Abstract:The mammary gland is an important organ for mammals to feed the offspring. It provides sufficient nutrients to the offspring by secreting milk. The healthy development of the mammary gland is of great significance to lactation and the survival rate of the offspring. The mammary gland develops through different stages, including embryonic period, puberty, pregnancy, lactation and regression period. The mammary gland is a highly dynamic organ. At different developmental stages, its morphology will undergo significant changes and the cells undergo extensive changes. Adipose tissue is an important part of the mammary gland. In the process of mammary gland development and circulatory remodeling, adipose tissue exhibits regular morphological and functional changes. The dynamic change of mammary gland adipose tissue is a significant feature of mammary gland circulatory development and reconstruction,and it is mainly manifested as changes in morphology and quantity. For example, adolescent mammary gland accounts for more adipocytes,the ratio of pregnancy and lactation decreases, and the ratio of degenerative phase increases, and this process will be repeated in different reproductive cycles. Studies have confirmed that adipose tissue can secrete special physiological factors to regulate the function of epithelial cells and the development of mammary glands, and has the potential to convert with epithelial cells. It is one of the indispensable cellular components in the development cycle of mammary glands. In addition, the abnormal development of adipose tissue also affects the development of epithelial cells and the function of secreting milk. However, it is still unclear how mammary gland adipocyte change in different periods, what is the mechanism, and what functions they play in mammary gland development. In addition, the research on mammary adipose tissue mainly focuses on mice, and there are few researches on other animals, which makes the research on mammary adipose tissue lack species integrity. In summary, this review synthesizes the relevant progress of mammary gland adipose tissue in recent years, and provides basic data for the follow-up study of the mechanism of adipose tissue regulating mammary gland development.

Abstract:Iron is an essential trace element for most organisms and plays a key role in health and disease, particularly in host-pathogen interactions. In bacteria, the intracellular iron concentration serves as a critical signal in not only controlling the expression of iron transport systems with high affinity, but also regulating the production of toxin and other important virulence factors. However, the overload of iron can lead to lethal cytotoxicity. Therefore, iron homeostasis is strictly regulated in most organisms, of which the iron binding global regulator, Fur (ferric uptake regulator) plays a pivotal role in the regulation of intracellular iron concentration. This review summarized the progress in the study of four aspects of Fur, including the composition of FUR superfamily, the structures of the Fur proteins and their difference, the regulation network of Fur, as well as its regulatory mechanism, thereby to provide insights for further research of Fur and iron homeostasis.

Abstract:Catch bond is a type of dynamic bond that exists in receptor protein and ligand interactions. The bond lifetime of catch bond is positively correlated with the pN-level external force that applied onto it within a certain range. Catch bond is mainly involved in cell adhesion and cell activation processes and it forms molecular switch with slip bond to regulate cell adhesion related cell activities. Catch bond has proven link with the urinary tract infection process that initiated by the pathogenic E. coli, T cell receptor-antigen recognition, microfilament depolymerization and Notch signaling pathway activation. This review summarized the progresses and new findings of catch bond research in cell adhesion, T cell activation, actin interaction. For cell adhesion of prokaryotes and eukaryote, catch bonds exist in a wide range of related proteins, including FimH, selectin, integrin. For T cell activation, recent research revealed that the catch bond in TCR-pMHC interaction is closely related to cancer cell development processes and this finding provides a new direction in improving T cell receptor-gene engineered T cells (TCR-T) immunotherapy. For actin interaction, the actin catch bond has been proven involving in RhoA-formin switch force-induced actin cytoskeleton alignment process. To further illustrate the prospect of catch bonds in medical research, we also discussed the potential of catch bonds in the development of anti-bacterial or anti-adhesion drugs and improvement for the TCR-T immunotherapy.

Abstract:Optogenetics has been developed to control the activities and functions of neural circuits with high cell-type specificity and spatiotemporal resolution. However, current optogenetic tools generally rely on visible light with poor tissue penetration ability that does require invasive optical fiber devices to deliver visible light into deep inside brain tissue. These often result in a series of side effects, such as tissue damage and restrict free movement of animals. Fortunately, upconversion nanoparticles (UCNPs)-mediated optogenetic systems facilitate the optogenetic regulation in complex living systems. In this review, the recent advances on design strategies of UCNP-mediated wireless optogenetics in biomedical research are summarized and the future perspectives for refining and advancing UCNP-mediated wireless optogenetics into in vivo for remote therapy are proposed.

