结球甘蓝CBF家族特征分析及低温诱导基因BoCBF1、BoCBF2a和BoCBF3表达分析

转录因子CBF在植物对低温胁迫的响应和增强植物的抗寒性方面发挥着重要作用。为分析结球甘蓝CBF家族成员的氨基酸序列特征,探究其是否受低温诱导表达,本研究利用结球甘蓝923全基因组数据库对其进行蛋白质理化特征、系统发育关系、编码基因结构以及2℃低温胁迫下编码基因表达水平分析。结果表明,共鉴定到7个BoCBF基因,系统发育分析后分成2个亚组(Ⅰ和Ⅱ)。BoCBF蛋白的氨基酸长度为203~283 aa,全部是亲水性蛋白质。在结球甘蓝02-12中,BoCBF1、BoCBF2a和BoCBF3基因在叶、花、芽和角果中基本不表达,在愈伤组织、根和茎中表达量较低。转录组测序和实时荧光定量PCR分析发现,在耐寒结球甘蓝923和不耐寒结球甘蓝D9中,BoCBF2b、BoCBF2c基因不受低温诱导表达,BoCBF2a基因低温诱导表达最为迅速,其次是BoCBF1和BoCBF3基因。BoCBF1、BoCBF2a和BoCBF3基因的相对表达量在低温胁迫3~6 h达到最大值,相对表达量达到最大值后急剧下降,在24 h降至最低。本研究结果为后续开展BoCBF1、BoCBF2a和BoCBF3基因调控结球甘蓝响应低温胁迫机理研究奠定了基础。

野生稻CBF/DREB1转录因子的鉴定与生物信息学分析

低温冷害是限制栽培稻地域分布和产量的重要因素之一,严重影响我国的粮食安全。以CBF/DREB1为核心的C-重复结合因子-冷调节基因(CBF-COR)途径是水稻适应低温的重要信号传导途径。基于稻属9种植物的全基因测序结果和隐马尔可夫模型(HMM)搜索,共鉴定出71个CBF/DREB1基因序列。所有基因均无内含子,由单个外显子组成。大部分DREB1s呈弱酸性,所有DREB1s亲水性平均值<0。进化树分析进一步将其分为3个组:DREB1A/1B/1H、DREB1C/1E/1F/1G和DREB1D/1I/1J,各组成员除AP2保守结构域和侧翼序列外,其他保守基序组成差别较大。适应性进化分析粳亚种和其他水稻的直系同源基因对,发现OsDREB1A/ObDREB1A、OsDREB1D/OnDREB1D、OsDREB1I/OsIDREB1I和OsDREB1J/OsIDREB1J四对基因非同义替换/同义替换(Ka/Ks)值均>1,受到正选择压力。旁系同源基因之间启动子顺式元件种类和数量差异较大,直系同源基因的启动子顺式元件种类和数量很相似。对日本晴、93-11和东乡野生稻7 d幼苗4℃冷处理2 h的实时荧光定量PCR分析发现早期冷响应基因可分为激活型(DREB1A/1B/1C/1E/1F/1G/1H)和抑制型(DREB1D/1I/1J)。在日本晴、93-11和东乡野生稻冷激活型基因中,DREB1B/1G/1H均是冷处理后响应最快的一级冷响应因子,且启动子均含有至少一个拷贝的CAMTA转录因子结合元件CM2(CCGCGT)。OrDREB1B/1C/1E/1F/1G/1H在东乡野生稻4℃冷处理4 h后的表达量均高于栽培稻同源基因的表达量。9种稻属植物的CBF/DREB1基因亚家族的分子进化分析结果为低温抗性基因的挖掘和利用提供了前期基础。

