A compact high‐speed full‐field optical coherence microscope for high‐resolution in vivo skin imaging

A compact high‐speed full‐field optical coherence microscope has been developed for high‐resolution in vivo imaging of biological tissues. The interferometer, in the Linnik configuration, has a size of 11 × 11 × 5 cm³ and a weight of 210 g. Full‐field illumination with low‐coherence light is achieved with a high‐brightness broadband light‐emitting diode. High‐speed full‐field detection is achieved by using part of the image sensor of a high‐dynamic range CMOS camera. En face tomographic images are acquired at a rate of 50 Hz, with an integration time of 0.9 ms. The image spatial resolution is 0.9 μm × 1.2 μm (axial × transverse), over a field of view of 245 × 245 μm². Images of human skin, revealing in‐depth cellular‐level structures, were obtained in vivo and in real‐time without the need for stabilization of the subject. The system can image larger fields, up to 1 × 1 mm², but at a reduced depth.      

Development and evaluation of high‐density Axiom®CicerSNP Array for high‐resolution genetic mapping and breeding applications in chickpea

To accelerate genomics research and molecular breeding applications in chickpea, a high‐throughput SNP genotyping platform ‘Axiom^®CicerSNP Array’ has been designed, developed and validated. Screening of whole‐genome resequencing data from 429 chickpea lines identified 4.9 million SNPs, from which a subset of 70 463 high‐quality nonredundant SNPs was selected using different stringent filter criteria. This was further narrowed down to 61 174 SNPs based on p‐convert score ≥0.3, of which 50 590 SNPs could be tiled on array. Among these tiled SNPs, a total of 11 245 SNPs (22.23%) were from the coding regions of 3673 different genes. The developed Axiom^®CicerSNP Array was used for genotyping two recombinant inbred line populations, namely ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261). Genotyping data reflected high success and polymorphic rate, with 15 140 (29.93%; ICCRIL03) and 20 018 (39.57%; ICCRIL04) polymorphic SNPs. High‐density genetic maps comprising 13 679 SNPs spanning 1033.67 cM and 7769 SNPs spanning 1076.35 cM were developed for ICCRIL03 and ICCRIL04 populations, respectively. QTL analysis using multilocation, multiseason phenotyping data on these RILs identified 70 (ICCRIL03) and 120 (ICCRIL04) main‐effect QTLs on genetic map. Higher precision and potential of this array is expected to advance chickpea genetics and breeding applications.     

Hydrogen Sulphide modulating mitochondrial morphology to promote mitophagy in endothelial cells under high‐glucose and high‐palmitate

Endothelial cell dysfunction is one of the main reasons for type II diabetes vascular complications. Hydrogen sulphide (H₂S) has antioxidative effect, but its regulation on mitochondrial dynamics and mitophagy in aortic endothelial cells under hyperglycaemia and hyperlipidaemia is unclear. Rat aortic endothelial cells (RAECs) were treated with 40 mM glucose and 200 μM palmitate to imitate endothelium under hyperglycaemia and hyperlipidaemia, and 100 μM NaHS was used as an exogenous H₂S donor. Firstly, we demonstrated that high glucose and palmitate decreased H₂S production and CSE expression in RAECs. Then, the antioxidative effect of H₂S was proved in RAECs under high glucose and palmitate to reduce mitochondrial ROS level. We also showed that exogenous H₂S inhibited mitochondrial apoptosis in RAECs under high glucose and palmitate. Using Mito Tracker and transmission electron microscopy assay, we revealed that exogenous H₂S decreased mitochondrial fragments and significantly reduced the expression of p‐Drp‐1/Drp‐1 and Fis1 compared to high‐glucose and high‐palmitate group, whereas it increased mitophagy by transmission electron microscopy assay. We demonstrated that exogenous H₂S facilitated Parkin recruited by PINK1 by immunoprecipitation and immunostaining assays and then ubiquitylated mitofusin 2 (Mfn2), which illuminated the mechanism of exogenous H₂S on mitophagy. Parkin siRNA suppressed the expression of Mfn2, Nix and LC3B, which revealed that it eliminated mitophagy. In summary, exogenous H₂S could protect RAECs against apoptosis under high glucose and palmitate by suppressing oxidative stress, decreasing mitochondrial fragments and promoting mitophagy. Based on these results, we proposed a new mechanism of H₂S on protecting endothelium, which might provide a new strategy for type II diabetes vascular complication.     

