The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights.

Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome-level Antarctic krill genome, whose large genome size appears to have resulted from inter-genic transposable element expansions. Our assembly reveals the molecular architecture of the Antarctic krill circadian clock and uncovers expanded gene families associated with molting and energy metabolism, providing insights into adaptations to the cold and highly seasonal Antarctic environment. Population-level genome re-sequencing from four geographical sites around the Antarctic continent reveals no clear population structure but highlights natural selection associated with environmental variables. An apparent drastic reduction in krill population size 10 mya and a subsequent rebound 100 thousand years ago coincides with climate change events. Our findings uncover the genomic basis of Antarctic krill adaptations to the Southern Ocean and provide valuable resources for future Antarctic research.

Designing efficient randstrobes for sequence similarity analyses.

MOTIVATION: Substrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis. However, k-mers are limited to exact matches between sequences leading to alternative constructs. We recently introduced a class of new constructs, strobemers, that can match across substitutions and smaller insertions and deletions. Randstrobes, the most sensitive strobemer proposed in Sahlin (Effective sequence similarity detection with strobemers. Genome Res 2021a;31:2080-94. https://doi.org/10.1101/gr.275648.121), has been used in several bioinformatics applications such as read classification, short-read mapping, and read overlap detection. Recently, we showed that the more pseudo-random the behavior of the construction (measured in entropy), the more efficient the seeds for sequence similarity analysis. The level of pseudo-randomness depends on the construction operators, but no study has investigated the efficacy. RESULTS: In this study, we introduce novel construction methods, including a Binary Search Tree-based approach that improves time complexity over previous methods. To our knowledge, we are also the first to address biases in construction and design three metrics for measuring bias. Our evaluation shows that our methods have favorable speed and sampling uniformity compared to existing approaches. Lastly, guided by our results, we change the seed construction in strobealign, a short-read mapper, and find that the results change substantially. We suggest combining the two results to improve strobealign's accuracy for the shortest reads in our evaluated datasets. Our evaluation highlights sampling biases that can occur and provides guidance on which operators to use when implementing randstrobes. AVAILABILITY AND IMPLEMENTATION: All methods and evaluation benchmarks are available in a public Github repository at https://github.com/Moein-Karami/RandStrobes. The scripts for running the strobealign analysis are found at https://github.com/NBISweden/strobealign-evaluation.

Oculocerebrorenal syndrome of Lowe (OCRL) controls leukemic T-cell survival by preventing excessive PI(4,5)P2 hydrolysis in the plasma membrane.

T-cell acute lymphoblastic leukemia (T-ALL) is one of the deadliest and most aggressive hematological malignancies, but its pathological mechanism in controlling cell survival is not fully understood. Oculocerebrorenal syndrome of Lowe is a rare X-linked recessive disorder characterized by cataracts, intellectual disability, and proteinuria. This disease has been shown to be caused by mutation of oculocerebrorenal syndrome of Lowe 1 (OCRL1; OCRL), encoding a phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] 5-phosphatase involved in regulating membrane trafficking; however, its function in cancer cells is unclear. Here, we uncovered that OCRL1 is overexpressed in T-ALL cells, and knockdown of OCRL1 results in cell death, indicating the essential role of OCRL in controlling T-ALL cell survival. We show OCRL is primarily localized in the Golgi and can translocate to plasma membrane (PM) upon ligand stimulation. We found OCRL interacts with oxysterol-binding protein-related protein 4L, which facilitates OCRL translocation from the Golgi to the PM upon cluster of differentiation 3 stimulation. Thus, OCRL represses the activity of oxysterol-binding protein-related protein 4L to prevent excessive PI(4,5)P2 hydrolysis by phosphoinositide phospholipase C ß3 and uncontrolled Ca2+ release from the endoplasmic reticulum. We propose OCRL1 deletion leads to accumulation of PI(4,5)P2 in the PM, disrupting the normal Ca2+ oscillation pattern in the cytosol and leading to mitochondrial Ca2+ overloading, ultimately causing T-ALL cell mitochondrial dysfunction and cell death. These results highlight a critical role for OCRL in maintaining moderate PI(4,5)P2 availability in T-ALL cells. Our findings also raise the possibility of targeting OCRL1 to treat T-ALL disease.

