Isolation and molecular identification of cellulolytic bacteria from Dig Rostam hot spring and study of their cellulase activity

Cellulose is the main structural component of lignocellulosic wastes that can be converted to sugars and biofuels by cellulase. Due to wide applications of this enzyme in various industries around the world, cellulase is considered as the third industrial enzyme. The ability of thermophilic bacteria in the production of heat-stable cellulases has made them valuable tools in biotechnology. The aim of this study was isolation and molecular identification of cellulolytic thermophile bacteria from Dig Rostam hot spring and investigating their cellulase activity. Samples were taken from water and sediments of this hot spring, and cellulolytic bacteria were enriched in media containing cellulose as the only carbon source. The bacteria were incubated at 60°C, and single colonies were then isolated on solid media. Congo red assay was used as a quick test for the qualitative screening of cellulase activity. According to these qualitative results, four colonies named CDB1, CDB2, CDB3, and CDB4 were isolated, and their growth curve and some other characteristics were determined by biochemical assays. Moreover, endoglucanase, exoglucanase, and FPase activities of the isolates were investigated quantitatively. Results indicated that CDB1 exhibited the highest endoglucanase (0.096 U/mL) and exoglucanase (0.156 U/mL) activities among other isolates. 16S rDNA partial sequencing indicated that CDB1 had 99% similarity to the genus Anoxybacillus, and the other isolates showed the highest similarity to the genus Geobacillus. The cellulase gene of CDB1 isolate with the highest cellulase activity was also cloned, and its sequence is reported for the first time. Further studies on this thermophilic enzyme might be useful for industrial applications.     

Effect of <i>Lycopus lucidus</i> Turcz. supplementation on gut microflora and short chain fatty acid composition in Crj: CD-1 mice

We investigated the diversity and composition of microflora in feces of Lycopus lucidus Turcz.-fed mice. In addition, we evaluated the production of major cytokines (Interleukin-6 and -10) which are related to inflammation and fatty acid composition of several tissues. 16S ribosomal DNA sequencing-based microbiome taxonomic profiling analysis was performed utilizing the EzBioCloud data base. Male mice fed on L. lucidus showed a significantly reduced number of lactic acid bacteria and coliform in the feces compared with the control group (p < 0.05). 16S rDNA sequencing analysis of fecal samples showed that L. lucidus supplementation decreased the community of harmful microflora (Enterobacteriaceae including Escherichia coli and Bacteroides sp.) in feces compared with the control group (p < 0.05). There were no significant differences in mRNA expression of cytokine IL-6 and IL-10 between the control and L. lucidus fed groups. The fecal fatty acid composition in the L. lucidus group had percentages of 4:0, 6:0, 8:0 and 10:0 in the intestine but those short chain fatty acids were not detected in the control group. Our results showed that L. lucidus supplementation influenced gut environment by decreasing harmful microflora and increased the percentages of several short fatty acids.     

Targeting the “undruggable” cancer driver genes: <i>Ras</i>, <i>myc</i>, and <i>tp53</i>

The term “undruggable” is to describe molecules that are not targetable or at least hard to target pharmacologically. Unfortunately, some targets with potent oncogenic activity fall into this category, and currently little is known about how to solve this problem, which largely hampered drug research on human cancers. Ras, as one of the most common oncogenes, was previously considered “undruggable”, but in recent years, a few small molecules like Sotorasib (AMG-510) have emerged and proved their targeted anti-cancer effects. Further, myc, as one of the most studied oncogenes, and tp53, being the most common tumor suppressor genes, are both considered “undruggable”. Many attempts have been made to target these “undruggable” targets, but little progress has been made yet. This article summarizes the current progress of direct and indirect targeting approaches for ras, myc, two oncogenes, and tp53, a tumor suppressor gene. These are potential therapeutic targets but are considered “undruggable”. We conclude with some emerging research approaches like proteolysis targeting chimeras (PROTACs), cancer vaccines, and artificial intelligence (AI)-based drug discovery, which might provide new cues for cancer intervention. Therefore, this review sets out to clarify the current status of targeted anti-cancer drug research, and the insights gained from this review may be of assistance to learn from experience and find new ideas in developing new chemicals that directly target such “undruggable” molecules.     

