Biology subjects

Levy, K.

Publications and source records attributed to Levy, K..

12 recordsLinked to original sources

bioRxiv2026

Genomovar-level resolution reveals rapid pathotype switching and genomovar-specific disease potential in diarrheagenic Escherichia coli populations in northern Ecuador

Diarrheagenic Escherichia coli (DEC) pathotypes are commonly defined by molecular detection of discrete virulence genes, yet how quickly these diagnostic genes emerge and move among co-circulating lineages remain unclear. Here, we classified 248 whole-genome-sequenced E. coli isolates from the EcoZUR case-control study in northern Ecuador into intra-species genomovar units using the recently described 99.5% ANI threshold. This framework exposed cryptic population structure, revealing that single sequence types, representing identical multilocus sequence types (MLST), can harbor multiple distinct genomovars. Within individual genomovars, we observed a few cases of different pathotypes among isolates showing ~99.7% ANI (and many such cases between genomovars). Coupled with synteny and phylogeny analyses that revealed pervasive incongruences between pathotype-diagnostic virulence genes and the core genome, these findings suggest recent horizontal gene transfer as the primary driver of pathotype evolution. Virulence gene profiling further revealed that accessory virulence repertoires are hierarchically structured by phylogroup across pathotypes, with genomovars assigned to phylogroups B2 and D exhibiting more conserved virulence architectures than those in phylogroup A and B1. Among DAEC isolates specifically, the B2- and D-associated genomovars showed elevated diarrhea-association rates relative to their phylogroup A counterparts. Rare virulence genes, including Type VI secretion systems, further distinguished diarrhea-associated from asymptomatic genomovars. These findings demonstrate that, although there seems to be within-lineage (phylogroup) conservation of virulence, pathotype identity is a labile state defined by horizontally acquired virulence genes at the genomovar level, and that the genomovar framework provides a biologically meaningful unit for linking intra-species diversity to pathogenic potential and outbreaks.

genomics↗

bioRxiv2025

Microbial source tracking of human and animal fecal contamination in Ecuadorian households

Exposures to both human and animal feces pose human health risks, particularly for young children in low- and middle-income country (LMIC) settings where domestic animals are common, water and sanitation infrastructure is often limited, and enteropathogen transmission is high. Microbial source tracking (MST) markers specific to feces from humans and particular animal types can be used to identify the provenance of microbial contamination, yet most MST studies explore few household environmental sample types, limiting understanding of how marker utility varies by matrix. We validated qPCR assays for six MST markers and quantified their prevalence in 585 samples from 59 households spanning an urban-rural gradient in northwestern Ecuador. We used GenBac3 to test for general fecal contamination, and HF183, Rum2Bac, Pig2Bac, DG37, and GFD to test for human, ruminant, swine, dog, and avian contamination, respectively. Approximately 10 sample types were collected per household, including: rinses of child and adult hands, swabs of floors and surfaces, soil, domestic and drinking water, and food. GenBac3 and HF183 were detected in 77.82% and 15.36% of samples, respectively. Animal-associated markers were detected less frequently, in 0.5-4.1% of samples. However, when present, animal marker concentrations were comparable to HF183. Host-associated markers were most often detected in adult and child hand rinse and floor samples, and GenBac3 concentrations were highest in hand rinses. HF183 detection on adult caregiver hands was associated with increased odds of HF183 detection on childrens hands and floors. ImportanceUnderstanding the sources and pathways of detectable household environmental fecal contamination is critical for identifying how exposures occur and for developing targeted interventions to reduce risk of enteric infection By linking contamination on caregiver hands to that on childrens hands and floors, we highlight a likely route for pathogen transfer in the home. The inclusion of multiple host-associated markers across a wide range of sample types reveals patterns that narrower studies may miss, offering new insights into the complex ecology of fecal contamination. These findings can inform sampling strategies, guide risk assessments, and support the design of interventions aimed at reducing child exposure to enteric pathogens in similar high-risk settings.

