Expression, purification, and characterization of transmembrane protein homogentisate solanesyltransferase

Homogentisate solanesyltransferase (HST) is a crucial enzyme in the plastoquinone biosynthetic pathway and has recently emerged as a promising target for herbicides. In this study, we successfully expressed and purified a stable and highly pure form of seven times transmembrane protein Chlamydomonas reinhardtii HST (CrHST). The final yield of CrHST protein obtained was 12.2 mg per liter of M9 medium. We evaluated the inhibitory effect on CrHST using Des-Morpholinocarbony Cyclopyrimorate (DMC) and found its IC50 value to be 3.63 ± 0.53 μM, indicating significant inhibitory potential. Additionally, we investigated the substrate affinity of CrHST with two substrates, determining the Km values as 22.76 ± 1.70 μM for FPP and 48.54 ± 3.89 μM for HGA. Through sequence alignment analyses and three-dimensional structure predictions, we identified conserved amino acid residues forming the active cavity in the enzyme. The results from molecular docking and binding energy calculations indicate that DMC has a greater binding affinity with HST compared to HGA. These findings represent substantial progress in understanding CrHST's properties and potential for herbicide development. KEY POINTS: • First high-yield transmembrane CrHST protein via E. coli system • Preliminarily identified active cavity composition via activity testing • Determined substrate and inhibitor modes via molecular docking.

An efficient method for detecting membrane protein oligomerization and complex using 05SAR-PAGE

Oligomerization is an important feature of proteins, which gives a defined quaternary structure to complete the biological functions. Although frequently observed in membrane proteins, characterizing the oligomerization state remains complicated and time-consuming. In this study, 0.05% (w/v) sarkosyl-polyacrylamide gel electrophoresis (05SAR-PAGE) was used to identify the oligomer states of the membrane proteins CpxA, EnvZ, and Ma-Mscl with high sensitivity. Furthermore, two-dimensional electrophoresis (05SAR/sodium dodecyl sulfate-PAGE) combined with western blotting and liquid chromatography-tandem mass spectrometry was successfully applied to study the complex of CpxA/OmpA in cell lysate. The results indicated that 05SAR-PAGE is an efficient, economical, and practical gel method that can be widely used for the identification of membrane protein oligomerization and the analysis of weak protein interactions.

Spatial distribution, movement, body damage, and feather condition of laying hens in a multi-tier system

The welfare and health of laying hens in the multitier system raise concern in public. The flock distributions during feeding time at 51 and 89 wk were studied in a multitier system. Furthermore, the ultra-high frequency radio frequency identification (UHF RFID) equipment was used to identify the transition between tiers and time spent in each tier of 48 focal hens (12 hens from each tier-group of the multitier system) at 92 wk of age. The body weight, tibia size (length and width), body damage (comb and rear part), and feather condition (neck, breast, back, tail, cloaca, and wings) of focal hens from different tier-groups were further compared. The results showed that the spatial distribution in flocks changed from top to bottom with increasing age. The hens at 51 wk of age were mainly distributed in the 4th tier (19.6 ± 5.0% in 1st tier, 9.6 ± 1.1% in 2nd tier, 23.6 ± 2.9% in 3rd tier and 47.3 ± 2.6% in 4th tier), and hens at 89 wk of age were mainly distributed in the lower tiers (33.5 ± 1.5% in 1st tier, 31.9 ± 5.1% in 2nd tier, 15.7 ± 3.4% in 3rd tier and 16.6 ± 3.1% in 4th tier). The spatial distribution of hens at 89 wk of age was more even than that at 51 wk of age. At 92 wk of age, the proportion of time spent in original tier of 4 tier-groups was 91.0 ± 5.7%, 51.9 ± 5.7%, 59.0 ± 7.0% and 63.0 ± 6.7%, respectively. Focal hens preferred to stay in the original tier and spent significantly less time in other tiers (P < 0.05). There was no significant difference in body weight, body damage score, tibia width and partial feather scores (neck, breast, tail, and cloaca) of focal hens among 4 tier-groups (P > 0.05). However, focal hens from 1st tier had worse feather scores on wings and back, and shorter tibia length compared to other tiers suggesting that there were more lower ranking birds that located in lower tier to avoid competition, but had equal access to resource, which is good for their welfare and health. In summary, the overcrowding situation was improved near the end of the laying cycle in the multitier system, thereby mitigating the potential negative effects to the lower ranking hens and maintain a satisfactory level of welfare and health for laying hens near the end of the laying cycle.

Effects of different light-emitting diode light on hatch performance, embryo development, eye structure, and plasma melatonin in layer incubation

Light intensity, wavelength, and photoperiod have a combined effect on chicken incubation. This study was conducted to evaluate the effect of 12-h light, 12-h dark (12L:12D) photoperiod of white light (380-780 nm, WL), blue light (455/447.5-462.5 nm, BL), and green light (525/515-535 nm, GL) in chicken perceived light intensity during layer incubation on hatching performance, embryo development, eye structure, and melatonin concentration. Three batches of eggs from Jinghong No. 1 layer breeder were used in this experiment. Light stimulation had no effect on hatchability, and no consistent effect on embryo weight and newly hatched chick weight. However, the average hatching time of white light group and green light group was 7.3 h and 5.5 h later than that of the control group. Therefore, the holding period of chicks was significantly shortened (P = 0.001) in these 2 light groups. Light stimulation had a significant effect on the thickness of retinal layers (P < 0.05), retinal layers of white light group was thicker than that of the other 3 groups. Melatonin levels of chicks hatched in the green light and blue light were significantly higher than that of chicks hatched in the white light and darkness (P < 0.05). It indicated that the monochrome green and blue light promoted the expression of melatonin in chicken embryos. No significant diurnal rhythms were found at the level of plasma melatonin in 4 groups on d 21 using cosine analysis. It was concluded that green light has a positive effect on embryo development and melatonin secretion, while white light probably has positive effect on eye development. Furthermore, both green and white light stimulation resulted in late hatch for layer egg incubation. The obtained results are important in determining the light protocol for chicken incubation.