腰果CBF基因家族的鉴定及响应冷胁迫的表达模式

腰果(Anacardium occidentalie Linn)属于典型的热带果树,主要在我国的云南省、海南省等地种植。腰果具有重要的经济价值、社会价值、生态价值,为农民增产创收,实现共同富裕和乡村振兴战略具有重要价值。腰果对于低温十分敏感,在8℃时就会受到严重伤害,生长停止。所以低温胁迫是制约腰果生长的重要非生物胁迫。CBF转录因子是植物在应对低温、干旱、盐等非生物胁迫下中发挥重要作用的转录因子。然而CBF基因家族在腰果中的作用尚未阐明,该家族在低温胁迫下的表达模式尚不清楚。本研究对腰果AoCBF基因家族的基本特性进行探究,通过生物信息学方法,在腰果转录组中鉴定并获得6个AoCBF基因家族成员,分别对其系统发育、理化性质、蛋白结构、低温诱导下表达模式和启动子作用元件进行分析。理化性质分析结果表明:6个AoCBF蛋白长度为189~334 aa,蛋白分子量为21.31~37.89 kDa,等电点均小于7,表明该蛋白呈酸性,且均包含AP2/ERF结构域。基序分析表明:AoCBF基因存在5个基序,不同AoCBF基因Motif的缺失暗示着相关功能的缺失性。系统发育树分析表明:6个AoCBFs可分为A、B两个亚组,其中A组包含1个基因,B组仅包含5个基因。启动子顺势作用元件分析得出,AoCBF可能参与激素响应及非生物胁迫响应过程。荧光定量表达分析显示,AoCBFs对低温冷胁迫均有不同程度的响应,表明AoCBF在响应低温胁迫生物学过程中发挥着一定的作用。本研究分析了AoCBF基因家族的基本特性,为后续AoCBF的深入研究和应用积累基础数据。

Combining stochastic density functional theory with deep potential molecular dynamics to study warm dense matter

In traditional finite-temperature Kohn–Sham density functional theory(KSDFT),the partial occupation of a large number of high-energy KS eigenstates restricts the use of first-principles molecular dynamics methods at extremely high temperatures.However,stochastic density functional theory(SDFT)can overcome this limitation.Recently,SDFT and the related mixed stochastic–deterministic density functional theory,based on a plane-wave basis set,have been implemented in the first-principles electronic structure software ABACUS[Q.Liu and M.Chen,Phys.Rev.B 106,125132(2022)].In this study,we combine SDFT with the Born–Oppenheimer molecular dynamics method to investigate systems with temperatures ranging from a few tens of eV to 1000 eV.Importantly,we train machine-learning-based interatomic models using the SDFT data and employ these deep potential models to simulate large-scale systems with long trajectories.Subsequently,we compute and analyze the structural properties,dynamic properties,and transport coefficients of warm dense matter.

The Probability Density Function Related to Shallow Cumulus Entrainment Rate and Its Influencing Factors in a Large-Eddy Simulation

The process of entrainment-mixing between cumulus clouds and the ambient air is important for the development of cumulus clouds.Accurately obtaining the entrainment rate(λ)is particularly important for its parameterization within the overall cumulus parameterization scheme.In this study,an improved bulk-plume method is proposed by solving the equations of two conserved variables simultaneously to calculateλof cumulus clouds in a large-eddy simulation.The results demonstrate that the improved bulk-plume method is more reliable than the traditional bulk-plume method,becauseλ,as calculated from the improved method,falls within the range ofλvalues obtained from the traditional method using different conserved variables.The probability density functions ofλfor all data,different times,and different heights can be well-fitted by a log-normal distribution,which supports the assumed stochastic entrainment process in previous studies.Further analysis demonstrate that the relationship betweenλand the vertical velocity is better than other thermodynamic/dynamical properties;thus,the vertical velocity is recommended as the primary influencing factor for the parameterization ofλin the future.The results of this study enhance the theoretical understanding ofλand its influencing factors and shed new light on the development ofλparameterization.

马铃薯CBFs基因家族的鉴定及其节律性表达分析

马铃薯对光照和温度等信号的敏感性是制约品种区域化种植的重要因素,CBF转录因子在维持植物生长发育和非生物胁迫响应之间的平衡过程中发挥重要作用,但马铃薯CBF基因家族缺少系统性分析.研究通过对马铃薯栽培种CBF基因家族的分析,发现8个StCBF蛋白的结构域较为保守,但基因启动子区存在较大差异.基因节律性表达分析结果显示,生物钟能调控StCBF1a、StCBF3a和StCBF4b的近日节律性表达,且在昼夜交替条件下,StCBF1a、StCBF3a和StCBF4b转录本积累的峰值在傍晚时段.为解析StCBF在环境适应性调控中的生物学功能和探索其在马铃薯遗传改良中的应用提供基础理论支持.

