Biology subjects

Bustamante, J.

Publications and source records attributed to Bustamante, J..

14 recordsLinked to original sources

bioRxiv2026

Determinants of CCT motif specificity in WNK signaling and expansion of CCT like domains

WNK kinases regulate ion transport and cell volume through interactions with partner proteins such as SPAK, OSR1, NRBP and TSC22D proteins. These interactions are mediated by conserved C-terminal (CCT) domains that recognize short sequence motifs, but the rules governing this recognition remain incompletely defined. Here we show that these domains can be grouped into distinct structural classes with different binding preferences for motif variants. We identify a previously unrecognized motif that mediates binding to the second CCT domain of WNKs and show that interaction specificity is determined by conserved physicochemical features, including electrostatic contacts and aromatic interactions, rather than strict sequence conservation. We further identify a similar domain in the protein FERRY3 that can bind TSC22D motifs in isolation. These findings define a framework for interaction specificity in WNK signaling and suggest that this binding mechanism may extend beyond this pathway.

cell biology↗

bioRxiv2025

Behavioral response of bed bugs (Hemiptera: Cimicidae) to wet surfaces

The behavioral response of bed bugs (Cimex lectularius) to wet surfaces was observed using motion-tracking software in a circular arena with a filter paper floor. Half of the arena floor was treated with varying amounts of deionized water, resulting in four treatment conditions: no water (control), low, medium, or high application rates. The other half was left untreated. For both sexes (adult) and all nymphal stages, the bed bugs spent significantly less time and walked significantly shorter distances on the wet surface. This result was amplified with increased water application rates. Some bed bugs made turns as they approached the wet zone. Bed bugs increased their speed by 38% when fleeing the wet zone relative to their approaching speed. On average, bed bugs made turns when they were 0.58 cm away from the wet zone. Furthermore, nymphs made turns when they were farther away from the wet zone relative to adults (by 60% on average). These findings suggest that overapplication of liquid pesticides may cause bed bugs to avoid treated areas, highlighting the need for precise application rates to enhance control efficacy. Additionally, this avoidance behavior likely reflects an adaptive strategy to reduce the risk of fungal infection or drowning, consistent with the evolutionary history of bed bugs as cave-dwelling insects.

animal behavior and cognition↗

bioRxiv2025

A simple method to classify behaviours of aerial predators using tri-axial high-frequency accelerometers

BackgroundRemote monitoring of animals has opened new avenues in behavioural research. The advent of animal-borne accelerometers makes it possible to derive the body posture and activity level, and thereby to identify fine-scale behaviours with no need for direct observation. This is particularly useful for species that forage or hunt beyond human sight in sometimes hard-to-access or remote areas. However, the complexity of numerous methods developed for this purpose may discourage researchers from effectively using acceleration data. ResultsWe present a simple and straightforward approach to identify and classify behaviours based on tri-axial high-frequency (25 Hz) acceleration data. This method relies on constructing a decision tree to assign predefined behaviours to time series of acceleration data using four accelerometer-based parameters that are biologically relevant and easy to interpret. Initially, we manually labelled sequences of acceleration data with the behaviours using paired high-frequency (i.e. 1 Hz) GPS tracking data as ground-truth. Then, threshold values of the acceleration-based parameters were objectively determined based on receiver operating characteristic (ROC) analysis. Finally, we built the decision tree to automatically classify the behaviours of the whole dataset and tested further improvements. As a case study, we used two falcon species (lesser kestrel Falco naumanni and common kestrel F. tinnunculus). Our simple method achieved an overall accuracy of 97.6% in classifying the following behaviours: perching (99.9%), soaring-gliding (99.3%), flapping (93.1%) and hovering (86.4%). We also showed that kestrels prey capture attempts can be identified from the tri-axial high-frequency accelerometers due to diagnostic signatures (the so-called spikes). ConclusionsOur simple method has broad applicability to free-ranging aerial predators. We show that behavioural categories can be accurately classified from a relatively small subset of manually labelled acceleration data (43,075 seconds). Although quantifying hunting success needs further investigation, the detection of prey capture attempts opens new possibilities for studying the hunting behaviour of aerial predators.

