Application of modern computer technology in classical genetics lab course--Development of a mobile, lightweight and high-precision batch identification system for genetic traits of Drosophila.

Drosophila is a crucial biological experimental teaching material extensively utilized in experimental teaching. In this experimental teaching, each student typically needs to manually identify hundreds of fruit flies and record multiple of each fly. This task involves substantial workload, and the classification standards can be inconsistent. To address this issue, we introduce a deep convolutional neural network that classifies the traits of every fruit fly, using a two-stage consisting of an object detector and a trait classifier. We propose a keypoint-assisted classification model with tailored training session for the trait classification task and significantly enhanced the model interpretability. Additionally, we've enhanced the RandAugment method to better fit the features of our task. The model is trained with progressive learning and adaptive regularization under limited computational resources. The final classification model, which utilizes MobileNetV3 as backbone, achieves an accuracy of 97.5%, 97.5% and 98% for the eyes, wings, gender tasks, respectively. After optimization, the model is highly lightweight, classifying 600 fruit fly traits from raw images in 10 seconds and having a size less than 5 MB. It can be easily deployed on any android device. The development of this system is conducive to promoting the experimental teaching, such as verifying genetic laws with Drosophila as the research object. It can also be used for scientific research involving a large number of Drosophila classifications, statistics and analyses.

Lindenane-Type Sesquiterpene Dimers Mitigate Lipopolysaccharide-Induced Inflammation by Inhibiting Toll-Like Receptor Signaling.

Toll-like receptors (TLRs) recognize pathogen-associated molecular patterns and trigger an inflammatory response via the myeloid differential factor 88 (MyD88)-dependent and toll-interleukin-1 receptor domain-containing adapter-inducing interferon-ß (TRIF)-dependent pathways. Lindenane type sesquiterpene dimers (LSDs) are characteristic metabolites of plants belonging to the genus Sarcandra (Chloranthaceae). The aim of this study was to evaluate the potential anti-inflammatory effects of the LSDs shizukaol D (1) and sarcandrolide E (2) on lipopolysaccharides (LPS)-stimulated RAW264.7 macrophages in vitro, and explore the underlying mechanisms. Both LSDs neutralized the LPS-induced morphological changes and production of nitric oxide (NO), as determined by CCK-8 assay and Griess assay, respectively. Furthermore, shizukaol D (1) and sarcandrolide E (2) downregulated interferon ß (IFNß), tumor necrosis factor α (TNFα) and interleukin-1ß (IL-1ß) mRNA levels as measured by reverse transcription polymerase chain reaction (RT-PCR), and inhibited the phosphorylation of nuclear factor kappa B p65 (p65), nuclear factor kappa-Bα (IκBα), Jun N-terminal kinase (JNK), extracellular regulated kinase (ERK), mitogen-activated protein kinase p38 (p38), MyD88, IL-1RI-associated protein kinase 1 (IRAK1), and transforming growth factor-ß-activated kinase 1 (TAK1) proteins in the Western blotting assay. In conclusion, LSDs can alleviate the inflammatory response by inhibiting the TLR/MyD88 signalling pathway.

Rhodomollosides A and B, glycosides of methyl everninate from the aerial parts of Rhododendron molle.

Two new glycosides of methyl everninate, rhodomollosides A (1) and B (2), were isolated from the aerial parts of a medicinal plant Rhododendron molle. The structures of 1 and 2 were elucidated on the basis of detailed spectroscopic analyses as well as HPLC analyses for thiazolidine derivatives of their sugar moieties. The sugar moiety of rhodomolloside A (1) was elucidated to be a rare monosaccharide, D-allose, while rhodomolloside B (2) was assigned as a D-glucoside of methyl everninate. Furthermore, they were evaluated for their cytotoxicity against RAW264.7 cells, and for their inhibitory effects with a lipopolysaccharide (LPS)-stimulated murine macrophages RAW 264.7 cells model.

TRIM31 enhances chemoresistance in glioblastoma through activation of the PI3K/Akt signaling pathway.

