Biology subjects

Lin, H.-H.

Publications and source records attributed to Lin, H.-H..

18 recordsLinked to original sources

bioRxiv2026

A comparison of scalable approaches for the pairwise analysis of large pathogen genomic and spatial datasets: an application to studying Mycobacterium tuberculosis transmission

Pairwise analysis of genomic and spatial data offers opportunities to identify and estimate the associations between covariates and the transmission of pathogens between individuals. However, such pairwise analyses are computationally intensive, and may not be feasible to conduct given the high dyad count in even moderately sized datasets. Here we compare two approaches to increase the efficiency of pairwise analysis for large datasets. We quantify and compare the performance of divide-and-conquer Bayesian model fitting and pairwise case-control approaches for estimating associations between individual- and pair-level covariates and shared membership in a transmission cluster. We utilize a large dataset (n=4,154) of spatially-referenced, genomically-sequenced Mycobacterium tuberculosis isolates collected from a single city for this analysis. We find that the case-control approach produces unbiased estimates of effect sizes with expected credible interval coverage and is more robust than the divide-and-conquer method when effect sizes are large. Thus, we recommend using the case-control approach with at least three controls per case to downscale datasets for pairwise analysis when analysis of the entire dataset is not possible. This approach mitigates the computational challenges of pairwise Bayesian modeling on datasets that require significant computational resources while maintaining desired inferential properties. Author SummaryPairwise analyses of large datasets to study pathogen transmission are computationally demanding because they typically require simultaneous analysis of each possible pair of individuals in a dataset; as datasets become larger these analyses often are not feasible to conduct even with access to high-performance computing resources. In this work, we compare a case-control approach and divide-and-conquer approaches for more efficient pairwise analysis of large datasets. Using a large dataset of Mycobacterium tuberculosis isolates including genetic and spatial data, we investigate the performance of each method for estimating the associations between host covariates and genetic clustering of isolates. We find that the case-control approach is generally preferred over methods which first divide the data into subsets and then combine results. While additional extensions of these analyses are needed to test the generality of these findings to other data settings, this work provides a practical way forward for the pairwise analysis of large datasets to study pathogen transmission.

microbiology↗

bioRxiv2026

An N-degron proteolytic pathway modulates recipient susceptibility to T6SS DNase effectors

The type VI secretion system (T6SS) is a contractile nanoweapon widely employed by Gram-negative bacteria to gain competitive advantages by injecting effector proteins into recipient cells. Although the biochemical activities of T6SS effectors have been well characterized, how recipient factors modulate effector toxicity remains poorly understood. Using Agrobacterium C58 as a model, previous work identified the Escherichia coli ClpAP protease as a recipient susceptibility (RS) factor that enhances T6SS-mediated interbacterial competition. Agrobacterium C58 deploys two DNase effectors, Tde1 and Tde2, as the major antibacterial weapon. Here, we demonstrate that the recipient ClpAP protease and its adaptor ClpS enhanced C58-mediated interbacterial competition in a Tde2-dependent manner in both intra- and interspecies competition. Ectopic expression of Tde2 in E. coli caused growth inhibition and DNA cleavage in the presence of a functional ClpAPS protease complex, but not in any of the clpP, clpA or clpS mutants. Notably, Tde2 accumulated in these mutants but not in wild-type cells, whereas a catalytic variant accumulated regardless of ClpAPS status, suggesting that Tde2 is not directly degraded by ClpAPS. Instead, Tde2 depends on ClpAPS for full toxicity, likely through degradation of inhibitory N-degron substrate(s). Affinity purification of His-tagged Tde2 in a clpP mutant background, followed by mass spectrometry, identified eight N-degron substrate candidates. Tde2-mediated interbacterial competition was significantly reduced by overexpression of three candidates. Among them, the Tde2 DNase domain directly associated with guanosine 5-monophosphate reductase GuaC, supporting a model in which Tde2 toxicity is blocked by binding of GuaC. Collectively, our findings reveal an unanticipated layer of recipient-mediated regulation in T6SS competition and highlight proteolytic control of inhibitory substrates as a determinant of bacterial susceptibility during interbacterial conflict.

microbiology↗

bioRxiv2026

Integrated microbiome and metabolomic profiling reveals alterations across the adenoma-colorectal cancer sequence

