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PubMed2025

Origin and evolution of mitochondrial inner membrane composition.

Unique membrane architectures and lipid building blocks underlie the metabolic and non-metabolic functions of mitochondria. During eukaryogenesis, mitochondria likely arose from an alphaproteobacterial symbiont of an Asgard archaea-related host cell. Subsequently, mitochondria evolved inner membrane folds known as cristae alongside a specialized lipid composition supported by metabolic and transport machinery. Advancements in phylogenetic methods and genomic and metagenomic data have suggested potential origins for cristae-shaping protein complexes, such as the mitochondrial contact site and cristae-organizing system (MICOS). MICOS protein homologs function in the formation of cristae-like intracytoplasmic membranes (ICMs) in diverse extant alphaproteobacteria. The machinery responsible for synthesizing key mitochondrial phospholipids - which cooperate with cristae-shaping proteins to establish inner membrane architecture - could have also evolved from a bacterial ancestor, but its origins have been less explored. In this Review, we examine the current understanding of mitochondrial membrane evolution, highlighting distinctions between prokaryotic and eukaryotic mitochondrial-specific proteins and lipids and their differing roles in shaping cristae and ICM architecture, and propose a model explaining the concurrent specialization of the mitochondrial lipidome and inner membrane structure in eukaryogenesis. We discuss how advancements across a range of disciplines are shedding light on how multiple membrane components co-evolved to support the central functions of eukaryotic mitochondria.

Mitochondrial Membranes↗
PubMed1976

The subacrosomal granule and its evolution during spermiogenesis in a lizard. Observations about the acrosomal fringe and the spermatid-sertoli cell relationship.

Some aspects of spermiogenesis have been studied in the testis of the teiid lizard Cnemidophorus lemniscatus lemniscatus by electron microscopy. Shortly after the acrosomal vesicle is lodged in a nuclear concavity of the spermatid, a dense granule differentiates in the center of the subacrosomal space. It is cone-shaped and shows a longitudinal striation. Its base applies to the acrosomal membrane and, through this, to the acrosomal granule. Its rounded vertex causes a depression of the nuclear membranes which, initially juxtaposed, separates at this point to form a vesicle. The granule develops and becomes a rod when spermiogenesis is advanced and the subacrosomal space has taken the form of a secondary cap. The rod is cylindrical, retains its original striation and has a convex acrosomal end. It encloses the vesicle formed by the nuclear envelope in its base and follows the apex of the nucleus. Meanwhile, the acrosomal granule loses its identity and the acrosomal cap is filled with a dense substance, in which a fringe of translucent material differentiates. This fringe lies in the dorsal and apical margins of the acrosome and is incompletely divided by longitudinal crests of the dense acrosomal substance. A projection of the Sertoli cell forms an accessory cap which envelops the acrosome and is in turn covered by the cytoplasm of the spermatid, constituting an intricate association. Two reflex membranes underlie the plasmalemma in the outer surface of the projection of the Sertoli cell. They are continuous with one another at their ends and with the cell membrane in the edge of pores. In the peripheral cytoplasm of the spermatid facing the accessory cap, numerous microtubules run longitudinally. By means of thin membranes some are interconnected or connected with the plasmalemma, from which they seem to originate.

Acrosome↗
PubMed1983

A thermodynamic study of sperm-egg interaction.

We have studied the binding of spermatozoa to the receptor sites on the vitelline coat (VC) of glycerol-treated eggs (ghost eggs) of the Ascidian, Ciona intestinalis (Protochordate). Glycerol treatment cytolyses the egg without affecting the ability of the VC to bind spermatozoa in a species-specific manner; however, in this system binding is not followed by the acrosome reaction. The ghost eggs are metabolically inert. As a base line for our analysis, we have studied the concentration-dependent heat evolved and oxygen consumption of spermatozoa when diluted in sea water. The process has been analyzed on the basis of equations derived by Liquori and Tripiciano to describe cell growth. Upon binding to the ghost eggs, the spermatozoa produce an explosive heat evolution (excess heat) which is not accompanied by oxygen consumption. The excess heat produced plotted against sperm concentration (at constant egg concentrations) gives an asymmetric bell-shaped curve. This is interpreted as being due to the competitive effect of sperm agglutination at a high sperm concentration. It is concluded that only spermatozoa that attach singly (monomeric spermatozoa) to the egg undergo metabolic activation.

