Biology subjects

Loh, E.

Publications and source records attributed to Loh, E..

8 recordsLinked to original sources

bioRxiv2026

Chemical tools to Detect and Inhibit IgA1 Proteases in Haemophilus influenzae

Non-encapsulated ("non-typeable") Haemophilus influenzae is a major cause of mucosal infections such as otitis media, conjunctivitis, and exacerbations of chronic obstructive pulmonary disease. Rising antibiotic resistance has increased interest in anti-virulence strategies that reduce pathogenicity without exerting selective pressure for resistance. A key virulence factor of H. influenzae is immunoglobulin A1 protease (IgA1P), a secreted serine protease that promotes colonization by cleaving human IgA1 at the hinge region and enabling immune evasion. Despite its therapeutic promise, progress has been limited by the lack of chemical tools to probe IgA1P activity in its native biological environment. Here, we report the first activity-based probes that enable direct detection of active IgA1Ps in complex samples and H. influenzae clinical isolates. Competitive activity-based screening using these probes identified novel IgA1P inhibitors, and structure-activity relationship guided optimization yielded a potent lead IgA1P inhibitor. This inhibitor preserves IgA1 at the bacterial surface, demonstrating effective inhibition of IgA1P activity in its native context and chemical disruption of an IgA1P-dependent immune-evasion mechanism. Together, these chemical tools establish a versatile platform for elucidating IgA1Ps role in H. influenzae colonization and virulence, and for validating IgA1Ps as diagnostic markers and antivirulence targets.

microbiology↗

bioRxiv2024

DNA methylation differences between the female and male X chromosomes in human brain

The mechanisms of X chromosome inactivation suggest fundamental epigenetic differences between the female and male X chromosomes. However, DNA methylation studies often exclude the X chromosomes. In addition, many previous studies relied on techniques that examine non-randomly selected subsets of positions such as array-based methods, rather than assessing the whole X chromosome. Consequently, our understanding of X chromosome DNA methylation lags behind that of autosomes. Here we addressed this gap of knowledge by studying X chromosome DNA methylation using 89 whole genome bisulfite sequencing (WGBS) maps from neurons and oligodendrocytes. Using this unbiased and comprehensive data, we show that DNA methylation of the female X chromosomes is globally reduced (hypomethylated) across the entire chromosome compared to the male X chromosomes and autosomes. On the other hand, the majority of X-linked promoters were more highly methylated (hypermethylated) in females compared to males, consistent with the role of DNA methylation in X chromosome inactivation and dosage compensation. Remarkably, hypermethylation of female X promoters was limited to a group of previously lowly methylated promoters. The other group of highly methylated promoters were both hyper- and hypo-methylated in females with no obvious association with gene expression. Therefore, X chromosome inactivation by DNA methylation was exclusive to a subset of promoters with distinctive epigenetic feature. Apart from this group of promoters, differentially methylated regions in the female and male X chromosomes were dominated by female hypomethylation. Our study furthers the understanding of X-chromosome dosage regulation by DNA methylation on the chromosomal level as well as on individual gene level.

genomics↗

bioRxiv2022

Decoding the IGF1 Signaling Gene Regulatory Network Behind Alveologenesis from A Mouse Model of Bronchopulmonary Dysplasia

Lung development is precisely controlled by underlying Gene Regulatory Networks (GRN). Disruption of genes in the network can interrupt normal development and cause diseases such as bronchopulmonary dysplasia (BPD)-a chronic lung disease in preterm infants with morbid and sometimes lethal consequences characterized by lung immaturity and reduced alveolarization. Here, we generated a transgenic mouse exhibiting a moderate severity BPD phenotype by blocking IGF1 signaling in secondary crest myofibroblasts (SCMF) at the onset of alveologenesis. Using approaches mirroring the construction of the model GRN in sea urchins development, we constructed the IGF1 signaling network underlying alveologenesis using this mouse model that phenocopies BPD. The constructed GRN, consisting of 43 genes, provides a birds-eye view of how the genes downstream of IGF1 are regulatorily connected. The GRN also reveals a mechanistic interpretation of how the effects of IGF1 signaling are transduced within SCMF from its specification genes to its effector genes and then from SCMF to its neighboring alveolar epithelial cells with WNT5A and FGF10 signaling as the bridge. Consistently, blocking WNT5A signaling in mice phenocopies BPD as inferred by the network. A comparative study on human samples suggests that a GRN of similar components and wiring underlies human BPD. Our network view of alveologenesis is transforming our perspective to understand and treat BPD. This new perspective calls for the construction of the full signaling GRN underlying alveologenesis, upon which targeted therapies for this neonatal chronic lung disease can be viably developed.