Oufti: an integrated software package for high‐accuracy,high‐throughput quantitative microscopy analysis

With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re‐emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today's single‐cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand‐alone, open‐source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non‐diffraction‐limited fluorescence signals and is scalable for high‐throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis and post‐processing analysis, makes the software broadly accessible to users irrespective of their computational skills.     

Small‐scale and automatable high‐throughput compositional analysis of biomass

Conventional wet chemistry methods to determine biomass composition are labor‐ and time‐intensive and require larger amounts of biomass (300 mg) than is often available. To overcome these limitations and to support a high‐throughput pretreatment and hydrolysis (HTPH) screening system, this article reports on the development of a downscaled biomass compositional analysis that is based on conventional wet chemistry techniques but is scaled down by a factor of 100 to use significantly less material. The procedure is performed in readily available high‐performance liquid chromatography vials and can be automated to reduce operator input and increase throughput. Comparison of the compositional analyses of three biomasses determined by the downscaled approach to those obtained by conventional methods showed that the downscaled method measured statistically identical carbohydrate compositions as standard procedures and also can provide reasonable estimates of lignin and ash contents. These results demonstrate the validity of the downscaled procedure for measuring biomass composition to enable the calculation of sugar yields and determination of trends in sugar release behavior in HTPH screening studies. Biotechnol. Bioeng. 2011;108: 306–312. © 2010 Wiley Periodicals, Inc.     

Broad‐scale vegetation‐environment relationships in Eurasian high‐latitude areas

Question: How is tundra vegetation related to climatic, soil chemical, geological variables and grazing across a very large section of the Eurasian arctic area? We were particularly interested in broad‐scale vegetation‐environment relationships and how well do the patterns conform to climate‐vegetation schemes. Material and Methods: We sampled vegetation in 1132 plots from 16 sites from different parts of the Eurasian tundra. Clustering and ordination techniques were used for analysing compositional patterns. Vegetation‐environment relationships were analysed by fitting of environmental vectors and smooth surfaces onto non‐metric multidimensional scaling scattergrams. Results: Dominant vegetation differentiation was associated with a complex set of environmental variables. A general trend differentiated cold and continental areas from relatively warm and weakly continental areas, and several soil chemical and physical variables were associated with this broad‐scaled differentiation. Especially soil chemical variables related to soil acidity (pH, Ca) showed linear relationships with the dominant vegetation gradient. This was closely related to increasing cryoperturbation, decreasing precipitation and cooler conditions. Remarkable differences among relatively adjacent sites suggest that local factors such as geological properties and lemming grazing may strongly drive vegetation differentiation. Conclusions: Vegetation differentiation in tundra areas conforms to a major ecocline underlain by a complex set of environmental gradients, where precipitation, thermal conditions and soil chemical and physical processes are coupled. However, local factors such as bedrock conditions and lemming grazing may cause marked deviations from the general climate‐vegetation models. Overall, soil chemical factors (pH, Ca) turned out to have linear relationship with the broad‐scale differentiation of arctic vegetation.     