Transplantation of fibrin-thrombin encapsulated human induced neural stem cells promotes functional recovery of spinal cord injury rats through modulation of the microenvironment

Recent studies have mostly focused on engraftment of cells at the lesioned spinal cord,with the expectation that differentiated neurons facilitate recovery.Only a few studies have attempted to use transplanted cells and/or biomaterials as major modulators of the spinal cord injury microenvironment.Here,we aimed to investigate the role of microenvironment modulation by cell graft on functional recovery after spinal cord injury.Induced neural stem cells reprogrammed from human peripheral blood mononuclear cells,and/or thrombin plus fibrinogen,were transplanted into the lesion site of an immunosuppressed rat spinal cord injury model.Basso,Beattie and Bresnahan score,electrophysiological function,and immunofluorescence/histological analyses showed that transplantation facilitates motor and electrophysiological function,reduces lesion volume,and promotes axonal neurofilament expression at the lesion core.Examination of the graft and niche components revealed that although the graft only survived for a relatively short period(up to 15 days),it still had a crucial impact on the microenvironment.Altogether,induced neural stem cells and human fibrin reduced the number of infiltrated immune cells,biased microglia towards a regenerative M2 phenotype,and changed the cytokine expression profile at the lesion site.Graft-induced changes of the microenvironment during the acute and subacute stages might have disrupted the inflammatory cascade chain reactions,which may have exerted a long-term impact on the functional recovery of spinal cord injury rats.

Small but big leaps towards neuroglycomics:exploring N-glycome in the brain to advance the understanding of brain development and function

Glycosylation is a process that involves the addition of sugar moieties or glycans to different types of molecules,including proteins,lipids,and nucleic acids.Among these,protein glycosylation is one of the most prevalent forms of post-translational modification,playing a crucial role in biological complexity.With more than ten monosaccharides identified within mammalian brain cells and more than 1×1012 possible combinations,the heterogeneity of glycosylation is extensive(Conroy et al.,2021).The diversity of glycans and the complexity of their structures allow for a wide range of protein functions.N-glycans are one of the most abundant forms of glycans and are involved in various cellular functions.N-glycans can be added to proteins at specific sequons,Asn-X-Ser/Thr,and are classified into three main types in mature glycoproteins:high mannose,complex,and hybrid.High mannose N-glycans consist of 5-9 mannose residues linked to a chitobiose core and undergo processing into complex or hybrid forms in the Golgi apparatus(Varki et al.,2017).Complex N-glycans are more diverse and contain various branched structures such as antennae with fucose,galactose,and sialic acid residues.Hybrid N-glycans contain one or more complex branches in conjunction with an oligomannose branch(Fisher and Ungar,2016).Understanding the specific functions of these different types of N-glycans in protein regulation,folding,and function is an active area of research in the life sciences,including glycobiology.

Elevated brain temperature under severe heat exposure impairs cortical motor activity and executive function