Animals↗
PubMed1993

The cytological spectrum of the monocytoid B-cell reaction: recognition of its large cell type.

To analyse the cytological features of benign monocytoid B-cells, we investigated, histologically and immunohistochemically, 78 reactive lymphadenopathies expressing monocytoid B-cell reactions. Within a broad cytological spectrum of reactive monocytoid B-cells, two cytological types can be recognized: 1 the common type composed of medium-sized cells with irregular or bean-shaped nuclei and inconspicuous nucleoli, and 2 the large cell type composed of cells considered to represent large transformed monocytoid B-cells, with less pleomorphic round nuclei with vesicular chromatin and moderately basophilic, prominent nucleoli. In between these variants transitional forms showing evolution to large transformed monocytoid B-cells occurred. While monocytoid B-cell reactions in 70.5% of all cases were composed predominantly of the common type of monocytoid B-cells, in 29.5% of cases the large transformed cells prevailed. The two distinctive cytological types of reactive monocytoid B-cells seem to have their neoplastic counterparts in monocytoid B-cell lymphoma, including its large cell variant.

Antigens, Differentiation, B-Lymphocyte↗
PubMed1989

Sound localization, use of binaural cues and the superior olivary complex in pigs.

Noise localization thresholds and the ability to localize pure tones at 60 degrees separation were determined for three domestic pigs using a conditioned avoidance procedure. The average threshold for localizing a brief noise burst was 4.5 degrees which is much more accurate than the thresholds of other hoofed mammals, such as horses, cattle and goats. The ability of pigs to localize low-frequency tones indicates that they can use the binaural phase-difference cue. However, they were unable to localize tones of 4 kHz and higher, indicating that, like other hoofed mammals, their ability to use binaural intensity cues is greatly restricted if not completely absent. An examination of the superior olivary complex of pigs revealed that in relative size, shape and cell density it is more like that of cats than that of other hoofed mammals.

Animals↗
PubMed1999

Evolution of antigen-specific T cell receptors in vivo: preimmune and antigen-driven selection of preferred complementarity-determining region 3 (CDR3) motifs.

Antigen (Ag)-driven selection of helper T cells (Th) in normal animals has been difficult to study and remains poorly understood. Using the major histocompatibility complex class II- restricted murine response to pigeon cytochrome c (PCC), we provide evidence for both preimmune and Ag-driven selection in the evolution of Ag-specific immunity in vivo. Before antigenic challenge, most Valpha11(+)Vbeta3(+) Th (70%) express a critical complementarity-determining region 3 (CDR3) residue (glutamic acid at TCR-alpha93) associated with PCC peptide contact. Over the first 5 d of the primary response, PCC-responsive Valpha11(+)Vbeta3(+) Th expressing eight preferred CDR3 features are rapidly selected in vivo. Clonal dominance is further propagated through selective expansion of the PCC-specific cells with T cell receptor (TCR) of the "best fit." Ag-driven selection is complete before significant emergence of the germinal center reaction. These data argue that thymic selection shapes TCR-alpha V region bias in the preimmune repertoire; however, Ag itself and the nongerminal center microenvironment drive the selective expansion of clones with preferred TCR that dominate the response to Ag in vivo.

Animals↗
PubMed1993

Red blood cell deformability, membrane material properties and shape: regulation by transmembrane, skeletal and cytosolic proteins and lipids.

