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1.
Angew Chem Int Ed Engl ; : e202410514, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38966937

ABSTRACT

Organic scintillators are praised for their abundant element reserves, facile preparation procedures, and rich structures. Herein, a new family of highly efficient organic phosphonium halide salts with thermally activated delayed fluorescence (TADF) are designed by innovatively adopting quaternary phosphonium as the electron acceptor, while dimethylamine group and halide anions (I-) serve as the electron donor. The prepared butyl(2-[2-(dimethylamino)phenyl]phenyl)diphenylphosphonium iodide (C4-I) exhibits bright blue emission and an ultra-high photoluminescence quantum yield (PLQY) of 100%. Efficient charge transfer is realized through the unique n-π and anion-π stacking in solid-state C4-I. Photophysical studies of C4-I suggest that the incorporation of I accounts for high intersystem crossing rate (kISC) and reverse intersystem crossing rate (kRISC), suppressing the intrinsic prompt fluorescence and enabling near-pure TADF emission at room temperature. Benefitting from the large Stokes shift, high PLQY, efficient exciton utilization, and remarkable X-ray attenuation ability endowed by I, C4-I delivers an outstanding light yield of 80721 photons/MeV and a low limit of detection (LoD) of 22.79 nGy·s-1. This work would provide a rational design concept and open up an appealing road for developing efficient organic scintillators with tunable emission, strong X-ray attenuation ability, and excellent scintillator performance.

2.
Article in English | MEDLINE | ID: mdl-38852918

ABSTRACT

BACKGROUND: The sex differences were co-shaped by innate biological differences and social environment, and were frequently observed in human emotional neural responses. Oral administration of oxytocin, as an alternative and noninvasive intake method, has been demonstrated to produce sex-dependent effects on emotional face processing. However, it is unclear whether oral oxytocin produces similar sex-dependent effects on processing continuous emotional scenes. METHODS: Current randomized, double-blind, placebo-controlled neuro-psychopharmacological fMRI experiment was conducted in 147 healthy participants (oxytocin=74, male/female=37/37; placebo=73, male/female=36/37) to examine the oral oxytocin effect on plasma oxytocin concentrations and neural response to emotional scenes in both sexes. RESULTS: At the neuroendocrine level, females showed lower endogenous oxytocin concentrations than males, but oral oxytocin equally increased the oxytocin concentrations in both sexes. Regarding neural activity, emotional scenes evoked opposite valence-independent effects on right amygdala activation (females>males) and its functional connectivity with the insula (males>females) in two sexes in the placebo group. This sex difference were either attenuated (amygdala response) or even completely eliminated (amygdala-insula functional connectivity) in the oxytocin group. The multivariate pattern analysis confirmed these findings by developing an accurate sex-predictive neural pattern that including the amygdala and the insula under the placebo but not oxytocin condition. CONCLUSION: Present study suggests a pronounced sex-difference in neural responses to emotional scenes which is abolished by oral oxytocin, with it having opposite modulatory effects in two sexes. Possibly this may reflect oral OXT enhancing emotional regulation to continuous emotional stimuli in both sexes by facilitating appropriate changes in sex-specific amygdala-insula circuitry.

3.
Medicine (Baltimore) ; 103(24): e38436, 2024 Jun 14.
Article in English | MEDLINE | ID: mdl-38875419

ABSTRACT

Cerebral embolism presents a significant challenge for recovery of motor and neurological function. Early integrated rehabilitation therapy (EIRT) has been proposed as a beneficial approach, yet its efficacy requires thorough evaluation. This retrospective study, conducted from January 2020 to January 2023, involved 117 patient's post-cerebral embolism, divided into an EIRT group (n = 56) receiving EIRT and a control group (n = 61) receiving standard care. The Fugl-Meyer Assessment (FMA) and the National Institutes of Health Stroke Scale (NIHSS) were used to evaluate motor and neurological functions, while muscle strength was categorized from Level 0 (complete paralysis) to Level V (normal strength) to assess physical recovery. Eligibility centered on confirmed cerebral embolism diagnosis, timing of poststroke admission, and baseline functional status. The study adhered to strict ethical standards, with informed consent obtained from all participants. The EIRT group showed substantial improvements in both FMA and NIHSS scores compared to the control group, indicating better motor and neurological recovery. Significant differences were found in the posttreatment FMA (P < .01) and NIHSS scores (P < .01). Muscle strength analysis further confirmed the positive impact of EIRT with more patients in the EIRT group achieving higher levels of muscle strength at discharge. The study demonstrates the potential of EIRT to significantly improve motor and neurological outcomes for patient's post-cerebral embolism. The marked improvements in the observation group suggest that EIRT should be considered for broader application in stroke rehabilitation to enhance recovery and improve quality of life.