Temozolomide (TMZ) resistance is a complication of treatment of glioma, and new strategies are urgently required to overcome chemoresistance in glioma cells. In the present study, it was demonstrated that tripartite motif-containing 31 (TRIM31) was abnormally upregulated in glioma tissues and cell lines compared with normal samples. Furthermore, the role of TRIM31 was assessed by overexpressing and knocking down its expression. Overexpression of TRIM31 increased cell viability, increased TMZ IC50 values and inhibited apoptosis in A172 and U251 cells; whereas overexpression of TRIM31 decreased the expression of the apoptosis-associated protein p53. Knockdown of TRIM31 increased apoptosis in cells treated with TMZ. Additionally, the mechanisms by which TRIM31 affected glioma cells treated with TMZ were determined. Overexpression of TRIM31 increased phosphorylation of AKT and inhibiting the PI3K/AKT signaling pathway abolished the increase in cell viability and decreased phospho-Akt protein expression in TRIM31 overexpressing A172 cells treated with TMZ. Together, the findings suggest that TRIM31 may be a potentially novel target for glioma chemotherapy.

Effect of Tong Xie Yao Fang on endogenous metabolites in urine of irritable bowel syndrome model rats.

BACKGROUND: Tong Xie Yao Fang is a representative traditional Chinese prescription for the treatment of liver and spleen deficiency, abdominal pain and diarrhea. It has a unique function in the treatment of gastrointestinal dysfunction including irritable bowel syndrome (IBS), is a common functional bowel disease. Its main symptoms are recurrent abdominal pain, diarrhea, constipation or alternations between diarrhea and constipation. There are obvious differences in metabolites between TCM syndromes. By comparing the body fluid metabolism maps of model animals, metabolomics can discover disease biomarkers, analyze the differences in metabolic pathways and understand the pathological process and the metabolic pathways of substances in the body. Thus, the evaluation of animal models tends to be comprehensive and objective. This may provide further understanding between the interaction between Tong Xie Yao Fang and the IBS model. AIM: To evaluate the effect of Tong Xie Yao Fang on IBS rats by using metabolomics method. METHODS: Wistar rats were used to establish IBS models, and then randomly divided into four groups: A model control group and three Tong Xie Yao Fang treatment groups (high, medium and low doses). A normal, non-IBS group was established. The rats were treated for 2 wk. On days 0 and 14 of the experimental model, urine was collected for 12 h and was analyzed by ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry. Nine potential biomarkers were identified, and six major metabolic pathways were found to be related to IBS. RESULTS: In the study of metabonomics, nine potential biomarkers including L-serine, 4-methylgallic acid, L-threonine, succinylacetone, prolyl-hydroxyproline, valyl-serine, acetyl citrate, marmesin rutinoside and 5-hydroxy-L-tryptophan were identified in urine, which were assigned to amino acids, organic acids, succinyl and glycosides. Furthermore, the metabolic pathway of L-serine, L-threonine and 5-hydroxy-L-tryptophan was found in the Kyoto Encyclopedia of Genes and Genomes, which mainly involved the metabolism of cysteine and methionine, vitamin B6 metabolism, serotonin synapse, tryptophan metabolism, sphingolipid metabolism, digestion, absorption of protein and amino acid metabolism. These pathways are related to intestinal dysfunction, inflammatory syndrome, nervous system dysfunction and other diseases. CONCLUSION: Tong Xie Yao Fang has pharmacological effects on IBS, and its mechanism may be related to the metabolism of the nine potential biomarkers identified above in urine.

Systematic tracking of altered modules identifies the key biomarkers involved in chronic lymphocytic leukemia.

Key genes in chronic lymphocytic leukemia (CLL) were investigated through systematically tracking the dysregulated modules from protein-protein interaction (PPI) networks. Microarray data of normal subjects and CLL patients recruited from ArrayExpress database were applied to extract differentially expressed genes (DEGs). Additionally, we re-weighted the PPI network of normal and CLL conditions by means of Pearsons correlation coefficient (PCC). Furthermore, clique-merging method was applied to extract the modules and then the altered modules were screened out. The intersection genes were selected from miss and add genes in the altered modules. The common genes were screened from the intersection genes and DEGs in CLL. A total of 734 DEGs were screened by statistical analysis. In this investigation, there were 1,805 and 703 modules in normal as well as disease PPI network. In addition, 875 altered modules were obtained which included 145 miss genes, 353 add genes and 85 intersection genes. Finally, in-depth analysis revealed 9 mutual genes between the intersection genes and DEGs in CLL. Our analysis revealed several key genes associated with CLL by systematically tracking the dysregulated modules, which might be candidate targets for diagnosis and management of CLL.

Association between polymorphisms of autophagy pathway and responses in non-small cell lung cancer patients treated with platinum-based chemotherapy.

