Biology subjects

Huang, C.-L.

Publications and source records attributed to Huang, C.-L..

18 recordsLinked to original sources

bioRxiv2026

Angiopoietin-like protein 7 (ANGPTL7)-mediated effects on resident immune cells contribute to neurodegeneration in glaucomatous optic nerve head

Glaucoma is an optic neuropathy characterized by progressive retinal degeneration. Population genetic analyses describe an association of variants in angiopoietin-like protein 7 (ANGPTL7) with lower intraocular pressure (IOP) and decreased glaucoma susceptibility. In addition to its reported role in the trabecular meshwork (TM), we demonstrate that ANGPTL7 is also expressed within disease-relevant cell types of the human posterior eye, specifically prelaminar optic nerve head astrocytes (ONHA). Contrasting with previously published findings, we observe no difference in IOP between Angptl7-/- mice and wild-type littermates. Despite absence of an IOP phenotype, loss of ANGPTL7 protects from IOPinduced retinal ganglion cell (RGC) damage in a rodent glaucoma neurodegeneration model. ANGPTL7 may signal through LAIR1-positive immune cells, potentially contributing to pro-inflammatory signaling and phenotypic modulation of resident immune cells, with evidence suggesting that oligomerization of ANGPTL7 is necessary for its activity. Comprehensively, our data highlight an unappreciated role of ANGPTL7 in modulating neuroinflammation in the posterior eye, contributing to glaucoma progression.

neuroscience↗

bioRxiv2026

Optimization of AAV tools to target M&uumlller glial cells for retinal gene therapy

Reprogramming of Muller glial (MG) cells into retinal neurons has the potential to treat vision loss by regenerating the retina. Development of efficient gene delivery systems to target the MG cells is critical. Adeno-associated virus (AAV) serotypes and promoter specificity are important factors that influence AAV transduction profile in the retina. However, studies that optimize these parameters to specifically target MG cells are limited, in particular in rats which are commonly used for eye research. Here we tested 4 AAV serotypes and 14 promoters to optimize gene delivery to human MG cells in vitro and/or rat MG cells in vivo. We showed that the combinatorial use of MG-specific serotypes and promoters achieved high specificity for MG cell targeting, with ShH10Y serotype and the GFAP (gfaABC1D) promoter as the best performing tool to target rat MG cells in vivo. We developed new AAV vectors using known and novel MG-specific promoters and engineered short promoter variants to improve the cargo capacity of AAV delivery. Our results highlighted a number of promoters that can target MG cells in vitro or in vivo. This study further expands the AAV toolbox to target MG cells, which has important implications for retinal gene therapy development.

bioengineering↗

bioRxiv2025

Optimization of AAV tools to target Muller glial cells for retinal gene therapy

molecular biology↗

bioRxiv2025

Endoplasmic reticulum-mitochondrion disconnection promotesmetabolic reprogramming and cystogenesis in polycystic kidneydisease

Mutations in PKD1 and PKD2 cause autosomal-dominant polycystic kidney disease (ADPKD), characterized by fluid-filled cysts, aberrant cell proliferation, and widespread genetic and epigenetic remodeling. While mitochondrial dysfunction and metabolic shifts are central to disease progression, the mechanisms linking PKD mutations to these changes remain unclear. Here, we demonstrate that ER-mitochondria connectivity was disrupted in Pkd1- and Pkd2-deleted mice, preceding cyst formation. This disconnection induces mitochondrial stress, triggering epigenetic remodeling and transcriptional activation of pathways driving proliferation and metabolic reprogramming. Remarkably, restoring PKD function in the ER or pharmacologically enhancing ER-mitochondria connection ameliorates mitochondrial dysfunction, epigenetic shifts, and cystogenesis. These findings reveal a critical role for ER-localized PKD in maintaining mitochondrial integrity and transcriptional homeostasis. Mitochondrial dysfunction resulting from ER-mitochondria uncoupling emerges as a key driver of cystogenesis in ADPKD, and correcting this defect may offer a promising therapeutic strategy. SignificanceAutosomal dominant polycystic kidney disease (ADPKD) is the most prevalent monogenic cause of kidney failure, marked by fluid-filled cysts, aberrant cell proliferation, metabolic reprogramming, and extensive genetic and epigenetic alterations. The mechanisms by which loss-of-function mutations in PKD1 and PKD2 drive disease progression remain poorly understood. Here, we demonstrate that ER-mitochondria contacts are disrupted in Pkd-mutant mice prior to cyst formation. This disconnection induces mitochondrial dysfunction and epigenetic remodeling, which in turn promote metabolic reprogramming and cystogenesis. Restoration of PKD function in the ER or pharmacological enhancement of ER-mitochondria coupling mitigates these pathological changes. Our findings uncover a critical role for ER-mitochondria crosstalk in suppressing cystogenesis and identify a promising therapeutic target for ADPKD.

