PNBACE: an ensemble algorithm to predict the effects of mutations on protein-nucleic acid binding affinity.

BACKGROUND: Mutations occurring in nucleic acids or proteins may affect the binding affinities of protein-nucleic acid interactions. Although many efforts have been devoted to the impact of protein mutations, few computational studies have addressed the effect of nucleic acid mutations and explored whether the identical methodology could be applied to the prediction of binding affinity changes caused by these two mutation types. RESULTS: Here, we developed a generalized algorithm named PNBACE for both DNA and protein mutations. We first demonstrated that DNA mutations could induce varying degrees of changes in binding affinity from multiple perspectives. We then designed a group of energy-based topological features based on different energy networks, which were combined with our previous partition-based energy features to construct individual prediction models through feature selections. Furthermore, we created an ensemble model by integrating the outputs of individual models using a differential evolution algorithm. In addition to predicting the impact of single-point mutations, PNBACE could predict the influence of multiple-point mutations and identify mutations significantly reducing binding affinities. Extensive comparisons indicated that PNBACE largely performed better than existing methods on both regression and classification tasks. CONCLUSIONS: PNBACE is an effective method for estimating the binding affinity changes of protein-nucleic acid complexes induced by DNA or protein mutations, therefore improving our understanding of the interactions between proteins and DNA/RNA.

Thiacalix[4]arene-Stabilized Sb/Ag Bimetallic Nanoclusters: Elucidating the Effects of Sb Doping on Electrocatalytic CO2 Reduction in Ag Clusters.

Accurately identifying the metal doping effects within heterogeneous catalysts presents a formidable challenge due to the complex nature of controlling the interfacial chemistry at the molecular level. Herein, we use two sets of atomically precise nanoclusters to demonstrate the impact of Sb doping on the electrocatalytic CO2 reduction activity in Ag nanoclusters. Leveraging the unique properties of the thiacalix[4]arene, we have pioneered a methodology for incorporating catalytic Ag1+ and Sb3+ sites, culminating in the synthesis of the pioneering Sb-Ag bimetallic cluster, Sb2Ag11. We refined this structure by replacing the two Sb3+ sites with Na+ sites, resulting in a Na2Ag10 cluster. Broadening our investigative scope, we isolated the core components from both Sb2Ag11 and Na2Ag10 and obtained two clusters: Sb2Ag4 and Ag4. The subtle compositional variations between two pairs of structurally analogous clusters, Sb2Ag11 and Na2Ag10, as well as Sb2Ag4 and Ag4, create opportunities to investigate how the Sb doping impacts the catalytic activity of Ag clusters. Clearly, compared to the undoped clusters, those doped with Sb exhibit higher catalytic current densities and enhanced CO selectivity. The theoretical calculations suggest that Sb doping can enhance the adsorption barrier of *H, thereby inhibiting hydrogen evolution activity and conversely promoting eCO2RR to CO activity.

In Situ Oxidative Ring-Opening of Calix[8]arene to Construct Stable Bismuth-Oxo Clusters with Exposed Catalytic Sites for Specific Electroreduction of CO2 to HCOOH.

Nanocluster catalysts typically face challenges in balancing stability with catalytic efficiency. This study introduces a unique bismuth-oxo cluster, solely protected by two ring-opened calixarenes, which demonstrates not only enhanced structural stability but also superior catalytic performance in the sustained conversion of CO2 to HCOOH via electrocatalysis. For the first time, we reveal that under specific solvothermal conditions, tert-butylcalix[8]arene (TBC[8]) can undergo in situ oxidative cleavage of its C-C bond, leading to ring-opened polyphenolic molecules. These molecules serve as protective ligands for the bismuth-oxo cluster, bestowing exceptional structural stability and offering a more flexible and diverse configuration compared to intact TBC[8]. This adaptability promotes the exposure of active bismuth sites on the cluster surface, enhancing catalytic efficiency. Notably, the Bi10 cluster, featuring a monobismuth active site, achieves an exceptional formate production efficiency of 98.79% at -1.25 V vs RHE while maintaining superb durability over 8 h. The stability and catalytic processes of Bi10 surpass those of the Bi13 cluster, which is structurally reinforced by two intact TBC[8] molecules and stabilized by four benzoic ligands. Through in situ infrared spectroscopy and density functional theory calculations, we demonstrate that the monobismuth active site in Bi10 more effectively stabilizes the *OCHO intermediate, thereby promoting the electrocatalytic reduction of CO2 to HCOOH compared to Bi13. This comparative performance underscores the potential of ring-opened calixarene ligands in enhancing the functionality of nanocluster catalysts.

