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PubMed2026

Population Genomics of Almond (Prunus dulcis) Reveals Region-Specific Selection and a Complex History of Domestication.

The domestication of perennial crops in the Mediterranean Basin remains unclear, particularly regarding the genomic consequences of human-mediated demographic shifts and selection. We analysed 8.1 million single nucleotide polymorphisms from 96 cultivated almond (Prunus dulcis) accessions from Europe, North America, Central Asia, and New Zealand, alongside four wild relatives. Population structure analyses revealed four geographically differentiated cultivated groups (Central Asian, North American, and two European) and three wild populations (P. spinosissima, P. orientalis, and P. fenzliana). Cultivated almonds retained high genetic diversity, consistent with weak domestication bottlenecks typical of outcrossing perennials. Elevated diversity and private allele counts in Central Asian cultivars, together with limited evidence of crop-wild gene flow, support Central Asia as an important reservoir of ancestral cultivated diversity that may have played a major role during the early stages of almond domestication. In contrast, allele sharing consistent with historical wild-to-crop introgression-especially involving P. orientalis-has contributed to the genomic composition of European and North American almonds. Genome-wide scans for selective sweeps showed most genes overlapping candidate sweep regions were population-specific, though often associated with similar biological functions, including stress responses and agronomic traits. This suggests repeated targeting of comparable pathways during and post-domestication, despite distinct selection histories. Notably, a subset of candidate genes detected in cultivated populations also occurs in wild relatives, particularly P. orientalis. This overlap is consistent with shared ancestral variation, introgression/gene flow between wild and cultivated lineages, and/or parallel adaptation. Altogether, our results support a complex domestication and diversification history for almonds, shaped by geographic expansion, gene flow with wild relatives, and recurrent selection acting in different regions. This study highlights wild relatives as important reservoirs of genetic diversity and emphasises the need for broader geographic sampling to clarify their contributions to almond domestication and adaptation.

Prunus dulcis↗

PubMed2006

Understanding urothelial carcinoma through cancer pathways.

Urothelial carcinoma (UC), the common histological subtype of bladder cancer, presents as a papillary tumor or as an invasive, often lethal form. To study UC molecular biology, candidate gene and genome-wide approaches have been followed. Here, it is argued that a 'cancer pathway' perspective is useful to integrate findings from both approaches. According to this view, papillary cancers typically exhibit activation of the MAPK pathway, as a consequence of oncogenic mutations in FGFR3 or HRAS, with increased Cyclin D1 expression. In contrast, invasive UC are characterized by severe disturbances in proximate cell cycle regulators, e.g. RB1 and CDKN2A/p16(INK4A), which decrease dependency on mitogenic signaling. In addition, these disturbances permit, promote and are in turn exacerbated by chromosomal instability, which is further enhanced by loss of TP53 function. In another vicious cycle, defective cell cycle regulation interacts with DNA methylation alterations. The transition toward invasive UC may require concomitant and interacting defects in cell cycle regulation and the control of genomic stability. Intriguingly, neither canonical WNT/beta-Catenin nor hedgehog signaling appear to play major roles in UC. This may reflect its origin from more differentiated urothelial cells possessing a high regenerative potential rather than a stem cell population.

Biomarkers, Tumor↗

PubMed2006

Gene expression profile signatures indicate a role for Wnt signaling in endothelial commitment from embryonic stem cells.

We have used global gene expression analysis to establish a comprehensive list of candidate genes in the developing vasculature during embryonic (ES) cell differentiation in vitro. A large set of genes, including growth factors, cell surface molecules, transcriptional factors, and members of several signal transduction pathways that are known to be involved in vasculogenesis or angiogenesis, were found to have expression patterns as expected. Some unknown or functionally uncharacterized genes were differentially regulated in flk1+ cells compared with flk1- cells, suggesting possible roles for these genes in vascular commitment. Particularly, multiple components of the Wnt signaling pathway were differentially regulated in flk1+ cells, including Wnt proteins, their receptors, downstream transcriptional factors, and other components belonging to this pathway. Activation of the Wnt signal was able to expand vascular progenitor populations whereas suppression of Wnt activity reduced flk1+ populations. Suppression of Wnt signaling also inhibited the formation of matured vascular capillary-like structures during late stages of embryoid body differentiation. These data indicate a requisite and ongoing role for Wnt activity during vascular development, and the gene expression profiles identify candidate components of this pathway that participate in vascular cell differentiation.

