Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression

Immunotherapy with CAR T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific exons (CSE) present a promising reservoir of targets; however, these have not been explored and validated systematically in a pan-cancer fashion. To identify CSE targets, we analyzed 1,532 RNA-seq datasets from 16 types of pediatric solid and brain tumors for comparison with normal tissues using a newly developed workflow. We found 2,933 exons in 157 genes encoding proteins of the surfaceome or matrisome with high cancer specificity either at the gene (n=148) or the alternatively spliced (AS) isoform (n=9) level. Expression of selected AS targets, including the EDB domain of FN1 (EDB), and gene targets, such as COL11A1, were validated in pediatric PDX tumors. We generated CAR T cells specific to EDB or COL11A1 and demonstrated that COL11A1-CAR T-cells have potent antitumor activity. The full target list, explorable via an interactive web portal (https://cseminer.stjude.org/), provides a rich resource for developing immunotherapy of pediatric solid and brain tumors using gene or AS targets with high expression specificity in cancer.

In ovo administration of the Marek's disease vaccine in conjunction with 25-hydroxyvitamin D3 and its subsequent effects on the performance and immunity-related characteristics of Ross 708 broiler hatchlings1,2,3

The combined effects of the in ovo injection of commercial Marek's disease vaccine (MDV) and various levels of 25-hydroxyvitamin D3 (25OHD3) on the hatch variables, immunological measurements, and gene expression of Ross 708 hatchling broilers were investigated. A total of 5 in ovo injection treatments that were applied at 18 d of incubation (doi) included: 1) noninjected (control); or a 50 μL solution volume of 2) MDV alone; or MDV combined with 3) 0.6 μg of 25OHD3; 4) 1.2 μg of 25OHD3; or 5) 2.4 μg of 25OHD3. At hatch, hatchability of set and live embryonated eggs, hatchling body weight, hatch residue analysis, serum IgY and alpha-1 acid glycoprotein (AGP) concentrations, and the expression of genes related to immunity (INFα, INFβ, INFγ, TLR-3, and TLR-21) and vitamin D3 activity (1 α-hydroxylase, 24 hydroxylase, and vitamin D receptor) were determined. No significant treatment differences were observed for hatchability of set and live embryonated eggs, or for serum IgY and AGP concentrations. However, hatchling body weight was higher when MDV was combined with either 1.2 or 2.4 μg of 25OHD3 than when MDV was provided alone or in combination with 0.6 μg of 25OHD3. Also, in comparison to the noninjected treatment group, the expression of the genes for 1 α-hydroxylase and 24 hydroxylase was improved when MDV was combined with either 1.2 or 2.4 μg of 25OHD3. Lastly, expression of the genes linked to viral detection (TLR-3) and antibody production (INF-β) was increased in those treatments that contained any level of 25OHD3. These results indicate that in comparison to controls, the effects of MDV were observed to be greater on hatchling BW and splenic gene expression when it was administered in combination with the 1.2 or 2.4 μg doses of 25OHD3. Further research is needed to determine the posthatch effects of the administration of various levels of 25OHD3 in combination with MDV.

An adaptive stress response that confers cellular resilience to decreased ubiquitination

Ubiquitination is a post-translational modification initiated by the E1 enzyme UBA1, which transfers ubiquitin to ~35 E2 ubiquitin-conjugating enzymes. While UBA1 loss is cell lethal, it remains unknown how partial reduction in UBA1 activity is endured. Here, we utilize deep-coverage mass spectrometry to define the E1-E2 interactome and to determine the proteins that are modulated by knockdown of UBA1 and of each E2 in human cells. These analyses define the UBA1/E2-sensitive proteome and the E2 specificity in protein modulation. Interestingly, profound adaptations in peroxisomes and other organelles are triggered by decreased ubiquitination. While the cargo receptor PEX5 depends on its mono-ubiquitination for binding to peroxisomal proteins and importing them into peroxisomes, we find that UBA1/E2 knockdown induces the compensatory upregulation of other PEX proteins necessary for PEX5 docking to the peroxisomal membrane. Altogether, this study defines a homeostatic mechanism that sustains peroxisomal protein import in cells with decreased ubiquitination capacity.

First Measurement of the Nuclear-Recoil Ionization Yield in Silicon at 100 eV

We measured the nuclear-recoil ionization yield in silicon with a cryogenic phonon-sensitive gram-scale detector. Neutrons from a monoenergetic beam scatter off of the silicon nuclei at angles corresponding to energy depositions from 4 keV down to 100 eV, the lowest energy probed so far. The results show no sign of an ionization production threshold above 100 eV. These results call for further investigation of the ionization yield theory and a comprehensive determination of the detector response function at energies below the keV scale.

Dissecting Detergent-Insoluble Proteome in Alzheimer's Disease by TMTc-Corrected Quantitative Mass Spectrometry

Protein aggregation of amyloid-β peptides and tau are pathological hallmarks of Alzheimer's disease (AD), which are often resistant to detergent extraction and thus enriched in the insoluble proteome. However, additional proteins that coaccumulate in the detergent-insoluble AD brain proteome remain understudied. Here, we comprehensively characterized key proteins and pathways in the detergent-insoluble proteome from human AD brain samples using differential extraction, tandem mass tag (TMT) labeling, and two-dimensional LC-tandem mass spectrometry. To improve quantification accuracy of the TMT method, we developed a complement TMT-based strategy to correct for ratio compression. Through the meta-analysis of two independent detergent-insoluble AD proteome datasets (8914 and 8917 proteins), we identified 190 differentially expressed proteins in AD compared with control brains, highlighting the pathways of amyloid cascade, RNA splicing, endocytosis/exocytosis, protein degradation, and synaptic activity. To differentiate the truly detergent-insoluble proteins from copurified background during protein extraction, we analyzed the fold of enrichment for each protein by comparing the detergent-insoluble proteome with the whole proteome from the same AD samples. Among the 190 differentially expressed proteins, 84 (51%) proteins of the upregulated proteins (n = 165) were enriched in the insoluble proteome, whereas all downregulated proteins (n = 25) were not enriched, indicating that they were copurified components. The vast majority of these enriched 84 proteins harbor low-complexity regions in their sequences, including amyloid-β, Tau, TARDBP/TAR DNA-binding protein 43, SNRNP70/U1-70K, MDK, PTN, NTN1, NTN3, and SMOC1. Moreover, many of the enriched proteins in AD were validated in the detergent-insoluble proteome by five steps of differential extraction, proteomic analysis, or immunoblotting. Our study reveals a resource list of proteins and pathways that are exclusively present in the detergent-insoluble proteome, providing novel molecular insights to the formation of protein pathology in AD.

