Abstract:贝时璋是著名实验生物学家，细胞生物学家，教育家， 我国细胞学、胚胎学创始人之一， 我国生物物理学奠基人，中国科学院生物物理研究所和中国科学技术大学生物物理系的创始人。 他是1948年第一届中央研究院院士、1955 年首批中国科学院学部委员（1993 年改称中国科学院院士），自1928年获得德国图宾根大学博士学位证书后，相继于1978 年（毕业50 周年）、 1988 年（毕业60 周年）、2003 年（毕业75 周年）和2008 年（毕业80 周年）被德国图宾根大学授予“金博士”、“钻石博士” 等博士学位荣誉证书，被德国政府授予“惟一学术公民” 称号。 为了纪念他对生命科学和航天事业的卓越贡献，太空中有一颗以他名字命名的小行星(36015 号)。
贝时璋出生于1903 年10 月10 日，他的一生与中国科学紧密联结在一起，见证并参与了新中国科学事业的发展与繁荣，为国家培养了一代代科技人才。 进入百岁高龄之后，他仍坚持工作，也依然时刻牵挂着国家的昌盛和科学的发展，是永不退休的科学家。 2003 年9 月，贝时璋用两年半时间主编完成的《细胞重建》论文集第二集正式出版，给了自己一份最好的百岁生日礼物。
2009 年诺贝尔奖公布以后，贝时璋心情很不平静，对我国科学创新问题陷入了深刻的思考之中。他想起，北京大学教授林克椿1981 年在美国斯坦福大学做访问学者时，发现了螺旋状脂质体，1982 年《自然》（Nature）杂志以封面文章的形式发表了这一成果。 他认为这是一项很有意义的创新课题，应该继续研究下去，因此特别邀请林克椿和一些研究人员10 月28 日上午来家里进行讨论。 当天，贝时璋问了林克椿很多关于实验情况的问题，问得很仔细。从贝时璋的询问中，可以感受到他心中对一项有意义工作被中断的那份惋惜。 林克椿虽然已退休，但贝时璋还是鼓励他要把这项研究进一步做下去，争取取得更大的成果，并语重心长地鼓励大家“我们要为国家争气”， 这句话，他说了好几遍，声音很大、很激动， 使当时在场的研究人员们深受感动和鼓舞。
那天，贝时璋精神特别好，特别高兴，和大家讨论了近一个小时。 然而，就在第二天，10 月29日上午9 点30 分，贝时璋在睡眠中安详辞世，永 远地离开了他所热爱的科学、他所热爱的国家和人民。 “我们要为国家争气” ， 成为了贝时璋留给科学界的最后嘱托和遗言，这也应当成为当今每一位科研工作者追求和践行的科学家精神。

Abstract:In previous understanding, microorganism was considered to be separated and living independently in the environment. However, recent studies have demonstrated that microorganism was capable of communicating intraspecific, interspecific, or even with other organisms in multiple ways. These communications are performed by specific signaling molecules, which we called microbial language. By using these microbial languages, microorganism in a specific ecological niche builds variety of interactions with their neighboring individuals or populations, such as cooperation, competition, and resource sharing, or even react to complex outer environment by coordinating group behaviors. With the profound modern molecular biology study of natural microbial community, researchers gradually accessed a clear and comprehensive understanding to microbial communication. In this review, we tried to summarize the signal substances (such as quorum sensing, quorum quenching, antibiotics, etc.) and communication methods used by both prokaryotic and eukaryotic microorganisms, and discussed the impact of these communication languages ??on the interaction in intraspecies (same microorganisms), interspecies (different microorganisms), and interkingdom communication (microorganisms and hosts). This review is aiming to interpret this interesting cross discipline deeply, to understand the form, mechanism and purpose of microbial communication language better, and to obtain a new approach for the interpretation of microbial behavior and the analysis of ecological events based on chemical ecology.

Abstract:Due to a highly developed echolocation system, bats can accurately process and integrate acoustic parameters of fluctuating environments to maintain optimum physiological and behavioral status. The neurophysiological mechanisms of this behavior have been extensively studied and it’s time to review the progress of this research. This review is mainly about the neural mechanism underlying in species-specific signal recognition, co-varying parameters processing, Doppler-shift compensation and multi-harmonic signals processing which is related to echolocation. It will not only help us understand the strategy of how the bat auditory system processes behavior-related acoustic signals, but also to raise some issues that remained unresolved, which need further intracellular studies in CF-FM bats as a model in the future.