Abstract:Brain stimulation is an important means in neuroscience research. Traditional brain stimulation such as transcranial magnetic stimulation and transcranial electrical stimulation can regulate motor function (including alleviation of motor disorders and improvement of motor ability), but they have low spatial resolution and are unable to stimulate deep brain tissue. In recent years, some brain stimulation methods with accurate positioning such as deep brain stimulation (DBS), optogenetics, transcranial ultrasound stimulation (TUS), temporal interference (TI) stimulation have achieved rapid development, showing higher spatial resolution and reaching deeper brain tissue. We summarized the principles and characteristics of the above brain stimulation methods, and progress in the regulation of these brain stimulation on motor function as well as their challenges and prospects, for providing more neuroscience research tool and clinical intervention means.

Abstract:RBM15 is an RNA binding protein that is known of involving in the m⁶A modification and the regulation of alternative splicing (AS). However, how RBM15 regulates AS is currently unclear. Here, using super-resolution microscopy, we found that RBM15 forms puncta structures that closely contact with or even embedded in the nuclear speckles. Nuclear speckles are enriched in splicing factors, which implies that RMB15 might be involved in RNA AS. To determine whether and how RBM15 regulates AS, we knocked down RBM15(RBM15-KD) using siRNA and performed RNA-seq for wildtype(WT) cells and RBM15-KD cells. We analyzed the RNA-seq of WT and RBM15-KD cells. We show that RBM15-KD cause 1 279 differential AS events in 1 111 transcripts. After comparing to public RBM15-CLIP data, we identify that 191 out of 1 111 transcripts are directly bound by RMB15, indicating that these 191 transcripts are probably direct targets of RBM15. Moreover, RBM15 promotes the retention of the adjacent regions proximal to its binding sites in 121 out of the 191 transcripts. This study reveals that how RBM15 regulates AS on a transcriptomic level.

Abstract:DNA methylation is an important epigenetic phenomena and plays crucial roles in the gene regulation. Many studies showed that DNA methylation can be used as clinical diagnostic biomarker. However, the ability to detect the DNA methylation status quickly and accurately is a prerequisite and key point for clinical application. By using two kinds of primers which can bind to methylated and unmethylated template respectively, methylation specific PCR (MSP) can distinguish DNA methylation status and prove to be a feasible and convenient diagnostic technique in clinical practice. Unlike traditional PCR, MSP mainly has four difficulties: how to enhance the specificity of binding to primer-methylated/unmethylated template, how to reduce the difference of Tm value of primer sequences, how to remove false positive amplification and how to improve sensitivity. Though most MSP primer design tools have proposed various solutions for those difficulties, there are still some defects in consideration of primer influencing factors, multitasking, prediction of specific amplification in MSP primer design and evaluation. Therefore, in this study, after deep exploration of existing MSP primer design tools, a novel MSP primer design and graphic evaluation tool named MethyScan was developed based on the integration of Bowtie, SAMtools, and BEDTools with Python graphic library Matplotlib and third-party functional libraries Biopython and Primer3-py. Three functional modules were involved in MethyScan including primer design, genome indexing and primer evaluation. MethyScan not only has the ability to perform MSP primers design and Nested primers adaptation, but also can evaluate primers specific/non-specific amplification with the analysis of primer binding information on four converted genomic templates and graphically displaying of the difference between non-specific amplification and target. Meanwhile, the comparison of MSP primer design for six potential biomarkers TFPI-2, NDRG4, CDKN2A, CD44, CASP8, and SDHD in esophageal cancer, colorectal cancer, and other malignant tumors suggested that MethyScan can not only obtain primers with more CpG sites, but also obtain primers with same or similar locations to those of other softwares, and the difference of Tm values of primers is even smaller. As the first MSP primer design tool for graphically displaying specific/non-specific amplification differences, MethyScan can effectively improve the accuracy of methylation primer design and provides strong support for the development of clinical DNA methylation detection projects, tests and diagnostic kits. The download address of MethyScan is: https://github.com/bioinfo-ibms-pumc/MethyScan.

