIP49 were localized in the nucleus.Moreover,PtbZIP49 was functionally identified as having an important role in salt stress via ectopic expression in A.thaliana and silenced in trifoliate orange using virus-induced gene silencing(VIGS).This study provided comprehensive information on PtbZIP transcription factors in citrus and highlights their potential functions in abiotic stress.

关键词： bZIP Citrus Trifoliate orange Abiotic stress Expression pattern

Evaluation of soil loss severity and ecological restoration approach for sustainable agriculture in the Hindu Kush, Karakoram and Himalaya region

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Journal of Mountain Science 2024年第5期21卷 1509-1521页

作者： Arshad ASHRAF Imran AHMAD Climate Energy and Water Research InstituteNational Agricultural Research Centre(NARC)Islamabad 44000Pakistan

Soil erosion has resulted in removal of the topsoils containing fine soil particles and plant nutrients, causing decrease in soil fertility in the Hindu Kush, Karakoram and Himalaya(HKH) region. The existing production of cereal crop grains has been reduced to one third of the potential crop grains production owing to land degradation and poor farming practices. It is necessary to assess risk of soil loss and identify appropriate controlling measures to address issues of low agriculture productivity and water insecurity in the region. In the present study, severity of soil loss was predicted using Revised Universal Loss Equation(RUSLE) and ecological measures were identified for sustainable mountain agriculture in the HKH region of Upper Indus Basin, Pakistan. Overall 62.6% area was found to have very low risk of soil loss, i.e., 100 t/(ha·yr) in about 6.8% and 7.4% areas respectively. The mean rate of soil loss was about 41.9 t/(ha·yr) in the Hindu Kush, 31.1 t/(ha·yr) in the Himalayas, 18.8 t/(ha·yr) in the Karakoram and overall 29.7 t/(ha·yr) in the three HKH ranges. As such no considerable measures have been adopted by the communities for restoration of the degraded areas except raising fruit/farm trees and supporting limited social forestry for their livelihoods. The slopes cleared for cultivation and susceptible to erosion may be stabilized through sowing/planting of multi-purpose plant species and formation of proper bench terraces. The conservation of forest ecosystem and pastures at higher elevations would help in reducing overland water flow, risk of flash flood hazard and minimizing sediment loads in the downstream. It is essential to adopt site-specific resource conservation techniques and restore possible ecosystem health for sustainable agriculture and economic development in the region in future.

关键词： Climate change Erodibility Indus basin Land degradation Slope stabilization