developmental biology↗

bioRxiv2021

Taxonomic classification methods reveal a new subgenus in the paramyxovirus subfamily Orthoparamyxovirinae

As part of a broad One Health surveillance effort to detect novel viruses in wildlife and people, we report several paramyxoviruses sequenced primarily from bats during 2013 and 2014 in Brazil and Malaysia, including seven from which we recovered full-length genomes. Of these, six represent the first full-length paramyxovirus genomes sequenced from the Americas, including two sequences which are the first full-length bat morbillivirus genomes published to date. Our findings add to the vast number of viral sequences in public repositories that have been increasing considerably in recent years due to the rising accessibility of metagenomics. Taxonomic classification of these sequences in the absence of phenotypic data has been a significant challenge, particularly in the paramyxovirus subfamily Orthoparamyxovirinae, where the rate of discovery of novel sequences has been substantial. Using pairwise amino acid sequence classification (PASC), we describe a novel genus within this subfamily tentatively named Jeishaanvirus, which we propose should include as subgenera Jeilongvirus, Shaanvirus, and a novel South American subgenus Cadivirus. We also highlight inconsistencies in the classification of Tupaia virus and Mojiang virus using the same demarcation criteria and show that members of the proposed subgenus Shaanvirus are paraphyletic. Importantly, this study underscores the critical importance of sequence length in PASC analysis as well as the importance of biological characteristics such as genome organization in the taxonomic classification of viral sequences.

microbiology↗

bioRxiv2019

Meningitis pathogens evade immune responses by thermosensing

Bacterial meningitis is a major cause of death and disability in children worldwide. Two human restricted pathogens, Streptococcus pneumoniae and Haemophilus influenzae, are the major causative agents of bacterial meningitis, attributing to 200,000 deaths annually. These pathogens are often part of the nasopharyngeal microflora of healthy carriers. However, what factors elicit them to disseminate and cause invasive diseases remain unknown. Elevated temperature and fever are hallmarks of inflammation triggered by infections and can act as warning signal to these pathogens. Here, we investigate whether these pathogens could sense environmental temperature to evade host complement-mediated killing. We show that expression of two vital virulence factors and vaccine components, the capsule and factor H binding proteins, are temperature dependent. We identify and characterize four novel RNA thermosensors in S. pneumoniae and H. influenzae within their 5'-untranslated regions of genes, responsible for capsular biosynthesis and production of factor H binding proteins. Our data further demonstrate that these pathogens have co-evolved thermosensing abilities independently with unique RNA sequences, but distinct secondary structures, to evade the human immune system.\n\nAuthor SummaryStreptococcus pneumoniae and Haemophilus influenzae are bacteria that reside in the upper respiratory tract. This harmless colonization may progress to severe and often lethal septicaemia and meningitis, but molecular mechanisms that control why these pathogens invade the circulatory system remain largely unknown. Here we show that both S. pneumoniae and H. influenzae can evade complement killing by sensing the temperature of the host. We identify and characterize four novel RNA thermosensors in S. pneumoniae and H. influenzae within their respective 5'-untranslated regions of genes, influencing capsular biosynthesis and production of factor H binding proteins. Moreover, we show that these RNA thermosensors evolved independently with exclusive unique RNA sequences to sense the temperature in the nasopharynx and in other body sites to avoid immune killing. Our finding that regulatory RNA senses temperatures and directly regulate expression of two important virulence factors and vaccine components of S. pneumoniae and H. influenzae, is most important for our understanding of bacterial pathogenesis and for vaccine development. Our work could pave the way for similar studies in other important bacterial pathogens and enables clinicians and microbiologists to adjust their diagnostic techniques, and treatments to best fit the condition of the patients.

