Biology subjects

Jimenez, P.

Publications and source records attributed to Jimenez, P..

8 recordsLinked to original sources

bioRxiv2026

Early vegetative development and ontogenetic phase transitions in Juglans neotropica Diels: a BBCH-scale approach

Juglans neotropica is an endangered South American walnut species for which standardized descriptions of early development are lacking, limiting its effective use in conservation and restoration programs. We developed a BBCH-scale description of early vegetative growth of J. neotropica based on observations under nursery and field conditions in Colombia. Three principal vegetative stages were described: seed germination (stage 0), leaf development (stage 1), and stem elongation (stage 3). Germination was hypogeal and occurred 30-140 d after sowing, occasionally extending to 180 d. During early growth, leaflet morphology, number, and architecture showed consistent and discrete changes between stages 1 and 3, including shifts in apex, base, margin type, and laminar shape. These modifications indicate that early development is organized into distinct ontogenetic phases rather than continuous variation, marking the transition from juvenile to vegetative adult stages. By providing a standardized, development-based framework independent of chronological age, this BBCH scale facilitates accurate identification and monitoring of seedlings in nursery production, restoration projects, and urban forestry programs. More broadly, this approach contributes to the characterization of ontogenetic phase transitions in tropical tree species and supports the use of development-based criteria for managing early establishment and performance.

plant biology↗

bioRxiv2025

'Guess Who?': Forensic genetics and archaeology converge to identify Cristopher Columbus descendants.

The generation of DNA profiles from skeletal remains is a core challenge in forensic genetics, particularly for the identification of missing persons and the resolution of cold cases. Factors such as diagenesis, DNA fragmentation, and the presence of PCR inhibitors severely compromise traditional methodologies, limiting the potential for successful identification. Similarly, in many archaeological studies, the presence of multiple individuals within a single burial site presents a significant challenge for accurate identification. This study shows how the most innovative forensic genetic techniques can be integrated into archaeological research, enabling the identification of individuals through the establishment of familial relationships between remains recovered from an archaeological site. A large-scale SNP assay, Forenseq(R) Kintelligence HT, has been applied to a familial group dating back to the 16th-17th century, allowing robust kinship calculations and lineage studies, that, in a first stage, lead to the identification of four individuals spanning four generations within the same family.

genomics↗

bioRxiv2025

Myc and Kras cooperate in adult acinar cells to drive phenotypic heterogeneity, metastasis, and therapeutic resistance in a novel pancreatic cancer mouse model

Pancreatic ductal adenocarcinoma (PDAc) is a deadly malignancy, most commonly diagnosed in advanced stages when no curative treatments are available. The development of new models that aid ongoing investigation into the mechanisms by which it initiates, disseminates, and evades treatment is of the utmost importance. In vivo models that accurately recapitulate the features and spectrum of human pancreatic cancer are paramount to make a dent in this disease as two decades of the standard-of-care have failed to substantially improve survival. Here, we take advantage of our finding that post-translational stabiliziation of MYC downstream of the canonical PDAc driver, mutant KRAS, is an early event in PDAc progression to design a novel mouse model of PDAc progression based on deregulated, constituitive expression of Myc and mutant Kras in adult pancreatic acinar cells. Tumors from this KMC model histologically and molecularly recapitulate heterogeneity seen in human PDAc, with a high rate of metastasis to the liver. Cell lines derived from KMC autochthonous PDAc provide new models for orthotopic primary tumors that reliably metastasize to the liver and lung, providing important new tools to efficiently study the metastatic cascade and aid in the develoment of new therapeutics addressing metastatic disease. Cell lines represent distinct molecular subtypes with corresponding differential drug sensitivity. Toghether, this model provides a new and additional tool in the study of pancreatic cancer and the means by which it so deftly evades our best efforts at treatment.

cancer biology↗

bioRxiv2025

MicroCT enables simultaneous longitudinal tracking of murine pancreatic cancer progression and cachexia

Preclinical models of pancreatic ductal adenocarcinoma (PDAC) can greatly benefit from non-invasive imaging for evaluating disease progression and therapeutic response. Imaging approaches that can accurately and simultaneously track primary tumor growth, metastatic dissemination, and host cachexia over time are lacking. Here, we report an optimized dual-contrast micro-computed tomography (microCT) protocol for longitudinal imaging in orthotopic murine models of PDAC. This method enables high-resolution, volumetric quantification of orthotopic primary tumors, liver and lung metastases, and paraspinal skeletal muscle, providing a dynamic view of both tumor and host physiology. MicroCT primary tumor measurements strongly correlated with endpoint tumor weights and outperformed 2D ultrasound in early detection and volumetric accuracy, particularly for small or irregularly shaped tumors. This platform revealed heterogeneous metastatic kinetics across PDAC models and uncovered early, heterogeneous onset of skeletal muscle wasting, a hallmark of cancer cachexia. Notably, this protocol mimics clinical CT surveillance by enabling opportunistic cachexia assessment from tumor imaging datasets and offers substantial advantages over destructive endpoint analyses. Further, microCT radiation had no effect on our model endpoints. By capturing the temporal dynamics of tumor progression and host response, dual contrast microCT serves as a powerful translational platform for preclinical PDAC research and therapeutic testing. SignificanceDual-contrast microCT provides high-resolution, whole-body, non-invasive imaging in orthotopic murine PDAC models, enabling simultaneous tracking of tumor growth, metastasis, and skeletal muscle wasting-offering a clinically relevant, translational imaging platform.