molecular biology↗

bioRxiv2025

Plant-soil feedback persists beyond host death to shape density-dependent plant competition

Background and AimsPlant-soil feedback (PSF) shapes plant competition, yet classic PSF experiments often overlook the density dependence and temporal complexities of PSFs, especially after host death. We ask whether microbial effects vary after host death and mediate density dependence in seedling competition. MethodsWe combined forest inventory data from a subtropical forest with a density-gradient greenhouse experiment to evaluate seedling competition among two tree species with different mycorrhizal associations (ectomycorrhizal versus arbuscular mycorrhizal). In 2023, we collected soil inocula from living and dead trees (died between 2014 and 2019) with unsterilized and sterilized treatments. We applied invasion analysis to infer seedling competitive outcomes and used bootstrapping to evaluate uncertainty. ResultsSoil microbial communities shaped seedling competition, favoring the ectomycorrhizal species. Using soils collected from living versus dead hosts as live inocula, we found similar plant competitive outcomes, indicating that PSF persists for over 4-9 years following host death. In contrast, when using sterilized inoculum, we found shifts in competition after host death, suggesting underlying abiotic changes which might masked by microbial effects. Moreover, we found significant evidence that soil microbes can mediate nonlinear density dependence in seedling competition. ConclusionWe provide experimental evidence of persistent microbial legacies that benefit ectomycorrhizal tree species in a subtropical forest. Our study demonstrates how integrating field-based census data with density-gradient experiments and explicit uncertainty estimation can better capture the temporal dimensions, complexities of density dependence, and uncertainties of PSF.

ecology↗

bioRxiv2025

Identification of cellular and molecular risk signatures for progression to late-stage age-related macular degeneration using the 9-step Minnesota Grading System

Age-related macular degeneration (AMD) is a complex multifactorial disease, and the molecular mechanisms underpinning the progression of intermediate AMD to geographic atrophy are not fully understood. To better understand mechanisms driving progression, we performed bulk RNA sequencing on dissected macular and peripheral RPE/choroid and neural retina tissue from postmortem human eyes graded using the 9-step Minnesota Grading System (MGS). Binning of intermediate AMD cases into three distinct groups (AMD3L, AMD3M, AMD3H) based on the 5-year risk of progression enabled identification of distinct gene and pathway changes associated with progression to late-stage disease. Identified changes in gene expression were validated using ELISA or histological methods. RPE-specific genes and lipid metabolic pathways showed a transient increase in AMD3L followed by a pronounced decrease in AMD3H. In AMD3H, immune response genes such as C3, TREM2, and OLR1 were upregulated when compared to AMD3L samples, as well as genes specific to Muller glia/astrocytes (NGFR, SPP1, GPX3). Our findings support complement inhibition as a promising therapeutic option for slowing conversion to advanced AMD and identify macrophage and Muller/astrocyte genes as potential cell types to target in AMD. Further, we demonstrate the value of combining emerging, outcomes-based, clinically relevant grading systems with profiling technologies to generate new insights into ocular diseases. HighlightsO_LIIntermediate AMD (AMD3) can be further divided into 3 stages - AMD3L (low risk), AMD3M (intermediate risk), AMD3H (high risk) - using the MGS9 grading system based on the risk of disease progression to late AMD. C_LIO_LIRNA sequencing of the macular RPE/choroid shows opposing changes in gene expression of multiple biological pathways for both RPE and immune cells between AMD3L and AMD3H stages. C_LIO_LIIn the macular neural retina, most biological pathways were downregulated in AMD2 (early AMD) but upregulated in AMD4 (late AMD) compared to AMD1 (non-AMD control). C_LIO_LIMolecular and cellular signatures associated with a high risk of progression to AMD4 include activation of complement C3, two subtypes of macrophages expressing either TREM2 or OLR1, and Muller glia/astrocytes as evidenced by the upregulation of GFAP and NGFR. C_LIO_LIUnderstanding the roles of these high-risk associated genes in AMD progression will facilitate the development of new treatments that prevent or delay the irreversible central vision loss in AMD patients. C_LI

