Biology subjects

Garcia, L.

Publications and source records attributed to Garcia, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Operando Failure Diagnosis and Performance Dynamics in Microbial Fuel Cells Treating Mine Waste

Artisanal gold-mining tailings carry dissolved mercury, copper and lead at concentrations requiring treatment before discharge. Bench-scale microbial fuel cells (MFCs) offer passive treatment of such streams, but exhibit operational variability that obscures whether removal is biologically driven. This study applies an integrated diagnostic framework to two bench-scale systems treating tailings from two artisanal gold-mining districts in Ecuador. System 1 evaluated Micractinium inermum bio-augmentation, while System 2 compared Psychrobacter alimentarius- and Trichococcus patagoniensis-dominated anodic consortia. The framework combines paired time-series statistical modeling, an adaptive percentile-floor change-point detector, equivalent-circuit modeling, and baseline-corrected XRD/FTIR spectroscopy. In System 1, treatment reduced mercury from 0.042 to 0.0027-0.0148 mg L^-1 and copper from 2.79 to 0.130-1.837 mg L^-1. Against the applicable discharge limits, copper complied in six of eight reactor--phase combinations, whereas mercury exceeded its limit throughout, identifying it as the limiting contaminant. Removal was governed by system-level physicochemical processes rather than algal-specific biocatalysis, with the non-algal control matching or exceeding the augmented reactors. Paired per-day testing showed that algal bio-augmentation conferred no voltage advantage under stable operation (+0.17%) but a +27.54% gain under diurnal perturbation, periodicity analysis attributed these shifts to the 24-h chamber photoperiod. An adaptive change-point detector distinguished recoverable excursions from terminal structural collapse in both systems, and equivalent-circuit fitting attributed System 2 consortium power difference to internal resistance and open-circuit voltage. The framework separates biological treatment effects from mechanical failure, supporting automated health monitoring in bio-electrochemical wastewater treatment.

bioengineering↗

bioRxiv2026

Deletion of TUBB4A mitigates the oligodendrocyte and neuronal deficits in human iPSCs derived from individuals affected by H-ABC

TUBB4A-related leukodystrophy (TUBB4A-LD) is a rare neurologic disorder with a broad spectrum of phenotypes, including severe early infantile encephalopathy, late infantile Hypomyelination with Atrophy of the Basal ganglia and Cerebellum (H-ABC), and milder late infantile forms. H-ABC is closely associated with a recurrent pathogenic variant, p.Asp249Asn, in the gene encoding tubulin beta class IVA (TUBB4A), a microtubule component. H-ABC presents with progressive dystonia, mobility loss, aphasia, and swallowing dysfunction in childhood. H-ABC results in cell-autonomous deficits in oligodendrocytes (OLs), cerebellar granule neurons, and medium spiny neurons (MSNs). Antisense oligonucleotides targeting Tubb4a can alleviate symptoms in H-ABC mouse models. However, the efficacy and safety of TUBB4A knockout in human cells remain poorly understood. We studied patient-derived TUBB4AD249N, TUBB4A KO, and control individual pluripotent stem cells (iPSCs). TUBB4AD249N iPSC-derived OLs failed to mature, showing less complexity and myelination, reduced microtubule acetylation and detyrosination. TUBB4AD249N iPSC-derived MSNs also showed impaired maturation and neurite extension. TUBB4A KO in mutant iPSCs reduced cellular deficits and was well tolerated. These findings support that suppression of TUBB4A could be a safe, effective therapy for TUBB4A-LD.

neuroscience↗

bioRxiv2026

Microbial induction of MHC-II expression in colon cancer cells overcomes immunotherapy resistance and limits metastasis

