We describe pLink 2, a search engine with higher speed and reliability for proteome-scale identification of cross-linked peptides. With a two-stage open search strategy facilitated by fragment ...indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, using simulated datasets, synthetic datasets,
N metabolically labeled datasets, and entrapment databases, four analysis methods were designed to evaluate the credibility of ten state-of-the-art search engines. This systematic evaluation shows that pLink 2 outperforms these methods in precision and sensitivity, especially at proteome scales. Lastly, re-analysis of four published proteome-scale cross-linking datasets with pLink 2 required only a fraction of the time used by pLink 1, with up to 27% more cross-linked residue pairs identified. pLink 2 is therefore an efficient and reliable tool for cross-linking mass spectrometry analysis, and the systematic evaluation methods described here will be useful for future software development.
Peroxisomes account for ~35% of total H2O2 generation in mammalian tissues. Peroxisomal ACOX1 (acyl‐CoA oxidase 1) is the first and rate‐limiting enzyme in fatty acid β‐oxidation and a major producer ...of H2O2. ACOX1 dysfunction is linked to peroxisomal disorders and hepatocarcinogenesis. Here, we show that the deacetylase sirtuin 5 (SIRT5) is present in peroxisomes and that ACOX1 is a physiological substrate of SIRT5. Mechanistically, SIRT5‐mediated desuccinylation inhibits ACOX1 activity by suppressing its active dimer formation in both cultured cells and mouse livers. Deletion of SIRT5 increases H2O2 production and oxidative DNA damage, which can be alleviated by ACOX1 knockdown. We show that SIRT5 downregulation is associated with increased succinylation and activity of ACOX1 and oxidative DNA damage response in hepatocellular carcinoma (HCC). Our study reveals a novel role of SIRT5 in inhibiting peroxisome‐induced oxidative stress, in liver protection, and in suppressing HCC development.
Synopsis
This study reveals a role for SIRT5 in regulating peroxisomal H2O2 and ROS homeostasis and indicates its potential function in liver protection and hepatocellular carcinoma suppression.
SIRT5 is localized in peroxisomes where it controls H2O2 metabolism.
SIRT5‐mediated desuccinylation inhibits ACOX1 activity by suppressing its active dimer formation.
SIRT5 downregulation increases ACOX1 activity and oxidative DNA damage response in HCC.
This study reveals a role for SIRT5 in regulating peroxisomal H2O2 and ROS homeostasis and indicates its potential function in liver protection and hepatocellular carcinoma suppression.
Although the substitution of Cu by Ag to suppress CuZn defects offers several advantages in overcoming the large open-circuit voltage (Voc) deficit for Cu2ZnSn(S,Se)4 (CZTSSe) solar cells, an ...excellent performance has not been achieved to date primarily due to the Fermi level pinning at the CdS/absorber interface and large recombination at the absorber/Mo interface. Herein, we developed a composition grading strategy to achieve a V-shaped Ag-graded structure with a higher Ag content on both the back and front surfaces of the (Cu,Ag)2ZnSn(S,Se)4 (CAZTSSe) layer. The key advantages of this Ag-graded structure are as follows: the higher content towards the CdS/absorber interface can create weak n-type donor defects and retard Fermi level pinning, whereas the lower content at the interlayer maintains the conductivity and light absorption; moreover, the other higher content towards Mo back contact can effectively suppress the recombination and improve the utilization of long-wave incident light. By appropriately adjusting the Ag gradient, we demonstrated a significant increase in Voc, and an unexpected conversion efficiency of 11.2% was achieved. This is the highest efficiency achieved to date for Ag-substituted CZTSSe solar cells, and the result supports a new aspect that synthesis of a composition-graded CAZTSSe absorber has great potential for future research.
