Wolfberry genome database: integrated genomic datasets for studying molecular biology.

Wolfberry, also known as goji berry or Lycium barbarum, is a highly valued fruit with significant health benefits and nutritional value. For more efficient and comprehensive usage of published L. barbarum genomic data, we established the Wolfberry database. The utility of the Wolfberry Genome Database (WGDB) is highlighted through the Genome browser, which enables the user to explore the L. barbarum genome, browse specific chromosomes, and access gene sequences. Gene annotation features provide comprehensive information about gene functions, locations, expression profiles, pathway involvement, protein domains, and regulatory transcription factors. The transcriptome feature allows the user to explore gene expression patterns using transcripts per kilobase million (TPM) and fragments per kilobase per million mapped reads (FPKM) metrics. The Metabolism pathway page provides insights into metabolic pathways and the involvement of the selected genes. In addition to the database content, we also introduce six analysis tools developed for the WGDB. These tools offer functionalities for gene function prediction, nucleotide and amino acid BLAST analysis, protein domain analysis, GO annotation, and gene expression pattern analysis. The WGDB is freely accessible at https://cosbi7.ee.ncku.edu.tw/Wolfberry/. Overall, WGDB serves as a valuable resource for researchers interested in the genomics and transcriptomics of L. barbarum. Its user-friendly web interface and comprehensive data facilitate the exploration of gene functions, regulatory mechanisms, and metabolic pathways, ultimately contributing to a deeper understanding of wolfberry and its potential applications in agronomy and nutrition.

Description of two new Megistophylla Burmeister, 1855 species from China, with a redescription of M. andrewesi Moser, 1913 (Coleoptera: Scarabaeidae: Melolonthinae).

This study presents descriptions and illustrations of two new melolonthine species: Megistophylla brevivirgata Wang & Gao, new species and M. keithi Wang & Gao, new species from Yunnan province in China. Additionally, a detailed redescription and illustration of the male of M. andrewesi Moser, 1913, and a description of its previously unknown female are provided. Finally, a key to identification of Megistophylla Burmeister, 1855 species from China is added.

Effects of Geographical Origin and Tree Age on the Stable Isotopes and Multi-Elements of Pu-erh Tea.

Pu-erh tea is a famous tea worldwide, and identification of the geographical origin of Pu-erh tea can not only protect manufacture's interests, but also boost consumers' confidence. However, tree age may also influence the fingerprints of Pu-erh tea. In order to study the effects of the geographical origin and tree age on the interactions of stable isotopes and multi-elements of Pu-erh tea, 53 Pu-erh tea leaves with three different age stages from three different areas in Yunnan were collected in 2023. The δ13C, δ15N values and 25 elements were determined and analyzed. The results showed that δ13C, δ15N, Mg, Mn, Fe, Cu, Zn, Rb, Sr, Y, La, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu had significant differences among different geographical origins (p < 0.05). Mn content was significantly influenced by region and tree age interaction. Based on multi-way analysis of variance, principal component analysis and step-wised discriminant analysis, 24 parameters were found to be closely related to the geographical origin rather than tree age, and the geographical origin of Pu-erh tea can be 100.0% discriminated in cross-validation with six parameters (δ13C, δ15N, Mn, Mg, La, and Tb). The study could provide references for the establishment of a database for the traceability of Pu-erh tea, and even the identification of tea sample regions with different tree ages.

Wolfberry genomes and the evolution of Lycium (Solanaceae).

Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.

[Site index model of Juglans mandshurica natural secondary mixed forest in Changbai Mountain area, Jilin Province, China]. / 吉林省长白山区胡桃楸天然次生混交林立地指数模型.