Antibacterial activity of lactose-binding lectins from <i>Bufo arenarum</i> skin

Amphibians respond to microbial infection through cellular and humoral defense mechanisms such as antimicrobial protein secretion. Most humoral defense proteins are synthetized in the skin. In this study we isolated two β-galactoside-binding lectins with molecular weights of 50 and 56 KDa from the skin of Bufo arenarum. These lectins have significant hemagglutination activity against trypsinized rabbit erythrocytes, which was inhibited by galactose-containing saccharides. They are water-soluble and independent of the presence of calcium. The antimicrobial analysis for each lectin was performed. At µmolar concentration lectins show strong bacteriostatic activity against Gram negative bacteria (Escherichia coli K12 4100 and wild strains of Escherichia coli and Proteus morganii) and Gram positive bacteria (Enterococcus faecalis). The antibacterial activity of these lectins may provide an effective defense against invading microbes in the amphibian Bufo arenarum.     

Response of <i>MaHMA2</i> gene expression and stress tolerance to zinc stress in mulberry (<i>Morus alba</i> L.)

HMA2 (heavy metal ATPase 2) plays a crucial role in extracellular and intracellular Zn²⁺ transport across biomembranes, maintaining ion homeostasis, and playing an important role in the normal physiological metabolism, growth, and development of plants. In our study, a novel HMA2 gene, named MaHMA2, was isolated and cloned from white mulberry (Morus alba L.). The gene sequence obtained was 1,342 bp long, with an open reading frame of 1,194 bp, encoding a protein of 397 amino acids, with a predicted molecular mass of 42.852 kD and an isoelectric point of 7.53. This protein belonged to the PIB-type ATPase transport protein family. We analyzed the expression of the MaHMA2 gene by quantitative real-time PCR. The results showed that the level of MaHMA2 gene expression decreased to a Zn concentration of 800 mg/kg. Malondialdehyde and proline levels increased and responded to increasing Zn when the MaHMA2 gene was silenced, whereas the activities of peroxidase and superoxide dismutase tended to increase in response to increasing Zn²⁺ ion stress concentrations but were lower in the gene-silenced plants. These findings suggested that the MaHMA2 gene played an active role in the tolerance response of mulberry to Zn stress.     

Human β-defensin 2 enhances IL-1β production and pyroptosis through P2X7-mediated NLRP3 expression in macrophages

Periodontal disease is the leading cause of tooth loss, which is also a high-risk factor for other diseases including oral cancer and cardiovascular disease. Periodontitis is one of the most common type of periodontal diseases. Interleukin-1β (IL-1β) plays a key role in the pathogenesis of periodontitis. However, the mechanism how IL-1β is produced during periodontitis is still unclear. In the present study, we found that human β-defensin 2 (hBD2) enhances IL-1β production through an LPS-primed human acute monocytic leukemia (THP-1) macrophage model. Inhibition of P2X purinoceptor 7 (P2X7) reduced hBD2-enhanced IL-1β production. Incubation of LPS-primed THP-1 macrophages with potassium chloride also suppressed hBD2-enhanced IL-1β production. Silence of inflammasome adaptor Nod-like receptor family pyrin domain containing 3 (NLRP3) led to reduced hBD2-enhanced IL-1β production. Likewise, inhibition of caspase-1 also resulted in the decrease of IL-1β. Moreover, an ethidium bromide uptake test indicated that hBD2-activated caspase-1 mediated pyroptotic pore formation. Subsequent lactate dehydrogenase detection and flow cytometric analysis indicated that hBD2 also induced pyroptosis. In brief, these findings illustrated not only the mechanism of hBD2 in enhancing the inflammatory response, but also provided novel therapeutic targets for periodontitis.     