In some cases of spontaneous miscarriage (SM), the exact etiology cannot be determined. Autophagy, which is responsible for cellular survival under stress conditions, has also been implicated in many ...diseases. Recently, it is also surmised to be correlated with SM. However, the detailed mechanism remains elusive. In fact, there are several essential steps during pregnancy establishment and maintenance: trophoblasts invasion, placentation, decidualization, enrichment and infiltration of decidua immune cells (e.g., natural killer, macrophage and T cells). Accordingly, upstream molecules and downstream effects of autophagy are discussed in these processes, respectively. Of note, autophagy regulates the crosstalk between these cells at the maternal-fetal interface as well. Aberrant autophagy is found in villi, decidual stromal cells, peripheral blood mononuclear cells in SM patients, although the findings are inconsistent among different studies. Furthermore, potential treatments targeting autophagy are included, during which rapamycin and vitamin D are hot-spots in recent literatures. To conclude, a moderately activated autophagy is deeply involved in pregnancy, suggesting that autophagy should be a regulator and promising target for treating SM.
Porous materials have been investigated as efficient photochromic platforms for detecting hazardous radiation, while the utilization of hydrogen bonded organic frameworks (HOFs) in this field has ...remained intact. Herein, two HOFs were synthesized through self‐assembly of tetratopic viologen ligand and formic acid (PFC‐25, PFC‐26), as a new class of “all‐organic” radiochromic smart material, opening a gate for HOFs in this field. PFC‐26 is active upon both X‐ray and UV irradiation, while PFC‐25 is only active upon X‐ray irradiation. The same building block yet different radiochromic behaviors of PFC‐25 and PFC‐26 allow us to gain a deep mechanistic understanding of the factors that control the detection specificity. Theoretical and experimental studies reveal that the degree of π‐conjugation of viologen ligand is highly related to the threshold energy of triggering a charge transfer, therefore being a vital factor for the particularity of radiochromic materials. Thanks to its convenient processibility, nanoparticle size, and UV silence, PFC‐25 can be further fabricated into a portable naked‐eye sensor for X‐ray detection, which shows obvious color change with the merits of high transmittance contrast, good sensitivity (reproducible dose threshold of 3.5 Gy), and excellent stability. The work exhibits the promising practical potentials of HOF materials in photochromic technology.
Hydrogen bonded organic frameworks (HOFs) were explored as radiochromic materials responsive to X‐ray irradiation, opening a new avenue for their application. The HOFs reported here have the same building block yet different radiochromic behaviors: one is sensitive to both X‐ray and UV light, while the other one is specifically responsive to X‐ray light. These phenomena provide a precious chance to understand the vital factors that account for the detection specificity of radiochromic materials.
To determine the change in refractive error and the incidence of myopia among school-aged children in the Yongchuan District of Chongqing City, Western China.
A population-based cross-sectional ...survey was initially conducted in 2006 among 3070 children aged 6 to 15 years. A longitudinal follow-up study was then conducted 5 years later between November 2011 and March 2012. Refractive error was measured under cycloplegia with autorefraction. Age, sex, and baseline refractive error were evaluated as risk factors for progression of refractive error and incidence of myopia.
Longitudinal data were available for 1858 children (60.5%). The cumulative mean change in refractive error was -2.21 (standard deviation SD, 1.87) diopters (D) for the entire study population, with an annual progression of refraction in a myopic direction of -0.43 D. Myopic progression of refractive error was associated with younger age, female sex, and higher myopic or hyperopic refractive error at baseline. The cumulative incidence of myopia, defined as a spherical equivalent refractive error of -0.50 D or more, among initial emmetropes and hyperopes was 54.9% (95% confidence interval CI, 45.2%-63.5%), with an annual incidence of 10.6% (95% CI, 8.7%-13.1%). Myopia was found more likely to happen in female and older children.
In Western China, both myopic progression and incidence of myopia were higher than those of children from most other locations in China and from the European Caucasian population. Compared with a previous study in China, there was a relative increase in annual myopia progression and annual myopia incidence, a finding which is consistent with the increasing trend on prevalence of myopia in China.