ecology↗

bioRxiv2023

Frequency variation and dose modification of benznidazole administration for the treatment of Trypanosoma cruzi infection in mice, dogs and non-human primates

Trypanosoma cruzi naturally infects a broad range of mammalian species and frequently results in the pathology that has been most extensively characterized in human Chagas disease. Currently employed treatment regimens fail to achieve parasitological cure of T. cruzi infection in the majority of cases. In this study, we have extended our previous investigations of more effective, higher dose, intermittent administration protocols using the FDA-approved drug benznidazole (BNZ), in experimentally infected mice and in naturally infected dogs and non-human primates (NHP). Collectively these studies demonstrate that twice-weekly administration of BNZ for more than 4 months at doses that are [~]2.5-fold that of previously used daily dosing protocols, provided the best chance to obtain parasitological cure. Dosing less frequently or for shorter time periods was less dependable in all species. Prior treatment using an ineffective dosing regimen in NHPs did not prevent the attainment of parasitological cure with an intensified BNZ dosing protocol. Furthermore, parasites isolated after a failed BNZ treatment showed nearly identical susceptibility to BNZ as those obtained prior to treatment, confirming the low risk of induction of drug resistance with BNZ and the ability to adjust the treatment protocol when an initial regimen fails. These results provide guidance for the use of BNZ as an effective treatment for T. cruzi infection and encourage its wider use, minimally in high value dogs and at-risk NHP, but also potentially in humans, until better options are available.

microbiology↗

bioRxiv2022

Kestrels of the same colony do not overwinter together

Coloniality is one of the most common strategies in birds. While the lesser kestrel (Falco naumanni) is a colonial raptor during the breeding period, it is not known whether individuals from the same breeding colony aggregate during the non-breeding period too. We GPS-tracked 40 adult lesser kestrels from different Spanish breeding colonies to study the degree of spatial aggregation between individuals from the same breeding colony in their West African non-breeding range. Lesser kestrels in our study used a large area from a wide longitudinal strip in the western Sahel: individuals used 143,697 {+/-} 98,048 km2 on average during the entire non-breeding period (95% KDE), and 1,359 {+/-} 1,424 km2 per week. On the other hand, the individuals traveled 6205 {+/-} 2407 km on average during the entire non-breeding period, and 41.1 {+/-} 11.8 km per day. There were no differences between the sexes in any of those variables. Individuals from the same breeding colony were not aggregated during the non-breeding period because the overlap between their areas (38.8 {+/-} 21.4 %) was not higher than that randomly expected. In conclusion, our study reveals some aspects of the non-breeding spatial ecology of the lesser kestrel, allowing a better understanding of the relationship of colonial birds out of the breeding season.

zoology↗

bioRxiv2022

Itinerant lifestyle and congregation of lesser kestrels in West Africa

Migratory birds often spend a large proportion of their annual cycle in their non-breeding areas. While some species are sedentary after arriving in their non-breeding areas, others engage in itinerary or nomadic movements. Using GPS-tracking we aimed to investigate the little known non-breeding movements of the lesser kestrel Falco namumanni in sub-Saharan Africa. We segment non-breeding tracks (n = 78 tracks by 54 individuals) into staging events (131{+/-} 25 days), itinerant movements between staging sites (11 {+/-} 10 days), and non-directed exploratory movements (6 {+/-} 5 days). We then describe timing and directionality of itinerary movements by male and female kestrels, and explore shifts in habitat use throughout the non-breeding season. Regardless of sex, lesser kestrels spent on average 89% of the non-breeding season at 2-3 staging sites in West Africa. Upon arrival at the end of September, kestrels used disparate sites throughout the Sahel. By December, however, they congregated into two clearly delineated areas in Senegal and along the Malian-Mauritanian border. The birds stayed longer and showed greater daily activity in the latter areas, which were situated closer to wetlands compared to their first and intermediate ones. While 20 of 24 individuals tracked across multiple annual cycles showed consistent staging sites, a few switched between the Senegal and Mauritanian/Malian staging clusters. These results show that rather than tracking suitable climatic conditions southward, lesser kestrels survive the West African dry season by moving into wetland areas within the Sahelian climatic belt. Our findings match reports of lesser kestrel super-roosts in West Africa and stress the conservation value of wetlands along the Senegal River and the Inner Niger Delta in West Africa for the Spanish lesser kestrel population. These areas host 81% of lesser kestrels during 20% of their annual cycle.

