HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a comprehensive laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. The bioinformatics pipeline code is available at https://github.com/lkalmar/HAM-ART.

Sex and blood group determination from hair using ATR-FTIR spectroscopy and chemometrics.

Examination of hair with its intact root is commonly used for DNA profiling of the donor. However, its use for gathering other types of information is less explored. Using attenuated total reflectance-Fourier transform infrared spectroscopy, the present study aims to explore other relevant aspects in a non-destructive manner for forensics. Determining the sex and blood group of human hair samples were the major goals of the study. Sex determination was accomplished by analyzing the differential vibrational intensities and stretching of various chemical groups associated with hair and its proteins. Statistical inference of spectral data was performed using chemometric algorithms such as PCA and PLS-DA. The PLS-DA model determined sex with 100% accuracy and blood grouping with an average accuracy of 95%. The present study is the first of its kind to determine sex and blood grouping from human scalp hair shafts, as far as the author knows. By acting as a preliminary screening test, this study could have significant implications for forensic analysis of crime scene samples. Human and synthetic hair were used in validation studies, resulting in 100% accuracy, specificity, and sensitivity, with 0% false positives and false negatives. The technique ATR FTIR spectroscopy could complement the currently used methods of hair analysis such as physical examination and mitochondrial or genomic DNA analysis.

Classic Hodgkin lymphoma in young people.

Classic Hodgkin lymphoma (CHL) is a unique form of lymphoid cancer featuring a heterogeneous tumor microenvironment and a relative paucity of malignant Hodgkin and Reed-Sternberg (HRS) cells with characteristic phenotype. Younger individuals (children, adolescents and young adults) are affected as often as the elderly, producing a peculiar bimodal age-incidence profile that has generated immense interest in this disease and its origins. Decades of epidemiological investigations have documented the populations most susceptible and identified multiple risk factors that can be broadly categorized as either biological or environmental in nature. Most risk factors result in overt immunodeficiency or confer more subtle alterations to baseline health, physiology or immune function. Epstein Barr virus, however, is both a risk factor and well-established driver of lymphomagenesis in a significant subset of cases. Epigenetic changes, along with the accumulation of somatic driver mutations and cytogenetic abnormalities are required for the malignant transformation of germinal center-experienced HRS cell precursors. Chromosomal instability and the influence of endogenous mutational processes are critical in this regard, by impacting genes involved in key signaling pathways that promote the survival and proliferation of HRS cells and their escape from immune destruction. Here we review the principal features, known risk factors and lymphomagenic mechanisms relevant to newly diagnosed CHL, with an emphasis on those most applicable to young people.

Spatially separating redox centers on 2D carbon nitride with cobalt single atom for photocatalytic H2O2 production.

Redox cocatalysts play crucial roles in photosynthetic reactions, yet simultaneous loading of oxidative and reductive cocatalysts often leads to enhanced charge recombination that is detrimental to photosynthesis. This study introduces an approach to simultaneously load two redox cocatalysts, atomically dispersed cobalt for improving oxidation activity and anthraquinone for improving reduction selectivity, onto graphitic carbon nitride (C3N4) nanosheets for photocatalytic H2O2 production. Spatial separation of oxidative and reductive cocatalysts was achieved on a two-dimensional (2D) photocatalyst, by coordinating cobalt single atom above the void center of C3N4 and anchoring anthraquinone at the edges of C3N4 nanosheets. Such spatial separation, experimentally confirmed and computationally simulated, was found to be critical for enhancing surface charge separation and achieving efficient H2O2 production. This center/edge strategy for spatial separation of cocatalysts may be applied on other 2D photocatalysts that are increasingly studied in photosynthetic reactions.

Testicular cavernous hemangioma masquerading as testicular malignancy.

Cavernous hemangiomas are benign tumors of vascular origin that can develop in any part of the body. However, its occurrence in the testis is rare. To the best of our knowledge, we are reporting the first case of a patient with cavernous hemangioma with concern for an extracapsular extension on ultrasound imaging.

Anti-membrane Antibodies Persist at Least One Year and Discriminate Between Past Coronavirus Disease 2019 Infection and Vaccination.

BACKGROUND: The consequences of past coronavirus disease 2019 (COVID-19) infection for personal and population health are emerging, but accurately identifying distant infection is a challenge. Anti-spike antibodies rise after both vaccination and infection and anti-nucleocapsid antibodies rapidly decline. METHODS: We evaluated anti-membrane antibodies in COVID-19 naive, vaccinated, and convalescent subjects to determine if they persist and accurately detect distant infection. RESULTS: We found that anti-membrane antibodies persist for at least 1 year and are a sensitive and specific marker of past COVID-19 infection. CONCLUSIONS: Thus, anti-membrane and anti-spike antibodies together can differentiate between COVID-19 convalescent, vaccinated, and naive states to advance public health and research.

