基于转录组测序的Cd胁迫下芹菜细胞自噬相关基因的筛选

细胞自噬是植物逆境应答过程中最常见的保护机制之一。动物中,自噬相关基因抵御镉(Cd)毒害的功能研究较清楚,但植物却知之甚少。文中以芹菜品种‘皇后’为试材,采用外源Cd(终浓度为0、2、4、8mg/L)添加营养液水培处理,利用转录组测序(RNA-seq)技术筛选细胞自噬相关差异基因并进行q RT-PCR验证。结果表明Cd胁迫对芹菜植株产生了明显的毒害作用,并与浓度间产生了量效关系。在筛选的8个差异表达的自噬相关基因中,ATG8a、ATG8f、ATG13、AMPK-1、AMPK-2基因随Cd浓度升高表达上调,ATG12、VPS30和VPS34则先上调后下降,说明自噬相关基因可能通过表达上调增加了自噬小体结构以抵御Cd毒性作用;而高浓度Cd(8mg/L)可能超出芹菜的耐受范围,导致多个自噬基因又出现表达下调趋势。以上结果有助于后期自噬相关基因的功能研究,为进一步探讨芹菜对Cd胁迫的耐性机制提供参考依据。     

PSMD: An extensive database for pan‐species microsatellite investigation and marker development

Microsatellites are widely distributed throughout nearly all genomes which have been extensively exploited as powerful genetic markers for diverse applications due to their high polymorphisms. Their length variations are involved in gene regulation and implicated in numerous genetic diseases even in cancers. Although much effort has been devoted in microsatellite database construction, the existing microsatellite databases still had some drawbacks, such as limited number of species, unfriendly export format, missing marker development, lack of compound microsatellites and absence of gene annotation, which seriously restricted researchers to perform downstream analysis. In order to overcome the above limitations, we developed PSMD (Pan‐Species Microsatellite Database, http://big.cdu.edu.cn/psmd/ ) as a web‐based database to facilitate researchers to easily identify microsatellites, exploit reliable molecular markers and compare microsatellite distribution pattern on genome‐wide scale. In current release, PSMD comprises 678,106,741 perfect microsatellites and 43,848,943 compound microsatellites from 18,408 organisms, which covered almost all species with available genomic data. In addition to interactive browse interface, PSMD also offers a flexible filter function for users to quickly gain desired microsatellites from large data sets. PSMD allows users to export GFF3 formatted file and CSV formatted statistical file for downstream analysis. We also implemented an online tool for analysing occurrence of microsatellites with user‐defined parameters. Furthermore, Primer3 was embedded to help users to design high‐quality primers with customizable settings. To our knowledge, PSMD is the most extensive resource which is likely to be adopted by scientists engaged in biological, medical, environmental and agricultural research.     

Manipulation of host ecdysteroid hormone levels facilitates infection by the fungal insect pathogen,Metarhizium rileyi

Entomopathogenic fungi such as Metarhizium rileyi and Beauveria bassiana are widely used insect biological control agents. Little, however, is known concerning genetic or enzymatic factors that differentiate the mechanisms employed by these two fungal pathogens to infect target hosts. Infection by either of these organisms is known to increase levels of the growth and molting hormone, ecdysone, which also regulates the expression of a number of innate immune pathways. M. rileyi, but not B. bassiana, has apparently evolved an ecdysteroid-22-oxidase (MrE22O) that inactivate ecdysone. We show that deletion of MrE22O impaired virulence compared with the wild-type strain, with an increase in ecdysone titer seen in hosts that was coupled to an increase in the expression of antimicrobial genes. An M. rileyi strain engineered to overexpress MrE22O (MrE22O^OE), as well as trans-expression in B. bassiana (Bb::MrE220^OE) resulted, in strains displaying enhanced virulence and dampening of host immune responses compared with their respective wild-type parental strains. These results indicate that ecdysone plays an important role in mediating responses to fungal infection and that some insect pathogenic fungi have evolved mechanisms for targeting this hormone as a means for facilitating infection.     

