From: stenzruthe622@gmail.com   
      
   Carbohydrates have various functions in biological systems. However, the   
   structural analysis of carbohydrates remains challenging. Most of the commonly   
   used methods involve derivatization of carbohydrates or can only identify part   
   of the structure. Here,    
   we report a de novo method for completely structural identification of   
   underivatised oligosaccharides. This method, which can provide assignments of   
   linkages, anomeric configurations, and branch locations, entails low-energy   
   collision-induced    
   dissociation (CID) of sodium ion adducts that enable the cleavage of selective   
   chemical bonds, a logical procedure to identify structurally decisive fragment   
   ions for subsequent CID, and the specially prepared disaccharide CID spectrum   
   databases. This    
   method was first applied to determine the structures of four underivatised   
   glucose oligosaccharides. Then, high-performance liquid chromatography and a   
   mass spectrometer with a built-in logical procedure were established to   
   demonstrate the capability of    
   the in situ CID spectrum measurement and structural determination of the   
   oligosaccharides in chromatogram. This consolidation provides a simple, rapid,   
   sensitive method for the structural determination of glucose oligosaccharides,   
   and applications to    
   oligosaccharides containing hexoses other than glucose can be made provided   
   the corresponding disaccharide databases are available.   
      
   Several advancements in the de novo structural identification of   
   monosaccharides and oligosaccharides have been demonstrated recently. Nagy et   
   al. reported a fixed-ligand kinetic method for the determination of   
   monosaccharide absolute configuration32.    
   However, this method was not used for the determination of the linkage   
   positions, anomeric configurations, sequences, and branch locations of   
   oligosaccharides. Konda et al. reported that the CID of anion m/z 163   
   exhibited distinct fragmentation    
   fingerprints corresponding to linkage positions. They applied the CID of anion   
   m/z 163 to the linkage determination of 18O-labelled linear olig   
   saccharides33. Bendiak et al. demonstrated that anion m/z 221 can be used to   
   identify the stereochemistry and    
   anomeric configuration of hexose in oligosaccharides34,35,36. This method has   
   the following limitations: The reducing end must be derivatised, resulting in   
   the structure of two hexoses on the reducing side cannot be determined, anion   
   intensities are    
   usually low that it may take several hours to obtain a mass spectrum with a   
   good signal-to-noise ratio, a complicated mass spectrometer is required, and   
   this method is currently used for only linear oligosaccharides.   
      
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   Recently we have proposed a new de novo method for determining the entire   
   structure of underivatised oligosaccharides through CID tandem MS of sodium   
   ion adducts37. In this study, the structural determination of glucose   
   trisaccharides and    
   tetrasaccharides was demonstrated. This method can be extended to larger   
   oligosaccharides and oligosaccharides containing hexoses other than glucose.   
      
   De novo root organogenesis is the process in which adventitious roots   
   regenerate from detached or wounded plant tissues or organs. In tissue   
   culture, appropriate types and concentrations of plant hormones in the medium   
   are critical for inducing    
   adventitious roots. However, in natural conditions, regeneration from detached   
   organs is likely to rely on endogenous hormones. To investigate the actions of   
   endogenous hormones and the molecular mechanisms guiding de novo root   
   organogenesis, we    
   developed a simple method to imitate natural conditions for adventitious root   
   formation by culturing Arabidopsis thaliana leaf explants on B5 medium without   
   additive hormones. Here we show that the ability of the leaf explants to   
   regenerate roots depends    
   on the age of the leaf and on certain nutrients in the medium. Based on these   
   observations, we provide examples of how this method can be used in different   
   situations, and how it can be optimized. This simple method could be used to   
   investigate the    
   effects of various physiological and molecular changes on the regeneration of   
   adventitious roots. It is also useful for tracing cell lineage during the   
   regeneration process by differential interference contrast observation of   
   β-glucuronidase staining,    
   and by live imaging of proteins labeled with fluorescent tags.   
      
   Mechanisms of de novo mutations. De novo mutations can arise because of static   
   properties of the genome, such as the underlying sequence (deamination of   
   methylated CpGs, transitions versus transversions) or due to erroneous pairing   
   of nucleotides during    
   DNA replication. However, de novo mutations can also occur in relation to   
   cell-specific properties such as the chromatin state, transcriptional status,   
   and gene expression levels. Mutational hotspots for genomic rearrangements are   
   largely determined by    
   the underlying genomic architecture. One such example is given for non-allelic   
   homologous recombination (NAHR). Arrows represent the influence of each   
   feature on the de novo mutation rate. Green arrows pointing upwards indicate   
   elevated mutability; red    
   arrows pointing downwards indicate lower mutability. M methyl group modifying   
   cytosine   
      
   In this review, we first touch on the biological aspects of de novo mutations   
   in humans, such as their origin, distribution throughout the genome, and   
   factors related to their occurrence and timing. Later, we discuss the   
   increasingly recognized role of    
   de novo mutations in human disease and other translational aspects.   
   Throughout, we will focus mostly on de novo SNVs; readers should refer to Box   
   2 and previous work from others for more information on the role of de novo   
   CNVs and other structural    
   genomic variation in human disease [36, 37].   
      
      
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