Backbone NMR resonance assignments for the C terminal domain of the Streptococcus mutans adhesin P1.

Adhesin P1 (aka AgI/II) plays a pivotal role in mediating Streptococcus mutans attachment in the oral cavity, as well as in regulating biofilm development and maturation. P1's naturally occurring truncation product, Antigen II (AgII), adopts both soluble, monomeric and insoluble, amyloidogenic forms within the bacterial life cycle. Monomers are involved in important quaternary interactions that promote cell adhesion and the functional amyloid form promotes detachment of mature biofilms. The heterologous, 51-kD C123 construct comprises most of AgII and was previously characterized by X-ray crystallography. C123 contains three structurally homologous domains, C1, C2, and C3. NMR samples made using the original C123 construct, or its C3 domain, yielded moderately resolved NMR spectra. Using Alphafold, we re-analyzed the P1 sequence to better identify domain boundaries for C123, and in particular the C3 domain. We then generated a more tractable construct for NMR studies of the monomeric form, including quaternary interactions with other proteins. The addition of seven amino acids at the C-terminus greatly improved the spectral dispersion for C3 relative to the prior construct. Here we report the backbone NMR resonance assignments for the new construct and characterize some of its quaternary interactions. These data are in good agreement with the structure predicted by Alphafold, which contains additional ß-sheet secondary structure compared to the C3 domain in the C123 crystal structure for a construct lacking the seven C-terminal amino acids. Its quaternary interactions with known protein partners are in good agreement with prior competitive binding assays. This construct can be used for further NMR studies, including protein-protein interaction studies and assessing the impact of environmental conditions on C3 structure and dynamics within C123 as it transitions from monomer to amyloid form.

Metagenome-Assembled Genomes from Photo-Oxidized and Nonoxidized Oil-Degrading Marine Microcosms.

We performed deep metagenomic sequencing on hydrocarbon-degrading marine microcosms designed to experimentally determine the effect of photo-oxidation on oil biodegradation dynamics. Assembly, binning, and dereplication yielded 73 unique metagenome-assembled genomes (MAGs) from 6 phyla, of which 61 are predicted to be over 90% complete.

EGFR Amplification in a Patient with Glioblastoma: A Case Report and Review of the Literature.

OBJECTIVES: Glioblastoma Multiforme (GBM) is the most malignant and frequently occurring primary brain tumor out of the different types of primary astrocytomas. It presents with an extremely poor prognosis, with a median survival of 14 to 15 months from the diagnosis. Herein, we present an 83-year-old female patient with a right frontal brain mass. A craniotomy for the frontal brain mass was performed, which revealed a tumor with high-grade glioma, necrosis, atypia, and vascular proliferation. The patient was subsequently diagnosed with Glioblastoma Multiforme Grade IV (GBM). Molecular cytogenetic studies showed an amplification of the EGFR gene in 100% nuclei scored. Amplification of EGFR appears in around 40-50% of individuals with Glioblastoma Multiforme Grade IV, leading to high levels of EGFR protein levels that contribute to tumorigenesis. Chromosomal deletions involving 1p36 and 19q13 are characteristic molecular features of solid tumors such as oligodendrocytes and mixed oligoastrocytomas, but in this case there was no evidence of a co-deletion of 1p36/19q13 in this case of glioblastoma.

An Idic(7)(q11.2) Resulting in Two Copies of 7p and Deletion 7q: A Rare Cytogenetic Event in a Case of Acute Myeloid Leukemia.