JUMPptm: Integrated software for sensitive identification of post-translational modifications and its application in Alzheimer's disease study

BACKGROUND

Mass spectrometry (MS)-based proteomic analysis of posttranslational modifications (PTMs) usually requires the pre-enrichment of modified proteins or peptides. However, recent ultra-deep whole proteome profiling generates millions of spectra in a single experiment, leaving many unassigned spectra, some of which may be derived from PTM peptides.

METHODS

Here we present JUMPptm, an integrative computational pipeline, to extract PTMs from unenriched whole proteome. JUMPptm combines the advantages of JUMP, MSFragger and Comet search engines, and includes de novo tags, customized database search and peptide filtering, which iteratively analyzes each PTM by a multi-stage strategy to improve sensitivity and specificity.

RESULTS

We applied JUMPptm to the deep brain proteome of Alzheimer's disease (AD), and identified 34,954 unique peptides with phosphorylation, methylation, acetylation, ubiquitination, and others. The phosphorylated peptides were validated by enriched phosphoproteome from the same sample. TMT-based quantification revealed 482 PTM peptides dysregulated at different stages during AD progression. For example, the acetylation of numerous mitochondrial proteins is significantly decreased in AD. A total of 60 PTM sites are found in the pan-PTM map of the Tau protein.

CONCLUSION

The JUMPptm program is an effective tool for pan-PTM analysis and the resulting AD pan-PTM profile serves as a valuable resource for AD research.

Alzheimer's disease-associated U1 snRNP splicing dysfunction causes neuronal hyperexcitability and cognitive impairment

Recent proteome and transcriptome profiling of Alzheimer's disease (AD) brains reveals RNA splicing dysfunction and U1 small nuclear ribonucleoprotein (snRNP) pathology containing U1-70K and its N-terminal 40-KDa fragment (N40K). Here we present a causative role of U1 snRNP dysfunction to neurodegeneration in primary neurons and transgenic mice (N40K-Tg), in which N40K expression exerts a dominant-negative effect to downregulate full-length U1-70K. N40K-Tg recapitulates N40K insolubility, erroneous splicing events, neuronal degeneration and cognitive impairment. Specifically, N40K-Tg shows the reduction of GABAergic synapse components (e.g., the GABA receptor subunit of GABRA2), and concomitant postsynaptic hyperexcitability that is rescued by a GABA receptor agonist. Crossing of N40K-Tg and the 5xFAD amyloidosis model indicates that the RNA splicing defect synergizes with the amyloid cascade to remodel the brain transcriptome and proteome, deregulate synaptic proteins, and accelerate cognitive decline. Thus, our results support the contribution of U1 snRNP-mediated splicing dysfunction to AD pathogenesis.

Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice

There are known associations between opioids, obesity, and the gut microbiome, but the molecular connection/mediation of these relationships is not understood. To better clarify the interplay of physiological, genetic, and microbial factors, this study investigated the microbiome and host inflammatory responses to chronic opioid administration in genetically obese, diet-induced obese, and lean mice. Samples of feces, urine, colon tissue, and plasma were analyzed using targeted LC-MS/MS quantification of metabolites, immunoassays of inflammatory cytokine levels, genome-resolved metagenomics, and metaproteomics. Genetic obesity, diet-induced obesity, and morphine treatment in lean mice each showed increases in distinct inflammatory cytokines. Metagenomic assembly and binning uncovered over 400 novel gut bacterial genomes and species. Morphine administration impacted the microbiome's composition and function, with the strongest effect observed in lean mice. This microbiome effect was less pronounced than either diet or genetically driven obesity. Based on inferred microbial physiology from the metaproteome datasets, a high-fat diet transitioned constituent microbes away from harvesting diet-derived nutrients and towards nutrients present in the host mucosal layer. Considered together, these results identified novel host-dependent phenotypes, differentiated the effects of genetic obesity versus diet induced obesity on gut microbiome composition and function, and showed that chronic morphine administration altered the gut microbiome.

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Soil microbiomes harbour unparalleled functional and phylogenetic diversity. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. As methylation was proposed to be catalysed by sulfate-reducing bacteria. However, to date, there are no available anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harbouring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.

29-Plex tandem mass tag mass spectrometry enabling accurate quantification by interference correction

Tandem mass tag (TMT) mass spectrometry is a mainstream isobaric chemical labeling strategy for profiling proteomes. Here we present a 29-plex TMT method to combine the 11-plex and 18-plex labeling strategies. The 29-plex method was examined with a pooled sample composed of 1×, 3×, and 10× Escherichia coli peptides with 100× human background peptides, which generated two E. coli datasets (TMT11 and TMT18), displaying the distorted ratios of 1.0:1.7:4.2 and 1.0:1.8:4.9, respectively. This ratio compression from the expected 1:3:10 ratios was caused by co-isolated TMT-labeled ions (i.e., noise). Interestingly, the mixture of two TMT sets produced MS/MS spectra with unique features for the noise detection: (i) in TMT11-labeled spectra, TMT18-specific reporter ions (e.g., 135N) were shown as the noise; (ii) in TMT18-labeled spectra, the TMT11/TMT18-shared reporter ions (e.g., 131C) typically exhibited higher intensities than TMT18-specific reporter ions, due to contaminated TMT11-labeled ions in these shared channels. We further estimated the noise levels contributed by both TMT11- and TMT18-labeled peptides, and corrected reporter ion intensities in every spectrum. Finally, the anticipated 1:3:10 ratios were largely restored. This strategy was also validated using another 29-plex sample with 1:5 ratios. Thus the 29-plex method expands the TMT throughput and enhances the quantitative accuracy.

Immunomodulatory effect of different statin regimens on regulatory T-cells among patients with acute coronary syndrome: a systematic review and network meta-analysis of randomized clinical trials

Funding Acknowledgements

Type of funding sources: None.