animal behavior and cognition↗

bioRxiv2022

Prophylactic low-dose, bi-weekly benznidazole treatment fails to prevent Trypanosoma cruzi infection in dogs under intense transmission pressure

Trypanosoma cruzi naturally infects a wide variety of wild and domesticated mammals, in addition to humans. Depending on the infection dose and other factors, the acute infection can be life-threatening, and in all cases, the risk of chagasic heart disease is high in persistently infected hosts. Domestic, working, and semi-feral dogs in the Americas are at significant risk of T. cruzi and in certain settings in the southern United States, the risk of new infections can exceed 30% per year, even with the use of vector control protocols. In this study, we explored whether intermittent low-dose treatment with the trypanocidal compound benznidazole (BNZ) during the transmission season, could alter the number of new infections in dogs in an area of known, intense transmission pressure. Preliminary studies in mice suggested that twice-weekly administration of BNZ could prevent or truncate infections when parasites were delivered at the mid-point between BNZ doses. Pre-transmission season screening of 126 dogs identified 53 dogs (42.1%) as T. cruzi infection positive, based upon blood PCR and Luminex-based serology. Serial monitoring of the 67 uninfected dogs during the high transmission season (May to October) revealed 15 (22.4%) new infections, 6 in the untreated control group and 9 in the group receiving BNZ prophylaxis, indicating no impact of this prophylaxis regimen on the incidence of new infections. Although these studies suggest that rigorously timed and more potent dosing regimen may be needed to achieve an immediate benefit of prophylaxis, additional studies would be needed to determine if drug prophylaxis reduced disease severity despite this failure to prevent new infections. Author SummaryTrypanosoma cruzi, the parasite that causes Chagas disease, circulates extensively in the southern U.S. and working dog populations in south-central Texas are at very high risk of infection, and morbidity and early mortality due to this infection. In this study, we used low level administration of an FDA-approved drug during the transmission season to attempt to prevent new infections in these dogs. Although that effort failed, the study revealed new information about the transmission dynamics and generation of antibody responses and immune control of infection in this high-transmission setting.

microbiology↗

bioRxiv2022

Abdominal movements in insect flight reshape the role of non-aerodynamic structures for flight maneuverability I: Model predictive control for flower tracking

Research on insect flight control has focused primarily on the role of wings. Yet abdominal deflections during flight can potentially influence the dynamics of flight. This paper assesses the role of airframe deformations in flight, and asks to what extent the abdomen contributes to flight maneuverability. To address this, we use a combination of both a Model Predictive Control (MPC)-inspired computational inertial dynamics model, and free flight experiments in the hawkmoth, Manduca sexta. We explored both underactuated (i.e. number of outputs are greater than the number of inputs) and fully actuated (equal number of outputs and inputs) systems. Using metrics such as the non-dimensionalized tracking error and cost of transport to evaluate flight performance of the inertial dynamics model, we show that fully actuated simulations minimized the tracking error and cost of transport. Additionally, we tested the effect of restricted abdomen movement on free flight in live hawkmoths by fixing a carbon fiber rod over the thoracic-abdomen joint. Moths with a restricted abdomen performed worse than sham treatment moths. This study finds that abdominal motions contribute to flight control and maneuverability. Such motions of non-aerodynamic structures, found in all flying taxa, can inform the development of multi-actuated micro air vehicles.