Colorectal cancer remains a major cause of cancer mortality, and most microsatellite stable tumors derive little benefit from immune checkpoint blockade. Here, we identify a microbiome-dependent mechanism that converts immune-refractory colorectal cancer into a more immunologically responsive state. Using orthotopic mouse models spanning distinct genetic and immunologic contexts, we show that a Helicobacter-containing microbiome suppresses primary tumor growth and limits metastasis. This protective state is associated with increased intratumoral lymphocyte infiltration and stronger effector programs. Mechanistically, microbial exposure induces MHC class II expression in colon cancer cells to promote anti-tumor immunity. Tumor-intrinsic loss of CIITA abrogates microbial protection, whereas enforced CIITA expression is sufficient to increase intratumoral T cell accumulation, restrict progression and metastasis, and sensitize microsatellite-stable tumors to PD-1 and CTLA-4 blockade. In human microsatellite-stable patient-derived organoids, increased cancer-cell MHC-II enhanced interactions with autologous immune cells and increased tumor cell apoptosis. Together, these findings define a microbiome-cancer cell antigen presentation axis that restrains metastasis and overcomes immunotherapy resistance in colorectal cancer.

immunology↗

bioRxiv2026

Astrocyte diversity and aging in the mouse lemur primate brain

Astrocytes play key roles in maintaining brain homeostasis, metabolism, and neurovascular integrity, yet their diversity and age-related modulation remain insufficiently understood, particularly across primate lineages. While rodent studies have generated extensive knowledge, notable species differences highlight the need for comparative analyses in non-human primates. The gray mouse lemur (Microcebus murinus), a small primate widely used in aging research, offers a valuable but underexplored model for studying astroglial aging. In this study, we characterized astrocyte distribution, morphology, and reactivity in 17 mouse lemurs aged 1.0-11.5 years using GFAP and vimentin immunohistochemistry. We identified marked regional and morphological heterogeneity, with dense astrocytic labeling in white matter, hippocampus, and sparse but diverse cortical populations. Distinct astrocyte subtypes--including fibrous, protoplasmic, projection, pial and subpial interlaminar, radial glia-like cells, tanycytes--were documented. Varicosity-bearing processes were common across multiple astroglial subtypes and may indicate altered physiological states. Quantitative analyses revealed pronounced age-related increases in astrocytic reactivity, particularly in white matter and interlaminar astrocytes. Cortical and hippocampal changes were comparatively modest. These findings indicate region-specific astrocytic vulnerability during aging and support the translational value of the mouse lemur for investigating glial aging in primates. Main PointsO_LIThe mouse lemur is the smallest primate on earth with a key role to understand primate brain characteristics. C_LIO_LIWe characterized seven different astrocyte subtypes: from fibrous to primate-specific astrocyte as interlaminar astrocytes in different brain regions of this primate. C_LIO_LIVaricosities were reported in different astrocyte subtypes found close to brain borders. C_LIO_LIMain age-related changes concerned fibrous astrocytes in the white matter and interlaminar astrocytes at the cortical border. C_LI

neuroscience↗

bioRxiv2025

Multi-omics characterization of IDH-mutant astrocytoma-derived cell lines reveals NOTCH-regulated plastic quiescent astrocyte-like state