Dynamic Interactions Between Brilliant Green and MscL Investigated by Solid-State NMR Spectroscopy and Molecular Dynamics Simulations

The mechanosensitive ion channel of large conductance (MscL) is a promising template for the development of new antibiotics due to its high conservation and uniqueness to microbes. Brilliant green (BG), a triarylmethane dye, has been identified as a new antibiotic targeted MscL. However, the detailed binding sites to MscL and the dynamic pathway of BG through the MscL channel remain unknown. Here, the dynamic interactions between BG and MscL were investigated using solid-state NMR spectroscopy and molecule dynamics (MD) simulations. Residue site-specific binding sites of BG to the MscL channel were identified by solid-state NMR. In addition, MD simulations revealed that BG conducts through the MscL channel via residues along the inner surface of the pore sequentially, in which the strong hydrophobic interactions between BG and hydrophobic residues F23 and I27 in the hydrophobic gate region of the MscL channel are major restrictions. Particularly, it was demonstrated that BG activates the MscL channel by reducing the hydrophobicity of the F23 in the gate region by water molecules that are bound to BG. Taken together, these simulations and experimental data provide novel insights into the dynamic interactions between BG and MscL, based on which new hydrophobic antibiotics and adjuvants targeting MscL can be developed.

Molecular Mechanisms of Mercury-Sensitive Aquaporins

Aquaporins are transmembrane channels that allow for the passive permeation of water and other small molecules across biological membranes. Their channel activities are sensitive to mercury ions. Intriguingly, while most aquaporins are inhibited by mercury ions, several aquaporins are activated by mercury ions. The molecular basis of the opposing aquaporin regulation by mercury remains poorly understood. Herein, we investigated AqpZ inhibition and AQP6 activation upon binding of mercury ions using solid-state NMR (ssNMR) and molecular dynamics (MD) simulations. Based on the structure of the Hg-AqpZ complex constructed by MD simulations and ssNMR, we identified that the pore closure was caused by mercury-induced conformational changes of the key residue R189 in the selectivity filter region, while pore opening was caused by conformational changes of residues H181 and R196 in the selectivity filter region in AQP6. Both conformational changes were caused by the disruption of the H-bond network of R189/R196 by mercury. The molecular details provided a structural basis for mercury-mediated functional changes in aquaporins.

Solid-state NMR 13C and 15 N resonance assignments of Vibrio sp. SemiSWEET transporter in lipid bilayers

The Sugar Will Eventually be Exported Transporter (SWEET) family is a new class of transporters that plays crucial roles in the cellular sugar transport process. Their bacterial homologs, known as SemiSWEETs, are among the smallest transporters and can be used as a prototype for studying the biological properties of sugar transporters. Here, a set of dipolar-based multidimensional solid-state NMR spectra were employed to investigate the structure of Vibrio sp. SemiSWEET (Vs-SemiSWEET) reconstituted in the native-like lipid bilayers. A nearly complete (88% of the amino acid residues) backbone and side-chain ¹³C and ¹⁵ N chemical shift assignments of Vs-SemiSWEET were obtained. The overall secondary structure of Vs-SemiSWEET predicted from the obtained ¹³C and ¹⁵ N chemical shifts is similar to that from X-ray crystallography, with some differences, reflecting the influence of the membrane environments to the structure of membrane proteins.

[Prevalence and trend analysis of severe multiple disabling birth defects in Chongqing City from 2007 to 2020]

Objective: To explore the prevalence and change trend of severe multiple disabling birth defects in Chongqing City from 2007 to 2020, and to provide a basis for comprehensive prevention and control measures of severe multiple disabling birth defects. Methods: Based on hospital monitoring data, 1 103 children with severe multiple disabling birth defects monitored by all birth defects monitoring institutions in Chongqing City from January 2007 to December 2020 were included in the study. They were grouped by year, perinatal gender, maternal permanent residence (urban/rural), maternal age, different regions and other categories. Chi-square test was used to analyze the differences in the incidence of severe multiple disabling birth defects in different categories, and linear trend test was used to analyze the change trend. Results: From 2007 to 2020, a total of 1 022 314 perinatal births and 1 103 severe multiple disabling birth defects were monitored in Chongqing City, with an incidence of 10.79/10 000, including 11.47/10 000 in urban areas and 9.48/10 000 in rural areas, with an incidence higher in urban areas than in rural areas(χ²=8.424,P=0.004). Male was 10.47/10 000, female was 10.97/10 000, there was no significant difference between male and female(χ²=0.606,P=0.436). The incidence of maternal in different age groups was u-shaped, and there was statistical difference in incidence among different age groups (χ²=59.465, P<0.001). The incidence of maternal in<20 years old and ≥35 years old was higher, and in 25-29 years old was lower. The incidence rate was 17.96/10 000 in 2007 and 7.18/10 000 in 2020, which decreased by 60.02% in 2007-2020. The incidence of neural tube defect, chromosome syndrome, limb shortening and abdominal wall defect decreased by 78.12%, 77.38%, 80.55% and 91.30%, respectively. Severe Congenital heart disease rose by 456.16%. From 2007 to 2020, the overall incidence of the disease showed a decreasing trend (χ²_trend =117.046, P<0.001), except for the rise of severe congenital heart disease, (χ²_trend=8.744, P=0.003), the other four types of diseases were on the decline (neural tube defects χ²_trend =48.618, P<0.001; chromosome syndrome χ²_trend=50.999, P<0.001; limb shortening χ²_trend=73.464, P<0.001; abdominal wall defect χ²_trend=79.863, P<0.001). Conclusion: From 2007 to 2020, the incidence of severe disabling birth defects in Chongqing City showed a downward trend, and there were regional and age differences. The incidence of severe congenital heart disease is on the rise.