physiology↗

bioRxiv2020

Detection of homozygous and hemizygous partial exon deletions by whole-exome sequencing

The detection of copy number variations (CNVs) in whole-exome sequencing (WES) data is important, as CNVs may underlie a number of human genetic disorders. The recently developed HMZDelFinder algorithm can detect rare homozygous and hemizygous (HMZ) deletions in WES data more effectively than other widely used tools. Here, we present HMZDelFinder_opt, an approach that outperforms HMZDelFinder for the detection of HMZ deletions, including partial exon deletions in particular, in typical laboratory cohorts that are generated over time under different experimental conditions. We show that using an optimized reference control set of WES data, based on a PCA-derived Euclidean distance for coverage, strongly improves the detection of HMZ deletions both in real patients carrying validated disease-causing deletions and in simulated data. Furthermore, we develop a sliding window approach enabling HMZDelFinder-opt to identify HMZ partial deletions of exons that are otherwise undiscovered by HMZDelFinder. HMZDelFinder_opt is a timely and powerful approach for detecting HMZ deletions, particularly partial exon deletions, in laboratory cohorts, which are typically heterogeneous.

bioinformatics↗

bioRxiv2020

Multi-batch cytometry data integration for optimal immunophenotyping

We describe the integration of multi-batch cytometry datasets (iMUBAC), a flexible, robust, and scalable computational framework for unsupervised cell-type identification across multiple batches of high-dimensional cytometry datasets. After overlaying cells from healthy controls across multiple batches, iMUBAC learns batch-specific cell-type classification boundaries and identifies aberrant immunophenotypes in patient samples. We illustrate unbiased and streamlined immunophenotyping, using both in-house and public mass and flow cytometry datasets.

bioinformatics↗

bioRxiv2020

Negative selection on human genes causing severe inborn errors depends on disease outcome and both the mode and mechanism of inheritance

BackgroundGenetic variants underlying severe diseases are less likely to be transmitted to the next generation, and are thus gradually and selectively eliminated from the population through negative selection. Here, we study the determinants of this evolutionary process in genes underlying severe diseases in humans. ResultsWe propose a novel approach, CoNeS, integrating known negative selection scores through principal component projection. We compare evidence for negative selection at 319 genes underlying inborn errors of immunity (IEI), which are life-threatening monogenic disorders. We find that genes underlying autosomal dominant (AD) or X-linked IEI are under stronger negative selection than those underlying autosomal recessive (AR) IEI, which are under no stronger selection than genes not known to be disease-causing. However, we find that genes with mutations causing AR IEI that are lethal before reproductive maturity and that display complete penetrance are under stronger negative selection than other genes underlying AR IEI. We also find that genes underlying AD IEI by haploinsufficiency are under stronger negative selection than other genes underlying AD IEI. Finally, we replicate these results in a study of 1,140 genes causing inborn errors of neurodevelopment. ConclusionsThese findings collectively show that the clinical outcomes of inborn errors, together with the mode and mechanism of inheritance of these errors, determine the strength of negative selection acting on severe disease-causing genes. These findings suggest that estimating the intensity of negative selection with CoNeS may facilitate the selection of candidate genes in patients suspected to carry an inborn error.

genetics↗

bioRxiv2020

A genome-wide case-only test for the detection of digenic inheritance in human exomes