Roles of the transcriptional regulators Fts1, YlNrg1, YlTup1, and YlSsn6 in the repression of the yeast-to-filament transition in the dimorphic yeast Yarrowia lipolytica.

In dimorphic fungi, the yeast-to-filament transition critical for cell survival under nutrient starvation is controlled by both activators and repressors. However, very few filamentation repressors are known. Here we report that, in the dimorphic yeast Yarrowia lipolytica, the conserved transcription factor YlNrg1 plays a minor role whereas Fts1, a newly identified Zn(II)2 Cys6 zinc cluster transcription factor, plays a key role in filamentation repression. FTS1 deletion caused hyperfilamentation whereas Fts1 overexpression drastically reduced filamentation. The expression of FTS1 is downregulated substantially during the yeast-to-filament transition. Transcriptome sequencing revealed that Fts1 represses 401 genes, including the filamentation-activating transcription factor genes MHY1, YlAZF1, and YlWOR4 and key cell wall protein genes. Tup1-Ssn6, a general transcriptional corepressor, is involved in the repression of many cellular functions in fungi. We show that both YlTup1 and YlSsn6 strongly repress filamentation in Y. lipolytica. YlTup1 and YlSsn6 together repress 1383 genes, including a large number of transcription factor and cell wall protein genes, which overlap substantially with Fts1-repressed genes. Fts1 interacts with both YlTup1 and YlSsn6, and LexA-Fts1 fusion represses a lexAop-promoter-lacZ reporter in a Tup1-Ssn6-dependent manner. Our findings suggest that Fts1 functions as a transcriptional repressor, directing the repression of target genes through the Tup1-Ssn6 corepressor.

ORP4L is a prerequisite for the induction of T-cell leukemogenesis associated with human T-cell leukemia virus 1.

Human T-cell leukemia virus 1 (HTLV-1) causes adult T-cell leukemia (ATL), but the mechanism underlying its initiation remains elusive. In this study, ORP4L was expressed in ATL cells but not in normal T-cells. ORP4L ablation completely blocked T-cell leukemogenesis induced by the HTLV-1 oncoprotein Tax in mice, whereas engineering ORP4L expression in T-cells resulted in T-cell leukemia in mice, suggesting the oncogenic properties and prerequisite of ORP4L promote the initiation of T-cell leukemogenesis. For molecular insight, we found that loss of miR-31 caused by HTLV-1 induced ORP4L expression in T-cells. ORP4L interacts with PI3Kδ to promote PI(3,4,5)P3 generation, contributing to AKT hyperactivation; NF-κB-dependent, p53 inactivation-induced pro-oncogene expression; and T-cell leukemogenesis. Consistently, ORP4L ablation eliminates human ATL cells in patient-derived xenograft ATL models. These results reveal a plausible mechanism of T-cell deterioration by HTLV-1 that can be therapeutically targeted.

PSMC5 regulates microglial polarization and activation in LPS-induced cognitive deficits and motor impairments by interacting with TLR4.