恒波长同步扫描固体基质室温磷光法测定水样中的咔唑

本文采用同步扫描固体基质室温磷光(SS-RTP)法测定水样中的咔唑。以β-环糊精修饰滤纸为固体基质,KI为重原子,考查咔唑在芴,7,8-苯并喹啉,苊,蒽等多环芳烃(PAHs)存在下同步扫描的最优条件,选择最佳的△λ值为150nm,建立咔唑的恒波长同步扫描固体基质室温磷光分析方法。咔唑的线性范围是6.30ng.mL-1~1.67μg.mL-1,检出限为6.30ng.mL-1,相对标准偏差(RSD)为3.67%,回收率为94%~109%。该方法简便快速,无需预分离,与常规激发和发射光谱相比分辨力显著提高。     

Oxidative effects of glyphosate on the lipophobic intracellular environment in the microalgae <i>Chlorella vulgaris</i>

The studied hypothesis is that the herbicide glyphosate (GLY) can affect the oxidative balance in the hydrophobic intracellular medium in non-target Chlorella vulgaris cells. Analytical GLY and RoundUp (RUP) supplementation, affected the growth profile. A significant 42% decrease in the cellular biomass in stationary (St) phase was observed in cultures supplemented with either 5 µM of GLY or RUP, as compared to control cultures. The treatment with 0.3 µM of GLY generated non-significant effects on the oxidation rate of 2’, 7’ dichlorofluorescein diacetate (DCFH-DA), neither in exponential (Exp) nor in St phase of development, as compared to control cultures. However, the treatment with either 5 µM GLY or 0.3 and 5 µM RUP lead to a significant decrease in the DCFH-DA oxidation rate, as compared to control cultures. The lipid radical (LR^●) generation rate, detected by Paramagnetic Resonance Spectroscopy (EPR), was significantly increased in the presence of RUP, in Lag and Exp phase of growth. The non-enzymatic antioxidants, α-Tocopherol (α-T) and β-Carotene (β-C), are aimed to protect membranes against the damage produced by the radical reactions. The content of β-C was not significantly affected, as compared to control cultures, by any of the treatments, in both growth phases of cellular development. The content of α-T was significantly decreased by the supplementation with either 0.3 or 5 µM of RUP or 5 µM GLY. The LR^●/α-T ratio, used as indicator of the oxidative balance in the hydrophobic cellular media, was significantly different between samples obtained from control and RUP-exposed microalgae in both, Exp and St phase of development, with either 0.3 or 5 μM RUP. The data presented here showed evidence that suggested that oxidative balance in the hydrophobic environment was affected by either GLY or RUP.

     

油菜核盘菌拮抗菌的筛选及鉴定

本文采用了平板对峙法初筛、复筛,得到了对油菜核盘菌具有较强拮抗性的细菌,命名为Z-05,对其进行了形态学观察,生理生化特性测定,并结合16SrDNA序列分析,确定其为假单孢杆菌。     

Co-ordinated combination of Embden-Meyerhof-Parnas pathway and pentose phosphate pathway in <i>Escherichia coli</i> to promote L-tryptophan production

In this study, phosphoenolpyruvate and erythrose-4-phosphate are efficiently supplied by collaborative design of Embden-Meyerhof-Parnas (EMP) pathway and pentose phosphate (PP) pathway in Escherichia coli, thus increasing the L-tryptophan production. Firstly, the effects of disrupting EMP pathway on L-tryptophan production were studied, and the results indicated that the strain with deletion of phosphofructokinase A (i.e., E. coli JW-5 ΔpfkA) produced 23.4 ± 2.1 g/L of L-tryptophan production. However, deletion of phosphofructokinase A and glucosephosphate isomerase is not conducive to glucose consumption and cell growth, especially deletion of glucosephosphate isomerase. Next, the carbon flux in PP pathway was enhanced by introduction of the desensitized glucose-6-phosphate dehydrogenase (zwf) and 6-phosphogluconate dehydrogenase (gnd) and thus increasing the L-tryptophan production (i.e., 26.5 ± 3.2 g/L vs. 21.7 ± 1.3 g/L) without obviously changing the cell growth (i.e., 0.41 h⁻¹ vs. 0.44 h⁻¹) as compared with the original strain JW-5. Finally, the effects of co-modifying EMP pathway and PP pathway on L-tryptophan production were investigated. It was found that the strain with deletion of phosphofructokinase A as well as introduction of the desensitized zwf and gnd (i.e., E. coli JW-5 zwf243 gnd361 ΔpfkA) produced 31.9 ± 2.7 g/L of L-tryptophan, which was 47.0% higher than that of strain JW-5. In addition, the glucose consumption rate of strain JW-5 zwf243 gnd361 ΔpfkA was obviously increased despite of the bad cell growth as compared with strain JW-5. The results of this study have important reference value for the following application of metabolic engineering to improve aromatic amino acids producing strains.     

