Biology subjects

Ordonez, A.

Publications and source records attributed to Ordonez, A..

11 recordsLinked to original sources

bioRxiv2026

Two decades of Novel Ecosystems: Literature analysis of topics, trends and connectivity

1. As human-driven climate change and other anthropogenic forces produce widespread impacts on biodiversity and ecosystem functioning, many ecosystems are shifting into unprecedented, novel states. The Novel Ecosystem Concept (NEC), formalized in 2006, was developed as an alternative framework for managing "novel ecosystems", human-altered systems that are challenging to restore to their historical state. In the years since, the NEC has been proposed as a broader lens for ecosystem management under ongoing global change. 2. We evaluated how the uptake and potential of the NEC have been realized over time using a bibliometric and linguistic toolkit. Using bibliometric data from the Web of Science, we clustered 40,914 applied ecology papers published between 2006 and 2025 into twenty research topics based on language use. We quantified the volume of NEC research within each topic, rates of publication over time, and cross-topic connectivity proxied by citations. 3. We found NEC research in most of the topics of applied ecology, particularly invasion biology, ecosystem services, soil research and studies of freshwater, urban and marine systems. In contrast, several major conservation-focused topics, including protected areas, threatened species, and human-wildlife interactions, contained little research with an explicit link to novel ecosystems. Publication rates increased across all topics, although growth slowed over time. At the same time, NEC research became more focused into ecosystem-specific topics, especially marine ecosystems. NEC research across different topics was well-connected by citations, with papers more likely to cite each other when they used similar language. 4. Overall, the NEC does not appear to have expanded beyond its origins in restoration to become a broadly applied framework across conservation and ecosystem management. Instead, the concepts behind the NEC have been integrated into restoration and management frameworks grappling with climate and other anthropogenic change, while "novelty" is emerging as a powerful quantitative variable for measuring ecological change over space and time. Our results highlight the potential value of bibliometric and linguistic tools to deconstruct the ecological literature to inform what we can, or should, do to intervene for benefit of nature and people.

ecology↗

bioRxiv2025

Both terminal misfolding and polymerisation contribute to disease-relevant phenotypic changes in cell models of α1-antitrypsin deficiency-associated liver disease

Polymerisation of 1-antitrypsin within hepatocytes is considered central to the pathogenesis of 1-antitrypsin deficiency-associated liver fibrosis, most commonly in homozygotes for the Z (p.Glu342Lys) allele. Polymerisation proceeds via self-association of monomeric intermediate states. In parallel, >50% of synthesised Z 1-antitrypsin is instead recognized as terminally-misfolded and degraded. It is unclear whether this contributes to Z 1-antitrypsin deficiency-associated liver disease. We characterised the relationships between polymer formation, terminal misfolding and their cellular consequences, using label-free proteomics mass spectrometry (MS), light and electron microscopy, and cellular assays. Proteomic analyses of well-established CHO cell models of hepatocyte handling of 1-antitrypsin variants indicated that cellular responses to the Z mutation were surprisingly similar to those seen with the NullHongKong variant (NHK), which can only misfold terminally and cannot polymerise. A minor set of proteins showed increases associated with Z and not NHK 1-antitrypsin expression, consistent with a polymer-specific response, characterized by association with increased organellar organization and vesicle-mediated transport. Conversely, proteostatic and pro-fibrotic integrin-associated pathways increased with the degree of terminal misfolding of the expressed 1-antitrypsin variant. Bioenergetic pathway changes indicated concomitant switching from oxidative to glycolytic metabolism. Cell studies further correlated fibrosis-associated behaviours with terminal misfolding rather than polymerisation. Terminal misfolding, as well as polymerisation behaviour, may therefore be important for pro-fibrotic responses including metabolic reprogramming and senescence in Z 1-antitrypsin deficiency. Molecular therapies may prove most efficacious for associated liver disease if they address terminal misfolding as well as polymerisation.