Subject(s)
Intracranial Embolism , Recovery of Function , Stroke Rehabilitation , Humans , Male , Female , Retrospective Studies , Middle Aged , Aged , Stroke Rehabilitation/methods , Intracranial Embolism/rehabilitation , Treatment Outcome , Muscle Strength/physiology
4.
J Colloid Interface Sci ; 669: 886-895, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38749227

ABSTRACT

Zinc metal anodes in aqueous electrolytes commonly face challenges such as dendrite growth and undesirable side reactions, limiting their application in the field of aqueous zinc-ion batteries (AZIBs) for energy storage. Drawing inspiration from industrial practices involving molybdenum salt solutions for metal modification, a polyoxometalate solution was formulated as a passivation solution for zinc anodes (referred to as MO solution). The formed passivation layer, referred to as the MO layer, exhibited a uniform and protective nature with a thickness of approximately 10 µm. The experimental results demonstrated that this passivation layer effectively suppressed side reactions at the zinc anode interface, as evidenced by lower corrosion current density for MO-Zn anodes. Additionally, the newly plated Zn was uniformly deposited atop the MO layer, ensuring coating integrity and inhibiting dendrite growth. As a result, under more demanding conditions such as a larger current of 8 mA cm-2, the MO-Zn anode displayed an extended cycle life exceeding 420 h in a symmetric battery, with an overpotential as low as 98 mV. This performance significantly outperformed that of commercially available pure Zn foils (with a cycle life of 60 h and an overpotential of 192 mV). Notably, a self-made Na-doped V2O5 served as the cathode (referred to as NaVO), forming the MO-Zn//NaVO full battery. Even under high current test conditions of 2 A/g, the specific capacity of the MO-Zn//NaVO full battery remained substantial at 152.83 mAh/g after 1000 cycles. Furthermore, pouch batteries assembled with NaVO//MO-Zn successfully illuminated small bulbs. This study offers a viable optimization strategy for AZIB anodes and demonstrates the potential of using polyoxometalate solution for etching zinc anodes to inhibit dendrite growth and interfacial corrosion of zinc metal anodes.

5.
Aging Cell ; : e14163, 2024 Apr 02.
Article in English | MEDLINE | ID: mdl-38566438

ABSTRACT

The transition from ordered to noisy is a significant epigenetic signature of aging and age-related disease. As a paradigm of healthy human aging and longevity, long-lived individuals (LLI, >90 years old) may possess characteristic strategies in coping with the disordered epigenetic regulation. In this study, we constructed high-resolution blood epigenetic noise landscapes for this cohort by a methylation entropy (ME) method using whole genome bisulfite sequencing (WGBS). Although a universal increase in global ME occurred with chronological age in general control samples, this trend was suppressed in LLIs. Importantly, we identified 38,923 genomic regions with LLI-specific lower ME (LLI-specific lower entropy regions, for short, LLI-specific LERs). These regions were overrepresented in promoters, which likely function in transcriptional noise suppression. Genes associated with LLI-specific LERs have a considerable impact on SNP-based heritability of some aging-related disorders (e.g., asthma and stroke). Furthermore, neutrophil was identified as the primary cell type sustaining LLI-specific LERs. Our results highlight the stability of epigenetic order in promoters of genes involved with aging and age-related disorders within LLI epigenomes. This unique epigenetic feature reveals a previously unknown role of epigenetic order maintenance in specific genomic regions of LLIs, which helps open a new avenue on the epigenetic regulation mechanism in human healthy aging and longevity.