Abstract:Eye gaze, as a type of unique nonverbal social cues, can trigger a reflexive attentional orienting effect that is crucial for human adaptive social behaviors. Adopting the central cueing paradigm and its variants, recent studies have been increasingly focused on the modulation of social information conveyed by faces, especially facial expressions, on this attentional effect. Specifically, facial expressions communicate other individuals’ internal affective states. When combined with gaze direction, they could reliably indicate others’ affective evaluation regarding the nature of the relevant object of interest and therefore modulate the gaze-triggered attentional effect. Such emotional modulation varies for different types of emotions and is more salient for fear and anger. Additionally, it would be further influenced by task-relevant (i.e., task dynamics, target valence) and individual factors (i.e., anxiety, fearfulness, autistic quotient, and social cognitive disorders). This modulation effect emerges from infancy and matures with age. It occurred rapidly and is associated with the two different attentional components (i.e., the early orienting and the later disengagement). Both the separate and integral neural processing of facial expressions and gaze directions, involving the brain regions of the amygdala and the posterior superior temporal sulcus, were implicated in this modulation. Apart from facial expressions, other types of social information contained in faces (e.g., trustworthiness, familiarity, facial dominance, social status, and groups) could also modulate the gaze-triggered orienting, which potentially engages the frontal eye field and the frontoparietal attention network. A systematic review of the behavioral evidence of the modulation and its neural mechanisms has significant theoretical and clinical implications. On the one hand, it will deepen our understandings of the relationship between face processing and gaze-triggered orienting. On the other hand, it may also contribute to the diagnosis and intervention of social cognitive disorders.

Abstract:Camel nanobody has a wide range of application prospects due to its simple structure, easy modification, and the characteristics of low immunogenicity, high stability, high specificity as well as high affinity. It is reported that nanobody with high stability could be stored and transported in more easily way compared with conventional antibodies. It can evenly refold and recover its antigen binding affinity after being denatured under polar conditions such as high temperature, high concentration organic solvents, high pressure, chemical reagents, extreme acid-base environments, and proteases. This review summarized the stability characterization of nanobody under these conditions. It is shown that nanobody can not only expand its application in the detection of targets under complex polar conditions but also enrich multiple routes of drug delivery in medical therapy, including intravenous and subcutaneous injection, nasal inhalation, and oral administration. Emphasis was made on describing the relationship between amino acid sequence, number and position of disulfide bonds, structural domains, and stability, which revealed that highly stable nanobody have common structural features such as higher net charge surfaces, disulfide bonds that limit conformational migration, framework regions with more hydrophilic amino acid substitutions, conserved hydrophobic pockets, and highly interacting structural domains. Based on these structural features, several strategies for stability structure optimization of nanobody were also discussed in this paper, including shared sequence-driven sequence repair, the substitution of easily modified amino acids, alteration of net protein charge, the introduction of unnatural disulfide bonds, and transposition of CDRs. It is expected to provide theoretical guidance on the stability regulation of nanobody to expand their wide applications as therapeutic drugs, diagnostic reagents, and biosensors.