Mapping drivers of second-generation South Asian American eating behaviors using a novel integration of qualitative and social network analysis methods.

This study explores a novel, mixed qualitative method to deconstruct the diet of second-generation South Asian Americans (SAAs). Online interviews of 32 second-generation SAAs were conducted usingintegrated free-listing and mind-mapping. Ranked free-lists were aggregated to identify salient drivers, while connections made within mind-maps were analyzed using social network analysis (SNA) methods. Overall, 34 distinct drivers and 247 unique connections were identified. Taste, family, and health had the highest adjusted rankings, while health displayed the strongest network centrality. Interventions aimed at second-generation SAA dietary behaviors may benefit from family-based or multi-level interventions, which consider the complex, unique dietary norms identified.

Exploring the Mechanisms of Selectivity for Environmentally Significant Oxo-Anion Removal during Water Treatment: A Review of Common Competing Oxo-Anions and Tools for Quantifying Selective Adsorption.

Development of novel adsorbents often neglects the competitive adsorption between co-occurring oxo-anions, overestimating realistic pollutant removal potentials, and overlooking the need to improve selectivity of materials. This critical review focuses on adsorptive competition between commonly co-occurring oxo-anions in water and mechanistic approaches for the design and development of selective adsorbents. Six "target" oxo-anion pollutants (arsenate, arsenite, selenate, selenite, chromate, and perchlorate) were selected for study. Five "competing" co-occurring oxo-anions (phosphate, sulfate, bicarbonate, silicate, and nitrate) were selected due to their potential to compete with target oxo-anions for sorption sites resulting in decreased removal of the target oxo-anions. First, a comprehensive review of competition between target and competitor oxo-anions to sorb on commonly used, nonselective, metal (hydr)oxide materials is presented, and the strength of competition between each target and competitive oxo-anion pair is classified. This is followed by a critical discussion of the different equations and models used to quantify selectivity. Next, four mechanisms that have been successfully utilized in the development of selective adsorbents are reviewed: variation in surface complexation, Lewis acid/base hardness, steric hindrance, and electrostatic interactions. For each mechanism, the oxo-anions, both target and competitors, are ranked in terms of adsorptive attraction and technologies that exploit this mechanism are reviewed. Third, given the significant effort to evaluate these systems empirically, the potential to use computational quantum techniques, such as density functional theory (DFT), for modeling and prediction is explored. Finally, areas within the field of selective adsorption requiring further research are detailed with guidance on priorities for screening and defining selective adsorbents.

Full genomic characterization of a porcine rotavirus strain detected in an asymptomatic piglet in Accra, Ghana.

BACKGROUND: The introduction of rotavirus A vaccination across the developing world has not proved to be as efficacious as first hoped. One cause of vaccine failure may be infection by zoonotic rotaviruses that are very variable antigenically from the vaccine strain. However, there is a lack of genomic information about the circulating rotavirus A strains in farm animals in the developing world that may be a source of infection for humans. We therefore screened farms close to Accra, Ghana for animals sub-clinically infected with rotavirus A and then sequenced the virus found in one of these samples. RESULTS: 6.1% of clinically normal cows and pigs tested were found to be Rotavirus A virus antigen positive in the faeces. A subset of these (33.3%) were also positive for virus RNA. The most consistently positive pig sample was taken forward for metagenomic sequencing. This gave full sequence for all open reading frames except segment 5 (NSP1), which is missing a single base at the 5' end. The virus infecting this pig had genome constellation G5-P[7]-I5-R1-C1-M1-A8-N1-T7-E1-H1, a known porcine genotype constellation. CONCLUSIONS: Farm animals carry rotavirus A infection sub-clinically at low frequency. Although the rotavirus A genotype discovered here has a pig-like genome constellation, a number of the segments most closely resembled those isolated from humans in suspected cases of zoonotic transmission. Therefore, such viruses may be a source of variable gene segments for re-assortment with other viruses to cause vaccine breakdown. It is recommended that further human and pig strains are characterized in West Africa, to better understand this dynamic.

Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape.