OBJECTIVES: A 67-year-old male patient was diagnosed with acute myeloid leukemia (AML) in April 2018. Chromosome analysis showed an abnormal male karyotype with an isodicentric chromosome 7q resulting in deletion 7q and two copies of 7p and a derivative chromosome 18 in 13 of the 20 metaphase cells examined. This karyotype was described as 46,XY,idic(7)(q11.2),der(18)t(1;18)(q23;q21.1)[13]/46,XY[7]. Additionally, subsequent sequencing analysis displayed FLT3-ITD and RUNX1 mutations (data not shown). The bone marrow showed an overwhelming number of blast cells, with co-expression of CD34, CD117, TdT, MPO, CD7, CD13, CD33, CD38, CD19, and HLA-DR. Molecular cytogenetic studies showed a deletion of one RELN/TES (7q22/7q31) signal in 80.5% of nuclei and a gain of a BCR/ABL1 (22q11.2/9q34) signal in 3.5% of interphase nuclei examined. These findings were described as nuc ish(RELN,TES)x1[161/200],(ABL1x2,BCRx3)[7/200], (EVI1,TAS2R1,EGR1,DEK,MYC,NUP214,KMT2A,DLEU1,DLEU2,Clone 163C9,PML,CBFB,RARA,PTPRT,MYBL2,RUNX1)x2[200]. The patient relapsed with AML in September 2019 and underwent treatment. However, all AML treatment options were exhausted by March 2020. An isodicentric chromosome 7 leading to two copies of the short arm of chromosome 7 (7p) and deletion 7q is a rare event in AML and is rarely described in the literature. The key element here is that this specific rearrangement leads to deletion 7q which is a well-known abnormality in AML that places the patient in the Poor/Adverse risk category.

Transient Myeloproliferative Disorder: A Cytogenomic Update.

OBJECTIVES: Transient myeloproliferative disorder (TMD), now more commonly known as transient abnormal myelopoiesis (TAM), is a condition closely associated with Down syndrome. Ninety-five percent of Down syndrome cases occur as a result of chromosomal nondisjunction and are rarely due to mosaicism or translocation. TMD is found exclusively in neonates and is most commonly characterized by trisomy 21, somatic GATA1 mutation, and the increased presence of megakaryoblasts. TMD often does not manifest clinically, but patients may show hepatomegaly, splenomegaly and other symptoms. While TMD is almost always present with trisomy 21, there are not many other cytogenetic abnormalities associated with TMD, with a few rare cases such as monosomy 7 and trisomy 8. Recent studies have suggested liver hematopoietic progenitor cells as the candidate for TMD origin. Furthermore, GATA1 mutations associated with TMD are found to encode for a stop codon in the N-terminal activation region of gene sequences. It has been shown that those mutations can cause overproliferation of megakaryocytes, which can cooperate with Down syndrome cells, which have trisomy 21, in the progression of TMD into acute megakaryoblastic leukemia (AMKL). Since GATA1 mutations are present in all cases of myeloid leukemia of Down Syndrome, monitoring GATA1 in patients with trisomy 21 may assist with earlier diagnosis of TMD. Another likely cause of TMD is the amplification of the RUNX1 transcription factor gene located on chromosome 21. It has been shown that RUNX1 is associated with leukemias of myeloid lineage. While most cases of TMD will spontaneously resolve, some will evolve into acute myeloid leukemia (AML). In this review, we will discuss the cytogenetic, molecular genetics and clinical aspects of TMD.

A Case of a Lymphoplasmacytic Lymphoma with Trisomy 12 in the Lymphoid Population and Deletion 13q in the Unstimulated Cell Culture.