The incidence of colorectal cancer (CRC) has been increasing in Taiwan and is associated with multiple risk factors, including aging, obesity, and dietary habits. Increasing evidence suggests that gut microbiota dysbiosis contributes to CRC development. This study aimed to characterize microbial and metabolic alterations across premalignant and malignant colorectal lesions and to identify potential microbiome-associated biomarkers. Individuals undergoing colonoscopy for screening or surveillance at Taipei Veterans General Hospital were enrolled. Gut microbial composition was analyzed using full-length 16S rRNA gene sequencing to achieve high-resolution taxonomic profiling. Predicted functional pathways were inferred from microbial communities, and targeted metabolomic profiling was performed to evaluate microbial metabolic outputs. A total of 122 individuals were included, comprising 62 healthy controls, 15 adenoma cases, and 45 CRC cases. Progressive shifts in microbial composition and predicted functional pathways were observed along the adenoma-carcinoma sequence. Several bacterial taxa, including Phocaeicola dorei, Anaerotignum faecicola, Negativibacillus massiliensis, and Dysosmobacter segnis, were enriched in CRC. At the functional level, CRC samples showed enrichment of pathways associated with energy metabolism and bacterial stress responses. Metabolomic analysis further revealed increased levels of tauro-ursocholanic acid in CRC samples, whereas short-chain fatty acids (SCFAs) were reduced compared with controls. Integrative analysis combining full-length 16S sequencing, functional pathway prediction, and metabolomic profiling revealed coordinated microbial and metabolic alterations across the adenoma-carcinoma sequence. These findings provide insight into microbiome-associated processes in colorectal tumorigenesis and suggest potential microbial and metabolic biomarkers for CRC. ImportanceColorectal cancer (CRC) develops through a adenoma-carcinoma sequence, yet the microbial and metabolic alterations accompanying this progression remain incompletely understood. In this study, we integrated full-length 16S rRNA gene sequencing with metabolomic profiling to characterize taxonomic, functional, and metabolic changes across healthy controls, adenoma, and CRC. Our results reveal synchronized shifts in specific microbial taxa, predicted metabolic pathways, and fecal metabolites along the adenoma-carcinoma sequence. Several bacterial species, including Phocaeicola dorei, Anaerotignum faecicola, and Dysosmobacter segnis, increased in CRC, whereas short-chain fatty acids decreased progressively from controls to adenoma and CRC. Functional pathway analysis further indicated alterations in microbial fermentation, amino acid metabolism, and energy-related pathways. Together, these findings highlight the potential role of microbiome-associated metabolic changes in colorectal tumorigenesis and suggest candidate microbial and metabolic markers that may aid in understanding disease development and improving risk stratification.

microbiology↗

bioRxiv2025

A topologically conserved unstructured region helps positioning the evolutionarily conserved Prp40 WW domains to promote non-canonical intron splicing

Newly transcribed introns are immediately identified by early splicing factors that recognize the intron 5 splice site (5SS) and branch site (BS). In the budding yeast, these critical splice-site sequences are generally constrained, whereas degeneracy is the rule in higher eukaryotes. Yet, [~]40% of the yeast introns do diverge, to a certain degree, from the canonical sequences. Exactly how these non-canonical introns are recognized and spliced remains unknown. Here we show that the conserved Prp40 WW domains promote non-canonical intron splicing by enhancing stable U1 snRNP and BBP recruitments. AlphaFold predicts a topologically conserved unstructured region between Prp40 WW and FF domains. Alignment of the AlphaFold Prp40 structure with published U1 snRNP structure positions WW domains adjacent to 5SS and Luc7, which is known to be critical for 5SS recognition. Indeed, deletion of this unstructured region negatively impacts on splicing of the non-canonical 5SS introns. Taken together, our results suggest that the conserved WW domains may have evolved to deal with the highly degenerate 5SS and BS sequences in higher eukaryotes, so as to accommodate increased splicing complexity. HighlightsO_LIThe evolutionarily conserved Prp40 WW domains promote splicing of introns harboring non-canonical 5 splice site or branch site. C_LIO_LIPrp40 WW domains enhance stable U1 snRNP and BBP recruitments to nascent transcripts containing non-canonical splice sites. C_LIO_LIA topologically conserved unstructured region between WW and FF domains helps to position Prp40 WW domains close to the 5 splice site. C_LIO_LIThe N-terminal WW domain sterically hinders conformational rearrangements required for efficient release of a BBP variant during spliceosome assembly. C_LIO_LIA reporter assay identified 13 non-canonical introns whose splicing, under various environmental conditions, depend on Prp40 WW domains. C_LI

biochemistry↗

bioRxiv2025

Engineered lignin composition in Brachypodium distachyon modulates the root-associated microbiome