Refined balloon pulmonary angioplasty for inoperable chronic thromboembolic pulmonary hypertension: a prospective multicenter registry

Funding Acknowledgements

Type of funding sources: Foundation. Main funding source(s): the National Key Research and Development Program of China

Background Chronic thromboembolic pulmonary hypertension (CTEPH) is a life-threatening disease with a poor prognosis if left untreated. Pulmonary endarterectomy is the standard treatment for CTEPH, but around 40% of CTEPH patients are non-eligible for surgery.

Purpose To investigate the efficacy and safety of refined balloon pulmonary angioplasty (BPA) for inoperable CTEPH in a prospective multicenter registry from China.

Methods We conducted a prospective multicenter cohort study using the data from National Rare Disease Registry System of China. Total 140 consecutive patients with inoperable CTEPH who completed BPA between Jan 2016 and Dec 2020 were enrolled. The key efficacy outcomes were changes from baseline to re-evaluation in mean pulmonary arterial pressure, pulmonary vascular resistance, and six-minute walking distance. The safety outcomes were procedure-related complications. The survival outcome was all-cause mortality.

Results Among the 140 patients who completed BPA, the mean age at diagnosis was 58 ± 14 years and 60.0% were female. At re-evaluation, the least-squares mean change from baseline was -18.3 mm Hg (95% confidence interval [CI], -19.9 to -16.6, P &lt; 0.001) in mean pulmonary arterial pressure, -5.3 Wood U (95% CI, -5.9 to -4.6, P &lt; 0.001) in pulmonary vascular resistance, and 87 meters (95% CI, 74 to 101, P &lt; 0.001) in six-minute walking distance. BPA procedure-related complications occurred in 109 of 650 BPA sessions (16.8%), but severe complications requiring noninvasive positive pressure ventilation only occurred in 4 (0.6%) BPA sessions. During a mean follow-up time of 32 ± 14 months, 4 patients died, including 2 peri-procedural deaths, contributing to the survival rates of 97.8% (95% CI, 93.4 to 99.3) at 1 year and 96.9% (95% CI, 91.9 to 98.8) at 3 and 5 years.

Conclusion Refined BPA appears to be an effective therapeutic option for inoperable CTEPH patients with acceptable safety profiles. Abstract Figure. Images of BPA Efficacy in a Patient  Abstract Figure. Efficacy outcomes of BPA

Dynamics properties of membrane proteins in native cell membranes revealed by solid-state NMR spectroscopy

Cell membranes provide an environment that is essential to the functions of membrane proteins. Cell membranes are mainly composed of proteins and highly diverse phospholipids. The influence of diverse lipid compositions of native cell membranes on the dynamics of the embedded membrane proteins has not been examined. Here we employ solid-state NMR to investigate the dynamics of E. coli Aquaporin Z (AqpZ) in its native inner cell membranes, and reveal the influence of diverse lipid compositions on the dynamics of AqpZ by comparing it in native cell membranes to that in POPC/POPG bilayers. We demonstrate that the dynamic rigidity of AqpZ generally conserves in both native cell membranes and POPC/POPG bilayers, due to its tightly packed tetrameric structure. In the gel and the liquid crystal phases of lipids, our experimental results show that AqpZ is more dynamic in native cell membranes than that in POPC/POPG bilayers. In addition, we observe that phase transitions of lipids in native membranes are less sensitive to temperature variations compared with that in POPC/POPG bilayers, which results in that the dynamics of AqpZ is less affected by the phase transitions of lipids in native cell membranes than that in POPC/POPG bilayers. This study provides new insights into the dynamics of membrane proteins in native cell membranes.

The economic impacts of traffic consumption during the COVID-19 pandemic in China: A CGE analysis

The transportation sector has played an important role during the COVID-19 pandemic. Like many industries, it experienced a sharp decline during the pandemic. The reduced traffic consumption has been caused by objective conditions, such as traffic control measures, and subjective factors, such as the perception of the COVID-19 pandemic. This study uses the computable general equilibrium (CGE) model to examine the economic impacts of traffic consumption during the COVID-19 pandemic in China. Moreover, to evaluate the impact of the government's economic stimulus policy related to transportation, this study examines the policy effects of transportation investment. This study suggests that, first, China's macroeconomy has been severely affected by reduced traffic consumption. The period when the pandemic was most severe had the largest GDP decrease (0.49%). Second, transportation consumption is closely associated with the output of all industries. As the pandemic worsens, the output of all sectors declines more. Of the transport sectors, road transport has the largest output decrease (10.17%), followed by railway (1.76%) and air sectors (1.53%). The service industry is the most negatively affected among the non-transportation sectors. Finally, transportation infrastructure investment can effectively promote the economy and create jobs. In addition, railway investment plays a more positive role in the economy than road and air transports. The findings provide a detailed understanding of the economic impact of the significantly reduced traffic consumption at different stages of the pandemic.