Down-regulated LINC00115 inhibits prostate cancer cell proliferation and invasion via targeting miR-212-5p/FZD5/Wnt/β-catenin axis

Prostate cancer is the second most frequent malignancy in men worldwide, and its incidence is increasing. Therefore, it is urgently required to clarify the underlying mechanisms of prostate cancer. Although the long non-coding RNA LINC00115 was identified as an oncogene in several cancers, the expression and function of LINC00115 in prostate cancer have not been explored. Our results showed that LINC00115 was significantly up-regulated in prostate cancer tissues, which was significantly associated with a poor prognosis for prostate cancer patients. Functional studies showed that knockdown LINC00115 inhibited cell proliferation and invasion. In addition, LINC00115 served as a competing endogenous RNA (ceRNA) through sponging miR-212-5p to release Frizzled Family Receptor 5 (FZD5) expression. The expression of miR-212-5p was noticeably low in tumour tissues, and FZD5 expression level was down-regulated with the knockdown of LINC00115. Knockdown LINC00115 inhibited the Wnt/β‑catenin signalling pathway by inhibiting the expression of FZD5. Rescue experiments further showed that LINC00115 inhibits prostate cancer cell proliferation and invasion via targeting miR-212-5p/ FZD5/ Wnt/β-catenin axis. The present study provided clues that LINC00115 may be a promising novel therapeutic target for prostate cancer patients.     

Reprogramming of sugar transport pathways in Escherichia coli using a permeabilized SecY protein-translocation channel

In the initial step of sugar metabolism, sugar-specific transporters play a decisive role in the passage of sugars through plasma membranes into cytoplasm. The SecY complex (SecYEG) in bacteria forms a membrane channel responsible for protein translocation. The present work shows that permeabilized SecY channels can be used as nonspecific sugar transporters in Escherichia coli. SecY with the plug domain deleted allowed the passage of glucose, fructose, mannose, xylose, and arabinose, and, with additional pore-ring mutations, facilitated lactose transport, indicating that sugar passage via permeabilized SecY was independent of sugar stereospecificity. The engineered E. coli showed rapid growth on a wide spectrum of monosaccharides and benefited from the elimination of transport saturation, improvement in sugar tolerance, reduction in competitive inhibition, and prevention of carbon catabolite repression, which are usually encountered with native sugar uptake systems. The SecY channel is widespread in prokaryotes, so other bacteria may also be engineered to utilize this system for sugar uptake. The SecY channel thus provides a unique sugar passageway for future development of robust cell factories for biotechnological applications.     

Deficiency of Macf1 in osterix expressing cells decreases bone formation by Bmp2/Smad/Runx2 pathway

Microtubule actin cross‐linking factor 1 (Macf1) is a spectraplakin family member known to regulate cytoskeletal dynamics, cell migration, neuronal growth and cell signal transduction. We previously demonstrated that knockdown of Macf1 inhibited the differentiation of MC3T3‐E1 cell line. However, whether Macf1 could regulate bone formation in vivo is unclear. To study the function and mechanism of Macf1 in bone formation and osteogenic differentiation, we established osteoblast‐specific Osterix (Osx) promoter‐driven Macf1 conditional knockout mice (Macf1^f/fOsx‐Cre). The Macf1^f/fOsx‐Cre mice displayed delayed ossification and decreased bone mass. Morphological and mechanical studies showed deteriorated trabecular microarchitecture and impaired biomechanical strength of femur in Macf1^f/fOsx‐Cre mice. In addition, the differentiation of primary osteoblasts isolated from calvaria was inhibited in Macf1^f/fOsx‐Cre mice. Deficiency of Macf1 in primary osteoblasts inhibited the expression of osteogenic marker genes (Col1, Runx2 and Alp) and the number of mineralized nodules. Furthermore, deficiency of Macf1 attenuated Bmp2/Smad/Runx2 signalling in primary osteoblasts of Macf1^f/fOsx‐Cre mice. Together, these results indicated that Macf1 plays a significant role in bone formation and osteoblast differentiation by regulating Bmp2/Smad/Runx2 pathway, suggesting that Macf1 might be a therapeutic target for bone disease.     

广州市湿地公园植物调查与分析

为更好地提高湿地公园的生态服务能力、加强湿地公园的物种保育功能并促进湿地公园建设和发展质量,对广州地区20个湿地公园植物进行了实地调查。结果表明,调查区域共有205种湿地植物;对其物种组成、生活型、生态习性、优势科属及应用频度等的分析表明,湿地公园的植物群落结构比较简单,主要植物种类同质化现象很严重,保护和珍稀植物种类应用较少等。基于此,推荐了55种本土植物作为广州市湿地公园进行生态改造和景观配置的候选物种,同时还提出了对未来湿地公园的建设和管理的若干建议。     

Fungal Diversity in Deep Sea Sediments from East Yap Trench and Their Denitrification Potential