Abstract:In bacteria fatty acids are synthesized by type II fatty acid synthase system, in which 3-hydroxylacyl -ACP dehydratase is one of the key enzymes for bacterial growth. Xanthomonas campestris pv. campestris (Xcc) causes black rot disease to all cruciferous plants, and great economic losses to the world. To study the 3-hydroxylacyl-ACP dehydratase in Xcc, XC_2876 (XcfabZ) was found based on the sequence alignment with E. coli FabZ. Moreover, XcFabZ shows 46.1% amino acid sequence identity with EcFabZ, and contains the conservative α-helix structure and active residue. XcfabZ was able to genetically complement the EcfabZ knock out mutant E.coli HW7 to restore the growth with inducer IPTG. In vitro assay also identified XcFabZ was able to dehydrated 3-hydroxyacyl-ACP in the initial and elongation reactions. However, XcfabZ in the chromosome could not be deleted directly, indicating XcfabZ is essential for growth. When expression plasmids harboring EcfabZ or XcfabZ was introduced, respectively, XcfabZ deletion mutants were constructed. The EcfabZ replaced mutant showed different fatty acid compositions, much lower tolerance to stressful conditions (high salty, low pH, H₂O₂ and SDS), and decreased motility compared to the wild-type. While mutant with XcfabZ in the plasmid showed similar phenotype to wild-type. These data demonstrated both XcFabZ and EcFabZ show 3-hydroxylacyl-ACP dehydratase activity, but they may contains different biological function in vivo.

Abstract:To investigate the effect of aerobic exercise on cardiac function in myocardial infarction rats, SD male rats were randomly divided into normal group (C group), sham operation group (S group), myocardial infarction group (MI group), normal+exercise group (CE group) and myocardial infarction+exercise group (ME group) after 1 week of adaptive feeding. Then, an MI model was established by ligating the left anterior descending coronary artery and group S only threading without ligation. One week after surgery, animals were randomly assigned to receive 4 weeks of no training or training (1 h/d, 5 d/week on a treadmill). In detail, the training consisted of two 10-minute sessions at speed of 10 m/min and 13 m/min, and the remaining 40 min at speed of 16 m/min. The next day after the training, blood flow mechanics was used to detect cardiac function. A single cell visual moving edge detection system (Ion Optix) was used to determine [Ca²⁺]_i amplitude, [Ca²⁺]_i fluorescence ratio, departure velocity, time to peak(TTP), time to peak50%(TTP50%), time to baseline50%(TTB50%), return velocity, ratio amplitude, maximum contraction and diastolic rate of sarcomere(±dl/dtmax), sarcomere length(SL), peak twitch amplitude(PTA) and SL shortening%. The related proteins of PI3K-AKT-PKG-1/p-PLN-SERCA2a signaling pathway and apoptosis were detected by PI3K-AKT-PKG-1/p-PLN-SERCA2a signaling pathway and apoptosis related proteins were detected by Western blotting. Compared with group S, in group MI, PI3K-Akt-PKG-1/p-PLN-SERCA2a signaling pathway is significantly inhibited, apoptosis and left ventricular end-diastolic pressure (LVEDP) are significantly increased, left ventricular systolic pressure (LVSP) and maximum pressure increasing and decreasing rate(±dp/dtmax), [Ca²⁺]_i amplitude, [Ca²⁺]_i ratio amplitude, departure velocity and return velocity all significantly reduce, and TTB50%, TTP and TTP50% both significantly increase. The myocardial cells were significantly reduced at the SL shortening%, PTA, ±dp/dtmax. Compared with MI group, PI3K-Akt-PKG-1/p-PLN-SERCA2a signaling pathway in ME group is significantly activated, apoptosis and LVEDP are significantly reduced, LVSP and ±dp/dtmax are significantly increased, ratio amplitude, [Ca²⁺]_i amplitude, ratio velocity and departure velocity are significantly increased, and TB50%, TTP and TTP50% are significantly shortened. The myocardial cells were significantly inaeased at the SL shortening%, PTA, ±dp/dtmax. It can be concluded that aerobic exercise improves the calcium transient and myocardial systolic function in peripheral infarction area of MI rats, activates the PI3K-Akt-PKG-1/p-PLN-SERCA2a signal, inhibits the apoptosis of myocardial cells, and improves myocardial infarction function. Moreover, the improvement of myocardial infarction function is closely related to the activation of PI3K-Akt-PKG-1/p-PLN-SERCA2a signaling pathway and the inhibition of myocardial cell apoptosis.