The role of the PZP domain of AF10 in acute leukemia driven by AF10 translocations

Chromosomal translocations of the AF10 (or MLLT10) gene are frequently found in acute leukemias. Here, we show that the PZP domain of AF10 (AF10_PZP), which is consistently impaired or deleted in leukemogenic AF10 translocations, plays a critical role in blocking malignant transformation. Incorporation of functional AF10_PZP into the leukemogenic CALM-AF10 fusion prevents the transforming activity of the fusion in bone marrow-derived hematopoietic stem and progenitor cells in vitro and in vivo and abrogates CALM-AF10-mediated leukemogenesis in vivo. Crystallographic, biochemical and mutagenesis studies reveal that AF10_PZP binds to the nucleosome core particle through multivalent contacts with the histone H3 tail and DNA and associates with chromatin in cells, colocalizing with active methylation marks and discriminating against the repressive H3K27me3 mark. AF10_PZP promotes nuclear localization of CALM-AF10 and is required for association with chromatin. Our data indicate that the disruption of AF10_PZP function in the CALM-AF10 fusion directly leads to transformation, whereas the inclusion of AF10_PZP downregulates Hoxa genes and reverses cellular transformation. Our findings highlight the molecular mechanism by which AF10 targets chromatin and suggest a model for the AF10_PZP-dependent CALM-AF10-mediated leukemogenesis.

Extensively sparse 13C labeling to simplify solid-state NMR 13C spectra of membrane proteins

Solid-state Nuclear Magnetic Resonance (ssNMR) is an emerging technique to investigate the structures and dynamics of membrane proteins in an artificial or native membrane environment. However, the structural studies of proteins by ssNMR are usually prolonged or impeded by signal assignments, especially the assignments of signals for collection of distance restraints, because of serious overlapping of signals in 2D ¹³C-¹³C spectra. Sparse labeling of ¹³C spins is an effective approach to simplify the ¹³C spectra and facilitate the extractions of distance restraints. Here, we propose a new reverse labeling combination of six types of amino acid residues (Ile, Leu, Phe, Trp, Tyr and Lys), and show a clean reverse labeling effect on a model membrane protein E. coli aquaporin Z (AqpZ). We further combine this reverse labeling combination and alternate ¹³C-¹²C labeling, and demonstrate an enhanced dilution effect in ¹³C-¹³C spectra. In addition, the influences of reverse labeling on the labeling of the other types of residues are quantitatively analyzed in the two strategies (1, reverse labeling and 2, reverse labeling combining alternate ¹³C-¹²C labeling). The signal intensities of some other types of residues in 2D ¹³C-¹³C spectra are observed to be 20-50% weaker because of the unwanted reverse labeling. The extensively sparse ¹³C labeling proposed in this study is expected to be useful in the collection of distance restraints using 2D ¹³C-¹³C spectra of membrane proteins.

[Comparative study on metagenomics of esophageal flora in elderly and middle-aged esophageal squamous cell carcinoma patients]

Objective: To explore the flora characteristics and differences of esophageal tissues between elderly esophageal squamous cell carcinoma (ESCC) patients and young and middle-aged ESCC patients, so as to assist in studying the potential biomarkers of elderly ESCC patients. Methods: In this study, a retrospective study was adopted. 72 ESCC patients diagnosed in Taihe Hospital, Shiyan City, Hubei Province from July 2018 to July 2019 were selected, including 49 patients in the elderly group (≥ 60 years old, 40 males and 9 females), 23 patients in the young and middle-aged group (<60 years old, 21 males and 2 females). In the same period, 20 healthy persons without abnormal gastroscopy in endoscopy center were selected as the control group (aged 35-78 years old, median age 57 years old, 16 males and 4 females). The genomic DNA was extracted from the affected esophageal tissues of patients with ESCC and the middle esophageal samples of the control group. The V4 hypervariable region of bacterial 16SrRNA gene sequence was amplified. Illumina HiSeq sequencing technology was adopted. The flora characteristics of elderly, young and middle-aged ESCC patients was compared and analyzed. QIIME and Rstudio software were used to analyze the sequence data, and nonparametric Kruskal-Wallis test or Wilcoxon rank sum test were used for statistical methods. Results: Shannon index [5.17 (4.53, 5.95) vs. 4.79 (3.74, 5.97)], Simpson index [0.94 (0.91, 0.96) vs. 0.92 (0.83, 0.96)] and Chao1 index [343.55 (259.76, 570.59) vs. 329.16 (268.88, 648.00)] were similar in flora of two groups, and there was no significant difference (Z=-0.791, -1.057, -0.380, all P>0.05). There was no significant difference in β-diversity between the elderly group and the young and middle-aged group (PC1=19.14%, PC2=6.95%, P_PC1=0.67, P_PC2=0.42). At the phyla level, the top 5 phyla in abundance were as follows: Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria in the young and middle-aged group, while the top 5 phyla in abundance were as follows: Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria and Actinobacteria in the elderly group; the significant difference between the two groups was Fusobacteria (Q=0.596, P<0.05). At the genus level, the top 5 genera in the young and middle-aged group in abundance were as follows: Prevotella, Bacteroides, Streptococcus, Selenomonas and Veillonella. In the elderly group, Prevotella, Bacteroides, Streptococcus, Selenomonas and Haemophilus were the top 5 in abundance, and there were significant difference in Fusobacterium between the two groups (Q=0.938, P<0.05). PICRUSt function prediction showed that the abundance of Aminoacyl.tRNA.biosynthesis, Nucleotide.excision.repair, RNA.polymerase, Ribosome, Clavulanic.acid.biosynthesis, Photosynthesis and Photosynthesis. proteins in the elderly group were lower than those in the young and middle-aged group (all Q=0.734, P<0.05). Conclusion: There is no significant difference in α-diversity and β-diversity between elderly ESCC patients and young and middle-aged patients, but the abundance of Fusobacterium flora increased.

