科研为导向的“环境生物学”研究性教学实践与思考

"环境生物学"是环境科学本科专业的基础课程,是生命科学与环境科学的新兴交叉学科,主要面向大学二年级学生。基于其实验性强以及学科交叉的特点,很适合使用研究性教学的方法。本文从当代"环境生物学"教学研究出发,结合"环境生物学"课程主讲教师的教学实践,提出新颖的教学思路:构建以科学素养为导向的"环境生物学"教学内容;以科研创新为导向的研究性教学方法;开展多种形式的科学研究活动。以此提高"环境生物学"的教学质量,培养具有科研能力和创新意识的高素质环境人才。

“环境微生物学”分层次模块化教学探讨

“环境微生物学”是一门由多门学科相互交叉、融合而成的课程,也是环境科学与工程专业必修课程,但学生学习微生物学的背景相对欠缺,学习效果参差不齐。针对教学过程中存在的问题,有机组合不同层次和不同模块,采取分层次模块化教学方式,根据学生个人想法将学生分为研究型和应用型,进行竞赛进而挖掘学生潜力,有效提升学生课堂积极性和学生自主创新能力。

Prognositic value of anoikis and tumor immune microenvironment-related gene in the treatment of osteosarcoma

Objective:Osteosarcoma is a highly aggressive primary malignant bone tumor commonly seen in children and adolescents,with a poor prognosis.Anchorage-dependent cell death(anoikis)has been proven to be indispensable in tumor metastasis,regulating the migration and adhesion of tumor cells at the primary site.However,as a type of programmed cell death,anoikis is rarely studied in osteosarcoma,especially in the tumor immune microenvironment.This study aims to clarify prognostic value of anoikis and tumor immune microenvironment-related gene in the treatment of osteosarcoma.Methods:Anoikis-related genes(ANRGs)were obtained from GeneCards.Clinical information and ANRGs expression profiles of osteosarcoma patients were sourced from the therapeutically applicable research to generate effective therapies and Gene Expression Omnibus(GEO)databases.ANRGs highly associated with tumor immune microenvironment were identified by the estimate package and the weighted gene coexpression network analysis(WGCNA)algorithm.Machine learning algorithms were performed to construct long-term survival predictive strategy,each sample was divided into high-risk and low-risk subgroups,which was further verified in the GEO cohort.Finally,based on single-cell RNA-seq from the GEO database,analysis was done on the function of signature genes in the osteosarcoma tumor microenvironment.Results:A total of 51 hub ANRGs closely associated with the tumor microenvironment were identified,from which 3 genes(MERTK,BNIP3,S100A8)were selected to construct the prognostic model.Significant differences in immune cell activation and immune-related signaling pathways were observed between the high-risk and low-risk groups based on tumor microenvironment analysis(all P<0.05).Additionally,characteristic genes within the osteosarcoma microenvironment were identified in regulation of intercellular crosstalk through the GAS6-MERTK signaling pathway.Conclusion:The prognostic model based on ANRGs and tumor microenvironment demonstrate good predictive power and provide more personalized treatment options for patients with osteosarcoma.

A New Model on Origin and Evolution of Biology

Modified classical Boltzmann entropy as generalized entropy, then proposed Maximum Generalized Entropy Principle fusing physics and biology, and established a new model for biological origin and evolutions based on this principle, finally took protein evolution for an example to analyze. The model provided some reference for biological complexity research.