Lignin is a key component of the plant cell wall and a barrier to microbial interaction and biomass digestibility. While lignin biosynthesis has been engineered in grasses to reduce recalcitrance for agroindustrial applications, the consequences for root-associated microbial communities remain poorly understood. Here, we show in the model grass species Brachypodium distachyon that genetic modification of lignin biosynthetic genes, particularly caffeic acid O-methyltransferase (COMT), alters root lignin syringyl/guaiacyl (S/G) ratios, root exudate composition, and significantly reshapes the rhizosphere microbiome. Using a synthetic microbial community (SYNCOM) in controlled fabricated ecosystem (EcoFAB) environments, we observed a distinct reduction in Burkholderia colonization and enrichment of Rhodococcus in COMT mutant lines. LC-MS/MS profiling of root exudates revealed increased p-coumaric acid, caffeic acid and hydroxycinnamic acid amides in these lines, potentially linked to both metabolic remodeling and plant stress responses. These findings demonstrate that altering lignin composition can have profound, genotype-specific impacts on rhizosphere microbiome assembly, with implications for plant-microbe interactions, nutrient cycling, and biomass conversion strategies in bioenergy crops.

plant biology↗

bioRxiv2024

Dynamic positioning of a TFIIE-related winged-helix domain in RNA polymerase elongation complex III underpins its multi-functionality

The tandem-winged-helix (tWH) domain of RNA polymerase III (Pol III) Rpc34 subunit is a multi-function hub in Pol III apparatus while the structure basis remains elusive. To probe tWH in Pol III elongation complex (EC), we engineered an azide-bearing unnatural amino acid into tWH and implemented a thiol-capping scheme to enable strain- promoted click reaction for selective dye labeling to suit single-molecule Forster resonance energy transfer (smFRET). Our discrete smFRET results and nano-positioning analysis reveal multiple docking sites of Rpc34 WH2 on Pol III EC with characteristic dwell-times, reflecting promiscuous and weak interactions underpinning tWHs multi-functionality. The docking sites include one overlapping with that during initiation and others on transcription bubble and downstream DNA, previously unreported. This work provides mechanistic insights into Pol III transcription re-initiation and elongation, with useful bio-orthogonal strategies for studying structural dynamics of large native protein complexes.

biophysics↗

bioRxiv2024

Assessing horizontal gene transfer in the rhizosphere of Brachypodium distachyon using fabricated ecosystems (EcoFABs)

Horizontal gene transfer (HGT) is a major process by which genes are transferred within microbes in the rhizosphere. However, examining HGT remains challenging due to the complexity of mimicking conditions within the rhizosphere. Fabricated ecosystems (EcoFABs) have been used to investigate several complex processes in plant associated environments. Here we show that EcoFABs are efficient tools to examine and measure HGT frequency in the rhizosphere. We provided the first demonstration of gene transfer via triparental conjugation system in the Brachypodium distachyon rhizosphere in the EcoFABs using Pseudomonas putida KT2440 as both donor and recipient bacterial strain with the donor having the mobilizable and non-self-transmissible plasmid. We also observed that the frequency of conjugal plasmid transfer in the rhizosphere is potentially dependent on the plant developmental stage, and composition and amount of root exudates. The frequency of conjugation also increased with higher numbers of donor cells. We have also shown the transfer of plasmid from P. putida to another B. distachyon root colonizer, Burkholderia sp. showing the possibility of HGT within a rhizosphere microbial community. Environmental stresses also influence the rate of HGT in the rhizosphere between species and genera. Additionally, we observed transfer of a non-self transmissible donor plasmid without the helper strain on agar plates when supplemented with environmental stressors, indicating reduced dependency on the helper plasmid under certain conditions. This study provides a robust workflow to evaluate conjugal transfer of engineered plasmids in the rhizosphere when such plasmids are introduced in a field or plant associated environment. ImportanceWe report the use of EcoFABs to investigate the HGT process in a rhizosphere environment. It highlights the potential of EcoFABs in recapitulating the dynamic rhizosphere conditions as well as their versatility in studying plant-microbial interactions. This study also emphasizes the importance of studying the parameters impacting the HGT frequency. Several factors such as plant developmental stages, nutrient conditions, number of donor cells and environmental stresses influence gene transfer within the rhizosphere microbial community. This study paves the way for future investigations into understanding the fate and movement of engineered plasmids in a field environment.