Multivalent Carbohydrate-Functionalized Polymer Nanocrystals

Nanoparticles with a covalently bound shell of carbohydrate or sulfate groups, respectively, and a polyethylene core were generated by Ni(II)-catalyzed aqueous copolymerization of ethylene with comonomers undec-10-en-1-yl sulfate, undec-10-en-1-yl β-d-glucoside or undec-10-en-1-yl α-d-mannoside, respectively. Via remote substituents of the catalyst, the degree of branching and consequently degree of crystallinity of the polyethylene core of the glyconanoparticles could be controlled. This in turn impacts particle shapes, from spherical to anisotropic platelets, as observed by cryo-transmission electron microscopy. Enzyme-linked lectin assays revealed the mannose-decorated nanocrystals to be efficient multivalent ligands for concavalin A.

Extraction of DNA from Sperm Cells in Mixed Stain by Nylon Membrane Bushing Separation Technique

OBJECTIVES

To establish a novel method for the separation of sperm cells in mixed stain, and to evaluate its application value.

METHODS

Totally 40 mixed stain samples were collected from sexual assault cases. Sperm cells were separated by the conventional differential lysis method and the nylon membrane bushing separation technique, respectively. The DNA of sperm cells was extracted with the silicon membrane kit （Forensic DNA Extraction Kit for Soft Tissues）. The PCR amplification was performed using AmpFℓSTR® Identifiler® Plus kit, and the products were electrophoresed by 3500xL genetic analyser. The results of two separation methods were then compared.

RESULTS

Complete and single-source male STR genotypes could be obtained from all the 40 mixed stain samples except three samples with minimal residual of female DNA by the nylon membrane bushing separation technique. The STR genotypes of sperm cells could not be detected in 25 samples, which were obtained in 15 samples （seven were of incomplete male STR genotypes, six with residual of female DNA, two were complete and single-source STR genotypes of sperm cells）.

CONCLUSIONS

The nylon membrane bushing separation technique developed in present study can be used in the separation of sperm cells in mixed stain, especially for the extraction of a small amount of sperm from a large quantity of female cells, which is inexpensive, rapid and simple.

The ZZ-type zinc finger of ZZZ3 modulates the ATAC complex-mediated histone acetylation and gene activation

Recognition of histones by epigenetic readers is a fundamental mechanism for the regulation of chromatin and transcription. Most reader modules target specific post-translational modifications on histones. Here, we report the identification of a reader of histone H3, the ZZ-type zinc finger (ZZ) domain of ZZZ3, a subunit of the Ada-two-A-containing (ATAC) histone acetyltransferase complex. The solution NMR structure of the ZZ in complex with the H3 peptide reveals a unique binding mechanism involving caging of the N-terminal Alanine 1 of histone H3 in an acidic cavity of the ZZ domain, indicating a specific recognition of H3 versus other histones. Depletion of ZZZ3 or disruption of the ZZ-H3 interaction dampens ATAC-dependent promoter histone H3K9 acetylation and target gene expression. Overall, our study identifies the ZZ domain of ZZZ3 as a histone H3 reader that is required for the ATAC complex-mediated maintenance of histone acetylation and gene activation.

Histones are recognized by epigenetic readers, which play essential roles in regulation of chromatin and transcription. Here the authors provide evidence that the ZZ-type zinc finger domain of ZZZ3 functions as a reader of histone H3, which is required for the ATAC complex-mediated maintenance of histone acetylation and gene activation.

Depth of field extension and objective space depth measurement based on wavefront imaging

When all the parts of the wavefront imaging system are kept static after wavefront measuring, the target's images are blurry, because the depth of field (DOF) of the system affects the imaging quality. In this paper, the method for extending the DOF of the wavefront imaging system through an integrated architecture of a liquid-crystal microlens array (LCMLA) powered by electricity and a common photosensitive array, is presented. The DOF can be extended remarkably only by stitching together several sub-images of the LCMLA. The problem that the wavefronts and imaging results are insensitive to the objective depth is also solved. Optimal driving voltage signals are found out according to Sobel mean gradient to efficiently calibrate the depth of objective space in order to quantitatively measure the depth. The approach indicates a viable way to effectively extend the DOF of imaging micro-systems and to measure the geometrical depth of targets at the same time.

Multivalent Chromatin Engagement and Inter-domain Crosstalk Regulate MORC3 ATPase

MORC3 is linked to inflammatory myopathies and cancer; however, the precise role of MORC3 in normal cell physiology and disease remains poorly understood. Here, we present detailed genetic, biochemical, and structural analyses of MORC3. We demonstrate that MORC3 is significantly upregulated in Down syndrome and that genetic abnormalities in MORC3 are associated with cancer. The CW domain of MORC3 binds to the methylated histone H3K4 tail, and this interaction is essential for recruitment of MORC3 to chromatin and accumulation in nuclear bodies. We show that MORC3 possesses intrinsic ATPase activity that requires DNA, but it is negatively regulated by the CW domain, which interacts with the ATPase domain. Natively linked CW impedes binding of the ATPase domain to DNA, resulting in a decrease in the DNA-stimulated enzymatic activity. Collectively, our studies provide a molecular framework detailing MORC3 functions and suggest that its modulation may contribute to human disease.