cell biology↗

bioRxiv2025

Metabolite import via SLC33A1 enables ATF6 activation by endoplasmic reticulum stress

The transcription factor ATF6 has a central role in adapting mammalian cells to endoplasmic reticulum (ER) stress via the Unfolded Protein Response (UPR). This has driven efforts to identify modulators of ATF6 signalling. Here, an unbiased genome-wide CRISPR-Cas9 screen performed in Chinese Hamster Ovary (CHO) cells revealed that proteolytic processing of the ATF6 precursor to its active form was impaired in CHO cells lacking the ER-resident solute carrier SLC33A1, a transporter involved in acetyl-CoA import, sialylation and N{varepsilon}-lysine protein acetylation. Cells lacking SLC33A1 constitutively trafficked the ATF6 precursor to the Golgi, but exhibit impaired subsequent Golgi processing, correlating with altered ATF6 Golgi glycosylation. SLC33A1 deficiency also deregulated activation of the IRE1 branch of the UPR, pointing to a selective loss of ATF6-mediated negative feedback in the UPR. Notably, Slc33a1-deleted cells accumulated higher levels of unmodified sialylated N-glycans, precursors to acetylated glycans, likely reflecting impaired glycan processing. By contrast, deletion of ER-localised acetyltransferases NAT8 and NAT8B, which catalyse protein N{varepsilon}-lysine acetylation in the secretory pathway, did not replicate the ATF6 processing defects observed in Slc33a1-deficient cells. Together, our findings highlight a role for SLC33A1-mediated metabolite transport in the post-ER maturation of ATF6 and point direct links between small-molecule metabolism and branch-specific signalling in the UPR.

cell biology↗

bioRxiv2024

Target deconvolution of an insulin hypersecretion-inducer acting through VDAC1 with a distinct transcriptomic signature in beta-cells

Obesity, insulin resistance, and a host of environmental and genetic factors can drive hyperglycemia, causing {beta}-cells to compensate by increasing insulin production and secretion. In type 2 diabetes (T2D), {beta}-cells under these conditions eventually fail. Rare {beta}-cell diseases like congenital hyperinsulinism (HI) also cause inappropriate insulin secretion, and some HI patients develop diabetes. However, the mechanisms of insulin hypersecretion and how it causes {beta}-cell dysfunction are not fully understood. We previously discovered small molecules (e.g. SW016789) that cause insulin hypersecretion and lead to a loss in {beta}-cell function without cell death. Here, we uncover the protein target of SW016789 and provide the first time-course transcriptomic analysis of hypersecretory responses versus thapsigargin-mediated ER stress in {beta}-cells. In mouse MIN6 and human EndoC-{beta}H1 {beta}-cells, we identified and validated VDAC1 as a SW016789 target using photoaffinity proteomics, cellular thermal shift assays, siRNA, and small molecule inhibitors. SW016789 raises membrane potential to enhance Ca2+ influx, potentially through VDAC1. Chronically elevated intracellular Ca2+ appears to underpin the negative impacts of hypersecretion, as nifedipine protected against each small molecule hypersecretion inducer we tested. Using time- course RNAseq, we discovered that hypersecretion induced a distinct transcriptional pattern compared to ER stress. Clustering analyses led us to focus on ER-associated degradation (ERAD) as a potential mediator of the adaptive response. SW016789 reduced the abundance of ERAD substrate OS-9 and pharmacological inhibition of ERAD worsened {beta}-cell survival in response to hypersecretory stress. Changes in other ERAD components in MIN6 and EndoC-{beta}H1 at the protein level were minor with either SW016789 or thapsigargin. However, immunostaining for core ERAD components SEL1L, HRD1, and DERL3 in non-diabetic and T2D human pancreas revealed altered distributions of SEL1L/HRD1 and SEL1L/DERL3 rations in {beta}-cells of T2D islets, in alignment with altered ERAD in stressed {beta}-cells. We conclude that hypersecretory stimuli, including SW016789- mediated VDAC1 activation, cause enhanced Ca2+ influx and insulin release. Subsequent differential gene expression represents a {beta}-cell hypersecretory response signature that is reflected at the protein level for some, but not all genes. A better understanding of how {beta}-cells induce hypersecretion and the mechanisms of negative feedback on secretory rate may lead to the discovery of novel therapeutic targets for T2D and HI.

