Biology subjects

Lee, A.

Publications and source records attributed to Lee, A..

At least 145 records · Page 8Linked to original sources

bioRxiv2019

Marizomib suppresses triple-negative breast cancer via proteasome and oxidative phosphorylation inhibition

Lacking effective targeted therapies, triple-negative breast cancer (TNBCs) is highly aggressive with development of metastasis especially brain, and remains clinically challenging breast cancer subtype to treat. Despite the survival dependency on the proteasome pathway genes, FDA-approved proteasome inhibitors induced minimal clinical response in breast cancer patients due to weak proteasome inhibition. Here, we show that a potent proteasome inhibitor Marizomib (Mzb) inhibits multiple proteasome catalytic activities and induces a better anti-tumor response in TNBC cell lines and patient-derived xenografts alone and in combination with the standard-of-care chemotherapy. Mechanistically, Mzb inhibits oxidative phosphorylation (OXPHOS) via PGC-1 suppression in conjunction with proteasome inhibition in TNBC cells. Mzb reduces lung and brain metastases by reducing the number of circulating tumor cells and the expression of multiple genes involved in the epithelial-to-mesenchymal transition. Furthermore, Mzb-induced OXPHOS inhibition upregulates glycolysis to meet the energetic demands of TNBC cells and, hence, combined inhibition of glycolysis with Mzb exposure leads to a synergistic anti-cancer activity. Collectively, our data provide a strong rationale for a clinical evaluation of Mzb in primary and metastatic TNBC patients.\n\nOne Sentence SummaryMarizomib inhibits primary tumor growth, and also reduces lung and brain metastases in pre-clinical models of triple-negative breast cancer.

cancer biology↗

bioRxiv2019

Riluzole does not ameliorate disease caused by cytoplasmic TDP-43 in a mouse model of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease commonly treated with riluzole, a small molecule that may act via modulation of glutamatergic neurotransmission. However, riluzole only modestly extends lifespan for people living with ALS and its precise mechanisms of action remain unclear. Most ALS cases are characterised by accumulation of cytoplasmic TAR DNA binding protein of 43 kDa (TDP-43), and understanding the effects of riluzole in models that closely recapitulate TDP-43 pathology may provide insights for development of improved therapeutics. We therefore investigated the effects of riluzole in transgenic mice that inducibly express nuclear localisation sequence (NLS)-deficient human TDP-43 in neurons (NEFH-tTA/tetO-hTDP-43{Delta}NLS, rNLS, mice). Riluzole treatment from the first day of hTDP-43{Delta}NLS expression did not alter disease onset, weight loss or performance on multiple motor behavioural tasks. Riluzole treatment also did not alter TDP-43 protein levels, solubility or phosphorylation. Although we identified a significant decrease in GluA2 and GluA3 proteins in the cortex of rNLS mice, riluzole did not ameliorate this disease-associated molecular phenotype. Likewise, riluzole did not alter the disease-associated atrophy of hindlimb muscle in rNLS mice. Finally, riluzole treatment beginning after disease onset in rNLS mice similarly had no effect on progression of late-stage disease or animal survival. Together, we demonstrate specific glutamatergic receptor alterations and muscle fibre-type changes reminiscent of ALS in rNLS mice, but riluzole had no effect on these or any other disease phenotypes. Future targeting of pathways directly related to accumulation of TDP-43 pathology may be needed to develop better treatments for ALS. Significance StatementAccumulation of cytoplasmic TDP-43 protein is the hallmark pathology of ALS. Riluzole is the most widely used drug for ALS treatment, but provides only a short extension of lifespan. We demonstrate here in the rNLS mouse model, which mimics TDP-43 pathology, that riluzole does not ameliorate progressive alterations in motor strength and coordination, muscle atrophy, glutamate receptor levels, or TDP-43 protein levels and solubility, and does not prolong animal survival. Riluzole similarly did not affect decreased levels of glutamate receptor subunits GluA2/GluA3 in rNLS mice. The inability of riluzole to rescue pathological or phenotypic changes in this TDP-43 model provides further impetus for the discovery of improved therapies targeting the key drivers of ALS pathogenesis.

