Cereal grain arabinoxylans contain a unique non-feruloylated disaccharide side-chain with alpha-xylose units: α-d-xylopyranosyl-(1 → 3)-l-arabinose.

Feruloylated side-chain oligosaccharide substituents are a distinctive feature of cereal grains' arabinoxylans (AX), but less is known about non-feruloylated oligosaccharide side-chain substituents. In this study we explored non-feruloylated disaccharide side-chains from corn (Zea mays L.) AX that had not been exposed to alkaline conditions and successfully isolated and unequivocally characterized the structure, α-d-xylopyranosyl-(1 → 3)-l-arabinose.

Lignin, extractives and structural carbohydrate characteristics of Thinopyrum intermedium biomass reveal additional valorization opportunities for dual-crop utilization.

Background: Thinopyrum intermedium (Host) Barkworth & D.R. Dewey, or intermediate wheat grass (IWG), is being developed as the first widely-available perennial grain candidate.

Genetic dissection of mutagenic repair and T-DNA capture at CRISPR-induced DNA breaks in .

A practical and powerful approach for genome editing in plants is delivery of CRISPR reagents via transformation. The double-strand break (DSB)-inducing enzyme is expressed from a transferred segment of bacterial DNA, the T-DNA, which upon transformation integrates at random locations into the host genome or is captured at the self-inflicted DSB site. To develop efficient strategies for precise genome editing, it is thus important to define the mechanisms that repair CRISPR-induced DSBs, as well as those that govern random and targeted integration of T-DNA.

Dissecting the genetic landscape of GPCR signaling through phenotypic profiling in C. elegans.

G protein-coupled receptors (GPCRs) mediate responses to various extracellular and intracellular cues. However, the large number of GPCR genes and their substantial functional redundancy make it challenging to systematically dissect GPCR functions in vivo. Here, we employ a CRISPR/Cas9-based approach, disrupting 1654 GPCR-encoding genes in 284 strains and mutating 152 neuropeptide-encoding genes in 38 strains in C.

DFT Study of Imine-Exchange Reactions in Iron(II)-Coordinated Pincers.

The imine bond is among the most applied motifs in dynamic covalent chemistry. Although its uses are varied and often involve coordination to a transition metal for stability, mechanistic studies on imine exchange reactions so far have not included metal coordination. Herein, we investigated the condensation and transimination reactions of an Fe -coordinated diimine pyridine pincer, employing wB97XD/6-311G(2d,2p) DFT calculations in acetonitrile.

Profiling of cool-season forage arabinoxylans a validated HPAEC-PAD method.

Cool-season pasture grasses contain arabinoxylans (AX) as their major cell wall hemicellulosic polysaccharide. AX structural differences may influence enzymatic degradability, but this relationship has not been fully explored in the AX from the vegetative tissues of cool-season forages, primarily because only limited AX structural characterization has been performed in pasture grasses. Structural profiling of forage AX is a necessary foundation for future work assessing enzymatic degradability and may also be useful for assessing forage quality and suitability for ruminant feed.

Improved methods for mare milk analysis: Extraction and quantification of mare milk carbohydrates and assessment of FTIR-based macronutrient quantification.

Accurately determining the macronutrient profile of mare milk is a precursor to studying how milk composition affects foals' growth and development. This study optimized and validated an extraction and quantification method for mare milk oligosaccharides, which make up a portion of the carbohydrate fraction of mare milk. Mare milk was extracted with chloroform and methanol, and oligosaccharides were selectively isolated from the carbohydrate fraction using porous-graphitized carbon solid-phase-extraction (SPE).

Chromosomal breaks at the origin of small tandem DNA duplications.

Small tandem DNA duplications in the range of 15 to 300 base-pairs play an important role in the aetiology of human disease and contribute to genome diversity. Here, we discuss different proposed mechanisms for their occurrence and argue that this type of structural variation mainly results from mutagenic repair of chromosomal breaks. This hypothesis is supported by both bioinformatical analysis of insertions occurring in the genome of different species and disease alleles, as well as by CRISPR/Cas9-based experimental data from different model systems.

SIQ: easy quantitative measurement of mutation profiles in sequencing data.

With the emergence of CRISPR-mediated genome editing, there is an increasing desire for easy-to-use tools that can process and overview the spectra of outcomes. Here, we present Sequence Interrogation and Quantification (SIQ), a simple-to-use software tool that enables researchers to retrieve, data-mine and visualize complex sets of targeted sequencing data. SIQ can analyse Sanger sequences but specifically benefit the processing of short- and long-read next-generation sequencing data (e.

Utilizing Design of Experiments Approach to Assess Kinetic Parameters for a Mn Homogeneous Hydrogenation Catalyst.

Homogeneous hydrogenation catalysts based on metal complexes provide a diverse and highly tunable tool for the fine chemical industry. To fully unleash their potential, fast and effective methods for the evaluation of catalytic properties are needed. In turn, this requires changes in the experimental approaches to test and evaluate the performance of the catalytic processes.

2D-HSQC-NMR-Based Screening of Feruloylated Side-Chains of Cereal Grain Arabinoxylans.

