Transcriptomic profiling of nuclei from paraformaldehyde-fixed and formalin-fixed paraffin-embedded brain tissues

BACKGROUND

Paraformaldehyde (PFA) fixation is necessary for histochemical staining, and formalin-fixed and paraffin-embedded (FFPE) tissue archives are the largest repository of clinically annotated specimens. Single-cell gene expression workflows have recently been developed for PFA-fixed and FFPE tissue specimens. However, for tissues where intact cells are hard to recover, including tissues containing highly interconnected neurons, single-nuclear transcriptomics is beneficial. Moreover, since RNA is very unstable, the effects of standard pathological practice on the transcriptome of samples obtained from such archived specimens like FFPE samples are largely anecdotal.

RESULTS

We evaluated the effects of polyformaldehyde (PFA) fixation and paraffin-embedding on transcriptional profiles of the mouse hippocampus obtained by RNA sequencing (RNA-seq). The transcriptomic signatures of nuclei isolated from fresh PFA-fixed and fresh FFPE tissues were comparable to those of cryopreserved samples. However, more differentially expressed genes were obtained for brains after PFA fixation for more than 3 days than in fresh PFA-fixed samples, especially genes involved in spliceosome and synaptic-related pathways. Importantly, the real cell states were destroyed, with oligodendrocyte precursor cells depleted in the 1day fixed hippocampus. After fixation for 3 days, the proportions of neuronal cells and oligodendrocytes decreased and microglia increased; however, relative frequencies remained constant for longer fixation durations. The storage time of FFPE samples had a negligible effect on the cell composition.

SIGNIFICANCE

This represents the first work to investigate the effects of fixation and storage time of brains on its nuclear transcriptome signatures in detail. The fixation time had more influences on the nuclear transcriptomic profiles than FFPE retention time, and the cliff-like effects appeared to occur over a fixed period of 1-3 days. These findings are expected to guide sample preparation for single-nucleus RNA-seq of FFPE samples, particularly in transcriptomic studies focused on brain diseases.

[Safety of double and a half layered esophagojejunal anastomosis in radical gastrectomy: A prospective, multi-center, single arm trial]

Objective: To evaluate the safety of double and a half layered esophagojejunal anastomosis in radical gastrectomy. Methods: This prospective, multi-center, single-arm study was initiated by the Affiliated Cancer Hospital of Zhengzhou University in June 2021 (CRAFT Study, NCT05282563). Participating institutions included Nanyang Central Hospital, Zhumadian Central Hospital, Luoyang Central Hospital, First Affiliated Hospital of Henan Polytechnic University, First Affiliated Hospital of Henan University, Luohe Central Hospital, the People's Hospital of Hebi, First People's Hospital of Shangqiu, Anyang Tumor Hospital, First People's Hospital of Pingdingshan, and Zhengzhou Central Hospital Affiliated to Zhengzhou University. Inclusion criteria were as follows: (1) gastric adenocarcinoma confirmed by preoperative gastroscopy;(2) preoperative imaging assessment indicated that R0 resection was feasible; (3) preoperative assessment showed no contraindications to surgery;(4) esophagojejunostomy planned during the procedure; (5) patients volunteered to participate in this study and gave their written informed consent; (6) ECOG score 0-1; and (7) ASA score I-III. Exclusion criteria were as follows: (1) history of upper abdominal surgery (except laparoscopic cholecystectomy);(2) history of gastric surgery (except endoscopic submucosal dissection and endoscopic mucosal resection); (3) pregnancy or lactation;(4) emergency surgery for gastric cancer-related complications (perforation, hemorrhage, obstruction); (5) other malignant tumors within 5 years or coexisting malignant tumors;(6) arterial embolism within 6 months, such as angina pectoris, myocardial infarction, and cerebrovascular accident; and (7) comorbidities or mental health abnormalities that could affect patients' participation in the study. Patients were eliminated from the study if: (1) radical gastrectomy could not be completed; (2) end-to-side esophagojejunal anastomosis was not performed during the procedure; or (3) esophagojejunal anastomosis reinforcement was not possible. Double and a half layered esophagojejunal anastomosis was performed as follows: (1) Open surgery: the full thickness of the anastomosis is continuously sutured, followed by embedding the seromuscular layer with barbed or 3-0 absorbable sutures. The anastomosis is sutured with an average of six to eight stitches. (2) Laparoscopic surgery: the anastomosis is strengthened by counterclockwise full-layer sutures. Once the anastomosis has been sutured to the right posterior aspect of the anastomosis, the jejunum stump is pulled to the right and the anastomosis turned over to continue to complete reinforcement of the posterior wall. The suture interval is approximately 5 mm. After completing the full-thickness suture, the anastomosis is embedded in the seromuscular layer. Relevant data of patients who had undergone radical gastrectomy in the above 12 centers from June 2021 were collected and analyzed. The primary outcome was safety (e.g., postoperative complications, and treatment). Other studied variables included details of surgery (e.g., surgery time, intraoperative bleeding), postoperative recovery (postoperative time to passing flatus and oral intake, length of hospital stay), and follow-up conditions (quality of life as assessed by Visick scores). Result: [1] From June 2021 to September 2022,457 patients were enrolled, including 355 men and 102 women of median age 60.8±10.1 years and BMI 23.7±3.2 kg/m2. The tumors were located in the upper stomach in 294 patients, mid stomach in 139; and lower stomach in 24. The surgical procedures comprised 48 proximal gastrectomies and 409 total gastrectomies. Neoadjuvant chemotherapy was administered to 85 patients. Other organs were resected in 85 patients. The maximum tumor diameter was 4.3±2.2 cm, number of excised lymph nodes 28.3±15.2, and number of positive lymph nodes five (range one to four. As to pathological stage,83 patients had Stage I disease, 128 Stage II, 237 Stage III, and nine Stage IV. [2] The studied surgery-related variables were as follows: The operation was successfully completed in all patients, 352 via a transabdominal approach, 25 via a transhiatus approach, and 80 via a transthoracoabdominal approach. The whole procedure was performed laparoscopically in 53 patients (11.6%), 189 (41.4%) underwent laparoscopic-assisted surgery, and 215 (47.0%) underwent open surgery. The median intraoperative blood loss was 200 (range, 10-1 350) mL, and the operating time 215.6±66.7 minutes. The anastomotic reinforcement time was 2 (7.3±3.9) minutes for laparoscopic-assisted surgery, 17.6±1.7 minutes for total laparoscopy, and 6.0±1.2 minutes for open surgery. [3] The studied postoperative variables were as follows: The median time to postoperative passage of flatus was 3.1±1.1 days and the postoperative gastrointestinal angiography time 6 (range, 4-13) days. The median time to postoperative oral intake was 7 (range, 2-14) days, and the postoperative hospitalization time 15.8±6.7 days. [4] The safety-related variables were as follows: In total, there were 184 (40.3%) postoperative complications. These comprised esophagojejunal anastomosis complications in 10 patients (2.2%), four (0.9%) being anastomotic leakage (including two cases of subclinical leakage and two of clinical leakage; all resolved with conservative treatment); and six patients (1.3%) with anastomotic stenosis (two who underwent endoscopic balloon dilation 21 and 46 days after surgery, the others improved after a change in diet). There was no anastomotic bleeding. Non-anastomotic complications occurred in 174 patients (38.1%). All patients attended for follow-up at least once, the median follow-up time being 10 (3-18) months. Visick grades were as follows: Class I, 89.1% (407/457); Class II, 7.9% (36/457); Class III, 2.6% (12/457); and Class IV 0.4% (2/457). Conclusion: Double and a half layered esophagojejunal anastomosis in radical gastrectomy is safe and feasible.

Exploration of Multiomic Profiles and Biomarkers as Predictors of Neoadjuvant Chemoradiotherapy Responsiveness in Esophageal Squamous Cell Carcinoma

PURPOSE/OBJECTIVE(S)

The current gold standard of care for resectable locally advanced esophageal cancer is neoadjuvant chemoradiotherapy (NCRT) followed by surgery. Given that only 30-40% of patients with esophageal squamous cell carcinoma (ESCC) achieved a pathologic complete response (pCR) following neoadjuvant chemoradiotherapy, it is critical to understand the biological basis of NCRT resistance in esophageal cancer and identify biomarkers for these patients in order to further personalize treatment plans. We aim to depict the biological landscape of ESCC responsiveness and resistance to neoadjuvant chemoradiotherapy.