6.
Hemoglobin ; 48(2): 121-124, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38450437

ABSTRACT

We report a new δ-chain hemoglobin (Hb) variant observed in a 5-year-old female living in Yulin, Guangxi, China. Capillary electrophoresis revealed splitting of the Hb A2 peak into two fractions (Hb A2 and Hb A2 variant), and the Hb A2 variant was also detected by high-performance liquid chromatography. However, it could not be detected using matrix-assisted laser desorption lonization-time of flight mass spectrometry. CD41-42 (-TCTT) heterozygosity was observed on the HBB gene by PCR and reverse dot-blot hybridization. Sanger sequencing showed a new transition (G > A) at codon 46 of the HBD gene, resulting in glycine changing to arginine. Based on the patient's place of residence, the new variant was named Hb A2-Yulin [δ46(CD5)Gly→Arg,HBD:c.139G > A].


Subject(s)
Hemoglobin A2 , Hemoglobins, Abnormal , delta-Globins , Humans , Female , delta-Globins/genetics , Child, Preschool , Hemoglobins, Abnormal/genetics , Hemoglobin A2/genetics , Amino Acid Substitution , China
7.
Aging Cell ; 23(1): e13916, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37400997

ABSTRACT

Somatic mutations accumulate with age and are associated closely with human health, their characterization in longevity cohorts remains largely unknown. Here, by analyzing whole genome somatic mutation profiles in 73 centenarians and 51 younger controls in China, we found that centenarian genomes are characterized by a markedly skewed distribution of somatic mutations, with many genomic regions being specifically conserved but displaying a high function potential. This, together with the observed more efficient DNA repair ability in the long-lived individuals, supports the existence of key genomic regions for human survival during aging, with their integrity being of essential to human longevity.


Subject(s)
Centenarians , Longevity , Aged, 80 and over , Humans , Longevity/genetics , Aging/genetics , Mutation/genetics , Genomics
8.
Math Biosci Eng ; 20(9): 16678-16704, 2023 Aug 21.
Article in English | MEDLINE | ID: mdl-37920029

ABSTRACT

Quick response (QR) codes have become increasingly popular as a medium for quickly and easily accessing information through mobile devices. However, the open-source nature of QR code encoding poses a risk of information leakage and potential attacks, especially with the growing use of QR codes in financial services and authentication applications. To mitigate the risk of information leakage due to open-source QR code encoding, this paper proposes a two-level QR code scheme based on a region matrix image secret sharing algorithm. In this scheme, the first-level public information can be directly obtained by scanning with any standard QR code scanner, while the two-level secret information can only be accessed by overlaying the shared images. To enhance the robustness of joint secret information recovery using shared images, this article designs a progressive image secret sharing algorithm based on region matrices. This algorithm meticulously processes high-priority share regions and generates multiple substitute shares. In the event of attacks on key shares, substitute shares can be employed to recover the secret information. For an increased payload capacity of each QR code, an adaptive pixel depth adjustment algorithm is devised. This algorithm ensures that the recovery of two-level secret information maintains high clarity, while not affecting the scanning functionality of each shared QR code. Experimental results validate the feasibility of this scheme, which simplifies the construction matrix, reduces matrix redundancy, and exhibits priority partitioning and higher robustness. Furthermore, QR codes embedding secret shares can safeguard the two-level information, and the recovered images exhibit exceptional clarity.