neuroscience↗

bioRxiv2019

Absence of pathogenic Short Tandem Repeat expansions in Systemic Lupus Erythematosus disease-associated genes

Short tandem repeat (STR) expansions have been shown to be pathogenic in human neurological diseases, such as Huntington disease. Yet, the potential role of STRs in non-neurological diseases has yet to be fully investigated. In this study, the potential role of STR expansions in the pathogenesis of systemic lupus erythematosus (SLE) was investigated using patient genomic data and two computational tools, HipSTR and exSTRa. The length variability of STRs in 76 SLE-associated genes was compared using exome data from 271 SLE affected individuals and 158 of their unaffected relatives. We conclude that no large STR expansions associated with SLE were present in these affected individuals within the 76 genes investigated. Lack of evidence does not negate a pathogenic role for STR expansions in SLE, yet given the number of individuals included in this study, we expect that this is not a common source of pathogenesis in SLE.\n\nSignificance statementThe increasing availability and decreasing cost of sequencing genomes lends itself to computational analysis, extracting information to aid diagnosis, guide treatment or discover disease mechanisms and new treatments. Computational tools have been developed to look for various types of mutations, including short tandem repeats (STRs), which has been shown to cause diseases such as Huntington disease. Limited research on the possible role of STR expansions in systemic lupus erythematosus (SLE) has been done. Here we use computational tools to compare the length of STRs in 76 SLE-associated genes in patients and their unaffected relatives. Our results did not identify any large STR expansions associated with SLE, and further research is required to gain a better understanding of this complex disease.

genomics↗

bioRxiv2019

State and trait characteristics of anterior insula time-varying functional connectivity

The human anterior insula (aINS) is a topographically organized brain region, in which ventral portions contribute to socio-emotional function through limbic and autonomic connections, whereas the dorsal aINS contributes to cognitive processes through frontal and parietal connections. Open questions remain, however, regarding how aINS connectivity varies over time. We implemented a novel approach combining seed-to-whole-brain sliding-window functional connectivity MRI and k-means clustering to assess time-varying functional connectivity of aINS subregions. We studied three independent large samples of healthy participants and longitudinal datasets to assess inter- and intra-subject stability, and related aINS time-varying functional connectivity profiles to dispositional empathy. We identified four robust aINS time-varying functional connectivity modes that displayed both "state" and "trait" characteristics: while modes featuring connectivity to sensory regions were modulated by eye closure, modes featuring connectivity to higher cognitive and emotional processing regions were stable over time and related to empathy measures.

neuroscience↗

bioRxiv2019

Histone acetylome-wide association study of tuberculosis

Host-cell chromatin changes are thought to play an important role in the pathogenesis of infectious diseases. Here, we describe the first histone acetylome-wide association study (HAWAS) of an infectious disease, based on genome-wide H3K27 acetylation profiling of peripheral granulocytes and monocytes from subjects with active Mycobacterium tuberculosis (Mtb) infection and healthy controls. We detected >2,000 differentially acetylated loci in either cell type in a Chinese discovery cohort, which were validated in a subsequent multi-ethnic cohort, thus demonstrating that HAWAS can be independently corroborated. Acetylation changes were correlated with differential gene expression in a third cohort. Differential acetylation was enriched near potassium channel genes, including KCNJ15, which modulated Akt-mTOR signaling and promoted Mtb clearance in vitro. We performed histone acetylation QTL analysis on the dataset and identified candidate causal variants for immune phenotypes. Our study serves as proof-of-principle for HAWAS to infer mechanisms of host response to pathogens.

immunology↗

bioRxiv2019

High-resolution and high-accuracy topographic and transcriptional maps of the nucleosome barrier

Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. A high-resolution description of the barrier topography, its modulation by epigenetic modifications, and their effects on Pol II nucleosome crossing dynamics, is still missing. Here, we obtain topographic and transcriptional (Pol II residence time) maps of canonical, H2A.Z, and monoubiquitinated H2B (uH2B) nucleosomes at near base-pair resolution and accuracy. Pol II crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression.\n\nHighlightsO_LIA single-molecule unzipping assay mimics DNA unwinding by Pol II and maps the topography of human canonical, H2A.Z and uH2B nucleosome barriers at high resolution\nC_LIO_LIReal-time dynamics and full molecular trajectories of Pol II crossing the nucleosomal barrier reveal the transcriptional landscape of the barrier at high accuracy\nC_LIO_LIH2A.Z enhances the width and uH2B the height of the barrier\nC_LIO_LIA unified mechanical model links position-dependent dwell times of Pol II on the nucleosome with energetics of the barrier\nC_LI

biophysics↗

bioRxiv2019

Aβ42 oligomers trigger synaptic loss through CAMKK2-AMPK-dependent effectors coordinating mitochondrial fission and mitophagy

During the early stages of Alzheimers disease (AD) in both mouse models and human patients, soluble forms of Amyloid-{beta}1-42 oligomers (A{beta}42o) trigger loss of excitatory synapses (synaptotoxicity) in cortical and hippocampal pyramidal neurons (PNs) prior to the formation of insoluble A{beta} plaques. We observed a spatially restricted structural remodeling of mitochondria in the apical tufts of CA1 PNs dendrites in the hAPPSWE,IND transgenic AD mouse model (J20), corresponding to the dendritic domain receiving presynaptic inputs from the entorhinal cortex and where the earliest synaptic loss is detected in vivo. We also observed significant loss of mitochondrial biomass in human neurons derived from a new model of human ES cells where CRISPR-Cas9-mediated genome engineering was used to introduce the Swedish mutation bi-allelically (APPSWE/SWE). Recent work uncovered that A{beta}42o mediates synaptic loss by over-activating the CAMKK2-AMPK kinase dyad, and that AMPK is a central regulator of mitochondria homeostasis in non-neuronal cells. Here, we demonstrate that A{beta}42o-dependent over-activation of CAMKK2-AMPK mediates synaptic loss through coordinated MFF-dependent mitochondrial fission and ULK2-dependent mitophagy in dendrites of PNs. We also found that the ability of A{beta}42o-dependent mitochondrial remodeling to trigger synaptic loss requires the ability of AMPK to phosphorylate Tau on Serine 262. Our results uncover a unifying stress-response pathway triggered by A{beta}o and causally linking structural remodeling of dendritic mitochondria to synaptic loss.

neuroscience↗

bioRxiv2019

The Moorfields AMD Database Report 2 - Fellow Eye Involvement with Neovascular Age-related Macular Degeneration

Background/AimsNeovascular age-related macular degeneration (nAMD) is frequently bilateral, and previous reports on fellow eyes have assumed sequential treatment after a period of treatment of the first eye only. The aim of our study was to analyse baseline characteristics and visual acuity (VA) outcomes of fellow eye involvement with nAMD, specifically differentiating between sequential and non-sequential (due to macular scarring in the first eye) anti-vascular endothelial growth factor treatment and timelines for fellow eye involvement.\n\nMethodsRetrospective, electronic medical record database study of the Moorfields AMD database of 8174 eyes/120,756 single entries with data extracted between October 21, 2008 and August 9, 2018. The dataset for analysis consisted of 1180 sequential, 413 nonsequential, and 1110 unilateral eyes.\n\nResultsMean VA of sequentially treated fellow eyes at baseline was significantly higher (62{+/-}13), VA gain over two years lower (0.65{+/-}14), and proportion of eyes with good VA ([≥]20/40 or 70 letters) higher (46%) than the respective first eyes (baseline VA 54{+/-}16, VA gain at two years 5.6{+/-}15, percentage of eyes with good VA 38%). Non-sequential fellow eyes showed baseline characteristics and VA outcomes similar to first eyes. Fellow eye involvement rate was 32% at two years, and median time interval to fellow eye involvement was 71 (IQR 27-147) weeks.\n\nConclusionThis reports shows sequentially treated nAMD fellow eyes have better baseline and final VA than non-sequentially treated eyes after 2 years of treatment. Sequentially treated eyes also had a greater proportion with good VA after 2 years of treatment.\n\nPRECISDepending on age, fellow eye involvement occurs in 32% of patients with neovascular AMD by two years. Fellow eyes generally maintain better vision, except in cases where late-stage disease in the first eye was untreated.

