RAMZIS: a bioinformatic toolkit for rigorous assessment of the alterations to glycoprotein composition that occur during biological processes.

Motivation: Glycosylation elaborates the structures and functions of glycoproteins; glycoproteins are common post-translationally modified proteins and are heterogeneous and non-deterministically synthesized as an evolutionarily driven mechanism that elaborates the functions of glycosylated gene products. Glycoproteins, accounting for approximately half of all proteins, require specialized proteomics data analysis methods due to micro- and macro-heterogeneities as a given glycosite can be divided into several glycosylated forms, each of which must be quantified. Sampling of heterogeneous glycopeptides is limited by mass spectrometer speed and sensitivity, resulting in missing values.

RAMZIS: a bioinformatic toolkit for rigorous assessment of the alterations to glycoprotein structure that occur during biological processes.

Motivation: Glycosylation elaborates the structures and functions of glycoproteins; glycoproteins are common post-translationally modified proteins and are heterogeneous and non-deterministically syn-thesized as an evolutionarily driven mechanism that elaborates the functions of glycosylated gene products. While glycoproteins account for approximately half of all proteins, their macro- and micro-heterogeneity requires specialized proteomics data analysis methods as a given glycosite can be divided into several glycosylated forms, each of which must be quantified. Sampling of heterogeneous glycopeptides is limited by mass spectrometer speed and sensitivity, resulting in missing values.

Improving Statistical Certainty of Glycosylation Similarity between Influenza A Virus Variants Using Data-Independent Acquisition Mass Spectrometry.

Amino acid sequences of immunodominant domains of hemagglutinin (HA) on the surface of influenza A virus (IAV) evolve rapidly, producing viral variants. HA mediates receptor recognition, binding and cell entry, and serves as the target for IAV vaccines. Glycosylation, a post-translational modification that places large branched polysaccharide molecules on proteins, can modulate the function of HA and shield antigenic regions allowing for viral evasion from immune responses.

Bringing families to the table: meaningful inclusion of families/significant others in adult eating disorder programmes.

In Ireland, traditionally, most public Adult Mental Health Services (AMHSs) had a small cohort of service users with eating disorders (EDs) in their service. However, over the last 5 years, the National Clinical Programmes have been encouraging Mental Health Services to develop ED programmes in each catchment area. This has culminated in a model of care for EDs for children and adults.

In-Depth Matrisome and Glycoproteomic Analysis of Human Brain Glioblastoma Versus Control Tissue.

Glioblastoma (GBM) is the most common and malignant primary brain tumor. The extracellular matrix, also known as the matrisome, helps determine glioma invasion, adhesion, and growth. Little attention, however, has been paid to glycosylation of the extracellular matrix components that constitute the majority of glycosylated protein mass and presumed biological properties.

Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein.

The spike protein of SARS-CoV-2, the virus responsible for the global pandemic of COVID-19, is an abundant, heavily glycosylated surface protein that plays a key role in receptor binding and host cell fusion, and is the focus of all current vaccine development efforts. Variants of concern are now circulating worldwide that exhibit mutations in the spike protein. Protein sequence and glycosylation variations of the spike may affect viral fitness, antigenicity, and immune evasion.

The Need for Community Standards to Enable Accurate Comparison of Glycoproteomics Algorithm Performance.

Protein glycosylation that mediates interactions among viral proteins, host receptors, and immune molecules is an important consideration for predicting viral antigenicity. Viral spike proteins, the proteins responsible for host cell invasion, are especially important to be examined. However, there is a lack of consensus within the field of glycoproteomics regarding identification strategy and false discovery rate (FDR) calculation that impedes our examinations.

Glycosylation of Serum Clusterin in Wild-Type Transthyretin-Associated (ATTRwt) Amyloidosis: A Study of Disease-Associated Compositional Features Using Mass Spectrometry Analyses.