Animals↗

PubMed2006

Coronary heart disease and depression: a review of recent mechanistic research.

OBJECTIVE: Both behavioural and physiological factors have been proposed as mechanisms that may explain the negative effect of depression on coronary heart disease (CHD). Our aim is to review some of the most important findings since our prior review. METHOD: We searched MEDLINE, PsycINFO, and other sources for recent studies of candidate mechanisms, with an emphasis on publications since 2002. RESULTS: Physiological pathways have received far greater attention than behavioural ones in the emerging literature. Recent studies have identified shared genetic determinants, inflammation, blood clotting, and vascular mechanisms as plausible explanatory mechanisms. CONCLUSIONS: Future research should focus on relations between behavioural and physiological mechanisms and on the effects of pharmacologic and psychotherapeutic treatments for depression on candidate mechanisms.

Acute Disease↗

PubMedDate not supplied

Loss of visual suppression of caloric nystagmus in cats.

Loss of visual suppression (VS) of caloric nystagmus was produced after creating flocculus lesions. The flocculus receives visual signals through a climbing fiber pathway via the inferior olive (IO) and through a mossy fiber pathway (MF) presumably via the superior colliculus (SC). In order to elucidate the prefloccular nuclei responsible for VS of caloric nystagmus, VS of caloric nystagmus was investigated after making lesions in such nuclei as the SC and the IO in 42 cats. After the IO lesion, VS of caloric nystagmus was revealed in all IO-lesioned cats throughout the whole experimental course. After the SC lesion, loss of VS was constantly observed and persisted in 7 out of 9 cats. Hence, the MF pathway via the SC is believed to be the most likely candidate for the immediate modification of the vestibuloocular reflex by visual stimuli.

Animals↗

PubMed2003

Olfactory input increases visual sensitivity in zebrafish: a possible function for the terminal nerve and dopaminergic interplexiform cells.

Centrifugal innervation of the neural retina has been documented in many species. In zebrafish Danio rerio, the only so-far described centrifugal pathway originates from terminal nerve (TN) cell bodies that are located in the olfactory bulb. Most of the TN axons terminate in the forebrain and midbrain, but some project via the optic nerve to the neural retina, where they synapse onto dopaminergic interplexiform cells (DA-IPCs). While the anatomical pathway between the olfactory and visual organs has been described, it is unknown if and how olfactory signals influence visual system functions. We demonstrate here that olfactory input is involved in the modulation of visual sensitivity in zebrafish. As determined by a behavioral assay and by electroretinographic (ERG) recording, zebrafish visual sensitivity was increased upon presentation of amino acids as olfactory stimuli. This effect, however, was observed only in the early morning hours when zebrafish are least sensitive to light. The effect of olfactory input on vision was eliminated after lesion of the olfactory bulbs or after the destruction of DA-IPCs. Intraocular injections of a dopamine D(2) but not a D(1) receptor antagonist blocked the effect of olfactory input on visual sensitivity. Although we cannot exclude the involvement of other anatomical pathways, our data suggest that the TN and DA-IPCs are the prime candidates for olfactory modulation of visual sensitivity.

Amino Acids↗

PubMed2006

Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation.

