Life Began When Evolution Began: A Lipidic Vesicle-Based Scenario

The research on the origin of life, as such, seems to have reached an impasse as a clear and universal scientific definition of life is probably impossible. On the contrary, the research on the origin of evolution may provide a clue. But it is necessary to identify the minimum requirements that allowed evolution to emerge on early Earth. The classical approach, the ‘RNA world hypothesis’ is one way, but an alternative based on nonlinear dynamics dealing with far-from-equilibrium self-organization and dissipative structures can also be proposed. The conditions on early Earth, near deep-sea hydrothermal sites, were favorable to the emergence of dissipative structures such as vesicles with bilayer membranes composed of a mixture of amphiphilic and hydrophobic molecules. Experimentally these vesicles are able to self-reproduce but not to evolve. A plausible scenario for the emergence of a positive feedback process giving them the capability of evolving on early Earth is suggested. The possibilities offered by such a process are described in regard to specific characteristics of extant biological organisms and leads for future research in the field are suggested.     

Terrestrial and extraterrestrial sources of molecular homochirality

The unique chirality of biomolecules is reviewed, and the prebiotic requirement for the absolute chiral homogeneity of such molecules prior to their capability of self-replication is emphasized. Biotic and abiotic theories embracing both chance and determinate mechanisms which have been proposed for the origin of terrestrial chiral molecules are briefly summarized and evaluated, as are abiotic mechanisms for the subsequent amplification of the small enantiomeric excesses (e.e.s) in the chiral molecules which might be formed by such processes. While amplification mechanisms are readily validated experimentally and are potentially viable on the primitive Earth, it is concluded that all terrestrial mechanisms proposed for the origin of chirality have one or more limitations which make them either intrinsically invalid or highly improbable in the chaotic and turbulent environment of the prebiotic Earth. To circumvent these difficulties we have proposed an extraterrestrial scenario for the production of terrestrial chirality in which circularly polarized synchrotron radiation from the neutron star remnant of a supernova interacts with the organic mantles on interstellar grains, producing chiral molecules by the partial asymmetric photolysis of racemic constituent in the mantles, after which the interstellar grains with their enantiomerically enriched mantles are transported to Earth either by direct accretion or through cometary impact. At this point one of the known terrestrial e.e. enrichment mechanisms could promote the small extraterrestrially produced e.e.s. into the state of chiral homogeneity required for self-replicating biomolecules.     

Conjugative DNA synthesis: R1162 and the question of rolling-circle replication

Strand-replacement synthesis during conjugative mating has been characterized by introducing into donor cells R1162 plasmid DNA containing a base-pair mismatch. Conjugative synthesis in donors occurs in the absence of vegetative plasmid replication, but with a lag between rounds of transfer, and with most strands being initiated at the normal site within the replicative origin. These characteristics argue against the idea that multiple plasmid copies are generated for successive rounds of transfer by rolling-circle replication. However, the R1162 relaxase protein can process molecules containing multiple transfer origins in the manner expected for the conversion of single-strand multimers, generated by rolling-circle replication, to unit-length molecules. This capability appears to be the result of a secondary cleavage reaction carried out by the protein. The possibility is raised that the processing of molecules with more than one origin of transfer might be a repair mechanism directed against adventitious DNA synthesis during transfer.     

Cytotoxic properties of CD4(+) T-cell clones which lyse HLA class II negative autologous non-small-cell lung cancer cells.

In this report, a subset of CD4(+) cells which kills autologous HLA class I positive and HLA class II negative non-small-cell lung cancer (NSCLC) cells is described. Killing was performed both by direct cytolytic mechanisms and by apoptosis. The peculiar characteristic of these effectors was their capability of lysing only interferon (IFN)-gamma-treated NSCLC target cells, expressing high numbers of HLA class I molecules. Analysis at the clonal level confirmed that cytolytic capability was distributed clonotypically. The addition of anti-HLA class I monoclonal IgM abrogated the susceptibility to lysis. Notably, the CD4-mediated cytolytic effect on IFN-gamma-treated targets was incomplete. Thus cytofluorimetric DNA and HLA class I expression analyses of target cells were performed: "resistant" targets consisted of large, aneuploid cells expressing a low number of HLA class I molecules. These findings suggested a direct role of HLA class I expression in the recognition of autologous cancer cells mediated by cytolytic CD4(+) cells.     