Wild-type transthyretin-associated (ATTRwt) amyloidosis is an age-related disease that causes heart failure in older adults. This disease frequently features cardiac amyloid fibril deposits that originate from dissociation of the tetrameric protein, transthyretin (TTR). Unlike hereditary TTR (ATTRm) amyloidosis, where amino acid replacements destabilize the native protein, in ATTRwt amyloidosis, amyloid-forming TTR lacks protein sequence alterations.

Calculating Glycoprotein Similarities From Mass Spectrometric Data.

Complex protein glycosylation occurs through biosynthetic steps in the secretory pathway that create macro- and microheterogeneity of structure and function. Required for all life forms, glycosylation diversifies and adapts protein interactions with binding partners that underpin interactions at cell surfaces and pericellular and extracellular environments. Because these biological effects arise from heterogeneity of structure and function, it is necessary to measure their changes as part of the quest to understand nature.

Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty.

Influenza A virus (IAV) mutates rapidly, resulting in antigenic drift and poor year-to-year vaccine effectiveness. One challenge in designing effective vaccines is that genetic mutations frequently cause amino acid variations in IAV envelope protein hemagglutinin (HA) that create new -glycosylation sequons; resulting -glycans cause antigenic shielding, allowing viral escape from adaptive immune responses. Vaccine candidate strain selection currently involves correlating antigenicity with HA protein sequence among circulating strains, but quantitative comparison of site-specific glycosylation information may likely improve the ability to design vaccines with broader effectiveness against evolving strains.

Protection of the oral mucosa by salivary histatin-5 against Candida albicans in an ex vivo murine model of oral infection.

The oral cavity is a primary target for opportunistic infections, particularly oral candidiasis caused by Candida albicans. A commensal fungus commonly colonizing mucosal surfaces, under conditions of immune dysfunction, C. albicans can become a pathogen causing recurrent infections.

Biochemical characterization of L-DOPA 2,3-dioxygenase, a single-domain type I extradiol dioxygenase from lincomycin biosynthesis.

L-DOPA-2,3-dioxygenase from Streptomyces lincolnensis is a single-domain type I extradiol dioxygenase of the vicinal oxygen chelate superfamily and catalyzes the second step in the metabolism of tyrosine to the propylhygric acid moiety of the antibiotic, lincomycin. S. lincolnensis L-DOPA-2,3-dioxygenase was overexpressed, purified and reconstituted with Fe(II).

Evidence that the phytochrome gene family in black cottonwood has one PHYA locus and two PHYB loci but lacks members of the PHYC/F and PHYE subfamilies.

The phytochrome photoreceptors play important roles in the photoperiodic control of vegetative bud set, growth cessation, dormancy induction, and cold-hardiness in trees. Interestingly, ecotypic differences in photoperiodic responses are observed in many temperate-zone tree species. Northern and southern ecotypes of black cottonwood (Populus trichocarpa Torr.

Differential Gene Expression in Response to Auxin Treatment in the Wild Type and rac, an Adventitious Rooting-Incompetent Mutant of Tobacco.

Histological analyses of auxin-treated cuttings from the wild type and the rac mutant of tobacco (Nicotiana tabacum cv Xanthii) previously revealed that some rac phloem parenchyma or inner cortical parenchyma cells form callus in response to exogenous auxin treatment but these cells never undergo the organized divisions associated with adventitious root initiation in the wild type. Here we report the effect of the rac mutation on the temporal and spatial expression patterns of three genes previously shown to be associated with adventitious root meristems, HRGPnt3, iaa4/5, and gh3. Using histochemical staining analyses of HRGPnt3-GUS transformant cuttings, we determined that the rac mutation blocks auxin activation of the HRGPnt3 promoter.

Changes in the pattern of cell arrangement at the surface of the shoot apical meristem in Hedera helix L. following gibberellin treatment.

The changes in the pattern of cell arrangement and surface topography at the shoot apical meristem of Hedera helix L., which occur during gibberellic acid (GA3)-induced transition from spiral to distichous phyllotaxis, were examined by scanning electron microscopy of rapidly frozen tissue. The technique preserves the original shape of the cells in their turgid state.

Gibberellin-induced reorganization of spatial relationships of emerging leaf primordia at the shoot apical meristem in Hedera helix L.