Expression and characterization of a bifunctional alginate lyase named Al163 from the Antarctic bacterium Pseudoalteromonas sp. NJ-21

In this study, an endolytic alginate lyase, named Al163, was identified, cloned, and characterized from the Antarctic bacterium Pseudoalteromonas sp. NJ-21. Comparative sequence analysis showed that the predicted amino acid sequence encoded by al163 belongs to the polysaccharide lyase 6(PL-6) family and has a molecular mass of about 80 kDa. Recombinant enzyme was purified by Ni-Sepharose affinity chromatography. Recombinant Al163 exhibited maximum activity(258 U/mg) at pH 7.0 and 40℃, and thermal stability assays showed retention of almost 90% activity after incubation at 30℃ for 30 min. Al163 activity was stimulated by Cd^(2+), Ca^(2+), Fe^(3+), and Mn^(2+), but inhibited by Cu^(2+), Si^(2+), Fe^(2+), and Ni^(2+). Thin-layer chromatographic analysis indicated that Al163 degraded sodium alginate, poly M, and poly G, generating disaccharides and trisaccharides as the final products. Only a few bacterial strains that produce a bifunctional alginate lyase have been reported. Our results indicate that recombinant Al163 exhibits broad substrate specificity and its products exhibit low degrees of polymerization. Both properties imply high potential for use of the enzyme in several industrial fields, including cosmetics and pharmaceuticals, based on the high demand for biologically active oligosaccharides.

Simulation of coupled pelagic-benthic ecosystem of the Yellow Sea Cold Water Mass

A one-dimensional coupled pelagic-benthic box model for the Yellow Sea Cold Water Mass (YSCWM) is developed. The model is divided into three boxes vertically according to the depths of thermocline and euphotic layer. It simulates well the oligotrophic shelf ecosystem of the YSCWM considering effects of nu- trients deposition and microbial loop. Main features of vertical structure of various variables in ecosystem of the YSCWM were captured and seasonal variability of the ecosystem was well reconstructed. Calculation shows that the contribution of microbial loop to the zooplankton can reach up to 60%. Besides, input of inorganic nutrients from atmospheric deposition is an important mechanism of production in upper layer of the YSCWM when stratified.

Assessment of different mcy genes for detecting the toxic to non-toxic Microcystis ratio in the field by multiplex qPCR

Harmful cyanobacterial blooms, especially Microcystis blooms, occur worldwide and draw widespread attention. The dynamics of microcystin-producing Microcystis and competition between microcystin-producing Microcystis and non-microcystin-producing Microcystis are key to predicting and treating Microcystis blooms. Multiplex qPCR is a useful tool to assess such issues. In this study, we developed multiplex qPCR methods with newly-designed probes and primers for the microcystin-synthesis related genes mcyA and mcyE. We used seven toxic Microcystis strains and four non-toxic Microcystis strains to compare the differences in the ratios of toxic and non-toxic Microcystis in mixed cultures, which were calculated using abundances of the genes mcyA, mcyB, mcyD, mcy E and phycocyanin( PC). We also compared traditional cell counting and multiplex qPCR. Hierarchical clustering and principal component analysis indicated that mcyD was the most suitable mcy gene for quantification in laboratory experiments. mcyB abundances were always higher; we suggest that the amount of toxic Microcystis measured using mcyB might overestimate the actual percentages.

Isothermal Microcalorimetry:A Review of Applications in Soil and Environmental Sciences

Isothermal microcalorimetry provides thermodynamic and kinetic information on various reactions and processes and is thereby a powerful tool to elucidate their mechanisms. Certain improvement in isothermal microcalorimetry with regard to the studies on soil and environmental sciences is briefly described. This review mainly focuses on the use of microcalorimetry in the determination of soil microbial activity, monitoring the toxicity and biodegradation of soil organic pollutants, the risk evaluation of metals and metalloids, the heat effect of ion exchange and adsorption in soil, and environmental researches. Promising prospects for the applications of the technique in the field are also discussed.