Luteolin is a flavonoid found in high concentrations in celery and green pepper, and acts as a neuroprotectant. PSMC5 (proteasome 26S subunit, ATPase 5) protein levels were reduced after luteolin stimulation in activated microglia. We aimed to determine whether regulating PSMC5 expression could inhibit neuroinflammation, and investigate the underlying mechanisms.BV2 microglia were transfected with siRNA PSMC5 before the addition of LPS (lipopolysaccharide, 1.0 µg/ml) for 24 h in serum free DMEM. A mouse model of LPS-induced cognitive and motor impairment was established to evaluate the neuroprotective effects of shRNA PSMC5. Intracerebroventricular administration of shRNA PSMC5 was commenced 7 days prior to i.p. injection of LPS (750 µg/kg). Treatments and behavioral experiments were performed once daily for 7 consecutive days. Behavioral tests and pathological/biochemical assays were performed to evaluate LPS-induced hippocampal damage. Molecular dynamics simulation was used to confirm the interaction between PSMC5 and TLR4 (Toll-like receptor 4) in LPS-stimulated BV2 microglia. SiRNA PSMC5 inhibited BV2 microglial activation, and suppressed the release of inflammatory factors (IL-1ß, COX-2, PGE2, TNF-α, and iNOS) upon after LPS stimulation in BV2 microglia. LPS increased IκB-α and p65 phosphorylation, which was attenuated by siRNA PSMC5. Behavioral tests and pathological/biochemical assays showed that shRNA PSMC5 attenuated LPS-induced cognitive and motor impairments, and restored synaptic ultrastructure and protein levels in mice. ShRNA PSMC5 reduced pro-inflammatory cytokine (TNF-α, IL-1ß, PGE2, and NO) levels in the serum and brain, and relevant protein factors (iNOS and COX-2) in the brain. Furthermore, shRNA PSMC5 upregulated the anti-inflammatory mediators interleukin IL-4 and IL-10 in the serum and brain, and promoted a pro-inflammation-to-anti-inflammation phenotype shift in microglial polarization. Mechanistically, shRNA PSMC5 significantly alleviated LPS-induced TLR4 expression. The polarization of LPS-induced microglial pro-inflammation phenotype was abolished by TLR4 inhibitor and in the TLR-4-/- mouse, as in shRNA PSMC5 treatment. PSMC5 interacted with TLR4 via the amino sites Glu284, Met139, Leu127, and Phe283. PSMC5 site mutations attenuated neuroinflammation and reduced pro-inflammatory factors by reducing TLR4-related effects, thereby reducing TLR4-mediated MyD88 (myeloid differentiation factor 88)-dependent activation of NF-κB. PSMC5 could be an important therapeutic target for treatment of neurodegenerative diseases involving neuroinflammation-associated cognitive deficits and motor impairments induced by microglial activation.

Homogenizing Zn Deposition in Hierarchical Nanoporous Cu for a High-Current, High Areal-Capacity Zn Flow Battery.

A Zn anode can offset the low energy density of a flow battery for a balanced approach toward electricity storage. Yet, when targeting inexpensive, long-duration storage, the battery demands a thick Zn deposit in a porous framework, whose heterogeneity triggers frequent dendrite formation and jeopardizes the stability of the battery. Here, Cu foam is transferred into a hierarchical nanoporous electrode to homogenize the deposition. It begins with alloying the foam with Zn to form Cu5 Zn8 , whose depth is controlled to retain the large pores for a hydraulic permeability ≈10-11  m2 . Dealloying follows to create nanoscale pores and abundant fine pits below 10 nm, where Zn can nucleate preferentially due to the Gibbs-Thomson effect, as supported by a density functional theory simulation. Morphological evolution monitored by in situ microscopy confirms uniform Zn deposition. The electrode delivers 200 h of stable cycles in a Zn-I2 flow battery at 60 mAh cm-2 and 60 mA cm-2 , performance that meets practical demands.

Salt-Assisted Selective Growth of H-phase Monolayer VSe2 with Apparent Hole Transport Behavior.

Vanadium diselenide (VSe2) exhibits versatile electronic and magnetic properties in the trigonal prismatic (H-) and octahedral (T-) phases. Compared to the metallic T-phase, the H-phase with a tunable semiconductor property is predicted to be a ferrovalley material with spontaneous valley polarization. Herein we report an epitaxial growth of the monolayer 2D VSe2 on a mica substrate via the chemical vapor deposition (CVD) method by introducing salt in the precursor. Our first-principles calculations suggest that the monolayer H-phase VSe2 with a large lateral size is thermodynamically favorable. The honeycomb-like structure and the broken symmetry are directly observed by spherical aberration-corrected scanning transmission electron microscopy (STEM) and confirmed by giant second harmonic generation (SHG) intensity. The p-type transport behavior is further evidenced by the temperature-dependent resistance and field-effect device study. The present work introduces a new phase-stable 2D transition metal dichalcogenide, opening the prospect of novel electronic and spintronics device design.

Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios.