Whole-exome sequencing (WES) has facilitated the discovery of genetic lesions underlying monogenic disorders. Incomplete penetrance and variable expressivity suggest a contribution of additional genetic lesions to clinical manifestations and outcome. Some monogenic disorders may therefore actually be digenic. However, only a few digenic disorders have been reported, all discovered by candidate gene approaches applied to at least one locus. We propose here a novel two-locus genome-wide test for detecting digenic inheritance in WES data. This approach uses the gene as the unit of analysis and tests all pairs of genes to detect pairwise gene x gene interactions underlying disease. It is a case-only method, which has several advantages over classic case-control tests, in particular by avoiding recruitment and bias of controls. Our simulation studies based on real WES data identified two major sources of type I error inflation in this case-only test: linkage disequilibrium and population stratification. Both were corrected by specific procedures. Moreover, our case-only approach is more powerful than the corresponding case-control test for detecting digenic interactions in various population stratification scenarios. Finally, we validated our unbiased, genome-wide approach by successfully identifying a previously reported digenic lesion in patients with craniosynostosis. Our case-only test is a powerful and timely tool for detecting digenic inheritance in WES data from patients. Significance statementDespite a growing number of reports of rare disorders not fully explained by monogenic lesions, digenic inheritance has been reported for only 54 diseases to date. The very few existing methods for detecting gene x gene interactions from next-generation sequencing data were generally studied in rare-variant association studies with limited simulation analyses for short genomic regions, under a case-control design. We describe the first case-only approach designed specifically to search for digenic inheritance, which avoids recruitment and bias related to controls. We show, through both extensive simulation studies on real WES datasets and application to a real example of craniosynostosis, that our method is robust and powerful for the genome-wide identification of digenic lesions.

genetics↗

bioRxiv2019

Homozygous STAT2 gain-of-function mutation by loss of USP18 activity in a patient with type I interferonopathy

Type I interferonopathies are monogenic disorders characterized by enhanced Type I interferon (IFN-I) activity. Inherited ISG15 and USP18 deficiencies underlie type I interferonopathies by preventing the regulation of late responses to IFN-I. Specifically, ISG15/USP18 are induced by IFN-I and sterically hinder JAK1 from binding to the IFNAR2 subunit of IFN-I receptor. We report an infant who died of autoinflammation due to a homozygous missense mutation (R148Q) in STAT2. The variant is gain-of-function (GOF) for ISGF3-dependent induction of late but not early response to IFN-I. Surprisingly, the mutation does not enhance the intrinsic transcriptional activity of ISGF3. Rather, the STAT2 R148Q variant is GOF because it fails to appropriately interact with and traffic USP18 to IFNAR2, preventing USP18 from negatively regulating responses to IFN-I. Overall, a STAT2 missense mutation that fails to facilitate USP18-mediated signal termination in the homozygous state underlies a novel genetic etiology of type I interferonopathy.

immunology↗

bioRxiv2017

IRF4 haploinsufficiency in a family with Whipples disease

The pathogenesis of Whipples disease (WD) remains largely unknown, as WD strikes only a very small minority of the individuals infected with Tropheryma whipplei (Tw). Asymptomatic carriage of Tw is less rare. We studied a large multiplex French kindred, containing four otherwise healthy WD patients (mean age: 76.7 years) and five healthy carriers of Tw (mean age: 55 years). We used a strategy combining genome-wide linkage analysis and whole-exome sequencing to test the hypothesis that WD is inherited in an autosomal dominant (AD) manner, with age-dependent incomplete penetrance. WD was linked to 12 genomic regions covering 27 megabases in the four patients. These regions contained only one very rare non-synonymous variation: the R98W variant of IRF4. The five Tw carriers were heterozygous for R98W. Interferon regulatory factor 4 (IRF4) is a transcription factor with pleiotropic roles in immunity. We showed that R98W was a loss-of-function allele, like only five other exceedingly rare IRF4 alleles of a total of 39 rare and common non-synonymous alleles tested. Furthermore, heterozygosity for R98W led to a distinctive pattern of transcription in leukocytes following stimulation with BCG or Tw. Finally, we found that IRF4 had evolved under purifying selection and that R98W was not dominant-negative, suggesting that the IRF4 deficiency in this kindred was due to haploinsufficiency. Overall, haploinsufficiency at the IRF4 locus selectively underlies WD in this multiplex kindred. This deficiency displays AD inheritance with incomplete penetrance, and chronic carriage probably precedes WD by several decades in Tw-infected heterozygotes.

immunology↗