neuroscience↗

bioRxiv2025

CNVPipe: An enhanced pipeline for accurate analysis of copy number variation from whole-genome sequencing

Copy number variations (CNVs) are critical contributors to the genetic architecture of complex diseases, yet many existing pipelines for whole-genome sequencing (WGS) data exhibit persistently high false discovery rates (FDR). Here, we introduce CNVPipe, an enhanced workflow that integrates widely used CNV-calling tools with a novel machine-learning framework to achieve lower FDR and higher sensitivity. CNVPipe also provides a specialised module for single-cell CNV analysis, featuring a new model that accurately estimates the ploidy of single cells to get integer copy number profile. Benchmark evaluations demonstrate that CNVPipe outperforms current pipelines in various genomic contexts. In addition to detecting recurrent CNVs in paediatric developmental disorders, CNVPipe enables large-scale functional genomics applications involving stem cell technologies. Moreover, its application to sparse single-cell DNA sequencing data provides a new aspect of research in cancer evolution. Collectively, these findings underscore the versatility and reliability of CNVPipe as a comprehensive solution for CNV detection in WGS-based research.

systems biology↗

bioRxiv2024

APOE Impacts Lipid Trafficking in Retinal Pigment Epithelium Cells

Age-related macular degeneration (AMD) is typified by the formation of lipid-rich drusen under the retinal pigment epithelium (RPE) layer. Apolipoprotein E (APOE) is a known genetic risk factor for AMD and a substantial component of drusen, however, the mechanism by which APOE variants contribute to AMD pathology remains unclear. APOE is the primary cholesterol and lipid transport protein of the central nervous system, as well as a component circulating lipoproteins. To better understand how APOE-dependent lipid transport may impact AMD risk, we generated isogenic APOE iPS-RPE cells expressing each of the common human APOE isoforms, as well as an APOE knockout line. APOE knockout cells showed significant morphological and barrier function deficits, suggesting that APOE is essential for RPE health. Furthermore, we observed that APOE abundance is isoform-dependent in RPE cells and that lipid transport is deficient in APOE knockout RPE cells, as well as in RPE cells expressing APOE2, a variant associated with higher risk of AMD. Contrastingly, cells expressing APOE4 seem to respond strongly to lipid challenges by upregulating APOE to support efficient lipid transport. Our results suggest that disease associated APOE variants may impact lipid transport in RPE, contributing to the formation of drusen and impairing cellular function.

cell biology↗

bioRxiv2024

Proteomic profile analysis of plasma and aqueous humor from glaucoma and non-glaucomatous patients