BACKGROUND: Activation of naïve B lymphocytes by extracellular ligands, e.g. antigen, lipopolysaccharide (LPS) and CD40 ligand, induces a combination of common and ligand-specific phenotypic changes through complex signal transduction pathways. For example, although all three of these ligands induce proliferation, only stimulation through the B cell antigen receptor (BCR) induces apoptosis in resting splenic B cells. In order to define the common and unique biological responses to ligand stimulation, we compared the gene expression changes induced in normal primary B cells by a panel of ligands using cDNA microarrays and a statistical approach, CLASSIFI (Cluster Assignment for Biological Inference), which identifies significant co-clustering of genes with similar Gene Ontology annotation. RESULTS: CLASSIFI analysis revealed an overrepresentation of genes involved in ion and vesicle transport, including multiple components of the proton pump, in the BCR-specific gene cluster, suggesting that activation of antigen processing and presentation pathways is a major biological response to antigen receptor stimulation. Proton pump components that were not included in the initial microarray data set were also upregulated in response to BCR stimulation in follow up experiments. MHC Class II expression was found to be maintained specifically in response to BCR stimulation. Furthermore, ligand-specific internalization of the BCR, a first step in B cell antigen processing and presentation, was demonstrated. CONCLUSION: These observations provide experimental validation of the computational approach implemented in CLASSIFI, demonstrating that CLASSIFI-based gene expression cluster analysis is an effective data mining tool to identify biological processes that correlate with the experimental conditional variables. Furthermore, this analysis has identified at least thirty-eight candidate components of the B cell antigen processing and presentation pathway and sets the stage for future studies focused on a better understanding of the components involved in and unique to B cell antigen processing and presentation.

Algorithms↗

PubMed2001

A conserved subtilisin-like protein TgSUB1 in microneme organelles of Toxoplasma gondii.

Proteolytic processing plays a significant role in the process of invasion by the obligate intracellular parasite Toxoplasma gondii. We have cloned a gene, TgSUB1, encoding for a subtilisin-type serine protease found in T. gondii tachyzoites. TgSUB1 protein is homologous to other Apicomplexan and bacterial subtilisins and is processed within the secretory pathway of the parasite. Initial cleavage occurs in the endoplasmic reticulum, after which the protein is transported to micronemes, vesicles that secrete early during host cell invasion. Upon stimulation of microneme secretion, TgSUB1 is cleaved into smaller products that are secreted from the parasite. This secondary processing is inhibited by brefeldin A and serine protease inhibitors. TgSUB1 is a candidate processing enzyme for several microneme proteins cleaved within the secretory pathway or during invasion.

Amino Acid Sequence↗

PubMed1999

In plants a putative isovaleryl-CoA-dehydrogenase is located in mitochondria.

In plants the degradation pathways of branched-chain amino acids have remained somewhat unclear with respect to both their biochemistry and their intracellular location. While biochemical evidence has localized some of the catabolic enzymes in peroxisomes/glyoxysomes, others cofractionate with mitochondria. We have now identified a candidate protein and corresponding cDNA for an enzyme of the leucine catabolic pathway, the isovaleryl-CoA-dehydrogenase (IVD). This polypeptide is a member of the acyl-CoA-dehydrogenase (ACDH) family and is encoded in the nuclear genome of Arabidopsis thaliana. Expression of the putative IVD gene in pea seedlings is documented by western blot analyses with an antibody against the mammalian IVD. Subcellular fractionation identifies the putative IVD enzyme in the mitochondrion. This localization suggests that in plants mitochondria contain at least part of the branched-chain amino acid degradation pathway(s).

Amino Acid Sequence↗

PubMed2006

Comparative insights into questions of lepidopteran wing pattern homology.