Abstract:Small interfering RNA (siRNA) is the initiator of RNA interference, which stimulates the silencing of complementary target mRNA. It is of great significance for gene regulation and disease treatment. It is used in viral infections, cancers, family genetic diseases and autoimmune diseases. As a new type of drug, siRNA is gradually being valued by researchers due to its high efficiency, strong specificity, and easy detection of therapeutic effects. siRNA used as a drug alone or co-delivered with anti-tumor drugs such as chemotherapy for cancer treatment shows greater application potential than traditional drugs. siRNA drugs have the advantages of designable targeting, convenient synthesis, instantaneous silencing, and strong target specificity. However, their delivery also faces obstacles that they are easily degraded in the blood circulation, cleared by the kidney, and difficult to break through the vascular endothelium/cell membrane/lysosome. Therefore, designing suitable nanocarriers to help siRNA successfully deliver into cells and play a role is an important goal for the development of siRNA drugs, and the amout of research in this area is also increasing year by year. The precise design of the nanocarrier material type, size, structure, surface modification, etc. are important factors for the successful delivery of siRNA drugs. At present, the design of siRNA drug nanocarriers mainly includes 4 strategies: loading siRNA drugs on the surface of nanocarriers, co-assembly of siRNA drugs and nanocarriers, nanocarriers encapsulating siRNA drugs, and siRNA self-assembly. At this stage, the use of nanocarriers to achieve siRNA drug delivery has made great progress. With the in-depth research and application development, the precise controlled preparation, precise targeted delivery and multifunctionalization of siRNA drug nanocarriers have achieved good results. However, there are still some problems that need to be overcome by researchers. For example, when siRNA drugs are used in the clinic, there are still problems such as inaccurate structure design of targeted drugs, serious off-target effects, difficulty in achieving endosome escape, and difficulties in large-scale preparation of nanocarriers. Because of this, only 3 siRNA drugs have been approved for marketing, namely Onpattro (Patisiran), Givlaari (Givosiran) and Oxlumo (Lumasiran) developed by Alnylam Pharmaceuticals. How to prepare siRNA drugs on a large scale is a major problem facing the clinical application of siRNA drugs, and it will become a research hotspot. At the same time, with the development of computer technology, combined with artificial intelligence, machine learning and other technologies, drug design with the aid of big data analysis is becoming a new research and development trend. Intelligent design and precise regulation of siRNA nanomedicine, and the design of multifunctional siRNA nanomedicine that integrates targeting, tracing, and co-delivery with other drugs to achieve synergy is also one of the future development directions of siRNA nanomedicine.

Abstract:Tumor immunotherapy is a novel strategy for cancers, which has great significance and application prospects in clinical treatment. It mainly includes adoptive cell therapy, tumor vaccines and monoclonal antibody therapy. Antibodies are widely used in tumor immunotherapy, but their price is too high, the quality is easily influenced by different batches and have immunogenicity. Aptamers, also known as “chemical antibodies”, are short single-stranded oligonucleotides which bind to their targets with high specificity and affinity. Aptamers which have low immunogenicity, are synthesized at low cost and quality stability. Based on these advantages, aptamers have been developed for tumor immunotherapy in recent years which mainly includes two aspects. One is to select immune-related aptamers, and the other is to expand the application of aptamers that have been reported to tumor immunotherapy. Using immune checkpoints, co-stimulatory receptors or cytokines as targets, the aptamers can be obtained through screening. However, it is uncertain whether the aptamer has the biological function of regulating the anti-tumor immune response. Therefore, the process of screening should be improved by adding appropriate screening pressure to obtain functional aptamers that can regulate antitumor immune response. There are many aptamers which have been reported, but rarely have been investigated for further research and application. So we can further develop these aptamers for tumor immunotherapy. For example, aptamers can be coupled with siRNA or nanomaterials to indirectly regulate tumor immune processes. The modification of membrane of immune cells with aptamers confers the immune cells targeted tumor-killing effects. Aptamers play an important role in tumor immunotherapy in a variety of ways, and have great potential to be developed for clinical treatment. We need to improve the aptamer screening process to obtain aptamers that have powerful biological functions quickly and maximize the use of the aptamers that have been obtained.

Abstract:Oxygen is essential for life growth and development, but hypoxia adaptation is also important in many physiological and pathological processes. At normal oxygen levels, hypoxia-inducible factor 2α (HIF-2α) is ubiquitinated by von Hippel-Lindau (VHL) and then rapidly degraded by the proteasome. Under hypoxia, HIF-2α is not degraded and enters the nucleus to form heterodimers with HIF-β subunit, and then activate target genes’ expression. Renal cell carcinoma (RCC) usually has high-frequency VHL gene inactivation, which leads to the accumulation of HIF-2α and ultimately promotes the initiation and progression of RCC. So, HIF-2α can act as a new therapeutic target in RCC. Although HIF-2α is generally regarded as “undruggable”, the allosteric inhibitors PT2385/PT2977 have been successfully developed, which perform pharmacological effects by specifically antagonizing the formation of HIF-2α/HIF-1β heterodimers. Based on the structure of HIF-2α/HIF-1β heterodimers, an extensive screening of small-molecule libraries was performed and 130 potential HIF-2α inhibitors were generated. After further considering the potency, selectivity and oral viability, PT2385 and PT2977 were chosen, in which PT2385 for in vitro studies and PT2977 for clinical development. PT2977 can selectively inhibit the expression of HIF-2α targeted genes in cultured RCC cells, but do not affect HIF-1α targeted genes. Preclinical and clinical trials have demonstrated that HIF-2α inhibitors are effective in blocking cancer cell growth, proliferation, and tumor regression in RCC. These data also indicated that these inhibitors are more effective and better tolerated and have few side effects than standard drugs in treating RCC. Prolonged HIF-2α inhibitors treatment can also produce drug resistance, which can be partly attributed to key amino acid mutations in binding domain of HIF-2α to inhibitors. These advances mean that HIF-2α allosteric inhibitors are expected to play an important role in the clinical treatment of RCC.