PurposeGlaucoma, a multifactorial ocular neuropathy, can lead to irreversible vision loss. Diagnosis involves assessing optic cupping (increased cup-to-disc ratios) and structural changes (like retinal nerve fiber layer thinning) through clinical imaging. Elevated intraocular pressure (IOP) is commonly associated with glaucoma, but not always. However, understanding disease progression is hindered by limited access to donor ocular tissue and consistent clinical data. We hypothesize that the proteome of aqueous humor and plasma may be altered in disease and correlates with clinical parameters such as IOP and cup-to-disc ratios. MethodsAqueous humor (AH) and plasma samples were collected from 36 glaucoma patients (17 male, 19 female), and 35 non-glaucomatous control patients (16 male, 19 female) undergoing cataract surgery. The protein profile was compared using the SOMAscan(R) assay system for proteome profiling. From glaucomatous donors, correlations between IOP and cup- to-disc ratios to proteome differences were determined. ResultsOverall proteomics profiles between both AH and plasma were compared by combining all samples (glaucoma and non-glaucoma) and then performing correlation analyses. This study revealed similar protein abundance in the two biological fluids. Additionally, it identified different abundance of proteins in plasma and AH between glaucoma and non- glaucoma samples. The differential proteins identified were involved in pathways related to vascular integrity, inflammation, immune response, cell adhesion, and complement activation. Generally, glaucomatous AH showed higher protein levels. Neurofilament light chain (NEFL) protein correlated with elevated IOP and inflammatory markers, but not with cup-to-disc ratios. ConclusionsTogether, our data demonstrate that the proteins identified in this study from glaucomatous donors correspond to markers of neurodegeneration and those that may inhibit cell proliferation or disrupt vascular integrity.

cell biology↗

bioRxiv2024

Conformational landscape of soluble α-klotho revealed by cryogenic electron microscopy

-Klotho (KLA) is a type-1 membranous protein that can associate with fibroblast growth factor receptor (FGFR) to form co-receptor for FGF23. The ectodomain of unassociated KLA is shed as soluble KLA (sKLA) to exert FGFR/FGF23-independent pleiotropic functions. The previously determined X-ray crystal structure of the extracellular region of sKLA in complex with FGF23 and FGFR1c suggests that sKLA functions solely as an on-demand coreceptor for FGF23. To understand the FGFR/FGF23-independent pleiotropic functions of sKLA, we investigated biophysical properties and structure of apo-sKLA. Mass photometry revealed that sKLA can form a stable structure with FGFR and/or FGF23 as well as sKLA dimer in solution. Single particle cryogenic electron microscopy (cryo-EM) supported the dimeric structure of sKLA. Cryo-EM further revealed a 3.3[A] resolution structure of apo-sKLA that overlays well with its counterpart in the ternary complex with several distinct features. Compared to the ternary complex, the KL2 domain of apo-sKLA is more flexible. 3D variability analysis revealed that apo-sKLA adopts conformations with different KL1-KL2 interdomain bending and rotational angles. The potential multiple forms and shapes of sKLA support its role as FGFR-independent hormone with pleiotropic functions. A comprehensive understanding of the sKLA conformational landscape will provide the foundation for developing klotho-related therapies for diseases.

biophysics↗

bioRxiv2024

Transport activity regulates mitochondrial bioenergetics and biogenesis in renal tubules

