Structures of S. pombe phosphofructokinase in the F6P-bound and ATP-bound states

Phosphofructokinase (Pfk1; EC 2.7.1.11) is the third enzyme of the glycolytic pathway catalyzing the formation of fructose-1,6-bisphosphate from fructose-6-phosphate (F6P) and ATP. Schizosaccharomyces pombe Pfk1 is a homo-octameric enzyme of 800 kDa molecular weight, distinct from its yeast counterparts which are mostly hetero-octameric enzymes composed of two different subunits. Having an "open" conformation and a tendency to aggregate into higher oligomeric structures, the S. pombe enzyme shows similarities to the mammalian muscle Pfk1. It has been proposed that due to the distinct N-terminal region of the S. pombe subunit, the oligomeric organization of subunits in this enzyme is different from other yeast phosphofructokinases. Electron microscopy studies were carried out to reveal the quaternary structure of the homo-octameric Pfk1 from S. pombe in the F6P-bound and in the ATP-bound state. Random conical tilt data sets have been collected from deep stain preparations of the enzyme in both states. The 0 degrees tilt images have been separated into different classes and a 3D reconstruction has been calculated for each class from the high tilt images. Our results confirm the presence of a variety of views of the particle, most of which can be interpreted as views of the molecule rotating around its long axis. Despite the biochemical differences, the structure of phosphofructokinase from S. pombe in the presence of either F6P or ATP is similar to the hetero-octameric structure of phosphofructokinase from Saccharomyces cerevisiae. The molecule can be described as composed of two subdomains, connected by two well-defined densities. We have been able to establish a correlation between the kinetic behavior and the structural conformation of Pfk1.     

An open‐source code for Mie extinction extended multiplicative signal correction for infrared microscopy spectra of cells and tissues

Infrared spectroscopy of single cells and tissue is affected by Mie scattering. During recent years, several methods have been proposed for retrieving pure absorbance spectra from such measurements, while currently no user‐friendly version of the state‐of‐the‐art algorithm is available. In this work, an open‐source code for correcting highly scatter‐distorted absorbance spectra of cells and tissues is presented, as well as several improvements of the latest version of the Mie correction algorithm based on extended multiplicative signal correction (EMSC) published by Konevskikh et al. In order to test the stability of the code, a set of apparent absorbance spectra was simulated. To this purpose, pure absorbance spectra based on a Matrigel spectrum are simulated. Scattering contributions where obtained by mimicking the scattering features observed in a set of experimentally obtained spectra . It can be concluded that the algorithm is not depending strongly on the reference spectrum used for initializing the algorithm and retrieves well the underlying pure absorbance spectrum. The calculation time of the algorithm is considerably improved with respect to the resonant Mie scattering EMSC algorithm used by the community today.      

基于植被信息季节变换的植被覆盖度变化——以福建省连江县为例

基于植被覆盖度的植被信息遥感变化检测已成为研究植被及其相关生态系统变化的主要途径,但由于云覆盖等天气条件的影响,很难获得不同年份同一季节覆盖整个研究区的光学遥感影像来进行植被变化检测,而采用季节差异的影像必然会影响植被变化检测的结果.为此,本研究利用中高分辨率遥感数据的空间分辨率优势和MODIS遥感数据的时间分辨率优势,基于二者关系的拟合,提出一种植被信息季节变换的方法,将不同季节影像的植被覆盖度变换到研究所需的季节上.结果表明: 将该方法应用到福建敖江流域连江片区发现,植被信息变换的效果较好,经过将覆盖研究区的2007年冬季和2013年春季的中高分辨率影像的植被信息统一变换到夏季后,2007年的植被覆盖度由66.5%上升到79.7%,2013年由58.6%上升到77.9%,有效消除了因季节差异而对植被覆盖度估算产生的误差,提高了结果的准确性.     