An unusual combination of membrane properties allows the RBC to undergo extensive deformation without cell fragmentation, enabling it to effectively perform its function of oxygen delivery during its long life span in circulation. These material properties are the consequence of slow evolution-driven "engineering" which evolved a composite structure in which a plasma membrane envelope composed of amphiphilic surfactant molecules is anchored to a network of skeletal proteins through tethering sites (transmembrane proteins) in the bilayer. Explosive growth in our understanding of the primary structure of the various RBC membrane proteins, definition of specific mutations in various RBC phenotypes, and detailed biophysical characterization of membrane properties of normal and mutant RBCs has enabled development of models of the molecular and structural basis for RBC properties. In this review, we have attempted to synthesize all of this currently available information and define the contributions of various membrane components to different RBC properties.

Bone and Bones↗
PubMed1996

Phenotypic characterization of the 3/A/1D-1M osteogenic cell line derived from in vivo transplantation of 3/A/1D-1 chondroprogenitor murine teratocarcinoma cells.

Bone cells involved in the replacement of cartilage by bone in the endochondral ossification process are known to enter via the medullar pathway. A hypothesis for the development of osteoblasts from chondroblasts was investigated by analyzing the phenotypic characteristics of the 3/A/1D-1M cell line derived from endochondral bone ossicle which was formed after in vivo transplantation of 3/A/1D-1 chondroprogenitor mouse teratocarcinoma cells. The 3/A/1D-1M cell cultures exhibited a triphasic evolution: after reaching confluence (day 3), cultures developed well-delimited cell clusters (days 6-8), which ultimately were organized into multilayered nodules (days 12-15). Electron-microscopic examination of such nodules at day 18 showed the presence of needle-shaped crystals associated with collagen fibrils in the extracellular space. The kinetics of collagen expression, investigated by an immunofluorescence staining procedure showed that, while confluent cultures mainly expressed type III collagen (70% of cells) with some type I (30-40% of cells) and V (30-40% of cells), the type I collagen became the major isoform beginning with day 6. From day 6 onwards, NP40-extracted alkaline phosphatase (AP) activity appeared concomitantly to cell cluster formation, and reached 160 nmol/min/mg of protein at the stage of nodule maturation (day 15). The strong inhibition of enzymatic activity by levamisole and L-homoarginine (IC50 = 0.9 microM and 5 mM, respectively) and its rapid heat inactivation at 56 degrees C (IT50 = 90 s), revealed the bone specificity of AP expressed by 3/A/1D-1M cells. In confluent cultures, brief exposure to parathyroid hormone (10 nM), known to be a bone-resorbing agent, showed a 60% increase in the intracellular cAMP level. In addition, while producing mRNA for the bone-specific protein osteocalcin, 3/A/1D-1M cells also produced type II procollagen mRNA, known to be the major cartilage-related characteristic. This in vitro study demonstrates that the 3/A/1D-1M clonal cell line, originating from 3/A/1D-1 chondroprogenitor cells after in vivo passage, was able to develop differentiated osteoblastic properties as well as the residual expression of the major chondrocytic RNA messenger.

Alkaline Phosphatase↗
PubMed2025

Enhancer activation from transposable elements in extrachromosomal DNA.

Extrachromosomal DNA (ecDNA) drives oncogene amplification and intratumoral heterogeneity in aggressive cancers. While transposable element (TE) reactivation is common in cancer, its role on ecDNA remains unexplored. Here, we map the 3D architecture of MYC-amplified ecDNA in colorectal cancer cells and identify 68 ecDNA-interacting elements (EIEs)-genomic loci enriched for TEs that are frequently integrated onto ecDNA. We focus on an L1M4a1#LINE/L1 fragment co-amplified with MYC, which functions only in the ecDNA amplified context. Using CRISPR-CATCH, CRISPR interference, and reporter assays, we confirm its presence on ecDNA, enhancer activity, and essentiality for cancer cell fitness. These findings reveal that repetitive elements can be reactivated and co-opted as functional rather than inactive sequences on ecDNA, potentially driving oncogene expression and tumor evolution. Our study uncovers a mechanism by which ecDNA harnesses repetitive elements to shape cancer phenotypes, with implications for diagnosis and therapy.