MATERIALS/METHODS

Endoscopic biopsied specimens of the primary tumors and paired peripheral blood samples were obtained from 24 patients before neoadjuvant chemoradiotherapy and tested for whole exosome sequencing, RNA sequencing, and DIA mass spectrometry. Genomic data were analyzed for significantly mutated genes, copy number alterations, MSI, TMB, and mutational signatures. Transcriptomics and proteomics data were used to examine differentially activated pathways. GSEA and ActivePathways were used for the single omics level and joint multi-omics analysis, respectively. Tumor microenvironment (TME) characteristics were deconvoluted by xCell upon RNA-seq data. Treatment resistance biomarkers were identified and validated in a separate cohort using mIHC.

RESULTS

In the study cohort, 54% (13/24) of the patients achieved pCR. WES data suggested that FBXW7 was more frequently mutated in the pCR group (fisher test p-value = 0.029), and the most significant cytoband loss in the pCR group was 9p21.3 (qval = 0.001). Differences in TMB, MSI, and mutational signatures were not significant between groups. Combined transcriptomics and proteomics analysis revealed that type I interferon signaling pathways and RIG-I-like receptor signaling pathways(p<0.05) were enriched in non-pCR tumors. Esophageal cancer cohort RNA-seq data from TCGA verified the correlation between the genetic variances (FBXW7 mutation and 9p21.3 loss) and the decreased expression of type I interferon signaling pathway genes. In TME analysis, tolerogenic dendritic cells and exhausted T cell signatures were significantly enriched in non-pCR tumors, indicating an immunosuppressive status in treatment resistant patients. Based on proteomics PPI network and differential expression genes from RNA-seq data, a biomarker panel consisted of 12 proteins predictive of non-pCR tumors was identified: STAT1, EIF2AK2, MX1, BST2, TRIM21, SAMHD1, IFI44L, GBP1, PARP14, ISG15, IFIT3, and HLA-B. The expression of selected genes was validated by mIHC in an independent cohort.

CONCLUSION

Through a multiomics approach, we described the biological characteristics of ESCC with distinct responses to neoadjuvant chemoradiotherapy and proposed a panel of 12 proteins as predictive biomarkers for non-pCR patients.

[Surgical treatment strategy of pulmonary artery sling: a series of 110 cases]

Objective: To examine the effect of surgical treatment in children with pulmonary artery sling and the surgical treatment strategy. Methods: Relevant data of 110 children with pulmonary artery sling admitted to the Department of Cardiac Surgery, Children's Hospital Affiliated to Shandong University from February 2017 to July 2022 were retrospectively analyzed. There were 55 males and 55 females, aging (M(IQR)) 9.0 (10.6) months (range: 1 to 96 months). The weight was 7.8 (3.5) kg (range: 2.5 to 25.0 kg). Of the 110 patients, 108 had different degrees of tracheal stenosis and 2 had normal trachea. Left pulmonary artery transplantation and tracheoplasty were performed in 78 patients. Left pulmonary artery transplantation was performed in 30 patients (11 in our hospital and 19 in other hospitals) due to the lack of an early tracheoplasty technique, in which 24 patients needed stage Ⅱ tracheoplasty due to obvious respiratory symptoms and limited activity endurance, and 6 cases did not intervene. Two children with normal trachea only underwent left pulmonary artery transplantation. Results: Among the 78 children who underwent surgery in the same period, 70 cases recovered smoothly after surgery, of whom respiratory symptoms were significantly reduced or disappeared during the 1 to 65 months follow-up, with similar activity endurance to normal children of the same age. Eight cases died, including 4 cases of postoperative multi-drug resistant bacteria infection, died from tracheal anastomotic opening or septic shock, 1 cases with severe congenital heart disease died from postoperative low cardiac output syndrome difficult to correct, 1 case died from blood pressure could not be maintained due to the compressed left pulmonary artery after transplantation, 2 cases of postoperative digestive system diseases (adhesive intestinal obstruction, gastrointestinal bleeding, etc.). The 24 patients in the staging group were followed for 1 to 84 months. All patients needed stage Ⅱ tracheoplasty due to respiratory symptoms and decreased endurance to activity. Eight cases of the non-intervention tracheal group were successfully separated from the ventilator, cured and discharged in a short period of time. Conclusions: Most children with pulmonary artery sling have tracheal stenosis. Children with low degree of tracheal stenosis and inconspicuous respiratory symptoms can only undergo left pulmonary artery transplantation by lateral thoracotomy. For patients combined with severe tracheal stenosis or obvious respiratory symptoms, a simultaneous left pulmonary artery transplantat and tracheoplasty is recommended.

Dominant constraints on the evolution of rhythmic gene expression

Although the individual transcriptional regulators of the core circadian clock are distinct among different organisms, the autoregulatory feedback loops they form are conserved. This unified design principle explains how daily physiological activities oscillate across species. However, it is unknown whether analogous design principles govern the gene expression output of circadian clocks. In this study, we performed a comparative analysis of rhythmic gene expression in eight diverse species and identified four common distribution patterns of cycling gene expression across these species. We hypothesized that the maintenance of reduced energetic costs constrains the evolution of rhythmic gene expression. Our large-scale computational simulations support this hypothesis by showing that selection against high-energy expenditure completely regenerates all cycling gene patterns. Moreover, we find that the peaks of rhythmic expression have been subjected to this type of selective pressure. The results suggest that selective pressure from circadian regulation efficiently removes unnecessary gene products from the transcriptome, thereby significantly impacting its evolutionary path.

Noncoding transcripts are linked to brain resting-state activity in non-human primates

Brain-derived transcriptomes are known to correlate with resting-state brain activity in humans. Whether this association holds in nonhuman primates remains uncertain. Here, we search for such molecular correlates by integrating 757 transcriptomes derived from 100 macaque cortical regions with resting-state activity in separate conspecifics. We observe that 150 noncoding genes explain variations in resting-state activity at a comparable level with protein-coding genes. In-depth analysis of these noncoding genes reveals that they are connected to the function of nonneuronal cells such as oligodendrocytes. Co-expression network analysis finds that the modules of noncoding genes are linked to both autism and schizophrenia risk genes. Moreover, genes associated with resting-state noncoding genes are highly enriched in human resting-state functional genes and memory-effect genes, and their links with resting-state functional magnetic resonance imaging (fMRI) signals are altered in the brains of patients with autism. Our results highlight the potential for noncoding RNAs to explain resting-state activity in the nonhuman primate brain.

scBrainMap: a landscape for cell types and associated genetic markers in the brain

The great variety of brain cell types is a fundamental element for neuronal circuits. One major goal of modern neuroscience is to decipher the various types of cellular composition and characterize their properties. Due to the high heterogeneity of neuronal cells, until recently, it was not possible to group brain cell types at high resolution. Thanks to the single-cell transcriptome technology, a dedicated database of brain cell types across species has been established. Here, we developed scBrainMap, a database for brain cell types and associated genetic markers for several species. The current scBrainMap database contains 4881 cell types with 26 044 genetic markers identified from 6 577 222 single cells, which link to 14 species, 124 brain regions and 20 different disease states. scBrainMap enables users to perform customized, cross-linked, biologically relevant queries for different cell types of interest. This quantitative information facilitates exploratory research on the role of cell types with regard to brain function in health and disease. Database URL https://scbrainmap.sysneuro.net/.

Cynomolgus-rhesus hybrid macaques serve as a platform for imprinting studies

Genomic imprinting can lead to allele-specific expression (ASE), where one allele is preferentially expressed more than the other. Perturbations in genomic imprinting or ASE genes have been widely observed across various neurological disorders, notably autism spectrum disorder (ASD). In this study, we crossed rhesus cynomolgus monkeys to produce hybrid monkeys and established a framework to evaluate their allele-specific gene expression patterns using the parental genomes as a reference. Our proof-of-concept analysis of the hybrid monkeys identified 353 genes with allele-biased expression in the brain, enabling us to determine the chromosomal locations of ASE clusters. Importantly, we confirmed a significant enrichment of ASE genes associated with neuropsychiatric disorders, including ASD, highlighting the potential of hybrid monkey models in advancing our understanding of genomic imprinting.