[Application of lymph node labeling with carbon nanoparticles by preoperative endoscopic subserosal injection in laparoscopic radical gastrectomy]

Objective: To evaluate the application value of carbon lymph node tracing technique by preoperative endoscopic subserosal injection in laparoscopic radical gastrectomy. Methods: From June 2013 to February 2015, seventy eight patients with gastric cancer were enrolled and randomly divided into trial group and control group. Subserosal injection of carbon nanoparticles around the tumor was performed by preoperative endoscopic subserosal injection one day before the operation in trial group, while the patients routinely underwent laparoscopic gastrectomy in control group. Results of harvested lymph nodes, postoperative complications were compared between the two groups. Carbon nanoparticle-related side effect was also evaluated. Results: The average number of harvested lymph node in trial group was significantly higher than that in control group (35.5±8.5 vs 29.5±6.5, P<0.05). The rate of overall black-dyed harvested lymph node was 74.7% (1 035/1 386) in trial group, the black-dyed lymph node rate in D1 lymph node was 80.1%, which was significantly higher than that in D2 lymph node (69.8%, χ²=19.38, P<0.01). When comparing the lymph node with and without black-dyed in trial group, the rate of metastasis lymph node was significantly higher in lymph node with black-dyed (17.3% vs 4.0%, χ²=38.67, P<0.01). There was no significant difference in postoperative complications rate between two group (trial group 10.2%; control group 12.8%, χ²=0.00, P>0.05), and no carbon nanoparticle-related side effect was observed. Conclusion: Given a higher harvested lymph node number and a similar rate of complications, preoperative endoscopic subserosal injection of carbon nanoparticles was safe and feasible.

An acetyl-methyl switch drives a conformational change in p53

Individual posttranslational modifications (PTMs) of p53 mediate diverse p53-dependent responses; however, much less is known about the combinatorial action of adjacent modifications. Here, we describe crosstalk between the early DNA damage response mark p53K382me2 and the surrounding PTMs that modulate binding of p53 cofactors, including 53BP1 and p300. The 1.8 Å resolution crystal structure of the tandem Tudor domain (TTD) of 53BP1 in complex with p53 peptide acetylated at K381 and dimethylated at K382 (p53K381acK382me2) reveals that the dual PTM induces a conformational change in p53. The α-helical fold of p53K381acK382me2 positions the side chains of R379, K381ac, and K382me2 to interact with TTD concurrently, reinforcing a modular design of double PTM mimetics. Biochemical and nuclear magnetic resonance analyses show that other surrounding PTMs, including phosphorylation of serine/threonine residues of p53, affect association with TTD. Our findings suggest a novel PTM-driven conformation switch-like mechanism that may regulate p53 interactions with binding partners.

Suppression of Inflammatory Responses by Dihydromyricetin, a Flavonoid from Ampelopsis grossedentata, via Inhibiting the Activation of NF-κB and MAPK Signaling Pathways

Ampelopsis grossedentata, an indigenous plant in southern China, has been used for treating pharyngitis in traditional Chinese medicine for hundreds of years. In this study, we explored the anti-inflammatory activity of dihydromyricetin (1), its major bioactive component, and the underlying mechanism of this action. We demonstrated that 1 suppressed the levels of pro-inflammatory cytokines such as tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6) as well as increased the level of the anti-inflammatory cytokine interleukin-10 (IL-10) in lipopolysaccharide (LPS)-treated mice. Moreover, 1 was found to markedly inhibit the production of nitric oxide (NO) and the levels of TNF-α, IL-1β, and IL-6, whereas it increased the level of IL-10 in LPS-induced RAW 264.7 macrophage cells. Compound 1 also reduced the protein expression of inducible nitric oxide synthase (iNOS), TNF-α, and cyclooxygenase-2 (COX-2) in macrophage cells. Furthermore, 1 suppressed the phosphorylation of NF-kappa B (NF-κB) and IκBα as well as the phosphorylation of p38 and JNK but not ERK1/2 in LPS-stimulated macrophages. Taken together, the present results suggest that 1 exerts its topical anti-inflammatory action through suppressing the activation of NF-κB and the phosphorylation of p38 and JNK. Thus, 1 may be a potentially useful therapeutic agent for inflammatory-related diseases.

An insight into the heat and mass transfer mechanisms of eggshells hatching broiler chicks and its effects to the hatcher environment

Thermodynamic study of incubated eggs is an important component in the optimisation of incubation processes. However, research on the interaction of heat and moisture transfer mechanisms in eggs is rather limited and does not focus on the hatching stage of incubation. During hatch, both the recently hatched chick and the broken eggshell add extra heat and moisture contents to the hatcher environment. In this study, we have proposed a novel way to estimate thermodynamically the amount of water evaporated from a broken eggshell during hatch. The hypothesis of this study considers that previously reported drops in eggshell temperature during hatching of chicks is the result remaining water content evaporating from the eggshell, released on the inner membrane by the recently hatched wet chick, just before hatch. To reproduce this process, water was sprayed on eggshells to mimic the water-fluid from the wet body of a chick. For each sample of eggshell, the shell geometry and weight, surface area and eggshell temperature were measured. Water evaporation losses and convection coefficient were calculated using a novel model approach considering the simultaneous heat and mass transfer profiles in an eggshell. The calculated average convective coefficient was 23.9 ± 7.5 W/m(2) °C, similar to previously reported coefficients in literature as a function of 0.5-1m/s air speed range. Comparison between measured and calculated values for the water evaporation showed 68% probability accuracy, associated to the use of an experimentally derived single heat transfer coefficient. The results support our proposed modelling approach of heat and mass transfer mechanisms. Furthermore, by estimating the amount of evaporated water in an eggshell post-hatch, air humidity levels inside the hatcher can be optimised to ensure wet chicks dry properly while not dehydrating early hatching chicks.

