Secure web book to store structural genomics research data

Recently established collaborative structural genomics programs aim at significantly accelerating the crystal structure analysis of proteins. These large-scale projects require efficient data management systems to ensure seamless collaboration between different groups of scientists working towards the same goal. Within the Berlin-based Protein Structure Factory, the synchrotron X-ray data collection and the subsequent crystal structure analysis tasks are located at BESSY, a third-generation synchrotron source. To organize file-based communication and data transfer at the BESSY site of the Protein Structure Factory, we have developed the web-based BCLIMS, the BESSY Crystallography Laboratory Information Management System. BCLIMS is a relational data management system which is powered by MySQL as the database engine and Apache HTTP as the web server. The database interface routines are written in Python programing language. The software is freely available to academic users. Here we describe the storage, retrieval and manipulation of laboratory information, mainly pertaining to the synchrotron X-ray diffraction experiments and the subsequent protein structure analysis, using BCLIMS.     

Terahertz Radiation at ANKA, the New Synchrotron Light Source in Karlsruhe

ANKA is a new synchrotron light source atthe Karlsruhe Research Center in southwestGermany. The acronym stands for Ångstrøm Source Karlsruhe.The ANKA-IR beamline provides a highbrilliance infrared beam through the near,mid and far-infrared range. Thefar-infrared range is of particularinterest, since at frequencies lower thanaround 200 cm^-1 (6 THz) synchrotronlight begins to outperform conventionalthermal sources in terms of total intensityas well as brilliance. The extraction ofthe entire flux is a challenge in the THzrange, since the natural verticaldivergence of synchrotron radiationincreases with wavelength and the openingangle for collection is limited by designconstraints. At ANKA-IR, this problem issolved by the collection of radiationemitted from a bending magnet edge source,which has a much smaller verticaldivergence than conventional synchrotronradiation emitted from the constantmagnetic field region within the dipolemagnet. Edge radiation at ANKA permits theextraction of the entire infrared flux downto around 100 cm^-1 (3 THz) while withconventional synchrotron radiation thiswould only be the case for frequencies downto 2500 cm^-1. ANKA-IR provides usableintensity down to 4 cm^-1 (120 GHz).     

Infrared analysis of contour feathers: The conservation of body heat radiation in birds

1. We examined infrared absorption spectra in contour feathers of 10 species of birds to compare infrared features of the downy and pennaceous regions with the mechanisms of conservation of body heat radiation.     

Synthesis,crystallization and preliminary crystallographic analysis of a 52-nucleotide DNA/2′-OMe-RNA oligomer mimicking 10–23 DNAzyme in the complex with a substrate

A 52-nucleotide DNA/2′-OMe-RNA oligomer mimicking 10–23 DNAzyme in the complex with its substrate was synthesized, purified and crystallized by the hanging-drop method using 0.8 M sodium potassium tartrate as a precipitant. A data set to 1.21 Å resolution was collected from a monocrystal at 100 K using synchrotron radiation on a beamline BL14.1 at BESSY. The crystal belonged to the P2₁ group with unit-cell a = 49.42, b = 24.69, c = 50.23, β = 118.48.     

前列腺癌根治性切除术后会阴部红外线照射提高患者控尿的 前瞻性的研究

目的:探讨对于前列腺癌根治术的患者,术后采用红外线会阴部照射,提高患者拔管后控尿的效果。方法:对76例前列腺癌根治术后患者,随机分为两组,实验组术后第一天起采用会阴部红外线照射治疗,连续10天,空白对照组不做任何处理,然后评估患者拔除尿管后控尿情况。结果:随访一年后发现,实验组中,37(97%)例的患者能够控制排尿,而对照组31(82%)例患者能够控制排尿(P=0.01)。实验组中可以控制排尿的患者,在拔除尿管以后,平均25±39天后可以控制排尿;而对照组中的患者则需要75±103天才能控制排尿(P<0.001)。接受红外线照射的患者尿控情况明显好于未接受治疗患者。结论:盆底红外线照射是前列腺癌根治术后提高患者尿控能力的有效的治疗方式。     