MiR-122-5p regulates the mevalonate pathway by targeting p53 in non-small cell lung cancer

The 5-year survival rate of non-small cell lung cancer (NSCLC) patients is very low. MicroRNAs (miRNAs) are involved in the occurrence of NSCLC. miR-122-5p interacts with wild-type p53 (wtp53), and wtp53 affects tumor growth by inhibiting the mevalonate (MVA) pathway. Therefore, this study aimed to evaluate the role of these factors in NSCLC. The role of miR-122-5p and p53 was established in samples from NSCLC patients, and human NSCLC cells A549 using the miR-122-5p inhibitor, miR-122-5p mimic, and si-p53. Our results showed that inhibiting miR-122-5p expression led to the activation of p53. This inhibited the progression of the MVA pathway in the NSCLC cells A549, hindered cell proliferation and migration, and promoted apoptosis. miR-122-5p was negatively correlated with p53 expression in p53 wild-type NSCLC patients. The expression of key genes in the MVA pathway in tumors of p53 wild-type NSCLC patients was not always higher than the corresponding normal tissues. The malignancy of NSCLC was positively correlated with the high expression of the key genes in the MVA pathway. Therefore, miR-122-5p regulated NSCLC by targeting p53, providing potential molecular targets for developing targeted drugs.

mvPPT: A Highly Efficient and Sensitive Pathogenicity Prediction Tool for Missense Variants

Next-generation sequencing technologies both boost the discovery of variants in the human genome and exacerbate the challenges of pathogenic variant identification. In this study, we developed Pathogenicity Prediction Tool for missense variants (mvPPT), a highly sensitive and accurate missense variant classifier based on gradient boosting. mvPPT adopts high-confidence training sets with a wide spectrum of variant profiles, and extracts three categories of features, including scores from existing prediction tools, frequencies (allele frequencies, amino acid frequencies, and genotype frequencies), and genomic context. Compared with established predictors, mvPPT achieves superior performance in all test sets, regardless of data source. In addition, our study also provides guidance for training set and feature selection strategies, as well as reveals highly relevant features, which may further provide biological insights into variant pathogenicity. mvPPT is freely available at http://www.mvppt.club/.

Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys

Integrative analyses of transcriptomic and neuroimaging data have generated a wealth of information about biological pathways underlying regional variability in imaging-derived brain phenotypes in humans, but rarely in nonhuman primates due to the lack of a comprehensive anatomically-defined atlas of brain transcriptomics. Here we generate complementary bulk RNA-sequencing dataset of 819 samples from 110 brain regions and single-nucleus RNA-sequencing dataset, and neuroimaging data from 162 cynomolgus macaques, to examine the link between brain-wide gene expression and regional variation in morphometry. We not only observe global/regional expression profiles of macaque brain comparable to human but unravel a dorsolateral-ventromedial gradient of gene assemblies within the primate frontal lobe. Furthermore, we identify a set of 971 protein-coding and 34 non-coding genes consistently associated with cortical thickness, specially enriched for neurons and oligodendrocytes. These data provide a unique resource to investigate nonhuman primate models of human diseases and probe cross-species evolutionary mechanisms.

RNAlight: a machine learning model to identify nucleotide features determining RNA subcellular localization

Different RNAs have distinct subcellular localizations. However, nucleotide features that determine these distinct distributions of lncRNAs and mRNAs have yet to be fully addressed. Here, we develop RNAlight, a machine learning model based on LightGBM, to identify nucleotide k-mers contributing to the subcellular localizations of mRNAs and lncRNAs. With the Tree SHAP algorithm, RNAlight extracts nucleotide features for cytoplasmic or nuclear localization of RNAs, indicating the sequence basis for distinct RNA subcellular localizations. By assembling k-mers to sequence features and subsequently mapping to known RBP-associated motifs, different types of sequence features and their associated RBPs were additionally uncovered for lncRNAs and mRNAs with distinct subcellular localizations. Finally, we extended RNAlight to precisely predict the subcellular localizations of other types of RNAs, including snRNAs, snoRNAs and different circular RNA transcripts, suggesting the generality of using RNAlight for RNA subcellular localization prediction.

[Active ingredients and in vitro anti-inflammatory effects of Polygoni Cuspidati Rhizoma et Radix decoction pieces by integrated processing and traditional processing: a comparative analysis]

The present study explored the differences in active ingredients and in vitro anti-inflammatory effects of the decoction pieces by integrated processing(IPDP) and traditional processing(TPDP) of Polygoni Cuspidati Rhizoma et Radix(PCRER).The content of polydatin, resveratrol, emodin-8-O-β-D-glucoside, emodin, and physcion in IPDP and TPDP was determined by high-performance liquid chromatography(HPLC).The inflammation model was induced by lipopolysaccharide(LPS) in RAW264.7 cells.The mRNA levels of inflammatory cytokines tumor necrosis factor-α(TNF-α), interleukin-6(IL-6), and interleukin-1β(IL-1β) in 60% ethanol extracts of IPDP and TPDP of different concentrations(5 and 10 μg·mL~(-1)) were determined by PCR.The results showed that the content of polydatin and emodin-8-O-β-D-glucoside in IPDP was significantly higher than that in TPDP, while the content of resveratrol, emodin, and physcion was higher in TPDP.The anti-inflammatory results showed that ethanol extracts of IPDP of different concentrations(5 and 10 μg·mL~(-1)) significantly inhibited the increase in the mRNA levels of IL-1β and TNF-α induced by LPS, whereas TPDP only had a significant inhibitory effect on IL-1β.This study preliminarily showed that the total content of five active ingredients in IPDP was higher than that in TPDP, and IPDP was superior to TPDP in anti-inflammatory activity in vitro, which provided an experimental basis for the production and application of IPDP.

[Effectiveness and safety of robotic assisted-bronchoscopy system in locating and removing spring coils placed in the peripheral lung of beagle dogs: a pilot study]

Objective: To evaluate the effectiveness and safety of the robotic assisted bronchoscope system for localizing and removing the spring coils that placed in the peripheral lung of beagle dogs. Methods: The study was conducted from June 18th to June 20th, 2021. Metallic lung coils were placed as the simulated lesions to the periphery of the lungs of two adult male beagle dogs using a bronchoscope under general anesthesia. The navigation path was planned by the navigation function that built in the robotic bronchoscope system. After training, the doctors operated the robotic bronchoscope system to locate and remove the coils from the lung. The navigation success rate, sampling success rate, position of the coil, navigation time, sampling time, and operation time were evaluated. The damage to the airway mucosa during the operation and the vital signs of the beagles during and post-operation were accessed. Chest computerized tomography (CT) was performed post-operation to detect if there were complications such as pneumothorax and bleeding. Results: A total of 12 spring coils were successfully inserted into the two beagles. All the navigation paths of the simulated lesions were successfully planned. The navigation success rate was 12/12. The navigation time was (43.9±19.8) seconds. The distance between the tip of the flexible endoscope arm and the target point measured by the navigation system was (6.93±2.15) mm. The locations of the simulated lesions were distributed in the 6th-8th generation of bronchi. The sampling success rate was 12/12. The sampling time was (42.4±11.3) seconds. There was no pneumothorax or mediastinal emphysema after the placement of the coil. The vital signs of the beagle dogs were stable throughout the operation, and no operation-related or postoperative complications occurred. Conclusions: The robotic bronchoscope system can be used to locate and remove the spring coils from the peripheral lung of beagle dogs, and the procedure is simple and safe. It suggests that the robotic bronchoscopy system has great clinical significance in the sampling and diagnosis of peripheral lung lesions.

Significant Evolutionary Constraints on Neuron Cells Revealed by Single-Cell Transcriptomics

Recent advances in single-cell RNA-sequencing technology have enabled us to characterize a variety of different cell types in each brain region. However, the evolutionary differences among these cell types remain unclear. Here, we analyzed single-cell RNA-seq data of >280,000 cells and developmental transcriptomes of bulk brain tissues. At the single-cell level, we found that the evolutionary constraints on the cell types of different organs significantly overlap with each other and the transcriptome of neuron cells is one of the most restricted evolutionarily. In addition, mature neurons are under more constraints than neuron stem cells as well as nascent neurons and the order of the constraints of various cell types of the brain is largely conserved in different subregions. We also found that although functionally similar brain regions have comparable evolutionary constraints, the early fetal brain is the least constrained and this pattern is conserved in the mouse, macaque, and humans. These results demonstrate the importance of maintaining the plasticity of early brain development during evolution. The delineation of evolutionary differences between brain cell types has great potential for an improved understanding of the pathogenesis of neurological diseases and drug development efforts aimed at the manipulation of molecular activities at the single-cell level.