Evidence for the existence of CD34+ angiogenic stem cells in human first-trimester decidua and their therapeutic for ischaemic heart disease.

Stem cell transplantation is nearly available for clinical application in the treatment of ischaemic heart disease (IHD), where it may be joined traditional methods (intervention and surgery). The angiogenic ability of seed cells is essential for this applicability. The aim of this study was to reveal the presence of CD34+ angiogenic stem cells in human decidua at the first trimester and to use their strong angiogenic capacity in the treatment of IHD. In vitro, human decidual CD34+ (dCD34+ ) cells from the first trimester have strong proliferation and clonality abilities. After ruling out the possibility that they were vascular endothelial cells and mesenchymal stem cells (MSCs), dCD34+ cells were found to be able to form tube structures after differentiation. Their angiogenic capacity was obviously superior to that of bone marrow mesenchymal stem cells (BMSCs). At the same time, these cells had immunogenicity similar to that of BMSCs. Following induction of myocardial infarction (MI) in adult rats, infarct size decreased and cardiac function was significantly enhanced after dCD34+ cell transplantation. The survival rate of cells increased, and more neovasculature was found following dCD34+ cell transplantation. Therefore, this study confirms the existence of CD34+ stem cells with strong angiogenic ability in human decidua from the first trimester, which can provide a new option for cell-based therapies for ischaemic diseases, especially IHD.

Sirtuin3 protects aged human mesenchymal stem cells against oxidative stress and enhances efficacy of cell therapy for ischaemic heart diseases.

Sirtuin3 (SIRT3) is associated with oxidative stress and lifespan. However, the possible mechanisms underlying its influence are unknown. We hypothesized that SIRT3 increases the antioxidant capacity of aged cells and improves the efficacy of human mesenchymal stem cell (hMSC) therapy for ischaemic heart diseases in aged patients. In vitro, the antioxidant capacity of old hMSCs (O-hMSCs) was increased after SIRT3 overexpression using a gene transfection technique, while the antioxidant capacity of young hMSCs (Y-hMSCs) was decreased by SIRT3 silencing. The levels of forkhead box O3a (FoxO3a) in the nucleus, and antioxidant enzymes Mn-superoxide dismutase (MnSOD) and catalase (CAT) increased in SIRT3-overexpressed O-hMSCs while they decreased in SIRT3-silenced Y-hMSCs after oxidative stress. Following myocardial infarction in adult rats in vivo, infarct size decreased and cardiac function was significantly enhanced after cell transplantation with SIRT3 overexpressed O-hMSCs. The number of apoptotic cells decreased and the survival rate of transplanted cells increased following SIRT3 overexpression in O-hMSCs. SIRT3 protects aged hMSCs against oxidative stress by positively regulating antioxidant enzymes (MnSOD and CAT) via increasing the expression of FoxO3a in the nucleus. The efficacy of aged hMSC transplantation therapy for ischaemic heart diseases can be improved by SIRT3 overexpression.

Identification and characterization of two novel C-type lectins from the larvae of housefly, Musca domestica L.

Lectins and antimicrobial peptides (AMPs) are widely distributed in various insects and play crucial roles in primary host defense against pathogenic microorganisms. Two AMPs (cecropin and attacin) have been identified and characterized in the larvae of housefly. In this study, two novel C-type lectins (CTLs) were obtained from Musca domestica, while their agglutinating and antiviral properties were evaluated. Real-time PCR analysis showed that the mRNA levels of four immune genes (MdCTL1, MdCTL2, Cecropin, and Attacin) from M. domestica were significantly upregulated after injection with killed Gram-negative Escherichia coli. Moreover, purified MdCTL1-2 proteins can agglutinate E. coli and Staphylococcus aureus in the presence of calcium ions, suggesting their immune function is Ca2+ dependent. Sequence analysis indicated that typical WND and QPD motifs were found in the Ca2+ -binding site 2 of carbohydrate recognition domain from MdCTL1-2, which was consistent with their agglutinating activities. Subsequently, antiviral experiments indicated that MdCTL1-2 proteins could significantly reduce the infection rate of Spodoptera frugiperda 9 cells by the baculovirus Autographa californica multicapsid nucleopolyhedrovirus, indicating they might play important roles in insect innate immunity against microbial pathogens. In addition, MdCTL1-2 proteins could effectively inhibit the replication of influenza H1 N1 virus, which was similar to the effect of ribavirin. These results suggested that two novel CTLs could be considered a promising drug candidate for the treatment of influenza. Moreover, it is believed that the discovery of the CTLs with antiviral effects in M. domestica will improve our understanding of the molecular mechanism of insect immune response against viruses.