Thermal priming of reef corals can enhance their heat tolerance; however, the legacy effects of heat stress during parental brooding on larval resilience remain understudied. This study investigated ...whether preconditioning adult coral Pocillopora damicornis to high temperatures (29°C and 32°C) could better prepare their larvae for heat stress. Results showed that heat‐acclimated adults brooded larvae with reduced symbiont density and shifted thermal performance curves. Reciprocal transplant experiments demonstrated higher bleaching resistance and better photosynthetic and autotrophic performance in heat‐exposed larvae from acclimated adults compared to unacclimated adults. RNA‐seq revealed strong cellular stress responses in larvae from heat‐acclimated adults that could have been effective in rescuing host cells from stress, as evidenced by the widespread upregulation of genes involved in cell cycle and mitosis. For symbionts, a molecular coordination between light harvesting, photoprotection and carbon fixation was detected in larvae from heat‐acclimated adults, which may help optimize photosynthetic activity and yield under high temperature. Furthermore, heat acclimation led to opposing regulations of symbiont catabolic and anabolic pathways and favoured nutrient translocation to the host and thus a functional symbiosis. Notwithstanding, the improved heat tolerance was paralleled by reduced light‐enhanced dark respiration, indicating metabolic depression for energy saving. Our findings suggest that adult heat acclimation can rapidly shift thermal tolerance of brooded coral larvae and provide integrated physiological and molecular evidence for this adaptive plasticity, which could increase climate resilience. However, the metabolic depression may be maladaptive for long‐term organismal performance, highlighting the importance of curbing carbon emissions to better protect corals.
Methyl-CpG binding protein 2 (MeCP2) has crucial roles in transcriptional regulation and microRNA processing. Mutations in the MECP2 gene are found in 90% of patients with Rett syndrome, a severe ...developmental disorder with autistic phenotypes. Duplications of MECP2-containing genomic segments cause the MECP2 duplication syndrome, which shares core symptoms with autism spectrum disorders. Although Mecp2-null mice recapitulate most developmental and behavioural defects seen in patients with Rett syndrome, it has been difficult to identify autism-like behaviours in the mouse model of MeCP2 overexpression. Here we report that lentivirus-based transgenic cynomolgus monkeys (Macaca fascicularis) expressing human MeCP2 in the brain exhibit autism-like behaviours and show germline transmission of the transgene. Expression of the MECP2 transgene was confirmed by western blotting and immunostaining of brain tissues of transgenic monkeys. Genomic integration sites of the transgenes were characterized by a deep-sequencing-based method. As compared to wild-type monkeys, MECP2 transgenic monkeys exhibited a higher frequency of repetitive circular locomotion and increased stress responses, as measured by the threat-related anxiety and defensive test. The transgenic monkeys showed less interaction with wild-type monkeys within the same group, and also a reduced interaction time when paired with other transgenic monkeys in social interaction tests. The cognitive functions of the transgenic monkeys were largely normal in the Wisconsin general test apparatus, although some showed signs of stereotypic cognitive behaviours. Notably, we succeeded in generating five F1 offspring of MECP2 transgenic monkeys by intracytoplasmic sperm injection with sperm from one F0 transgenic monkey, showing germline transmission and Mendelian segregation of several MECP2 transgenes in the F1 progeny. Moreover, F1 transgenic monkeys also showed reduced social interactions when tested in pairs, as compared to wild-type monkeys of similar age. Together, these results indicate the feasibility and reliability of using genetically engineered non-human primates to study brain disorders.