Abstract:Breast cancer has become the first rank cancer in the world, and the exploration of the pathogenesis and treatment of breast cancer deserves more and more attention. Lipid metabolism dysfunction is one of the most prominent metabolic changes in cancer cells. It is very important to explore the changes of lipid metabolism in breast cancer cells in order to find new diagnostic indicators and therapeutic targets. This paper introduces the research progress of lipid metabolism dysfunction in breast cancer from 4 aspects: (1) the expression of abnormal fatty acid metabolism in breast cancer from three aspects of fatty acid synthesis, oxidation and uptake and the related research progress; (2) introduction to the abnormal expression of triglyceride metabolism in breast cancer from the aspects of triglyceride synthesis and degradation and the related research progress; (3) to introduce the abnormal expression of cholesterol synthase in breast cancer and the related research progress; (4) to introduce the abnormal expression of lipid metabolism signaling pathways in breast cancer from five signaling pathways, namely Notch, Hippo, Hedgehog, Wnt and mTOR, and the related research progress. The aim is to provide new ideas and methods for targeting lipid metabolism in the treatment of breast cancer.

Abstract:Endothelial cells, as non-excitable cells, were previously thought to lack functional voltage-gated calcium channels (VGCC), such as human umbilical vein endothelial cells, bovine pulmonary artery endothelial cells, bovine aortic endothelial cells, and bovine aorta endothelial cells. With the development of patch clamp technology, fluorescence microscopy technology, and polymerase chain reaction (PCR) technology, more and more VGCC are found in various endothelial cells, such as human aortic endothelial cells, rat aortic endothelial cells, and rat pulmonary microvascular endothelial cells. At present, there are 3 main detection methods for the existence of VGCC: the detection of ion channel current by patch clamp technology, the detection of intracellular calcium ion concentration change by fluorescence microscopy technology, and the detection of ion channel gene or protein expression by PCR. Endothelial cells are not only the physical barrier between blood and other adjacent tissue cells and matrix proteins, but more importantly, exert a significant influence on the physiological changes of cell and vascular tissues through the opening and closing of VGCC on the cell membrane. On the one hand, the effect of VGCC on the change of intracellular calcium ion concentration controls the release of vasodilators such as nitric oxide (NO) and regulates the balance of vascular tone. On the other hand, VGCC, which is an important route for calcium ion inflow, affects endothelial cell migration and proliferation through the induction of a kind of small G protein (Ras) and mitogen-activated proteinkinase kinase (MEK) pathways, the phosphonic acidification of phosphatidylinositol 3 kinase (PI3K) and serine/threonine protein kinase (Akt) pathways. In addition, some physiological phenomena, such as mechanical strain generated by intravascular pressure and shear stress associated with blood flow, activate VGCC by activating mechanical bodies, causing the ATP-sensitive potassium channel () channel to close, causing endothelial cell membranes to depolarize; the binding of some receptors and ligands and the opening and closing of ion channels require the participation of VGCC, such as the opening and closing of potassium ion channels with bradykinin as activator and cation channels with histamine as activator. Hence,in view of the important functions of VGCC in regulating the excitability, secretion and migration of endothelial cells, in-depth and extensive research on VGCC is of great significance for revealing and treating endothelial functional diseases such as essential hypertension and atherosclerosis.