microbiology↗

bioRxiv2024

The Structure of the Lujo Virus Spike Complex

Lujo virus is a human pathogen that emerged as the etiology agent of a deadly viral disease in Africa. While it is a member of the Arenaviridae, it is a distinct virus that does not classify with the classical Old World or New World groups of viruses in this family. It further utilizes neuropilin-2 (NRP2) as an entry receptor, a property that is not shared by other arenaviruses. So far, structural information is limited to the receptor binding domain of LUJV, and the overall organization of the trimeric complex, as well as the way NRP2 is recognized in the context of the complete viral spike, were unknown. Here, we present the cryo-EM structure of the complete, native, membrane-embedded spike complex of LUJV. We found that NRP2 is bound at the apex of the spike in a way that allows each trimer to engage with a single NRP2. Also, the complete receptor binding site is quaternary, depending on interactions contributed by neighboring protomers. Recognition of NRP2 involves an overlooked arginine-methionine interaction, which we have now characterized. This LUJVs spike structure, which is the second determined structure of a complete arenaviral spike, points to similarities and differences in the structures of these viral spikes, informing vaccine design and allowing us to be better prepared to combat future outbreaks of this virus.

microbiology↗

bioRxiv2023

When Night Becomes Day: Artificial Light at Night Alters Insect Behavior under Semi-Natural Conditions

Light is the most important Zeitgeber for temporal synchronization in nature. Artificial light at night (ALAN) disrupts the natural light-dark rhythmicity and thus negatively affects animal behavior. However, to date, ALAN research has been mostly conducted under laboratory conditions in this context. Here, we used the field cricket, Gryllus bimaculatus, to investigate the effect of ALAN on insect behavior under semi-natural conditions, i.e., under shaded natural lighting conditions, natural temperature and soundscape. Male crickets were placed individually in outdoor enclosures and exposed to ALAN conditions ranging from <0.01 to 1,500 lx intensity. The crickets stridulation behavior was recorded for 14 consecutive days and nights and their daily activity patterns were analysed. ALAN impaired the crickets stridulation rhythm, evoking a change in the crickets naturally synchronized daily activity period. This was manifested by a light-intensity-dependent increase in the proportion of insects demonstrating an intrinsic circadian rhythm (free-run behavior). This also resulted in a change in the populations median activity cycle period. These ALAN-induced effects occurred despite the crickets exposure to almost natural conditions. Our findings provide further validity to our previous studies on ALAN conducted under lab conditions and establish the deleterious impacts of ALAN on animal behavioral patterns. HighlightsO_LIALAN presents a threat for insect populations and biodiversity C_LIO_LIThe impact of ALAN on insect behavior is mostly studied under laboratory conditions C_LIO_LIWe studied the effects of ALAN on cricket stridulation in semi-natural conditions C_LIO_LIALAN clearly affected the crickets behavior in a light-intensity dependent manner C_LIO_LIThe behavioral effects of ALAN were revealed despite the semi-natural environment C_LIO_LIALAN represents a threat for cricket populations fitness C_LI

animal behavior and cognition↗

bioRxiv2023

Distribution of blaCTX-M-gene variants in E. coli from different origins in Ecuador

The increasing abundance of extended spectrum {beta}-lactamase (ESBL) genes in E. coli, and other commensal and pathogenic bacteria, endangers the utility of third or more recent generation cephalosporins, which are major tools for fighting deadly infections. The role of domestic animals in the transmission of ESBL carrying bacteria has been recognized, especially in low- and middle-income countries, however the horizontal gene transfer of these genes is difficult to assess. Here we investigate blaCTX-M gene diversity (and flanking nucleotide sequences) in E. coli from chicken and humans, in an Ecuadorian rural community and from chickens in another location in Ecuador. The blaCTX-M associated sequences in isolates from humans and chickens in the same remote community showed greater similarity from those found in E. coli in a chicken industrial operation 200 km away. Our study may provide evidence of blaCTX-M transfer between chickens and humans in the community.

microbiology↗

bioRxiv2022

Transcriptional response of circadian clock genes to an 'artificial light at night' pulse in the cricket Gryllus bimaculatus

Light is the major signal entraining the circadian clock that regulates physiological and behavioral rhythms in most organisms, including insects. Artificial Light at Night (ALAN) disrupts the natural light-dark cycle and negatively impacts animals at various levels. We simulated ALAN using dim light stimuli and tested their impact on gene expression in the cricket Gryllus bimaculatus, a model of insect physiology and chronobiology. At night, adult LD crickets were exposed for 30 minutes to a light pulse of 2-40 lx. The relative expression of five circadian clock associated genes was compared using qPCR. A dim ALAN pulse elicited tissue-dependent differential expression in some of these genes. The strongest effect was observed in the brain and in the optic lobe, the crickets circadian pacemaker. Expression of opsin-Long Wave (opLW) was upregulated, as well as cryptochrome1-2 (cry), and period (per). Our findings demonstrate that even a dim ALAN exposure may affect insects at the molecular level, underscoring the detrimental impact of ALAN on the circadian clock system.