According to slope direction and position of the distribution of Juglans mandshurica natural secondary mixed forest in 12 sites of Changbai Mountain in Jilin Province, and combined with the age structure of J. mandshurica, we set up 109 plots. Based on the age-tree height data, we complied the site index of the forests. We used the three times tree height standard deviation method to eliminate abnormal data, 379 pairs age and tree height data were obtained from the 80 plots. Then, we used seven mathematical models for comparison and got simplex site index-oriented curve equation as H=28.0181(1-e-0.0341A)1.0503. The coefficient of determination R2 and the sum of squared residuals were 0.85 and 0.89, respectively, the base age was 50 years, the exponential interval was 2 m, and 7 site index curves of 16-28 m were obtained. According to different site types, polymorphic sites index model was established, and the power function fitting effect was best. Its equation was H=B0tB1, in which B0=10-9e0.9213SI, B1=-0.2139SI+5.6183. Finally, the polymorphic site index model equation was H=10-9e0.9213SIt-0.2139SI+5.6183. The exponential difference method and drop point test were conducted to check the accuracy of the two site index models. The results showed that the polymorphic site index had higher precision and it could accurately reflect the difference in tree height growth under different site types of J. mandshurica. Therefore, it could evaluate the site quality of natural secondary mixed forests of J. mandshurica in Changbai Mountain area of Jilin Province.

Pathological evaluation of neoadjuvant chemotherapy in advanced gastric cancer.

BACKGROUND: Although pathological evaluation has been considered an effective evaluation method, some problems still exist in practice. Therefore, we explored whether there are more reasonable and practical pathological evaluation criteria for neoadjuvant chemotherapy in patients with advanced gastric cancer. Here, we aim to determine pathological judgment criteria for neoadjuvant chemotherapy in patients with advanced gastric cancer. METHODS: Eighty-seven patients with cT2-4 or cN+ were enrolled in this study. Pathological factors for overall survival (OS) were investigated using univariate and multivariate analyses, and the pathological criteria for neoadjuvant chemotherapy were then determined. RESULTS: A total of 87 patients underwent 3-4 cycles of neoadjuvant chemotherapy, with 67 (77.0%), 15 (17.2%), and 5 (5.8%) receiving Folfox6, Xelox, and SOX regimens, respectively. All patients showed different levels of graded histological regression (GHR) of the primary tumor, with a ≥ 50% regression rate of 50.6%. The univariate analysis showed that GHR ≥ 50% (p = 0.022), 66.7% (p = 0.013), and 90% (p = 0.028) were significantly correlated with OS. The multivariate analysis demonstrated that ypTNM (II/III) stage was significantly associated with OS compared with ypTNM (0+I) stage [HR = 3.553, 95% CI 1.886-6.617; HR = 3.576, 95% CI 1.908-6.703, respectively] and that the Lauren classification of diffuse type was also an independent risk factor for OS compared with the intestinal type (HR = 3.843, 95% CI 1.443-10.237). CONCLUSIONS: The Lauren classification and ypTNM stage after neoadjuvant chemotherapy are independent prognostic factors in advanced gastric cancer. A GHR ≥ 50%/< 50% can be used as the primary criterion for advanced gastric cancer after neoadjuvant chemotherapy to determine postoperative adjuvant chemotherapy regimens.

[Comparison of Different Leaching Methods for Heavy Metals in Sludge Fly Ash and Comprehensive Toxicity Evaluation].

Fly ash from sludge incineration was separated into five different sizes (<1 µm, 1-2.5 µm, 2.5-10 µm, 10-50 µm, and > 50 µm) by high-precision air classification equipment. The leaching of heavy metals was contrastively studied using the HJT 299-2007-sulfuric acid/nitric acid method, HJ 557-2009-Horizontal Oscillation Method, toxicity characteristic leaching procedure (TCLP), and European standard protocol (EN 12457-3) for the different size fractions of the fly ash. Based on the leaching results, an evaluation method for the comprehensive toxicity of heavy metal leaching was established. The results show that the content of heavy metals and the amount of leaching from the fly ash decrease with the increase in fly ash particle size. The leaching of the heavy metals Zn and Cu in the < 1 µm particle size range of TCLP leaching method was the highest, at 107.34 mg·kg-1 and 318 mg·kg-1, respectively. The TCLP and sulfuric acid/nitric acid methods of heavy metal leaching were more effective than the EU (EN 12457-3) and horizontal oscillation methods. According to the value of OPTI, the OPTI value of < 10 µm fly ash was much larger than that of fly ash that was > 10 µm. This indicated that the fly ash of particle size < 10 µm was more toxic and more harmful.