MOLECULAR CHARACTERIZATION OF AUTOPHAGY-RELATED GENE 5 FROM Spodoptera exigua AND EXPRESSION ANALYSIS UNDER VARIOUS STRESS CONDITIONS.

Autophagy is not only involved in development, but also has been proved to attend immune response against invading pathogens. Autophagy protein 5 (ATG5) is an important autophagic protein, which plays a crucial role in autophagosome elongation. Although ATG5 has been well studied in mammal, yeast, and Drosophila, little is known about ATG5 in lepidopteran insects. We cloned putative SeAtg5 gene from Spodoptera exigua larvae by the rapid amplification of cDNA ends method, and its characteristics and the influences of multiple exogenous factors on its expression levels were then investigated. The results showed that the putative S. exigua SeATG5 protein is highly homologous to other insect ATG5 proteins, which has a conserved Pfm domain and multiple phosphorylation sites. Next, fluorescence microscope observation showed that mCherry-SeATG5 was distributed in both nucleus and cytoplasm of Spodoptera litura Sl-HP cells and partially co-localized with BmATG6-GFP, but it almost has no significant co-localization with GFP-HaATG8. Then, the Western blot analysis demonstrated that GFP-SeATG5 conjugated with ATG12. Moreover, real-time PCR revealed that its expression levels significantly increased at the initiation of pupation and the stage of adult. In addition, the expression levels of SeAtg5 can be enhanced by the starvation, UV radiation, and infection of baculovirus and bacterium. However, the expression levels of SeAtg5 decreased at 24 h post treatments in all these treatments except in starvation. These results suggested that SeATG5 might be involved in response of S. exigua under various stress conditions.

Decreased SIRT3 in aged human mesenchymal stromal/stem cells increases cellular susceptibility to oxidative stress.

Sirtuin3 (SIRT3) is an important member of the sirtuin family of protein deacetylases that is localized to mitochondria and linked to lifespan extension in organisms ranging from yeast to humans. As aged cells have less regenerative capacity and are more susceptible to oxidative stress, we investigated the effect of ageing on SIRT3 levels and its correlation with antioxidant enzyme activities. Here, we show that severe oxidative stress reduces SIRT3 levels in young human mesenchymal stromal/stem cells (hMSCs). Overexpression of SIRT3 improved hMSCs resistance to the detrimental effects of oxidative stress. By activating manganese superoxide dismutase (MnSOD) and catalase (CAT), SIRT3 protects hMSCs from apoptosis under stress. SIRT3 expression, levels of MnSOD and CAT, as well as cell survival showed little difference in old versus young hMSCs under normal growth conditions, whereas older cells had a significantly reduced capacity to withstand oxidative stress compared to their younger counterparts. Expression of the short 28 kD SIRT3 isoform was higher, while the long 44 kD isoform expression was lower in young myocardial tissues compared with older ones. These results suggest that the active short isoform of SIRT3 protects hMSCs from oxidative injury by increasing the expression and activity of antioxidant enzymes. The expression of this short isoform decreases in cardiac tissue during ageing, leading to a reduced capacity for the heart to withstand oxidative stress.

Al12Co4: a pioneering heterometallic aluminum oxo cluster with surface-exposed Co sites for the oxygen evolution reaction.