Background:Excessive heat exposure can lead to hyperthermia in humans,which impairs physical performance and disrupts cognitive function.While heat is a known physiological stressor,it is unclear how severe heat stress affects brain physiology and function.Methods:Eleven healthy participants were subjected to heat stress from prolonged exercise or warm water immersion until their rectal temperatures(T_(re))attained 39.5℃,inducing exertional or passive hyperthermia,respectively.In a separate trial,blended ice was ingested before and during exercise as a cooling strategy.Data were compared to a control condition with seated rest(normothermic).Brain temperature(T_(br)),cerebral perfusion,and task-based brain activity were assessed using magnetic resonance imaging techniques.Results:T_(br)in motor cortex was found to be tightly regulated at rest(37.3℃±0.4℃(mean±SD))despite fluctuations in T_(re).With the development of hyperthermia,T_(br)increases and dovetails with the rising T_(re).Bilateral motor cortical activity was suppressed during high-intensity plantarflexion tasks,implying a reduced central motor drive in hyperthermic participants(T_(re)=38.5℃±0.1℃).Global gray matter perfusion and regional perfusion in sensorimotor cortex were reduced with passive hyperthermia.Executive function was poorer under a passive hyperthermic state,and this could relate to compromised visual processing as indicated by the reduced activation of left lateral-occipital cortex.Conversely,ingestion of blended ice before and during exercise alleviated the rise in both T_(re)and T_(bc)and mitigated heat-related neural perturbations.Conclusion:Severe heat exposure elevates T_(br),disrupts motor cortical activity and executive function,and this can lead to impairment of physical and cognitive performance.

Functional near-infrared spectroscopy in non-invasive neuromodulation

Non-invasive cerebral neuromodulation technologies are essential for the reorganization of cerebral neural networks,which have been widely applied in the field of central neurological diseases,such as stroke,Parkinson’s disease,and mental disorders.Although significant advances have been made in neuromodulation technologies,the identification of optimal neurostimulation paramete rs including the co rtical target,duration,and inhibition or excitation pattern is still limited due to the lack of guidance for neural circuits.Moreove r,the neural mechanism unde rlying neuromodulation for improved behavioral performance remains poorly understood.Recently,advancements in neuroimaging have provided insight into neuromodulation techniques.Functional near-infrared spectroscopy,as a novel non-invasive optical brain imaging method,can detect brain activity by measuring cerebral hemodynamics with the advantages of portability,high motion tole rance,and anti-electromagnetic interference.Coupling functional near-infra red spectroscopy with neuromodulation technologies offe rs an opportunity to monitor the cortical response,provide realtime feedbac k,and establish a closed-loop strategy integrating evaluation,feedbac k,and intervention for neurostimulation,which provides a theoretical basis for development of individualized precise neuro rehabilitation.We aimed to summarize the advantages of functional near-infra red spectroscopy and provide an ove rview of the current research on functional near-infrared spectroscopy in transcranial magnetic stimulation,transcranial electrical stimulation,neurofeedback,and braincomputer interfaces.Furthermore,the future perspectives and directions for the application of functional near-infrared spectroscopy in neuromodulation are summarized.In conclusion,functional near-infrared spectroscopy combined with neuromodulation may promote the optimization of central pellral reorganization to achieve better functional recovery form central nervous system diseases.

百香果CBF基因家族鉴定与表达分析

百香果(Passiflora edulis Sims)原产热带地区,对低温十分敏感。CBF(C-repeat binding factor)基因家族是AP2转录因子家族的一类成员,在植物应对低温、干旱和盐等非生物胁迫中发挥重要作用。对百香果CBF基因家族进行鉴定和分析,并探究其在低温胁迫下的表达模式,可为进一步研究百香果CBF基因功能提供重要的参考信息。采用生物信息学方法鉴定百香果CBF基因家族成员,并对家族成员的序列组分、理化性质、系统进化关系、染色体定位、基因结构、保守基序、启动子顺式作用元件和转录因子结合位点等进行分析,通过qRT-PCR方法分析其在低温胁迫下的表达模式。结果显示,百香果基因组中共有5个CBF基因家族成员,其中3个分布在1号染色体上,2个分布在7号染色体上,被预测定位到细胞核、质膜和过氧化物酶体中;含有1~2个外显子,11~12个motif;系统进化显示5个百香果CBF基因、10个水稻CBF基因及6个拟南芥CBF基因共分成了2大亚组:亚组Ⅰ中包括拟南芥的全部6个CBF基因、百香果的全部5个CBF基因和水稻的4个CBF基因,水稻剩下的6个CBF基因分到了亚组Ⅱ中;启动子区域含有25种顺式作用元件,以光响应、激素与逆境胁迫响应元件为主;共有20个转录因子结合位点;3个百香果CBF基因在低温胁迫下表达量极显著上升,推测上述基因参与了百香果低温胁迫响应。