OBJECTIVES: Lymphoplasmacytic lymphoma (LPL, previously termed lymphoplasmacytoid lymphoma) is an uncommon mature B-cell lymphoma usually involving the bone marrow and less commonly the spleen and/or lymph nodes. The majority of patients with LPL have a circulating monoclonal immunoglobulin M (IgM) that can lead to a hyperviscosity syndrome known as Waldenström macroglobulinemia (WM). Although LPL appears to be a sporadic disease in the majority of cases, a familial predisposition is present in some cases. The main chromosomal abnormalities are trisomy 12, trisomy 3, isochromosome 6p, and 14q rearrangements involving IgH among complex karyotypes. Herein, we present an 89-year-old male patient who presents with LPL involving 80% of the marrow cellularity with circulating lymphoma cells. Chromosomal analysis detected two unrelated abnormal clonal populations: one clone has trisomy 12 as the sole abnormality in the stimulated culture, while the other clone has a 13q deletion as the sole abnormality in the cells from the non-stimulated culture. Trisomy 12 is one of the most common abnormalities in B-CLL and it is associated with an intermediate prognosis. Deletions 13q have been identified in B-cell malignancies, non-Hodgkin's lymphomas (NHL), as well as myelodysplastic syndromes and chronic myeloproliferative neoplasms (Heim and Mitelman, 2015). Trisomy 12/13q- FISH slide was reviewed looking at the segmented cells. Fifty segmented cells were scored and a 13q- pattern was detected in 36% (18/50) of the cells suggesting that this finding (the 13q- clone) may be myeloid in origin. Clinicopathologic correlation of these results was recommended.

Characterization of an intermolecular quaternary interaction between discrete segments of the Streptococcus mutans adhesin P1 by NMR spectroscopy.

Cell surface-localized P1 adhesin (aka Antigen I/II or PAc) of the cariogenic bacterium Streptococcus mutans mediates sucrose-independent adhesion to tooth surfaces. Previous studies showed that P1's C-terminal segment (C123, AgII) is also liberated as a separate polypeptide, contributes to cellular adhesion, interacts specifically with intact P1 on the cell surface, and forms amyloid fibrils. Identifying how C123 specifically interacts with P1 at the atomic level is essential for understanding related virulence properties of S. mutans. However, with sizes of ~ 51 and ~ 185 kDa, respectively, C123 and full-length P1 are too large to achieve high-resolution data for full structural analysis by NMR. Here, we report on biologically relevant interactions of the individual C3 domain with A3VP1, a polypeptide that represents the apical head of P1 as it is projected on the cell surface. Also evaluated are C3's interaction with C12 and the adhesion-inhibiting monoclonal antibody (MAb) 6-8C. NMR titration experiments with 15 N-enriched C3 demonstrate its specific binding to A3VP1. Based on resolved C3 assignments, two binding sites, proximal and distal, are identified. Complementary NMR titration of A3VP1 with a C3/C12 complex suggests that binding of A3VP1 occurs on the distal C3 binding site, while the proximal site is occupied by C12. The MAb 6-8C binding interface to C3 overlaps with that of A3VP1 at the distal site. Together, these results identify a specific C3-A3VP1 interaction that serves as a foundation for understanding the interaction of C123 with P1 on the bacterial surface and the related biological processes that stem from this interaction. DATABASE: BMRB submission code: 27935.

Precolumn derivatization liquid chromatography method for analysis of dietary supplements for glucosamine: single laboratory validation study.

A precolumn derivatization liquid chromatography (LC) method was developed for the analysis of various dietary supplement formulations and raw materials for glucosamine. A 1 mL sample or standard water solution (containing about 0.05 mg glucosamine) was mixed with 1 mL pH 8.3 buffer, 1 mL 5% phenylisothiocyanate methanolic solution, and derivatized at 80 degrees C in a water bath for 30 min. After derivatization, the solution was cooled in a cold water bath and centrifuged at 3000-5000 rpm. The clear upper layer was ready for injection. The LC system was equipped with a C18 reversed-phase column and an ultraviolet detector set at 240 nm. The column was developed with a linear gradient composed of 0.1% phosphoric acid in deionized water and 0.1% phosphoric acid in methanol. The method was subjected to Single Laboratory Validation. The method precision was 0.50% relative standard deviation, accuracy was less than +/-1.5%, method linearity in the range 0-2 mg glucosamine/mL was 1.00, the detection limit was 0.0705 microg/mL, and the quantitation limit was 0.235 microg/mL. Chondroitin sulfate, amino acids, and excipients did not interfere with glucosamine testing. After derivatization, both standard and sample preparations were stable for at least 48 h. Due to its high sensitivity, this method can be used to assay glucosamine in functional foods and pet foods. The validation data will be published separately.