Rapid Body-Wide Transcriptomic Turnover During Rhesus Macaque Perinatal Development

An hourglass cup-shape pattern of regulation at the molecular level was detected during the development of the primate brain. Specifically, a peak of temporally differentially expressed genes around the time of birth has been observed in the human brain. However, to what extend this peak of regulation exists among species has not been investigated in great detail. Here, by integrating multiple large-scale transcriptome data from rhesus macaques, we confirmed that a similar differential expression peak exists during the development of the macaque brain. We also found that a similar peak exists during the development of other organs, such as liver, testis, kidney and heart. Furthermore, we found that distinct pathways are regulated in the peak period of those organs. Our results highlight the importance of co-evolution of diverse organs during critical periods of perinatal development in primates.

Chromatin-Binding Protein PHF6 Regulates Activity-Dependent Transcriptional Networks to Promote Hunger Response

Understanding the mechanisms of activity-dependent gene transcription underlying adaptive behaviors is challenging at neuronal-subtype resolution. Using cell-type specific molecular analysis in agouti-related peptide (AgRP) neurons, we reveal that the profound hunger-induced transcriptional changes greatly depend on plant homeodomain finger protein 6 (PHF6), a transcriptional repressor enriched in AgRP neurons. Loss of PHF6 in the satiated mice results in a hunger-state-shifting transcriptional profile, while hunger fails to further induce a rapid and robust activity-dependent gene transcription in PHF6-deficient AgRP neurons. We reveal that PHF6 binds to the promoters of a subset of immediate-early genes (IEGs) and that this chromatin binding is dynamically regulated by hunger state. Depletion of PHF6 decreases hunger-driven feeding motivation and makes the mice resistant to body weight gain under repetitive fasting-refeeding conditions. Our work identifies a neuronal subtype-specific transcriptional repressor that modulates transcriptional profiles in different nutritional states and enables adaptive eating behavior.

Formation of a Key Intermediate Complex Species in Catalytic Hydrolysis of NH3BH3 by Bimetal Clusters: Metal-Dihydride and Boron-Multihydroxy

The hydrolysis of AB (AB, NH₃BH₃) with the help of transition metal catalysts has been identified as one of the promising strategies for the dehydrogenation in numerous experiments. Although great progress has been achieved in experiments, evaluation of the B-N bond cleavage channel as well as the hydrogen transfer channel has not been performed to gain a deep understanding of the kinetic route. Based on the density functional theory (DFT) calculation, we presented a clear mechanistic study on the hydrolytic reaction of AB by choosing the smallest NiCu cluster as a catalyst model. Two attacking types of water molecules were considered for the hydrolytic reaction of AB: stepwise and simultaneous adsorption on the catalyst. The Ni and Cu metal atoms play the distinctive roles in catalytic activity, i.e., Ni atom takes reactions for the H₂O decomposition with the formation of [OH]⁻ group whereas Cu atom takes reactions for the hydride transfer with the formation of metal-dihydride complex. The formation of Cu-dihydride and B-multihydroxy complex is the prerequisite for the effectively hydrolytic dehydrogenation of AB. By analyzing the maximum barrier height of the pathways which determines the kinetic rates, we found that the hydride hydrogen transferring rather than the N-B bond breaking is responsible to the experimentally measured activation energy barrier.

Epigenetic inheritance of circadian period in clonal cells

Circadian oscillations are generated via transcriptional-translational negative feedback loops. However, individual cells from fibroblast cell lines have heterogeneous rhythms, oscillating independently and with different period lengths. Here we showed that heterogeneity in circadian period is heritable and used a multi-omics approach to investigate underlying mechanisms. By examining large-scale phenotype-associated gene expression profiles in hundreds of mouse clonal cell lines, we identified and validated multiple novel candidate genes involved in circadian period determination in the absence of significant genomic variants. We also discovered differentially co-expressed gene networks that were functionally associated with period length. We further demonstrated that global differential DNA methylation bidirectionally regulated these same gene networks. Interestingly, we found that depletion of DNMT1 and DNMT3A had opposite effects on circadian period, suggesting non-redundant roles in circadian gene regulation. Together, our findings identify novel gene candidates involved in periodicity, and reveal DNA methylation as an important regulator of circadian periodicity.

Twin-peak temporal regulation during human neocortical development

Understanding the temporal and spatial expression patterns of the human cerebral cortex is essential for expanding knowledge of its functionality. Previous analysis focused on the differentially expressed genes (DEGs) among cortical subregions revealed an hourglass model for interareal differences. However, the overall pattern of transcriptional differences during the development of every region remains to be fully explored. Here, analysing more than 800 neocortex samples from lifespan transcriptional profiles revealed that excitatory neurons are more regulated than inhibitory neurons in the foetal brain. Developmental DEGs tend to be resting state or memory encoding-related and are also involved in autism and Alzheimer’s disease. In addition, twin peaks of DEGs occur during the development of each neocortex region, with a first peak appearing in the perinatal period and an unexpected second peak appearing around childhood. Genes in these peaks have similar functions, but the second peak is more inhibitory neuron related. All these results emphasize the significance of this unique temporal regulatory pattern for human neocortical development.

A single factor dominates the behavior of rhythmic genes in mouse organs

Background

Circadian rhythm, regulated by both internal and external environment of the body, is a multi-scale biological oscillator of great complexity. On the molecular level, thousands of genes exhibit rhythmic transcription, which is both organ- and species-specific, but it remains a mystery whether some common factors could potentially explain their rhythmicity in different organs. In this study we address this question by analyzing the transcriptome data in 12 mouse organs to determine such major impacting factors.

Results

We found a strong positive correlation between the transcriptional level and rhythmic amplitude of circadian rhythmic genes in mouse organs. Further, transcriptional level could explain over 70% of the variation in amplitude. In addition, the functionality and tissue specificity were not strong predictors of amplitude, and the expression level of rhythmic genes was linked to the energy consumption associated with transcription.

Conclusion

Expression level is a single major factor impacts the behavior of rhythmic genes in mouse organs. This single determinant implicates the importance of rhythmic expression itself on the design of the transcriptional system. So, rhythmic regulation of highly expressed genes can effectively reduce the energetic cost of transcription, facilitating the long-term adaptive evolution of the entire genetic system.

Application of Computational Biology to Decode Brain Transcriptomes

The rapid development of high-throughput sequencing technologies has generated massive valuable brain transcriptome atlases, providing great opportunities for systematically investigating gene expression characteristics across various brain regions throughout a series of developmental stages. Recent studies have revealed that the transcriptional architecture is the key to interpreting the molecular mechanisms of brain complexity. However, our knowledge of brain transcriptional characteristics remains very limited. With the immense efforts to generate high-quality brain transcriptome atlases, new computational approaches to analyze these high-dimensional multivariate data are greatly needed. In this review, we summarize some public resources for brain transcriptome atlases and discuss the general computational pipelines that are commonly used in this field, which would aid in making new discoveries in brain development and disorders.

Clinical practice guideline for image-guided multimode tumour ablation therapy in hepatic malignant tumours

Multimode tumour ablation therapy is a treatment method that combines cryoablation with radiofrequency ablation, guided by medical imaging technology and based on precise planning, targeting, monitoring, and control of the thermal energy delivered, with the aim of achieving a whole-body antitumour immune response to malignant tumours. To develop standardized criteria for the application of multimode tumour ablation therapy to malignant hepatic tumours, to facilitate actualization of the criteria in various hospitals, and to ensure therapeutic efficacy and safety, the Society of Interventional Therapy of the Chinese Anti-Cancer Association and the Solid Tumor Theranostics Committee of the Shanghai Anti-Cancer Association assembled experts who specialize in oncology to discuss this treatment method and to arrive at a clinical practice consensus guideline for the indications, contraindications, and techniques of multimode tumour ablation therapy for malignant hepatic tumours.