microbiology↗

bioRxiv2023

Impact of inoculation practices on microbiota assembly and community stability in a fabricated ecosystem

Studying plant-microbe-soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacteria inoculation practices and plant harvesting time points affect the reproducibility of a microbial synthetic community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices: seed inoculation, transplant inoculation, and seedling inoculation; and two harvesting points: early (14-day-old plants) and late (21 days post-inoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community only when harvesting at an early time point but not at the late stage. As the SynCom showed a persistent association with B. distachyon at 21 days post-inoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacteria inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB-B. distachyon-SynCom fabricated ecosystem and recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems.

plant biology↗

bioRxiv2022

RE2DC: a robust and efficient 2D classifier with visualization for processing massive and heterogeneous cryo-EM data

Single-particle cryo-electron microscopy (cryo-EM) increasingly generates millions of particle images, yet two-dimensional (2D) classification remains a major bottleneck because existing approaches balance computational efficiency against robustness to noise, outliers and structural heterogeneity. We introduce RE2DC (Robust and Efficient 2D Classifier), an algorithmic framework that resolves this trade-off through dynamic linear-time clustering, dimension-reduction multi-reference alignment, and offers real-time interactive t-SNE visualization. Rather than relying primarily on hardware acceleration, RE2DC reduces the computational cost of robust clustering and employs de-noised images for alignment, enabling efficient execution on standard multi-core CPUs. Across diverse benchmark datasets, RE2DC achieves class homogeneity comparable to ISAC while processing datasets three- to ten-fold faster per classification round than RELION. Notably, RE2DC resolves rare, structurally coherent particle populations, enabling detection of transient conformational intermediates and supporting near real-time cryo-EM analysis. By addressing algorithmic complexity, RE2DC establishes a general framework for robust, scalable analysis of massive and heterogeneous image datasets.

bioinformatics↗

bioRxiv2021

Machine learning prediction of antiviral-HPV protein interactions for anti-HPV pharmacotherapy

Persistent infection with high-risk types Human Papillomavirus could cause diseases including cervical cancers and oropharyngeal cancers. Nonetheless, so far there is no effective pharmacotherapy for treating the infection from high-risk HPV types, and hence it remains to be a severe threat to the health of female. Based on drug repositioning strategy, we trained and benchmarked multiple machine learning models so as to predict potential effective antiviral drugs for HPV infection in this work. Through optimizing models, measuring models predictive performance using 182 pairs of antiviral-target interaction dataset which were all approved by the United States Food and Drug Administration, and benchmarking different models predictive performance, we identified the optimized Support Vector Machine and K-Nearest Neighbor classifier with high precision score were the best two predictors (0.80 and 0.85 respectively) amongst classifiers of Support Vector Machine, Random forest, Adaboost, Naive Bayes, K-Nearest Neighbors, and Logistic regression classifier. We applied these two predictors together and successfully predicted 57 pairs of antiviral-HPV protein interactions from 864 pairs of antiviral-HPV protein associations. Our work provided good drug candidates for anti-HPV drug discovery. So far as we know, we are the first one to conduct such HPV-oriented computational drug repositioning study.