Stimulation of Oligonucleotide-Directed Gene Correction by Redβ Expression and MSH2 Depletion in Human HT1080 Cells

The correction of disease-causing mutations by single-strand oligonucleotide-templated DNA repair (ssOR) is an attractive approach to gene therapy, but major improvements in ssOR efficiency and consistency are needed. The mechanism of ssOR is poorly understood but may involve annealing of oligonucleotides to transiently exposed single-stranded regions in the target duplex. In bacteria and yeast it has been shown that ssOR is promoted by expression of Redβ, a single-strand DNA annealing protein from bacteriophage lambda. Here we show that Redβ expression is well tolerated in a human cell line where it consistently promotes ssOR. By use of short interfering RNA, we also show that ssOR is stimulated by the transient depletion of the endogenous DNA mismatch repair protein MSH2. Furthermore, we find that the effects of Redβ expression and MSH2 depletion on ssOR can be combined with a degree of cooperativity. These results suggest that oligonucleotide annealing and mismatch recognition are distinct but interdependent events in ssOR that can be usefully modulated in gene correction strategies.     

Beam angle optimization using angular dependency of range variation assessed via water equivalent path length (WEPL) calculation for head and neck proton therapy

PurposeTo investigate angular sensitivity of proton range variation due to anatomic change in patients and patient setup error via water equivalent path length (WEPL) calculations.MethodsProton range was estimated by calculating WEPL to the distal edge of target volume using planning CT (pCT) and weekly scatter-corrected cone-beam CT (CBCT) images of 11 head and neck patients. Range variation was estimated as the difference between the distal WEPLs calculated on pCT and scatter-corrected CBCT (cCBCT). This WEPL analysis was performed every five degrees ipsilaterally to the target. Statistics of the distal WEPL difference were calculated over the distal area to compare between different beam angles. Physician-defined contours were used for the WEPL calculation on both pCT and cCBCT, not considering local deformation of target volume. It was also tested if a couch kick (10°) can mitigate the range variation due to anatomic change and patient setup error.ResultsFor most of the patients considered, median, 75% quantile, and 95% quantile of the distal WEPL difference were largest for posterior oblique angles, indicating a higher chance of overdosing normal tissues at distal edge with these angles. Using a couch kick resulted in decrease in the WEPL difference for some posterior oblique angles.ConclusionsIt was demonstrated that the WEPL change has angular dependency for the cohort of head and neck cancer patients. Selecting beam configuration robust to anatomic change in patient and patient setup error may improve the treatment outcome of head and neck proton therapy.     

Empirical orthogonal function regression: Linking population biology to spatial varying environmental conditions using climate projections

Ecologists and oceanographers inform population and ecosystem management by identifying the physical drivers of ecological dynamics. However, different research communities use different analytical tools where, for example, physical oceanographers often apply rank‐reduction techniques (a.k.a. empirical orthogonal functions [EOF]) to identify indicators that represent dominant modes of physical variability, whereas population ecologists use dynamical models that incorporate physical indicators as covariates. Simultaneously modeling physical and biological processes would have several benefits, including improved communication across sub‐fields; more efficient use of limited data; and the ability to compare importance of physical and biological drivers for population dynamics. Here, we develop a new statistical technique, EOF regression, which jointly models population‐scale dynamics and spatially distributed physical dynamics. EOF regression is fitted using maximum‐likelihood techniques and applies a generalized EOF analysis to environmental measurements, estimates one or more time series representing modes of environmental variability, and simultaneously estimates the association of this time series with biological measurements. By doing so, it identifies a spatial map of environmental conditions that are best correlated with annual variability in the biological process. We demonstrate this method using a linear (Ricker) model for early‐life survival (“recruitment”) of three groundfish species in the eastern Bering Sea from 1982 to 2016, combined with measurements and end‐of‐century projections for bottom and sea surface temperature. Results suggest that (a) we can forecast biological dynamics while applying delta‐correction and statistical downscaling to calibrate measurements and projected physical variables, (b) physical drivers are statistically significant for Pacific cod and walleye pollock recruitment, (c) separately analyzing physical and biological variables fails to identify the significant association for walleye pollock, and (d) cod and pollock will likely have reduced recruitment given forecasted temperatures over future decades.     