MOTIVATION: Achieving a near complete understanding of how the genome of an individual affects the phenotypes of that individual requires deciphering the order of variations along homologous chromosomes in species with diploid genomes. However, true diploid assembly of long-range haplotypes remains challenging. RESULTS: To address this, we have developed Haplotype-resolved Assembly for Synthetic long reads using a Trio-binning strategy, or HAST, which uses parental information to classify reads into maternal or paternal. Once sorted, these reads are used to independently de novo assemble the parent-specific haplotypes. We applied HAST to cobarcoded second-generation sequencing data from an Asian individual, resulting in a haplotype assembly covering 94.7% of the reference genome with a scaffold N50 longer than 11 Mb. The high haplotyping precision (∼99.7%) and recall (∼95.9%) represents a substantial improvement over the commonly used tool for assembling cobarcoded reads (Supernova), and is comparable to a trio-binning-based third generation long-read-based assembly method (TrioCanu) but with a significantly higher single-base accuracy [up to 99.99997% (Q65)]. This makes HAST a superior tool for accurate haplotyping and future haplotype-based studies. AVAILABILITY AND IMPLEMENTATION: The code of the analysis is available at https://github.com/BGI-Qingdao/HAST. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Tailored Linker Defects in UiO-67 with High Ligand-to-Metal Charge Transfer toward Efficient Photoreduction of CO2.

Defect engineering can be used as a potential tool to activate metal-organic frameworks by regulating the pore structure, electronic properties, and catalytic activity. Herein, linker defects were effectively controlled by adjusting the amount of formic acid, and UiO-67 with different CO2 reduction capabilities was obtained. Among them, UiO-67-200 had the highest ability to selectively reduce CO2 to CO (12.29 µmol g-1 h-1). On the one hand, the results based on time-resolved photoluminescence decay curves and photochemical experiments revealed that UiO-67-200 had the highest charge separation efficiency. On the other hand, the linker defects affected the band structure of UiO-67 by changing the lowest unoccupied molecular orbital (LUMO) based on the density functional theory and UV-vis spectra. Hence, the proper linker defects enhanced the ligand-to-metal charge transfer process by promoting the transfer of electrons between the highest occupied molecular orbital and LUMO. Additionally, in situ Fourier transform infrared spectra and 13CO2 labeling experiments also indicated that COOH* was an important intermediate for CO formation and that CO originated from the photoreduction of CO2.

Construction of a ZnIn2S4/Au/CdS Tandem Heterojunction for Highly Efficient CO2 Photoreduction.

Photocatalytic CO2 reduction technology is of great importance to alleviate energy crisis and environmental pollution; however, it remains a serious challenge due to the fast recombination of carriers. In this study, we report a three-dimensional structure of a ZnIn2S4/Au/CdS composite photocatalyst for the CO2 reduction reaction, where Au nanoparticles (NPs) are evenly anchored on the surface of ZnIn2S4 by photodeposition and Au NPs are wrapped around by CdS. In ZnIn2S4/Au/CdS composite photocatalysts, Au NPs act as a bridge to construct a "semiconductor-metal-semiconductor" tandem electron transfer mechanism (ZnIn2S4 → Au → CdS) heterojunction, which greatly promotes the transfer of photogenerated electrons. It is worth noting that Au NPs, as a local surface plasmon resonance (LSPR) effect excited source to generate excited-state electrons, further improve the photoreduction CO2 activity. Under UV-vis light irradiation, the CO yield of ZnIn2S4/Au/CdS can reach 63.07 µmol·g-1·h-1, which is higher than that of 6.37 µmol·g-1·h-1 for pure ZnIn2S4, 0.93 µmol·g-1·h-1 for CdS, 8.9 µmol·g-1·h-1 for ZnIn2S4/CdS, 31.04 µmol·g-1·h-1 for ZnIn2S4/Au, and 5.37 µmol·g-1·h-1 for CdS/Au. In addition, the ternary ZnIn2S4/Au/CdS composite photocatalyst has good cyclic stability. This study broadens the idea of designing photocatalysts with good carrier separation efficiency.

OSBP-Related Protein 5L Maintains Intracellular IP3/Ca2+ Signaling and Proliferation in T Cells by Facilitating PIP2 Hydrolysis.