一种新型相干辐射--THz辐射在生物学中的应用

脉冲THz辐射是一种新型的远红外相干辐射源,近年来在不同的研究领域得到了广泛的应用。本文简要介绍THz辐射产生、探测的基本原理和方法;THz辐射的基本性质和它在生物学研究中应用的物理基础;对生物体系进行时域光谱分析和成像研究所取得的成果和最新进展,以及对该领域研究前景的展望。     

Polarized infrared microspectroscopy of single spruce fibers: hydrogen bonding in wood polymers

We studied wood polymers in their native composite structure using mechanically isolated single spruce (Picea abies [L.] Karst.) fibers. Dichroic infrared spectra of fibers placed in a custom-built microfluidic cuvette were acquired in air, in liquid (heavy) water, and in liquid dimethylacetamide using a novel combination of synchrotron-based Fourier transform infrared microspectroscopy with polarization modulation. Differences were observed in the O-H stretching frequency region of the spruce spectra upon changing the ambient conditions. Analysis of these spectral variations provides information on hydrogen bonding, orientation, and accessibility of structural units of the wood polymers in the spruce cell walls. Our in situ approach contributes to a further understanding of the structural details of wood polymers in their native setting.     

Biological applications of synchrotron radiation infrared spectromicroscopy

Extremely brilliant infrared (IR) beams provided by synchrotron radiation sources are now routinely used in many facilities with available commercial spectrometers coupled to IR microscopes. Using these intense non-thermal sources, a brilliance two or three order of magnitude higher than a conventional source is achievable through small pinholes (< 10 μm) with a high signal to-noise ratio. IR spectroscopy is a powerful technique to investigate biological systems and offers many new imaging opportunities. The field of infrared biological imaging covers a wide range of fundamental issues and applied researches such as cell imaging or tissue imaging. Molecular maps with a spatial resolution down to the diffraction limit may be now obtained with a synchrotron radiation IR source also on thick samples. Moreover, changes of the protein structure are detectable in an IR spectrum and cellular molecular markers can be identified and used to recognize a pathological status of a tissue. Molecular structure and functions are strongly correlated and this aspect is particularly relevant for imaging. We will show that the brilliance of synchrotron radiation IR sources may enhance the sensitivity of a molecular signal obtained from small biosamples, e.g., a single cell, containing extremely small amounts of organic matter. We will also show that SR IR sources allow to study chemical composition and to identify the distribution of organic molecules in cells at submicron resolution is possible with a high signal-to-noise ratio. Moreover, the recent availability of two-dimensional IR detectors promises to push forward imaging capabilities in the time domain. Indeed, with a high current synchrotron radiation facility and a Focal Plane Array the chemical imaging of individual cells can be obtained in a few minutes. Within this framework important results are expected in the next years using synchrotron radiation and Free Electron Laser (FEL) sources for spectro-microscopy and spectral-imaging, alone or in combination with Scanning Near-field Optical Microscopy methods to study the molecular composition and dynamic changes in samples of biomedical interest at micrometric and submicrometric scales, respectively.     

Radiobiological effects and medical applications of non-ionizing radiation

Radiation is used in medicine to diagnose and treat diseases but it can also cause harm to the body by burning or mutation. This depends on whether the radiation is ionizing or nonionizing. Despite its vast applications in surgery, dermatology and cosmetics, little is taught and thus known about non-ionizing radiation.This review article discusses the fundamentals of non-ionizing electromagnetic radiations. The main aim is to extensively explain the different types of non-ionizing radiation. This will equip students and medical personnel with knowledge on different medical applications and expose them to a variety of specializations in medicine that utilize non-ionizing radiation. The article discusses the physics, hazard, means of protection and medical application of each type of radiation: ultraviolet radiation, light (both visible light and LASER), infrared radiation, microwaves and extremely low frequency radiation separately. It presents these terms in a simple manner that avoids rigors mathematics and physics, which makes them comprehensible for medical students.The development of new diagnostic and therapeutic approaches could also lead to increased hazards to the body unless they are treated with precaution. If not adequately monitored, a significant health risk may be posed to potentially exposed employees. Hence proper dosage should be used for non-ionizing radiation. This is only possible through understanding of the risks/benefits of these radiations by studying the physics and radiobiological effects of each individual radiation.     