epidemiology↗

bioRxiv2019

A putative enoyl-CoA hydratase contributes to biofilm formation and the antibiotic tolerance of Achromobacter xylosoxidans

Achromobacter xylosoxidans has attracted increasing attention as an emerging pathogen in patients with cystic fibrosis. Intrinsic resistance to several classes of antimicrobials and the ability to form robust biofilms in vivo contribute to the clinical manifestations of persistent A. xylosoxidans infection. Still, much of A. xylosoxidans biofilm formation remains uncharacterized due to the scarcity of existing genetic tools. Here we demonstrate a promising genetic system for use in A. xylosoxidans; generating a transposon mutant library which was then used to identify genes involved in biofilm development in vitro. We further described the effects of one of the genes found in the mutagenesis screen, encoding a putative enoyl-CoA hydratase, on biofilm structure and tolerance to antimicrobials. Through additional analysis, we find that a cis-2 fatty acid signaling compound is essential to A. xylosoxidans biofilm ultrastructure and maintenance. This work describes methods for the genetic manipulation of A. xylosoxidans and demonstrated their use to improve our understanding of A. xylosoxidans pathophysiology.

microbiology↗

bioRxiv2019

Aging induces Nlrp3 inflammasome dependent adipose B cell expansion to impair metabolic homeostasis

Visceral adiposity in elderly is associated with alterations in adipose tissue immune cells leading to inflammation and metabolic dysfunction. The Nlrp3 inflammasome is a critical regulator of macrophage activation, inflammation, and immunometabolism in visceral adipose tissue during aging; however, the potential contribution of adipose tissue B cells is unexplored. Here, we show that aging expands adipose-resident B cells and fat-associated lymphoid clusters (FALCs) in visceral white adipose tissue. Adipose tissue B cells exhibit a memory-like B cell profile similar to the phenotype of aged B cells that are increased in spleen of old mice. Mechanistically, the age-induced FALC formation and adipose B cell expansion, but not B cell transcriptional program, is dependent on the Nlrp3 inflammasome. Furthermore, B cell depletion in aged mice restores lipolysis and defense against loss of core body temperature during cold stress. These data reveal that inhibiting Nlrp3-dependent B cell accumulation can be targeted to reverse metabolic impairment in aging adipose tissue.\n\nHighlights- Adipose-resident aged B cells are increased in fat-associated lymphoid clusters (FALC)\n\n- FALC formation and adipose-resident B cell expansion during aging are regulated by the Nlrp3 inflammasome\n\n- Nlrp3 and B cell depletion in aging restores lipolysis and improves cold tolerancea

immunology↗

bioRxiv2019

Reproductive success of Eastern Bluebirds (Sialia sialis) varies with the timing and severity of drought