9.
J Psychiatr Res ; 167: 23-31, 2023 Oct 06.
Article in English | MEDLINE | ID: mdl-37820447

ABSTRACT

Comorbidity has been frequently observed between generalized anxiety disorder (GAD) and major depressive disorder (MDD), however, common and distinguishable alterations in the topological organization of functional brain networks remain poorly understood. We sought to determine a robust and sensitive functional connectivity marker for diagnostic classification and symptom severity prediction. Multi-layered dynamic functional connectivity including whole brain, network-node and node-node layers via graph theory and gradient analyses were applied to functional MRI resting-state data obtained from 31 unmedicated GAD and 34 unmedicated MDD patients as well as 33 age and education matched healthy controls (HC). GAD and MDD symptoms were assessed using Penn State Worry Questionnaire and Beck Depression Inventory II, respectively. Three network measures including global properties (i.e., global efficiency, characteristic path length), regional nodal property (i.e., degree) and connectivity gradients were computed. Results showed that both patient groups exhibited abnormal dynamic cortico-subcortical topological organization compared to healthy controls, with MDD > GAD > HC in degree of randomization. Furthermore, our multi-layered dynamic functional connectivity network model reached 77% diagnostic accuracy between GAD and MDD and was highly predictive of symptom severity, respectively. Gradients of functional connectivity for superior frontal cortex-subcortical regions, middle temporal gyrus-subcortical regions and amygdala-cortical regions contributed more in this model compared to other gradients. We found shared and distinct cortico-subcortical connectivity features in dynamic functional brain networks between GAD and MDD, which together can promote the understanding of common and disorder-specific topological organization dysregulations and facilitate early neuroimaging-based diagnosis.

10.
Hum Cell ; 36(6): 2162-2178, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37642832

ABSTRACT

Ferroptosis is a form of cell death and has great potential application in the treatment of many cancers, including clear cell renal cell carcinoma (ccRCC). Herein, we identified the essential roles of Krüppel-like factor 11 (KLF11) in suppressing the progression of ccRCC. By analyzing mRNA expression data from the Gene Expression Omnibus (GEO) database, we found that KLF11 was a significantly downregulated gene in ccRCC tissues. The results of subsequent functional assays verified that KLF11 played an antiproliferative role in ccRCC cells and xenograft tumors. Furthermore, gene set enrichment analysis indicated that ferroptosis was involved in ccRCC development, and correlation analysis revealed that KLF11 was positively related to ferroptosis drivers. We also found that KLF11 promoted ferroptosis in ccRCC by downregulating the protein expression of ferritin, system xc (-) cystine/glutamate antiporter (xCT), and glutathione peroxidase 4 (GPX4), acting as the inhibitory factors of ferroptosis and increasing the intracellular levels of lipid reactive oxygen species (ROS). As a transcriptional regulator, KLF11 significantly increased the promoter activity of nuclear receptor coactivator 4 (NCOA4), a gene significantly downregulated in ccRCC and whose low expression is associated with poor survival. The characteristics of ccRCC cells caused by KLF11 overexpression were reversed after NCOA4 silencing. In summary, the present study suggests that KLF11 suppresses the progression of ccRCC by increasing NCOA4 transcription. Therefore, the KLF11/NCOA4 axis may serve as a novel therapeutic target for human ccRCC.

12.
Neuroimage ; 277: 120263, 2023 08 15.
Article in English | MEDLINE | ID: mdl-37399932

ABSTRACT

The mirror neuron system (MNS), including the inferior frontal gyrus (IFG), inferior parietal lobule (IPL) and superior temporal sulcus (STS) plays an important role in action representation and imitation and may be dysfunctional in autism spectrum disorder (ASD). However, it's not clear how these three regions respond and interact during the imitation of different basic facial expressions and whether the pattern of responses is influenced by autistic traits. Thus, we conducted a natural facial expression (happiness, angry, sadness and fear) imitation task in 100 healthy male subjects where expression intensity was measured using facial emotion recognition software (FaceReader) and MNS responses were recorded using functional near-infrared spectroscopy (fNIRS). Autistic traits were measured using the Autism Spectrum Quotient questionnaire. Results showed that imitation of happy expressions produced the highest expression intensity but a small deactivation in MNS responses, suggesting a lower processing requirement compared to other expressions. A cosine similarity analysis indicated a distinct pattern of MNS responses during imitation of each facial expression with functional intra-hemispheric connectivity between the left IPL and left STS being significantly higher during happy compared to other expressions, while inter-hemispheric connectivity between the left and right IPL differed between imitation of fearful and sad expressions. Furthermore, functional connectivity changes during imitation of each different expression could reliably predict autistic trait scores. Overall, the results provide evidence for distinct patterns of functional connectivity changes between MNS regions during imitation of different emotions which are also associated with autistic traits.