Accumulation of a non-binding form of estrogen receptor in MCF-7 cells under hydroxytamoxifen treatment

It is well known that MCF-7 cells, when incubated with hydroxytamoxifen (OH-Tam) loose their capacity to bind [³H]estradiol. By using Western blotting and [³H]tamoxifen aziridine labeling of KCl extracts from these cells we found that this loss in binding capacity was not associated with a disappearance of the estrogen receptor (ER) protein, an event known to occur after incubation with estradiol. Attempts to label under exchange conditions these ER molecules, which, on the basis of enzyme immunoassays appear to accumulate under OH-Tam treatment, were unsuccessful. Cell fractionation suggested that their origin is nuclear. Assessment of a few triphenylethylenic antiestrogens, as far as their inhibitory potency towards the in vitro MCF-7 cell growth is concerned, indicated a correlation between accumulation of these non-binding ER molecules and the antiestrogen antiproliferative action. However, we were unable to demonstrate absence of such an ER accumulation in two tamoxifen-resistant variants. Impaired folding of the ER protein or impaired phosphorylation of its hormone-binding domain are attractive hypotheses to account for these non-binding ER molecules. Whether these ER molecules have any physiological role, such as competition with the “normal” receptor molecules for the estrogen responsive elements on the DNA is unknown and deserves further study.     

Does quantum mechanics play a non-trivial role in life?

There have been many claims that quantum mechanics plays a key role in the origin and/or operation of biological organisms, beyond merely providing the basis for the shapes and sizes of biological molecules and their chemical affinities. These range from Schr?dinger's suggestion that quantum fluctuations produce mutations, to Hameroff and Penrose's conjecture that quantum coherence in microtubules is linked to consciousness. I review some of these claims in this paper, and discuss the serious problem of decoherence. I advance some further conjectures about quantum information processing in bio-systems. Some possible experiments are suggested.     

Origin of life: hypothesized roles of high-energy electrical discharges, infrared radiation, thermosynthesis and pre-photosynthesis

The hypothesis is proposed that during the organization of pre-biotic bacterial cell(s), high-energy electrical discharges, infrared radiation (IR), thermosynthesis and possibly pre-photosynthesis were central to the origin of life. High-energy electrical discharges generated some simple organic molecules available for the origin of life. Infrared radiation, both incoming to the Earth and generated on the cooling Earth with day/night and warming/cooling cycles, was a component of heat engine thermosynthesis before enzymes and the genetic code were present. Eventually, a primitive forerunner of photosynthesis and the capability to capture visible light emerged. In addition, the dual particle-wave nature of light is discussed from the perspective that life requires light acting both as a wave and particle.     

The echinoderm surface and its role in preventing microfouling

Antifouling is a property of the epidermis in echinoderms. There is neither production of biocides that act at any distance from the surface nor is the sloughing rate of the entire surface capable of explaining the observed antifouling capability. As with many invertebrates, the epidermis in echinoderms is overlain by thin surface coats, often termed the cuticle. The outermost coat has attenuated fibrils radiating outwards from the underlying cuticle. As these fibrils are the "real"; surface of the echinoderm, this is the level at which any antifouling defense must operate. It is suggested that their function is primarily antifouling. The cuticle contains chondroitin sulphate proteoglycan molecules and is negatively charged. The cuticle appears to be a highly extended glycocalyx. It is suggested that the primitive function of cellular glycocalyces is to modulate adhesive interactions at the cell or organismal surface.     

The topology of circular DNA]

A non-orientable structure, said M?bius stripe, is proposed for certain types of circular DNA. This structure could account for particular forms, such as dimers, double length molecules, or catenans which are molecules topologically interwomen. On the other hand, it is suggested that a second structure derived from the same principal of non-orientability could have gendered the dynamics of DNA replication at the origin of life: this is hypothesis of archetype M?bius strip.     

A method for the covalent capture and screening of diverse small molecules in a microarray format

This protocol describes a robust method for the covalent capture of small molecules with diverse reactive functional groups in microarray format, and outlines a procedure for probing small-molecule microarrays (SMMs) with proteins of interest. A vapor-catalyzed, isocyanate-mediated surface immobilization scheme is used to attach bioactive small molecules, natural products and small molecules derived from diversity-oriented synthesis pathways. Additionally, an optimized methodology for screening SMMs with purified proteins and cellular lysates is described. Finally, a suggested model for data analysis that is compatible with commercially available software is provided. These procedures enable a platform capability for discovering novel interactions with potential applications to immunoglobulin profiling, comparative analysis of cellular states and ligand discovery. With the appropriate materials and experimental setup, the printing of SMMs can be completed in 14 hours over 3 days. Screening and data analysis requires 2 days. A detailed timeline is provided.     