Diffuse IDH-mutant astrocytomas are brain tumors typically diagnosed as low-grade but capable of progressing to higher grades. They exhibit three cellular states resembling astrocytes, oligodendrocytes, and neural progenitor (NPC) cells. Understanding their biology has been challenging due to the lack of relevant in vitro models. Here we established and extensively characterized four astrocytoma cell lines (LGG275, LGG336, LGG85, LGG349) derived from IDH-mutant astrocytoma at different grades, cultured in defined media and analyzed by multi-omics. These lines display growth rates in vitro and in vivo consistent with tumor grade and recapitulate key molecular alterations observed in patient tumors, including IDH1, ATRX, and TP53 mutations, activation of the alternative lengthening of telomeres (ALT) pathway and, in the most aggressive line, amplification of MET and PDGFRA. Single-cell RNA sequencing showed that the 4 astrocytoma lines maintain the three major cellular states observed in patient tumors. A hallmark of higher-grade-derived lines (LGG85, LGG349) is the persistence of NPC-like populations without growth factors, reflecting tumor progression. The LGG275 line most accurately mirrors slow-growing astrocytomas. Using CD44 and GLAST, we isolated astrocyte-like (CD44+/GLAST+) cells from LGG275 that preferentially adopt a quiescent state yet retain remarkable plasticity, generating oligodendrocyte-like cells (CD44-/GLAST-). Transcriptomic and proteomic analyses revealed that astrocyte-like and oligodendrocyte-like cells populations resemble quiescent and activated neural stem (NSC) cells from the adult subventricular zone (SVZ). Finally, we found that NOTCH signaling regulates the balance between astrocytic and oligodendrocytic states, while DLL3, expressed by oligodendrocyte-like cells, modulates both proliferation and phenotype. These cell lines represent valuable resources for dissecting lineage dynamics, heterogeneity, and progression mechanisms in IDH-mutant astrocytomas. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/696808v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@953108org.highwire.dtl.DTLVardef@c6234aorg.highwire.dtl.DTLVardef@3703fcorg.highwire.dtl.DTLVardef@1e6c3a9_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightO_LIWe constituted a richly annotated biobank derived from 4 astrocytomas, showing similar characteristics to those found in patients, providing valuable tools to investigate cellular heterogeneity and plasticity, and link with tumor progression. C_LIO_LIscRNA-sequencing revealed three cell states (oligodendrocyte-like, astrocyte-like, and stem cell-like cells) akin to those found in tumors. C_LIO_LIAstrocyte-like cells are quiescent cells, plastic and similar to quiescent neural stem cell (qNSC) from the sub-ventricular zone (SVZ), while oligodendrocyte-like cells are similar to active NSC (aNSC). C_LIO_LIThe Notch pathway plays a role in cell plasticity, enabling a shift towards an astrocyte-like state. C_LI

cancer biology↗

bioRxiv2025

Detection of Anopheles pseudopunctipennis (Diptera: Culicidae) in Cochabamba, Bolivia, after 90 years of suspected presence

Objectives.This study provides the first confirmed record of the malaria vector Anopheles pseudopunctipennis in Cochabamba city, Bolivia, ending nearly 90 years of suspected presence since the malaria epidemics of the 1930s and 1940s. Additionally, it assesses the potential suitability of the region for this mosquito species. MethodsMosquito larvae were collected as part of a comprehensive survey of Culicidae in Cochabamba city and its suburbs. Larvae of An. pseudopunctipennis were collected on April 16, 2024, and reared to the fourth instar in the laboratory. One male specimen obtained from collected larvae was pinned. Specimens were morphologically identified using a standard identification key and species re-description. The larval identification was based on its unique spiracular apparatus, while adults were identified by their characteristic black hind tarsomeres and unspotted wing costa. The specimens are preserved in the Laboratory of Medical Entomology at UMSS, Cochabamba. ResultsA single larval habitat was identified in Lincoln Park, in the center of Cochabamba. It consisted of a 184 m{superscript 2} pond with a cement bottom, clear water with very slow flow from a small spring, and abundant Rhizoclonium algae. A Maxent habitat suitability model indicated that the Cochabamba Valley provides suitable environmental conditions for An. pseudopunctipennis. ConclusionsThis study provides the first concrete evidence of An. pseudopunctipennis in Cochabamba city, confirming its presence after decades of speculation. However, its low abundance and limited larval habitats due to urbanization and pollution suggest that it poses no significant malaria transmission risk in the area.

ecology↗

bioRxiv2025

Statistical analysis of larval postspiracular filament length reveals continuous variation in Bolivian Anopheles pseudopunctipennis (Diptera: Culicidae)

