生物信息学课程教学的初步探讨

结合教学实践,对在生物学专业开设生物信息学课程的必要性及具体的教学实施作初步探讨,为生物信息学课程教学提供参考。     

The effect of gold and silver nanoparticles,chitosan and their combinations on bacterial biofilms of food-borne pathogens

Abstract

The antimicrobial activity of gold and silver nanoparticles (AuNPs, AgNPs), chitosan (CS) and their combinations was established by determining the minimum inhibitory concentration for planktonic (MICPC₈₀) and biofilm growth (MICBC₈₀), for biofilm formation (MICBF₈₀), metabolic activity (MICBM₈₀) and reduction (MICBR₈₀), and for the metabolic activity of preformed biofilm (MICMPB₈₀). Biofilms were quantified in microtitre plates by crystal violet staining and metabolic activity was evaluated by the MTT assay. Chitosan effectively suppressed biofilm formation (0.31–5?mg ml^?1) in all the tested strains, except Salmonella enterica Infantis (0.16–2.5?mg ml^?1) where CS and its combination with AgNPs induced biofilm formation. Nanoparticles inhibited biofilm growth only when the highest concentrations were used. Even though AuNPs, AgNPs and CS were not able to remove biofilm mass, they reduced its metabolic activity by at least 80%. The combinations of nanoparticles with CS did not show any significant positive synergistic effect on the tested target properties.     

The Use of Polarization-dependent SERS from Scratched Gold Films to Selectively Eliminate Solution-phase Interference

Polarization-dependent surface-enhanced Raman scattering (SERS) was studied for oxazine 720 molecules adsorbed on a scratched gold surface placed in situ and under electrochemical control. A quantitative method for evaluating the observed polarization dependence will be introduced. This method takes into account the polarization artifacts caused by optical elements in the light microscope used for Raman microscopy. Intensity of the SERS obtained from oxazine 720 adsorbed on scratches in gold showed a polarization dependence after correction was made for these artifacts. In contrast, intensity of the ordinary Raman signal obtained from perchlorate ions in the solution above a scratched gold surface was found to be polarization-independent. Therefore, polarization effects can be used to selectively remove solution-phase interference signals from the SERS spectrum of an adsorbed analyte. These polarization effects were found to be independent of the applied potential, meaning the methodology is applicable to electrochemical SERS studies.     

Highlighting the roles of transition metals and speciation in chemical biology

Transition metal ions play key structural and functional roles, affecting structures of biomolecules and enzyme function. The importance of transition metal ions in chemical biology is, thus, undisputed. However, the aqueous chemistry of metal ions is complicated because they form species in several protonation and redox states. In the presence of metabolites, metal ions can also form coordination complexes. The existence of several species is relevant because enzymes and membrane receptors can distinguish between species even when they are rapidly equilibrating. Thus, metal ions, enzyme cofactors, and therapeutic agents are sensitive to the metal ion speciation chemistry because it affects their interaction with enzymes and other biomolecules. Speciation is also crucial for metal-containing bioorthogonal reactions, since water and metabolites stabilize active catalysts, affect chemoselectivity and reaction yields.     

Bacterial Oxidation of Refractory Sulfide Ores for Gold Recovery

Abstract

The microbiological leaching of refractory sulfide ores (pyrite, arsenopyrite) for recovery of gold is reviewed in this article. The underlying physiological, biochemical, and genetic fundamentals of the bacteria involved (Thiobacillus and Sulfolobus spp.) are complex and have yet to be elucidated in depth. The chemistry of acid and biological leaching of pyrite and arsenopyrite minerals is also complex, and many of the individual reactions are not known in detail. Bacterial leaching is discussed in relation to chemical speciation at acid pH values. Attempts to develop models for a better understanding of bioleaching processes are summarized. The importance of pH, redox potential, temperature, sulfur balance, and toxic metals is evaluated for optimizing conditions for bacterial activity. Gold is finely disseminated in refractory sulfide ores, thereby decreasing Au recoveries upon conventional cyanidation for gold dissolution. In the bioleaching process, bacteria remove the sulfide minerals by oxidative dissolution and thus expose Au to extraction with cyanide solution. Stirred tank reactors appear most suited for this biological leaching process. The overall oxidation of the sulfides is an important variable for gold recovery. Pilot- and commercial-scale bioleaching processes for gold-containing pyrite and arsenopyrite ores are reviewed. This application of mineral biotechnology competes favorably with pressure leaching and roasting processes, both of which are problematic and energy-intensive alternatives for pretreatment of auriferous pyrite/arsenopyrite ores.     