Hypercycles,parasites and packages

The hypercycle model considers a functional rather than spatial coupling of primitive tRNA molecules the essential phenomenon at the origin of life. We will critically discuss this model with special regard to the problems of selecting for functionally improved mutant molecules.To overcome these difficulties compartmentalization must become effective much earlier than suggested by the hypercycle model. Consequently, we sketch some features relevant for the genetics of primitive compartments.     

Optical and electronic coupling of the redox copper Azurin on ITO-coated quartz substrate

We have investigated the hybrid system constituted by the redox copper protein Azurin integrated with the semiconductor indium tin oxide (ITO) coated on quartz substrate. The system appears to be a good candidate for bio-sensing and bio-optoelectronics applications, especially due to the coupling between the optical and electron transfer features of Azurin with the conductive properties and optical transparency of ITO. The optical, morphological and electrical properties of the system have been investigated by combining optical absorption and transmission, steady-state fluorescence, resonance Raman spectroscopy and scanning probe microscopies. We found that Azurin molecules are firmly anchored on ITO and retain their structural and optical features underlying the physiological electron transfer activity. Scanning tunnelling spectroscopy evidenced a good electric coupling between the protein molecules and the substrate and a concomitant modulation of the ITO semiconductor properties upon deposition of Azurin. Some interplay between the conduction and valence bands of ITO and the electronic levels of Azurin is therefore suggested. These results are of a significant relevance in the perspective of developing bio-nanodevices able to process both optical and electrical signals, in conjugation also with the biorecognition capability of the protein molecules.     

Effect of bile on the amylolytic activity of various biological media

It has been established in experiments in vitro that bile activates amylase in blood, saliva and homogenates of the pancreas and small intestinal mucosa. Activation was found to depend on the amount of bile added and enzyme origin. It is suggested that bile has a direct effect on conformation of the amylase molecules.     

Tumour-released exosomes and their implications in cancer immunity

Tumour cells release vesicular structures, defined as microvesicles or exosomes, carrying a large array of proteins from their originating cell. The expression of antigenic molecules recognized by T cells has originally suggested a role for these organelles as a cell-free antigen source for anticancer vaccines. However, recent evidence shows that tumour exosomes may also exert a broad array of detrimental effects on the immune system, ranging from apoptosis in activated antitumour T cells to impairment of monocyte differentiation into dendritic cells and induction of myeloid suppressive cells. Immunosuppressive exosomes of tumour origin can be found in neoplastic lesions and sera from cancer patients, implying a potential role of this pathway in in vivo tumour progression. Through the expression of molecules involved in angiogenesis promotion, stromal remodelling, delivery of signalling pathways through growth factor/receptor transfer, chemoresistance and genetic intercellular exchange, tumour exosomes could represent a versatile tool for moulding host environment. Hence, their secretion by neoplastic cells may in the future become a novel pathway to target for therapeutic intervention in cancer patients.     

The origin of large molecules in primordial autocatalytic reaction networks

Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we know that can accomplish this task consist of large molecules. Thus the origin of large molecules is a chicken and egg problem in chemistry. Here we present a mechanism, based on autocatalytic sets (ACSs), that is a possible solution to this problem. We discuss a mathematical model describing the population dynamics of molecules in a stylized but prebiotically plausible chemistry. Large molecules can be produced in this chemistry by the coalescing of smaller ones, with the smallest molecules, the 'food set', being buffered. Some of the reactions can be catalyzed by molecules within the chemistry with varying catalytic strengths. Normally the concentrations of large molecules in such a scenario are very small, diminishing exponentially with their size. ACSs, if present in the catalytic network, can focus the resources of the system into a sparse set of molecules. ACSs can produce a bistability in the population dynamics and, in particular, steady states wherein the ACS molecules dominate the population. However to reach these steady states from initial conditions that contain only the food set typically requires very large catalytic strengths, growing exponentially with the size of the catalyst molecule. We present a solution to this problem by studying 'nested ACSs', a structure in which a small ACS is connected to a larger one and reinforces it. We show that when the network contains a cascade of nested ACSs with the catalytic strengths of molecules increasing gradually with their size (e.g., as a power law), a sparse subset of molecules including some very large molecules can come to dominate the system.     