Beyond functional MRI signals:molecular and cellular modifiers of the functional connectome and cognition

Our brain is constantly active.Even at rest,the brain carries out essential functions such as maintenance of resting potentials,subthreshold synaptic activity,and spiking activity related to information processing.This resting activity can be assessed with several in vivo tools,such as resting-state functional magnetic resonance imaging.This technique measures subtle changes in blood flow,volume,and oxygenation that occur over time.Although vascular in nature,resting-state functional magnetic resonance imaging is considered a reliable proxy of neural activity and several studies have shown that the brain is functionally divided into interacting neural networks called the“functional connectome”.

Tau's function and dysfunction in the brain:when small changes have big consequences

With the increase of life expectancy and population growth,neurodegenerative diseases have risen too and are projected to be a major health public concern by 2050.Neurodegenerative diseases are characterized by the progressive decline of cognitive function leading to the subsequent loss of autonomy.Although the underlying causes of neurodegeneration are not well understood,aging is the main risk factor.

A divergent pattern in functional connectivity: a transdiagnostic perspective

Functional magnetic resonance imaging(fMRI)is a popular tool used to investigate not only how the brain responds to specific stimuli during sensorimotor or cognitive tasks,but also brain activity at rest.The physics beyond this approach is based on the analysis of the blood oxygenation level-dependent signal.

Influence of ecological function protection zone on the water conservation in Gansu-Qinghai Contiguous Region of the upper Yellow River

The implementation of Ecological Function Protection Zone(EFPZ)policy is significant for the ecological restoration and conservation of soil and water in the territory space.This manuscript analyzed and quantified the impact of EFPZ on the regional water conservation function,based on land use data from 2005,2008,2010,2015 and 2020,by conducting a counterfactual simulation along with the GeoSOS-FLUS model and the InVEST model.The results demonstrate that the delineation of EFPZ can significantly influence the water conservation.(1)From 2010 to 2020,as the EFPZ was implemented,the water conservation in the study area was increasing year by year,with a growth rate of 0.03×10^(8) m^(3)∙a^(-1).On the other hand,the simulated water conservation capacity without the implementation of EFPZ decreased year by year,with a decrease rate of 0.01×10^(8) m^(3)∙a^(-1).(2)The EFPZ accounts for only 23%of the total area,but the contribution rate of water conservation reaches 80%.The actual values of water conservation and average water yield per unit pixel in the EFPZ show an increasing trend both internally and externally,while the counterfactual simulation values exhibit a decreasing trend.(3)The water conservation is much higher within the EFPZ than without EFPZ.The implementation of EFPZ has a significant effect on the improvement of the water conservation capacity in Maqu EFPZ and Yellow River Source EFPZ.The protection effectiveness should be enhanced in Qilian Mountain EFPZ and afforestation activities need to be carefully considered in Loess Plateau EFPZ.

Random Green's Function Method for Large-Scale Electronic Structure Calculation

We report a linear-scaling random Green's function(rGF) method for large-scale electronic structure calculation. In this method, the rGF is defined on a set of random states and is efficiently calculated by projecting onto Krylov subspace. With the rGF method, the Fermi–Dirac operator can be obtained directly, avoiding the polynomial expansion to Fermi–Dirac function. To demonstrate the applicability, we implement the rGF method with the density-functional tight-binding method. It is shown that the Krylov subspace can maintain at small size for materials with different gaps at zero temperature, including H_(2)O and Si clusters. We find with a simple deflation technique that the rGF self-consistent calculation of H_(2)O clusters at T = 0 K can reach an error of~ 1 me V per H_(2)O molecule in total energy, compared to deterministic calculations. The rGF method provides an effective stochastic method for large-scale electronic structure simulation.

Probability Laws Derived from the Gamma Function

Several densities or probability laws of continuous random variables derive from the Euler Gamma function. These laws form the basis of sampling theory, namely hypothesis testing and estimation. Namely the gamma, beta, and Student law, through the chi-square law and the normal law are all distributions resulting from applications of Euleur functions.