Anopheles pseudopunctipennis is a neotropical malaria vector widely distributed from northern Argentina and Chile to the southern United States. At the larval stage, it is characterized by posterior-lateral caudal filaments, which vary markedly in length within the same samples in Bolivia, with some individuals displaying unusually long filaments. The coexistence of individuals with relatively long and relatively short filaments raises the question of whether at least two distinct populations could be differentiated based on caudal filament length. This study examined filament-length distributions in two Bolivian dry-valley populations, El Chaco and Mataral, to determine whether variation reflects distinct subpopulations or continuous phenotypic variation within a single population. Distributions deviated from normality, exhibiting moderate skewness and tail heaviness, and the Generalized Error Distribution provided the best statistical fit. Examination of outliers and a targeted analysis of the distribution tail using multiple complementary methods showed that extreme values did not form a discrete secondary cluster but rather represented the upper continuum of the trait range. The two sites showed broadly comparable distributions, consistent with similar environmental conditions. These results emphasize the importance of using appropriate distributional models for continuous traits, highlight the occurrence of rare extreme phenotypes within otherwise homogeneous populations, and provide a baseline for future studies on the ecological and genetic determinants of caudal filament variation in An. pseudopunctipennis.

zoology↗

bioRxiv2025

Hippo/YAP1 Signaling Regulates the Oligodendrocyte-Astrocyte Fate Switch and Ependymal Gene Expression in Adult Spinal Cord Stem Cells

The adult mammalian spinal cord harbors ependymal cells that retain neural stem-cell properties. Although they possess a latent capacity to generate oligodendrocytes, these cells predominantly differentiate into astrocytes after injury. The molecular cues that govern their lineage commitment toward astrocytic versus oligodendroglial fates remain poorly defined. In this study, we addressed this gap in vitro by investigating the emergence of PDGFRA oligodendrocyte precursor cells (OPCs) in neurosphere cultures derived from adult spinal cord stem cells. We first observed that neurosphere cells exhibited a hybrid identity, co-expressing transcription factors of both astrocytic (NFIA, SOX9) and oligodendrocytic (OLIG1/2, SOX4, NKX2.2, TCF4) lineages. Upon differentiation, oligodendrocytic transcription factors were selectively maintained in OPCs but reduced in other cells. Using PdgfraH2B-GFP mice, we then isolated newly formed PDGFRA OPCs from neurospheres and performed multi-omic profiling. OPC formation was associated with the upregulation of chromatin remodelers and the downregulation of stem-cell markers such as EGFR, HES1, and TNC. Strikingly, OPC specification coincided with reduced expression of YAP1 and its partner TEAD1, key effectors of the Hippo pathway. Functional analyses revealed that YAP1 loss enhanced oligodendrocytic differentiation while reducing astrocytic and ependymal/cilia-associated gene expression. Conversely, constitutive YAP1 activation blocked differentiation into both lineages and promoted an ependymal-like transcriptional program, including upregulation of the ependymal marker CD24a and cilia-related proteins such as CROCC (Rootletin). Collectively, these findings uncover previously unrecognized roles for YAP1 in adult spinal cord stem-cell fate decisions and provide a molecular framework for leveraging these cells in regenerative strategies targeting spinal cord repair.

cell biology↗

bioRxiv2025

Endothelin Signaling via EDNRB receptor Reduces Proliferation and Promotes Proneural-to-Mesenchymal Transition in Gliomas