Renal tubules are featured with copious mitochondria and robust transport activity. Mutations in mitochondrial genes cause congenital renal tubulopathies, and changes in transport activity affect mitochondrial morphology, suggesting mitochondrial function and transport activity are tightly coupled. Current methods of using bulk kidney tissues or cultured cells to study mitochondrial bioenergetics are limited. Here, we optimized an extracellular flux analysis (EFA) to study mitochondrial respiration and energy metabolism using microdissected mouse renal tubule segments. EFA detects mitochondrial respiration and glycolysis by measuring oxygen consumption and extracellular acidification rates, respectively. We show that both measurements positively correlate with sample sizes of a few centimeter-length renal tubules. The thick ascending limbs (TALs) and distal convoluted tubules (DCTs) predominantly utilize glucose/pyruvate as energy substrates, whereas proximal tubules (PTs) are significantly much less so. Acute inhibition of TALs transport activity by ouabain treatment reduces basal and ATP-linked mitochondrial respiration. Chronic inhibition of transport activity by 2-week furosemide treatment or deletion of with-no-lysine kinase 4 (Wnk4) decreases maximal mitochondrial capacity. In addition, chronic inhibition downregulates mitochondrial DNA mass and mitochondrial length/density in TALs and DCTs. Conversely, gain-of-function Wnk4 mutation increases maximal mitochondrial capacity and mitochondrial length/density without increasing mitochondrial DNA mass. In conclusion, EFA is a sensitive and reliable method to investigate mitochondrial functions in isolated renal tubules. Transport activity tightly regulates mitochondrial bioenergetics and biogenesis to meet the energy demand in renal tubules. The system allows future investigation into whether and how mitochondria contribute to tubular remodeling adapted to changes in transport activity. Key pointsO_LIA positive correlation between salt reabsorption and oxygen consumption in mammalian kidneys hints at a potential interaction between transport activity and mitochondrial respiration in renal tubules. C_LIO_LIRenal tubules are heterogeneous in transport activity and mitochondrial metabolism, and traditional assays using bulk kidney tissues cannot provide segment-specific information. C_LIO_LIHere, we applied an extracellular flux analysis to investigate mitochondrial respiration and energy metabolism in isolated renal tubules. This assay is sensitive in detecting oxygen consumption and acid production in centimeter-length renal tubules and reliably recapitulates segment-specific metabolic features. C_LIO_LIAcute inhibition of transport activity reduces basal and ATP-linked mitochondrial respirations without changing maximal mitochondrial respiratory capacity. Chronic alterations of transport activity further adjust maximal mitochondrial respiratory capacity via regulating mitochondrial biogenesis or non-transcriptional mechanisms. C_LIO_LIOur findings support the concept that renal tubular cells finely adjust mitochondrial bioenergetics and biogenesis to match the new steady state of transport activity. C_LI

physiology↗

bioRxiv2024

Effects of local and landscape factors on paddy field arthropod diversity: from species to communities

Agricultural landscapes are dynamic mosaics where environmental conditions vary across spatial scales. Identifying the spatial scales of environmental variables relevant to biodiversity is therefore essential for safeguarding biodiversity and the ecosystem services they provide. Although species richness is a useful aggregate metric the captures the responses of biodiversity as a whole, few studies have examined how species-specific responses to environmental variables give rise to community-level patterns. Failure to account for the heterogeneity in species responses may undermine potential processes that structure biodiversity. In this study, we sampled paddy-field inhabiting arthropods across the first growing season and examined how local (organic farming, water depth, and crop height) and landscape factors (forest cover and connectivity) affect their abundance and distribution. We built a spatio-temporally explicit joint species distribution model (JSDM) to answer three main questions. 1) How do species differ in their response to local and landscapes factors. 2) Can trophic guild explain the variation in species responses to environmental covariates, and 3) How do species-specific responses scale-up to structure species richness at the community-level? Our results show that the mean importance of environmental covariates was low overall (mean R2 = 0.21), suggesting the prevalence of stochasticity in structuring species abundances. However, environmental importance varied substantially across species (highest R2 = 0.87 and lowest R2 = 0.01) and that trophic guild explained only approximately 15% of species responses, which indicates high idiosyncrasy in species responses both within and among guilds. At the community-level, we found that species richness responds negligibly to local factors while increasing with forest cover at the landscape scale. The importance of each environmental covariate was reflected by the variability of species responses. Lastly, we found no evidence of dispersal limitation in structuring species abundances. Taken together, our study suggests that many paddy field arthropods exhibit transient dynamics and that environmental effects are highly species-specific, even within the same trophic guild. Most importantly, our study highlights the need to understand biodiversity from the species level to understand the processes that structure them in dynamic mosaic landscapes.