Theory and performance of an infrared heater for ecosystem warming

In order to study the likely effects of global warming on future ecosystems, a method for applying a heating treatment to open-field plant canopies (i.e. a temperature free-air controlled enhancement (T-FACE) system) is needed which will warm vegetation as expected by the future climate. One method which shows promise is infrared heating, but a theory of operation is needed for predicting the performance of infrared heaters. Therefore, a theoretical equation was derived to predict the thermal radiation power required to warm a plant canopy per degree rise in temperature per unit of heated land area. Another equation was derived to predict the thermal radiation efficiency of an incoloy rod infrared heater as a function of wind speed. An actual infrared heater system was also assembled which utilized two infrared thermometers to measure the temperature of a heated plot and that of an adjacent reference plot and which used proportional–integrative–derivative control of the heater to maintain a constant temperature difference between the two plots. Provided that it was not operated too high above the canopy, the heater system was able to maintain a constant set-point difference very well. Furthermore, there was good agreement between the measured and theoretical unit thermal radiation power requirements when tested on a Sudan grass (Sorghum vulgare) canopy. One problem that has been identified for infrared heating of experimental plots is that the vapor pressure gradients (VPGs) from inside the leaves to the air outside would not be the same as would be expected if the warming were performed by heating the air everywhere (i.e. by global warming). Therefore, a theoretical equation was derived to compute how much water an infrared-warmed plant would lose in normal air compared with what it would have lost in air which had been warmed at constant relative humidity, as is predicted with global warming. On an hourly or daily basis, it proposed that this amount of water could be added back to plants using a drip irrigation system as a first-order correction to this VPG problem.     

Infrared spectral characterization of peptidic material produced by ionizing radiation in aqueous cyanides

Summary Oligomers formed by ionizing radiation in aqueous cyanide solutions, under various experimental conditions, have been characterized by infrared spectroscopy. IR bands appear in the region known to be characteristic for amides and peptides. The results are discussed in relation to radiation-induced formation of peptidic material and the potential role of ionizing radiation as an energy source for some processes in prebiotic molecular evolution.     

The Effect of Red and Infrared Light on the Growth of Escherichia coli and the Production of the Recombinant Protein Barstar

Incoherent red and infrared low-intensity light enhanced the growth of the auxotrophic strain Escherichia coli AD494(DE3)pLysS and the production of the recombinant polypeptide barstar. Illumination also stimulated the growth of nonrecombinant E. coli cells.     

Selective light transmittance of translucent bracts in the Himalayan giant glasshouse plant Rheum nobile Hook. f. & Thomson (Polygonaceae)

Translucent bract transmittance of ultraviolet (UV) to infrared (IR) radiation (between 320 and 800 nm) and leaf anatomy were examined in a glasshouse plant, Rheum nobile Hook. f. & Thomson (Polygonaceae) to assess the function of avoiding injury by UV radiation while keeping the inflorescence warm by photosynthetically active (PA) and IR radiation. Although the translucent bracts and rosulate leaves transmitted little UV radiation, the former always transmit more PA and IR radiation. Additionally, the bracts transmit much more scattered solar radiation than direct radiation. The bracts are also anatomically different from the rosulate leaves. They have two or three layers of mesophyll cells with neither palisade nor spongy parenchymatous cells; in addition, the uppermost layer of mesophyll and the epidermis stain easily, and both are thought to play a role in attenuating UV radiation. The leaf epidermis of many land plants has UV absorbing pigments such as flavonoids, which absorb almost all UV radiation. Thus the role of the bracts of R. nobile is to protect the reproductive organs by absorbing UV radiation and to keep them warm by transmitting PA and IR radiation. The bracts are believed to have adapted function and form to the environment, in particular, to the weather conditions of the eastern Himalaya.     