Drought affects avian communities in complex ways. We used our own and citizen science-generated reproductive data acquired through The Cornell Lab of Ornithologys NestWatch Program, combined with drought and vegetation indices obtained from governmental agencies, to determine drought effects on Eastern Bluebird (Sialia sialis L.) reproduction across their North American breeding range for the years 2006-2013. Our results demonstrate that some aspects of bluebird reproductive success varies with the timing and severity of drought. Clutch size was unaffected by drought occurrence or severity during or within one and two months of clutch initiation, but hatching and fledging rates decreased as drought severity increased. Drought conditions occurring one month prior to the month during which eggs should have hatched, and two months prior to the month nestlings should have fledged also reduced the numbers of fledged offspring. We also demonstrate the value of datasets generated by citizen scientists in combination with climate data for examining biotic responses at large temporal and spatial scales.

ecology↗

bioRxiv2018

Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function

11.1 BackgroundChildren with oropharyngeal dysphagia have impaired airway protection mechanisms and are at higher risk for pneumonia and other pulmonary complications. Aspiration of gastric contents is often implicated as a cause for these pulmonary complications, despite being supported by little evidence. The goal of this study is to determine the relative contribution of oropharyngeal and gastric microbial communities to perturbations in the lung microbiome of children with and without oropharyngeal dysphagia and aspiration.\n\n1.2 MethodsWe conducted a prospective cohort study of 222 patients consecutively recruited from a tertiary aerodigestive center undergoing simultaneous esophagogastroduodenoscopy and flexible bronchoscopy. Bronchoalveolar lavage, gastric and oropharyngeal samples were collected and 16S sequencing was performed. A subset of patients also underwent video fluoroscopic swallow studies to assess swallow function and were categorized as aspiration/no aspiration. Microbial communities across the aerodi-gestive tract were compared in patients with and without aspiration by calculating within-patient beta diversities and quantifying microbial exchange across sites.\n\n1.3 ResultsWithin all patients, lung, oropharyngeal and gastric microbiomes overlap. The degree of similarity is the lowest between the oropharynx and lungs (median Jensen-Shannon distance (JSD) = 0.90), and as high between the stomach and lungs as between the oropharynx and stomach (median JSD = 0.55 and 0.56, respectively; p = 0.6). Unlike the oropharyngeal microbiome, lung and gastric communities are highly variable across people and driven primarily by person rather than body site. In patients with aspiration, the lung microbiome more closely resembles oropharyngeal rather than gastric communities and there is greater prevalence of microbial exchange between the lung and oropharynx than between gastric and lung sites (p = 0.04 and 3x10-5, respectively).\n\n1.4 ConclusionsThe gastric and lung microbiomes display significant overlap in patients with intact airway protective mechanisms while the lung and oropharynx remain distinct. In patients with impaired swal-low function and aspiration, the lung microbiome shifts towards oropharyngeal rather than gastric communities. This finding may explain why antireflux surgeries fail to show benefit in pediatric pulmonary outcomes.

microbiology↗

bioRxiv2018

Multi-scale Loading and Damage Mechanisms of Rat Tail, Plantaris, and Achilles Tendons

Tendinopathy, degeneration of tendon that leads to pain and dysfunction, is common in both sports and occupational settings, but multi-scale mechanisms for tendinopathy are still unknown. We recently showed that micro-scale sliding (shear) is responsible for both load transfer and damage mechanisms in rat tail tendon; however, rat tail tendon is a specialized non-load bearing tendon, and thus the load transfer and damage mechanisms are still unknown for load-bearing tendons. The objective of this study was to investigate the load transfer and damage mechanisms of load-bearing tendons using rat plantaris and Achilles tendons. We demonstrated that the micro-scale sliding is a key component for both mechanisms in plantaris tendon, similar to tail tendon. Namely, the micro-scale sliding was correlated with applied strain, demonstrating that load was transferred via micro-scale sliding in the plantaris and tail tendons. In addition, while the micro-scale strain fully recovered, the micro-scale sliding was non-recoverable and strain-dependent, and correlated with a tissue-scale mechanical parameters. When the applied strain was normalized, the % magnitudes of non-recoverable sliding was similar between the plantaris and tail tendons. Achilles tendon demonstrated some of the mechanical responses observed in plantaris and tail tendons, yet the results were inconclusive due to its complex structure. Statement of Clinical Significance: Understanding the mechanisms responsible for the pathogenesis and progression of tendinopathy can improve prevention and rehabilitation strategies and guide therapies and design of engineered constructs.