cell biology↗

bioRxiv2024

A genome wide CRISPR/Cas9 screen identifies calreticulin as a selective repressor of ATF6

Activating transcription factor 6 (ATF6) is one of three endoplasmic reticulum (ER) transmembrane stress sensors that mediate the unfolded protein response (UPR). Despite its crucial role in long-term ER stress adaptation, regulation of ATF6 alpha () signalling remains poorly understood, possibly because its activation involves ER-to-Golgi and nuclear trafficking. Here, we generated an ATF6/IRE1 dual UPR reporter CHO-K1 cell line and performed an unbiased genome-wide CRISPR/Cas9 mutagenesis screen to systematically profile genetic factors that specifically contribute to ATF6 signalling in the presence and absence of ER stress. The screen identified both anticipated and new candidate genes that regulate ATF6 activation. Among these, calreticulin (CRT), a key ER luminal chaperone, selectively repressed ATF6 signalling: Cells lacking CRT constitutively activated a BiP::sfGFP ATF6-dependent reporter, had higher BiP levels and an increased rate of trafficking and processing of ATF6. Purified CRT interacted with the luminal domain of ATF6 in vitro and the two proteins co-immunoprecipitated from cell lysates. CRT depletion exposed a negative feedback loop implicating ATF6 in repressing IRE1 activity basally and overexpression of CRT reversed this repression. Our findings indicate that CRT, beyond its known role as a chaperone, also serves as an ER repressor of ATF6 to selectively regulate one arm of the UPR.

cell biology↗

bioRxiv2023

Ecological Network Resilience & Extinction Proxies - Updating Projections of Ecological Networks

Forecasting biodiversity and functioning changes to ecosystem composition and functioning under climate change requires using multi-species approaches that explicitly consider ecological interactions. Here, we propose a framework with which to incorporate considerations of (1) localised extinction risk proxies, (2) resilience mechanisms of ecological networks, and (3) extinction cascade directionality as a driving force of ecological change. These three aspects are seldomly considered when establishing ecosystems responses to climate change and biodiversity loss. Using this framework, we demonstrate that current practices may severely underpredict ecological change measured as loss of biodiversity and change in connectedness. Our novel framework which explicitly explores two-dimensional resilience landscapes defined by network resilience mechanisms (i.e., link loss sensitivity and realisation of rewiring potential) represents the most complete toolbox for assessment of vulnerability of ecological networks to extinction cascades. Ultimately, we propose that using localised extinction proxies, explicitly quantifying ecological network resilience through link-loss sensitivity and realisation of rewiring potential, as well as simulation of bidirectional extinction cascades will lead to improved capabilities of estimating ecosystem trajectories throughout the Anthropocene.

ecology↗

bioRxiv2023

Ecological network inference is not consistent across sales or approaches

Identifying the most suitable method of ecological network inference in line with individual research considerations is a non-trivial task, which significantly hinders adoption of network approaches to forest management applications. To advance the study of ecological networks and better guide their use in managing forest ecosystems, we propose a framework that aligns pairwise species-association inference methods with specific research questions, biological interaction types, data availability, and spatial scales of study. We motivate the adoption of this framework through an empirical comparison of multiple inference methods, highlighting substantial inconsistencies that arise across scales and methodologies. Using data on species distributions and attributes at local, regional, and continental scales for temperate conifer forests in North America, we show that network inference varies significantly depending on whether occurrence, abundance, or performance data are used and the degree to which confounding factors are accounted for. Across four widely used and/or cutting-edge inference methods (COOCCUR, NETASSOC, HMSC, NDD-RIM), we find notable disparities in both whole-network metrics and pairwise species associations, particularly at continental scales. These findings underscore that no single method is likely to universally outperforms others across scales, emphasizing the importance of choosing an inference approach that aligns with specific ecological and spatial contexts. Our framework aids in interpreting network topologies and interactions in light of these method- and datatype-driven variances, providing a structured approach to more reliably infer ecological associations and address complex network dynamics in forest management practices.