Arabinoxylans of commelinid monocots are characterized by high contents of ferulic acid that is incorporated into arabinose-bearing side-chains of varying complexity. Species-related differences in the feruloylated side-chain profiles of grain arabinoxylans are observed and lead to differences in arabinoxylan functionality. Here, a semi-quantitative assay based on H-C-correlation NMR spectroscopy (HSQC experiment) was developed to profile feruloylated side-chains of cereal grain arabinoxylans.

THO complex deficiency impairs DNA double-strand break repair via the RNA surveillance kinase SMG-1.

The integrity and proper expression of genomes are safeguarded by DNA and RNA surveillance pathways. While many RNA surveillance factors have additional functions in the nucleus, little is known about the incidence and physiological impact of converging RNA and DNA signals. Here, using genetic screens and genome-wide analyses, we identified unforeseen SMG-1-dependent crosstalk between RNA surveillance and DNA repair in living animals.

Distinct mechanisms for genomic attachment of the 5' and 3' ends of Agrobacterium T-DNA in plants.

Agrobacterium tumefaciens, a pathogenic bacterium capable of transforming plants through horizontal gene transfer, is nowadays the preferred vector for plant genetic engineering. The vehicle for transfer is the T-strand, a single-stranded DNA molecule bound by the bacterial protein VirD2, which guides the T-DNA into the plant's nucleus where it integrates. How VirD2 is removed from T-DNA, and which mechanism acts to attach the liberated end to the plant genome is currently unknown.

Helicase Q promotes homology-driven DNA double-strand break repair and prevents tandem duplications.

DNA double-strand breaks are a major threat to cellular survival and genetic integrity. In addition to high fidelity repair, three intrinsically mutagenic DNA break repair routes have been described, i.e.

Gene targeting in polymerase theta-deficient Arabidopsis thaliana.

Agrobacterium tumefaciens-mediated transformation has been for decades the preferred tool to generate transgenic plants. During this process, a T-DNA carrying transgenes is transferred from the bacterium to plant cells, where it randomly integrates into the genome via polymerase theta (Polθ)-mediated end joining (TMEJ). Targeting of the T-DNA to a specific genomic locus via homologous recombination (HR) is also possible, but such gene targeting (GT) events occur at low frequency and are almost invariably accompanied by random integration events.

High-resolution breakpoint junction mapping of proximally extended D4Z4 deletions in FSHD1 reveals evidence for a founder effect.

Facioscapulohumeral muscular dystrophy (FSHD) is an inherited myopathy clinically characterized by weakness in the facial, shoulder girdle and upper a muscles. FSHD is caused by chromatin relaxation of the D4Z4 macrosatellite repeat, mostly by a repeat contraction, facilitating ectopic expression of DUX4 in skeletal muscle. Genetic diagnosis for FSHD is generally based on the sizing and haplotyping of the D4Z4 repeat on chromosome 4 by Southern blotting (SB), molecular combing or single-molecule optical mapping, which is usually straight forward but can be complicated by atypical rearrangements of the D4Z4 repeat.

Small tandem DNA duplications result from CST-guided Pol α-primase action at DNA break termini.

Small tandem duplications of DNA occur frequently in the human genome and are implicated in the aetiology of certain human cancers. Recent studies have suggested that DNA double-strand breaks are causal to this mutational class, but the underlying mechanism remains elusive. Here, we identify a crucial role for DNA polymerase α (Pol α)-primase in tandem duplication formation at breaks having complementary 3' ssDNA protrusions.

Preservation of lagging strand integrity at sites of stalled replication by Pol α-primase and 9-1-1 complex.

During genome duplication, the replication fork encounters a plethora of obstacles in the form of damaged bases, DNA-cross-linked proteins, and secondary structures. How cells protect DNA integrity at sites of stalled replication is currently unknown. Here, by engineering "primase deserts" into the genome close to replication-impeding G-quadruplexes, we show that de novo DNA synthesis downstream of the blocked fork suppresses DNA loss.

Robust and efficient hydrogenation of carbonyl compounds catalysed by mixed donor Mn(I) pincer complexes.

Any catalyst should be efficient and stable to be implemented in practice. This requirement is particularly valid for manganese hydrogenation catalysts. While representing a more sustainable alternative to conventional noble metal-based systems, manganese hydrogenation catalysts are prone to degrade under catalytic conditions once operation temperatures are high.

BRCA1-associated structural variations are a consequence of polymerase theta-mediated end-joining.

Failure to preserve the integrity of the genome is a hallmark of cancer. Recent studies have revealed that loss of the capacity to repair DNA breaks via homologous recombination (HR) results in a mutational profile termed BRCAness. The enzymatic activity that repairs HR substrates in BRCA-deficient conditions to produce this profile is currently unknown.

Translesion synthesis polymerases are dispensable for C. elegans reproduction but suppress genome scarring by polymerase theta-mediated end joining.

Bases within DNA are frequently damaged, producing obstacles to efficient and accurate DNA replication by replicative polymerases. Translesion synthesis (TLS) polymerases, via their ability to catalyze nucleotide additions to growing DNA chains across DNA lesions, promote replication of damaged DNA, thus preventing checkpoint activation, genome instability and cell death. In this study, we used C.