Abstract:Tumor microenvironment (TME) not only promotes the early formation and distant metastasis of tumors but also changes constantly with the progress of tumors. Cancer stem cells (CSCs) are self-renewing cells that facilitate tumor initiation, promote metastasis, and enhance cancer therapy resistance. The crosstalk between CSCs with cancer cells and other non‐CSCs occurs in cancers, which is possible under the control of signals from CSCs and TME, including CSCs niche. As an important immune cell in CSCs niche, tumor-associated macrophages (TAMs) are among the most influential cells for promoting CSCs survival, and self-renewal. TAMs can activate IL-6 /STAT3, TGF-β, Wnt/β-catenin, and other signaling pathways by secreting a series of cytokines to promote survival, self-renewal, and resistance to chemotherapy of CSCs. At the same time, CSCs also play an important role in promoting the recruitment of macrophages and inducing their transformation into M2 TAMs to promote tumor progression. CSCs recruit macrophages into TME through various secretory factors such as POSTN, MIF, CCL2, M-CSF, IL-6, IL-1β, TNF-α, etc, and then polarize to the M2 phenotype under the action of PGE2, WISP, IL-10, GM-CSF, MIC-1, and other chemokines and cytokines, shaping immunosuppressive and tumor-promoting TME. Therefore, the interaction between TAMs and CSCs plays an important role in promoting tumor growth, metastasis, and chemoresistance. This paper reviews the research progress on the interaction between CSCs and TAMs in TME and the potential target in the interaction of CSCs and TAMs for novel cancer therapy. These emerging insights provide a roadmap for the development of novel anti-cancer therapeutic strategies that disrupt this dynamic circuit in specific tumor types.

Abstract:Objective DNA end resection is a common mechanism for the formation of 3"-ssDNA tails in homologous recombination (HR) and is mainly mediated by 5"-3" exonuclease. However, whether DNA end configurations directly regulate 5"-3" exonuclease activity remains unclear. In this study, we explored the regulation and mechanisms of DNA end configurations on RecJ, the only 5"-3" exonuclease of RecF recombination pathway in Escherichia coli.Methods To investigate the regulation of DNA 3"-end configurations on RecJ exonuclease, single-stranded DNAs (ssDNAs) containing different lengths of 3"-ssDNA overhangs (9 nt and 18 nt) and 3"-end modifications (phosphorylation and phosphorothioation) were used for exonuclease assays in the presence of Mg²⁺. To elucidate the mechanisms, RecJ was incubated with substrates containing different 3"-end configurations in the absence of Mg²⁺ and analyzed by electrophoretic mobility shift assays (EMSA). Furthermore, the coordination of DNA 3" end configurations and two other RecJ regulatory factors, DNA 5"-end phosphorylation and single-stranded DNA binding protein (SSB), were determined by exonuclease assays and EMSA on substrates with different 3"-end configurations respectively.Results DNA 3"-end configurations inhibited the RecJ exonuclease activity, including DNA 3"-overhang length and 3"-end modifications (phosphorylation and phosphorothioation). 3"-End phosphorylation and phosphorothioation of DNA reshaped the RecJ-DNA binding patterns to inhibit RecJ exonuclease activity. DNA 5"-end phosphorylation overcame RecJ inhibition of 3"-end modifications and remodeled the RecJ-DNA binding patterns. In addition, SSB partially overcame the 3"-end modifications mediated inhibition by enhancing RecJ-DNA binding.Conclusion The RecJ exonuclease activity was regulated and orchestrated by the DNA configurations of 3" and 5" ends.

Abstract:Objective The T cell receptor-co-receptor complex (TCR-CD3) plays an important role in the adaptive immune response, and the interaction between its subunits has always been a research hotspot. Due to the limitations of traditional experiments, the study of transmembrane protein TCR-CD3 complexes cannot go deep into the microscopic level.Methods Therefore, we used molecular dynamics simulation methods to analyze the self-assembly mechanism of TCR-CD3 complexes.Results Through coarse-grained simulation (CGMD), we found that the TCR-CD3 complex has an assembly sequence in which αβ sequentially binds δε", γε, and ζζ" during the assembly process, and explained that the α^R253 mutation reduces the interaction between α^K258 and δε".Conclusion We demonstrated that only the transmembrane region of the TCR-CD3 complex is not sufficient to mediate the specific interaction between the subunits of the TCR-CD3 complex. The results of steered dynamics (SMD) and all-atom simulation (AAMD) indicate that the extracellular interaction between ζζ" and the rest of TCR-CD3 is stronger than the transmembrane region. The absence of ζζ" makes the stability of αβδε"γε little change, while the absence of δε" greatly reduces the stability of αβγεζζ".

