Morphometric and genetic structure of the edible dormouse (Glis glis): a consequence of forest fragmentation in Turkey

Past climatic fluctuations influenced forest habitats and impacted heavily the distribution of forest species, such as the edible dormouse, by changing the distribution and composition of forests themselves. Such effects may be valid for ongoing climate change as well. To improve our understanding of the edible dormouse's history and how it responded to changes in its environment, we investigated its variation across the understudied zone of Northern Turkey using two complementary markers of differentiation: the mitochondrial cytochrome b gene for genetics, and size and shape of the first upper molar for phenotypic differences. Genetic and morphometric results were strongly discrepant. Genetic analyses evidenced an amazing homogeneity throughout the Eurasian range of the edible dormouse, whereas morphometrics pointed to a complex, step‐wise differentiation along the Black Sea coast, the main signal being an opposition between Easternmost and Westernmost Turkish dormice. The genetic homogeneity suggests that this phenotypic differentiation is not the inheritance of glacial refuges, but the consequence of a more recent post‐glacial isolation. The transition between the European and Asian groups is located eastwards from the Marmara straits, undermining its claimed role as an efficient barrier but stressing the importance of climatic and vegetational factors. A secondary differentiation between populations from the Central Black Sea coast and Easternmost regions was evidenced, attributed to a complex interplay of climatic, topographic, anthropogenic, and ecological factors. Turkey, at the crossroad of European and Asian species, heavily impacted by the current global change including climatic and anthropogenic factors, appears of importance for understanding the historical dynamics of differentiation and exchanges between populations that shaped the current distribution of Eurasian species and their future survival. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 611–623.     

Concentration-dependent oligomerization and oligomeric arrangement of LptA

Gram-negative bacteria such as Escherichia coli have an inner membrane and an asymmetric outer membrane (OM) that together protect the cytoplasm and act as a highly selective permeability barrier. Lipopolysaccharide (LPS) is the major component of the outer leaflet of the OM and is essential for the survival of nearly all Gram-negative bacteria. Recent advances in understanding the proteins involved in the transport of LPS across the periplasm and into the outer leaflet of the OM include the identification of seven proteins suggested to comprise the LPS transport (Lpt) system. Crystal structures of the periplasmic Lpt protein LptA have recently been reported and show that LptA forms oligomers in either an end-to-end arrangement or a side-by-side dimer. It is not known if LptA oligomers bridge the periplasm to form a large, connected protein complex or if monomeric LptA acts as a periplasmic shuttle to transport LPS across the periplasm. Therefore, the studies presented here focus specifically on the LptA protein and its oligomeric arrangement and concentration dependence in solution using experimental data from several biophysical approaches, including laser light scattering, crosslinking, and double electron electron resonance spectroscopy. The results of these complementary techniques clearly show that LptA readily associates into stable, end-to-end, rod-shaped oligomers even at relatively low local protein concentrations and that LptA forms a continuous array of higher order oligomeric end-to-end structures as a function of increasing protein concentration.     

Detection of disordered regions in globular proteins using 13C‐detected NMR

Characterization of disordered regions in globular proteins constitutes a significant challenge. Here, we report an approach based on ¹³C‐detected nuclear magnetic resonance experiments for the identification and assignment of disordered regions in large proteins. Using this method, we demonstrate that disordered fragments can be accurately identified in two homologs of menin, a globular protein with a molecular weight over 50 kDa. Our work provides an efficient way to characterize disordered fragments in globular proteins for structural biology applications.     

Microrheology of human synovial fluid of arthritis patients studied by diffusing wave spectroscopy

The viscoelastic properties of synovial fluid (SF) are critical to its functions of lubrication and shock‐absorption of joints in human body; a change in the viscoelastic properties, even of only a few percents, is often concomitant with arthritis. In this work, the elastic modulus G ′(f) and the viscous modulus G ′′(f) of SF from patients suffering from three kinds of joint diseases, namely, osteoarthritis (OA), rheumatoid arthritis (RA), and gouty arthritis (GA), were determined as a function of frequency “f ” (in the low frequency range from f ～ 0.1 to 10 Hz) by Diffusing Wave Spectroscopy (DWS) and correlated with the white blood cell (WBC) count. A strong correlation was observed, showing a higher WBC count corresponding to lower elastic and viscous moduli, G ′ and G ′′; further details depend on inflammatory vs. non‐inflammatory, and on the severity of inflammation. Different types of arthritis lead to different degrees of decreasing viscoelasticity. Identical measurements were carried out with a commercial visco‐supplementation (or artificial SF) to serve as reference. In general, the reduction in both G ′ and G ′′ was most severe in the case of GA and least severe in the case of OA. Besides, in all cases, the reduction in G ′ was more prominent than the reduction in G ′′, indicating that in general, the deterioration in the elasticity of SF by inflammation is more severe than that in the viscosity. This simple method for quantitative physical characterization of synovial fluid may serve as a useful complementary metric to the conventional biochemical analysis in clinical diagnosis of arthritis. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Interpreting CARS images of tissue within the C–H‐stretching region