Platinum-based chemotherapy is an important treatment for non-small cell lung cancer. However, the effectiveness of the treatment varies among the patients. We investigated the association between DNA polymorphisms of the autophagy pathway and responses of such treatment among 1004 Chinese patients. Ninety-nine SNPs located on 13 genes of the autophagy pathway were genotyped and assessed for their association with clinical benefit, progression-free survival (PFS) and overall survival (OS). The results showed that rs7953348 (G>A) (P=0.017, OR: 0.67, 95%CI: 0.49-0.93) and rs12303764 (A>C) (P=0.009, OR: 0.63, 95%CI: 0.45-0.89) at the ULK1 gene, and rs17742719 (C>A) (P=0.002, OR: 1.83, 95%CI: 1.26-2.66), rs8003279 (A>G) (P=0.006, OR: 1.65, 95%CI: 1.16~2.35) and rs1009647 (G>A) (P=0.002, OR: 1.70, 95%CI: 1.22-2.37) at the ATG14 gene were associated with clinical benefit. Polymorphisms at rs7955890 (G>A) (P=0.004, HR: 0.63; 95%CI: 0.46-0.86) and rs17032060 (G>A) (P=0.006, HR: 0.65, 95%CI: 0.48-0.88) at the DRAM gene, and rs13082005 (G>A) (P=0.012, HR: 1.27, 95%CI: 1.05-1.53) at the ATG3 gene were significantly associated with PFS. We also found that rs7953348 (G>A) (P=0.011, HR: 0.74, 95%CI: 0.58-0.93) at the ULK1 gene and rs1864183 (G>A) (P=0.016, HR: 0.42, 95%CI: 0.21-0.85) at the ATG10 gene were associated with OS. Thus, the study demonstrated that the autophagy pathway might play important role(s) in platinum-based chemotherapy. DNA polymorphisms in its component genes can potentially be predictors for clinical responses of platinum-based chemotherapy among the patients with non-small lung cancer.

Fabrication of Metal-Organic Framework and Infinite Coordination Polymer Nanosheets by the Spray Technique.

We have developed a rapid and convenient method for fabricating metal-organic framework (MOF) and infinite coordination polymer (ICP) nanosheets by spraying the atomized solution of metal ions onto the organic ligand solution. Nanosheet formation could be attributed to the anisotropic diffusion of metal ions in the ligand solution, which may give rise to a lateral interface of metal ions and organic ligands, where the crystals tend to grow laterally in the form of nanosheets. Three kinds of Zn- and Cu-based MOF nanosheets and two kinds of Co-based ICP nanosheets have been successfully obtained by spraying under mild conditions. The two-dimensional structures of nanosheets with a nanometer thickness and a homogeneous size can be evidenced by scanning electron microscopy, atomic force microscopy, X-ray diffraction, Brunauer-Emmett-Teller, and Fourier transform infrared spectroscopy measurements. Furthermore, the fabricated ICP nanosheets have exhibited efficient catalytic performance for the conversion of CO2 to high-value-added chemicals. This spray technique simplifies the nanosheet production process by industrialized means and enhances its controllability by the fast liquid-liquid interfacial fabrication, thus allowing access to the industrialized fabrication of MOF and ICP nanosheets.

Tong Xie Yao Fang relieves irritable bowel syndrome in rats via mechanisms involving regulation of 5-hydroxytryptamine and substance P.

AIM: To investigate whether the Chinese medicine Tong Xie Yao Fang (TXYF) improves dysfunction in an irritable bowel syndrome (IBS) rat model. METHODS: Thirty baby rats for IBS modeling were separated from mother rats (1 h per day) from days 8 to 21, and the rectum was expanded by angioplasty from days 8 to 12. Ten normal rats were used as normal controls. We examined the effects of TXYF on defection frequency, colonic transit function and smooth muscle contraction, and the expression of 5-hydroxytryptamine (5-HT) and substance P (SP) in colonic and hypothalamus tissues by Western blot and RT-PCT techniques in both normal rats and IBS model rats with characterized visceral hypersensitivity. RESULTS: Defecation frequency was 1.8 ± 1.03 in normal rats and 4.5 ± 1.58 in IBS model rats (P < 0.001). However, the defecation frequency was significantly decreased (3.0 ± 1.25 vs 4.5 ± 1.58, P < 0.05), while the time (in seconds) of colon transit function was significantly increased (256.88 ± 20.32 vs 93.36 ± 17.28, P < 0.001) in IBS + TXYF group rats than in IBS group rats. Increased colonic smooth muscle tension and contract frequency in IBS model rats were significantly decreased by administration of TXYF. Exogenous agonist stimulants increased spontaneous activity and elicited contractions of colon smooth muscle in IBS model rats, and all of these actions were significantly reduced by TXYF involving 5-HT and SP down-regulation. CONCLUSION: TXYF can modulate the activity of the enteric nervous system and alter 5-HT and SP activities, which may contribute to the symptoms of IBS.