We report an unprecedented heterometallic aluminum oxo cluster (AlOC) containing four surface-exposed CoII sites, designated as Al12Co4, protected by four t-butylcalix[4]arene (TBC[4]) molecules. The Al12Co4 nanocluster represents a significant advancement on multiple innovative fronts. First, it stands as an pioneering example of an AlIII-based metallocalixarene nanocluster. It is also the first instance of heterometallic AlOCs shielded by macrocyclic ligands. Notably, this cluster also holds the distinction of being the highest nuclearity Al-Co bimetallic nanocluster known to date. Additionally, by depositing Al12Co4 on carbon nanotubes (CNTs) as a supported catalyst, we investigated its electrocatalytic performance for the oxygen evolution reaction in alkaline media. To reach a 10 mA cm-2 current density in alkaline solution, the Al12Co4@CNT electrode needs overpotential as low as 320 mV.

Sirtuin 3 Ameliorates Lung Senescence and Improves Type II Alveolar Epithelial Cell Function by Enhancing the FoxO3a-Dependent Antioxidant Defense Mechanism.

Lung aging alters the intrinsic structure of the lung and pulmonary surfactant system and increases the mortality and morbidity due to respiratory diseases in elderly individuals. We hypothesized that lung aging results from an insufficiency of type II alveolar epithelial cells (AECIIs) in the lung tissue. Sirtuin 3 (SIRT3) is a member of the sirtuin family of proteins that promote longevity in many organisms. Increased SIRT3 expression has been linked to an extended life span in humans. Hence, we speculated that the overexpression of SIRT3 may help to ameliorate lung senescence and improve AECII function. AECIIs were isolated from young and old patients with pneumothorax caused by pulmonary bullae. The expression of SIRT3, manganese superoxide dismutase, and catalase, as well as cell function and senescence indicators of young and old AECIIs, was measured before and after SIRT3 overexpression. After SIRT3 overexpression, the aged state of old AECIIs improved, and antiapoptotic activity, proliferation, and secretion were dramatically enhanced. Surfactant protein C (SPC), which is secreted by AECIIs, reduces alveolar surface tension, repairs the alveolar structure, and regulates inflammation. SPC deficiency in patients is associated with increased inflammation and delayed repair. SIRT3 deacetylated forkhead box O3a, thereby protecting mitochondria from oxidative stress and improving cell function and the senescent state of old AECIIs. These findings provide a possible direction for aging-delaying therapies and interventions for diseases of the respiratory system.

Simultaneous characterization of the shape and refractive index of transparent living cells by an optical aperture.

We report a method of using optical aperture diffraction to simultaneously detect the image and the refractive index of a living cell. By simulation, it is found that, when a suitable gap is introduced between the cell and the aperture, the image of the cell on the detection plane can be amplified hundreds to thousands of times, and a limit of detection of 3e-4 to 9e-5 can be reached for the refractive index of the cell. Experiments show that this method is feasible to realize, but the achievement of such a detection system is yet to be proved.

A de novo DDX3X Variant Is Associated With Syndromic Intellectual Disability: Case Report and Literature Review.

De novo DDX3X variants account for 1%-3% of intellectual disability (ID) in females and have been occasionally reported in males. Here, we report a female patient with severe ID and various other features, including epilepsy, movement disorders, behavior problems, sleep disturbance, precocious puberty, dysmorphic features, and hippocampus atrophy. With the use of family-based exome sequencing, we identified a de novo pathogenic variant (c.1745dupG/p.S583*) in the DDX3X gene. However, our patient did not present hypotonia, which is considered a frequent clinical manifestation associated with DDX3X variants. While hand stereotypies and sleep disturbance have been occasionally associated with the DDX3X spectrum, hippocampus atrophy has not been reported in patients with DDX3X-related ID. The investigation further expands the phenotype spectrum for DDX3X variants with syndromic intellectual disability, which might help to improve the understanding of DDX3X-related intellectual disability or developmental delay.

SIRT3 Transfection of Aged Human Bone Marrow-Derived Mesenchymal Stem Cells Improves Cell Therapy-Mediated Myocardial Repair.