BACKGROUND: Butterfly and moth eyespots can share a similar appearance, involving multiple concentric rings of colored scales, but usually occurring in non-homologous positions on the wing. Within the butterflies, on the other hand, spots that share the same homologous position may not share the concentric ring structure; and, in butterfly species that have eyespots with concentric rings, ectopic eyespots with a similar ring structure can be induced by means of a simple epidermal wound. The extent to which all these eyespots, natural or induced, share similar genes and developmental mechanisms is investigated here by means of protein in-situ localizations in selected butterfly and moth species. In addition to looking at some of the transcription factors previously identified as being involved in eyespot formation, we also tested the involvement of candidate genes from the Wingless and TGF-beta signaling pathways as putative morphogens for eyespot development. RESULTS: Saturniid moth and nymphalid butterfly eyespots with concentric rings of color express at least two transcription factors, Distal-less and Engrailed, in the center of the future pattern. Nymphalid eyespots centers also express the ligand Wingless and an activated signal transducer, a phosphorylated Smad protein, but neither these proteins nor the previous two proteins are found in pierid spot centers, which consist of a single patch of color. Both butterfly wing patterns, however, express a third transcription factor, Spalt, a portion of whose expression domain maps to the black scales on the adult wing. Wounding a nymphalid wing, on the other hand, leads to upregulation of Distal-less, engrailed and spalt in subsets of cells around the wounding site, mimicking concentric eyespot development. CONCLUSION: Wingless and TGF-beta ligands are both candidate morphogens involved in nymphalid butterfly eyespot formation. These eyespots, as well as saturniid moth eyespots with concentric circles, share two genes that are associated with the differentiation of the signaling cells in nymphalid eyespots. This commonality suggests that they may be produced via the same developmental mechanism despite their non-homologous location. By contrast, pierid butterfly spots of a single color share some of the same genes but appear to be produced by a different mechanism. Eyespots with concentric rings may have co-opted a wound healing genetic network during their evolution.

Animals↗

PubMed1984

Visual and auditory pathways contain cholecystokinin: evidence from immunofluorescence and retrograde tracing.

The distribution of cholecystokinin (CCK) in the visual and auditory systems of the rat was studied with combined immunofluorescence and fluorescence retrograde tracing techniques. Double-labeled projection neurons in the pathway from the dorsal lateral geniculate nucleus to area 17 of visual cortex, and from the superior olive to the inferior colliculus demonstrated the presence of CCK-containing pathways in the ascending visual and auditory systems. Thus, CCK can be viewed as a neurotransmitter/neuromodulator candidate in ascending sensory systems.

Animals↗

PubMed2001

Interconnectivity between the amygdaloid complex and the amygdalostriatal transition area: a PHA-L study in rat.

The amygdala orchestrates the formation of behavioral responses to emotionally arousing stimuli. Many of these responses are initiated by the central nucleus, which converges information from other amygdaloid nuclei. Recently, we observed substantial projections from the amygdala to the amygdalostriatal transition area, which is located dorsal to the central nucleus. These projections led us to question whether the amygdalostriatal transition area has a role in the initiation of behavioral responses in emotionally arousing circumstances. To explore this anatomically, we traced the interconnections between the amygdalostriatal transition area and the amygdaloid complex using the anterograde tracer Phaseolus vulgaris-leucoagglutinin. The lateral (the medial division and the caudal portion of the dorsolateral division) and the accessory basal nuclei (the parvicellular division) provide moderate-to-heavy projections to the amygdalostriatal transition area. Projections back to the amygdala are light and are composed of thin, faintly stained varicose fibers that resemble the labeling of cholinergic terminals. The extra-amygdaloid outputs of the amygdalostriatal transition area are sparse and include moderate projections to the caudoventral globus pallidus, the ansa lenticularis, and the substantia nigra pars lateralis. These data suggest that the amygdalostriatal transition area is one of the major targets for projections originating in the lateral and accessory basal nuclei of the amygdala. Via these pathways, emotionally significant stimuli can evoke behavioral responses that are different from those initiated via projections from the amygdala to the central nucleus. One such candidate response is the orienting response (i.e., saccadic eye movements and head direction) in a pathway that includes a projection from the lateral/accessory basal nucleus of the amygdala to the amygdalostriatal transition area, and from there to the substantia nigra, pars lateralis.

Amygdala↗

PubMed2006

Mechanisms of disease: angiogenesis in urologic malignancies.