Corrigendum: MicroRNA-502-3p regulates GABAergic synapse function in hippocampal neurons

There is an error in the name of the cell line in the abstract of the published paper“MicroRNA-502-3p regulates GABAergic synapse function in hippocampal neurons”published on pages 2698-2707,Issue 12,Volume 19 of Neural Regeneration Research(Sharma et al.,2024),because of oversight during final proof checking.The correct description should be“human-GABA receptor A-α1/β2/γ2L human embryonic kidney(HEK)recombinant cell line.”The authors apologize for any inconvenience this correction may cause for readers and editors of Neural Regeneration Research.

Interaction between systemic iron parameters and left ventricular structure and function in the preserved ejection fraction population:a two-sample bidirectional Mendelian randomization study

BACKGROUND Left ventricular(LV)remodeling and diastolic function in people with heart failure(HF)are correlated with iron status;however,the causality is uncertain.This Mendelian randomization(MR)study investigated the bidirectional causal relationship between systemic iron parameters and LV structure and function in a preserved ejection fraction population.METHODS Transferrin saturation(TSAT),total iron binding capacity(TIBC),and serum iron and ferritin levels were extracted as instrumental variables for iron parameters from meta-analyses of public genome-wide association studies.Individuals without myocardial infarction history,HF,or LV ejection fraction(LVEF)<50%(n=16,923)in the UK Biobank Cardiovascular Magnetic Resonance Imaging Study constituted the outcome dataset.The dataset included LV end-diastolic volume,LV endsystolic volume,LV mass(LVM),and LVM-to-end-diastolic volume ratio(LVMVR).We used a two-sample bidirectional MR study with inverse variance weighting(IVW)as the primary analysis method and estimation methods using different algorithms to improve the robustness of the results.RESULTS In the IVW analysis,one standard deviation(SD)increased in TSAT significantly correlated with decreased LVMVR(β=-0.1365;95%confidence interval[CI]:-0.2092 to-0.0638;P=0.0002)after Bonferroni adjustment.Conversely,no significant relationships were observed between other iron and LV parameters.After Bonferroni correction,reverse MR analysis showed that one SD increase in LVEF significantly correlated with decreased TSAT(β=-0.0699;95%CI:-0.1087 to-0.0311;P=0.0004).No heterogeneity or pleiotropic effects evidence was observed in the analysis.CONCLUSIONS We demonstrated a causal relationship between TSAT and LV remodeling and function in a preserved ejection fraction population.

Tetraethylenepentamine-functionalized magnetic mesoporous composites as a novel adsorbent for the removal Cr(III)-ethylenediaminetetraacetic acid in complex solution

A novel tetraethylenepentamine(TEPA)functionalized magnetic mesoporous silica adsorbent(FNMs/TEPA)was prepared for the adsorption of Cr(III)-ethylenediaminetetraacetic acid(EDTA)from wastewater.The characterization of the prepared adsorbent certified that TEPA was modified onto the magnetic mesoporous silicon(FNMs),while FNMs/TEPA maintained the ordered mesoporous and pristine magnetic properties.The batch adsorption experiments demonstrated that TEPA significantly enhanced the removal capacity of the adsorbent for Cr(III)-EDTA.FNMs/TEPA exhibited an excellent adsorption property(13.84 mg·g^(-1))at pH 4.0.Even in the presence of high concentrations of coexisting ions and organic acids,the adsorption performance of FNMs/TEPA was stable.Experimental characterization and DFT demonstrated that the adsorption of Cr(III)-EDTA was ascribed to the electrostatic interaction,hydrogen bonding,and complexation between Cr(III)-EDTA and amino groups on the adsorbent surface.The analysis of the independent gradient model(IGM)shows that electrostatic interaction is the main mode of action in the adsorption process.Moreover,FNMs/TEPA demonstrated remarkable reusability in three regeneration cycles.These findings indicated that FNMs/TEPA possessed excellent application prospects in the disposal of wastewater containing Cr(III)-EDTA.