99Non-ruptured plaque and platelet-rich thrombi in ST-segment elevation myocardial infarction: new insight into early spontaneous reperfusion

Objectives

To detect the potential mechanism of early spontaneous reperfusion (ESR) in STEMI.

Background

Early spontaneous reperfusion occurs in around 20% of STEMI and is associated with favorable outcomes. Optical coherence tomography (OCT) is more accurate in detecting subtle morphological details of the culprit lesion.

Methods

In this prospective study, a total of 107 consecutive patients with STEMI were enrolled from July 2016 to May 2017. Of that total, 21 (19.6%) met the criteria of angiographic ESR (TIMI-3 flow in the initial angiogram). Among those without ESR (TIMI-0 flow in the initial angiogram), 21 patients were assigned into the control group according to propensity score matching with the ESR group. The OCT findings and one-year clinical outcomes were compared between the two groups.

Results

Although baseline characteristics were comparable, plaque features significantly differed between the ESR and control group (P<0.001), including plaque rupture (23.8% vs. 66.7%), plaque erosion (47.6% vs. 33.3%), calcified nodule (9.5% vs. 0%) and vasospasm (19.1% vs. 0%). Red thrombus (19.1% vs. 85.7%) was far less found whereas white thrombus (61.9% vs. 14.3%) was more common in the ESR group. In addition, despite of less stent placement (0.6±0.5 vs. 1.3±0.9, P<0.001), patients in the ESR group had a non-statistically lower rate of cardiac adverse events (4.8% vs. 14.3%, P=0.269) during one-year follow up.

The OCT finding Variables ESR group (n=21) Control group (n=21) P value The OCT imaging <0.001   Plaque erosion 10 (47.6) 7 (33.3)   Plaque rupture 5 (23.8) 14 (66.7)   Calcified nodule 2 (9.5) 0 (0)   Vasospasm 4 (19.1) 0 (0) The Type of Thrombus <0.001   Red thrombus 4 (19.1) 18 (85.7)   White thrombus 13 (61.9) 3 (14.3)   No thrombus (vasospasm) 4 (19.1) 0 (0)   MLA (mm2) 2.7±2.2 2.3±2.4 0.534 Values are n (%), mean ± SD. ESR = early spontaneous reperfusion; MLA = Minimum lumen area; OCT = optical coherence tomography.

ESR and control group

Conclusions

Relief of coronary occlusion induced by non-ruptured plaque and platelet-rich thrombi may be one of the main mechanism underlying early spontaneous reperfusion in STEMI.

Acknowledgement/Funding

No.81470491 from the National Natural Science Foundation of China and No.7192078 from Beijing Municipal Natural Science Foundation to Dr. Li.

Structural analysis of fungal CENP-H/I/K homologs reveals a conserved assembly mechanism underlying proper chromosome alignment

The kinetochore is a proteinaceous complex that is essential for proper chromosome segregation. As a core member of the inner kinetochore, defects of each subunit in the CENP-H/I/K complex cause dysfunction of kinetochore that leads to chromosome mis-segregation and cell death. However, how the CENP-H/I/K complex assembles and promotes kinetochore function are poorly understood. We here determined the crystal structures of CENP-I N-terminus alone from Chaetomium thermophilum and its complex with CENP-H/K from Thielavia terrestris, and verified the identified interactions. The structures and biochemical analyses show that CENP-H and CENP-K form a heterodimer through both N- and C-terminal interactions. CENP-I integrates into the CENP-H/K complex by binding to the C-terminus of CENP-H, leading to formation of the ternary complex in which CENP-H is sandwiched between CENP-K and CENP-I. Our sequence comparisons and mutational analyses showed that this architecture of the CENP–H/I/K complex is conserved in human. Mutating the binding interfaces of CENP-H for either CENP-K or CENP-I significantly reduced their localizations at centromeres and induced massive chromosome alignment defects during mitosis, suggesting that the identified interactions are critical for CENP-H/I/K complex assembly at the centromere and kinetochore function. Altogether, our findings unveil the evolutionarily conserved assembly mechanism of the CENP-H/I/K complex that is critical for proper chromosome alignment.

Human Genomic Signatures of Brain Oscillations During Memory Encoding

Memory encoding is an essential step for all learning. However, the genetic and molecular mechanisms underlying human memory encoding remain poorly understood, and how this molecular framework permits the emergence of specific patterns of brain oscillations observed during mnemonic processing is unknown. Here, we directly compare intracranial electroencephalography recordings from the neocortex in individuals performing an episodic memory task with human gene expression from the same areas. We identify genes correlated with oscillatory memory effects across 6 frequency bands. These genes are enriched for autism-related genes and have preferential expression in neurons, in particular genes encoding synaptic proteins and ion channels, supporting the idea that the genes regulating voltage gradients are involved in the modulation of oscillatory patterns during successful memory encoding across brain areas. Memory-related genes are distinct from those correlated with other forms of cognitive processing and resting state fMRI. These data are the first to identify correlations between gene expression and active human brain states as well as provide a molecular window into memory encoding oscillations in the human brain.

Understanding Molecular Mechanisms of the Brain Through Transcriptomics

The brain is the most complicated organ in the human body with more than ten thousand genes expressed in each region. The molecular activity of the brain is divergent in various brain regions, both spatially and temporally. The function of each brain region lies in the fact that each region has different gene expression profiles, the possibility of differential RNA splicing, as well as various post-transcriptional and translational modification processes. Understanding the overall activity of the brain at the molecular level is essential for a comprehensive understanding of how the brain works. Fortunately, the development of next generation sequencing technology has made it possible to measure the molecular activity of a specific tissue as a daily routine approach of research. Therefore, at the molecular level, the application of sequencing technology to investigate the molecular organization of the brain has become a novel field, and significant progress has been made recently in this field. In this paper, we reviewed the major computational methods used in the analysis of brain transcriptome, including the application of these methods to the research of human and non-human mammal brains. Finally, we discussed the utilization of transcriptome methods in neurological diseases.

[Clinical significance of low-dose CT performed for three consecutive years in diagnosis of lung nodules in coal mine workers with 20 working years]

Objective: To investigate the clinical significance of low-dose CT (LDCT) in coal mine workers with relatively long working years. Methods: A total of 907 coal mine workers with ≥20 working years were enrolled, among whom there were 863 male and 44 female workers with a mean age of 49.5 years. Digital radiography (DR) was performed for these workers in 2013, and LDCT was performed for three consecutive years from 2014 to 2016. Results: A total of 32 workers were found to have lung nodules by DR in 2013, while in 2014, 269 workers were found to have non-calcified lung nodules by LDCT, and there was a significant difference in the number of workers with lung nodules (χ(2)=233.73, P<0.005) . There was also a significant difference in the detection rate of nodules between the workers with different working years of dust exposure (χ(2)=6.648, P=0.00) . The male workers had a significantly higher detection rate of nodules than the female workers (χ(2)=5.690, P=0.017) . There was no significant difference in the number of nodules between workers with different types of work (χ(2)=16.985, P=0.05) . There were 443 lung nodules in total, among which 71.56% were solid nodules and 55.75% had a size of ≤4mm; malignant nodules were confirmed by surgery in 6 (0.66%) of the 907 workers after baseline LDCT. LDCT reexamination in 2015 and 2016 found new nodules in 8 workers and enlarged nodules in 3 workers, and there was no significant change in the number of nodules with a size of ≤4 mm. Conclusions: It is necessary to perform high-risk population screening for coal mine workers by LDCT. The follow-up strategies for nodules with a size of ≤4mm are the same as those for negative results; annual reexamination is recommended for nodules with a size of >4-8 mm, and clinical treatment should be considered for nodules with a size of >8 mm.