Effect of species-specific sound stimulation on the development and hatching of broiler chicks

1. Previous research has reported that chicken embryos develop a functionary auditory system during incubation and that prenatal sound may play an important role in embryo development and alter the hatch time. In this study the effects of prenatal auditory stimulation on hatch process, hatch performance, the development of embryo and blood parameters were investigated. 2. Four batches of Ross 308 broiler breeder eggs were incubated either in control or in sound-stimulated groups. The sound-stimulated embryos were exposed to a discontinuous sound of species-specific calls by means of a speaker at 72 dB for 16 h a day: maternal calls from d 10 to d 19 of incubation time and embryo/chick calls from d 19 until hatching. The species-specific sound was excluded from the control group. 3. The onset of hatch was delayed in the sound-stimulated group compared to the controls. This was also supported by comparison of the exact hatching time of individual focal chicks within the two groups. However, the sound-stimulated embryos had a lower hatchability than the control group, mainly due to significantly increased numbers of late deaths. 4. The embryos exhibited a similar growth pattern between the sound-stimulated group and the control group. Although sound exposure decreased body weight at d 16, no consistent effect of sound on body weight at incubation stage was observed. Species-specific sound stimulation also had no impact on chick quality, blood values and plasma corticosterone concentrations during hatch.

Structural plasticity of methyllysine recognition by the tandem tudor domain of 53BP1

p53 is dynamically regulated through various posttranslational modifications (PTMs), which differentially modulate its function and stability. The dimethylated marks p53K370me2 and p53K382me2 are associated with p53 activation or stabilization and both are recognized by the tandem Tudor domain (TTD) of 53BP1, a p53 cofactor. Here we detail the molecular mechanisms for the recognition of p53K370me2 and p53K382me2 by 53BP1. The solution structures of TTD in complex with the p53K370me2 and p53K382me2 peptides show a remarkable plasticity of 53BP1 in accommodating these diverse dimethyllysine-containing sequences. We demonstrate that dimeric TTDs are capable of interacting with the two PTMs on a single p53K370me2K382me2 peptide, greatly strengthening the 53BP1-p53 interaction. Analysis of binding affinities of TTD toward methylated p53 and histones reveals strong preference of 53BP1 for p53K382me2, H4K20me2, and H3K36me2 and suggests a possible role of multivalent contacts of 53BP1 in p53 targeting to and accumulation at the sites of DNA damage.

Depletion of white adipocyte progenitors induces beige adipocyte differentiation and suppresses obesity development

Overgrowth of white adipose tissue (WAT) in obesity occurs as a result of adipocyte hypertrophy and hyperplasia. Expansion and renewal of adipocytes relies on proliferation and differentiation of white adipocyte progenitors (WAP); however, the requirement of WAP for obesity development has not been proven. Here, we investigate whether depletion of WAP can be used to prevent WAT expansion. We test this approach by using a hunter-killer peptide designed to induce apoptosis selectively in WAP. We show that targeted WAP cytoablation results in a long-term WAT growth suppression despite increased caloric intake in a mouse diet-induced obesity model. Our data indicate that WAP depletion results in a compensatory population of adipose tissue with beige adipocytes. Consistent with reported thermogenic capacity of beige adipose tissue, WAP-depleted mice display increased energy expenditure. We conclude that targeting of white adipocyte progenitors could be developed as a strategy to sustained modulation of WAT metabolic activity.

Effect of transportation duration of 1-day-old chicks on postplacement production performances and pododermatitis of broilers up to slaughter age

This experiment studied the effect of transportation duration of 1-d-old chicks on dehydration, mortality, production performance, and pododermatitis during the growout period. Eggs from the same breeder flock (Ross PM3) were collected at 35, 45, and 56 wk of age, for 3 successive identical experiments. In each experiment, newly hatched chicks received 1 of 3 transportation duration treatments from the hatchery before placement in the on-site rearing facility: no transportation corresponding to direct placement in less than 5 min (T00), or 4 (T04) or 10 h (T10) of transportation. The chicks were housed in 35-m(2) pens (650 birds each) and reared until 35 d old. Hematocrit and chick BW were measured on sample chicks before and after transportation. During the growout period, bird weight, feed uptake, and feed conversion ratio were measured weekly until slaughter. Transportation duration affected BW; T00 groups had a significantly higher BW than T04 and T10 transported birds but this effect lasted only until d 21. No clear effect on hematocrit, feed uptake, feed conversion ratio, or mortality was observed for birds transported up to 10 h. The decrease in weight in T10 birds was associated with less severe pododermatitis. Increasing age of the breeder flock was correlated with reduced egg fertility and hatchability, and also with higher quality and BW of hatched chicks. Chicks from older breeders also exhibited reduced mortality during the growout period.

Crystal design using multipolar electrostatic interactions: A concept study for organic electronics

Using a simple synthetic protocol, heterohexacene analogues with a quadrupolar distribution of partial charges are readily available. In contrast to most other acenes, these compounds crystallize with a slipped-stack, brickwork-like packing which is mainly controlled by electrostatic interactions. This type of packing offers an advantage for organic semiconductors, because it allows more isotropic charge transport compared to the “herring bone” stacking observed for other acenes.

Exchange of associated factors directs a switch in HBO1 acetyltransferase histone tail specificity

Histone acetyltransferases (HATs) assemble into multisubunit complexes in order to target distinct lysine residues on nucleosomal histones. Here, we characterize native HAT complexes assembled by the BRPF family of scaffold proteins. Their plant homeodomain (PHD)-Zn knuckle-PHD domain is essential for binding chromatin and is restricted to unmethylated H3K4, a specificity that is reversed by the associated ING subunit. Native BRPF1 complexes can contain either MOZ/MORF or HBO1 as catalytic acetyltransferase subunit. Interestingly, while the previously reported HBO1 complexes containing JADE scaffold proteins target histone H4, the HBO1-BRPF1 complex acetylates only H3 in chromatin. We mapped a small region to the N terminus of scaffold proteins responsible for histone tail selection on chromatin. Thus, alternate choice of subunits associated with HBO1 can switch its specificity between H4 and H3 tails. These results uncover a crucial new role for associated proteins within HAT complexes, previously thought to be intrinsic to the catalytic subunit.

