Ancestry of RNA/RNA interaction regions within segmented ribosomes.

The ribosome is the universally conserved ribozyme that translates DNA coded instructions into proteins with the assistance of other RNA molecules, including transfer and messenger RNAs. Of particular interest is the segmentation phenomena, which is found in trypanosomatids and other protists. In these organisms, the large subunit ribosomal RNA is assembled from multiple smaller RNAs. This phenomenon posits several challenges to the folding and stabilization of such ribosomes to retain functionality and efficiency. In earlier studies, RNA/protein interactions were suggested to fully compensate for the fragmentation. Recently, several conserved RNA/RNA interaction regions were described in the cryo-EM structures of segmented ribosomes from trypanosomatids. These regions also seemed to aid in the folding and stabilization of such ribosomes, even before the ribosomal proteins start their association. In the present study, the existence of conserved RNA/RNA interaction regions shared between trypanosomatid and Euglena gracilis segmented ribosomes was confirmed, despite differences in segmentation patterns. Analysis of the crystallographic structures of unsegmented ribosomes from other Eukaryotes, Bacteria, and Archaea allowed us to estimate the relative age of highly conserved RNA/RNA interaction regions. These results strongly suggest that common interaction regions likely date far back into the ribosomes of the last common ancestor. Results also revealed that single hydrogen bonds are overwhelmingly facilitated by the 2'OH, a distinctive RNA feature. This supports the notion that RNA predates DNA and places some constraints on alternative nucleic acids proposals.

Morbidity and mortality in hip surgery patients due to fracture during the COVID-19 pandemic.

BACKGROUND: The COVID-19 epidemic generated major changes in general surgical management protocols. The literature has reported high mortality rates for hip fracture surgery in patients with COVID-19. This study describes the morbidity and mortality in patients undergoing surgery due to hip fractures in 12 Colombian institutions between March and September 2020. METHODOLOGY: This was a retrospective observational descriptive study. Medical records of 12 hospitals were reviewed. Consecutive patients who underwent hip fracture surgery from March 6 to September 6, 2020, were included. Data collected were sociodemographic profile, type of fracture, surgical treatment, complications, and early (1 month) or mid-term (1-6 months) mortality associated or not with COVID-19. RESULTS: Five hundred twenty patients with hip fractures requiring surgery in the 12 institutions were included. 364 (70%) were women; mean age was 77.7 years (SD: 13.8), mean BMI was 25.1, 91.73% of patients had at least one comorbidity, 60.38% were classified as ASA II and 25.77% as ASA III. There were 267 (51.34%) pertrochanteric fractures, 227 (43.65%) femoral neck fractures, and 26 (5.0%) subtrochanteric fractures. 274 (52.69%) patients were treated with osteosynthesis, 244 (46.92%) with arthroplasty, and 2 (0.38%) with girdlestone. Surgery was performed less than 24 h after the fracture for 115 (22.11%) patients, between 24 and 72 h for 208 (40.0%) patients, and more than 72 h for 197 (37.88%) patients. One hundred six patients in total suffered a medical or surgical complication throughout the different follow-up stages, amongst the most frequent were respiratory failure, coronary events, surgical site infection, cutting-out and peri­implant fracture. 25 (4.8%) patients required attention in the Intensive Care Unit (ICU). 13 patients had COVID-19 throughout the follow-up period. 27 patients died due to any cause, and 3 of them had reported a positive COVID-19 test any time during follow-up period, of which one died during the first month, and two died between 1 and 6 months. Statistically significant associations were found between age older than 75 years old, ASA classification, ICU requirement, and death. CONCLUSION: 520 patients received surgical treatment for hip fracture during the first six months of the COVID-19 pandemic in 12 medical centers in Colombia. 21.10% suffered a complication during the early stage (30 days) and 4.77% during the midterm stage (1-6 months). 4.8% were admitted in the ICU during the early stage. All-cause death was 27 patients, early death was 11 (40.74%) and midterm death was 16 (59.25%). 13 patients were positive for COVID-19, 3 died, one (1/5=20%) on the first 30 days and the other two (2/8=25%) from month 1 to 6.

How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active.

The modern ribosome catalyzes all coded protein synthesis in extant organisms. It is likely that its core structure is a direct descendant from the ribosome present in the last common ancestor (LCA). Hence, its earliest origins likely predate the LCA and therefore date further back in time. Of special interest is the pseudosymmetrical region (SymR) that lies deep within the large subunit (LSU) where the peptidyl transfer reaction takes place. It was previously proposed that two RNA oligomers, representing the P- and A-regions of extant ribosomes dimerized to create a pore-like structure, which hosted the necessary properties that facilitate peptide bond formation. However, recent experimental studies show that this may not be the case. Instead, several RNA constructs derived exclusively from the P-region were shown to form a homodimer capable of peptide bond synthesis. Of special interest will be the origin issues because the homodimer would have allowed a pre-LCA ribosome that was significantly smaller than previously proposed. For the A-region, the immediate issue will likely be its origin and whether it enhances ribosome performance. Here, we reanalyze the RNA/RNA interaction regions that most likely lead to SymR formation in light of these recent findings. Further, it has been suggested that the ability of these RNA constructs to dimerize and enhance peptide bond formation is sequence-dependent. We have analyzed the implications of sequence variations as parts of functional and nonfunctional constructs.