Immunomodulatory effect of different statin regimens on regulatory T-cells  among patients with acute coronary syndrome: a systematic review  and network meta-analysis of randomized clinical trials

Introduction

In patients with acute coronary syndrome (ACS), studies suggest that statin therapy, besides its role in reducing the progression of atherosclerosis through its pharmacological effect, plays a pivotal role in controlling the pathogenesis of ACS through the anti-inflammatory effects of suppressor regulatory T cells (Tregs).

Purpose

We conducted a network meta-analysis (NMA) to determine the effects of low-dose conventional statin therapy (CST) (20 mg/day or less) and high-dose intensive statin therapy (IST) (40 mg/day or more) on the frequency of Tregs and their associated cytokines (IFN-γ, IL-10, TGF-β), compared to placebo.

Methods

The PubMed, Cochrane Library, and EMBASE databases were searched for randomized clinical trials (RCTs) to identify relevant articles published until June 2021. We pooled data extracted from the included studies using the standardized mean difference (SMD). A random-effects model was used to conduct this NMA. Heterogeneity was evaluated using Cochran's Q- and the I2-test. GRADE(Grading of Recommendations, Assessment, Development and Evaluations) was used to assess the study's quality. Data analysis was conducted using R software.

Results

A total of 505 patients were enrolled in the 5 RCTs. The NMA indicated a significant increase in Treg frequency in the CST group compared with the control group (SMD 1.77; 95% CI: 0.77 – 2.76; P-value = 0.0005) and a larger increase in the Treg frequency associated with the IST group compared with the control group (SMD 2.12; 95% CI: 1.15 – 3.10; P-value < 0.0001). However, there was significant heterogeneity and inconsistency among the included studies (τ2 = 0.6096; τ = 0.7808; I2 = 91.2% [80.5%; 96.0%]). When compared to the placebo, both CST and IST increased levels of secreted IL-10 (SMD 2.69; 95% CI: 2.07 – 3.31; P-value < 0.0001 and (SMD 2.14; 95% CI: 1.76 – 2.52; P-value < 0.0001), respectively. In comparison to the control group, CST was associated with increased levels of TGF-β (SMD 3.83; 95% CI: 0.63 – 7.0; P-value = 0.0189). This association was not seen in the IST group. IFN-γ levels decreased significantly in both the IST and CST groups (SMD -1.52; 95% CI: -1.94 – -1.10; P-value < 0.0001) and (SMD -2.34; 95% CI: -2.73 – -1.95; P-value < 0.0001) respectively.

Conclusions

Our study suggests that both high and low dose statin groups showed increased Treg frequency compared to the placebo group. IST showed larger benefits. Statin therapy also increased IL-10 and TGF-β cytokine levels and decreased IFN-γ levels. Therefore, statins have the potential to be the main treatment to reduce the incidence of cardiovascular events and improve cardiac function in patients with ACS through immunomodulatory effect on Treg.

Health Promoting Lifestyle during Covid-19 Pandemic among Residents of Gandaki Province, Nepal

Background Lifestyle is an important factor to individual's health and quality of life. Although, the emergence of Corona virus disease 2019 (COVID-19) has forced billions of people to change their lifestyle overnight. Objective To identify health promoting lifestyle during COVID-19 pandemic among the residents of Gandaki Province, Nepal. Method Descriptive cross sectional web based study was conducted among 386 respondents from Gandaki Province. Adults from 18 years and above, who could fill the form online were included using purposive and snowball sampling technique. Data were collected using Health Promoting Lifestyle Profile II (HPLP II) scale and analysed using descriptive (frequency, percentage, median) and inferential statistics (Mann Whitney U test and Kruskal Wallis test). Result Only 18.7% of the respondents had an excellent health promoting lifestyle followed by good health promoting lifestyle among 60.4%. Highest median score was observed in spiritual 27(10-36), and interpersonal relationship subscale 27(9-36). Whereas, the lowest was observed in physical activity 21(8-32) followed by stress management 24(10-32). Statistically significant difference was observed in age and perception of own health status with spirituality; gender, chronic illness and perception of own health status with interpersonal subscale and age, gender, marital status, occupation and perception of own health status with physical subscale. Conclusion The study concludes the need of health education and awareness to promote healthy lifestyle behaviours with a particular emphasis on indoor physical activities and stress management skills with specific consideration to female and elderly.

Deep Single-Cell-Type Proteome Profiling of Mouse Brain by Nonsurgical AAV-Mediated Proximity Labeling

Proteome profiling is a powerful tool in biological and biomedical studies, starting with samples at bulk, single-cell, or single-cell-type levels. Reliable methods for extracting specific cell-type proteomes are in need, especially for the cells (e.g., neurons) that cannot be readily isolated. Here, we present an innovative proximity labeling (PL) strategy for single-cell-type proteomics of mouse brain, in which TurboID (an engineered biotin ligase) is used to label almost all proteins in a specific cell type. This strategy bypasses the requirement of cell isolation and includes five major steps: (i) constructing recombinant adeno-associated viruses (AAVs) to express TurboID driven by cell-type-specific promoters, (ii) delivering the AAV to mouse brains by direct intravenous injection, (iii) enhancing PL labeling by biotin administration, (iv) purifying biotinylated proteins, followed by on-bead protein digestion, and (v) quantitative tandem-mass-tag (TMT) labeling. We first confirmed that TurboID can label a wide range of cellular proteins in human HEK293 cells and optimized the single-cell-type proteomic pipeline. To analyze specific brain cell types, we generated recombinant AAVs to coexpress TurboID and mCherry proteins, driven by neuron- or astrocyte-specific promoters and validated the expected cell expression by coimmunostaining of mCherry and cellular markers. Subsequent biotin purification and TMT analysis identified ∼10,000 unique proteins from a few micrograms of protein samples with excellent reproducibility. Comparative and statistical analyses indicated that these PL proteomes contain cell-type-specific cellular pathways. Although PL was originally developed for studying protein-protein interactions and subcellular proteomes, we extended it to efficiently tag the entire proteomes of specific cell types in the mouse brain using TurboID biotin ligase. This simple, effective in vivo approach should be broadly applicable to single-cell-type proteomics.