Diffuse gliomas are incurable primary brain tumors encompassing three histo-molecular subtypes: glioblastomas (GB), astrocytomas, and oligodendrogliomas. The latter two harbor IDH1 mutations and exhibit slower progression than glioblastomas. Diffuse gliomas are composed of highly plastic tumor cells capable of transitioning between astrocyte-like, oligodendrocyte-like, progenitor-like, and mesenchymal-like states, driven by genetic alterations and microenvironmental cues. The proneural-to-mesenchymal transition (PMT), associated with increased malignancy, is notably influenced by cytokines in the tumor microenvironment. Endothelin cytokines (ET-1, ET-2, ET-3), primarily secreted by vascular cells, regulate not only vascular tone but also astrocyte and neural stem cell proliferation via the G-protein-coupled receptors EDNRA and EDNRB. Prior studies using serum-cultured glioma lines suggested pro-proliferative effects of endothelins; however, such models poorly recapitulate the in vivo glioma context. In this study, we comprehensively revisited endothelin signaling - covering receptor expression, regulation, downstream pathways, and cellular responses-using eleven serum-free, patient-derived glioma lines (glioblastomas, IDH-wt and IDH-mutant oligodendrogliomas and astrocytomas), along with primary tumor samples. Multi-omics and electrophysiological analyses revealed EDNRB as the predominant receptor, enriched in astrocyte-like cells, upregulated by BMPs or growth factor withdrawal, and downregulated by interferons, IL-6 cytokines, endothelins, and Hippo/YAP activation. In contrast, EDNRA was expressed by a perivascular tumor subpopulation and induced by Notch signaling in glioblastomas but not in IDH1-mutant cells. Functionally, endothelins reduced proliferation across all models while promoting migration and PMT. Mechanistically, EDNRB activation increased intracellular Ca{superscript 2} and activated ERK, STAT3, and apamin-sensitive SK2/SK3 potassium channels. These findings identify endothelin signaling as an important regulator of glioma cell plasticity and behavior. HighlightsO_LIEDNRB is the predominant endothelin receptor expressed in glioma cells, with a small subset of tumor cells expressing EDNRA in close proximity to blood vessels C_LIO_LIEndothelin signaling reduces proliferation while promoting cell migration and Proneural-to-Mesenchymal transition C_LIO_LIEndothelin activates downstream Ca2+, K+, ERK, and STAT3 signaling pathways C_LIO_LIEDNRB expression is both positively and negatively regulated by inflammatory cytokines and the Hippo/YAP1 pathway, whereas EDNRA is upregulated by Notch signaling and hypoxia C_LI

cancer biology↗

bioRxiv2025

CD44v6 Drives Tumor Aggressiveness and Chemoresistance in Bladder Cancer

Bladder cancer is a fast-moving and recurrent malignancy where survival hinges on early detection and precise risk stratification. The search for robust biomarkers is urgent, and CD44v6 has emerged as a compelling candidate. In this study, we reveal that CD44v6 is not merely a marker but a driver of urothelial carcinoma aggressiveness. Through integrated clinical and functional analyses, we show that high CD44v6 expression is strongly associated with poor patient outcomes. Mechanistic investigations demonstrate that CD44v6 amplifies the proliferative, migratory, and invasive potential of bladder cancer cells, while conferring marked resistance to cisplatin. These findings position CD44v6 at the intersection of tumor progression and therapeutic failure, underscoring its value as both a prognostic biomarker and a promising therapeutic target. Targeting CD44v6 could pave the way for strategies that curb disease aggressiveness and overcome chemoresistance in bladder cancer.

cancer biology↗

bioRxiv2025

Improving angiogenesis ameliorates the efficacy of ASO-based exon-skipping for the treatment of Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is a severe X-linked disease caused by mutations in the DMD gene, resulting in the absence of functional dystrophin. Antisense oligonucleotide (ASO)-based therapies aim to restore the open reading frame and produce a truncated but functional dystrophin protein. Although several ASOs are FDA-approved, dystrophin restoration in patient biopsies remains low, underlining the need to improve ASO efficacy. One major limitation is poor ASO biodistribution to skeletal muscle, influenced by both ASO chemistry and pathological features of dystrophic tissue. In DMD patients and mdx mice, microvascular abnormalities and impaired angiogenesis likely restrict ASO delivery. Here, we hypothesized that enhancing muscle vascularization could improve ASO biodistribution and therapeutic outcomes. Mdx mice were treated with a pro-angiogenic treatment prior to ASO administration targeting exon 23 of dystrophin pre-mRNA. Angiogenic stimulation increased capillary density and improved ASO delivery, exon skipping, and dystrophin expression compared to ASO alone. These molecular improvements were associated with increased myofiber size, larger mean cross-sectional area, and decreased serum myomesin levels, without signs of toxicity. This study provides proof-of-concept that promoting angiogenesis can enhance the efficacy of ASO-based treatments, offering a complementary strategy to improve therapeutic outcomes in DMD.