Journal Article↗
PubMed1991

The structure of plasmodesmata as revealed by plasmolysis, detergent extraction, and protease digestion.

Plasmodesmata or intercellular bridges that connect plant cells are cylindrical channels approximately 40 nm in diameter. Running through the center of each is a dense rod, the desmotubule, that is connected to the endoplasmic reticulum of adjacent cells. Fern, Onoclea sensibilis, gametophytes were cut in half and the cut surfaces exposed to the detergent, Triton X 100, then fixed. Although the plasma membrane limiting the plasmodesma is solubilized partially or completely, the desmotubule remains intact. Alternatively, if the cut surface is exposed to papain, then fixed, the desmotubule disappears, but the plasma membrane limiting the plasmodesmata remains intact albeit swollen and irregular in profile. Gametophytes were plasmolyzed, and then fixed. As the cells retract from their cell walls they leave behind the plasmodesmata still inserted in the cell wall. They can break cleanly when the cell proper retracts or can pull away portions of the plasma membrane of the cell with them. Where the desmotubule remains intact, the plasmodesma retains its shape. These images and the results with detergents and proteases indicate that the desmotubule provides a cytoskeletal element for each plasmodesma, an element that not only stabilizes the whole structure, but also limits its size and porosity. It is likely to be composed in large part of protein. Suggestions are made as to why this structure has been selected for in evolution.

Cell Wall↗
PubMed1995

Convergent evolution within the V3 loop domain of human immunodeficiency virus type 1 in association with disease progression.

Phylogenetic analysis was used to study in vivo genetic variation of the V3 region of human immunodeficiency virus type 1 in relation to disease progression in six infants with vertically acquired human immunodeficiency virus type 1 infection. Nucleotide sequences from each infant formed a monophyletic group with similar average branch lengths separating the sets of sequences. In contrast to the star-shaped phylogeny characteristic of interinfant viral evolution, the shape of the phylogeny formed by sequences from the infants who developed AIDS tended to be linear. A computer program, DISTRATE, was written to analyze changes in DNA distance values over time. For the six infants, the rate of divergence from the initial variant was inversely correlated with CD4 cell counts averaged over the first 11 to 15 months of life (r = -0.87, P = 0.024). To uncover evolutionary relationships that might be dictated by protein structure and function, tree-building methods were applied to inferred amino acid sequences. Trees constructed from the full-length protein fragment (92 amino acids) showed that viruses from each infant formed a monophyletic group. Unexpectedly, V3 loop protein sequences (35 amino acids) that were found at later time points from the two infants who developed AIDS clustered together. Furthermore, these sequences uniquely shared amino acids that have been shown to confer a T-cell line tropic phenotype. The evolutionary pattern suggests that viruses from these infants with AIDS acquired similar and possibly more virulent phenotypes.

Acquired Immunodeficiency Syndrome↗
PubMed2025

A mouse organoid platform for modeling cerebral cortex development and cis-regulatory evolution in vitro.

Natural selection has shaped the gene regulatory networks that orchestrate cortical development, leading to structural and functional variation across mammals, but the molecular and cellular mechanisms underpinning these changes have only begun to be characterized. Here, we develop a reproducible protocol for cerebral cortex organoid generation from mouse epiblast stem cells (EpiSCs), which recapitulates the timing and cellular differentiation programs of the embryonic cortex. We generated cortical organoids from F1 hybrid EpiSCs derived from crosses between laboratory mice (C57BL/6J) and four wild-derived inbred strains spanning ∼1 M years of evolutionary divergence to comprehensively map cis-acting transcriptional regulatory variation across developing cortical cell types, using single-cell RNA sequencing (scRNA-seq). We identify hundreds of genes that exhibit dynamic allelic imbalances, providing the first insight into the developmental mechanisms underpinning changes in cortical structure and function between subspecies. These experimental methods and cellular resources represent a powerful platform for investigating gene regulation in the developing cerebral cortex.

Organoids↗
PubMed1996

Intracellular endosymbiotic bacteria of Camponotus species (carpenter ants): systematics, evolution and ultrastructural characterization.