Apoptogenic effect of the lipophilic <i>o</i>-naphthoquinone CG 10-248 on rat hepatocytes: light and electron microscopy studies

CG 10-248 (3,4-dihydro-2,2-dimethyl-9-chloro-2H-naphtho[1,2b]pyran- 5,6-dione; CG-NQ), a β-lapachone analogue, modified the ultrastructure of rat hepatocytes, as demonstrated by light and electron microscopy. After 4 h incubation with 100 µM CG-NQ, the following effects were observed: (a) nuclear chromatin condensation; (b) chromatin fragmentation; (c) displacement of mitochondria, concentrated around the nucleus; (d) disruption or expansion of mitochondrial outer or inner membranes, respectively; (e) displacement and alteration of endoplasmic reticulum (rough and smooth); (f) decrease of microvilli; (g) blebbing of plasma membrane and production of apoptotic bodies formed by folding of plasma membrane fragments around mitochondria or peroxysomes; and (h) production of hydrogen peroxide. Expression of such effects varied according to hepatocyte samples and taken together strongly support an apoptotic action of CG-NQ dependent on “reactive oxygen species”.     

The chloroplast genome comparative characteristic of artificial breeding tree,a case about <i>Broussonetia kazinoki</i> × <i>Broussonetia papyrifera</i>

Broussonetia kazinoki × Broussonetia papyrifera (ZJGS) is a hybrid species in Moraceae family, which has a very complicated hybrid origin. The excellent characteristics of fast growth, strong soil and water conservation ability, high leaf protein content and stem fiber content in ZJGS make it both ecological benefits in the mining area and economically valuable. This study aims to further understand ZJGS and other Moraceae taxa through the ZJGS chloroplast (cp) genome structure and the comparison with 12 closely related Moraceae species. Among the 13 Moraceae species, the cp genome length of seven Broussonetia species (ranges from 160,239 bp to 162,594 bp) is larger than that of six Morus species (ranges from 158,459 bp to 159,265 bp). Among the 77 shared protein-coding genes (PCGs) in Moraceae species, the obvious positive selection of Ka/Ks ratios acted on petD and rpl16 genes of B. kazinoki and B. papyrifera, respectively. Phylogenetic analysis based on shared PCGs from 28 species shows that ZJGS is closely related to maternal B. kazinoki. These findings provide data support for the origin of ZJGS hybridization and provide genomic resources for future ZJGS resource development and molecular breeding.     

Isolation and biological characterization of a basic phospholipase A₂ from <i>Bothrops jararacussu</i> snake venom