[Comparison of safety between continued warfarin therapy and bridging anticoagulation therapy in patients undergoing coronary intervention]

Objective: To compare the safety of continued warfarin therapy and bridging anticoagulation therapy during hospital stay in patients undergoing percutaneous coronary intervention (PCI). Methods: We retrospectively analyzed patients on warfarin therapy referred for PCI in Beijing Anzhen Hospital from January 2008 to December 2016. The patients were divided into continued warfarin therapy (n=195) or bridging anticoagulation therapy (n=311) groups. After Propensity Score Matching, data from matched patients (n=123 in each group) were analyzed. Bleeding complications and major adverse cardiac events including death, myocardial infarction, target vessel revascularization, and stent thrombosis were assessed. Results: There were no significant difference in the rate of death (2.4%(3/123) vs. 1.6%(2/123),P=0.54), acute myocardial infarction (4.1%(5/123) vs. 4.9%(6/123), P=0.78),re-revascularization (0.8%(1/123) vs. 1.6%(2/123),P=0.16), stent thrombosis (1.6%(2/123) vs. 1.6%(2/123),P=1.00) and stroke between the two groups. Prevalence of minor bleeding complications was significantly higher in the bridging therapy group (15.4%(19/123) vs. 9.8%(12/123),P=0.01). Rate of access-site complications (hematoma:4.1%(5/123) vs. 2.4%(3/123),P=0.20; pseudoaneurysm:2.4%(3/123) vs. 2.4%(3/123),P=1.00; arteriovenous fistula:0.8%(1/123) vs. 1.6%(2/123),P=0.09; and retroperitoneal hematoma:0(0/123) vs. 0.8%(1/123),P=0.23) were similar between the two groups. Conclusion: For patients receiving chronic warfarin therapy, the uninterrupted oral anticoagulant treatment is as safe as bridging therapy in PCI patients.

A combustion method to synthesize nanoporous graphene

In this paper, we introduce a combustion method which is rapid, low cost, mass-producing and environmentally friendly to produce nanoporous graphene. After loading a graphene oxide aerogel (GOA)/paper (GOP) on a preheated hot plate (as the heat source, with a temperature as low as 200 °C) under an ambient environment, in a few seconds, the GOA/GOP would self-combust and change into reduced graphene oxide (RGO) with nanopores mainly concentrated in the 0.4-2.0 nm range and a large specific surface area of 536 m2 g-1. Supercapacitors fabricated with the synthesized porous RGO (P-RGO) showed a high specific capacitance of 245 F g-1 at 0.1 A g-1, and a retention rate of about 96.9% after 12 000 cycle tests with respect to the initial specific capacitance with a scan rate of 10.0 A g-1. The production yield of this method was as high as 77.0%.

Analysis of genetic diversity of Chinese dairy goats via microsatellite markers

In this study, 15 polymorphic microsatellite markers were used to analyze the genetic structure and phylogenetic relationships of 6 dairy goat breeds in China, including 4 native developed breeds and 2 introduced breeds. The results showed that a total of 172 alleles were detected in 347 samples of the dairy goat breeds included in this study. The mean number of effective alleles per locus was 4.92. Except for BMS0812, all of the remaining microsatellite loci were highly polymorphic (polymorphism information content [PIC] > 0.5). The analysis of genetic diversity parameters, including the number of effective alleles, PIC, and heterozygosity, revealed that the native developed dairy goat breeds in China harbored a rich genetic diversity. However, these breeds showed a low breeding degree and a high population intermix degree, with a certain degree of inbreeding and within-subpopulation inbreeding coefficient ( > 0). The analysis of population genetic differentiation and phylogenetic tree topologies showed a moderate state of genetic differentiation among subpopulations of native developed breed dairy goats in China (0.05 < gene fixation coefficient [] < 0.15). The native developed breeds shared a common ancestor, namely, the Saanen dairy goat, originating from Europe. The results showed that there was a close genetic relationship between Wendeng and Laoshan dairy goats while the Guanzhong dairy goat and the Xinong Saanen dairy goat were also found to have a close genetic relationship, which were both in agreement with the formation history and geographical distribution of the breeds. This study revealed that adopting genetic management strategies, such as expanding pedigree source and strengthening multi-trait selection, is useful in maintaining the genetic diversity of native developed breeds and improving the population uniformity of dairy goats.

[Factors influencing antiretroviral therapy adherence among HIV-infected people on antiretroviral therapy in Ili Kazakh Autonomous Prefecture]

Objective: To analyze factors influencing antiretroviral therapy (ART) adherence among human immunodeficiency virus (HIV) patients receiving ART at the town level in Ili Kazakh Autonomous Prefecture (Ili) in May 2015 and to document enhanced ART for acquired immunodeficiency syndrome (AIDS) cases. Methods: A cross-sectional survey was conducted using one-on-one interviews and data collection from the system of AIDS follow-up management in three ART services centers at the town level of Ili. The subjects were HIV-infected individuals, aged 18 years or older, who were receiving ART during the survey. The surveys collected demographic characteristics, information related to ART and status of engaging ART, smoking and drinking behavior, depression, and quality of life. Results: A total of 412 participants completed the survey. The age was (41.1±8.0) years (range, 19-67 years). Approximately 60.9% (251) were male and 39.1% (161) were female. The survey showed that 75.0% (309) of participants were in good adherence and the P(50) (P(25), P(75)) of quality of life was 56.31 (50.55, 59.42). Females demonstrated better adherence to ART (82.6% (n=133)) than males (70.1% (n=76)) (χ(2)=8.16, P=0.005). The compliance rate of participants (78.0% (n=54)) with depression was higher than non-depressed participants (63.5% (n=255)) (χ(2)=7.52, P=0.008). Multivariate logistic regression analyses showed that the probability of good adherence to ART increased with increasing quality of life (OR=1.06, 95%CI:1.02-1.09). Moreover, participants who consumed alcohol or disclosed their HIV infection status to families were less likely to have good adherence to ART (OR=0.26, 95% CI:0.13-0.53 and OR=0.31, 95% CI:0.13-0.72, respectively). Additionally, employed participants were also less likely to have good adherence to ART compared with unemployed participants (OR=0.45, 95% CI:0.21-0.97). Conclusion: HIV/AIDS patients primarily showed good adherence to ART. Factors related to ART adherence included alcohol consumption, informing family of infection, work status, and quality of life.

Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity

Motivation

Formation of homodimers by identical Dscam1 protein isomers on cell surface is the key factor for the self-avoidance of growing neurites. Dscam1 immense diversity has a critical role in the formation of arthropod neuronal circuit, showing unique evolutionary properties when compared to other cell surface proteins. Experimental measures are available for 89 self-binding and 1722 hetero-binding protein samples, out of more than 19 thousands (self-binding) and 350 millions (hetero-binding) possible isomer combinations.

Results

We developed Dscam1 Web Server to quickly predict Dscam1 self- and hetero- binding affinity for batches of Dscam1 isomers. The server can help the study of Dscam1 affinity and help researchers navigate through the tens of millions of possible isomer combinations to isolate the strong-binding ones.

Availability and Implementation

Dscam1 Web Server is freely available at: http://bioinformatics.tecnoparco.org/Dscam1-webserver . Web server code is available at https://gitlab.com/ne1s0n/Dscam1-binding .

Contact

simone.marini@unipv.it or guangzhong.wang@picb.ac.cn.

Supplementary information

Supplementary data are available at Bioinformatics online.

[Analysis of Koch phenomenon of Mycobacterium tuberculosis-infected guinea pigs vaccinated with recombinant tuberculosis vaccine AEC/BC02]

OBJECTIVE

To observe the Koch phenomenon of Mycobacterium tuberculosis(MTB)-infected guinea pigs after vaccinated with killed H37Ra bacteria or tuberculosis vaccine candidate AEC/BC02.

METHODS

Eighteen guinea pigs were challenged subcutaneously with 5.0×10(3) CFU MTB and after 40 days were divided into 3 groups (6 per group): NS group, AEC/BC02 group and H37Ra group, which were injected intramuscularly 3 times at 1 day interval with normal saline, AEC/BC02 vaccine and killed H37Ra bacteria respectively. Three weeks after the first vaccination, all guinea pigs were sacrificed to evaluate gross pathological scores for liver, spleen and lung, bacterial loads in lung and spleen, and lung inflammation.