bioinformatics↗

bioRxiv2021

Macrophage Circadian Rhythms are Differentially Affected Based on Stimuli

Macrophages are white blood cells of the innate immune system that play disparate roles in homeostasis and immune responses. As a result, they have the capability to alter their phenotypes to pro-inflammatory (M1) or anti-inflammatory (M2) subtypes in response to their environment. 8-15% of the macrophage transcriptome has circadian oscillations, including genes closely related to their functioning. As circadian rhythms are also associated with cellular phenotypes, we hypothesized that the polarization of macrophages to opposing subtypes might differently affect their circadian rhythms. We tested this by tracking the circadian rhythms of the mouse model macrophage cell line, RAW 264.7, which was stably transfected with Bmal1:luc and Per2:luc reporters, representing a positive and a negative component of the core molecular clock. The strength of rhythmicity was assessed using three measures: the relative power of the circadian band in the power spectral density, the rhythmicity index computed as the height of the third peak of the correlogram, and the maximum value of the chi square periodorgram. The period and amplitudes of the de-trended, smoothed time-series were estimated both by fitting to a damped cosine curve and by identifying the peak and trough of each cycle. M1 polarization decreased amplitudes and rhythmicities of both Bmal1:luc and Per2:luc, but did not significantly affect periods, while M2 polarization increased periods and caused no substantial alterations to amplitudes or rhythmicity. As macrophage phenotypes are also altered in the presence of cancer cells, we then tested the circadian effects of conditioned media from two mouse breast cancer cell lines on macrophage circadian rhythms. Media from highly agressive 4T1 cells caused loss of rhythmicity, while media from less aggressive EMT6 cells yielded no changes. As macrophages are known to play roles in tumors, and oncogenic features are associated with circadian rhythms, we also tested whether conditioned media from macrophages can alter circadian rhythms of cancer cells. We found that conditioned media from RAW 264.7 cells resulted in lower circadian rhythmicities and periods, but higher circadian amplitudes in human osteosarcoma, U2OS-Per2:luc cells. Taken together, our study shows that different circadian characteristics exist based on macrophage phenotypes, and suggests further that there is an association between circadian rhythms and macrophage polarization state. Additionally, our data shows that macrophages treated with breast cancer-conditioned media have circadian phenotypes similar to those of the M1 subtype, and cancer cells treated with macrophage-conditioned media have circadian alterations, providing insight to another level of cross-talk between macrophages and cancer cells that merits further investigation.

immunology↗

bioRxiv2021

Circadian Alterations Increase with Progression in a Patient-Derived Cell Culture Model of Breast Cancer

Circadian rhythms are critical regulators of many physiological and behavioral functions; disruption of this time-tracking system can elicit the development of various diseases, including breast cancer. While multiple studies have used cell lines to study the correlation between altered circadian rhythms and cancer, these cells generally have different genetic backgrounds and do not mirror the changes that occur with disease development. Isogenic cell models can represent and recapitulate changes across cancer progression. Hence in the present study, a patient-derived breast cancer model, the 21T series, was used to evaluate changes to circadian oscillations of core clock protein transcription and translation as cells progress from normal to malignant states. Three cell lines from the series were used: H16N2, from normal breast epithelium; 21PT, from Atypical Ductal Hyperplasia; and 21MT, from Invasive Metastatic Carcinoma. Both of the cancerous cell lines are HER2 positive. We assessed the transcriptional profiles of two core circadian clock proteins, BMAL1 and PER2, which represent a positive and negative component of the molecular oscillator. In the normal H16N2 cells, BMAL1 and PER2 both possessed rhythmic mRNA oscillations with close to standard periods and the expected anti-phase relationship. However, in the cancerous cells, consistent changes were observed: both clock genes had periods that deviated farther from normal and did not have an anti-phase relationship. To provide a more complete understanding of circadian alterations in breast cancer, luciferase reporters and real-time luminometry should be used in future studies.

biochemistry↗

bioRxiv2020

Nobiletin Affects Circadian Rhythms and Oncogenic Characteristics in a Cell-Dependent Manner