bioinformatics↗

bioRxiv2021

Sex differences in lung imaging and SARS-CoV-2 antibody responses in a COVID-19 golden Syrian hamster model

In the ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), more severe outcomes are reported in males compared with females, including hospitalizations and deaths. Animal models can provide an opportunity to mechanistically interrogate causes of sex differences in the pathogenesis of SARS-CoV-2. Adult male and female golden Syrian hamsters (8-10 weeks of age) were inoculated intranasally with 105 TCID50 of SARS-CoV-2/USA-WA1/2020 and euthanized at several time points during the acute (i.e., virus actively replicating) and recovery (i.e., after the infectious virus has been cleared) phases of infection. There was no mortality, but infected male hamsters experienced greater morbidity, losing a greater percentage of body mass, developing more extensive pneumonia as noted on chest computed tomography, and recovering more slowly than females. Treatment of male hamsters with estradiol did not alter pulmonary damage. Virus titers in respiratory tissues, including nasal turbinates, trachea, and lungs, and pulmonary cytokine concentrations, including IFN{beta} and TNF, were comparable between the sexes. However, during the recovery phase of infection, females mounted two-fold greater IgM, IgG, and IgA responses against the receptor-binding domain of the spike protein (S-RBD) in both plasma and respiratory tissues. Female hamsters also had significantly greater IgG antibodies against whole inactivated SARS-CoV-2 and mutant S-RBDs, as well as virus neutralizing antibodies in plasma. The development of an animal model to study COVID-19 sex differences will allow for a greater mechanistic understanding of the SARS-CoV-2 associated sex differences seen in the human population. ImportanceMen experience more severe outcomes from COVID-19 than women. Golden Syrian hamsters were used to explore sex differences in the pathogenesis of a human clinical isolate of SARS-CoV-2. After inoculation, male hamsters experienced greater sickness, developed more severe lung pathology, and recovered more slowly than females. Sex differences in disease could not be reversed by estradiol treatment in males and were not explained by either virus replication kinetics or the concentrations of inflammatory cytokines in the lungs. During the recovery period, antiviral antibody responses in the respiratory tract and plasma, including to newly emerging SARS-CoV-2 variants, were greater in females than male hamsters. Greater lung pathology during the acute phase combined with reduced antiviral antibody responses during the recovery phase of infection in males than females illustrate the utility of golden Syrian hamsters as a model to explore sex differences in the pathogenesis of SARS-CoV-2 and vaccine-induced immunity and protection. One Sentence SummaryFollowing SARS-CoV-2 infection, male hamsters experience worse clinical disease and have lower antiviral antibody responses than females.

microbiology↗

bioRxiv2020

Cargo receptor-assisted endoplasmic reticulum export of pathogenic α1-antitrypsin polymers

Circulating polymers of alpha1-antitrypsin (1AT) are chemo-attractant for neutrophils and contribute to inflammation in pulmonary, vascular and adipose tissues. Cellular factors affecting the intracellular itinerary of mutant polymerogenic 1AT remain obscure. Here, we report on an unbiased genome-wide CRISPR/Cas9 screen for regulators of trafficking of the polymerogenic 1ATH334D variant. Single guide RNAs targeting genes whose inactivation enhanced accumulation of polymeric 1AT were enriched by iterative construction of CRISPR libraries based on genomic DNA from fixed cells selected for high polymer content by fluorescence-activated cell sorting. This approach bypassed the limitation to conventional enrichment schemes imposed by cell fixation and identified 121 genes involved in polymer retention at false discovery rate < 0.1. From that set of genes, the pathway cargo loading into COPII-coated vesicles was overrepresented with 16 significant genes, including two transmembrane cargo receptors, LMAN1 (ERGIG-53) and SURF4. LMAN1 and SURF4-disrupted cells displayed a secretion defect extended beyond 1AT monomers to polymers, whose low-level secretion was especially dependent on SURF4 and correlated with SURF4-1ATH334D physical interaction and with enhanced co-localisation of polymeric 1ATH334D with the endoplasmic reticulum (ER). These findings suggest that ER cargo receptors co-ordinate intracellular progression of 1AT out of the ER and modulate the accumulation of polymeric 1AT not only by controlling the concentration of precursor monomers but also through a previously-unrecognised role in secretion of the polymers themselves.