Angiogenesis is critical for growth of tumors and their metastasis. In this article we review the literature on studies of angiogenesis pathways and markers for renal cancer, prostate cancer and bladder cancer. Overall, there is clear evidence that markers of angiogenesis and expression of angiogenic factors are associated with adverse outcomes in each of these tumor types. Relatively few angiogenic pathways have been investigated so far, although over 50 factors are known to be involved, and little has been studied on the antiangiogenic pathways and their suppression. The failing in many of the studies is small size and lack of suitable statistical analysis. Nevertheless, this review demonstrates the importance of these pathways and the need to develop selection criteria for patients who are candidates for antiangiogenic therapies. On the basis of the expression profiles reported so far, therapies that target vascular endothelial growth factor should be considered for the treatment of renal, prostate and bladder cancers. As most tumors express factors that are involved in multiple angiogenic pathways, further research is needed to determine which are coregulated and what the most common patterns are.

Humans↗

PubMed2025

Multi-omics Mendelian randomization integrating RNA-seq, eQTL and pQTL data revealed CPXM1 as a potential drug target for osteoporosis.

Osteoporosis, a prevalent skeletal disorder characterized by decreased bone mineral density and increased fracture risk, continues to be a major global health concern. Traditional treatments for osteoporosis have limited efficacy and safety profiles, highlighting the need for novel therapeutic targets. This study integrates multi-omics data, including RNA-seq, expression quantitative trait loci (eQTL), and protein quantitative trait loci (pQTL) data, through Mendelian randomization (MR) to identify potential drug targets for osteoporosis. By leveraging bidirectional two-sample MR analysis, we identified CPXM1 (Carboxypeptidase X, M14 family member 1) as a novel gene that is causally linked to osteoporosis risk. Through transcriptomic and proteomic validation, we demonstrate that CPXM1 was upregulated in aged bone tissues and osteoporotic conditions in both human and murine models. Gene set enrichment analysis (GSEA) revealed significant dysregulation of bone homeostasis pathways, including increased extracellular matrix degradation and suppression of osteoblast differentiation in aged mice. Furthermore, phenome-wide association studies (PheWAS) confirmed minimal off-target effects of CPXM1, reinforcing its potential as a therapeutic target. Finally, computational drug repurposing predicted several promising drug candidates, including Doxorubicin, 5-Fluorouracil, and 2-Methylcholine, which may target CPXM1 pathways for osteoporosis treatment. These findings highlight CPXM1 as a potential biomarker and therapeutic target, offering new avenues for osteoporosis therapy.

Osteoporosis↗

PubMed2004

Two distinct pathways for thymidylate (dTMP) synthesis in (hyper)thermophilic Bacteria and Archaea.

The hyperthermophilic anaerobic archaeon Pyrococcus abyssi, which lacks thymidine kinase, incorporates label from extracellular uracil, but not from thymidine, into its DNA. This implies that P. abyssi must synthesize dTMP (thymidylate), an essential precursor for DNA synthesis, de novo. However, iterative similarity searches of the three completed Pyrococcus genomes fail to detect candidate genes for canonical thymidylate synthase ThyA, suggesting the presence of alternative pathways for dTMP synthesis. Indeed, by identifying a novel class of flavin-dependent thymidylate synthases, ThyX, we have recently proven that two distinct pathways for de novo synthesis of dTMP are operational in the microbial world. While both thyX and thyA can be found in hyperthermophilic micro-organisms, the phylogenetic distribution of thyX among hyperthermophiles is wider than that of thyA. In this contribution, we discuss the differences in the distinct mechanisms of dTMP synthesis, with a special emphasis on hyperthermophilic micro-organisms.

Archaea↗

PubMed1991

Movement of IgM antibody from blood to bile in rats.