The use of environmentally sustainable bio-derived solvents in solvent extraction applications——A review

Replacement of volatile organic compounds （VOCs） by greener or more environmentally sustainable solvents is becoming increasingly important due to the increasing health and environmental concerns as well as economic pressures associated with VOCs. Solvents that are derived from biomass, namely bio-derived solvents, are a type of green solvent that have attracted intensive investigations in recent years because of their advantages over con- ventional VOCs, such as low toxicity, biodegradability and renewability. This review aims to summarize the use of bio-derived solvents in solvent extraction applications, with special emphasis given to utilization of biodiesels and terpenes. Compared with the conventional VOCs, the overall performance of these bio-derived solvents is comparable in terms of extraction yields and selectivity for natural product extraction and no difference was found for metal extraction. To date most researchers have focused on laboratory scale thermodynamics studies. Future work is required to develop and test new bio-derived solvents and understand the kinetic performance as well as solvent extraction nilnt nlant studies.

Performance of BAC process for treatment of micro-polluted water

Biological activated carbon (BAC) has been developed on the granular activated carbon by immobilization of selected and acclimated species of bacteria to treat the micro-polluted water. The BAC removal efficiencies for nitrobenzene, permanganate index, turbidity and ammonia were investigated. Effects of shock loading and SEM (Scanning Electron Microscope) observation on BAC were studied. Backwashing and its intensity of BAC were also discussed. The results showed that BAC took short time to start up and recover to the normal condition after shock loading. The shock loading studies showed that the removal efficiency of BAC was not completely inhibited even at high concentration of nitrobenzene. Backwashing performed once every 10-20 d, or an average of 15 d. Backwashing intensity was 12-14 L/(s·m2) with air and 3-4 L/(s·m2) with water.

ANALYSIS OF HABITAT PATTERN CHANGE OF RED-CROWNED CRANES IN THE LIAO HE DELTA USING SPATIAL DIVERSITY INDEX

Habitat pattern change of red-crowned cranes (Grus japonensis) in t he Liaohe Delta between 1988 and 1998 was analyzed with the help of Spatial Dive rsity Index based on remote sensing data and field investigation. The result sho wed that the influence from human activities on the wetland habitat of red-crow ned cranes was prominent with the development of oil and agricultural exploitati on, and the habitat pattern of red-crowned cranes had been obviously changed by the human disturbance during the ten years. The areas with high Spatial Diversi ty values (SD≥0.65) and that with mid-high values (0.5≤SD< 0.65), which const ituted the main part of suitable habitat of red-crowned cranes,had reduced to 9142ha and 5576ha respectively, with the shrinking of natural land cover, such a s reed and Suaeda community. The habitat pattern became more fragmented, which w as caused by roads and wells during oil exploration. It was indicated that the s uitability and quality of habitat for red-crowned cranes in the Liaohe Delta we re degraded in the last decade. The results also showed that diversity index cou ld reflect the habitat suitability of red-crowned cranes quantitatively and des cribe the spatial pattern of the habitat explicitly. This study will provide a s cientific basis for habitat protection of red-crowned cranes and other rare spe cies in wetlands.

Microbial Remediation of Heavy Metal(loid)Contaminated Soil: A Review

Because of the rapid development of industrial processes, increased urban pollution and agricultural chemicals applied in recent years, heavy metal(loid) pollution in soil has been very serious, and there is an urgent need for fast and efficient removal of heavy metal(loid) pollution. Currently, environmental microorganisms are always used to perform biological alteration or improvement of soils and sewage. Using functional microorganisms that are resistant to toxic heavy metal(loid) ions for alteration and transformation of heavy metal(loid)s in ionic form is an effective measure for microbial remediation of heavy metal(loid)contaminated soil. This paper reviewed the microbial remediation mechanism of heavy metal(loid) contaminated soils, and the approaches for breeding bacteria those can be used for highly efficient removal of heavy metal(loid)s, as well as the application examples of microbial remediation and transformation of heavy metal(loid) contaminated soil, and finally described the future trends and further research work of heavy metal(loid) contaminated soils by microbial remediation.

Ecological control of forest pest： a new strategy for forest pest control

In comparison with integrated pest management and chemical control, the authors put forward a new strategy of forest pest control, named ecological control of forest pest （ECFP）. This paper reviewed the development history, summarized the concept and principles of ECFP, discussed the technology and methods of ECFP, and evaluated the ECFP and its application conditions.