Biosynthesis of reduced graphene oxide nanosheets and their in vitro cytotoxicity against cardiac cell lines of Catla catla.

This work reports a one-step simple synthesis method for functionalized reduced graphene oxide (RGO) nanosheets by a Platanus orientalis leaf extract polyphenol-mediated deoxygenation of graphene oxide (GO). Microscopic and spectroscopic characterization revealed the successful deoxygenation of GO and subsequent stabilization by oxidized polyphenols of plant extract. X-ray photoelectron spectroscopy, Raman spectroscopy, and X-ray diffraction analyses were used to examine the reduction of GO. Fourier-transform infrared spectroscopy results revealed capping of RGO with oxidized polyphenols of Platanus orientalis extract, which prevented aggregation of graphene sheets. Transmission electron microscopy and atomic force microscopy images revealed the formation of thin, transparent, sheet-like graphene. The in vitro cytotoxicity of synthesized RGO exhibited a dose-dependent toxicity against cardiac cell lines of Catla catla. Further, this work opens up a green synthesis route for the development of new graphene-based technologies.

Design and discovery of 2-(4-(1H-tetrazol-5-yl)-1H-pyrazol-1-yl)-4-(4-phenyl)thiazole derivatives as cardiotonic agents via inhibition of PDE3.

A series of novel 2-(4-(1H-tetrazol-5-yl)-1H-pyrazol-1-yl)-4-(4-phenyl)thiazole derivatives, 6(a-o) were designed, synthesized and evaluated for inhibitory activity against human PDE3A and PDE3B. In PDE3 assay, entire set of targeted analogs showed considerable inhibition of PDE3A (IC50=0.24 ± 0.06-16.42 ± 0.14 µM) over PDE3B (IC50=2.34 ± 0.13-28.02 ± 0.03 µM). Among the synthesized derivatives, compound 6d exhibited most potent inhibition of PDE3A with IC50=0.24 ± 0.06 µM than PDE3B (IC50=2.34 ± 0.13 µM). This compound was further subjected for evaluation of cardiotonic activity (contractile and chronotropic effects) in comparison with Vesnarinone. Results showed that, it selectively modulates the force of contraction (63%± 5) rather than frequency rate (23% ± 2) at 100 µM. Docking study of above compound was also carried out in the active site of PDE3 protein model to give proof to the mechanism of action of designed inhibitor. Further, in sub-acute toxicity experiment in Swiss-albino mice, it was found to be non-toxic up to 100mg/kg dose for 28days.

Highly efficient synthesis of novel methyl 13(2)-methylene mesopyropheophorbide a and its stereoselective Michael addition reaction.

Treatment of methyl mesopyropheophorbide a with formaldehyde under basic conditions gave a novel 13(2)-methylene derivative in 85% yield; under acidic conditions, the corresponding 20-hydroxymethyl derivative was obtained in 65% yield. The high reactivity of the enone structural motif existed in the former product provides a unique way to construct some novel chlorophyll a derivatives for various applications. Stereoselective Michael reaction of this compound is studied and discussed.

Expression of tissue levels of matrix metalloproteinases and tissue inhibitors of metalloproteinases in renal cell carcinoma.