Abstract:Objective Magnetic seizure therapy (MST) is an emerging neuromodulation intervention technique that is widely used in the treatment of major depressive disorder (MDD), but its antidepressant mechanism is still unclear. Therefore, exploring the regulatory effect of MST on the brain functional network of MDD patients with different therapeutic effects is of great significance for the study of the antidepressant mechanism of MST treatment.Methods In this study, the resting-state EEG of 18 MDD patients pre- and post-MST was recorded, and the Pearson correlation method was used to construct the brain functional network; the complex network theory was used to compare and analyze the changes in the topology of the brain functional network; according to the rate of change of the HDRS-17 score, it was further distinguished. The network characteristics were performed a secondary comparison between responders and non-responders.Results The brain functional network connectivity, mean node degree, mean clustering coefficient, and mean global efficiency values were significantly higher than that pre-MST treatment. Mean path length values were significantly lower, and small world attribute significantly increased post-MST treatment. Compared with the group of non-responders, the changes in the characteristic parameters of the brain functional network in the group of responders were significantly larger.Conclusion MST significantly changes the topology of the brain functional network in patients with MDD, and it has a certain modulation effect on the brain functional network of patients. These results provide experimental support and a theoretical basis for the study of the antidepressant mechanism of MST treatment.

Abstract:Objective The phenotypes of population, such as biogeographical and physical characteristics, are the result of the interaction between genotype and environment. A large number of genomic studies have shown that the Han Chinese are admixed population which displayed obvious genetic differences between the north and the south. The purpose of this study is to explore whether there are differences in epigenomes between northern and southern Han populations, and to screen biogeographical specific genetic loci.Methods Glint software was used to perform epigenome-wide association study (EWAS) analysis on genome-wide methylation microarray data of 483 Han Chinese individuals, and Lasso regression was used to screen the sites. Multiple logistic regression algorithm was used to construct the prediction model for the Han population in the south and the north, and the evaluation was conducted by the method of 10-fold cross validation.Results A group of CpG sites with significant differences between southern and northern Han populations were screened out, with accuracy of 99.03% and Kappa of 0.979 6.Conclusion This study shows that there are epigenetic differences between the southern and northern Han populations, which lays a foundation for further studies on epigenetic differences between the Han populations in different regions.

Abstract:Objective Current forensic SNP genotyping methods often require imported platforms and are labor-intensive, time-consuming and costly. Droplet digital PCR (ddPCR) is a new generation of PCR technology that allows rapid qualification of rare target DNA sequence, and is less susceptible to PCR inhibitors. This study is intended to establish a SNP genotyping method on domestic ddPCR platform and explore the applicability of ddPCR in forensics.Methods Genotyping system of the high altitude adaptive EPAS1 haplotype (rs115321619, rs73926263, rs73926264, rs73926265 and rs55981512) was established by ddPCR. Then we tested the specificity of primers and probes, evaluated its accuracy, stability, sensitivity and adaptability separately. Meanwhile, ddPCR and SNaPshot minisequencing technology were compared in terms of inhibitor resistance ability. Finally, preliminary application in 70 samples were conducted.Results The ddPCR assay only required a total run time within 2.5 h, and showed high accuracy and repeatability in SNP genotyping. The detection sensitivity was 0.312 5 ng. DdPCR assays also exhibited better tolerance to inhibitors than SNaPshot. The tested individuals showed good consistence with their background information.Conclusion The SNP genotyping assay based on ddPCR is accurate, rapid, easily-used and shows great resistance to perturbations by inhibitors, which has strong application potential in the field of rapid forensic detection, and is suitable for forensic analysis.

Abstract:Objective TRIM28 (TRIpartate motif-containing protein 28), also called KAP1 (KRAB-associated protein1) or TIF1β (transcription intermediary factor 1β), is a heterochromatin related protein, composed of RBCC domain in N terminal and PHD,BROMO,NHD domain in C terminal, which participates in the establishment of H3K9me3 modification and SUMOylation pathway. The present study is to further explore the function of TRIM28.Methods We used CRISPR/cas9 technology, chromatin imm unoprecipitation assay, Western blot, quantitative real-time assay in HEK293F cell line to further study the function of TRIM28. We knocked out Trim28 gene in HEK293F cell line by CRISPR/cas9 technology.Results By analyzing experimental data, we found that TRIM28 mainly suppresses the transcription of genes with low endogenous expression level. Further analysis by GO bioinformation assay, we found that TRIM28 regulates zinc finger protein family genes and protocadherin protein family genes. According to the results of ChIP-seq, we found that in Trim28 knockout cell lines, the global distribution pattern of H3K9me3 decreased dramatically and H3K4me3 dropped moderately in TRIM28 target sites, indicating TRIM28 not only regulates the establishment of heterochromatin but also affects cis-acting elements. Meanwhile, H3K27ac modification, H3K4me1 modification and H3K4me3 modification in zinc finger protein family genes increased significantly, H3K9me3 decreased dramatically. H3K4me3 modification in protocadherin protein family genes increased significantly, H3K9me3 decreased dramatically. Previous study showed that protocadherin protein family genes mainly engaged in the identification and recognition of axon and dendrites in neuron cell.Conclusion In our study, it’s the first time to show the relationship between TRIM28 and protocadherin protein family genes. These results suggest that TRIM28 regulates zinc finger and protocadherin β genes by changing the chromatin accessibility and provide a new idea for further study of the relationship between TRIM28 and chromatin higher order structure.

