Additional file 2: of A systematic literature review of time to return to work and narcotic use after lumbar spinal fusion using minimal invasive and open surgery techniques

List of included studies. A list of studies that were finally included after title/abstract and full text evaluations in this SLR. (DOCX 18 kb

LC–MS/MS Characterization of O‑Glycosylation Sites and Glycan Structures of Human Cerebrospinal Fluid Glycoproteins

The GalNAc <i>O</i>-glycosylation on Ser/Thr residues of extracellular proteins has not been well characterized from a proteomics perspective. We previously reported a sialic acid capture-and-release protocol to enrich tryptic <i>N</i>- and <i>O</i>-glycopeptides from human cerebrospinal fluid glycoproteins using nano-LC–ESI–MS/MS with collision-induced dissociation (CID) for glycopeptide characterization. Here, we have introduced peptide <i>N</i>-glycosidase F (PNGase F) pretreatment of CSF samples to remove the <i>N</i>-glycans facilitating the selective characterization of <i>O</i>-glycopeptides and enabling the use of an automated CID–MS²/MS³ search protocol for glycopeptide identification. We used electron-capture and -transfer dissociation (ECD/ETD) to pinpoint the glycosylation site(s) of the glycopeptides, identified as predominantly core-1-like HexHexNAc-<i>O</i>- structure attached to one to four Ser/Thr residues. We characterized 106 <i>O</i>-glycosylations and found Pro residues preferentially in the <i>n</i> – 1, <i>n</i> + 1, and/or <i>n</i> + 3 positions in relation to the Ser/Thr attachment site (<i>n</i>). The characterization of glycans and glycosylation sites in glycoproteins from human clinical samples provides a basis for future studies addressing the biological and diagnostic importance of specific protein glycosylations in relation to human disease

Data_Sheet_1_Characterization of MdpS: an in-depth analysis of a MUC5B-degrading protease from Streptococcus oralis.PDF

Oral biofilms, comprising hundreds of bacteria and other microorganisms on oral mucosal and dental surfaces, play a central role in oral health and disease dynamics. Streptococcus oralis, a key constituent of these biofilms, contributes significantly to the formation of which, serving as an early colonizer and microcolony scaffold. The interaction between S. oralis and the orally predominant mucin, MUC5B, is pivotal in biofilm development, yet the mechanism underlying MUC5B degradation remains poorly understood. This study introduces MdpS (Mucin Degrading Protease from Streptococcus oralis), a protease that extensively hydrolyses MUC5B and offers an insight into its evolutionary conservation, physicochemical properties, and substrate- and amino acid specificity. MdpS exhibits high sequence conservation within the species and also explicitly among early biofilm colonizing streptococci. It is a calcium or magnesium dependent serine protease with strict physicochemical preferences, including narrow pH and temperature tolerance, and high sensitivity to increasing concentrations of sodium chloride and reducing agents. Furthermore, MdpS primarily hydrolyzes proteins with O-glycans, but also shows activity toward immunoglobulins IgA1/2 and IgM, suggesting potential immunomodulatory effects. Significantly, MdpS extensively degrades MUC5B in the N- and C-terminal domains, emphasizing its role in mucin degradation, with implications for carbon and nitrogen sequestration for S. oralis or oral biofilm cross-feeding. Moreover, depending on substrate glycosylation, the amino acids serine, threonine or cysteine triggers the enzymatic action. Understanding the interplay between S. oralis and MUC5B, facilitated by MdpS, has significant implications for the management of a healthy eubiotic oral microenvironment, offering potential targets for interventions aimed at modulating oral biofilm composition and succession. Additionally, since MdpS does not rely on O-glycan removal prior to extensive peptide backbone hydrolysis, the MdpS data challenges the current model of MUC5B degradation. These findings emphasize the necessity for further research in this field.</p

Table_1_Characterization of MdpS: an in-depth analysis of a MUC5B-degrading protease from Streptococcus oralis.XLSX