cancer biology↗

bioRxiv2024

THE FIRST COMPREHENSIVE FORENSIC GENETIC STUDY OF A MEMBER OF CHRISTOPHER COLUMBUS' FAMILY: HIS GREAT-GREAT-GRANDSON

The present study has successfully obtained genetic information that allow the identification from direct descendants of Christopher Columbus, dating from 1526 to 1734. This represents the first achievement of this unique objective. The results obtained from the analysed samples, characterized by their significant antiquity, yield exceptional insights into forensic genetics and its newest protocols and methodologies applied to the study of ancient skeletal remains. This work presents the preliminary results of the whole family study using massive parallel sequencing, focusing on the autosomal Single Nucleotide Polymorphism (SNP) and Short Tandem Repeats (STR) markers, including their flanking region sequences, as well as ancestry informative markers (AIMS) of the great-great-grandson of the discoverer. The results of this project pave the way towards the application of new sequencing technologies for the study of genetic evolution, biogeographical origins and forensic identification of historical characters.

genomics↗

bioRxiv2023

SF3B1-dependent alternative splicing is critical for maintaining endometrial homeostasis and the establishment of pregnancy

The remarkable potential of human endometrium to undergo spontaneous remodeling is shaped by controlled spatiotemporal gene expression patterns. Although hormone-driven transcription shown to govern these patterns, the post-transcriptional processing of these mRNA transcripts, including the mRNA splicing in the endometrium is not studied yet. Here, we report that the splicing factor, SF3B1 is central in driving alternative splicing (AS) events that are vital for physiological responses of the endometrium. We show that loss of SF3B1 splicing activity impairs stromal cell decidualization as well as embryo implantation. Transcriptomic analysis revealed that SF3B1 depletion decidualizing stromal cells led to differential mRNA splicing. Specifically, a significant upregulation in mutually exclusive AS events (MXEs) with SF3B1 loss resulted in the generation of aberrant transcripts. Further, we found that some of these candidate genes phenocopy SF3B1 function in decidualization. Importantly, we identify progesterone as a potential upstream regulator of SF3B1-mediated functions in endometrium possibly via maintaining its persistently high levels, in coordination with deubiquitinating enzymes. Collectively, our data suggest that SF3B1-driven alternative splicing plays a critical role in mediating the endometrial-specific transcriptional paradigms. Thus, the identification of novel mRNA variants associated with successful pregnancy establishment may help to develop new strategies to diagnose or prevent early pregnancy loss.

molecular biology↗

bioRxiv2020

Density-dependent private benefit leads to bacterial mutualism

Microorganisms produce materials leaked from the cell which are beneficial for themselves and their neighbors. We modeled the situation when cells can produce different costly secretions which increase the carrying capacity of the population. Strains that lose the function of producing one or more secretions avoid the cost of production and can exhaust the producers. However, secreting substances provides a private benefit for the producers in a density-dependent way. We developed a model to examine the outcome of the selection among different type of producer strains from the non-producer strain to the partial producers, to the full producer one. We were particularly interested in circumstances under which selection maintains partners that produce complementary secreted materials thus forming an interdependent mutualistic interaction. We show that interdependent mutualism is selected under broad range of conditions if private benefit decreases with density. Selection frequently causes the coexistence of more and less generalist cooperative strains, thus cooperation and exploitation co-occur. Interdependent mutual-ism is evolved under more specific circumstances if private benefit increases with density and these general observations are valid in a well-mixed and in a structured deme model. We show that the applied population structure supports cooperation in general, which, depending on the level of private benefit and intensity of mixing helps either the specialist or the generalist cooperators.

evolutionary biology↗

bioRxiv2020

Phylodynamics of SARS-CoV-2 transmission in Spain

ObjectivesSARS-CoV-2 whole-genome analysis has identified three large clades spreading worldwide, designated G, V and S. This study aims to analyze the diffusion of SARS-CoV-2 in Spain/Europe. MethodsMaximum likelihood phylogenetic and Bayesian phylodynamic analyses have been performed to estimate the most probable temporal and geographic origin of different phylogenetic clusters and the diffusion pathways of SARS-CoV-2. ResultsPhylogenetic analyses of the first 28 SARS-CoV-2 whole genome sequences obtained from patients in Spain revealed that most of them are distributed in G and S clades (13 sequences in each) with the remaining two sequences branching in the V clade. Eleven of the Spanish viruses of the S clade and six of the G clade grouped in two different monophyletic clusters (S-Spain and G-Spain, respectively), with the S-Spain cluster also comprising 8 sequences from 6 other countries from Europe and the Americas. The most recent common ancestor (MRCA) of the SARS-CoV-2 pandemic was estimated in the city of Wuhan, China, around November 24, 2019, with a 95% highest posterior density (HPD) interval from October 30-December 17, 2019. The origin of S-Spain and G-Spain clusters were estimated in Spain around February 14 and 18, 2020, respectively, with a possible ancestry of S-Spain in Shanghai. ConclusionsMultiple SARS-CoV-2 introductions have been detected in Spain and at least two resulted in the emergence of locally transmitted clusters, with further dissemination of one of them to at least 6 other countries. These results highlight the extraordinary potential of SARS-CoV-2 for rapid and widespread geographic dissemination.

microbiology↗