[Application of Ion Torrent PGM™ System in Detection of Fetal DNA in Maternal Plasma].

OBJECTIVE: To explore the feasibility of detecting of Y-STR of fetal DNA in maternal plasma using Ion Torrent PGM™ System. METHODS: A total of 16 fetal DNA samples from maternal plasmas (8 cases from 38 weeks gestational age and 8 ones from 12 weeks) were prepared and a multiplex assay with 7 STR loci (DYS390, DYS391, DYS393, DYS438, DYS437, DYS456, DYS635) was designed for multiplex-PCR amplification. Using Ion Torrent PGM™ System, the results of Y-STR sequences and capillary electrophoresis were obtained and compared. RESULTS: Y-STR specific alleles were detected in the maternal plasma of all the pregnant women having male babies of second and third trimester, which were higher than that detected by capillary electrophoresis. Consistent Y-STR genotypes were observed between fetal DNA from maternal plasma and genomic DNA from the newborn babies. CONCLUSION: Based on Ion Torrent PGM™ System, the prenatal Y-STR detection method may provide a high-sensitive and high-throughput choice for prenatal STR detection in forensic testing.

[Clinical observation on effect of danzhi xiaoyao powder in treating depression].

OBJECTIVE: To observe the effect and side effect of Danzhi Xiaoyao powder (DXP) in treating depression. METHODS: A randomized controlled and double-blinded study was conducted in 63 cases of depression by divided them into the western medicine group (WMG, 31 cases) treated with maprotiline, and the Chinese medicine group (CMG, 32 cases) treated with DXP. The effect of therapy was evaluated before and at the 2nd, 4th and 6th week of the treatment with Hamilton's depressive scale (HAMD), self-rating depression scale (SDS), self-rating anxiety scale (SAS) and the scale for TCM syndrome and symptom differentiation (TCM-SSD), and the side-effect of therapy was assessed with Asberg side-effect scale as well. RESULTS: There was no significant difference between the two groups in scores of HAMD, SDS, SAS, and TCM-SSD. The markedly effective rate in CMG was 84% and in WMG 87%, showed no significance between them (P > 0.05). The scores of HAMD, SDS and SAS of both groups were remarkably lowered after therapy (P < 0.05). However, the score of Asberg in CMG was lower than that in WMG (P < 0.05). CONCLUSION: DXP shows the effect equivalent to that of maprotiline, but with obviously less side-effect.

[Visual and histologic analysis of laparoscopic diagnosis of endometriosis].

OBJECTIVE: To determine the characteristics of anatomical distribution of pelvic endometriosis and the correlation between visual and histologic findings of endometriosis at laparoscopy. METHODS: A prospective study of 62 patients undergoing laparoscopy for the pelvic pain, infertility and/or pelvic masses was carried out. All lesions with the diagnosis of endometriosis laparoscopically were excised and examined pathologically. Normal-appearing peritoneal biopsies were obtained randomly. All lesions were identified by anatomical site and color of the foci. The positive predictive value (PPV), sensitivity, negative predictive value (NPV), and specificity were determined for visually identified endometriosis versus the histologic findings. RESULTS: Totally, 219 peritoneal endometriotic lesions, 54 normal peritoneal biopsies, and 71 ovarian endometriotic cysts were obtained. Peritoneal lesions tended to locate in posterior part of the pelvis (80.8%, 177/219) and in left (58.0%, 127/219) with most in black (39.2%). The PPV was 67.6%; sensitivity, 93.7%; NPV, 81.4%; and specificity, 38.3% for visual versus histologic diagnosis of peritoneal endometriosis. Lesions in black or from sacral ligaments were confirmed histologically in 94.2% and 84.7% respectively, and 80.3% (57/71) of ovarian endometriotic cysts diagnosed by laparoscopy were confirmed histologically with 43.6% in the left, 27.3% in the right; and 29.1% (16/55) in both sides of the ovary. In addition, 18.5% (10/54) of normal-appearing peritoneal biopsy were identified as endometriosis by pathological examination. Laparoscopy was confirmed to be in 100% diagnostic accordance with pathology for patients with endometriosis. CONCLUSIONS: Our study showed asymmetrical distribution of pelvic endometriosis. Peritoneal lesions in black or from sacral ligament are more likely to be histologically confirmed, and microscopic lesions are not a rare phenomenon of endometriosis.