Subject(s)
Autism Spectrum Disorder , Autistic Disorder , Mirror Neurons , Humans , Male , Facial Expression , Mirror Neurons/physiology , Autism Spectrum Disorder/diagnostic imaging , Brain Mapping/methods , Imitative Behavior/physiology , Emotions/physiology
13.
J Acupunct Meridian Stud ; 16(3): 109-118, 2023 Jun 30.
Article in English | MEDLINE | ID: mdl-37381033

ABSTRACT

Background: In clinics, Ziwuliuzhu acupuncture is widely considered an effective method of treating insomnia; however, there is currently limited information available regarding its possible mechanisms. Although the method of Ziwuliuzhu acupuncture possesses a unique rhythmic pattern. Objectives: In this study, we have creatively combined the traditional Chinese medicine of Ziwuliuzhu with a modern biological rhythm to investigate the internal mechanism of insomnia. Methods: Pathological tissue from the hypothalamus was analyzed using hematoxylin-eosin staining. The level of TNF (tumor necrosis factor)-α in the SCN (suprachiasmatic nucleus) area of the hypothalamus was detected in situ using the TUNEL fluorescence staining assay. The concentration of hypothalamic melatonin was detected using the enzyme-linked immunosorbent assay (ELISA). The mRNA expression of Clock and Bmal1 was measured using RT-qPCR. Results: In the Ziwuliuzhu acupuncture groups, the structural damage in the hypothalamic neurons was alleviated compared to the model group and the expression of inflammatory factors was reduced. The mRNA expression levels of Clock and Bmal1 were significantly increased (p < 0.05). The concentration of melatonin was significantly increased (p < 0.001). Although there were no significant differences between the treatment groups (diazepam group, Nazi group, Najia group, and routine group) (p > 0.05). Conclusion: Ziwuliuzhu acupuncture alleviated neuronal damage and modulated the inflammatory reaction in the hypothalamus of rats with insomnia. Moreover, Ziwuliuzhu acupuncture increased the expression levels of Clock and Bmal1 mRNA, and MT content. This study has potentially highlighted one of the mechanisms through which Ziwuliuzhu acupuncture can be used to treat insomnia.


Subject(s)
Acupuncture Therapy , Melatonin , Sleep Initiation and Maintenance Disorders , Animals , Rats , Medicine, Chinese Traditional , RNA, Messenger/genetics , Sleep Initiation and Maintenance Disorders/genetics , Sleep Initiation and Maintenance Disorders/therapy
15.
Ying Yong Sheng Tai Xue Bao ; 34(5): 1187-1193, 2023 May.
Article in English | MEDLINE | ID: mdl-37236934

ABSTRACT

We compared the interspecific differences in leaf nutrient resorption of two dominant understory species (Lophatherum gracile and Oplimenus unulatifolius), and analyzed the correlations between the intraspecific efficiency of leaf nutrient resorption and nutrient properties of soil and leaves in Chinese fir plantation. The results showed high soil nutrient heterogeneity in Chinese fir plantation. Soil inorganic nitrogen content and available phosphorus content varied from 8.58 to 65.29 mg·kg-1 and from 2.43 to 15.20 mg·kg-1 in the Chinese fir plantation, respectively. The soil inorganic nitrogen content in O. undulatifolius community was 1.4 times higher than that in L. gra-cile community, but there was no significant difference in soil available phosphorus content between the two communities. Both leaf nitrogen and phosphorus resorption efficiency of O. unulatifolius was significantly lower than that of L. gracile under the three measurement bases of leaf dry weight, leaf area, and lignin content. Resorption efficiency in L. gracile community expressed on leaf dry weight was lower than that expressed on leaf area and lignin content, while resorption efficiency expressed on leaf area was the lowest in O. unulatifolius community. The intraspecific resorption efficiency was significantly correlated with leaf nutrient contents, but was less correlated with soil nutrient content, and only the nitrogen resorption efficiency of L. gracile had significant positive correlation with soil inorganic nitrogen content. The results indicated that there was significant difference in the leaf nutrient resorption efficiency between the two understory species. Soil nutrient heterogeneity exerted a weak effect on the intraspecific nutrient resorption, which might be attributed to high soil nutrient availability and potential disturbance from canopy litter in Chinese fir plantation.