molecular biology↗

bioRxiv2025

Social experience alters behaviors by reprogramming the Fruitless pathway and circadian state in Drosophila

From flies to humans, social experience affects various cognitive and behavioral processes. Previous studies have shown that group housing suppresses many behaviors like courtship, aggression, and feeding in Drosophila melanogaster, in addition to resetting the circadian state. Here, we focus on group housing-induced courtship suppression. To determine the mechanisms by which social experience modulates courtship behaviors, we performed bulk tissue RNAseq and single-cell RNAseq from cells expressing FruitlessM (FruM) and DoublesexM (DsxM), two transcription factors that label interconnected neural circuits for socially driven behaviors, from grouped or isolated male brains. These revealed that social isolation alters fru and dsx levels throughout the brain. Knocking down fruM in different fruM-positive neuron subpopulations in the brains has diverse effects on social experience-dependent changes in courtship. Furthermore, group housing increases the expression of stripe (sr) and Hormone receptor-like in 38 (Hr38) genes encoding neural activity-induced transcription factors in most neurons within social circuits. We found that knocking down sr in fruM-positive neurons effectively eliminates the impact of social experience by increasing courtship in group-housed males. Importantly, social experience also alters the expression of FruM/DsxM putative target genes regulating circadian states throughout the brain. Disrupting the function of multiple circadian genes diminishes the effect of group housing on courtship. Our findings suggest that group housing/social enrichment suppresses courtship by reprogramming the circadian arousal state, whereas courtship-elevating effects of social experience rely on unique influences of FruM expression and function in different neurons within social and clock circuits. These results are significant as they point to modulation of circadian arousal state as a possible central strategy for mediating the pleiotropic effects of social experience on organismal responses.

neuroscience↗

bioRxiv2025

Increased white matter microglial reaction and perivascular macrophages in the aging microcebe primate

As populations age, the incidence of neurodegenerative disorders is rising. Early age-related neuropathological changes are the breeding ground for the development of these disorders. Microglia are the resident macrophages of the central nervous system. They play crucial roles in maintaining brain homeostasis, yet their age-related changes remain not fully understood. While age-related microglia changes have been strongly characterized in rodents, studies in non-human primates are scarce. The microcebe primate (mouse lemur (Microcebus murinus)) is widely used as a model for cerebral aging and to investigate age-related neurodegenerative processes. HLA-DR is a major histocompatibility class II cell surface receptor which presents antigens to cells of the immune response. It is a major marker of microglia reaction. In this study, we explored microglia in the whole brains of middle-aged and old microcebes using HLA-DR immunolabeling. We analyzed microglial morphology and quantified HLA-DR+ cell density and protein expression. A wide range of microglial morphologies was observed in the white matter, including thin processes microglia, "rod-like" elongated and polarized shape, hypertrophic, and amoeboid microglia. Aging was associated with increased HLA-DR+ microglial expression in the white matter while very few HLA-DR+ microglia were observed in the parenchyma of cortical gray matter regions. A second finding was the higher number of HLA-DR+ perivascular macrophages in old animals. This study in a primate outlines that, in the absence of neurodegenerative processes, the most prominent signs of age-related microglia/macrophage changes are region-specific and concern white matter and perivascular regions. This emphasizes the need to target these regions to prevent cerebral aging. Main PointsO_LIHLA-DR+ microglia in Microcebus murinus primate show diverse morphologies and increase with age in white matter. C_LIO_LIHLA-DR+ perivascular macrophage load increase in aged animals. C_LI Table of Contents Image (TOCI) O_FIG O_LINKSMALLFIG WIDTH=167 HEIGHT=200 SRC="FIGDIR/small/645519v2_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@edb574org.highwire.dtl.DTLVardef@23f606org.highwire.dtl.DTLVardef@ed2e0borg.highwire.dtl.DTLVardef@169f059_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