Sirtuin 3 (SIRT3) is a deacetylase important for antioxidant protection, cell longevity, and aging. We hypothesized that SIRT3 improve oxidative resistance of aged cells and improve cell therapy in aged patients. In vitro, the proliferation and oxidative resistance of human mesenchymal stem cells (hMSCs) significantly declined with age. The expression and activity of antioxidant enzymes, including catalase (CAT) and manganese superoxide dismutase (MnSOD), increased after transfection of SIRT3 in hMSCs from older donors (O-hMSCs). The protein level of Forkhead box O3a (FOXO3a) in nucleus increased after SIRT3 overexpression. The antioxidant capacity of O-hMSCs increased after SIRT3 overexpression. 3-Amino-1,2,4-triazole (3-AT, CAT inhibitor) or diethyldithiocarbamate (DETC, SOD inhibitor) that was used to inhibit CAT or SOD activity significantly blocked the antioxidant function of SIRT3. When two inhibitors were used together, the antioxidant function of SIRT3 almost disappeared. Following myocardial infarction and intramyocardial injections of O-hMSCs in rats in vivo, the survival rate of O-hMSCs increased by SIRT3 transfection. The cardiac function of rats was improved after SIRT3-overexpressed O-hMSC transplantation. The infarct size, collagen content, and expression levels of matrix metalloproteinase 2 (MMP2) and MMP9 decreased. Besides, the protein level of vascular endothelial growth factor A and vascular density increased after cell transplantation with SIRT3-modified O-hMSCs. These results indicate that damage resistance of hMSCs decline with age and SIRT3 might protect O-hMSCs against oxidative damage by activating CAT and MnSOD through transferring FOXO3a into nucleus. Meanwhile, the therapeutic effect of aged hMSC transplantation can be improved by SIRT3 overexpression.

Algorithm and simulation for analysis of bio-images obtained by aperture diffraction based optical MEMS.

This paper proposes a novel method to detect transparent living cells in a transparent microfluidic chamber by optical diffraction of an aperture or an aperture array. Through the analysis of the far-field diffraction pattern, one of the parameters of the cells, including the size, refractive index, or position, can be extracted by the analysis software developed in this paper. Calculations are carried out to discuss the key issues of this MEMS device, and our simulation is verified by diffraction patterns of transparent microparticles on fabricated apertures, recorded via a digital camera.

Fabrication of gold nanocrescents by angle deposition with nanosphere lithography for localized surface plasmon resonance applications.

The gold nanostructures fabricated on a substrate yield localized surface plasmon resonance. We describe the fabrication and characterization of nanocrescents on a silicon substrate, which are fabricated by depositing a gold film at an oblique angle through nanosphere lithography. Following the etching of the gold perpendicular to the substrate and the removal of the nanospheres by dissolution, nanocrescents with fine nanostructures are generated. By varying the deposition angle of the gold film from 0 degrees to 72 degrees , nanorings, 2D and 3D nanocrescents can be obtained. During the nanocrescent fabrication, we also compared the deposition angle difference between the e-beam and thermal evaporators for oblique depositions of the gold. The 3D nanocrescents fabricated in our experiments are expected to have improved sensitivity in localized surface plasmon resonance measurements when compared to the previously reported 2D nanocrescents, which enable broader biosensor applications. Simulations of the profiles of these 3D nanocrescents using solid geometry show good consistency with the fabricated ones.

[A comparison between the effects on DNA-protein cross-links of Saccharomyces and E. coli induced by formaldehyde].

To explore the effect of formaldehyde on DNA-protein cross-links (DPC) in eucaryotic cells and prokaryotic cells, Pichia pastoris and E. coli DH5alpha were chosen as materials to evaluate the amount of DPC induced by liquid formaldehyde in vivo by the method of KCl-SDS assay. The results showed that formaldehyde could not induce DPC at low dose(25micromol/L,P > 0.05), but could obviously induce DPC at higher dose (125 and 625micromol/L, P < 0.05). The DPC coefficient in Pichia pastoris was 10-fold higher than that in E. coli DH5alpha. It is concluded that formaldehyde could induce DPC in eucaryotic cells and prokaryotic cells with a dose-dependent manner and the DPC coefficient in Pichia pastoris is higher than that in E. coli DH5alpha.

Genome-wide dissection of heterosis for yield traits in two-line hybrid rice populations.