RESULTS

The gross pathological score in H37Ra group (48±26) was lower than that in NS group(62±15), but the difference was not significant (t=1.093, P=0.300). The AEC/BC02 group had a significantly lower gross pathological score (36±15) than NS group (t=2.980, P=0.014). No significant difference between H37Ra group and AEC/BC02 group was observed (t=1.009, P=0.337). The spleen bacterial load [(5.31±0.80) log10 CFU]in H37Ra group was slightly lower than that in NS group[(5.57±0.75) log10 CFU] but the difference was not significant (t=1.581, P=0.574). In AEC/BC02 group bacterial load in the spleen was (4.64±0.64) log10 CFU and significantly lower than NS group (t=2.306, P=0.044) and no significant difference between H37Ra group and AEC/BC02 group was observed (t=1.602, P=0.140). Meanwhile, the lung bacterial load in AEC/BC02 group was (3.71±1.01) log10 CFU and in H37Ra group was (3.82±1.25) log10 CFU. Compared to (4.15±0.69) log10 CFU in the NS group, no significant differences were found (t=0.881, P=0.399; t=0.566, P=0.584, respectively). For the lung inflammation, the inflamed areas in H37Ra group were significantly larger [(33.0±4.4%)] than those in both NS group [(14.8±8.4) %, t=4.719, P=0.001] and AEC/BC02 group [(14.8±8.4) %, t=3.616, P=0.005], and no significant differences were seen between AEC/BC02 group and NS group (t=1.041, P=0.322).

CONCLUSION

The lung inflammation indicated that killed H37Ra bacteria evoked an obvious Koch reaction in the MTB-infected guinea pigs, whereas AEC/BC02 vaccine showed a low risk of causing Koch phenomenon.

[Influencing factors for trauma-induced tibial infection in underground coal mine]

Objective: To investigate the influencing factors for trauma-induced tibial infection in underground coal mine. Methods: A retrospective analysis was performed for the clinical data of 1 090 patients with tibial fracture complicated by bone infection who were injured in underground coal mine and admitted to our hospital from January 1995 to August 2015, including the type of trauma, injured parts, severity, and treatment outcome. The association between risk factors and infection was analyzed. Results: Among the 1 090 patients, 357 had the clinical manifestations of acute and chronic bone infection, 219 had red and swollen legs with heat pain, and 138 experienced skin necrosis, rupture, and discharge of pus. The incidence rates of tibial infection from 1995 to 2001, from 2002 to 2008, and from 2009 to 2015 were 31%, 26.9%, and 20.2%, respectively. The incidence rate of bone infection in the proximal segment of the tibia was significantly higher than that in the middle and distal segments (42.1% vs 18.9%/27.1%, P<0.01) . As for patients with different types of trauma (Gustilo typing) , the patients with type III fracture had a significantly higher incidence rate of bone infection than those with type I/II infection (52.8% vs 21.8%/24.6%, P<0.01) . The incidence rates of bone infection after bone traction, internal fixation with steel plates, fixation with external fixator, and fixation with intramedullary nail were 20.7%, 43.5%, 21.4%, and 26.1%, respectively, suggesting that internal fixation with steel plates had a significantly higher incidence rate of bone infection than other fixation methods (P<0.01) . The multivariate logistic regression analysis showed that the position of tibial fracture and type of fracture were independent risk factors for bone infection. Conclusion: There is a high incidence rate of trauma-induced tibial infection in workers in underground coal mine. The position of tibial fracture and type of fracture are independent risk factors for bone infection. Vacuum sealing drainage and Ilizarov technique can achieve a satisfactory therapeutic effect.

[A new kinematics method of determing elbow rotation axis and evaluation of its feasibility]

OBJECTIVE

To study a new positioning method of elbow external fixation rotation axis, and to evaluate its feasibility.

METHODS

Four normal adult volunteers and six Sawbone elbow models were brought into this experiment. The kinematic data of five elbow flexion were collected respectively by optical positioning system. The rotation axes of the elbow joints were fitted by the least square method. The kinematic data and fitting results were visually displayed. According to the fitting results, the average moving planes and rotation axes were calculated. Thus, the rotation axes of new kinematic methods were obtained. By using standard clinical methods, the entrance and exit points of rotation axes of six Sawbone elbow models were located under X-ray. And The kirschner wires were placed as the representatives of rotation axes using traditional positioning methods. Then, the entrance point deviation, the exit point deviation and the angle deviation of two kinds of located rotation axes were compared.

RESULTS

As to the four volunteers, the indicators represented circular degree and coplanarity of elbow flexion movement trajectory of each volunteer were both about 1 mm. All the distance deviations of the moving axes to the average moving rotation axes of the five volunteers were less than 3 mm. All the angle deviations of the moving axes to the average moving rotation axes of the five volunteers were less than 5°. As to the six Sawbone models, the average entrance point deviations, the average exit point deviations and the average angle deviations of two different rotation axes determined by two kinds of located methods were respectively 1.697 2 mm, 1.838 3 mm and 1.321 7°. All the deviations were very small. They were all in an acceptable range of clinical practice.

CONCLUSION

The values that represent circular degree and coplanarity of volunteer's elbow single curvature movement trajectory are very small. The result shows that the elbow single curvature movement can be regarded as the approximate fixed axis movement. The new method can replace the traditional method in accuracy. It can make up the deficiency of the traditional fixed axis method.

Regulatory effect of miRNA on multi-directional differentiation ability of mesenchymal stem cell in treatment of osteoporosis

This study was designed to evaluate the effect of miRNA acting in regulating multi-directional differentiation ability of mesenchymal stem cell in treatment of osteoporosis (OP), with the aim of finding a new idea and approach for clinical treatment of OP. Estrogen deficiency-induced OP mice model was established by means of ovariectomy (OVX). Additionally, a sham group was set up for control. Bone Marrow Mesenchymal Stem Cells (BMMSCs) of OVX group (O/BMMSCs) and BMMSCs of sham group (S/BMMSCs) were separately cultured. Then surface markers of BMMSCs were detected. Multi-directional differentiation ability was identified in the two groups by giving cells targeted induced stimulation. It was found that the bone trabecula, bone density and bone volume fraction of distal femoral metaphysis in the OVX group were much lower than those of the sham group. Moreover, trabecular bone space in the OVX group became larger; O/BMMSCs and S/BMMSCs both had normal expression of surface markers as well as potentials of osteogenic and adipogenic differentiation; O/BMMSCs had a weaker osteogenic capability but a stronger adipogenic capability than S/BMMSCs. All the findings suggest that the regulatory effect of miRNA on multi-directional differentiation ability plays a vital role in the treatment of OP, and there is a close correlation between them; deficiency or functional defect of BMMSCs can result in the occurrence of OP.

Correspondence between Resting-State Activity and Brain Gene Expression

The relationship between functional brain activity and gene expression has not been fully explored in the human brain. Here, we identify significant correlations between gene expression in the brain and functional activity by comparing fractional amplitude of low-frequency fluctuations (fALFF) from two independent human fMRI resting-state datasets to regional cortical gene expression from a newly generated RNA-seq dataset and two additional gene expression datasets to obtain robust and reproducible correlations. We find significantly more genes correlated with fALFF than expected by chance and identify specific genes correlated with the imaging signals in multiple expression datasets in the default mode network. Together, these data support a population-level relationship between regional steady-state brain gene expression and resting-state brain activity.

Investigation of the diversity and origins of Chinese dairy goats via the mitochondrial DNA D-loop

To determine the genetic diversity, origins, and the phylogeography of Chinese dairy goats, we analyzed 162 complete mitochondrial DNA (mtDNA) D- loop sequences from 9 dairy goat breeds and compared them with 8 goat sequences that were previously reported in GenBank. The length of the mtDNA D-loop was 1,212 to 1,215 bp, and 97 polymorphic sites were identified. We also defined 62 haplotypes, including 35 unique haplotypes. The haplotype diversity value of all the dairy goats was 0.952, and the nucleotide diversity was 0.011 per site. Phylogenetic analyses revealed that Chinese dairy goats were divided into haplogroups A and B, with haplogroup A serving as the predominant group. Median-joining network and analyses of molecular variance indicated that Chinese dairy goats were more weakly phylogeographically structured than other domestic goats. A mismatch distribution analysis and Fu's test revealed that at least 1 population expansion event occurred in the demographic history of Chinese dairy goats.

Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale

Genes expressing circadian RNA rhythms are enriched for metabolic pathways, but the adaptive significance of cyclic gene expression remains unclear. We estimated the genome-wide synthetic and degradative cost of transcription and translation in three organisms and found that the cost of cycling genes is strikingly higher compared to non-cycling genes. Cycling genes are expressed at high levels and constitute the most costly proteins to synthesize in the genome. We demonstrate that metabolic cycling is accelerated in yeast grown under higher nutrient flux and the number of cycling genes increases ∼40%, which are achieved by increasing the amplitude and not the mean level of gene expression. These results suggest that rhythmic gene expression optimizes the metabolic cost of global gene expression and that highly expressed genes have been selected to be downregulated in a cyclic manner for energy conservation.