The movement from blood to bile of passively injected autologous IgM antibody against horse erythrocytes was studied in rats. Both native and neuraminidase-treated antibody entered bile intact, with the peak titers for both measured between 60 and 90 min after injection. A small part (0.38%) of the injected dose of native antibody and 1.05% of the asialo-IgM antibody appeared in bile over 24 hr. These recoveries represented only a small fraction of the activity, which apparently disappeared from serum over the period. The pathways used by IgM antibody to enter bile were partially assessed. Prior injection of fetuin was found to abrogate the biliary secretion of native antibody and to significantly reduce the recovery of asialo-antibody in bile. In contrast, the presence of asialofetuin reduced (but not significantly) the secretion of native antibody and markedly changed the kinetics of appearance of asialo-IgM activity in bile. Some candidate routes to bile can be excluded as unlikely. The parahepatocellular pathway to bile canaliculi appears uninvolved because the secretion of antibody is slow and the inhibitory effects of fetuin argue against secretory component-mediated transport. Instead, two secretory pathways appear to be present. The first appears to be available to both native and asialo-IgM antibody, and may involve the peribiliary capillary plexus. The second route to bile is available to asialo-IgM antibody alone and is probably initiated by binding to the hepatic asialoglycoprotein receptor.

Animals↗

PubMed2004

Molecular imaging of drug-modulated protein-protein interactions in living subjects.

Networks of protein interactions mediate cellular responses to environmental stimuli and direct the execution of many different cellular functional pathways. Small molecules synthesized within cells or recruited from the external environment mediate many protein interactions. The study of small molecule-mediated interactions of proteins is important to understand abnormal signal transduction pathways in cancer and in drug development and validation. In this study, we used split synthetic renilla luciferase (hRLUC) protein fragment-assisted complementation to evaluate heterodimerization of the human proteins FRB and FKBP12 mediated by the small molecule rapamycin. The concentration of rapamycin required for efficient dimerization and that of its competitive binder ascomycin required for dimerization inhibition were studied in cell lines. The system was dually modulated in cell culture at the transcription level, by controlling nuclear factor kappaB promoter/enhancer elements using tumor necrosis factor alpha, and at the interaction level, by controlling the concentration of the dimerizer rapamycin. The rapamycin-mediated dimerization of FRB and FKBP12 also was studied in living mice by locating, quantifying, and timing the hRLUC complementation-based bioluminescence imaging signal using a cooled charged coupled device camera. This split reporter system can be used to efficiently screen small molecule drugs that modulate protein-protein interactions and also to assess drugs in living animals. Both are essential steps in the preclinical evaluation of candidate pharmaceutical agents targeting protein-protein interactions, including signaling pathways in cancer cells.

Animals↗

PubMed2006

Wnt/Frizzled signaling in hepatocellular carcinoma.

The Wnt/Frizzled (FZD) signaling cascade is important for cell fate determination during embryonic development as well as maintaining tissue homeostasis in the adult. In addition to these physiologic roles, studies have shown that deregulation of Wnt/FZD signaling occurs during carcinogenesis. As an example, over 90% of the colorectal cancers have mutations in adenomatous polyposis coli (APC) or beta-catenin genes. In addition, hepatocellular carcinoma (HCC) is another tumor with frequent aberrant activation of beta-catenin signaling. Nuclear and/or cellular beta-catenin accumulation, a hallmark of the activated canonical Wnt/FZD signaling, has been observed in 33-67% of tumors. However, mutations of APC and/or beta-catenin genes are found only in about 20-30% of HCCs, suggesting that the predominant mechanism(s) activating Wnt/FZD signaling pathway may be different from that found in colorectal cancers. There is accumulating evidence to suggest that regulatory mechanisms other than mutations involving beta-catenin or proteins in its destruction complex, many of which involve upstream components of the Wnt/FZD cascade, are important in HCC. Furthermore, information on the target genes of Wnt/FZD signaling and their roles in hepatocarcinogenesis is limited despite the recent discovery of several candidate genes. This review focuses on the alterations of Wnt/FZD signaling pathways and their relationship to the pathogenesis of HCC. A better understanding of the precise mechanisms of altered Wnt/FZD signaling may provide new molecular targets for therapy of HCC.

Adenomatous Polyposis Coli↗