animal behavior and cognition↗

bioRxiv2021

Impact of an Urban Sanitation Intervention on Enteric Pathogen Detection in Soils

Environmental fecal contamination is common in many low-income cities, contributing to a high burden of enteric infections and associated negative sequelae. To evaluate the impact of a shared onsite sanitation intervention in Maputo, Mozambique on enteric pathogens in the domestic environment, we collected 179 soil samples at shared latrine entrances from intervention (n= 49) and control (n= 51) compounds during baseline (pre-intervention) and after 24 months (post-intervention) as part of the Maputo Sanitation Trial. We tested soils for the presence of nucleic acids associated with 20 enteric pathogens using a multiplex reverse transcription qPCR platform. We detected at least one pathogen-associated target in 91% (163/179) of soils and a median of 3 (IQR=1.5, 5) pathogens. Using a difference-in-difference analysis and adjusting for compound population, visibly wet soil, sun exposure, wealth, temperature, animal presence, and visible feces, we estimate the intervention reduced the probability of [≥]1 pathogen detected by 15% (adjusted prevalence ratio, aPR=0.85; 95% CI: 0.70, 1.0) and the total number of pathogens detected by 35% (aPR =0.65; 0.44, 0.95) in soil 24 months following the intervention. These results suggest that the intervention reduced the presence of some fecal contamination in the domestic environment, but pathogen detection remained prevalent 24-months following the introduction of new latrines.

molecular biology↗

bioRxiv2021

Ciliary control of meiotic chromosomal pairing mechanics and germ cell morphogenesis

The hallmark of meiosis is chromosomal pairing and synapsis via synaptonemal complexes, but chromosomal pairing also depends on cytoplasmic counterparts that tether and rotate telomeres on the nuclear envelope. Telomeres slide on perinuclear microtubules, shuffling chromosomes and mechanically driving their homology searches. Pull of telomeres towards the centrosome drives formation of the "zygotene chromosomal bouquet". These telomere dynamics are essential for pairing and fertility, and the bouquet, discovered in 1900, is universally conserved. Nevertheless, how cytoplasmic counterparts of bouquet formation are mechanically regulated has remained enigmatic. Here, we report the "zygotene cilium" - a previously unrecognized cilium, in oocytes. We show in zebrafish that this cilium specifically connects to the bouquet centrosome, constituting a cable system of the cytoplasmic bouquet machinery. Furthermore, zygotene cilia extend throughout the germline cyst, a conserved germ cell organization. Using multiple ciliary mutants and laser-induced excision, we demonstrate that the zygotene cilium is essential for chromosomal bouquet and synaptonemal complex formation, germ cell morphogenesis, ovarian development and fertility. Mechanistically, we provide evidence that the cilium functions at least partly via anchoring the bouquet centrosome in order to counterbalance telomere rotation and pulling. We also show that the zygotene cilium is conserved in both male and female meiosis in zebrafish, as well as in mammals. Our work uncovers the novel concept of a cilium as a critical player in meiosis and sheds new light on reproduction phenotypes in ciliopathies. We propose a cellular paradigm that cilia can control chromosomal dynamics.

cell biology↗

bioRxiv2021

Cooperative Communication with Humans Evolved to Emerge Early in Dogs

While we know that dogs evolved from wolves through a process of domestication, it remains unclear how this process may have affected dog cognitive development. Here we tested dog (N=44) and wolf (N=37) puppies, 5-18 weeks old, on a battery of temperament and cognition tasks. Dog puppies were more attracted to humans, read human gestures more skillfully and made more eye contact with humans than wolf puppies. The two species were similarly attracted to objects and performed similarly on nonsocial measures of memory and inhibitory control. These results demonstrate the role of domestication in enhancing the cooperative communication skills of dogs through selection on attraction to humans, which altered developmental pathways. One Sentence Summary Domestication altered dogs developmental pathways to enhance their cooperative communication with humans.

animal behavior and cognition↗

bioRxiv2019

FLASH irradiation enhances the therapeutic index of abdominal radiotherapy in mice