Menopause, a risk factor for brain dysfunction in women, is characterized by neuropsychological symptoms including depression and dementia, which are closely related to alterations in different brain ...regions after menopause. However, little is known about the variability in pathophysiologic changes associated with menopause in the brain. Here, we observed that menopause in rats induced by bilateral ovariectomy (OVX) showed depressive and dementia‐related behaviors along with neuronal loss in the prefrontal cortex (PFC), hippocampus (HIP), hypothalamus (HYP), and amygdala (AMY) by Nissl staining. Meanwhile, by immunohistochemical staining, increased microglia in the HIP and AMY and increased astrocytes in the PFC, HYP, and AMY were shown. Using quantitative proteomics, we identified 146 differentially expressed proteins in the brains of OVX rats, for example, 20 in the PFC, 41 in the HIP, 17 in the HYP, and 79 in the AMY, and performed further detection by western blotting. A link between neuronal loss and apoptosis was suggested, as evidenced by increases in adenylate kinase 2 (AK2), B‐cell lymphoma 2 associated X (Bax), cleaved caspase 3, and phosphorylated p53 and decreases in Huntingtin‐interacting protein K, hexokinase, and phosphorylated B‐cell lymphoma 2 (Bcl‐2), and apoptosis might be triggered by endoplasmic reticulum stress (probed by increased glucose‐regulated protein 78 (GRP78), cleaved caspase 12, phosphorylated protein kinase R (PKR)‐like endoplasmic reticulum kinase, inositol‐requiring enzyme‐1 and activating transcription factor 6), and mitochondrial dysfunction (probed by increased cytochrome c and cleaved caspase 3 and decreased sideroflexin‐1 (SFXN1) and NADH dehydrogenase (ubiquinone) 1 α subcomplex 11 (NDUFA11)). Activation of autophagy was also indicated by increased autophagy‐related 7, γ‐aminobutyric acid (GABA) receptor‐associated protein‐like 2, and oxysterol‐binding protein‐related protein 1 and confirmed by increased microtubule‐associated protein light chain 3 (LC3II/I), autophagy‐related 5, and Beclin1 in the HIP and AMY. In the AMY, which is important in emotion, higher GABA transporter 3 and lower vesicular glutamate transporter 1 levels indicated an imbalance between excitatory and inhibitory neurotransmission, and the increased calretinin and decreased calbindin levels suggested an adjustment of GABAergic transmission after OVX. In addition, cytoskeletal abnormalities including tau hyperphosphorylation, dysregulated Ca²+ signals, and glutamic synaptic impairments were observed in the brains of OVX rats. Collectively, our study showed the changes in different brain regions related to depression and dementia during menopause.
The variability in pathophysiologic changes in different brain regions, for example, the prefrontal cortex (PFC), hippocampus (HIP), hypothalamus (HYP), and amygdala (AMY), of rats after menopause were studied. Rats with bilateral ovariectomy (OVX) showed dementia and depression with neuronal loss in PFC/HIP/HYP/AMY, increased astrocytes in PFC/HYP/AMY, and increased microglia in HIP/AMY. Endoplasmic reticulum (ER) stress, autophagy dysregulation, mitochondrial dysfunction, and Ca2+ signal dysregulation were involved in apoptosis, cytoskeletal abnormalities, and synaptic impairments in the brains of OVX rats. Furthermore, myelin injury in HIP/HYP/AMY, neurodegeneration with cytoskeletal abnormalities and synaptic impairments in HIP/HYP/AMY, and excitatory/inhibitory dysregulation in AMY were also found.
•B. amyloliquefaciens B4 inhibited eight of the fungal pathogens isolated from loquat fruits.•B4 suspension was more effective than its supernatant against fungi in postharvest fruit.•Oral toxicity ...test in mice suggested that B. amyloliquefaciens B4 was actually non-toxic.•Treatment with B4 obviously reduced decay incidence of loquat fruit during natural storage.
Loquat fruit is a subtropical fruit with high commercial values in the international market, but it actually has a short postharvest life due to mechanical damage and microbial decay. Until now, there exist few appropriate storage methods or biocontrol agents to control postharvest diseases and prolong storage period of postharvest loquat fruit. Recently, by comparing twelve Bacillus strains with biocontrol activity, a potential Bacillus amyloliquefaciens B4 was found to be effective in controlling various pathogens of loquat fruit. The in vivo results displayed that the active constituent in B4 exerting antifungal activity was bacterium itself, rather than metabolites. Scanning electron microscope was applied to observe the interaction between B4 and pathogens, and bacterial colonization and site occupancy on postharvest loquat fruit appeared to be one of the reasons why B4 could inhibit growth of fungal pathogens. In brief, Bacillus amyloliquefaciens B4 tends to be the most broad-spectrum antifungal biological agent available so far against postharvest pathogens of loquat fruit. Furthermore, oral toxicity test results suggested Bacillus B4 is actually non-toxic, making it a really suitable biocontrol agent for postharvest loquat fruit. The treatment for loquat fruit with B4 resulted in a lower disease incidence, with only 62.5 % compared to all decayed in the untreated group 20 d after inoculation at 25 ℃. This study provides a promising biological agent to control diseases of postharvest loquat fruit and improves our understanding of the possible biocontrol mechanisms of the Bacillus strain.
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