Abstract

In recent years, the hadal trenches have been recognized as biological hot spots for deep sea researchers. Due to high hydrostatic pressure, low temperatures, high salinity and low nutrients, the microorganisms in hadal trenches may have unique community structure with potential for biotechnical application. Compared with bacteria and archaea, the diversity and ecological roles of fungi in hadal trenches remain largely unknown. The purpose of this study was to explore fungal diversity in deep-sea sediments of the Yap trench and their denitrification potential. In the present study, a total of 106 fungal strains were isolated from six sediment samples collected in the East Yap Trench. These fungi belonged to five classes (Dothideomycetes, Eurotiomycetes, Sordariomycetes, Cystobasidiomycetes, and Microbotryomycetes), thirteen genera (Acremonium, Alternaria, Aureobasidium, Aspergillus, Cladosporium, Cystobasidium, Engyodontium, Gliomastix, Lecanicillium, Penicillium, Phoma, Rhodotorula and Trichoderma) and eighteen species, based on morphological identification and ITS-rDNA sequence analysis. Among them, the dominant genus is Cladosporium, which accounting for 42.45% of the total fungal strains. Meanwhile, the denitrification potential of the fungal strains was also examined with two different denitrifying media (nitrate and nitrite as sole substrate, respectively). Two fungal strains (Acremonium sp. and Aspergillus versicolor), were found to be able to produce N₂O ex situ in the presence of nitrite. No fungus was found to produce N₂O by using nitrate. Our results suggest that fungi in hadal sediments, play important roles in nitrogen cycles.     

Thermal stress responses in the bacterial biosphere of the Great Barrier Reef sponge,Rhopaloeides odorabile

Marine sponges are diverse, abundant and provide a crucial coupling point between benthic and pelagic habitats due to their high filtration rates. They also harbour extensive microbial communities, with many microbial phylotypes found exclusively in sponge hosts and not in the seawater or surrounding environment, i.e. so‐called sponge‐specific clusters (SCs) or sponge‐ and coral‐specific clusters (SCCs). We employed DNA (16S rRNA gene) and RNA (16S rRNA)‐based amplicon pyrosequencing to investigate the effects of sublethal thermal stress on the bacterial biosphere of the Great Barrier Reef sponge Rhopaloeides odorabile. A total of 8381 operational taxonomic units (OTUs) (97% sequence similarity) were identified, affiliated with 32 bacterial phyla from seawater samples, 23 bacterial phyla from sponge DNA extracts and 18 bacterial phyla from sponge RNA extracts. Sublethal thermal stress (31°C) had no effect on the present and/or active portions of the R. odorabile bacterial community but a shift in the bacterial assemblage was observed in necrotic sponges. Over two‐thirds of DNA and RNA sequences could be assigned to previously defined SCs/SCCs in healthy sponges whereas only 12% of reads from necrotic sponges could be assigned to SCs/SCCs. A rapid decline in host health over a 1°C temperature increment suggests that sponges such as R. odorabile may be highly vulnerable to the effects of global climate change.     

Thermodynamically Self‐Healing 1D–3D Hybrid Perovskite Solar Cells

Thermal degradation in perovskite solar cells is still an unsettled issue that limits its further development. In this study, 2‐(1H‐pyrazol‐1‐yl)pyridine is introduced into lead halide 3D perovskites, which allows 1D–3D hybrid perovskite materials to be obtained. The heterostructural 1D–3D perovskites are proved to be capable of remarkably prolonging the photoluminescence decay lifetime and suppressing charge carrier recombination in comparison to conventional 3D perovskites. The intrinsic properties of thermodynamically stable yet kinetically labile 1D materials allow the system to alleviate the lattice mismatch and passivate the interface traps of heterojunction region of 1D–3D hybrid perovskites that may occur during the crystal growth process. Importantly, the as‐fabricated 1D–3D perovskite solar cells display a thermodynamic self‐healing ability, which is induced through blocking the ion‐migration channels of A‐site ions by the flexible 1D perovskite with less densely close‐packed structure. Particularly, the power conversion efficiency of as‐fabricated unencapsulated 1D–3D perovskite solar cells is demonstrated to be reversible under temperature cycling (25–85 °C) at 55% relative humidity, which largely outperforms the pure 3D perovskite solar cell. The present study provides a facile approach to fabricate 1D–3D perovskite solar cells with high efficiency and long‐term stability.