Campylobacter jejuni is the leading cause of bacterial food borne illness. While helical cell shape is considered important for C. jejuni pathogenesis, this bacterium is capable of adopting other morphologies. To better understand how helical-shaped C. jejuni maintain their shape and thus any associated colonisation, pathogenicity or other advantage, it is first important to identify the genes and proteins involved. So far, two peptidoglycan modifying enzymes Pgp1 and Pgp2 have been shown to be required for C. jejuni helical cell shape. We performed a visual screen of ∼2000 transposon mutants of C. jejuni for cell shape mutants. Whole genome sequence data of the mutants with altered cell shape, directed mutants, wild type stocks and isolated helical and rod-shaped 'wild type' C. jejuni, identified a number of different mutations in pgp1 and pgp2, which result in a change in helical to rod bacterial cell shape. We also identified an isolate with a loss of curvature. In this study, we have identified the genomic change in this isolate, and found that targeted deletion of the gene with the change resulted in bacteria with loss of curvature. Helical cell shape was restored by supplying the gene in trans. We examined the effect of loss of the gene on bacterial motility, adhesion and invasion of tissue culture cells and chicken colonisation, as well as the effect on the muropeptide profile of the peptidoglycan sacculus. Our work identifies another factor involved in helical cell shape.

Flowcytometric comparative analysis in acute leukemias between Indian and proposed minimal screening panel.

BACKGROUND: Acute myeloid leukemia and acute lymphoid leukemia differ substantially in response to therapy and course, and accurate differentiation of the two is fundamental to therapeutic decisions. Immunophenotyping is used for this purpose, and various guidelines have been proposed regarding a minimal screening antibody panel. Most of them have been found inefficient. METHODS: Eighty-two cases of consecutive acute leukemias reporting to this hospital over a period of two years were included in the study. Peripheral blood smear, bone marrow aspirate, and bone marrow biopsy were studied using morphology, cytochemical stains, and relevant immunohistochemical stains on selected biopsy specimens. Flowcytometry analysis was carried out using Indian consensus screening panel and our proposed minimal screening panel (PMSP) for comparison. RESULT: Immunophenotyping using PMSP resulted in 95.12% accurate diagnosis versus Indian consensus minimal screening panel (ICMSP) with an accuracy of 92.68%. This result was statistically significant as per Chi Square tests. CONCLUSION: PMSP can be used as a substitute for ICMSP, since it includes lineage-specific cytoplasmic antibodies, as well as lesser number of monoclonal antibodies, and enables us to diagnose mixed lineage leukemia. Fewer markers can be linked to a lower cost as well, which is relevant in a developing economy.

Motility defects in Campylobacter jejuni defined gene deletion mutants caused by second-site mutations.

Genetic variation due to mutation and phase variation has a considerable impact on the commensal and pathogenic behaviours of Campylobacter jejuni. In this study, we provide an example of how second-site mutations can interfere with gene function analysis in C. jejuni. Deletion of the flagellin B gene (flaB) in C. jejuni M1 resulted in mutant clones with inconsistent motility phenotypes. From the flaB mutant clones picked for further analysis, two were motile, one showed intermediate motility and two displayed severely attenuated motility. To determine the molecular basis of this differential motility, a genome resequencing approach was used. Second-site mutations were identified in the severely attenuated and intermediate motility flaB mutant clones: a TA-dinucleotide deletion in fliW and an A deletion in flgD, respectively. Restoration of WT fliW, using a newly developed genetic complementation system, confirmed that the second-site fliW mutation caused the motility defect as opposed to the primary deletion of flaB. This study highlights the importance of (i) screening multiple defined gene deletion mutant clones, (ii) genetic complementation of the gene deletion and ideally (iii) screening for second-site mutations that might interfere with the pathways/mechanisms under study.

Bone marrow findings post allogeneic transplant for myeloproliferative neoplasms and chronic myelomonocytic leukemia with increased fibrosis.