ecology↗

bioRxiv2023

WNK1 enforces macrophage lineage fidelity

The appropriate development of macrophages, the bodys professional phagocyte, is essential for organismal development, especially in mammals. This dependence is exemplified by the observation that loss-of-function mutations in colony stimulating factor 1 receptor (CSF1R) results in multiple tissue abnormalities owing to an absence of macrophages. Despite this importance, little is known about the molecular and cell biological regulation of macrophage development. Here, we report the surprising finding that the chloride-sensing kinase With-no-lysine 1 (WNK1) is required for development of tissue-resident macrophages (TRMs). Myeloid-specific deletion of Wnk1 resulted in a dramatic loss of TRMs, disrupted organ development, systemic neutrophilia, and mortality between 3 and 4 weeks of age. Strikingly, we found that myeloid progenitors or precursors lacking WNK1 not only failed to differentiate into macrophages, but instead differentiated into neutrophils. Mechanistically, the cognate CSF1R cytokine macrophage-colony stimulating factor (M-CSF) stimulates macropinocytosis by both mouse and human myeloid progenitors and precursor cells. Macropinocytosis, in turn, induces chloride flux and WNK1 phosphorylation. Importantly, blocking macropinocytosis, perturbing chloride flux during macropinocytosis, and inhibiting WNK1 chloride-sensing activity each skewed myeloid progenitor differentiation from macrophages into neutrophils. Thus, we have elucidated a role for WNK1 during macropinocytosis and discovered a novel function of macropinocytosis in myeloid progenitors and precursor cells to ensure macrophage lineage fidelity. Highlights- Myeloid-specific WNK1 loss causes failed macrophage development and premature death - M-CSF-stimulated myeloid progenitors and precursors become neutrophils instead of macrophages - M-CSF induces macropinocytosis by myeloid progenitors, which depends on WNK1 - Macropinocytosis enforces macrophage lineage commitment

immunology↗

bioRxiv2023

Refined novel techniques for long term cryo-storage using vitrification and laser warming

Vitrification and ultra-rapid laser warming technique is an important approach for cryopreservation of animal embryos and oocytes, as well as other cells with medicinal, genetic, and agricultural value. We believe that the long term cryo-storage after vitrification and for the following laser warming has only been achieved to date using our customized device which was first attempted to be developed in our study. In the present study, we focused on developing alignment and bonding techniques for special cryo-jig which were assembling jig tool and jig holder in one piece. This newly produced customized cryo-jig was demonstrated to have significantly high laser striking accuracy of 95% and a successful rewarming rate of 62%. This study was experimentally demonstrate an refined novel device for improvement of laser striking accuracy after long term cryo-storage using vitrification and laser warming technique. In addition, the customized device described herein was successfully applied to a biological sample with over a thousand coral larvae in long term cryo-storage (The first cryo-repository for coral larvae; the results related to coral cryobanking and repositry described in this preprint will be published separately in details). We anticipate that our core findings will provide further examples of cryobanking applications that use vitrification and nano-laser warming to help a wide range of cells and tissues from diverse species.

bioengineering↗

bioRxiv2021

Chloride oscillation in pacemaker neurons regulates circadian rhythms through a chloride-sensing WNK kinase signaling cascade

Central pacemaker neurons regulate circadian rhythms and undergo diurnal variation in electrical activity in mammals and flies. In mammals, circadian variation in the intracellular chloride concentration of pacemaker neurons has been proposed to influence the response to GABAergic neurotransmission through GABAA receptor chloride channels. However, results have been contradictory, and a recent study demonstrated circadian variation in pacemaker neuron chloride without an effect on GABA response. Therefore, whether and how intracellular chloride regulates circadian rhythms remains controversial. Here, we demonstrate a signaling role for intracellular chloride in the Drosophila ventral lateral (LNv) pacemaker neurons. In control flies, intracellular chloride increases in LNv neurons over the course of the morning. Chloride transport through the sodium-potassium-2-chloride (NKCC) and potassium-chloride (KCC) cotransporters is a major determinant of intracellular chloride concentrations. Drosophila melanogaster with loss-of-function mutations in the NKCC encoded by Ncc69 have abnormally low intracellular chloride six hours after lights on, and a lengthened circadian period. Loss of kcc, which is expected to increase intracellular chloride, suppresses the long-period phenotype of Ncc69 mutant flies. Activation of a chloride-inhibited kinase cascade, consisting of the WNK (With No Lysine (K)) kinase and its downstream substrate, Fray, is necessary and sufficient to prolong period length. Fray activation of an inwardly rectifying potassium channel, Irk1, is also required for the long-period phenotype. These results indicate that the NKCC-dependent rise in intracellular chloride in Drosophila LNv pacemaker neurons restrains WNK-Fray signaling and overactivation of an inwardly rectifying potassium channel to maintain normal circadian period length.