biophysics↗

bioRxiv2018

One and Two Year Visual Outcomes from the Moorfields AMD Database - an Open Science Resource for the Study of Neovascular Age-related Macular Degeneration

ObjectivesTo analyse treatment outcomes and share clinical data from a large, single-center, well-curated database (8174 eyes / 6664 patients with 120,756 single entries) of patients with neovascular age related macular degeneration (AMD) treated with anti-vascular endothelial growth factor (VEGF). By making our depersonalised raw data openly available, we aim to stimulate further research in AMD, as well as setting a precedent for future work in this area.\n\nSettingRetrospective, comparative, non-randomised electronic medical record (EMR) database cohort study of the UK Moorfields AMD database with data extracted between 2008 and 2018.\n\nParticipants3357 eyes/patients (61% female). Extraction criteria were [≥] 1 ranibizumab or aflibercept injection, entry of \"AMD\" in the diagnosis field of the EMR, and a minimum of one year of follow-up. Exclusion criteria were unknown date of first injection and treatment outside of routine clinical care at Moorfields before the first recorded injection in the database.\n\nMain outcome measuresPrimary outcome measure was change in VA at one and two years from baseline as measured in Early Treatment Diabetic Retinopathy Study (ETDRS) letters. Secondary outcomes were the number of injections and predictive factors for VA gain.\n\nResultsMean VA gain at one-year and two years were +5.5{+/-}0.5 and +4.9{+/-}0.68 letters respectively. Fifty-four percent of eyes gained [≥]5 letters at two years, 63% had stable VA ({+/-}[≤]14 letters), forty-four percent of eyes maintained good VA ([≥]70 letters). Patients received a mean of 7.7{+/-}0.06 injections during year one and 13.0{+/-}0.2 injections over two years.\n\nYounger age, lower baseline VA, and more injections were associated with higher VA gain at two years.\n\nConclusionThis study benchmarks high quality EMR study results of real life AMD treatment and promotes open science in clinical AMD research by making the underlying data publicly available.\n\nStrengths and limitations of this study- Large sample size, retrospective, single centre, electronic medical record database study\n- High quality real life data\n- Open science approach with sharing of depersonalised raw data

epidemiology↗

bioRxiv2018

Does the strength of women’s attraction to male vocal masculinity track changes in steroid hormones?

Recent studies that either used luteinizing hormone tests to confirm the timing of ovulation or measured steroid hormones from saliva have found little evidence that womens preferences for facial or body masculinity track within-subject changes in womens fertility or hormonal status. Fewer studies using these methods have examined womens preferences for vocal masculinity, however, and those that did report mixed results. Consequently, we used a longitudinal design and measured steroid hormones from saliva to test for evidence of hormonal regulation of womens (N=351) preferences for two aspects of male vocal masculinity (low pitch and low formants). Analyses suggested that preferences for masculine pitch, but not masculine formants, may track within-woman changes in estradiol. Although these results present some evidence for the hypothesis that within-subject hormones regulate womens attraction to masculine men, we do not discount the possibility that the effect of estradiol on pitch preferences in the current study is a false positive.

animal behavior and cognition↗

bioRxiv2018

Bradycardic mice undergo effective heart rate improvement after specific homing to the sino-atrial node and differentiation of adult muscle derived stem cells.