Heterosis has been widely utilized in agriculture and is important for world food safety. Many genetic models have been proposed as mechanisms underlying heterosis during the past century, yet more evidence is needed to support such models. To investigate heterosis in two-line hybrid rice, we generated a partial diallel crossing scheme, which consisted of approximately 500 F1 hybrids derived from 14 male sterile lines and 39 restorer lines. In this population, increased panicle number played the most important role in yield heterosis of hybrid rice. Genome-wide association studies identified many QTLs related to the yield traits of F1 hybrids, better paternal heterosis and special combining ability. Relevant genes, including Hd3a, qGL3, OsmiR156h, and LAX2, were identified as candidates within these QTLs. Nearly forty percent of the QTLs had only two genotypes in the F1 hybrids, mainly because the maternal lines were under intense selective pressure. Further analysis found male sterile lines and restorer lines made different superior allele contributions to F1 hybrids, and their contributions varied among different traits. These results extend our understanding of the molecular basis of heterosis in two-line hybrid rice.

Suppression of miR-34a Expression in the Myocardium Protects Against Ischemia-Reperfusion Injury Through SIRT1 Protective Pathway.

MicroRNA-34a (miR-34a) is expressed in the myocardium and expression is altered after myocardial injury. We investigated the effects of miR-34a on heart function after ischemia-reperfusion (IR) injury. Cardiomyocytes were isolated from neonatal rat hearts and simulated IR injury was induced in vitro. Following IR injury in rats, infarct size was measured and left ventricular (LV) function was evaluated using echocardiography. Protein expression of silent information regulator 1 (SIRT1), acetylated p53 (ac-p53), Bcl-2 and Bax, and miR-34a and SIRT1 gene levels were analyzed. miR-34a overexpression exacerbated myocardial injury by increasing apoptosis and infarct size and decreasing LV function. Suppression of miR-34a attenuated myocardial IR injury. SIRT1 was negatively regulated by miR-34a and the expression of downstream genes, such as ac-p53, Bcl-2, and Bax were altered correspondingly. Increased expression of miR-34a aggravates injury after IR; miR-34a suppression therapy may represent a new line of treatment for myocardial IR injury.

[Diversity and function of symbiotic microbes in the gut of lower termites].

The gut of lower termites harbor a complex microbial community, including eukaryotic flagellates and prokaryotic bacteria and archaea, which play important roles in the wood-cellulose digestion of these termites. The hindguts of lower termites are characterized with an enlarged paunch with steep oxygen and hydrogen gradient and not randomly distributed abundant microorganisms. The symbiotic flagellates in the gut of lower termites, which are normally associated with epibionts or endobionts, are phylogenetically affiliated with Trichomonadida, Hypermastigida and Oxymonadida. They endocytose wood particles and ferment the polysaccharide components to acetate, CO2 and H2, which are further metabolized by symbiotic prokaryotes as energy and nutrition sources in the termites. Cellulose genes such as glycosyl hydrolase family 45 have been identified in gut protists with molecular approach. Phylogenetic analysis have revealed that in the gut of lower termites, such as several Reticulitermites species, most of the dominant bacteria belong to phyla like "Termite group 1", Spirochaetes, Firmicutes, Bacteroidetes, and Proteobacteria. These bacteria clones normally form distinct termite clusters in phylogenetic trees, which show the existence of specific microbial diversity in the termite guts. Most of the symbiotic archaea in the gut of lower termites are methanogens and affiliated with the genus Methanobrevibacter by phylogenetic analysis and pure culture. The symbiotic bacteria and archaea may involve in the reduction of CO2 and the metabolism of N2 in these termite guts. However, the functions and metabolic mechanisms of the symbiotic flagellates and prokaryotes in the gut of lower termites are still remaining to be further elucidated.

Inhibitory effect of arsenic trioxide on neuronal migration in vitro and its potential molecular mechanism.

Primary neuron cultures were established from the brains of neonatal rats and the effects of arsenic trioxide (As2O3) on the migration of neurons and the potential mechanism of As2O3 were investigated. Boyden chamber assay was used to detect the effect of AS2O3 on neuronal migration. Matrix metalloproteinase-2 (MMP-2) and MMP-9 RNA expression and doublecortin (DCX) protein expression were measured. Neuronal migration ability was significantly lower in the 20 µmol/L group compared with the other three groups (all p < 0.001). The expression of both MMP-2 and MMP-9 was significantly inversely correlated with As2O3 concentration. The expression of DCX was significantly higher in the control group compared with the other three groups (all p ≤ 0.003). Thus, the inhibitory effect of As2O3 on the migration of primary neurons might be related to the reduction in MMP-2 and MMP-9 activities and decrease in ß-actin and DCX expression.