Abstract:Objective Opioid receptor, a kind of G protein-coupled receptors (GPCRs), mainly mediates an analgesic response via allosterically transducing the signal of endogenous ligand binding in the extracellular domain to couple to effector proteins in the intracellular domain. δ opioid receptor (DOP) is associated with emotional control besides pain control, which makes it an attractive therapeutic target. However, its allosteric mechanism and key residues responsible for structural stability and signal transmission are not completely clear. This paper aims to analyze the structural dynamics and allosteric effects of DOP.Methods Firstly, the relationships between DOP structure dynamics and function were explored by means of residue fluctuations in slow motion mode and fast motion mode from the anisotropic network model (ANM). Then, perturbation response scanning (PRS) was used to identify key residues related to allosteric communication in DOP.Results The DOP segments and functional sodium-binding sites can be well identified by the slowest motion modes, and the key residues that play a crucial role in protein structural stability can be identified by the fastest motion modes. Correlation analysis of residue motions reveals positive correlations between extracellular/intracellular transmembrane helices and loops, which promote the DOP structural stability and the binding of DOP with ligands. Key residues with high sensitivity and high effectiveness in PRS analysis play an important role in the allosteric communication of DOP.Conclusion This work sheds light on the allosteric communication mechanism of δ opioid receptor and provides valuable information for drug design.

Abstract:Objective Nowadays, how to determine an accurate three-dimensional protein structure from nuclear magnetic resonance (NMR) spectroscopy experiments is a hot topic in biophysics, because understanding the spatial structure of a protein is crucial to research its function. However, this is a large challenge due to the serious lack of experimental data.Methods In this paper, the problem of protein structure determination was solved by matrix completion (MC) algorithms of recovering a distance matrix. Firstly, the initial distance matrix model was established, then its missing data were recovered by the MC algorithms at different sampling ratios. The subsequent stage involved adding the noise model to evaluate the noise resistance of the algorithms. Four proteins with different topological structures and 6 off-the-shelf MC algorithms were selected for testing.Results The results show that these algorithms have good performance in a certain range of sampling ratios and noises. More specifically, the advantages of different algorithms in the case of accurate sampling and noisy sampling are compared by analyzing the average and standard deviation of the root-mean-square deviation (RMSD) and computational time, which are two important indexes about algorithms.Conclusion We can conclude that 6 different MC algorithms have different performances and advantages for the problem of protein structure determination. These characteristics provide a basis for the development of a new MC algorithm. The results of this paper have potential promotion in the field of protein research based on MC algorithms.

Abstract:Objective Different patients may have different responses to the same anticancer drug. Understanding differences in anticancer drug responses among patients is crucial for cancer precision medicine.Methods High-throughput sequencing data make it possible to construct anti-cancer drug response classification models. Based on two classic data sets, Cancer Cell Line Encyclopedia (CCLE) and Genomics of Drug Sensitivity in Cancer (GDSC), this paper proposed a classification model, mRMR-SVM, by employing Max-Relevance and Min-Redundancy (mRMR) algorithm and Support Vector Machine (SVM). Feature genes were extracted by using variance ranking and mRMR algorithm on gene expression data,and SVM was applied to predict that an anticancer drug is sensitive or resistant to a given cell line.Results The experimental results showed that the average accuracy of mRMR-SVM is 0.904 for 22 drugs in CCLE, and 0.851 for 11 drugs in GDSC, higher than traditional SVM, Random Forest, Deep Response Forest, Deep Neural Network and CDCN.Conclusion mRMR-SVM also has good generalization due to its satisfactory classification prediction on three specific tissues. In addition, mRMR-SVM could identify biomarkers closely related to the occurrence and development of cancer.