Phospholipase C (PLC) isoforms play central roles in signaling cascades by cleaving PIP2 into the second messengers IP3 and DAG. In this study, to our knowledge, we uncover that ORP5L interacts physically with PLCγ1 in T cells, extracts PIP2 from the plasma membrane via its ORD domain (OSBP-related domain), presents it to PLCγ1 (enabling IP3 generation), and eventually maintains intracellular Ca2+ homeostasis. Through this mechanism, ORP5L promotes T cell proliferation in a Ca2+-activated NFAT2-dependent manner. To our knowledge, our study uncovers a new key function of ORP5L as a critical cofactor for PLCγ1 catalysis and its crucial role in human T cell proliferation.

SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme.

BACKGROUND: Synthetic long reads (SLR) with long-range co-barcoding information are now widely applied in genomics research. Although several tools have been developed for each specific SLR technique, a robust standalone scaffolder with high efficiency is warranted for hybrid genome assembly. RESULTS: In this work, we developed a standalone scaffolding tool, SLR-superscaffolder, to link together contigs in draft assemblies using co-barcoding and paired-end read information. Our top-to-bottom scheme first builds a global scaffold graph based on Jaccard Similarity to determine the order and orientation of contigs, and then locally improves the scaffolds with the aid of paired-end information. We also exploited a screening algorithm to reduce the negative effect of misassembled contigs in the input assembly. We applied SLR-superscaffolder to a human single tube long fragment read sequencing dataset and increased the scaffold NG50 of its corresponding draft assembly 1349 fold. Moreover, benchmarking on different input contigs showed that this approach overall outperformed existing SLR scaffolders, providing longer contiguity and fewer misassemblies, especially for short contigs assembled by next-generation sequencing data. The open-source code of SLR-superscaffolder is available at https://github.com/BGI-Qingdao/SLR-superscaffolder . CONCLUSIONS: SLR-superscaffolder can dramatically improve the contiguity of a draft assembly by integrating a hybrid assembly strategy.

Phomaligols F-I, polyoxygenated cyclohexenone derivatives from marine-derived fungus Aspergillus flavus BB1.

By tracing the 13C NMR resonances for carbonyls and enols, four new oxidized phomaligol derivatives, phomaligols F-I (1-4), along with seven known compounds (5-11) were isolated from the culture of the fungus Aspergillus flavus BB1 isolated from the marine shellfish Meretrix meretrix collected on Hailing Island, Yangjiang, China. The chemical structures and the absolute configurations of the new compounds were elucidated by MS, NMR, ECD, optical rotation, and 13C NMR calculations. Compounds 1 and 2 represent the first examples of phomaligol derivatives that contain an unusual bicyclic skeleton. All isolated compounds were tested for their cytotoxic activity. Among them, sporogen-AO 1 (8) showed potent inhibitory activity against the cancer cell lines A549, H1299, SK-BR-3, and HCT116 with IC50 values of 0.13, 0.78, 1.19, and 1.32 µM, respectively. Phomaligol G (2) displayed cytotoxic activity against the A549 and H1299 cell lines with IC50 values of 46.86 and 51.87 µM respectively. Additionally, phomaligol H (3) demonstrated cytotoxic activity against the A549 cell line with an IC50 value of 65.53 µM. Mechanistic studies of compound 8 showed that it induced apoptosis of HCT116 cells in a dose-dependent manner.

Evaluating the Impact of Four Major Nutrients on Gut Microbial Metabolism by a Targeted Metabolomics Approach.

Gut microbiome plays fundamental roles in host physiology, and gut microbial metabolism is important to the host-microbiome homeostasis. As major contributors to gut microbial metabolism, the medium nutritional components are essential to in vitro gut microbiome growths, and four nutrients, namely, inorganic salts, bile salts, short-chain fatty acids (SCFAs), and mucin, have gained particular attention because of their significant variation found in different growth environments and their ability to modulate the gut microbial population and functions. However, a systematic study is lacking to evaluate the effects of these four nutrients on the gut microbiome in terms of their impact on the microbial metabolic profiles. To fill the gap of the knowledge, we applied mass-spectrometry-based targeted metabolomics approach to study the regulation effects of these four medium components on in vitro-cultured gut microbiota. Our results show that inorganic salts and mucin had the greatest impacts on the gut microbiome metabolic profile compared to the other components studied, with gut microbial cultures grown with low-concentration inorganic salts and mucin-supplemented medium demonstrating greater numbers of metabolites detected. We also applied metabolic pathway impact analysis, which revealed several significantly impacted metabolic pathways during the comparison of different medium supplements, which could further assist our understanding of the overall impacts of certain critical nutrients on gut microbial metabolism. In summary, this pilot study can serve as a first attempt to evaluate the individual nutritional component in their contribution to gut microbial metabolic functions.