BACKGROUND: Allogeneic hematopoietic stem cell transplant for myeloid neoplasms with increased fibrosis is uncommon; morphologic features posttransplant can be concerning for persistent disease. METHODS: In this retrospective study, we identified 22 patients transplanted for myeloproliferative neoplasms or chronic myelomonocytic leukemia with fibrosis at our institution, and reviewed slides from pretransplant and posttransplant bone marrow biopsies. Clinical features and results of molecular, chimerism, and cytogenetic studies were retrieved from the medical record. RESULTS: Pretransplant bone marrow biopsies commonly exhibited hypercellularity, atypical megakaryocytes, and reticulin fibrosis. At day 100, 36% of biopsies had reticulin grade >MF1 and 33% of those tested had positive molecular studies, with no significant associations between day 100 marrow characteristics and molecular profile or peripheral count recovery times. In the 1 year posttransplant biopsies (n = 12), 7 of 9 had negative molecular studies; of these, none had reticulin grade >MF1, 1 had trichrome 1+, 2 had atypical megakaryocytes, and 1 was hypercellular. CONCLUSIONS: Supporting recent literature, our study indicates that persistent day 100 reticulin fibrosis/collagen deposition does not show an association with day 100 molecular status. Our study additionally provides data for 12 patients with 1 year posttransplant marrow biopsies, with the majority of those lacking either increased fibrosis or molecular evidence of persistent disease.

ADAMTS13 regulates angiogenic markers via Ephrin/Eph signaling in human mesenchymal stem cells under serum-deprivation stress.

Mesenchymal stem cells (MSCs) are known to facilitate angiogenesis and promote neo-vascularization via secretion of trophic factors. Here, we explored the molecular mechanism adopted by ADAMTS13 in modulating the expression of some key angiogenic markers in human umbilical cord-derived MSCs under serum-deprivation stress. Wharton's jelly MSCs (WJ-MSCs) were isolated from the perivascular region of human umbilical cords by explant culture. ADAMTS13 was upregulated at both mRNA and protein levels in WJ-MSCs under serum-deprivation stress. Correspondingly, some key angiogenic markers were also seen to be upregulated. By screening signaling pathways, p38 and JNK pathways were identified as negative and positive regulators for expression of ADAMTS13, and the angiogenic markers, respectively. Our results also indicated the Notch pathway and p53 as other probable partners modulating the expression of ADAMTS13 and the angiogenic markers. Knockdown of ADAMTS13 using siRNA led to reversal in the expression of these angiogenic markers. Further, ADAMTS13 was shown to act via the EphrinB2/EphB4 axis followed by ERK signaling to control expression of the angiogenic markers. Interestingly, stronger expression levels were noted for ADAMTS13, VEGF and PDGF under a more stringent nutrient stress condition. Thus, we highlight a novel role of ADAMTS13 in WJ-MSCs under nutrient stress condition.

Performance of MYC, BCL2, and BCL6 break-apart FISH in small biopsies with large B-cell lymphoma: a retrospective Cytopathology Hematopathology Interinstitutional Consortium study.

Introduction: Fluorescence in situ hybridization (FISH) is an essential ancillary study used to identify clinically aggressive subsets of large B-cell lymphomas that have MYC, BCL2, or BCL6 rearrangements. Small-volume biopsies such as fine needle aspiration biopsy (FNAB) and core needle biopsy (CNB) are increasingly used to diagnose lymphoma and obtain material for ancillary studies such as FISH. However, the performance of FISH in small biopsies has not been thoroughly evaluated or compared to surgical biopsies. Methods: We describe the results of MYC, BCL2, and BCL6 FISH in a series of 222 biopsy specimens, including FNAB with cell blocks, CNBs, and surgical excisional or incisional biopsies from 208 unique patients aggregated from 6 academic medical centers. A subset of patients had FNAB followed by a surgical biopsy (either CNB or excisional biopsy) obtained from the same or contiguous anatomic site as part of the same clinical workup; FISH results were compared for these paired specimens. Results: FISH had a low hybridization failure rate of around 1% across all specimen types. FISH identified concurrent MYC and BCL2 rearrangements in 20 of 197 (10%) specimens and concurrent MYC and BCL6 rearrangements in 3 of 182 (1.6%) specimens. The paired FNAB and surgical biopsy specimens did not show any discrepancies for MYC or BCL2 FISH; of the 17 patients with 34 paired cytology and surgical specimens, only 2 of the 49 FISH probes compared (4% of all comparisons) showed any discrepancy and both were at the BCL6 locus. One discrepancy was due to necrosis of the CNB specimen causing a false negative BCL6 FISH result when compared to the FNAB cell block that demonstrated a BCL6 rearrangement. Discussion: FISH showed a similar hybridization failure rate in all biopsy types. Ultimately, MYC, BCL2, or BCL6 FISH showed 96% concordance when compared across paired cytology and surgical specimens, suggesting FNAB with cell block is equivalent to other biopsy alternatives for evaluation of DLBCL or HGBCL FISH testing.

Investigating the functional hierarchy of Bacillus megaterium PV361 spore germinant receptors.