Origin and Direction of Simian Virus 40 Deoxyribonucleic Acid Replication

Double-branched, circular, replicating deoxyribonucleic acid (DNA) molecules of simian virus 40 (SV40) have been cleaved by the R(1) restriction endonuclease from Escherichia coli. This enzyme introduces one double-strand break in SV40 DNA, at a specific site. The site of cleavage in the replicating molecules was used in this study to position the origin and the two branch points. Radioactively labeled molecules fractionated according to their extent of replication were evaluated after cleavage by sedimentation analysis and electron microscopy. The results demonstrate that the R(1) cleavage site is 33% of the genome length from the origin of replication and that both branch points are growing points. These data indicate that SV40 DNA replication is bidirectional and confirm other reports which have shown a unique origin of replication.     

In situ photochemical crosslinking of HeLa cell mitochondrial DNA by a psoralen derivative reveals a protected region near the origin of replication.

The in vivo association with proteins of HeLa cell mitochondrial DNA (mtDNA) has been investigated by analyzing the pattern of in situ crosslinking of the DNA by 4'-hydroxymethyl-4, 5',8-trimethylpsoralen (HMT). Either isolated mitochondria or whole cells were irradiated with long wavelength UV light in the presence of ths psoralen derivative, and the mtDNA was then isolated and analyzed in the electron microscope under totally denaturing conditions. No evidence of nucleosomal structure was found. The great majority of the molecules (approximately 90%) had a double-stranded DNA appearance over most of their contour length, with one to several bubbles occupying the rest of the contour, while the remaining 10% of the molecules appeared to be double-stranded over their entire length. Analysis of restriction fragments indicated the presence, in approximately 80% of the molecules, of a protected segment (300 to 1500 bp long) in a region which was centered asymmetrically around the origin of replication so as to overlap extensively the D-loop. Control experiments showed that at most 30% of the bubbles found near the origin could represent D-loops or expanded D-loops: furthermore, it could be excluded that some sequence peculiarity would account for the preferential location of bubbles near the origin of replication. The data have been interpreted to indicate that, in at least 55% of HeLa cell mtDNA molecules, the region around the origin is protected from in situ psoralen crosslinking by proteins or protein complexes which are associated in vivo with the DNA.     

Regenerated luminal epithelial cells are derived from preexisting luminal epithelial cells in adult mouse prostate

Determining the source of regenerated luminal epithelial cells in the adult prostate during androgen deprivation and replacement will provide insights into the origin of prostate cancer cells and their fate during androgen deprivation therapy. Prostate stem cells in the epithelial layer have been suggested to give rise to luminal epithelium. However, the extent of stem cell participation to prostate regrowth is not clear. In this report, using prostate-specific antigen-CreER(T2)-based genetic lineage marking/tracing in mice, preexisting luminal epithelial cells were shown to be a source of regenerated luminal epithelial cells in the adult prostate. Prostatic luminal epithelial cells could survive androgen deprivation and were capable of proliferating upon androgen replacement. Prostate cancer cells, typically exhibiting a luminal epithelial phenotype, may retain this intrinsic capability to survive and regenerate in response to changes in androgen signaling, providing part of the mechanism for the ultimate failure of androgen deprivation therapy in prostate cancer.     

Complex-formation between reduced xanthine oxidase and purine substrates demonstrated by electron paramagnetic resonance

The origin of the Rapid molybdenum electron-paramagnetic-resonance signals, which are obtained on reducing xanthine oxidase with purine or with xanthine, and whose parameters were measured by Bray & Vänngård (1969), was studied. It is concluded that these signals represent complexes of reduced enzyme with substrate molecules. Xanthine forms one complex at high concentrations and a different one at low concentrations. Purine forms a complex indistinguishable from the low-concentration xanthine complex. There are indications that some other substrates also form complexes, but uric acid, a reaction product, does not appear to do so. The possible significance of the complexes in the catalytic cycle of the enzyme is discussed and it is suggested that they represent substrate molecules bound at the reduced active site, waiting their turn to react there, when the enzyme has been reoxidized. Support for this role for the complexes was deduced from experiments in which frozen samples of enzyme–xanthine mixtures, prepared by the rapid-freezing method, were warmed until the signals began to change. Under these conditions an increase in amplitude of the Very Rapid signal took place. Data bearing on the origin of the Slow molybdenum signal are also discussed. This signal disappears only slowly in the presence of oxygen, and its appearance rate is unaffected by change in the concentration of dithionite. It is concluded that, like other signals from the enzyme, it is due to Mo^v but that a slow change of ligand takes place before it is seen. The Slow species, like the Rapid, seems capable of forming complexes with purines.