Effect of low intensity pulsed ultrasound on expression of TIMP-2 in serum and expression of mmp-13 in articular cartilage of rabbits with knee osteoarthritis

OBJECTIVE

To study the effect of low intensity pulsed ultrasound (LIPUS) on the expression of tissue inhibitor of metalloproteinase-2 (TIMP-2) in the serum and expression of matrix metallopeptidase 13 (MMP-13) in the articular cartilage cells of rabbits with knee osteoarthritis (OA).

METHODS

Inner patellar ligament defect method was used to establish the model of knee OA. Four weeks after the modeling, the arterial blood was drawn from the ear of each rabbit, while ELISA was employed to detect the expression of TIMP-2 in the serum. The chondrocytes were separated from animals in each group and then cultured in vitro. All rabbits were divided into control group, OA model group and OA + LIPUS group. Cells in the control and OA groups were not treated, while cells in the OA + LIPUS group were treated with LIPUS (40 mW/cm(2), 1 time/day). Cells were collected 7 d later and the RNA and total protein were extracted respectively. Real-time PCR and Western blotting were employed to analyze the expression of MMP-13 in chondrocytes at the mRNA and protein level, respectively.

RESULTS

The success rate of establishment of OA model was 83%. The results of ELISA showed that the content of TIMP-2 in the serum of animals with OA was 22.3%, lower than the one in the control group (P < 0.05). Compared with the normal control group, the expression of TIMP-2 in the OA model group was significantly increased, while the expression of MMP-13 was significantly increased (P < 0.05). After the stimulation of LIPUS, the expression of TIMP-2 and MMP-13 was close to the one in the normal control group.

CONCLUSIONS

The inner patellar ligament defect method is a mature method to establish the rabbit OA model, with high success rate. The expression of serum TIMP-2 in the OA model group is significantly decreased. LIPUS can up-regulate TIMP-2 and down-regulate MMP-13.

Interleukin-6 gene -174G>C polymorphism and chronic obstructive pulmonary disease risk: a meta-analysis

Association studies of interleukin-6 (IL-6) -174G>C polymorphism and chronic obstructive pulmonary disease (COPD) have yielded inconsistent results, possibly because single studies often lack sufficient statistical power. A comprehensive search was performed in the PubMed, Embase, Elsevier, Web of Science databases, Wanfang, and the Chinese National Knowledge Infrastructure (CNKI) databases for published studies investigating the associations between IL-6 -174G>C polymorphism and COPD. Odds ratios (OR) and 95% confidence intervals (95%CI) were used to assess the possible associations. Seven studies with a total of 2701 subjects were included in this meta-analysis. A significantly increased risk was detected in the C allele of the IL-6 -174G>C in Caucasians (C vs G: OR = 1.16, 95%CI = 1.03-1.30; CC+GC vs GG: OR = 1.21, 95%CI = 1.02-1.42; CC vs GG: OR = 1.32, 95%CI = 1.03-1.70). This meta-analysis suggests that the C allele of the IL-6 -174G>C might act as a COPD risk factor in Caucasians. Further well-designed case-control studies with larger sample sizes are needed to confirm these conclusions.

First Report of Cladobotryum protrusum causing Cobweb Disease on the Edible Mushroom Coprinus comatus

Coprinus comatus is one of the most commercially important mushrooms in China. Its fruiting body possesses rich nutritional and medicinal value. In November 2013, unusual symptoms were observed on C. comatus on a mushroom farm in Wuhan, Hubei, China. At first, fruiting bodies were covered by white and cobweb-like mycelia. Later, the cap and stipe turned brown or dark before rotting and cracking. The pathogen was isolated from infected tissue of C. comatus. Colonies of the pathogen on potato dextrose agar (PDA) medium first appeared yellowish, followed by an obvious ochraceous or pinkish color. Aerial mycelia grew along the plate wall, cottony, 1 to 4 mm high. Conidiophores were borne on the tops of hyphae, had two to four branches, and were cylindrical, long clavate, or fusiform. Conidia were borne on the tops of the branches of conidiophores, had one to two separates, and were long and clavate. The spores ranged from 15.3 to 22.1 μm long and were 5.1 to 8.3 μm wide, which was consistent with the characteristics of Cladobotryum protrusum (1). The species was identified by ribosomal internal transcribed spacer sequencing. The ribosomal ITS1-5.8S-ITS2 region was amplified from the isolated strain using primers ITS1 and ITS4. A BLAST search in GenBank revealed the highest similarity (99%) to C. protrusum (GenBank Accession Nos. FN859408.1 and FN859413.1). The pathogen was grown on PDA at 25°C for 3 days, and the inoculation suspension was prepared by flooding the agar surface with sterilized double-distilled water for spore suspension (1 × 10⁵ conidia/ml). In one treatment, the suspension was sprayed on casing soil (10⁶ conidia/m²) and mixed thoroughly with it, then cased with treated soil for 2 to 3 cm thickness on the surface of compost in cultivation pots (35 × 25× 12 cm), with sterile distilled water as a control (2). Eight biological replicates were included in this treatment. In the second treatment, mycelia plugs (0.3 × 0.3 cm) without spore production were added to 20 fruiting bodies. Mushrooms treated with blank agar plugs (0.3 × 0.3 cm) were used as a control. The plugs were covered with sterilized cotton balls to avoid loss of moisture. Tested cultivation pots were maintained at 18°C and 85 to 95% relative humidity. In the samples where casing soil was sprayed with conidia suspension, white mildew developed on the pileus, and a young fruiting body grew out from the casing soil. Eventually, the surface of the mushroom was overwhelmed by the mycelia of the pathogen and the pileus turned brown or black. For the other group inoculated with mycelia plugs, only the stipe and pileus inoculated with mycelia turned brown or dark; it rotted and cracked 2 to 3 days later. The symptoms were similar to those observed on the C. comatus cultivation farm. Pathogens re-isolated from pathogenic fruiting bodies were confirmed to be C. protrusum based on morphological characteristics and ITS sequence. To our knowledge, this is the first report of the occurrence of C. protrusum on the edible mushroom C. comatus (3). Based on the pathogenicity test results, C. protrusum has the ability to severely infect the fruiting body of C. comatus. References: (1) K. Põldmaa. Stud. Mycol. 68:1, 2011. (2) F. J. Gea et al. Plant Dis. 96:1067, 2012. (3) W. H. Dong et al. Plant Dis. 97:1507, 2013.

Improvement of Dscam homophilic binding affinity throughout Drosophila evolution

Background

Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is known that thousands of isoforms bind themselves through specific homophilic interactions, a process which provides the basis for cellular self-recognition. Detailed biochemical studies of specific isoforms strongly suggest that homophilic binding, i.e. the formation of homodimers by identical Dscam1 isomers, is of great importance for the self-avoidance of neurons. Due to experimental limitations, it is currently impossible to measure the homophilic binding affinities for all 19,000 potential isoforms.

Results

Here we reconstructed the DNA sequences of an ancestral Dscam form (which likely existed approximately 40 ~ 50 million years ago) using a comparative genomic approach. On the basis of this sequence, we established a working model to predict the self-binding affinities of all isoforms in both the current and the ancestral genome, using machine-learning methods. Detailed computational analysis was performed to compare the self-binding affinities of all isoforms present in these two genomes. Our results revealed that 1) isoforms containing newly derived variable domains exhibit higher self-binding affinities than those with conserved domains, and 2) current isoforms display higher self-binding affinities than their counterparts in the ancient genome. As thousands of Dscam isoforms are needed for the self-avoidance of the neuron, we propose that an increase in self-binding affinity provides the basis for the successful evolution of the arthropod brain.

Conclusions

Our data presented here provide an excellent model for future experimental studies of the binding behavior of Dscam isoforms. The results of our analysis indicate that evolution favored the rise of novel variable domains thanks to their higher self-binding affinities, rather than selection merely on the basis of simple expansion of isoform diversity, as that this particular selection process would have established the powerful mechanisms required for neuronal self-avoidance. Thus, we reveal here a new molecular mechanism for the successful evolution of arthropod brains.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0186-z) contains supplementary material, which is available to authorized users.