Peritoneal metastases are the leading cause of morbidity and mortality in ovarian cancer. Despite current surgery, chemotherapy and targeted therapies, the majority of patients diagnosed with advanced epithelial ovarian cancer develop recurrent disease and overall survival rates remain poor. It is known that ovarian cancer is a radiosensitive tumor. Historically, total abdominal irradiation (TAI) was used as an effective postsurgical adjuvant therapy in the management of chemotherapy sensitive and resistant ovarian cancer. However, TAI fell out of favor due to high toxicity, particularly of the gastrointestinal tract. We have developed a preclinical irradiation platform that allows for total abdominal ultrahigh dose rate FLASH irradiation. We demonstrate that TAI-FLASH reduces radiation-induced intestinal injury in both healthy and tumor-bearing mice compared to conventional dose rate (CONV) irradiation. Single high dose TAI-FLASH reduced mortality from gastrointestinal syndrome, spared gut function and epithelial integrity, and decreased cell death in crypt base columnar cells. Importantly, FLASH and CONV irradiation had similar efficacy in the reduction of ovarian cancer peritoneal metastases. These findings suggest that FLASH irradiation may be an effective strategy to enhance the therapeutic index of radiotherapy for the treatment of metastatic ovarian cancer in women.

cancer biology↗

bioRxiv2017

Effects of Human-Animal Interaction on Dog Salivary and Plasma Oxytocin and Vasopressin

Oxytocin (OT) and Vasopressin (AVP) are neuropeptides with diverse effects on social behavior, cognition and stress responses. Recent studies suggest that OT facilitates and responds to affiliative forms of human-animal interaction (HAI). However, previous studies measuring OT and AVP in dogs have been limited to measures from blood or urine, which present concerns related to the invasiveness of sample collection, the potential for matrix interference in immunoassays, and whether samples can be collected at precise time points to assess event-linked endocrine responses. Previous studies from our laboratory validated salivary measures of OT and AVP in dogs, however, it is currently unknown whether these measures respond dynamically to aspects of HAI. Here, we investigated the effects of affiliative forms of HAI on both plasma and salivary OT and AVP in dogs. We employed a between-subjects design with a group of Labrador retrievers and Labrador retriever X golden retriever crosses (23 females, 15 males). Half of the dogs engaged in 10 minutes of free-form friendly interaction with a human experimenter (HAI condition), and the other half rested quietly in the same environment, without human interaction (control condition). We collected blood and saliva samples before, and immediately following both experimental conditions, and all samples were analyzed using enzyme-linked immunosorbent assays (ELISAs) following previously validated protocols. Dogs participating in HAI exhibited a significant increase in both salivary OT (+39%) and plasma OT (+5.7%) whereas dogs in the control group did not. Salivary AVP showed no change in the HAI group but increased significantly (+33%) in the control group. Plasma AVP decreased significantly following HAI (-13%) but did not change across time in the control condition. Within the dogs exposed to HAI, increases in salivary OT, and decreases in plasma AVP, were predicted by the extent of affiliative behaviour between the dog and human (indexed by scores from a principal components analysis of social behaviours between the dog and human). Collectively our results suggest that measures of salivary OT and AVP provide useful biomarkers in studies of HAI, and afford a flexible and noninvasive toolkit than can be employed in diverse research contexts.

animal behavior and cognition↗

bioRxiv2017

Validation of Salivary Oxytocin and Vasopressin as Biomarkers in Domestic Dogs

BackgroundOxytocin (OT) and Vasopressin (AVP) are phylogenetically conserved neuropeptides with effects on social behavior, cognition and stress responses. Although OT and AVP are most commonly measured in blood, urine and cerebrospinal fluid (CSF), these approaches present an array of challenges including concerns related to the invasiveness of sample collection, the potential for matrix interference in immunoassays, and whether samples can be collected at precise time points to assess event-linked endocrine responses.\n\nNew MethodWe validated enzyme-linked immunosorbent assays (ELISAs) for the measurement of salivary OT and AVP in domestic dogs.\n\nResultsBoth OT and AVP were present in dog saliva and detectable by ELISA and high performance liquid chromatography - mass spectrometry (HPLC-MS). OT concentrations in dog saliva were much higher than those typically detected in humans. OT concentrations in the same samples analyzed with and without sample extraction were highly correlated, but this was not true for AVP. ELISA validation studies revealed good accuracy and parallelism, both with and without solid phase extraction. Collection of salivary samples with different synthetic swabs, or following salivary stimulation or the consumption of food led to variance in results. However, samples collected from the same dogs using different techniques tended to be positively correlated. We detected concurrent elevations in salivary and plasma OT during nursing.\n\nComparison with Existing MethodsThere are currently no other validated methods for measuring OT/AVP in dog saliva.\n\nConclusionsOT and AVP are present in dog saliva, and ELISAs for their detection are methodologically valid.

animal behavior and cognition↗