Intracellular endosymbiotic bacteria inherent to ants of the genus Camponotus were characterized. The bacteria were localized in bacteriocytes, which are specialized cells of both workers and queen ants; these cells are intercalated between epithelial cells of the midgut. The bacteriocytes show a different morphology from the normal epithelial cells and carry a large number of the rod-shaped Gram-negative bacteria free in the cytoplasm. The bacteria were never observed in the neighbouring epithelial cells, but they were found intracellularly in oocytes, strongly indicating a maternal transmission of the bacteria. The 16S DNA encoding rrs loci of the endosymbionts of four species of the genus Camponotus derived either from Germany (C. herculeanus and C. ligniperdus), North America (C. floridanus) or South America (C. rufipes) were cloned after polymerase chain reaction (PCR) amplification using oligonucleotides complementary to all so far known eubacterial rrs sequences. The DNA sequences of the rrs loci of the four endosymbionts were determined, and, using various genus- and species-specific oligonucleotides derived from variable regions in the rrs sequences, the identity of the bacteria present in the bacteriocytes and the ovarian cells was confirmed by PCR and in situ hybridization techniques. Comparison of the 16S DNA sequences with the available database showed the endosymbiotic bacteria to be members of the gamma-subclass of Proteobacteria. They formed a distinct taxonomic group, a sister taxon of the taxons defined by the tsetse fly and aphid endosymbionts. Within the gamma-subclass, the cluster of the ant, tsetse fly and aphid endosymbionts are placed adjacent to the family of Enterobacteriaceae. The evolutionary tree of the ant endosymbionts reflects the systematic classification and geographical distribution of their host insects, indicating an early co-evolution of the symbiotic partners and a vertical transmission of the bacteria.

Animals↗
PubMed2026

Cytonuclear conflict and reticulate evolution in the Morelloid clade (Solanum, Solanaceae): Insights from genome skimming and network Phylogenomics.

The Morelloid clade (black nightshades) is one of the most strongly supported clades within the megadiverse Solanum genus. It comprises 76 globally distributed, non-spiny herbaceous and suffrutescent species. While often erroneously considered poisonous weeds, several species are economically important as orphan crops. The clade is closely related to tomato and potato but, due to a lack of focused breeding efforts, remains a putative reservoir of genetic diversity for crop improvement. Despite this potential, we lack fundamental knowledge on the evolution of the Morelloid clade. The group includes polyploid species with unknown parental origins-likely reflecting reticulate processes such as hybridization, introgression, and associated backcrossing events. Prior analyses have been unable to disentangle these processes, leaving the mechanisms underlying reticulate evolution in the Morelloid clade poorly understood. Here, we use genome skimming to produce a well-supported maximum likelihood plastid phylogeny from complete circularized plastomes and a coalescent-based species tree from combined Angiosperms353 and conserved ortholog set nuclear markers. Our dataset, composed of previously published data and deep genome skimming from herbarium samples, spans 26 Morelloid species. To investigate phylogenetic discordance, we used a nuclear phylogenetic network, multispecies coalescent simulations, a fused rooted nuclear chloroplast tree, and quantification of nuclear gene tree concordance. We show that incongruence between nuclear and plastid trees is pervasive and cannot be explained by incomplete lineage sorting alone. Instead, our results demonstrate that events consistent with repeated chloroplast capture have shaped the reticulate evolutionary history of the clade, especially among African polyploid and Pan-American diploid lineages.

Phylogeny↗
PubMed1986

Development of ultrastructural specializations during the formation of acetylcholine receptor aggregates on cultured myotubes.

