Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid ...analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.
Bark beetles play an important role as agents of natural renovation and regeneration in coniferous forests. Several studies have documented the metabolic capacity of bacteria associated with the gut, ...body surface, and oral secretions of these insects; however, little is known about how the bacterial community structure changes during the life cycle of the beetles. This study represents the first comprehensive analysis of the bacterial community of the gut of the bark beetle D. rhizophagus during the insect's life cycle using 454 pyrosequencing. A total of 4 bacterial phyla, 7 classes, 15 families and 23 genera were identified. The α-diversity was low, as demonstrated in previous studies. The dominant bacterial taxa belonged to the Enterobacteriaceae and Pseudomonadaceae families. This low α-diversity can be attributed to the presence of defensive chemical compounds in conifers or due to different morpho-physiological factors in the gut of these insects acting as strong selective factors. Members of the genera Rahnella, Serratia, Pseudomonas and Propionibacterium were found at all life stages, and the first three genera, particularly Rahnella, were predominant suggesting the presence of a core microbiome in the gut. Significant differences in β-diversity were observed, mainly due to bacterial taxa present at low frequencies and only in certain life stages. The predictive functional profiling indicated metabolic pathways related to metabolism of amino acids and carbohydrates, and membrane transport as the most significant in the community. These differences in the community structure might be due to several selective factors, such as gut compartmentalization, physicochemical conditions, and microbial interactions.
Significance
The detection of ethanolamine (
N
H
2
C
H
2
C
H
2
OH) in a molecular cloud in the interstellar medium confirms that a precursor of phospholipids is efficiently formed by interstellar ...chemistry. Hence, ethanolamine could have been transferred from the proto-Solar nebula to planetesimals and minor bodies of the Solar System and thereafter to our planet. The prebiotic availability of ethanolamine on early Earth could have triggered the formation of efficient and permeable amphiphilic molecules such as phospholipids, thus playing a relevant role in the evolution of the first cellular membranes needed for the emergence of life.
Cell membranes are a key element of life because they keep the genetic material and metabolic machinery together. All present cell membranes are made of phospholipids, yet the nature of the first membranes and the origin of phospholipids are still under debate. We report here the presence of ethanolamine in space,
N
H
2
C
H
2
C
H
2
OH, which forms the hydrophilic head of the simplest and second-most-abundant phospholipid in membranes. The molecular column density of ethanolamine in interstellar space is
N
= (1.51
±
0.07)
×
10
13
c
m
−
2
, implying a molecular abundance with respect to
H
2
of
(
0.9
−
1.4
)
×
10
−
10
. Previous studies reported its presence in meteoritic material, but they suggested that it is synthesized in the meteorite itself by decomposition of amino acids. However, we find that the proportion of the molecule with respect to water in the interstellar medium is similar to the one found in the meteorite (
10
−
6
). These results indicate that ethanolamine forms efficiently in space and, if delivered onto early Earth, could have contributed to the assembling and early evolution of primitive membranes.
One of the proposed scenarios for the origin of life is the primordial RNA world, which considers that RNA molecules were likely responsible for the storage of genetic information and the catalysis ...of biochemical reactions in primitive cells, before the advent of proteins and DNA. In the last decade, experiments in the field of prebiotic chemistry have shown that RNA nucleotides can be synthesized from relatively simple molecular precursors, most of which have been found in space. An important exception is hydroxylamine, NH2OH, which, despite several observational attempts, it has not been detected in space yet. Here we present the first detection of NH2OH in the interstellar medium toward the quiescent molecular cloud G+0.693-0.027 located in the Galactic Center. We have targeted the three groups of transitions from the J = 2−1, 3−2, and 4−3 rotational lines, detecting five transitions that are unblended or only slightly blended. The derived molecular abundance of NH2OH is (2.1 0.9) × 10−10. From the comparison of the derived abundance of NH2OH and chemically related species, with those predicted by chemical models and measured in laboratory experiments, we favor the formation of NH2OH in the interstellar medium via hydrogenation of NO on dust grain surfaces, with possibly a contribution of ice-mantle NH3 oxidation processes. Further laboratory studies and quantum chemical calculations are needed to completely rule out the formation of NH2OH in the gas phase.