Constraints on Lightly Ionizing Particles from CDMSlite

The Cryogenic Dark Matter Search low ionization threshold experiment (CDMSlite) achieved efficient detection of very small recoil energies in its germanium target, resulting in sensitivity to lightly ionizing particles (LIPs) in a previously unexplored region of charge, mass, and velocity parameter space. We report first direct-detection limits calculated using the optimum interval method on the vertical intensity of cosmogenically produced LIPs with an electric charge smaller than e/(3×10^{5}), as well as the strongest limits for charge ≤e/160, with a minimum vertical intensity of 1.36×10^{-7}  cm^{-2} s^{-1} sr^{-1} at charge e/160. These results apply over a wide range of LIP masses (5  MeV/c^{2} to 100  TeV/c^{2}) and cover a wide range of βγ values (0.1-10^{6}), thus excluding nonrelativistic LIPs with βγ as small as 0.1 for the first time.

Proteomic landscape of Alzheimer's Disease: novel insights into pathogenesis and biomarker discovery

Mass spectrometry-based proteomics empowers deep profiling of proteome and protein posttranslational modifications (PTMs) in Alzheimer's disease (AD). Here we review the advances and limitations in historic and recent AD proteomic research. Complementary to genetic mapping, proteomic studies not only validate canonical amyloid and tau pathways, but also uncover novel components in broad protein networks, such as RNA splicing, development, immunity, membrane transport, lipid metabolism, synaptic function, and mitochondrial activity. Meta-analysis of seven deep datasets reveals 2,698 differentially expressed (DE) proteins in the landscape of AD brain proteome (n = 12,017 proteins/genes), covering 35 reported AD genes and risk loci. The DE proteins contain cellular markers enriched in neurons, microglia, astrocytes, oligodendrocytes, and epithelial cells, supporting the involvement of diverse cell types in AD pathology. We discuss the hypothesized protective or detrimental roles of selected DE proteins, emphasizing top proteins in "amyloidome" (all biomolecules in amyloid plaques) and disease progression. Comprehensive PTM analysis represents another layer of molecular events in AD. In particular, tau PTMs are correlated with disease stages and indicate the heterogeneity of individual AD patients. Moreover, the unprecedented proteomic coverage of biofluids, such as cerebrospinal fluid and serum, procures novel putative AD biomarkers through meta-analysis. Thus, proteomics-driven systems biology presents a new frontier to link genotype, proteotype, and phenotype, accelerating the development of improved AD models and treatment strategies.

Light Dark Matter Search with a High-Resolution Athermal Phonon Detector Operated above Ground

We present limits on spin-independent dark matter-nucleon interactions using a 10.6 g Si athermal phonon detector with a baseline energy resolution of σ_{E}=3.86±0.04(stat)_{-0.00}^{+0.19}(syst)  eV. This exclusion analysis sets the most stringent dark matter-nucleon scattering cross-section limits achieved by a cryogenic detector for dark matter particle masses from 93 to 140  MeV/c^{2}, with a raw exposure of 9.9 g d acquired at an above-ground facility. This work illustrates the scientific potential of detectors with athermal phonon sensors with eV-scale energy resolution for future dark matter searches.

Abstract 1543: Mining cancer-specific isoforms as CAR T-cell therapy targets for pediatric solid and brain tumors

Immunotherapy with T-cells expressing chimeric antigen receptors (CARs) holds the promise to improve outcomes for children with solid and brain tumors. However, at present, there is a limited array of targetable antigens. We posit here that targets generated by alternative splicing events (ASEs) in cancer cells present an untapped class of CAR targets since many of these are tumor-specific and overexpressed in malignant cells. Thus, we developed Cancer-Specific Isoform Miner (CSI-Miner), a pipeline to perform a comprehensive ASE analysis of pediatric cancers to discover CSIs as CAR T-cell therapy targets. We analyzed 1,938 solid and brain tumor samples collected from PCGP, TARGET, and St. Jude's real-time clinical sequencing data sets. In addition, 7,527 GTEx RNAseq samples across 31 human tissues were harmonized to prioritize exon candidates with minimal expression in normal tissue. Through CSI-Miner, we identified 40,748 highly expressed exons from the tumor's surfaceome and secretome, of which 185 were unannotated novel exons. Taking advantage of available mass-spectrometry proteome data from the Clinical Proteomic Tumor Analysis Consortium and St. Jude's proteomics facility, we validated the presence of peptides encoded by these novel exons for rhabdomyosarcoma, medulloblastoma, high-grade glioma, low-grade glioma, and ependymoma. Moreover, non-malignant mass-spectrometry data from muscle and brain samples were incorporated as negative controls. Several secretome targets were identified that adhered to the surface of cancer cells, including EDB, an oncofetal splice variant of fibronectin. EDB was expressed in a broad range of pediatric solid and brain tumors, including Ewing sarcoma and high-grade glioma. We generated T-cells expressing a 2nd generation EDB-CAR (EDB-CAR T-cells) by standard retroviral transduction. EDB-CAR T-cells recognized and killed EDB+ cancer cells in vitro and had potent antitumor activity in xenograft models, resulting in improved overall survival compared to control mice. Importantly, EDB-CAR T-cells did not induce ‘on target/off cancer' toxicities in mice, which is encouraging since EDB is identical in mice and humans. c-MET was also identified as a candidate surfaceome CAR target for rhabdomyosarcoma and melanoma. In summary, we developed CSI-Miner, an integrative analysis pipeline to discover CSIs as CAR T-cell therapy targets, comprised of 248 surfaceome and 51 secretome candidates, for pediatric solid and brain tumors. At present we have validated these CSIs by mass-spectrometry and successfully generated CAR T-cells for one of the candidates. Collectively, CSIs present an untapped class of immunotherapy targets that hold the promise to improve current CAR T-cell therapy approaches for a wide range of pediatric solid and brain tumors. A web portal has been developed supporting access and visualization of this data set to the research community.

Citation Format: Timothy I. Shaw, Jessica Wagner, Elizabeth Wickman, Liqing Tian, Dong Li, Suresh Poudel, Elizabeth Stewart, Yuxin Li, Hong Wang, Mingming Niu, Robin Paul, Colleen Reilly, Xin Zhou, Michael Dyer, Suzanne Baker, Junmin Peng, Jiyang Yu, Paulina Velasquez, Chris DeRenzo, Giedre Krenciute, Jinghui Zhang, Stephen Gottschalk. Mining cancer-specific isoforms as CAR T-cell therapy targets for pediatric solid and brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1543.

Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets

BACKGROUND

Mass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research.