Oral biofilms, comprising hundreds of bacteria and other microorganisms on oral mucosal and dental surfaces, play a central role in oral health and disease dynamics. Streptococcus oralis, a key constituent of these biofilms, contributes significantly to the formation of which, serving as an early colonizer and microcolony scaffold. The interaction between S. oralis and the orally predominant mucin, MUC5B, is pivotal in biofilm development, yet the mechanism underlying MUC5B degradation remains poorly understood. This study introduces MdpS (Mucin Degrading Protease from Streptococcus oralis), a protease that extensively hydrolyses MUC5B and offers an insight into its evolutionary conservation, physicochemical properties, and substrate- and amino acid specificity. MdpS exhibits high sequence conservation within the species and also explicitly among early biofilm colonizing streptococci. It is a calcium or magnesium dependent serine protease with strict physicochemical preferences, including narrow pH and temperature tolerance, and high sensitivity to increasing concentrations of sodium chloride and reducing agents. Furthermore, MdpS primarily hydrolyzes proteins with O-glycans, but also shows activity toward immunoglobulins IgA1/2 and IgM, suggesting potential immunomodulatory effects. Significantly, MdpS extensively degrades MUC5B in the N- and C-terminal domains, emphasizing its role in mucin degradation, with implications for carbon and nitrogen sequestration for S. oralis or oral biofilm cross-feeding. Moreover, depending on substrate glycosylation, the amino acids serine, threonine or cysteine triggers the enzymatic action. Understanding the interplay between S. oralis and MUC5B, facilitated by MdpS, has significant implications for the management of a healthy eubiotic oral microenvironment, offering potential targets for interventions aimed at modulating oral biofilm composition and succession. Additionally, since MdpS does not rely on O-glycan removal prior to extensive peptide backbone hydrolysis, the MdpS data challenges the current model of MUC5B degradation. These findings emphasize the necessity for further research in this field.</p

Common-garden experiment

Data from 937 common-garden reared juveniles (35 days old) including offspring from 64 parental crossings originating from three sympatric subpopulations. The following phenotypic traits are included: total length (mm), weight (g) and specific growth rate (mm/day)

Size-at-age

Body size (length, cm) data from 95 adults of known age (3-6 years old) originating from three subpopulations

Growth trajectories

Data of reconstructed growth trajectories for 109 adults (≥ 4 years old) by using growth increment in cleithra bones. The file includes annual increment in the cleithra (mm) for each adult

Emigrating juveniles body size

Body size (total length, mm) data of 3517 field-sampled emigrating juveniles. Includes data from three different years and two subpopulations

Adult body size

Body size (total length, cm) data of 4097 adults. Individuals were sampled during spawning migration in five streams (subpopulaitions)

<i>SweetNET</i>: A Bioinformatics Workflow for Glycopeptide MS/MS Spectral Analysis

Glycoproteomics has rapidly become an independent analytical platform bridging the fields of glycomics and proteomics to address site-specific protein glycosylation and its impact in biology. Current glycopeptide characterization relies on time-consuming manual interpretations and demands high levels of personal expertise. Efficient data interpretation constitutes one of the major challenges to be overcome before true high-throughput glycopeptide analysis can be achieved. The development of new glyco-related bioinformatics tools is thus of crucial importance to fulfill this goal. Here we present <i>SweetNET</i>: a data-oriented bioinformatics workflow for efficient analysis of hundreds of thousands of glycopeptide MS/MS-spectra. We have analyzed MS data sets from two separate glycopeptide enrichment protocols targeting sialylated glycopeptides and chondroitin sulfate linkage region glycopeptides, respectively. Molecular networking was performed to organize the glycopeptide MS/MS data based on spectral similarities. The combination of spectral clustering, oxonium ion intensity profiles, and precursor ion <i>m</i>/<i>z</i> shift distributions provided typical signatures for the initial assignment of different N-, O- and CS-glycopeptide classes and their respective glycoforms. These signatures were further used to guide database searches leading to the identification and validation of a large number of glycopeptide variants including novel deoxyhexose (fucose) modifications in the linkage region of chondroitin sulfate proteoglycans