Subject(s)
Cunninghamia , Soil , Nitrogen/analysis , Phosphorus , Lignin , Plants , Nutrients , Plant Leaves/chemistry
16.
Aging Dis ; 14(4): 1374-1389, 2023 Aug 01.
Article in English | MEDLINE | ID: mdl-37163432

ABSTRACT

Aging is characterized by persistent low-grade systematic inflammation, which is largely responsible for the occurrence of various age-associated diseases. We and others have previously reported that long-lived people (such as centenarians) can delay the onset of or even escape certain major age-related diseases. Here, by screening blood transcriptome and inflammatory profiles, we found that long-lived individuals had a relatively lower inflammation level (IL6, TNFα), accompanied by up-regulation of activating transcription factor 7 (ATF7). Interestingly, ATF7 expression was gradually reduced during cellular senescence. Loss of ATF7 induced cellular senescence, while overexpression delayed senescence progress and senescence-associated secretory phenotype (SASP) secretion. We showed that the anti-senescence effects of ATF7 were achieved by inhibiting nuclear factor kappa B (NF-κB) signaling and increasing histone H3K9 dimethylation (H3K9me2). In Caenorhabditis elegans, ATF7 overexpression significantly suppressed aging biomarkers and extended lifespan. Our findings suggest that ATF7 is a longevity-promoting factor that lowers cellular senescence and inflammation in long-lived individuals.

17.
Cell Rep ; 42(5): 112413, 2023 05 30.
Article in English | MEDLINE | ID: mdl-37164007

ABSTRACT

Although it is widely recognized that the ancestors of Native Americans (NAs) primarily came from Siberia, the link between mitochondrial DNA (mtDNA) lineage D4h3a (typical of NAs) and D4h3b (found so far only in East China and Thailand) raises the possibility that the ancestral sources for early NAs were more variegated than hypothesized. Here, we analyze 216 contemporary (including 106 newly sequenced) D4h mitogenomes and 39 previously reported ancient D4h data. The results reveal two radiation events of D4h in northern coastal China, one during the Last Glacial Maximum and the other within the last deglaciation, which facilitated the dispersals of D4h sub-branches to different areas including the Americas and the Japanese archipelago. The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs.


Subject(s)
Genome, Mitochondrial , Humans , Japan , Americas , China , DNA, Mitochondrial/genetics , Haplotypes/genetics , Phylogeny
18.
Ying Yong Sheng Tai Xue Bao ; 34(3): 631-638, 2023 Mar.
Article in English | MEDLINE | ID: mdl-37087645

ABSTRACT

Plants can alter soil microbial biomass and extracellular enzyme activities related with carbon (C), nitrogen (N), and phosphorus (P), through litter and root exudates, with consequences on soil carbon, nitrogen and phosphorus (P) cycling. However, it is not well known how the changes in soil phosphorus availability affect the relationships between plants and soil microorganisms. In this study, a factorial experiment was conducted to investigate the effects of Chinese fir (Cunninghamia lanceolata) planting and different levels of P addition (0, 1.95, 3.9, 7.8 and 15.6 g P·m-2·a-1) on soil microbial biomass and extracellular enzyme activities. The results showed that planting Chinese fir planting significantly altered soil microbial biomass and C- and N- and P-related extracellular enzyme activities, but the effects were dependent on P addition levels. Without P addition, Chinese fir planting significantly reduced soil nutrient availability and pH, which led to the aggravation of P limitation and lower soil microbial biomass. P addition relieved P limitation, and reduced soil acid phosphatase (ACP) activities by 30.0%, 30.5%, 35.3% and 47.1% with the increasing P addition level (1.95, 3.9, 7.8 and 15.6 g P·m-2·a-1). Under three P addition levels (1.95, 3.9 and 7.8 g P·m-2·a-1), the negative effects of Chinese fir planting on soil microbial growth were alleviated. Under the high P addition level (15.6 g P·m-2·a-1), the negative effects of Chinese fir planting on soil microbial growth occurred again due to soil N limitation. Taken together, Chinese fir planting and soil P availability generally affected soil microbial biomass and extracellular enzyme activities, and changed P limitation.