The transition from spiral to distichous leaf arrangement during gibberellic-acid (GA3)-induced rejuvenation in Hedera was studied in detail by scanning electron microscopy of the shoot apical meristem. The transition, which involves the initiation of about 14 new leaf primordia, is accomplished by progressive increments in the divergence angle between the leaf primordia from an initial average value of 138.9 ° until it approaches 180 °.

Dihydroflavonol Reductase Activity in Relation to Differential Anthocyanin Accumulation in Juvenile and Mature Phase Hedera helix L.

Juvenile phase English ivy (Hedera helix L.) plants accumulate anthocyanin pigment in the hypodermis of stems and petioles, whereas genetically identical plants of the mature phase do not. The objective of this work was to assess which enzyme(s) might limit anthocyanin accumulation in mature phase ivy.

Flowering in bougainvillea: a function of assimilate supply and nutrient diversion.

Reproductive development, whether expressed as first node to flower or numbers of inflorescences developing, is promoted in direct relationship to leaf area and in inverse relationship to the numbers of axillary branches developing. Per cent soluble solids in the reproductive shoots vary with reproductive development. Cytokinin treatments promote inflorescence development and per cent soluble solids, further supporting a nutritional hypothesis in the control of flowering in Bougainvillea "San Diego Red.

Control of flowering in bougainvillea "san diego red.": metabolism of benzyladenine and the action of gibberellic Acid in relation to short day induction.

Benzyladenine (BA) and short day (SD) induction promote and gibberellic acid (GA) inhibits flowering in Bougainvillea "San Diego Red." GA is an overriding vegetative signal maintaining plants in a vegetative state even when BA is applied in SD conditions. SD promotes a more rapid conversion of BA to the ribotide and other "polar derivatives" (containing adenine derivatives).

Callus and shoot formation in organ and tissue cultures of Hedera helix L., English ivy.

Whole embryos and organs excised from ungerminated embryos and from seedlings of H. helix were cultured to assess their capacity to form callus and regenerate organs. There is a high potential for shoot formation in the explanted cotyledons and in the explanted hypocotyl of the ungerminated embryo.

Microbial decomposition of synthetic C-labeled lignins in nature: lignin biodegradation in a variety of natural materials.

Lignin biodegradation in a variety of natural materials was examined using specifically labeled synthetic C-lignins. Natural materials included soils, sediments, silage, steer bedding, and rumen contents. Both aerobic and anaerobic incubations were used.

Preparation and microbial decomposition of synthetic [14C]ligins.

A definitive assay for microbiological and biochemical research on the biodegradation of lignin was developed using radioactive synthetic lignins specifically labeled in the side chains, aromatic rings or in the methoxyl groups. The [14C]lignins were prepared by oxidative polymerization with peroxidase and H2O2 Of specifically labeled coniferyl alcohol (4-hydroxy-3-methyoxycinnamyl alcohol). The synthetic polymers were shown by spectroscopic and chemical methods to contain the same intermonomer linkages found in natural lignins.

Enhanced inflorescence development in bougainvillea "san diego red" by removal of young leaves and cytokinin treatments.

Removal of young leaves and application of the cytokinin, N-benzyla-alpha-(tetrahydro-2H-pyran-2yl)-adenine promote inflorescence development in Bougainvillea "San Diego Red". Defoliation greatly increased the amount of assimilate accumulated at the shoot tip 1 to 2 days after treatment. Cytokinin applications further increased the amount accumulated and this increase was apparent 4 days before morphological changes could be detected at the inflorescence axes.

Terpene Biosynthesis in Cell-free Extracts and Excised Shoots from Wedgwood Iris.

Excised shoots and cell-free extracts prepared from Wedgwood iris (Iris hollandica Hoog. "Wedgwood") shoots metabolized (14)C-labeled mevalonic acid (MVA). By using cell-free extracts, the (14)C from MVA-1-(14)C was recovered as (14)CO(2), while that from MVA-2-(14)C was recovered as neutral terpenes, acid-hydrolyzable terpenes, or (14)CO(2).