RESULTS

We optimized and employed a pipeline integrating various "guilt-by-association" (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum. Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum. In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions.

CONCLUSIONS

This work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.

Coculture with hemicellulose-fermenting microbes reverses inhibition of corn fiber solubilization by Clostridium thermocellum at elevated solids loadings

BACKGROUND

The cellulolytic thermophile Clostridium thermocellum is an important biocatalyst due to its ability to solubilize lignocellulosic feedstocks without the need for pretreatment or exogenous enzyme addition. At low concentrations of substrate, C. thermocellum can solubilize corn fiber > 95% in 5 days, but solubilization declines markedly at substrate concentrations higher than 20 g/L. This differs for model cellulose like Avicel, on which the maximum solubilization rate increases in proportion to substrate concentration. The goal of this study was to examine fermentation at increasing corn fiber concentrations and investigate possible reasons for declining performance.

RESULTS

The rate of growth of C. thermocellum on corn fiber, inferred from CipA scaffoldin levels measured by LC-MS/MS, showed very little increase with increasing solids loading. To test for inhibition, we evaluated the effects of spent broth on growth and cellulase activity. The liquids remaining after corn fiber fermentation were found to be strongly inhibitory to growth on cellobiose, a substrate that does not require cellulose hydrolysis. Additionally, the hydrolytic activity of C. thermocellum cellulase was also reduced to less-than half by adding spent broth. Noting that > 15 g/L hemicellulose oligosaccharides accumulated in the spent broth of a 40 g/L corn fiber fermentation, we tested the effect of various model carbohydrates on growth on cellobiose and Avicel. Some compounds like xylooligosaccharides caused a decline in cellulolytic activity and a reduction in the maximum solubilization rate on Avicel. However, there were no relevant model compounds that could replicate the strong inhibition by spent broth on C. thermocellum growth on cellobiose. Cocultures of C. thermocellum with hemicellulose-consuming partners-Herbinix spp. strain LL1355 and Thermoanaerobacterium thermosaccharolyticum-exhibited lower levels of unfermented hemicellulose hydrolysis products, a doubling of the maximum solubilization rate, and final solubilization increased from 67 to 93%.

CONCLUSIONS

This study documents inhibition of C. thermocellum with increasing corn fiber concentration and demonstrates inhibition of cellulase activity by xylooligosaccharides, but further work is needed to understand why growth on cellobiose was inhibited by corn fiber fermentation broth. Our results support the importance of hemicellulose-utilizing coculture partners to augment C. thermocellum in the fermentation of lignocellulosic feedstocks at high solids loading.

A Viable New Strategy for the Discovery of Peptide Proteolytic Cleavage Products in Plant-Microbe Interactions

Small peptides that are proteolytic cleavage products (PCPs) of less than 100 amino acids are emerging as key signaling molecules that mediate cell-to-cell communication and biological processes that occur between and within plants, fungi, and bacteria. Yet, the discovery and characterization of these molecules is largely overlooked. Today, selective enrichment and subsequent characterization by mass spectrometry-based sequencing offers the greatest potential for their comprehensive characterization, however qualitative and quantitative performance metrics are rarely captured. Herein, we addressed this need by benchmarking the performance of an enrichment strategy, optimized specifically for small PCPs, using state-of-the-art de novo-assisted peptide sequencing. As a case study, we implemented this approach to identify PCPs from different root and foliar tissues of the hybrid poplar Populus × canescens 717-1B4 in interaction with the ectomycorrhizal basidiomycete Laccaria bicolor. In total, we identified 1,660 and 2,870 Populus and L. bicolor unique PCPs, respectively. Qualitative results supported the identification of well-known PCPs, like the mature form of the photosystem II complex 5-kDa protein (approximately 3 kDa). A total of 157 PCPs were determined to be significantly more abundant in root tips with established ectomycorrhiza when compared with root tips without established ectomycorrhiza and extramatrical mycelium of L. bicolor. These PCPs mapped to 64 Populus proteins and 69 L. bicolor proteins in our database, with several of them previously implicated in biologically relevant associations between plant and fungus.

Biogeography of microbial bile acid transformations along the murine gut

Bile acids, which are synthesized from cholesterol by the liver, are chemically transformed along the intestinal tract by the gut microbiota, and the products of these transformations signal through host receptors, affecting overall host health. These transformations include bile acid deconjugation, oxidation, and 7α-dehydroxylation. An understanding of the biogeography of bile acid transformations in the gut is critical because deconjugation is a prerequisite for 7α-dehydroxylation and because most gut microorganisms harbor bile acid transformation capacity. Here, we used a coupled metabolomic and metaproteomic approach to probe in vivo activity of the gut microbial community in a gnotobiotic mouse model. Results revealed the involvement of Clostridium scindens in 7α-dehydroxylation, of the genera Muribaculum and Bacteroides in deconjugation, and of six additional organisms in oxidation (the genera Clostridium, Muribaculum, Bacteroides, Bifidobacterium, Acutalibacter, and Akkermansia). Furthermore, the bile acid profile in mice with a more complex microbiota, a dysbiosed microbiota, or no microbiota was considered. For instance, conventional mice harbor a large diversity of bile acids, but treatment with an antibiotic such as clindamycin results in the complete inhibition of 7α-dehydroxylation, underscoring the strong inhibition of organisms that are capable of carrying out this process by this compound. Finally, a comparison of the hepatic bile acid pool size as a function of microbiota revealed that a reduced microbiota affects host signaling but not necessarily bile acid synthesis. In this study, bile acid transformations were mapped to the associated active microorganisms, offering a systematic characterization of the relationship between microbiota and bile acid composition.