A phospholipase A₂ has been isolated from Bothrops jararacussu venom from snakes that inhabit the northeast region of Argentina. The present study describes in vivo and in vitro biological activities of phospholipase A₂ from B. jararacussu as well as isolation details of its. Venom was obtained by milking of adult snakes which were housing in wood reptile cages of varying dimensions in heated (20–30ºC) rooms. Snakes received a weekly diet of mice and water was available ad libitum for drinking and soaking. The enzyme was purified by gel filtration on a Sephadex G-75 column followed by ion exchange chromatography on a SP-Sephadex C25 column. The major peak belonging to proteins was retained in the cation exchanger and then eluted using a concentration gradient of KCl that exhibited phospholipase activity.
This basic PLA₂ consists of a single polypeptide chain with a molecular mass of 15.6 kDa. It had a high indirect hemolytic activity and produced a significant paw edema reaction in mice. The enzyme showed a low lethality (LD₅₀ 148.6 µg) when was administered i.p. but exhibited elevated myotoxic effects in vivo by increasing plasma CK activity of injected mice, corroborated results by the histological observations of samples of gastrocnemius muscle. Myonecrosis is the result of intense destruction of muscular fibers that involves local infiltration of inflammatory cells and leads to the highest peak of CK level just after 1 hour mice injection. Moreover, the isolated enzyme showed anticoagulant activity, evaluated on sheep platelet-poor plasma which recalcification time was prolonged after incubation with the isolated phospholipase A₂ . These findings showed that this phospholipase, isolated by only two simple chromatographic steps, possesses high edematogenic and myotoxic activities. However, despite the low lethal activity, this enzyme would contribute markedly to the pathophysiology of the bothropic envenomation.     

LncRNA <i>ZFAS1</i> regulates cardiomyocyte differentiation of human embryonic stem cells

Background: Cardiomyocytes derived from human embryonic stem cells (hESCs) are regulated by complex and stringent gene networks during differentiation. Long non-coding RNAs (lncRNAs) exert critical epigenetic regulatory functions in multiple differentiation processes. However, the involvement of lncRNAs in the differentiation of hESCs into cardiomyocytes has not yet been fully elucidated. Here, we identified the key roles of ZFAS1 (lncRNA zinc finger antisense 1) in the differentiation of cardiomyocytes from hESCs. Methods: A model of cardiomyocyte differentiation from stem cells was established using the monolayer differentiation method, and the number of beating hESCs-derived cardiomyocytes was calculated. Gene expression was analyzed by quantitative real-time PCR (qRT-PCR). Immunofluorescence assays were performed to assess the expression of cardiac troponin T (cTnT) and α-actinin protein in cardiomyocytes. Results: qRT-PCR showed that ZFAS1 expression in the mesoderm was significantly higher than that in embryonic stem cells, cardiac progenitor cells, and cardiomyocytes. Knockdown of ZFAS1 inhibited cardiomyocyte differentiation from hESCs, which was characterized by reduced expression of the cardiac-specific markers cTnT, α-actinin, myosin heavy chain 6 (MYH6), and myosin heavy chain 7 (MYH7). In contrast, ZFAS1 overexpression remarkably increased the percentage of spontaneously beating cardiomyocytes. In terms of the mechanism, we found that ZFAS1 is an antisense lncRNA at the 5′ end of the protein-coding gene ZNFX1. Knockdown of ZFAS1 could increase the mRNA expression level of ZNFX1. Furthermore, qRT-PCR demonstrated that the silencing of ZNFX1 led to an increase in cardiac-specific markers that predicted the promotion of cardiomyocyte differentiation. Conclusion: Altogether, these data suggest that lncRNA-ZFAS1 is required for cardiac differentiation by functionally inhibiting the expression of ZNFX1, which may provide a reference for the treatment of heart disease to a certain extent.     

Expression analysis of <i>OsSERK</i>, <i>OsLEC1</i> and <i>OsWOX4</i> genes in rice (<i>Oryza</i> sativa L.) callus during somatic embryo development