DMEM and EMEM are suitable surrogate media to mimic host environment and expand leptospiral pathogenesis studies using in vitro tools

Pathogenic Leptospira species can survive and thrive in a wide range of environments. Distinct environments expose the bacteria to different temperatures, osmolarities, and amounts and sources of nutrition. However, leptospires are mostly cultured, in a laboratory setting under in vitro conditions that do not reflect natural environments. This constraint on laboratory cultures limits the applicability of in vitro studies to the understanding of even simple pathogenic processes. Here we report, investigate, and identify a medium and conditions that mimic the host environment during leptospirosis infection, expanding the available in vitro tools to evaluate leptospiral pathogenesis. We quantified genome-wide gene expression of pathogenic Leptospira interrogans cultured in different in vitro media compositions (EMJH, DMEM, EMEM, and HAN). Using EMJH as standard, we compared gene expression in these compositions to genome-wide gene expression gathered in a host environment: whole blood (WB) of hamsters after infection with pathogenic leptospires. Leptospires cultured in DMEM and EMEM media shared 40% and 47% of all differentially expressed genes (DEGs) of leptospires present within WB (FDR<0.01), while leptospires cultured in HAN media only shared 20% of DEGs with those from WB. Furthermore, gene and pathway expression of leptospires cultured on DMEM and EMEM media exhibited a better correlation with leptospires grown in WB, including promoting expression of a similar leptospiral lipid A profile to the one identified directly in host tissues. Taken together, these results indicate that commercial cell-culture media EMEM or DMEM are better surrogates for in vivo pathogenic studies than EMJH or HAN media in Leptospira. These alternative culture conditions, using media that are a standard supply worldwide, provide a reproducible and cost-effective approach that can accelerate research investigation and reduce the number of animal infections necessary for basic research of leptospirosis.

microbiology↗

bioRxiv2025

Decaying and expanding Erk gradients process memory of skeletal size during zebrafish fin regeneration

Regeneration of an amputated salamander limb or fish fin restores pre-injury size and structure, illustrating the phenomenon of positional memory. Although appreciated for centuries, the identity of position-dependent cues and how they control tissue growth are not resolved. Here, we quantify Erk signaling events in whole populations of osteoblasts during zebrafish fin regeneration. We find that osteoblast Erk activity is dependent on Fgf receptor signaling and organized into millimeter-long gradients that extend from the distal tip to the amputation site. Erk activity scales with the amount of tissue amputated, predicts the likelihood of osteoblast cycling, and predicts the size of regenerated skeletal structures. Mathematical modeling suggests gradients are established by the transient deposition of long-lived ligands that are transported by tissue growth. This concept is supported by the observed scaling of expression of the essential epidermal ligand fgf20a with extents of amputation. Our work provides evidence that localized, scaled expression of pro-regenerative ligands instructs long-range signaling and cycling to control skeletal size in regenerating appendages.

developmental biology↗

bioRxiv2024

The topography of gene tree topology space in a plant genus with a legacy of recent polyploidy and introgression