The natural product nobiletin is a small molecule, widely studied with regard to its therapeutic effects, including in models of cancer. Recently, nobiletin has also been shown to affect circadian rhythms via their enhancement, resulting in protection against metabolic syndrome. We hypothesized that nobiletins anti-oncogenic effects are correspondingly accompanied by modulation of circadian rhythms. Concurrently, we wished to determine whether the circadian and anti-oncogenic effects of nobiletin differed across cell culture models of cancer. In this study, we assessed nobiletins circadian and therapeutic characteristics to ascertain whether these effects depend on cell line, which here also vary in terms of baseline circadian rhythmicity. Three cell culture models where nobiletins anti-cancer effects have been studied previously were evaluated here: U2OS (bone osteosarcoma), which possesses robust circadian rhythms; MCF7 (breast adenocarcinoma), which has weak circadian rhythms; and MDA-MB-231 (breast adenocarcinoma), which is arrhythmic. We found that both circadian and anti-cancer effects following nobiletin treatment were subtle in the U2OS and MCF7 cells. On the other hand, changes were clear in MDA-MB-231s, where nobiletin rescued rhythmicity, and substantially reduced oncogenic features. Based on these results and those previously described, we posit that a positive correlation exists between nobiletins circadian and therapeutic effects.

cancer biology↗

bioRxiv2019

Identification of Escherichia coli ClpAP in regulating susceptibility to type VI secretion system-mediated attack by Agrobacterium tumefaciens

Type VI secretion system (T6SS) is an effector delivery system used by gram-negative bacteria to kill other bacteria or eukaryotic host to gain fitness. In Agrobacterium tumefaciens, T6SS has been shown to kill other bacteria such as Escherichia coli. Interestingly, the A. tumefaciens T6SS killing efficiency differs when using different E. coli strains as recipient cells. Thus, we hypothesize that a successful T6SS killing not only relies on attacker T6SS activity but also depends on recipient factors. A high-throughput interbacterial competition assay was employed to test the hypothesis by screening for mutants with reduced killing outcomes caused by A. tumefaciens strain C58. From the 3909 E. coli Keio mutants screened, 16 candidate mutants were filtered out. One strain, {Delta}clpP::Kan, showed ten times more resistant to T6SS-mediating killing but restored its susceptibility when complemented with clpP in trans. ClpP is a universal and highly conserved protease that exists in both prokaryotes and eukaryotic organelles. In E. coli, ClpP uses either ClpA or ClpX as an adaptor for substrate specificity. Therefore, the susceptibility of the {Delta}clpA::Kan and {Delta}clpX::Kan was also tested. The T6SS attack susceptibility of {Delta}clpA::Kan is at the same level as {Delta}clpP::Kan, while {Delta}clpX::Kan showed no difference as compared to that of wild-type E. coli BW25113. The data also suggest that ClpA-ClpP interaction, rather than its protease activity, is responsible for enhancing susceptibility to T6SS killing. This study highlights the importance of recipient factors in determining the outcome of T6SS killing.

microbiology↗

bioRxiv2019

Circadian Oscillations Persist in Low Malignancy Breast Cancer Cells

Epidemiological studies have shown that humans with altered circadian rhythms have higher cancer incidence, with breast cancer being one of the most cited examples. To uncover how circadian disruptions may be correlated with breast cancer and its development, prior studies have assessed the expression of BMAL1 and PER2 core clock genes via RT-qPCR and western blot analyses. These and our own low-resolution data show that BMAL1 and PER2 expression are suppressed and arrhythmic. We hypothesized that oscillations persist in breast cancer cells, but due to limitations of protocols utilized, cannot be observed. This is especially true where dynamic changes may be subtle. In the present work, we generated luciferase reporter cell lines representing high- and low-grade breast cancers to assess circadian rhythms. We tracked signals for BMAL1 and PER2 to determine whether and to what extent oscillations exist and provide initial correlations of circadian rhythm alterations with breast cancer aggression. In contrast to previous studies, where the clock was deemed to be \"broken\" in breast cancer, our luminometry data reveal that circadian oscillations of BMAL1 and PER2 do in fact exist in the low-grade, luminal A cell line, MCF7 but are not apparent in high-grade, basal MDA-MB-231 cells. To our knowledge, this is the first evidence of core circadian clock oscillations in breast cancer cells. This work also suggests that circadian rhythms are increasingly disrupted with breast cancer tumor grade/aggressiveness, and that use of real time luminometry to study additional representatives of breast and other cancer subtypes is highly merited.

molecular biology↗

bioRxiv2019

Oncogenic and Circadian Effects of Small Molecules Directly and Indirectly Targeting the Core Circadian Clock