BACKGROUND: Matrix metalloproteinases (MMPs) are one of the major classes of proteolytic enzymes involved in tumor invasion and metastasis and are inhibited by naturally occurring tissue inhibitors of metalloproteinases (TIMPs). {AU Query: Please verify that corrections made to previous sentence did not alter intended meaning}. In this study, we examined the expression of MMP-2, MMP-9, membrane-type 1 (MT1)-MMP, TIMP-1, and TIMP-2 in renal tissue samples of renal cell cancer and examined the correlation between their expression and clinicopathological parameters. METHODS: Renal tissue samples from 76 patients with renal cell carcinoma were available for this study. To determine the expression of MMP-2, MMP-9, MT1-MMP, TIMP-1, and TIMP-2, semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) was carried out on tumor and normal tissues. RESULTS: Mean MMP-2, MMP-9, MT1-MMP, TIMP-1, and TIMP-2 mRNA expression in the renal cell carcinomas was significantly higher than in the normal renal tissue (P <0.05). The RT-PCR data of MMP-2, MMP-9, MT1-MMP, TIMP-1, and TIMP-2 did not show any significant correlation with tumor type or pathologic grade of renal cell carcinoma. MMP-2, MMP-9 and MT1-MMP mRNA expression increased significantly with the TNM stage of the tumor. CONCLUSIONS: Mean MMP-2, MMP-9, MT1-MMP, TIMP-1, and TIMP-2 mRNA expression in the renal cell carcinomas was significantly higher than in the normal renal tissue.

[Effects of ultrasonic pretreatment on drying characteristics of sewage sludge].

The high water content of sewage sludge has engendered many inconveniences to its treatment and disposal. While ultrasonic takes on unique advantages on the sludge drying because of its high ultrasonic power, mighty penetrating capability and the ability of causing cavitations. Thus this research studies the characteristics influences of ultrasonic bring to the sludge drying and effects of the exposure time, ultrasonic generator power, temperatures of ultrasonic and drying temperature on the drying characteristics of dewatered sludge. Results indicate that ultrasonic pretreatment could speed up evaporation of the free water in sludge surface and help to end the drying stage with constant speed. In addition, ultrasonic treatment can effectively improve the sludge drying efficiency which could be more evident with the rise of the ultrasonic power (100-250 W), ultrasonic temperature and drying temperature. If dried under low temperature such as 105 degrees C, sludge will have premium drying characteristics when radiated under ultrasound for a shorter time such as 3 min. In the end, the ultrasonic treatment is expected to be an effective way to the low-cost sludge drying and also be an important reference to the optimization of the sludge drying process because of its effects on the increase of sludge drying efficiency.

Simulation study of stimulation parameters in desynchronisation based on the Hodgkin-Huxley small-world neural networks and its possible implications for vagus nerve stimulation.

Adopting small-world neural networks of the Hodgkin-Huxley (HH) model, the stimulation parameters in desynchronisation and its possible implications for vagus nerve stimulation (VNS) are numerically investigated. With the synchronisation status of networks to represent epilepsy, then, adding pulse to stimulations to 10% of neurons to simulate the VNS, we obtain the desynchronisation status of networks (representing antiepileptic effects). The simulations show that synchronisation evolves into desynchronisation in the HH neural networks when a part (10%) of neurons are stimulated with a pulse current signal. The network desynchronisation appears to be sensitive to the stimulation parameters. For the case of the same stimulation intensity, weakly coupled networks reach desynchronisation more easily than strongly coupled networks. The network desynchronisation reduced by short-stimulation interval is more distinct than that of induced by long stimulation interval. We find that there exist the optimal stimulation interval and optimal stimulation intensity when the other stimulation parameters remain certain.

[Migration characteristics of heavy metals during pilot melting process of incineration fly ash].

The characteristics of heavy metals (Cd, Pb, Zn, Cu, Cr and Ni) were studied during pilot melting process of waste incineration fly ash, and it mainly focused on the solidification of those heavy metals in molten slag. The experiment factors include temperature (1290 degrees C, 1320 degrees C and 1360 degrees C), additive (10% glass powder), slag cooling mode(water or air cooling), whose influence on the heavy metals' solidification in the molten slag was studied. The result shows: the solidification of the heavy metals (Pb, Zn, Cu, Cr and Ni) increase on certain degree with temperature's increasing; Adding 10% glass powder makes the solidification of heavy metals increase greatly except Zn; For Zn, Cu, Cr and Ni, the solidification using air cooling mode is higher than that using water cooling mode.