Subject(s)
Cunninghamia , Biomass , Soil/chemistry , Phosphorus , Soil Microbiology , Carbon , Nitrogen/analysis
19.
Yi Chuan ; 45(4): 324-340, 2023 Apr 20.
Article in English | MEDLINE | ID: mdl-37077166

ABSTRACT

It has been reported that the aberrant DNA methylation may result in copy number variations (CNVs), and the CNVs may alter the levels of DNA methylation. Whole genome bisulfite sequencing (WGBS) is able to generate the sequencing data of DNAs, and shows the potential ability to detect CNVs. However, the evaluations and performances on the detections of CNVs using WGBS data is still unclear. In this study, five software with different strategies for CNV detections, e.g., BreakDancer, cn.mops, CNVnator, DELLY and Pindel, were selected to explore and benchmark the performances of CNV detections with WGBS data. Based on the real (2.62 billion reads) and simulated (12.35 billion reads) WGBS data of humans, we calculated the number, precision, recall, relative ability, memory usage, and running time of CNV detections by 150 times, and tried to figure out the optimal strategy for CNV detections with WGBS data. Based on the real WGBS data, Pindel detected the most deletions and duplications, CNVnator detected the deletions with the highest precision, cn.mops detected the duplications with the highest precision, Pindel detected the deletions with the highest recall, and cn.mops detected the duplications with the highest recall. Based on the simulated WGBS data, BreakDancer detected the most deletions, and cn.mops detected the most duplications. The CNVnator showed the highest precision and recall for both deletions and duplications. In real and simulated WGBS data, the ability of CNVnator to detect CNVs was likely to overtake that in the whole genome sequencing data. Additionally, DELLY and BreakDancer displayed the lowest peak of memory usage and the lest CPU runtime, while CNVnator expressed the highest peak of memory usage and the most CPU runtime. Taken together, CNVnator and cn.mops showed the excellent performances of CNV detections with WGBS data. These results suggested that it was feasible to detect CNVs using WGBS data, and provided the useful information to further investigate both CNVs and DNA methylation using WGBS data alone.


Subject(s)
DNA Copy Number Variations , Genome, Human , Humans , Whole Genome Sequencing
20.
Ying Yong Sheng Tai Xue Bao ; 34(4): 937-945, 2023 Apr.
Article in English | MEDLINE | ID: mdl-37078311

ABSTRACT

Acid rain is one of most serious environment problems in China. The types of acid rain have gradually transformed from sulfuric acid rain (SAR) to mixed acid rain (MAR) and nitric acid rain (NAR) in recent years. Roots are one source of soil organic carbon and play an important role in the formation of soil aggregates. However, the changes in acid rain type and the effect of root removal on soil organic carbon in forest ecosystems are poorly understood. In this study, we removed roots and simulated acid rain with different types (SO42-:NO3- ratio of 4:1, 1:1, and 1:4) for three years in Cunninghamia lanceolata (CP) and Michelia macclurei (MP) plantations to analyze the changes of soil organic carbon and physical properties and to measure the size and mean weight diameter (MWD) of aggregates. Results showed that root removal in C. lanceolata and M. macclurei remarkably reduced soil organic carbon pool by 16.7 % and 21.5%, and soil recalcitrant carbon by 13.5% and 20.0%, respectively. Root removal substantially decreased the MWD and proportion and organic carbon content of soil macroaggregates in M. macclurei, but not in C. lanceolata. Acid rain did not affect soil organic carbon pool and soil aggregate structures. Our results indicated that roots promote soil organic carbon stabilization and that their contribution to the stability of soil organic carbon varies with forest types. Moreover, soil organic carbon stabilization is not affected by different types of acid rain in the short term.


Subject(s)
Acid Rain , Cunninghamia , Magnoliaceae , Ecosystem , Carbon/analysis , Soil/chemistry , China
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