ORP4L couples IP3 to ITPR1 in control of endoplasmic reticulum calcium release.

Oxysterol-binding protein-related protein (ORP) 4L acts as a scaffold protein assembling CD3-ε, G-αq/11, and PLC-ß3 into a complex at the plasma membrane that mediates inositol (1,4,5)-trisphosphate (IP3)-induced endoplasmic reticulum (ER) Ca2+ release and oxidative phosphorylation in T-cell acute lymphoblastic leukemia cells. Here, we offer new evidence that ORP4L interacts with the carboxyl terminus of the IP3 receptor type 1 (ITPR1) in Jurkat T cells. ORP4L enables IP3 binding to ITPR1; a truncated construct that lacks the ITPR1-binding region retains the ability to increase IP3 production but fails to mediate IP3 and ITPR1 binding. In association with this ability of ORP4L, it enhances Ca2+ release from the ER and subsequent cytosolic and mitochondrial parallel Ca2+ spike oscillations that stimulate mitochondrial energetics and thus maintains cell survival. These data support a novel model in which ORP4L is a cofactor of ITPR1, which increases ITPR1 sensitivity to IP3 and enables ER Ca2+ release.-Cao, X., Chen, J., Li, D., Xie, P., Xu, M., Lin, W., Li, S., Pan, G., Tang, Y., Xu, J., Olkkonen, V. M., Yan, D., Zhong, W. ORP4L couples IP3 to ITPR1 in control of endoplasmic reticulum calcium release.

Monitoring the Diversity and Metabolic Shift of Gut Microbes during Green Tea Feeding in an In Vitro Human Colonic Model.

The human gut microbiome plays an important role in human health, and many factors such as environment, host genetics, age, and diet have been found to influence the microbial composition. Tea, as one of the widely consumed beverages, has been known for centuries to have antioxidant, anti-inflammatory, and anticancer effects. To investigate the impact of green tea polyphenol on the diversity and metabolic functions of human gut microbes, we applied an in vitro human colonic model (HCM) in this study to mimic a short-term green tea ingestion event and investigate its related changes to gut microbial composition and their metabolic functions. The pH, temperature, anaerobic environment, feeding nutrient, and time point in each compartment of the HCM were tightly controlled to simulate the intestinal system, and pooled human fecal samples of two healthy volunteers were used for the colon microbiota inoculation within the colonic model. By adding green tea extract (GTE) to the growth medium, the detailed impacts of GTE polyphenol on gut microbial population/diversity, gut microbial metabolites, metabolic pathways, and their associations were investigated via 16 S ribosomal DNA sequencing and liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) analyses. Our data indicated that the treatment of green tea extract applied to gut microbiota can induce a significant decrease in the abundance of Firmicutes and a slight decrease in the abundance of Bacteroidetes, and these changes result in a decreased Firmicutes/Bacteroidetes ratio, which can be an effective indicator for successful GTE intervention, which may generate beneficial health effect to human. Meanwhile, the relative abundances of many detected bacteria genera among three HCM vessels changed through the GTE intervention. The overall effects of GTE on gut microbial beta-diversity were observed by multivariate statistical analyses, and the differences in metabolic profiles from different GTE treatment stages were detected. Moreover, we identified several associations between microbial population and microbial metabolites, which may assist us in establishing new hypotheses for future related studies. In summary, our study suggested that the microbial compositional changes induced by GTE also changed their metabolic functions, and consequentially, may change the host metabolism and impact human health.