Slow‐growth high‐mortality: A meta‐analysis for insects

The slow growth‐high mortality hypothesis (SG‐HG) predicts that slower growing herbivores suffer greater mortality due to a prolonged window of vulnerability. Given diverse plant–herbivore–natural enemy systems resulting from different feeding ecologies of herbivores and natural enemies, this hypothesis might not always be applicable to all systems. This is evidenced by mixed support from empirical data. In this study, a meta‐analysis of the SG‐HM hypothesis for insects was conducted, aiming to find conditions that favor or reject SG‐HM. The analysis revealed significant within‐ and between‐group heterogeneity for almost all explanatory variables and overall did not support SG‐HM. In this analysis, SG‐HM was supported when any of the following 5 conditions was met: (1) host food consisted of artificial diet; (2) herbivore growth was measured as larval mass; (3) herbivores were generalists; (4) no or multiple species of natural enemies were involved in the study; and (5) parasitoids (i.e., parasitic insects) involved in the study were gregarious. SG‐HM was rejected when any of the following 5 conditions was met: (1) herbivores were from the order Hymentoptera; (2) parasitoids from more than 1 order caused herbivore mortality; (2) parasitoids were specialists; (3) parasitoids were solitary; (4) parasitoids were idiobionts or koinobionts; and (5) single species of natural enemy caused mortality of specialist herbivores. All known studies investigated herbivore mortality for a short period of their life cycle. Researchers are encouraged to monitor herbivore mortality during the entire window of susceptibility or life cycle using life tables. Studies involving multiple mortality factors (i.e., both biotic and abiotic) or multiple natural enemy species are also encouraged since herbivores in nature face a multitude of risks during the entire life cycle. More comprehensive studies may increase our understanding of factors influencing the relationships between herbivore growth and mortality.     

A high‐affinity putrescine‐cadaverine transporter from Trypanosoma cruzi

Whereas mammalian cells and most other organisms can synthesize polyamines from basic amino acids, the protozoan parasite Trypanosoma cruzi is incapable of polyamine biosynthesis de novo and therefore obligatorily relies upon putrescine acquisition from the host to meet its nutritional requirements. The cell surface proteins that mediate polyamine transport into T. cruzi, as well as most eukaryotes, however, have by‐in‐large eluded discovery at the molecular level. Here we report the identification and functional characterization of two polyamine transporters, TcPOT1.1 and TcPOT1.2, encoded by alleles from two T. cruzi haplotypes. Overexpression of the TcPOT1.1 and TcPOT1.2 genes in T. cruzi epimastigotes revealed that TcPOT1.1 and TcPOT1.2 were high‐affinity transporters that recognized both putrescine and cadaverine but not spermidine or spermine. Furthermore, the activities and subcellular locations of both TcPOT1.1 and TcPOT1.2 in intact parasites were profoundly influenced by extracellular putrescine availability. These results establish TcPOT1.1 and TcPOT1.2 as key components of the T. cruzi polyamine transport pathway, an indispensable nutritional function for the parasite that may be amenable to therapeutic manipulation.     

Introgression browser: high‐throughput whole‐genome SNP visualization

Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker‐assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (iBrowser ), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP (Single Nucleotide Polymorphisms) accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, multi‐nucleotide polymorphisms (MNPs) and insertion–deletions (InDels). For data analysis iBrowser makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the iBrowser in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP‐free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of iBrowser makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes iBrowser a valuable breeding tool.     

Storage‐induced changes of the cytosolic red blood cell proteome analyzed by 2D DIGE and high‐resolution/high‐accuracy MS

The storage of packed red blood cells (RBCs) is associated with the development of morphological and biochemical changes leading to a reduced posttransfusion functionality and viability of the cells. Within this study, 2D DIGE and high‐resolution/high‐accuracy Orbitrap MS were used to analyze the storage‐induced changes of the cytosolic RBC proteome and identify characteristic protein patterns and potential marker proteins for the assessment of RBC storage lesions. Leukodepleted RBC concentrates were stored according to standard blood bank conditions for 0, 7, 14, 28, and 42 days and analyzed by using a characterized and validated protocol. Following statistical evaluation, a total of 14 protein spots were found to be significantly altered after 42 days of ex vivo storage. Protein identification was accomplished by tryptic digestion and LC‐MS/MS and three proteins potentially useful as biomarkers for RBC aging comprising transglutaminase 2, beta actin, and copper chaperone for superoxide dismutase were selected and validated by western blot analysis. These can serve as a basis for the development of a screening assay to detect RBC storage lesions and autologous blood doping in sports.