Assessment of relationships between pigs based on pedigree and genomic information

Relationships play a very important role in studies on quantitative genetics. In traditional breeding, pedigree records are used to establish relationships between animals; while this kind of relationship actually represents one kind of relatedness, it cannot distinguish individual specificity, capture the variation between individuals or determine the actual genetic superiority of an animal. However, with the popularization of high-throughput genotypes, assessments of relationships among animals based on genomic information could be a better option. In this study, we compared the relationships between animals based on pedigree and genomic information from two pig breeding herds with different genetic backgrounds and a simulated dataset. Two different methods were implemented to calculate genomic relationship coefficients and genomic kinship coefficients, respectively. Our results show that, for the same kind of relative, the average genomic relationship coefficients (G matrix) were very close to the pedigree relationship coefficients (A matrix), and on average, the corresponding values were halved in genomic kinship coefficients (K matrix). However, the genomic relationship yielded a larger variation than the pedigree relationship, and the latter was similar to that expected for one relative with no or little variation. Two genomic relationship coefficients were highly correlated, for farm1, farm2 and simulated data, and the correlations for the parent-offspring, full-sib and half-sib were 0.95, 0.90 and 0.85; 0.93, 0.96 and 0.89; and 0.52, 0.85 and 0.77, respectively. When the inbreeding coefficient was measured, the genomic information also yielded a higher inbreeding coefficient and a larger variation than that yielded by the pedigree information. For the two genetically divergent Large White populations, the pedigree relationship coefficients between the individuals were 0, and 62 310 and 175 271 animal pairs in the G matrix and K matrix were greater than 0. Our results demonstrated that genomic information outperformed the pedigree information; it can more accurately reflect the relationships and capture the variation that is not detected by pedigree. This information is very helpful in the estimation of genomic breeding values or gene mapping. In addition, genomic information is useful for pedigree correction. Further, our findings also indicate that genomic information can establish the genetic connection between different groups with different genetic background. In addition, it can be used to provide a more accurate measurement of the inbreeding of an animal, which is very important for the assessment of a population structure and breeding plan. However, the approaches for measuring genomic relationships need further investigation.     

Calibration and uncertainties in personal exposure measurements of radiofrequency electromagnetic fields

In the past 5 years radiofrequency personal exposure meters have been used to characterize the exposure during daily activities. We found from calibration tests for the 12 frequency bands of the EME Spy 121 exposimeter in a Gigahertz Transverse Electromagnetic cell and an Open Area Test Site, that these measurements tend to underestimate the actual exposure. Therefore, a maximum frequency‐dependent correction factor of 1.1–1.6 should be applied to the electric field. This correction factor consists of three multipliers correcting for calibration, elevation arrival angle, and influence of the body. The calibration correction factor should be determined per exposimeter, as the maximum range of response between exposimeters in a frequency band is 2.4 dB. Since the range of response for different elevation angles could reach 10.2 dB, a strict protocol for wearing the exposimeter during fieldwork should be followed to be able to compare and combine measurements made by different persons in the same microenvironments. Because the influence of the body depends on the azimuth angle of arrival, it may lead to an over‐ or underestimation. Thus, the body correction factor is an average over the angles and should only be applied in activities involving movement through the full 360° range of random angles of arrival. Bioelectromagnetics. Bioelectromagnetics 32:652–663, 2011. © 2011 Wiley Periodicals, Inc.     

山丘区苹果树花期冠层反射率的定量遥感反演

采用山东省栖霞市苹果树花期不同分辨率的TM和ALOS影像,充分考虑坡向系数和冠层花叶比,通过地形辐射校正获取地表反演反射率,再经混合像元分解获取苹果树冠层的反演反射率,将30个果园样方的反演结果与同时段实测反射率及表观反射率进行比较,分析反演效果和精度.结果表明:地形辐射校正有效减弱了地形和大气的影响,恢复了阴影处地物,地表反演反射率影像的解析力大幅提高;无论是TM还是ALOS影像,冠层反演反射率的绝对误差和相对误差均最小,所有波段的相对误差表现出一致性,且样方间变化趋势与实测值最一致,说明混合像元分解是必要的.反演方法应用于不同分辨率影像,表现出相似的反射率变化特点,高分辨率图像更具优势,但受波段限制,可与中分辨率影像结合使用.