Peeling back the layers of crassulacean acid metabolism: functional differentiation between Kalanchoë fedtschenkoi epidermis and mesophyll proteomes

Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that offers the potential to engineer improved water-use efficiency (WUE) and drought resilience in C₃ plants while sustaining productivity in the hotter and drier climates that are predicted for much of the world. CAM species show an inverted pattern of stomatal opening and closing across the diel cycle, which conserves water and provides a means of maintaining growth in hot, water-limited environments. Recent genome sequencing of the constitutive model CAM species Kalanchoë fedtschenkoi provides a platform for elucidating the ensemble of proteins that link photosynthetic metabolism with stomatal movement, and that protect CAM plants from harsh environmental conditions. We describe a large-scale proteomics analysis to characterize and compare proteins, as well as diel changes in their abundance in guard cell-enriched epidermis and mesophyll cells from leaves of K. fedtschenkoi. Proteins implicated in processes that encompass respiration, the transport of water and CO₂ , stomatal regulation, and CAM biochemistry are highlighted and discussed. Diel rescheduling of guard cell starch turnover in K. fedtschenkoi compared with that observed in Arabidopsis is reported and tissue-specific localization in the epidermis and mesophyll of isozymes implicated in starch and malate turnover are discussed in line with the contrasting roles for these metabolites within the CAM mesophyll and stomatal complex. These data reveal the proteins and the biological processes enriched in each layer and provide key information for studies aiming to adapt plants to hot and dry environments by modifying leaf physiology for improved plant sustainability.

Impact of Fatty-Acid Labeling of Bacillus subtilis Membranes on the Cellular Lipidome and Proteome

Developing cultivation methods that yield chemically and isotopically defined fatty acid (FA) compositions within bacterial cytoplasmic membranes establishes an in vivo experimental platform to study membrane biophysics and cell membrane regulation using novel approaches. Yet before fully realizing the potential of this method, it is prudent to understand the systemic changes in cells induced by the labeling procedure itself. In this work, analysis of cellular membrane compositions was paired with proteomics to assess how the proteome changes in response to the directed incorporation of exogenous FAs into the membrane of Bacillus subtilis. Key findings from this analysis include an alteration in lipid headgroup distribution, with an increase in phosphatidylglycerol lipids and decrease in phosphatidylethanolamine lipids, possibly providing a fluidizing effect on the cell membrane in response to the induced change in membrane composition. Changes in the abundance of enzymes involved in FA biosynthesis and degradation are observed; along with changes in abundance of cell wall enzymes and isoprenoid lipid production. The observed changes may influence membrane organization, and indeed the well-known lipid raft-associated protein flotillin was found to be substantially down-regulated in the labeled cells – as was the actin-like protein MreB. Taken as a whole, this study provides a greater depth of understanding for this important cell membrane experimental platform and presents a number of new connections to be explored in regard to modulating cell membrane FA composition and its effects on lipid headgroup and raft/cytoskeletal associated proteins.

JUMPm: A Tool for Large-Scale Identification of Metabolites in Untargeted Metabolomics

Metabolomics is increasingly important for biomedical research, but large-scale metabolite identification in untargeted metabolomics is still challenging. Here, we present Jumbo Mass spectrometry-based Program of Metabolomics (JUMPm) software, a streamlined software tool for identifying potential metabolite formulas and structures in mass spectrometry. During database search, the false discovery rate is evaluated by a target-decoy strategy, where the decoys are produced by breaking the octet rule of chemistry. We illustrated the utility of JUMPm by detecting metabolite formulas and structures from liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) analyses of unlabeled and stable-isotope labeled yeast samples. We also benchmarked the performance of JUMPm by analyzing a mixed sample from a commercially available metabolite library in both hydrophilic and hydrophobic LC-MS/MS. These analyses confirm that metabolite identification can be significantly improved by estimating the element composition in formulas using stable isotope labeling, or by introducing LC retention time during a spectral library search, which are incorporated into JUMPm functions. Finally, we compared the performance of JUMPm and two commonly used programs, Compound Discoverer 3.1 and MZmine 2, with respect to putative metabolite identifications. Our results indicate that JUMPm is an effective tool for metabolite identification of both unlabeled and labeled data in untargeted metabolomics.

Integrated Proteomics and Lipidomics Reveal That the Swarming Motility of Paenibacillus polymyxa Is Characterized by Phospholipid Modification, Surfactant Deployment, and Flagellar Specialization Relative to Swimming Motility

Paenibacillus polymyxa is a Gram-positive bacterium commonly found associated with plant roots. P. polymyxa can exhibit two forms of flagellar motility: swimming in liquid culture and swarming on a surface. Here, swimming cells were compared to swarming cells using an integrated proteomic and lipidomic approach, yielding information about how lipid modifications and protein/enzyme pathways are tailored for these specific phenotypes. Observed differences in both phospholipid composition and metabolism between the two conditions suggest membrane remodeling in response to the surrounding environment. Key enzymes involved in glycerophospholipid metabolism were abundant in swimming bacteria, while enzymes associated with glycerol-3-phosphate metabolism were more abundant in swarming bacteria. Several glycoside hydrolases were either unique to or more abundant during swarming. This likely reflects the degradation of their own exopolysaccharides to both enhance swarming and supply the necessary chemical energy to compensate for increased flagellar synthesis. The observed upregulation of biosynthetic gene clusters (polyketides, lantibiotics, and surfactin) in swarming bacteria suggest the importance of signaling, antimicrobial activity, and surfactin production during this mode of motility – the latter of which is confirmed via RT-PCR.

Primary Laryngotracheal Amyloidosis Masquerading as Malignancy

Amyloidosis represents a heterogeneous group of disorders characterized by the deposition of amyloid protein in various target organs of the body. Amyloidosis is classified as systemic or local. Larynx is the common site for localized amyloid deposition and patient usually presents with hoarseness of voice. Because of the similar clinical and imaging features to malignant laryngeal mass, diagnostic confusion occurs and histopathological confirmation is usually needed. Although laryngeal tracheo-bronchial amyloidosis is rare, it should be considered among the differentials of benign laryngeal tumors.

Erratum: First Dark Matter Constraints from a SuperCDMS Single-Charge Sensitive Detector [Phys. Rev. Lett. 121, 051301 (2018)]

This corrects the article DOI: 10.1103/PhysRevLett.121.051301.

First Dark Matter Constraints from a SuperCDMS Single-Charge Sensitive Detector

We present the first limits on inelastic electron-scattering dark matter and dark photon absorption using a prototype SuperCDMS detector having a charge resolution of 0.1 electron-hole pairs (CDMS HVeV, a 0.93 g CDMS high-voltage device). These electron-recoil limits significantly improve experimental constraints on dark matter particles with masses as low as 1  MeV/c^{2}. We demonstrate a sensitivity to dark photons competitive with other leading approaches but using substantially less exposure (0.49 g d). These results demonstrate the scientific potential of phonon-mediated semiconductor detectors that are sensitive to single electronic excitations.