Dido3 PHD modulates cell differentiation and division

Death Inducer Obliterator 3 (Dido3) is implicated in the maintenance of stem cell genomic stability and tumorigenesis. Here, we show that Dido3 regulates the expression of stemness genes in embryonic stem cells through its plant homeodomain (PHD) finger. Binding of Dido3 PHD to histone H3K4me3 is disrupted by threonine phosphorylation that triggers Dido3 translocation from chromatin to the mitotic spindle. The crystal structure of Dido3 PHD in complex with H3K4me3 reveals an atypical aromatic-cage-like binding site that contains a histidine residue. Biochemical, structural, and mutational analyses of the binding mechanism identified the determinants of specificity and affinity and explained the inability of homologous PHF3 to bind H3K4me3. Together, our findings reveal a link between the transcriptional control in embryonic development and regulation of cell division.

MicroRNA-145 inhibits the growth, invasion, metastasis and angiogenesis of neuroblastoma cells through targeting hypoxia-inducible factor 2 alpha

Recent evidence shows that hypoxia-inducible factor 2 alpha (HIF-2α) may have critical roles in the growth and progression of neuroblastoma (NB) under non-hypoxic conditions. However, the underlying mechanisms and clinical potentials of normoxic HIF-2α expression in NB still remain largely unknown. In this study, HIF-2α immunostaining was identified in 26/42 NB tissues, which was correlated with clinicopathological features. In subtotal 20 NB cases, microRNA-145 (miR-145) was downregulated and inversely correlated with HIF-2α expression. Bioinformatics analysis revealed a putative miR-145 binding site in the 3'-untranslated region (3'-UTR) of HIF-2α messenger RNA (mRNA). Overexpression or knockdown of miR-145 responsively altered both the mRNA and protein levels of HIF-2α and its downstream genes, cyclin D1, matrix metalloproteinase 14 and vascular endothelial growth factor, in normoxically cultured NB cell lines SH-SY5Y and SK-N-SH. In a luciferase reporter system, miR-145 downregulated the luciferase activity of HIF-2α 3'-UTR, and these effects were abolished by a mutation in the putative miR-145-binding site. Overexpression of miR-145 suppressed the growth, invasion, metastasis and angiogenesis of SH-SY5Y and SK-N-SH cells in vitro and in vivo, while restoration of HIF-2α expression rescued the tumor cells from miR-145-mediated defects in these biological features. Furthermore, anti-miR-145 inhibitor rescued the HIF-2α knockdown-mediated repression on the growth, migration, invasion and angiogenesis of NB cells. These data indicate that miR-145 suppresses HIF-2α expression via the binding site in the 3'-UTR under normoxic conditions, thus inhibiting the aggressiveness and angiogenesis of NB.

Identification of complex vertebral malformation carriers in Holstein cattle in south China

Complex vertebral malformation (CVM) is a recently described monogenic autosomal recessive hereditary defect of Holstein dairy cattle that causes premature birth, aborted fetuses and stillborn calves. Guanine is substituted by thymine (G>T) in the solute carrier family 35 member A3 gene (SLC35A3). A valine is changed to a phenylalanine at position 180 of uridine 5'-diphosphate-N-acetyl-glucosamine transporter protein. CVM is expected to occur in many countries due to the widespread use of sire semen. We developed a created restriction site PCR (CRS-PCR) method to diagnose CVM in dairy cows. This was tested on 217 cows and 125 bulls selected randomly from a Holstein cattle population in south China. Five Holstein cows and five Holstein bulls were identified to be CVM carriers; the percentages of CVM carriers were estimated to be 2.3, 4.0 and 2.9% in the cows, bulls and entire Holstein cattle sample, respectively.

Deacetylation of FOXO3 by SIRT1 or SIRT2 leads to Skp2-mediated FOXO3 ubiquitination and degradation

Sirtuin deacetylases and FOXO (Forkhead box, class O) transcription factors have important roles in many biological pathways, including cancer development. SIRT1 and SIRT2 deacetylate FOXO factors to regulate FOXO function. Because acetylation and ubiquitination both modify the ɛ-amino group of lysine residues, we investigated whether FOXO3 deacetylation by SIRT1 or SIRT2 facilitates FOXO3 ubiquitination and subsequent proteasomal degradation. We found that SIRT1 and SIRT2 promote FOXO3 poly-ubiquitination and degradation. Proteasome-inhibitor treatment prevented sirtuin-induced FOXO3 degradation, indicating that this process is proteasome dependent. In addition, we demonstrated that E3 ubiquitin ligase subunit Skp2 binds preferentially to deacetylated FOXO3. Overexpression of Skp2 caused poly-ubiquitination of FOXO3 and degradation, whereas knockdown of Skp2 increased the amount of FOXO3 protein. We also present evidence that SCF-Skp2 ubiquitinates FOXO3 directly in vitro. Furthermore, mutating four known acetylated lysine residues (K242, K259, K290 and K569) of FOXO3 into arginines to mimic deacetylated FOXO3 resulted in enhanced Skp2 binding but with inhibition of FOXO3 ubiquitination; this suggests that some or all of these four lysine residues are likely the sites for ubiquitination. In the livers of mice deficient in SIRT1, we detected increased expression of FOXO3, indicating SIRT1 regulates FOXO3 protein levels in vivo. Furthermore, we found that the elevation of SIRT1 and Skp2 expression in malignant PC3 and DU145 prostate cells is responsible for the downregulation of FOXO3 protein levels in these cells. Taken together, our data support the notion that deacetylation of FOXO3 by SIRT1 or SIRT2 facilitates Skp2-mediated FOXO3 poly-ubiquitination and proteasomal degradation.