Circadian rhythms are essential for controlling the cell cycle, cellular proliferation, and apoptosis, and hence, are tightly linked to cell fate. Disruption of circadian rhythms has been shown to trigger various pathological developments, including cancer. Several recent studies have used a variety of small molecules to affect circadian oscillations, however, their concomitant cellular effects were not assessed. Here, we use five molecules, grouped into direct versus indirect effectors of the circadian clock, to modulate periods in a human osteosarcoma cell line (U2OS), and determined their influences on cellular behaviors, including motility and colony formation. Luciferase reporters, whose expression were driven via Bmal1- and Per2-promoters (positive and negative protein components of the core clock), were used to facilitate the visualization and quantitative analysis of circadian oscillations. We show that all molecules significantly increase or decrease the circadian periods of Bmal1 and Per2 in a dose-dependent manner, but period length does not correlate with the extent of cell migration or proliferation. We observed that only molecules that affected circadian oscillations to a greater extent showed significant influence on cell functions (e.g. motility and colony formation). Because it is important to consider the likelihood of biological effects resulting from non-circadian targets, we also provide a thorough discussion of potential modes of action. Future studies should employ additional compounds that directly target circadian proteins and/or have different circadian effects, and evaluation in other cancer models to determine whether results obtained here remain consistent.\n\nFor Table of Contents Only\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC=\"FIGDIR/small/645861v1_fig1u.gif\" ALT=\"Figure 1U\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@ec8881org.highwire.dtl.DTLVardef@f601f1org.highwire.dtl.DTLVardef@f98f5aorg.highwire.dtl.DTLVardef@3278e1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2018

The ligand-mediated affinity of escort proteins determines the directionality of lipophilic cargo transport

Intracellular cargo transport is a highly dynamic process. In eukaryotic cells, the uptake and release of lipophilic ligands are executed by escort proteins. However, how these carriers control the directionality of cargo trafficking remains unclear. Here, we have elucidated the unliganded structure of an archetypal fatty acid-binding protein (FABP) and found that it possesses stronger binding affinity than its liganded counterpart towards empty nanodiscs. Titrating unliganded FABP and nanodiscs with long-chain fatty acids (LCFAs) rescued the broadening of FABP cross-peak intensities in HSQC spectra due to decreased protein-membrane interaction. Crystallographic studies revealed that the tails of bound LCFAs obstructed the charged interfaces of the FABP-nanodisc complexes. We conclude that the lipophilic ligands, by taking advantage of escort proteins with high conformational homogeneity and nanodiscs as the third interaction partner involved in this transport study, participate directly in the control of their own transportation in an irreversible, unidirectional fashion.

biophysics↗

bioRxiv2018

Bloodstream Infection with Extended-spectrum Beta-lactamase-producing Escherichia coli: the role of virulence genes

BackgroundVarious bacterial putative virulence factors are involved in the pathogenesis of bacterial infection. However, the effect of comorbidities or infection syndrome in the association of virulence factors and mortality remains inconclusive.\n\nMethodThis study addressed whether specific sequence type (ST) and virulence factors of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) are associated with different outcomes in patients with bloodstream infection.121 adults from southern Taiwan with ESBL-producing E. coli bloodstream infections were enrolled during a 6-year period. Demographic data, including infection syndromes, underlying disease and outcomes, were collected. The virulence factors in isolates were analyzed by PCR and multilocus sequence typing.\n\nResultPositivity for the virulence genes iha, hlyD, sat, iut, fyu, malX, ompT, usp and traT was associated with ST131 positivity (P<0.05). Some ESBL-EC virulence genes associated with urinary tract infection (UTI) were revealed. Positivity for ST405 and the virulence genes iroN and iss was significantly associated with increased 30-day mortality (death within 30 days) on univariate analysis (P<0.05). Independent risk factors of 30-day mortality in bacteremic patients with UTI included underlying chronic liver disease and malignancy. ST131 was borderline associated with 30-day mortality. Independent risk factors associated with 30-day mortality among bacteremic patients without UTI included comorbidities and iroN positivity.\n\nConclusionIn bacteremic patients with UTI, and the ST131 clone was borderline associated with mortality. Positivity for the virulence gene iroN may be linked to mortality in bacteremic patients without UTI.

microbiology↗