The ultrastructure of cultured rat myotubes was examined at stages in the initial assembly of acetylcholine receptor (AChR) aggregates in order to elucidate the role of cell-surface specializations in aggregate formation. Within 4-6 hr, embryonic brain extract (EBX) induces the formation of sites of AChR density elevated 5-9 X above that of surrounding regions, and the appearance of these aggregates is preceded by the formation of clouds of punctate microaggregates (Olek et al., 1983). A video image-intensification system was used to monitor this redistribution of fluorescently labeled AChR, and sites of aggregation were mapped on identified myotubes. After processing the cultures for electron microscopy, thin sections were taken through identified aggregate sites at various stages in assembly. Specializations, including a basal lamina, mound-shaped plasma membrane contours with occasional deep infoldings, and a subjacent dense cytoskeletal specialization, which tended to exclude other cytoplasmic organelles, were associated with newly formed aggregates found 4-6 hr after adding EBX to the cultures. Analysis of random thin sections through EBX-treated and untreated myotubes showed that the extent of specializations of the basal lamina and cytoplasm was approximately threefold greater in cells exposed to EBX for 4 hr, suggesting a concurrent, and possibly interdependent, organization of such specializations with AChR aggregate assembly. Examination of sections through clouds of microaggregates, which formed within 90 min, revealed mound-shaped plasma membrane contours and underlying cytoplasm depleted of organelles but relatively little basal lamina and submembrane cytoskeletal density. These results suggest that the initial stage of AChR aggregate assembly involves relatively subtle changes in the structure of the cell cortex and that the evolution of microaggregates to aggregates may require the formation of additional cytoskeletal and extracellular matrix structures.

Animals↗
PubMed2002

Evolution of octopod sperm I: comparison of nuclear morphogenesis in Eledone and Octopus.

Morphogenesis of the Eledone cirrhosa sperm nucleus, as studied by electron microscopic techniques, is compared with that of Octopus vulgaris. Both species of cephalopods belong to the family Octopodidae. The results indicate that extensive nuclear helicoidization during E. cirrhosa spermiogenesis is brought about by modifications of the function of structural components already present in the late steps of O. vulgaris spermiogenesis. In particular, changes in the regulation of perinuclear microtubule contraction in E. cirrhosa spermatids, as well as a decrease in basicity of protamines, promote nuclear helicoidization. Disulphide bond formation between protamine molecules fixes the completely helicoidal shape of the nucleus in mature sperm of E. cirrhosa.

Animals↗
PubMed1998

Biogenesis and function of IgM: the role of the conserved mu-chain tailpiece glycans.

The tailpiece of secretory Ig-mu-chains (mu(s)tp) is highly conserved throughout evolution: in particular, a carboxy-terminal cysteine residue (Cys575) and a glycan linked to Asn563 are found in all species sequenced so far. Here we show that the mu(s)tp oligosaccharide moieties are important for the binding of J-chains and for the process of IgM polymerization. In the absence of the mu(s)tp glycans, pentamers cannot be assembled and polymers containing six or more subunits are secreted. Despite their increased valency, these molecules have a lower association rate with antigen than wild-type polymers. Unexpectedly, the C-terminal oligosaccharides also affect kinetic parameters on unpolymerized subunits. Thus, monomers lacking the C-terminal sugars because of either site-directed mutagenesis or selective enzymatic deglycosylation with endoglycosidase H, have a lower k(on) for the antigen. Taken together, our results indicate that the C-terminal mu-chain glycans can shape the structure of mu(s2)L2 subunits and their further assembly into polymers.

Animals↗
PubMed2001

The shaping of the T cell repertoire.

By combining a TCRbeta transgene with a TCRalpha minilocus comprised of a single V and two J gene segments, we engineered a mouse line exhibiting ample but focused TCR diversity, restricted to CDR3alpha. Using single-cell PCR and high-throughput sequencing, we have exploited this system to scrutinize T cell repertoire selection and evolution. Some striking observations emerged: (1) thymic selection produces a repertoire that is very "bumpy," with marked overrepresentation of a subset of sequences; (2) MHC class I- and class II-restricted TCRs can be distinguished by minute, single-residue changes in CDR3alpha; and (3) homeostatic expansion and survival in the periphery can markedly remold the postselection repertoire, likely reflecting variability in the potential of cells displaying different TCRs to respond to homeostatic cues.

Animals↗