Abstract The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, ...their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from “symbiotic” relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain.
Water agreements between Mexico and the United States have been crucial to preserving and restoring the Colorado River Delta's wetlands. Nowadays, increased water demand and climate change in the ...Colorado River Basin could threaten the conservation of the Ciénega de Santa Clara, a 4709 ha coastal wetland at the Sonoran Desert's edge. The international Ramsar convention recognizes the Ciénega de Santa Clara ecosystem for providing vital ecological services, including habitat for endemic, endangered, and migratory species. The hydrology of this wetland has not been completely understood since the 2010–2011 trial run of the Yuma Desalting Plant. Therefore, this study was conducted to identify and quantify the hydrological elements essential for the conservation of this wetland, under three scenarios: (a) normal inflow conditions of the water source – the Wellton‐Mohawk canal; (b) inflow reductions, and; (c) an increase of temperature due to global warming. Water and mass balances estimates were conducted every month during 2014–2015; in situ measurements of inflows were carried out on Southern International Boundary in Wellton‐Mohawk canal, the Riíto Drain, groundwater, and precipitation: evapotranspiration outputs were estimated using local weather stations and Penman‐Monteith formulations. Temperature increases were based on the Intergovernmental Panel on Climate Change projections for the next 100 years. Results showed disconnection in the surface flow of water from the wetland to the adjacent Gulf of California. This behaviour was observed mainly in the summer months in the three scenarios. The disconnections reduced the wetland area and water storage. The hydrological functionality of the Ciénega de Santa Clara wetland depends on the water supply from the Wellton‐Mohawk canal, with a minimum continuous discharge of 5.10 m3 s−1 during the summer months.
The water and mass balance of the Ciénega de Santa Clara, the most important remnant wetland of the Colorado River Delta, was analysed during 2014–2015. We examined different scenarios of future conditions based on variations of inflow from its principal binational source and the effects of the increase of temperatures in the watershed due to climate change. Maintenance of the Ciénega de Santa Clara's hydrological equilibrium will require at least 5.10 m3 s−1 of water during the summer months.
In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular ...species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided.
The properties of water at the nanoscale are crucial in many areas of biology, but the confinement of water molecules in sub-nanometre channels in biological systems has received relatively little ...attention. Advances in nanotechnology make it possible to explore the role played by water molecules in living systems, potentially leading to the development of ultrasensitive biosensors. Here we show that the adsorption of water by a self-assembled monolayer of single-stranded DNA on a silicon microcantilever can be detected by measuring how the tension in the monolayer changes as a result of hydration. Our approach relies on the microcantilever bending by an amount that depends on the tension in the monolayer. In particular, we find that the tension changes dramatically when the monolayer interacts with either complementary or single mismatched single-stranded DNA targets. Our results suggest that the tension is mainly governed by hydration forces in the channels between the DNA molecules and could lead to the development of a label-free DNA biosensor that can detect single mutations. The technique provides sensitivity in the femtomolar range that is at least two orders of magnitude better than that obtained previously with label-free nanomechanical biosensors and with label-dependent microarrays.
A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on ...mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.
The hepatitis C virus (HCV) RNA genome contains multiple structurally conserved domains that make long-distance RNA–RNA contacts important in the establishment of viral infection. Microarray ...antisense oligonucelotide assays, improved dimethyl sulfate probing methods and 2′ acylation chemistry (selective 2’-hydroxyl acylation and primer extension, SHAPE) showed the folding of the genomic RNA 3′ end to be regulated by the internal ribosome entry site (IRES) element via direct RNA–RNA interactions. The essential
cis
-acting replicating element (CRE) and the 3′X-tail region adopted different 3D conformations in the presence and absence of the genomic RNA 5′ terminus. Further, the structural transition in the 3′X-tail from the replication-competent conformer (consisting of three stem-loops) to the dimerizable form (with two stem-loops), was found to depend on the presence of both the IRES and the CRE elements. Complex interplay between the IRES, the CRE and the 3′X-tail region would therefore appear to occur. The preservation of this RNA–RNA interacting network, and the maintenance of the proper balance between different contacts, may play a crucial role in the switch between different steps of the HCV cycle.
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