Abstract:As advanced cognitive activities, it is poorly understood if visual weakening affects auditory fear conditioning. Here we investigated the responses in auditory Pavlovian fear conditioning, using mutant rd/rd, cl/cl mice as visual weakening group. Freezing behaviors were recorded during fear conditioning, fear extinction, and extinction recall phases. The results indicated that mice with shape vision deprivation are more conducive to auditory fear conditioning. We discuss the possible neuro-mechanism of visual-auditory system interactions.

Abstract:The paper presents a method to use the photothermal phase difference to map metal nanoparticle (NP) reagent with optical coherence tomography (OCT). The depth-resolved, real-time, and highly localized light-to-heat conversion can be traced by recording the photothermal phase. For adiabatic absorption, the photothermal phase difference represents the localized light absorption characteristics of the NPs. In order to prove the effectiveness of our method, we firstly used FD-OCT imaging system to do agar phantom experiments with different concentrations of NP reagent. The results show that the photothermal phase difference can be used to distinguish different concentrations of NP reagent in agar model. Subsequently, a 3-month-old male C57BL / 6J mouse weighing about 25 g was used to verify the feasibility of our method for reconstructing the distribution of NP reagent in tissues. Before the experiment, 0.12 ml chloral hydrate with a concentration of 0.15 g/ml was used for anesthesia, and then 100 ml NP solution with a concentration of 60 μg/L was injected into the bladder of mice through a trocar inserted into the urethra. After about 4 hours, the mouse bladder was used to reconstruct the photothermal image. By analyzing the OCT structural image of mouse bladder, we can clearly observe two distinguishable layers. The first layer is detrusor and the second layer is muscularis mucosa. The results are consistent with those reported. In conclusion, we have proved theoretically and experimentally that the distribution of NP reagent in tissues can be reconstructed by photothermal phase difference. Owing to thermal expansion and thermal refractive index effect, the photothermal phase difference can produce local temperature changes in the tissue. For adiabatic absorption, the photothermal phase difference is related to the concentration of NPs. Therefore, it has been used to distinguish different concentrations of NP in the model and reconstruct the distribution of NP in the bladder of mice.

Abstract:Due to the unique structure of circular RNAs (circRNAs) and their widespread presence in body fluids, circRNAs are considered to have the potential as tumor biomarkers. At present, real-time fluorescent quantitative polymerase chain reaction (PCR) technology is thought as one of the main detection methods for molecular diagnosis in clinical practice. However, this technology has limitations with relatively higher false negatives. The digital PCR technology, the third generation PCR, optimizes and improves the detection sensitivity. More important, it does not require a standard curve to achieve absolute quantitative detection, which greatly improving the accuracy of detection, especially for the detection of low-expressed RNAs. In this study, to establish a new method for the quantitative detection of circRNAs in plasma, hsa_circ_0061276 was used as an example. Its specific primers were first designed, and then the economical droplet digital PCR (ddPCR) EvaGreen dye method was used to determine its absolute copy number in plasma samples from 12 patients with gastritis and 13 patients with gastric cancer. Besides, a negative control (without template) was set. The results showed that the total number of droplets in all samples exceeded 14 000. The absolute copy numbers in patients with gastritis are 2.90 Copies/μl, 2.20 Copies/μl, 3.20 Copies/μl, 1.40 Copies/μl, 3.00 Copies/μl, 1.02 Copies/μl, 0.81 Copies/μl, 0.41 Copies/μl, 1.40 Copies/μl, 0.69 Copies/μl, 0.41 Copies/μl, and 2.30 Copies/μl, respectively. The absolute copy numbers in patients with gastric cancer are 1.80 Copies/μl, 2.30 Copies/μl, 0.90 Copies/μl, 0.62 Copies/μl, 0.06 Copies/μl, 3.30 Copies/μl, 0.26 Copies/μl, 0.59 Copies/μl, 1.04 Copies/μl, 0.65 Copies/μl, 0.06 Copies/μl, 1.38 Copies/μl, and 0.18 Copies/μl, respectively. The bands of positive droplets and negative droplets are clearly distinguished, indicating that the specific copy number of hsa_circ_0061276 in plasma has been successfully detected. In conclusion, ddPCR may become a new technology for the detection of DNA/RNA-based biomarkers in biomedical researches and clinical applications with greater promotion value.