microbiology↗

bioRxiv2019

A regulatory RNA is associated to invasive meningococcal disease in Europe

The strictly human pathogen Neisseria meningitidis is a commensal bacterium but can occasionally turn lethal causing septicaemia and meningitis. The mechanisms of how the meningococcus shifts to invasive infection remain poorly understood. Here we demonstrate that an eight base-pair tandem repeat deletion in the 5-untranslated region of the polysaccharide capsular biosynthesis operon results in a hypercapsulation phenotype in clinical isolates. The increased capsule production significantly improves the bacterium survival in human serum while impairing its ability to adhere and colonise human pharyngeal cells. Among 4501 reported meningococcal cases in Europe from 2010-2018, the loss of an eight base-pair tandem repeat is three times more prevalent in invasive isolates (16.3%) compared to carrier isolates (5.1%).Combined results indicate that polymorphisms in this regulatory RNA contributes to meningococcal virulence.\n\nImportanceIn this study we report a regulatory RNA to be directly involved in clinical manifestation of meningococcal disease. Using readily accessible WGS of meningococcus, we have now demonstrated that regulatory RNAs directly contribute to the progression of invasive meningococcal infection. We believe this novel combination of molecular and comparative regulatory RNA study could be used for the identification of additional RNAs involved in not only meningococcus but also pave the way for similar studies in other important bacterial pathogens. The identification of specific regulatory RNAs will no doubt facilitate clinicians, microbiologists, and public health practitioners to adjust their diagnostic techniques and treatments to best fit the condition of the patients.

microbiology↗

bioRxiv2019

Effects of flavorless electronic cigarette aerosol on the survival and growth of common oral commensal streptococci

The use of electronic cigarettes (ECIG) has become very common. Consequently, critical analysis of the biological effects of ECIG aerosol deserves attention. Since the mouth is the first anatomical cavity exposed to aerosol, the oral bacteria within are also exposed. We hypothesize that while cigarette smoke has a detrimental effect on the survival and growth of oral commensal streptococci, flavorless ECIG aerosol does not. Survival and growth of several strains of commensal streptococci were measured after exposure to flavorless ECIG aerosol {+/-} nicotine and smoke. Peristaltic pumps were used to transport flavorless aerosol {+/-} nicotine or cigarette smoke into chambers containing recently seeded colony forming units of four strains of oral commensal streptococci on agar plates. Bacterial survival and growth, based on colony counts and sizes, were determined 24 hours post-exposure. Lastly, aerosol or smoke were delivered into chambers containing the four strains of streptococci pre-adhered to plastic coverslips. Bacterial survival and growth, as indicated by biofilm formation, were determined 24 hours post-exposure via scanning electron microscopy. The results suggest that flavorless aerosol {+/-} nicotine has a modest effect on bacterial growth both as colonies on agar and as biofilms. In contrast, smoke dramatically decrease bacterial survival and growth in all parameters measured. Therefore, unlike cigarette smoke, flavorless ECIG aerosol has only a small effect on the survival and growth of oral commensal streptococci.

microbiology↗

bioRxiv2018

Evaluating the effects of data visualisation techniques on interpretation and preference in clinical quality reports: A cross-sectional study.

ObjectiveTo evaluate the different methods of data visualisation and how it affects preference and data interpretation.\n\nDesignA cross-sectional survey, assessing interpretation and preference for four methods of data presentation, was distributed to participants.\n\nSettingMelbourne, Victoria\n\nParticipantsMembers of Prostate Cancer Outcome Registry-Victoria (PCOR-Vic) and senior hospital staff in three metropolitan Victorian hospitals.\n\nInterventionsDifferent methods of data visualisation. Mainly, funnel plots, league charts, risk adjusted sequential probability ratio test (RASPRT) charts and dashboard.\n\nMain Outcome MeasureInterpretation scores assessed capacity by participants to identify outliers and poor performers. Preference was based on a 9-point Likert-scale (0 - 9).\n\nResultsIn total, 113 participants responded to the online survey (16/58 urologists and 97/297 senior hospital staff, response rate 32%). Respondents reported that funnel plots were easier to interpret compared to league charts (mean interpretability score difference of 28% (95% CI: 19.2% - 37.0%, P<0.0001). Predictors of worse interpretability of charts in the adjusted model were being a hospital executive compared to a urologist (coefficient= -2.50, 95% CI = -3.82, - 1.18, P<0.01) and having no statistical training compared to those with statistical training (coefficient = -1.71, 95% CI=-2.85, -0.58, P=0.003). Participants preferred funnel plots and dashboards compared to league charts and RASPRT charts (median score 7/9 vs 5/9), and preferred charts which were traffic-light coloured versus greyscale charts (43/60 (71.6%) vs 17/60 (28.3%)).\n\nConclusionWhen developing reports for clinicians and hospitals, consideration should be given to preference of end-users and ability of groups to interpret the graphs.

epidemiology↗