Role of laparoscopy in the diagnosis and treatment of adnexal masses.

BACKGROUND: Laparoscopy has been accepted for years as a management of benign ovarian tumors. The aim of this study was to estimate the feasibility and safety of laparoscopy in diagnosis and management of adnexal masses. METHODS: A total of 2083 patients with benign adnexal mass were treated by laparoscopy at Peking Union Medical College Hospital from January 2000 to December 2003. Their clinical data were reviewed retrospectively. All the adnexal masses suspicious of malignancy at the time of laparoscopy were sent for frozen section evaluation intraoperatively. The rates of unexpected intracystic vegetation and low malignant potential (LMP) tumor or malignancy were investigated. The sensitivity, specificity, positive predictive value, and negative predictive value of laparoscopic diagnosis for LMP or ovarian malignancies were calculated. The ratios were compared by Chi-square test and the continuous variables were tested using two-tailed t test. RESULTS: Of the 2083 patients, 16 had LMP or invasive tumors (0.77%), among which 14 were diagnosed histologically intraoperatively and 2 postoperatively. Fifty-five (2.6%) of the 2083 patients had unexpected intracystic vegetations. Their frozen sections showed benign tumors in 41 (74.5%), LMP tumors in 8 (14.5%), and focal invasive ovarian cancers (stage Ic) in 6 (10.9%). The final pathological diagnosis were benign tumors in 41 (74.5%), LMP tumors 7 (12.7%), and focal invasive ovarian cancers (stage Ic) in 7 (12.7%). Laparoscopy achieved a sensitivity of 87.5%, specificity of 98%, positive predictive value of 25.5%, and negative predictive value of 99.9% in the diagnosis of ovarian malignancies. 2067 cases with benign adnexal masses underwent laparoscopy successfully. No conversion to laparotomy, or intra- and postoperative complications in this series. Of the 16 patients with LMP or invasive ovarian cancer, seven underwent laparoscopic surgery including immediate staging laparoscopy in 3. The mean follow-up was 17.3 months for the 16 patients. Among them, 1 developed a recurrent LMP tumor in the contralateral ovary 36 months after laparoscopic salpingo-oophorectomy, and received subsequent laparoscopic cystectomy and pelvic lymph node sampling; the others had no evidence of recurrent tumor during the follow-up. CONCLUSION: Laparoscopy is feasible for diagnosis of adnexal masses, and the surgery is safe for patients with benign ovarian tumors.

[Clinical characteristics of abdominal wall endometrioma and its recurrence-related factors].

OBJECTIVE: To analyze the clinical characteristics, and treatment, recurrence-related factors of abdominal wall endometriomas (AWE). METHODS: Fifty-seven cases of AWE treated at Peking Union Medical College Hospital from 1983 to 2002 were reviewed. RESULTS: The incidence of AWE was 1.04% (57/5478) in patients with endometriosis after surgical treatment. It was 0.046% in patients undergoing cesarean section in the same period. Of 57 cases with AWE, 56 had low-abdominal operation previously and one was primary umbilicus endometrioma. Fifty-five cases of AWE were secondary to cesarean section. The latent period of AWE was positively correlated to patient's age at onset (P < 0.001). Fifty-five cases received surgical treatment while 2 were given medical treatment. Follow-up duration was 1.1 - 235 months. Five cases recurred and one was transformed to malignancy. The recurrence was correlated to the size and depth of the lesions. CONCLUSIONS: AWE could be diagnosed prior to operation according to its typical clinical manifestations. Ultrasonic examination may be valuable for the diagnosis of atypical cases. Surgical treatment is effective. A complete excision with clear margin is very important to prevent recurrence.

[Sentinel lymph notes in female reproductive tract cancer].

To reduce extensive radical procedures and decrease morbidity in gynecologic malignancies, much effort is being focused on implementing less aggressive interventions. Two different approaches such as lymphatic mapping and lymphoscintigraphy are currently used to identify sentinel lymph nodes. In vulvar and cervical carcinomas, metastatic spread of disease commonly follows stepwise progressive drainage. Thus, sentinel lymph node identification may significantly reduce the number of patients undergoing unnecessary, extensive lymphadenectomy in the absence of metastatic disease. The addition of novel techniques, such as histopathologic ultrastaging, step sectioning, and immunohistochemistry staining, will help increase the accuracy and rate of detection of the disease. Any definitive statements can be made to the validity of sentinel lymphadenectomy until we got data with long-term follow-up.