Manila clam Venerupis philippinarum as a biomonitor to metal pollution

The Manila clam Venerupis philippinarum is a good biomonitor/bioindicator to marine metal pollution and is frequently used in aquatic toxicology. Two dominant pedigrees (white and zebra) of clam are distributed in the Bohai Sea; however, little attention has been paid to potential biological differences between these two pedigrees. In this study, we tested the sensitivity of both pedigrees to marine metal (cadmium and zinc) pollution biomonitoring and marine environmental toxicology. Results demonstrate significant biological differences in gills of white and zebra clams based on metabolic profiles and antioxidant enzyme activities. In addition, we found that hypotaurine, malonate and homarine were relatively high in white clam gills, while alanine, arginine, glutamate, succinate, 4-aminobutyrate, taurine and betaine were high in zebra clam gills. Zebra clam gills were also more sensitive to a mixture of Cd and Zn, as shown by antioxidant enzyme activities and metabolic profiles, but white clam gills could accumulate more Zn. Therefore, we suggest that the white pedigree can be used as a biomonitor to marine Zn pollution, whereas the zebra pedigree can be used for toxicology studies on Cd and Zn mixed pollution.

How do soil fauna and soil microbiota respond to beech forest growth?

The dynamics and performance of soil biota during forest rotation were studied in monoculture beech stands forming a chronosequence of four different age-classes(30,62,111,153 yr).Biomass was monitored in major groups of microflora,microfauna,mesofauna,and macrofauna.Resource availability(litter layer,soil organic mater),biomass of the two dominant decomposer groups(microflora,earthworms)as well as the biomass of mesofauna and microfauna were found to remain quite stable during forest succession.Nevertheless,the marked increase of the biomasses of primary decomposers(fungi,saprophagous macroinvertebrates)in the 62-year-old stand,followed by an increase of the biomasses of macropredators in the 111-year-old stand,indicate substantial changes of several components of edaphic communities during forest development.However,constant values of soil respiration suggest that the overall performance of the soil food web does not change during beech forest succession.Thus,the decomposer system of lowland managed beech forests on calcareous soils seems to be very stable over time.We suggest that earthworm activity might have masked impacts of forest development on other soil biota and led to an astounding stability of decomposer assemblages during beech forest rotation.

Microbiostratigraphy and depositional environment of Eocene Shahbazan deposits at Chenareh section,southwest of Iran

The Shahbazan Formation was deposited in the foreland basin in southwestern Iran( Lorestan Basin). In this research,microbiostratigraphy and depositional environmental implications related to the Shahbazan Formation at the northern flank of Chenaerh anticline are discussed. Carbonate sequences of the Shahbazan Formation consist mainly of large benthic foraminifera along with other skeletal and non-skeletal components.Two biozones have been recognized by distribution of large foraminifera in the studied area that indicate middle Eocene age( Lutetian). Based on analysis of large benthic foraminiferal assemblages and microfacies features,7 different microfacies have been recognized,which can be grouped into three depositional environments: inner,middle and outer ramps.

Biological Autonomy

We argue that genuine biological autonomy, or described at human level as free will, requires taking into account quantum vacuum processes in the context of biological teleology. One faces at least three basic problems of genuine biological autonomy： （1） if biological autonomy is not physical, where does it come from？ （2） Is there a room for biological causes？ And （3） how to obtain a workable model of biological teleology？ It is shown here that the solution of all these three problems is related to the quantum vacuum. We present a short review of how this basic aspect of the fundamentals of quantum theory, although it had not been addressed for nearly 100 years, actually it was suggested by Bohr, Heisenberg, and others. Realizing that the quantum mechanical measurement problem associated with the ＂collapse＂ of the wave function is related, in the Copenhagen Interpretation of quantum mechanics, to a process between self-consciousness and the external physical environment, we are extending the issue for an explanation of the different processes occurring between living organisms and their internal environment. Definitions of genuine biological autonomy, biological aim, and biological spontaneity are presented. We propose to improve the popular two-stage model of decisions with a biological model suitable to obtain a deeper look at the nature of the mind-body problem. In the newly emerging picture biological autonomy emerges as a new, fundamental and inevitable element of the scientific worldview.