cell biology↗

bioRxiv2020

Development of a small molecule that corrects misfolding and increases secretion of Z α1-antitrypsin

Severe 1-antitrypsin deficiency results from the Z allele (Glu342Lys) that causes the accumulation of homopolymers of mutant 1-antitrypsin within the endoplasmic reticulum of hepatocytes in association with liver disease. We have used a DNA-encoded chemical library to undertake a high throughput screen to identify small molecules that bind to, and stabilise Z 1-antitrypsin. The lead compound blocks Z 1-antitrypsin polymerisation in vitro, reduces intracellular polymerisation and increases the secretion of Z 1-antitrypsin three-fold in mammalian cells including an iPSC model of disease. Crystallographic and biophysical analyses demonstrate that GSK716 and related molecules bind to a cryptic binding pocket, negate the local effects of the Z mutation and stabilise the bound state against progression along the polymerization pathway. Oral dosing of transgenic mice at 100 mg/kg three times a day for 20 days increased the secretion of Z 1-antitrypsin into the plasma by 7-fold. There was no observable clearance of hepatic inclusions with respect to controls. This study provides proof-of-principle that mutation ameliorating small molecules are a viable approach to treat protein conformational diseases.

pharmacology and toxicology↗

bioRxiv2018

The integrated stress response mediates type I interferon driven necrosis in Mycobacterium tuberculosis granulomas

Necrosis in the tuberculous granuloma is a hallmark of tuberculosis that enables pathogen survival and transmission. Susceptibility to tuberculosis and several other intracellular bacteria is controlled by a mouse genetic locus, sst1, and mice carrying the sst1-suscepible (sst1S) genotype develop necrotic inflammatory lung lesions, similar to human TB granulomas. Our previous work established that increased disease severity in sst1S mice reflects dysfunctional macrophage effector or tolerance mechanisms, but the molecular mechanisms have remained unclear. Here we demonstrate that sst1S macrophages develop aberrant, biphasic responses to TNF characterized by super-induction of stress and type I interferon pathways after prolonged TNF stimulation with this late-stage response being initiated by oxidative stress and Myc activation and driven via a JNK - IFN{beta} - PKR circuit. This circuit leads to induction of the integrated stress response (ISR) mediated by eIF2 phosphorylation and the subsequent hyper-induction of ATF3 and ISR-target genes Chac1, Trib3, Ddit4. The administration of ISRIB, a small molecule inhibitor of the ISR, blocked the development of necrosis in lung granulomas of M. tuberculosis-infected sst1S mice and concomitantly reduced the bacterial burden revealing that induction of the ISR and the locked-in state of escalating stress driven by type I IFN pathway in sst1S macrophages plays a causal role in the development of necrosis. Our data support a generalizable paradigm in intracellular pathogen-host interactions wherein host susceptibility emerges within inflammatory tissue due to imbalanced macrophage responses to growth, differentiation, activation and stress stimuli. Successful pathogens such as M. tuberculosis may exploit this aberrant response in susceptible hosts to induce necrotic lesions that favor long-term pathogen survival and transmission. Interruption of the aberrant stress response with inhibitors such as ISRIB may offer novel therapeutic strategies.

immunology↗