The eukaryotic genome has been described as a collection of different histories; for any set of taxa one of these histories is the record of cladogenic events that together comprise the species tree. Among the other histories expected to occur are those attributable to deep coalescence/lineage sorting; to biological causes such as introgression and horizontal transfer; or to pseudo-orthology, long branch attraction, and other technical issues. Gene tree topology space is the portion of tree space occupied by the gene trees reconstructed for a particular dataset of sampled genetic loci. Because coalescent theory predicts that the species tree topology will generally be the most frequent among gene trees, a reasonable expectation is that there will be a peak in gene tree topology space at the species tree topology, with secondary peaks present due to trees tracking other histories. Gene tree topology space in the small ([~]30 species, including the cultivated soybean) legume genus, Glycine should not only have signals from the species tree and from lineage sorting, but also from a likely introgression event that created incongruence between the plastid and nuclear genomes. Additionally, Glycine is the product of a relatively recent (<13 million years) whole genome duplication, raising the possibility of pseudo-orthology. We explored this space using a set of 2389 nuclear genes and representative accessions from a 570-taxon concatenation tree, reconstructing gene trees for all nuclear loci and from complete plastid genomes and partial mitochondrial genomes. Species trees (ASTRAL) and maximum likelihood (ML) concatenation trees were congruent for a 61-taxon dataset but were incongruent with organellar genome trees. Gene tree topology space was flat: No topology was represented by more than one gene tree. This was also true for a reduced dataset of 27 taxa; only when the dataset was reduced to six ingroup taxa were multiple gene trees having the species tree topology observed, along with a topology congruent with the chloroplast genome topology, presumably representing nuclear loci introgressed along with the plastome. Clustering failed to identify any regional differentiation of gene tree topology space populated by loci with similar topologies. Pseudo-orthology did not contribute meaningfully to incongruence, in agreement with recent modeling work that minimizes concerns about this phenomenon. Clearly, different genes have different historical signals, but these signals are complex and exist at the level of clades within trees rather than as entire gene trees.

evolutionary biology↗

bioRxiv2024

Breaking out of the cell cycle: Including quiescence in cell cycle classification

Single-cell transcriptomics has unveiled a vast landscape of cellular heterogeneity in which the cell cycle is a significant component. We trained a high-resolution cell cycle classifier (ccAFv2) using single cell RNA-seq (scRNA-seq) characterized human neural stem cells. The ccAFv2 classifies six cell cycle states (G1, Late G1, S, S/G2, G2/M, and M/Early G1) and a quiescent-like G0 state (Neural G0), and it incorporates a tunable parameter to filter out less certain classifications. The ccAFv2 classifier performed better than or equivalent to other state-of-the-art methods even while classifying more cell cycle states, including G0. We demonstrate that the ccAFv2 classifier effectively generalizes the S, S/G2, G2/M, and M/Early G1 states across cell types derived from all three germ layers. While the G0, G1, and Late G1 states perform well in neuroepithelial cell types, their accuracy is lower in other cell types. However, misclassifications are confined to the G0, G1, and Late G1 states. We showcased the versatility of ccAFv2 by successfully applying it to classify cells, nuclei, and spatial transcriptomics data in humans and mice, using various normalization methods and gene identifiers. We provide methods to regress the cell cycle expression patterns out of single cell or nuclei data to uncover underlying biological signals. The classifier can be used either as an R package integrated with Seurat or a PyPI package integrated with SCANPY. We proved that ccAFv2 has enhanced accuracy, flexibility, and adaptability across various experimental conditions, establishing ccAFv2 as a powerful tool for dissecting complex biological systems, unraveling cellular heterogeneity, and deciphering the molecular mechanisms by which proliferation and quiescence affect cellular processes.

cell biology↗

bioRxiv2024

Presence of Triatoma breyeri (Reduviidae, Triatominae) in Bolivia

The study focuses on identifying and understanding the ecological dynamics of Triatoma breyeri in Bolivia. Morphological identification and molecular analysis using gene fragments (COI, CytB and 16S) confirms T. breyeris presence and its relation to other species. The species has been consistently found in the Estancia-Mataral - La Palma region since 2010 but has not spread to other regions in Bolivia. The region of occurrence is a small characteristic dry inter-Andean valley. A MaxEnt model suggests part of the Bolivian Montane Dry Forest ecoregion serves as a unique habitat within its range. The infrequent presence in Bolivia and the distance from its main range in Argentina suggest recent accidental introduction, possibly through human transport. Further research is needed to comprehend its persistence in this small area of Bolivia.

ecology↗