Spores of Bacillus megaterium QM B1551 germinate rapidly when exposed to a number of single-trigger germinant compounds, including glucose, proline, leucine, and certain inorganic salts. However, spores of strain PV361, a plasmidless QM B1551 derivative that lacks the GerU germinant receptor (GR) responsible for mediating germination in response to single-trigger compounds, can germinate efficiently when incubated in nutritionally rich media, presumably via activation of additional germinant receptors. In this work, we have identified five chromosomally encoded GRs and attempted to characterize, by mutational analysis, germinant recognition profiles associated with the respective receptors in strain PV361. Of strains engineered with single GR insertion-deletions, only GerK-null spores displayed significant defective germination phenotypes when incubated in 5% (wt/vol) beef extract or plated on rich solid medium. Cumulative decreases in viability were observed in GerK-null spores that also lacked GerA or GerA2, indicating that these GRs, which exerted little effect on spore germination when disrupted individually, have a degree of functionality. Unexpectedly, an efficient germination response to combinations of germinants was restored in GerA(+) spores, which lack all other functional GRs, providing evidence for negative cooperativity between some GRs within the spore. Tetrazolium-based germinative assays conducted with purified spores indicated that these newly characterized B. megaterium GRs are cognate for a wide and chemically diverse range of germinant molecules, but unlike GerU, can only be induced to trigger germination when stimulated by at least two different germinants.

Identification of new proteins that modulate the germination of spores of bacillus species.

A number of operons encoding the nutrient germinant receptors (GRs) in dormant spores of Bacillus megaterium and Bacillus subtilis species have small open reading frames (ORFs) of unknown function within or immediately adjacent to the operons. Inactivation of the genes in these ORFs, encoding proteins now termed D proteins, either significantly increased or decreased spore germination via the associated GR but had no effects on germination via non-GR-dependent germinants. These effects on GR-dependent germination were complemented by ectopic expression of the appropriate D gene (gene encoding D protein). However, substitution of noncognate D genes in two GR operons resulted in inhibition of germination via the GR manipulated, although ectopic overexpression of a D gene had no effect on overall GR-dependent germination. The various D genes studied were expressed in the forespore during sporulation in parallel with the associated GR operon, and transcription of a B. subtilis D gene was controlled by RNA polymerase sigma factor σ(G). These results indicate that proteins encoded by small ORFs within or adjacent to operons encoding GRs play major roles in modulating GR function in spores of Bacillus species. In B. subtilis, deletion of a D gene (B. subtilis gerKD [gerKDbs]) adjacent to the gerK operon encoding the GerK GR or ectopic expression or overexpression of gerKDbs had no major effect on the levels of GR subunits or of two other germination proteins.

Understanding the Effect of Single Atom Cationic Defect Sites in an Al2O3 (012) Surface on Altering Selenate and Sulfate Adsorption: An Ab Initio Study.

Adsorption is a promising under-the-sink selenate remediation technique for distributed water systems. Recently it was shown that adsorption induced water network re-arraignment control adsorption energetics on the α-Al2O3 (012) surface. Here, we aim to elucidate the relative importance of the water network effects and surface cation identity on controlling selenate and sulfate adsorption energy using density functional theory calculations. Density functional theory (DFT) calculations predicted the adsorption energies of selenate and sulfate on nine transition metal cations (Sc-Cu) and two alkali metal cations (Ga and In) in the α-Al2O3 (012) surface under simulated acidic and neutral pH conditions. We find that the water network effects had larger impact on the adsorption energy than the cationic identity. However, cation identity secondarily controlled adsorption. Most cations decreased the adsorption energy weakening the overall performance, the larger Sc and In cations enabled inner-sphere adsorption in acidic conditions because they relaxed outward from the surface providing more space for adsorption. Additionally, only Ti induced Se selectivity over S by reducing the adsorbing selenate to selenite but not reducing the sulfate. Overall, this study indicates that tuning water network structure will likely have a larger impact than tuning cation-selenate interactions for increasing adsorbate effectiveness.

Enzyme-free isolation of mesenchymal stem cells from decidua basalis of the human placenta.

Mesenchymal stem cells (MSCs), also referred to as "medicinal signaling cells," have gained prominence as candidates for cell-based therapy and in clinical trials owing to their regenerative and therapeutic properties. Here, we present a protocol for isolating MSCs from the decidua basalis layer of human placenta using an explant culture approach. We describe steps for collecting, disinfecting, and plating placental tissue. We then detail procedures for characterizing the isolated MSCs through flow cytometry and in vitro differentiation.