Current treatments for heart automaticity disorders still lack a safe and efficient source of stem cells to restore normal biological pacemaking. Since adult Muscle-Derived Stem Cells (MDSC) show multi-lineage differentiation in vitro including into spontaneously beating cardiomyocytes, we questioned whether they could effectively differentiate into cardiac pacemakers, a specific population of cardiomyocytes producing electrical impulses in the sino-atrial node (SAN) of adult heart. We show here that beating cardiomyocytes, differentiated from MDSC in vitro, exhibit typical characteristics of cardiac pacemakers: expression of markers of the SAN lineage Hcn4, Tbx3 and Islet1, as well as spontaneous calcium transients and hyperpolarization-activated "funny" current and L-type Cav1.3 channels. Pacemaker-like myocytes differentiated in vitro from Cav1.3-deficient mouse stem cells produced slower rate of spontaneous Ca2+ transients, consistent with the reduced activity of native pacemakers in mutant mice. In vivo, undifferentiated wild type MDSC migrated and homed with increased engraftment to the SAN of bradycardic mutant Cav1.3-/- within 2-3 days after systemic I.P. injection. The increased homing of MDSCs corresponded to increased levels of the chemokine SDF1 and its receptor CXCR4 in mutant SAN tissue and was ensued by differentiation of MDSCs into Cav1.3-expressing pacemaker-like myocytes within 10 days and a significant improvement of the heart rate maintained for up to 40 days. Optical mapping and immunofluorescence analyses performed after 40 days on SAN tissue from transplanted wild type and mutant mice showed MDSCs integrated as pacemaking cells both electrically and functionally within recipient mouse SAN. These findings identify MDSCs as directly transplantable stem cells that efficiently home, differentiate and improve heart rhythm in mouse models of congenital bradycardia.

cell biology↗

bioRxiv2018

Addition of Degenerate Bases to DNA-based Data Storage for Increased Information Capacity

Introductory paragraphDNA-based data storage has emerged as a promising method to satisfy the exponentially increasing demand for information storage. However, practical implementation of DNA-based data storage remains a challenge because of the high cost of DNA per unit data. Here, we propose the use of eleven degenerate bases as encoding characters in addition to A, C, G, and T, which increases the information capacity (the amount of data that can be stored per length of DNA sequence designed) and reduce the cost of DNA per unit data. Using the proposed method, we experimentally achieved an information capacity of 3.37 bits/character, which is more than twice when compared to the highest information capacity previously achieved. Finally, the platform was projected to reduce the cost of DNA-based data storage by 50%.

synthetic biology↗

bioRxiv2018

Redesign of an Undergraduate General Microbiology Lab to Include Authentic Discovery-Driven Research on Cucumber Fermentations

Many undergraduate introductory microbiology laboratory courses teach basic principles of bacteriology using classical protocol-based experiments, with limited critical thinking and inquiry-based learning practices. We initiated a comprehensive redesign in our General Microbiology Laboratory course to promote scientific critical and creative thinking, while strengthening core microbiology concepts and skills. As part of the redesign, a series of authentic discovery-driven labs, based on cucumber fermentations, were developed as an independent research module within the course curriculum. Integrating discovery-driven labs allowed students to be engaged problem solvers, applying the scientific process to develop hypotheses, design experiments, utilize quantitative reasoning, and effectively communicate results. The inquiry-guided research project was developed to evaluate the minimum concentration of salt (NaCl) required in fermentation brine to safely, and effectively, ferment cucumbers. Over 5 weeks, students assess different aspects of the fermentation process, including quantifying bacterial populations with differential and selective media, measuring pH and glucose concentration of brine solutions, and characterizing the microbial metabolic potential. Additionally, students isolate an unknown bacterium from their fermentations, identifying and characterizing the isolate using 16S rRNA gene sequencing and metabolic tests. Throughout the research project, students collect, graph, and analyze their observations, culminating in students creating and presenting a scientific research poster. With this lab redesign, students generate new knowledge contributing to our understanding of microbial ecology within food fermentations, learn core microbiology skills and techniques, and develop critical and creative thinking skills. The impact of their research is valuable to science educators, researchers, and industry partners.

scientific communication and education↗