Somatic embryogenesis is an asexual reproduction process that occurs in many plant species, including rice. This process contains several totipotency markers such as Somatic Embryogenesis Receptor-like Kinase (SERK), Leafy Cotyledon1 (LEC1) and WUSCHEL-Related Homeobox4 (WOX4) and also a helpful model for embryo development and clones and transformations. Here, we report the gene expression during somatic embryo development correlates with regeneration frequency in 14 Javanica rice (pigmented and non-pigmented) using modifified N6 media supplemented with Kinetin (2.0 mg/L) and NAA (1.0 mg/L). Although there have been advances in understanding the genetic basis of somatic embryogenesis in other varieties, rice is still unexplored, especially during somatic embryo development. Moreover, for the formation of callus induction from immature embryos, 2,4-D (2.0 mg/L, 3.0 mg/L) was used. This study analysed the gene expression of OsSERK, OsWOX4 and OsLEC1 genes through RT-PCR analysis. Higher expression of the OsLEC1 gene indicates that their function may correlate in the in vitro with the high response of rice after transfer to regeneration media. This study found that rice varieties of pigmented rice (MS Pendek and Gogoniti II) and non-pigmented rice (Pandan Ungu) showed high regeneration frequency, showing higher OsLEC1 expression than other varieties because OsLEC1 promotes the maturation of somatic embryos in plant regeneration on day 14. However, the contrast with Genjah nganjuk may be effective because of other regulatory genes. RT-PCR analysis showed OsSERK had less expression level than OsLEC1 and OsWOX4 in the varieties, which correlate with the percentage of plant regeneration, but not for Gogoniti II. In conclusion, the higher percentage of plant regeneration correlates with the higher expression level of OsLEC1 at day 14 of media regeneration of rice.     

Genome-wide identification of <i>U-box</i> gene family and expression analysis under abiotic stresses in <i>Salvia miltiorrhiza</i>

Plant U-box (PUB) E3 ubiquitin ligases play important roles in hormone signaling pathways and in response to different abiotic stresses, but little is known about U-box genes in Danshen (root of Salvia miltiorrhiza Bunge). Here, we identified and characterized 70 SmPUB genes based on its genome sequence. Phylogenetic analysis of U-box genes from S. miltiorrhiza and Arabidopsis suggested that they can be clustered into seven subgroups (I–VII). Typical U-box domains were found in all identified SmPUB genes through the analysis of conserved motifs. Moreover, qRT-PCR was applied to analyze the relative expression levels of U-box genes in S. miltiorrhiza roots and leaves under PEG-induced water deficit and salt stresses. Results revealed that the SmPUB genes exhibited stronger response to drought than to salt stress. To the best of our knowledge, this report is the first to perform genome-wide identification and analysis of the U-box gene family in S. miltiorrhiza, and the results provide valuable information for better understanding of the function of U-box in S. miltiorrhiza.     

Tanshinone IIA protects intestinal epithelial cells from ferroptosis through the upregulation of <i>GPX4</i> and <i>SLC7A11</i>

Background: Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract. The destruction of the intestinal epithelial barrier is one of the major pathological processes in IBD pathology. Growing evidence indicated that epithelial cell ferroptosis is linked to IBD and is considered a target process. Methods: RAS-selective lethal 3 (RSL3) was used to induce ferroptosis in intestinal epithelial cell line No. 6 (IEC-6) cells, and cell ferroptosis and the effects of tanshinone IIA (Tan IIA) were determined by cell counting kit-8 (CCK-8), reactive oxygen species (ROS) staining, Giemsa staining and transmission electron microscope (TEM). The cell viability of natural product library compounds was determined by CCK-8. The expression of ferroptosis-related genes were detected by real-time quantitative polymerase chain reaction (RT-qPCR) and western blot. Results: Treatment of IEC-6 cells results in the accumulation of ROS and typical morphological characteristics of ferroptosis. RSL3 treatment caused rapid cellular cytotoxicity which could be reversed by ferrostatin-1 (Fer-1) in IEC-6 cells. Natural product library screening revealed that Tan IIA is a potent inhibitor of IEC-6 cell ferroptosis. Tan IIA could significantly protect the RSL3-induced ferroptosis of IEC-6 cells. Furthermore, the ferroptosis suppressors, glutathione peroxidase 4 (GPX4), solute carrier family 7 member 11 (SLC7A11), and miR-17-92 were found to be early response genes in RSL3-treated cells. Treatment of IEC-6 cells with Tan IIA resulted in upregulation of GPX4, SLC7A11, and miR-17-92. Conclusion: Our study demonstrated that Tan IIA protects IEC-6 cells from ferroptosis through the upregulation of GPX4, SLC7A11, and miR-17-92. The findings might provide a theoretical grounding for the future application of Tan IIA to treat or prevent IBD.