Microbial Community and Urban Water Quality

Urbanization of China is substantial and growing, and water resources are crucial for both economic and social sustainable development. Unfortunately, the frequency and intensity of water contamination events are increasing at an unprecedented rate and often accompanied by increased pollutant loading due to human activities such as irreversible industrialization and urbanization. The impacts of human pollution are most evident and of greatest concern at the microbial level. The research of the Aquatic Ecohealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, has been focusing mainly on aquatic microorganisms in the urban environment, from drinking water and landscape water to waste water. Its projects fall into three categories: biomonitoring and bioassessment, microbial ecology and diversity, ecotoxicology and environmental microbiology. Its scientif ic topics include the aquatic ecological safety and microbial food web.

Colloid's influences on microalgae growth as a potential environmental factor

The role of colloid as “colloid pump” in the ocean is well known. The important influence of colloid in seawater on the growth of microalga was found in our 1999—2000 study. Colloid concentrates were obtained by employing a cross flow filtration system to ultrafilter seawater (which had been pre filtrated by 0.45 μm acetate cellulose membrane) successively with different membranes. Ultrafiltration retentions (we called them colloid concentrates) together with control sample (seawater without colloid) were then inoculated with two species of microalgae and cultivated in selected conditions. Monitoring of microalgae growth during cultivation showed that all colloid concentrates had obvious influence on the growth of the microalgae studied. Addition of Fe(OH) 3 colloid or organic colloid (protein or carbohydrate) to the control sample enhanced the microalgae’s growth.

FIRST AMMONITE AND INOCERAMID DATA FROM THE UPPER CRETACEOUS OF THE TINGRI SECTION IN SE-TIBET:BIOSTRATIGRAPHICAL AND PALAEOENVIRONMENTAL IMPLICATIONS

A section in the Zhepure Mountains near Old Tingri in SE-Tibet,ranging from the Upper Albian to Paleogene,was described in detail by Willems et al.(1996).These authors worked on the litho-and microfacies and set up the biostratigraphical framework by planktonic foraminifera.Willems et al.(1996)established their section as a standard for southern Tibet and compared it to the Gamba area.During the 2004 Tibet-expedition of Chengdu University of Technology in China,in co-operation with Bremen and Kiel universities in Germany,the locality was revisited for the purpose of collecting invertebrate fossils.This field-work included only the Upper Cretaceous part of the Tingri section and its invertebrate faunal content.Until today almost no ammonite and inoceramid data existed for this section.This is true for most Cretaceous sections in Tibet,although the Upper Cretaceous succession was interpreted as shelf environment.which in other parts of the world contains rich faunas of these macrofossil groups.The newly discovered continuous record of rare ammonites and inoceramids is probably limited since the preservation in the wacke-and packstones is poor.In addition,sampling conditions were unfavorable and the environmental conditions disadvantageous for most groups of invertebrates,as possibly indicated by larger amounts of small bivalve debris(filaments)in the upper part of the Gamba Group.Although the collected fauna is sparse and poorly preserved,the following biostratigraphical data can be added to the hitherto described microfauna:Calycoceras?from the Upper Gamba Group is Late Cenomanian in age and is accompanied by indeterminable juvenile desmoceratids.Superjacent follows a record of the ammonite Forresteria sp.,indicating that this level in the upper part of the Gamba Group belongs to the Lower Coniacian.This supports the finding of Inoceramus(Cremnoceramus)waltersdorfensis?hannovrensis?from the same interval.Anagaudryceras?is an individual ammonite finding from the Zhepure Shanbei or Zhepure Shanpo Formation,corresponding to the Santonian-Maastrichtian part of the succession.