落叶阔叶林反照率的时间变化与影响因素

反照率原位测量对生态系统能量收支及其遥感应用至关重要,但目前坡面地形反照率的测量方式有局限且可见光与近红外波段反照率时间变化的差异尚不清楚。本研究以东北地区帽儿山森林生态站的落叶阔叶林为例,探究入射和反射太阳辐射(SR,300～2800 nm)、光合有效辐射(PAR,400～700 nm)、近红外辐射(NIR,700～2800 nm)的反照率时间变化特征及其影响因子,同时分析了两种辐射表安装方式反照率的差异。结果表明: 晴天SR和NIR反照率日变化呈上下午不对称的U型曲线,但PAR从早到晚递增;阴天反照率均先急剧下降后趋于稳定。平行于坡面测量增大了反照率的日均值,但缓和了SR、NIR反照率日不对称的现象。从整个生长季来看,SR、NIR与PAR反照率水平测量时最大值分别为0.16、0.27和0.11,最小值分别为0.07、0.11和0.03。SR和NIR反照率季节变化均为先增大后减小(7月为峰值),PAR则相反,SR反照率主要受NIR而不是PAR控制。各波段反照率季节变化的影响因子按照贡献率排序为宽带归一化植被指数(61.7%～78.5%,可表征叶面积指数)>太阳高度角(15.4%～36.9%)>晴空指数(0.4%～36.9%)。     

Activation of Molecular Oxygen by Infrared Laser Radiation in Pigment-Free Aerobic Systems

With the goal of mimicking the mechanisms of the biological effects of low energy laser irradiation, we have shown that infrared low intensity laser radiation causes oxygenation of the chemical traps of singlet oxygen dissolved in organic media and water saturated by air at normal atmospheric pressure. The photooxygenation rate was directly proportional to the oxygen concentration and strongly inhibited by the singlet oxygen quenchers. The maximum of the photooxygenation action spectrum coincided with the maximum of the oxygen absorption band at 1270 nm. The data provide unambiguous evidence that photooxygenation is determined by the reactive singlet ¹_g state formed as a result of direct laser excitation of molecular oxygen. Hence, activation of oxygen caused by its direct photoexcitation may occur in natural systems.     

Calorimetric measurements of the effect of 330-MHz radiofrequency radiation on human erythrocyte ghosts

Irreversible changes in the heat capacity of human erythrocyte ghost suspensions due to the effect of 330-MHz radiofrequency radiation (at a specific absorption rate of approximately 9 mW/g) were detected by the method of scanning differential microcalorimetry. Using the data obtained from the analysis of infrared spectra of air-dried films of erythrocyte membranes, it can be postulated that the observed microcalorimetric changes are connected with the local interaction of electromagnetic radiation with the channel-forming portion of band-3 protein.     

Activity of murine peritoneal macrophages upon weak red and infrared laser irradiation in vitro and in vivo

The phagocytic activity and production of proinflammatory cytokines by murine peritoneal macrophages was examined upon in vitro and in vivo exposure to low doses (up to 150 mJ/cm²) of red (650 nm) and infrared (850 nm) light generated by semiconductor lasers. Infrared irradiation proved stimulatory in a dose-dependent way for phagocytosis and killing of enteropathogenic Escherichia coli as well as for cytokine production. Red light markedly enhanced cytokine production but was detrimental to macrophage activity and at higher doses caused their destruction.     

长白山阔叶红松林太阳辐射分光谱特征

根据对林冠上方和林下太阳辐射的观测及气象站资料,分析了长白山阔叶红松林太阳辐射分光谱特征。结果表明,长白山阔叶红松林区太阳总辐射、直接辐射、散射辐射的光合有效辐射系数有一定的日变化和年变化,年平均值分别为０．４６、０．４３、０．５６。阔叶红松林中不同树种的单叶对于太阳总辐射的反射率、透射率、吸收率的平均值分别为２７．０％、２３．４％、４９．６％。单叶的分光谱反射、透射和吸收的特点是,单叶对紫外辐射     

低能铁离子束辐照氨基酸衍生物的红外光谱结构表征

利用傅里叶变换红外光谱（FTIR）技术研究了能量为110keV的Fe^ 离子束辐照L（ ）-半胱氨酸盐酸盐单晶水合物固态样品的结构变化情况。对辐照样品的两次红外光谱分析结果有所不同,表明固态样品不同部位受低能铁离子束作用后可发生不同的分子改性;但二者又具有一定的相似性,都反映了原分子中氨基、羧基和巯基等基团的受损及硝基和酰胺基团等的生成。