Single band coherent anti‐Stokes Raman scattering (CARS) microscopy is one of the fastest implementation of nonlinear vibrational imaging allowing for video‐rate image acquisition of tissue. This is due to the large Raman signal in the C—H‐stretching region. However, the chemical specificity of such images is conventionally assumed to be low. Nonetheless, CARS imaging within the C—H‐stretching region enables detection of single cells and nuclei, which allows for histopathologic grading of tissue. Relevant information such as nucleus to cytoplasm ratio, cell density, nucleus size and shape is extracted from CARS images by innovative image processing procedures. In this contribution CARS image contrast within the C—H‐stretching region is interpreted by direct comparison with Raman imaging and correlated to the tissue composition justifying the use of CARS imaging in this wavenumber region for biomedical applications. (© 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Hybrid modeling framework for process analytical technology: application to Bordetella pertussis cultures

In the process analytical technology (PAT) initiative, the application of sensors technology and modeling methods is promoted. The emphasis is on Quality by Design, online monitoring, and closed-loop control with the general aim of building in product quality into manufacturing operations. As a result, online high-throughput process analyzers find increasing application and therewith high amounts of highly correlated data become available online. In this study, an hybrid chemometric/mathematical modeling method is adopted for data analysis, which is shown to be advantageous over the commonly used chemometric techniques in PAT applications. This methodology was applied to the analysis of process data of Bordetella pertussis cultivations, namely online data of near-infrared, (NIR), pH, temperature and dissolved oxygen, and off-line data of biomass, glutamate, and lactate concentrations. The hybrid model structure consisted of macroscopic material balance equations in which the specific reactions rates are modeled by nonlinear partial least square (PLS). This methodology revealed a significant higher statistical confidence in comparison to PLSs, translated in a reduction of mean squared prediction errors (e.g., individual root mean squared prediction errors calibration/validation obtained through the hybrid model for the concentrations of lactate: 0.8699/0.7190 mmol/L; glutamate: 0.6057/0.2917 mmol/L; and biomass: 0.0520/0.0283 OD; and obtained through the PLS model for the concentrations of lactate: 1.3549/1.0087 mmol/L; glutamate: 0.7628/0.3504 mmol/L; and biomass: 0.0949/0.0412 OD). Moreover, the analysis of loadings and scores in the hybrid approach revealed that process features can, as for PLS, be extracted by the hybrid method.     

近红外光谱技术预测猪肉的pH、嫩度和蒸煮损失

以冷却猪肉为研究对象,评价近红外光谱（NIR）技术用于肉类物理特性预测的可行性以及不同的光谱处理方法和建模方法对预测准确性的影响。试样取自排酸24h的同一批猪胴体的小里脊肉,采集4000—10000cm-1的光谱。经外部验证的偏最小二乘（PLS）模型在预测pH时表现出良好的相关性（Rc^2=0．88,Rp^2=0．80,SEC=0．08,SEP=0．084）,嫩度与蒸煮损失模型的相关性分别是Rc^2=0．50和0．57,R;=0．34和0．50。在各种光谱预处理方法中,平滑处理结合多元散射校正（MSC）或标准正态变量变换（SNV）的效果最好。     

红外-核磁共振光谱-免疫亲和柱法解析梨孢镰孢菌代谢产物成分

利用红外光谱,核磁共振光谱结合免疫亲和柱的方法解析梨孢镰孢菌代谢产物成分,为真菌代谢产物的分析提供新的信息.将F.Poae菌株在GYM培养基上25℃条件下培养12 h后转至8℃培养12h,交替进行4周,将其代谢产物分离纯化、结晶,80℃干燥后用红外光谱议分析产物结构,然后利用免疫亲和柱特异性,比较产物经T-2免疫亲和柱纯化前后的1H核磁谱图.由红外谱图可判断目标组分存在与单端孢霉烯族毒素相同的特征官能团,初步判定产物为单端孢霉烯族毒素.通过1H核磁谱图比较T-2免疫亲和柱纯化前后物质结构一致.梨孢镰孢菌代谢产物成分为T-2毒素.红外-核磁共振光谱结合免疫亲和柱的方法解析梨孢镰孢菌代谢产物的方法在国内外尚未见报道.