Headspace Gas Monitoring of Gut Microbiota Using Targeted and Globally Optimized Targeted Secondary Electrospray Ionization Mass Spectrometry.

This study aimed to develop and incorporate a secondary electrospray ionization (SESI) setup in combination with both targeted tandem mass spectrometry (MS/MS) and a hybrid metabolomics technique, globally optimized targeted mass spectrometry (GOT-MS), to sensitively detect volatile metabolites from the headspace of in vitro gut microbial culture in a human colonic model (HCM). Two SESI-tandem mass spectrometry panels with a comparable number of targeted metabolites/features (77 compounds in the targeted SESI-MS/MS panel and 75 features in the SESI-GOT-MS/MS panel) were established. The analytical performance of the SESI-GOT-MS/MS method, as well as its biological capability, were examined and compared with the targeted SESI-MS/MS method. As a result, the SESI-GOT-MS/MS method detected a similar number of metabolic features with good reproducibility (coefficient of variation <10%) compared to the targeted SESI-MS/MS method. Both methods showed a comparable ability to differentiate the gut microbial culture with or without the addition of green tea extract (GTE) to a HCM. The results from analysis of variance (ANOVA) showed that similar numbers of compounds from targeted SESI-MS/MS and metabolic features from SESI-GOT-MS/MS have significant differences when comparing samples collected from different HCM treatment stages. Partial least-squares discriminant analysis (PLS-DA) indicated that both methods could clearly differentiate the stages of GTE treatment. In summary, we demonstrated that SESI-MS/MS in combination with either targeted or GOT approaches can be a useful tool for monitoring gut microbial metabolism and their response to perturbations.

An APE1 inhibitor reveals critical roles of the redox function of APE1 in KSHV replication and pathogenic phenotypes.

APE1 is a multifunctional protein with a DNA base excision repair function in its C-terminal domain and a redox activity in its N-terminal domain. The redox function of APE1 converts certain transcription factors from inactive oxidized to active reduced forms. Given that among the APE1-regulated transcription factors many are critical for KSHV replication and pathogenesis, we investigated whether inhibition of APE1 redox function blocks KSHV replication and Kaposi's sarcoma (KS) phenotypes. With an shRNA-mediated silencing approach and a known APE-1 redox inhibitor, we demonstrated that APE1 redox function is indeed required for KSHV replication as well as KSHV-induced angiogenesis, validating APE1 as a therapeutic target for KSHV-associated diseases. A ligand-based virtual screening yielded a small molecular compound, C10, which is proven to bind to APE1. C10 exhibits low cytotoxicity but efficiently inhibits KSHV lytic replication (EC50 of 0.16 µM and selective index of 165) and KSHV-mediated pathogenic phenotypes including cytokine production, angiogenesis and cell invasion, demonstrating its potential to become an effective drug for treatment of KS.

Comparative Metabolomics Elucidates Postprandial Metabolic Modifications in Plasma of Obese Individuals with Metabolic Syndrome.

Although higher intakes of dairy milk are associated with a lower risk of metabolic syndrome (MetS), the underlying protective mechanism remains unclear. This study investigated the dynamic metabolic profile shift following the ingestion of low-fat milk or an isocaloric volume of rice milk in obese individuals with metabolic syndrome (MetS). In a randomized, double-blind, crossover study, postprandial plasma samples ( n = 266) were collected from 19 MetS participants. Plasma samples were analyzed by a targeted metabolomics platform which specifically detects 117 metabolites from 25 metabolic pathways. The comprehensive time-course metabolic profiling in MetS participants indicated that the postprandial metabolic profiles distinguish low-fat milk and rice milk consumption in a time-dependent manner. Metabolic biomarkers, such as orotate, leucine/isoleucine and adenine, showed significantly different trends in the two test beverages. Bayesian statistics identified 12 metabolites associated with clinical characteristics of postprandial vascular endothelial function, such as flow-mediated dilation (FMD), postprandial plasma markers of oxidative stress and NO status. Furthermore, metabolic pathway analysis based on these metabolite data indicated the potential utility of metabolomics to provide mechanistic insights of dietary interventions to regulate postprandial metabolic excursions.