Results from the Super Cryogenic Dark Matter Search Experiment at Soudan

We report the result of a blinded search for weakly interacting massive particles (WIMPs) using the majority of the SuperCDMS Soudan data set. With an exposure of 1690 kg d, a single candidate event is observed, consistent with expected backgrounds. This analysis (combined with previous Ge results) sets an upper limit on the spin-independent WIMP-nucleon cross section of 1.4×10^{-44} (1.0×10^{-44})  cm^{2} at 46  GeV/c^{2}. These results set the strongest limits for WIMP-germanium-nucleus interactions for masses >12  GeV/c^{2}.

The diversity and specificity of the extracellular proteome in the cellulolytic bacterium Caldicellulosiruptor bescii is driven by the nature of the cellulosic growth substrate

BACKGROUND

Caldicellulosiruptor bescii is a thermophilic cellulolytic bacterium that efficiently deconstructs lignocellulosic biomass into sugars, which subsequently can be fermented into alcohols, such as ethanol, and other products. Deconstruction of complex substrates by C. bescii involves a myriad of highly abundant, substrate-specific extracellular solute binding proteins (ESBPs) and carbohydrate-active enzymes (CAZymes) containing carbohydrate-binding modules (CBMs). Mass spectrometry-based proteomics was employed to investigate how these substrate recognition proteins and enzymes vary as a function of lignocellulosic substrates.

RESULTS

Proteomic analysis revealed several key extracellular proteins that respond specifically to either C5 or C6 mono- and polysaccharides. These include proteins of unknown functions (PUFs), ESBPs, and CAZymes. ESBPs that were previously shown to interact more efficiently with hemicellulose and pectin were detected in high abundance during growth on complex C5 substrates, such as switchgrass and xylan. Some proteins, such as Athe_0614 and Athe_2368, whose functions are not well defined were predicted to be involved in xylan utilization and ABC transport and were significantly more abundant in complex and C5 substrates, respectively. The proteins encoded by the entire glucan degradation locus (GDL; Athe_1857, 1859, 1860, 1865, 1867, and 1866) were highly abundant under all growth conditions, particularly when C. bescii was grown on cellobiose, switchgrass, or xylan. In contrast, the glycoside hydrolases Athe_0609 (Pullulanase) and 0610, which both possess CBM20 and a starch binding domain, appear preferential to C5/complex substrate deconstruction. Some PUFs, such as Athe_2463 and 2464, were detected as highly abundant when grown on C5 substrates (xylan and xylose), also suggesting C5-substrate specificity.

CONCLUSIONS

This study reveals the protein membership of the C. bescii secretome and demonstrates its plasticity based on the complexity (mono-/disaccharides vs. polysaccharides) and type of carbon (C5 vs. C6) available to the microorganism. The presence or increased abundance of extracellular proteins as a response to specific substrates helps to further elucidate C. bescii's utilization and conversion of lignocellulosic biomass to biofuel and other valuable products. This includes improved characterization of extracellular proteins that lack discrete functional roles and are poorly/not annotated.

Comparison of cardiac and lung doses for breast cancer patients with free breathing and deep inspiration breath hold technique in 3 dimensional conformal radiotherapy - a dosimetric study

Purpose: To investigate the cardio-pulmonary doses between Deep Inspiration Breath Hold (DIBH) and Free Breathing (FB) technique in left sided breast irradiation.

Materials & Methods: DIBH CT and FB CT were acquired for 10 left sided breast patients who underwent whole breast irradiation with or without nodal irradiation. Three fields single isocenter technique were used for patients with node positive patients along with two tangential conformal fields whereas only two tangential fields were used in node negative patients. All the critical structures like lungs, heart, esophagus, thyroid, etc., were delineated in both DIBH and FB scan. Both DIBH and FB scans were fused with the Dicom origin as they were acquired with the same Dicom coordinates. Plans were created in the DIBH scan for a dose range between 50 Gy in 25 fractions. Critical structures doses were recorded from the Dose Volume Histogram for both the DIBH and FB data set for evaluation.

Results: The average mean heart dose in DIBH vs FB was 13.18 Gy vs 6.97 Gy, (p = 0.0063) significantly with DIBH as compared to FB technique. The relative reduction in average mean heart dose was 47.12%. The relative V5 reduced by 14.70% (i.e. 34.42% vs 19.72%, p = 0.0080), V10 reduced by 13.83% (i.e. 27.79 % vs 13.96%, p = 0.0073). V20 reduced by 13.19% (i.e. 24.54 % vs 11.35%, p = 0.0069), V30 reduced by 12.38% (i.e. 22.27 % vs 9.89 %, p = 0.0073) significantly with DIBH as compared to FB. The average mean left lung dose reduced marginally by 1.43 Gy (13.73 Gy vs 12.30 Gy, p = 0.4599) but insignificantly with DIBH as compared to FB. Other left lung parameters (V5, V10, V20 and V30) shows marginal decreases in DIBH plans compare to FB plans.

Conclusion: DIBH shows a substantial reduction of cardiac doses but slight and insignificant reduction of pulmonary doses as compared with FB technique. Using the simple DIBH technique, we can effectively reduce the cardiac morbidity and at the same time radiation induced lung pneumonitis is unlikely to increase.

Patterns of scrotal pain in a hospital setting

Introduction: Scrotal pain is a common urological condition. Common causes of scrotal pain are testicular torsion, epididymitis, epididymo-orchitis and occasionally due to post vasectomy pain, varicocele, testicular trauma etc. The objective of our study is to review the different disease patterns in patients presenting with scrotal pain in a tertiary care hospital.Methods: Patients presenting with scrotal pain to the out-patient clinic and the emergency department were included in the study. All patients were subjected to urinalysis and ultrasound of scrotum with color Doppler study when needed. Descriptive variables were studied and analyzed.Results: Eighty three patients were enrolled in the study during the period of one year. Age ranged from 13 to 72 years; most of the patients were less than 40 years and more than 20 years. Among this age group non-specific orchalgia was very common. Isolated epididymitis was seen in only 4 (4.81%) patients. Epididymo-orchitis was found in 16 (19.27%) patients. Torsion of testis was found in 6 patients (7.22%). The major bulk of the patients presenting with scrotal pain were nonspecific which was found in 39 (46.98%) and exact cause could not be found in them. Total of 15 (18%) patients had acute presentation.Conclusion: Management of Scrotal pain can be simple or at times organ threatening, proper diagnosis and treatment by clinical judgment and necessary investigation is very important.Journal of Society of Surgeons of NepalVol. 17, No. 2, 2014, Page: 31-34

Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

BACKGROUND

Clostridium thermocellum is capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe's growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand its metabolism on more complex, lignocellulosic substrates to identify relevant industrial bottlenecks that could undermine efficient biofuel production. To this end, we have examined a time course progression of C. thermocellum grown on switchgrass to assess the metabolic and protein changes that occur during the conversion of plant biomass to ethanol.