Could preoperative short-course radiotherapy be the treatment of choice for localized advanced rectal carcinoma?

Short-course preoperative radiotherapy (RT) is widely used in northern Europe for locally advanced resectable rectal cancer, but its role in the era of advanced imaging techniques is uncertain. Here, we reviewed articles and abstracts on SCRT published from 1974 through 2013 with the goal of identifying patients who might be best suited for short-course RT. We included relevant articles comparing surgery with or without preoperative radiation published before and after the advent of total mesorectal excision. We also analyzed two randomized trials directly comparing short-course RT with conventionally fractionated chemoradiation (the Polish Colorectal Study Group and the Trans-Tasman Radiation Oncology Group) that compared short-course RT with conventional chemoradiotherapy. We conclude from our review that short-course RT can be generally applied for operable rectal cancer and produces high rates of pelvic control with acceptable toxicity; it reduces local recurrence rates but does not increase overall survival. SCRT seems to be best used for tumors considered “low risk,” i.e., those that are >5 cm from the anal margin, without circumferential margin involvement, and involvement of fewer than 4 lymph nodes. Whether sequential chemotherapy can further improve outcomes remains to be seen, as does the best time for surgery (immediately or 6–8 weeks after RT). We further recommend that selection of patients for short-course RT should be based on findings from magnetic resonance imaging or transrectal ultrasonography.     

Comparison of lag times in plant physiology

Abstract Comparison of lag (or latent) times is a useful tool in plant physiology for investigating potential mechanisms involved in a response. There are two main ways of deriving the lag time, but only one of these can be properly used for comparative purposes. The other method is biased by the faster responding plants and may not give a representative estimate for the lag time in the population. The fact that the two methods give different, non-comparable results has been widely overlooked. We suggest more care should be taken for their correct use, and propose two terms which can be used to describe the different estimates of the lag time to avoid confusion.     

A Comparison of Photosynthetic Capacity between Myrica Gale var. Tomentosa a Nitrogen-Fixing Shrub,and Co-Occurring Species in an Oligotrophic Moor

Photosynthetic and transpiration (E) rates, stomatal conductance, and leaf nitrogen content were surveyed for Myrica gale var. tomentosa, a N₂-fixing wetland shrub, Betula platyphylla var. japonica, and Rhododendron japonicum in Ozegahara moor, an oligotrophic moor in Central Japan. Net photosynthetic rate saturated with irradiance (P_max) of M. gale was 15.2-16.5 μmol(CO₂) m^-2 s^-1, higher than those of the other species throughout the growing season. P_max was positively correlated with leaf N content among the three species. The large leaf N content in M. gale was due to N₂-fixation in root nodules. In a comparison of M. gale in two habitats, P_max, leaf N content, and root nodule development were larger in the wetter habitat. M. gale showed high E and no midday depression of P_max even under high irradiance and large vapour pressure deficit between leaves and ambient air on a midsummer day. These traits of photosynthesis and water relations were associated with the dominance of this shrub in wetter sites such as stream sides and hollows. This revised version was published online in September 2006 with corrections to the Cover Date.     

Visualization photofragmentation‐induced rhodamine B release from gold nanorod delivery system by combination two‐photon luminescence imaging with correlation spectroscopy

Plasmon‐enhanced gold nanorod (AuNR) with high photothermal conversion efficiency is a promising light‐controllable nanodrug delivery system for cancer therapy. Understanding the mechanism for the light‐controllable drug release of AuNR delivery systems is important for the development of nanomedicine. In this study, the rhodamine B (RB) released from AuNR‐RB nanodelivery system was quantitated and visualized by using two‐photon luminescence (TPL) imaging combined with correlation spectroscopy. The photofragmentation of AuNR induced by femtosecond pulsed laser was revealed by TPL correlation spectroscopy when the laser energy was above the thermal damage threshold of AuNR, and the RB released from this nanodrug delivery system was visualized by TPL imaging. Furthermore, the photofragmentation‐induced release of RB from AuNR‐RB nanodelivery system was visualized in living MCF‐7 breast cancer cells by TPL imaging combined with correlation spectroscopy. These results provided a novel optical approach to quantify the release of drugs from gold nanocarriers in complex biological media.