neuroscience↗

bioRxiv2021

Kidney-Specific WNK1 Amplifies NCC Responsiveness to Potassium Imbalance

To maintain potassium homeostasis, the kidneys distal convoluted tubule (DCT) converts small changes in blood [K+] into robust effects on salt reabsorption. This process requires NaCl cotransporter (NCC) activation by WNK kinases. During hypokalemia, the Kidney-Specific WNK1 isoform (KS-WNK1) scaffolds the DCT-expressed WNK signaling pathway within biomolecular condensates of unknown function termed WNK bodies. Here, we show that KS-WNK1 amplifies the dynamic range of NCC activity in response to potassium imbalance, in part via WNK bodies. Targeted condensate disruption traps the WNK pathway, causing renal salt-wasting that is more pronounced in females. In humans, WNK bodies accumulate as plasma potassium falls below 4.0mmol/L, suggesting avid condensate-mediated salt reabsorption even when [K+] is low-normal. These data identify WNK bodies as signal amplifiers that mediate tubular potassium responsiveness, nephron sexual dimorphism, and blood pressure salt-sensitivity. Our results illustrate how condensate specialization can optimize a mammalian physiologic stress response that impacts human health.

physiology↗

bioRxiv2020

DNA barcodes and reliable molecular identifications in a diverse group of invasive pests: lessons from Bactrocera fruit flies on variation across the COI gene, introgression, and standardization

The utility of a universal DNA barcode fragment of 658 base pairs of the Cytochrome C Oxidase I (COI) gene for the recognition of all animal species has been a widely debated topic on theoretical and practical levels. Regardless of its challenges, large amounts of COI sequence data have been produced in the last two decades. To optimally use the data towards reliable species identification will require further steps to validate the method and reference libraries. The fruit fly tribe Dacini holds about a thousand species, of which eighty are pests of economic concern, including some of the worlds foremost fruit and vegetable pests, and there are many morphologically cryptic species complexes in the tribe. Where previous studies showed limited success in using COI to identify Dacini, our results with a highly curated morphological dataset indicate high congruence between morphology and COI: 90% of the species in our 5,576 sequences, 262-species global dataset can be identified with COI alone based on a monophyly criterion. However, in some key pest species belonging to complexes that were previously thought diagnosable with COI, we found that expanded sampling and independent validation of identifications using genomic data revealed introgression of mitochondrial DNA. We find that the informative SNPs are uniformly distributed across the COI gene, and we provide recommendations for standardization. We conclude that reliable molecular identifications with COI require extensive species coverage, population sampling, and genomics-supported reference identifications before they can be validated as a "diagnostic" marker for specific groups.

evolutionary biology↗

bioRxiv2020

Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin

Since the SARS outbreak 18 years ago, a large number of severe acute respiratory syndrome related coronaviruses (SARSr-CoV) have been discovered in their natural reservoir host, bats1-4. Previous studies indicated that some of those bat SARSr-CoVs have the potential to infect humans5-7. Here we report the identification and characterization of a novel coronavirus (nCoV-2019) which caused an epidemic of acute respiratory syndrome in humans, in Wuhan, China. The epidemic, started from December 12th, 2019, has caused 198 laboratory confirmed infections with three fatal cases by January 20th, 2020. Full-length genome sequences were obtained from five patients at the early stage of the outbreak. They are almost identical to each other and share 79.5% sequence identify to SARS-CoV. Furthermore, it was found that nCoV-2019 is 96% identical at the whole genome level to a bat coronavirus. The pairwise protein sequence analysis of seven conserved non-structural proteins show that this virus belongs to the species of SARSr-CoV. The nCoV-2019 virus was then isolated from the bronchoalveolar lavage fluid of a critically ill patient, which can be neutralized by sera from several patients. Importantly, we have confirmed that this novel CoV uses the same cell entry receptor, ACE2, as SARS-CoV.

microbiology↗