RESULTS

The most striking feature of the metabolome was the observed accumulation of long-chain, branched fatty acids over time, implying an adaptive restructuring of C. thermocellum's cellular membrane as the culture progresses. This is undoubtedly a response to the gradual accumulation of lignocellulose-derived inhibitory compounds as the organism deconstructs the switchgrass to access the embedded cellulose. Corroborating the metabolomics data, proteomic analysis revealed a corresponding time-dependent increase in various enzymes, including those involved in the interconversion of branched amino acids valine, leucine, and isoleucine to iso- and anteiso-fatty acid precursors. Additionally, the metabolic accumulation of hemicellulose-derived sugars and sugar alcohols concomitant with increased abundance of enzymes involved in C5 sugar metabolism/pentose phosphate pathway indicates that C. thermocellum shifts glycolytic intermediates to alternate pathways to modulate overall carbon flux in response to C5 sugar metabolites that increase during lignocellulose deconstruction.

CONCLUSIONS

Integrated omic platforms provided complementary systems biological information that highlight C. thermocellum's specific response to cytotoxic inhibitors released during the deconstruction and utilization of switchgrass. These additional viewpoints allowed us to fully realize the level to which the organism adapts to an increasingly challenging culture environment-information that will prove critical to C. thermocellum's industrial efficacy.

Microbialite response to an anthropogenic salinity gradient in Great Salt Lake, Utah

A railroad causeway across Great Salt Lake, Utah (GSL), has restricted water flow since its construction in 1959, resulting in a more saline North Arm (NA; 24%-31% salinity) and a less saline South Arm (SA; 11%-14% salinity). Here, we characterized microbial carbonates collected from the SA and the NA to evaluate the effect of increased salinity on community composition and abundance and to determine whether the communities present in the NA are still actively precipitating carbonate or if they are remnant features from prior to causeway construction. SSU rRNA gene abundances associated with the NA microbialite were three orders of magnitude lower than those associated with the SA microbialite, indicating that the latter community is more productive. SSU rRNA gene sequencing and functional gene microarray analyses indicated that SA and NA microbialite communities are distinct. In particular, abundant sequences affiliated with photoautotrophic taxa including cyanobacteria and diatoms that may drive carbonate precipitation and thus still actively form microbialites were identified in the SA microbialite; sequences affiliated with photoautotrophic taxa were in low abundance in the NA microbialite. SA and NA microbialites comprise smooth prismatic aragonite crystals. However, the SA microbialite also contained micritic aragonite, which can be formed as a result of biological activity. Collectively, these observations suggest that NA microbialites are likely to be remnant features from prior to causeway construction and indicate a strong decrease in the ability of NA microbialite communities to actively precipitate carbonate minerals. Moreover, the results suggest a role for cyanobacteria and diatoms in carbonate precipitation and microbialite formation in the SA of GSL.

Insights from 20 years of bacterial genome sequencing

Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.

Still-birth--a tragic journey: a critical analysis

Despite improvement in antenatal and intrapartum care, late intrauterine fetal death at and after 28 weeks of gestation remains a persistent and challenging problem to the obstetricians. We undertook the retrospective review of the medical records of 89 women with singleton pregnancy who gave birth to still-born infants at or more than 28 weeks gestation during the period from April 1998 to April 2007 at Nepal Medical College Teaching Hospital to know the prevalence rate and devise preventive measures for still-born infants which accounts more than 50.0% of perinatal death in Nepal. Major malformations were present in 5 (5.6%) of 89 infants including three infants with neural tube abnormalities. Pre-eclampsia preceded the stillbirth and might have been an indirect cause of stillbirth in 16 (19.0%) of 84 women whose infants had normal formations. The cause of still birth in 68 non-pre-eclamptic women was unclear in 31 (45.6%) home breech delivery with head stuck in 11 (16.0%), abruptio placentae in 5 (7.3%), intrauterine fetal growth restriction in 10 (14.7%), infection in 6 (8.8%) and cord accidents in 5 (7.3%). The causes of still births were many and varied, with large population having no obvious cause, although autopsy was not done in any case in this study. Proper monitoring of women with preeclampsia and early diagnosis and prompt delivery for women with abruption placenta might be helpful in reducing the number of stillbirths. Great advocacy with community education on importance of community focused antenatal care and increasing institutional delivery with availability of emergency obstetric care is necessary to decrease the number of stillbirths and perinatal mortality in developing countries like Nepal.

Tamoxifen for Breast Cancer

Breast cancer is one of the common cancers. Hormonal therapy along with surgery, chemotherapy, radiotherapy and targeted therapy are vital modalities for the management of breast cancer. Tamoxifen has been the most widely used hormonal therapy for more than two decades. In this article we review the benefits, dose, duration and timing of Tamoxifen therapy in patients with breast cancer. Keywords: breast cancer, hormonal therapy, tamoxifen.

Tamoxifen for breast cancer

Breast cancer is one of the common cancers. Hormonal therapy along with surgery, chemotherapy, radiotherapy and targeted therapy are vital modalities for the management of breast cancer. Tamoxifen has been the most widely used hormonal therapy for more than two decades. In this article we review the benefits, dose, duration and timing of Tamoxifen therapy in patients with breast cancer.

Live birth following treatment of post molar choriocarcinoma

A G3P(1+1) who underwent dilatation and curettage (D and C) for persistent vaginal bleeding after a month of molar evacuation, underwent successful treatment of choriocarcinoma with methotrexate and was able to have normal baby weighing 2800 gms with good Apgar score and normal placenta. This shows that a normal menstruation and uncomplicated term delivery can be expected after complete chemotherapy for gestational trophoblastic neoplasia (GTN).