Residual formaldehyde contents in fresh white cheese in El Salvador: Seasonal changes associated with temperature.

Detection of residual formaldehyde (FA) in dairy products could be explained by direct addition of this preservative to extend the shelf life of raw material or final product at room temperature. FA is not authorized as a preservative by international standards and its addition to dairy products is prohibited due to its potentially harmful effects on consumers. Although the carcinogenicity of FA by oral exposure has not been proven, it is also known it cause histopathological and cytogenic changes in tissues at first contact, so its toxicity by ingestion should not be underestimated. This research determined both residual FA levels in locally produced fresh white cheese and its variation according to the seasons of the year and its association with ambient temperature. None of the FA levels quantified in cheese exceeded the maximum tolerable concentration (2.6 mg/kg) and although average FA contents did not vary significantly with seasonal changes (0.093-0.181 mg/kg), the number of positive cases did, since the highest prevalence occurred in the dry (60.9 %) and transitional dry-rainy (79.7 %) seasons of 2021, which are characterized by having the highest average ambient temperatures (27.5 °C and 28.3 °C, respectively). It was also shown that 79.6 % of the variability of FA-positive samples is explained by changes in the average temperature according to the year´s season. The association between these variables and quantified levels of aldehyde in raw milk sampled at the plant could indicate that FA was used to prevent milk and/or the final product from decomposing due to the effect of high ambient temperature. In addition, residual FA contents decreased in both milk and cheese, depending on added preservative levels, and the time elapsed prior to analysis.

Entropy Engineering and Tunable Magnetic Order in the Spinel High-Entropy Oxide.

Spinel oxides are an ideal setting to explore the interplay between configurational entropy, site selectivity, and magnetism in high-entropy oxides (HEOs). In this work, we characterize the magnetic properties of the spinel (Cr, Mn, Fe, Co, Ni)3O4 and study the evolution of its magnetism as a function of nonmagnetic gallium substitution. Across the range of compositions studied here, from 0 to 40% Ga, magnetic susceptibility and powder neutron diffraction measurements show that ferrimagnetic order is robust in the spinel HEO. However, we also find that the ferrimagnetic order is highly tunable, with the ordering temperature, saturated and sublattice moments, and magnetic hardness all varying significantly as a function of Ga concentration. Through X-ray absorption and magnetic circular dichroism, we are able to correlate this magnetic tunability with strong site selectivity between the various cations and the tetrahedral and octahedral sites in the spinel structure. In particular, we find that while Ni and Cr are largely unaffected by the substitution with Ga, the occupancies of Mn, Co, and Fe are each significantly redistributed. Ga substitution also requires an overall reduction in the transition metal valence, and this is entirely accommodated by Mn. Finally, we show that while site selectivity has an overall suppressing effect on the configurational entropy, over a certain range of compositions, Ga substitution yields a striking increase in the configurational entropy and may confer additional stabilization. Spinel oxides can be tuned seamlessly from the low-entropy to the high-entropy regime, making this an ideal platform for entropy engineering.

Self-medication in hospitalized patients with COVID-19: A cross-sectional study in northern Peru.

Introduction: This study aimed to identify factors associated with self-medication in patients with COVID-19. Methods: A cross-sectional study was conducted using medical records of patients with COVID-19 who self-medicated before admission to a hospital in Piura, Peru. Prevalence ratios and 95% confidence intervals were estimated using generalized linear models with Poisson distribution family, log link function, and robust variance. Results: Out of 301 patients, 165 (54.8%) self-medicated before hospital admission, being more frequent self-medication with ivermectin (85.5%) and azithromycin (71.5%). The frequency of self-medication in those aged between 30-59 years was 2.53-fold higher than in those between 18-29 years. Male patients, dyslipidemia, smoking, and hepatic steatosis were associated with self-medication. Clinical characteristics associated with self-medication were fever, cough, headache, anosmia, dysgeusia, nausea/vomiting, and gastroesophageal reflux. Conclusions: A high frequency of self-medication before hospital admission was observed in Peruvian patients with COVID-19, mainly of drugs without proven efficacy.

Factores asociados al impacto emocional de la pandemia por Covid-19 en profesionales sanitarios / [Factors associated with the emotional impact of the Covid-19 pandemic on health professionals]

El objetivo de este trabajo fue explorar el impacto emocional de la Covid-19 en profesionales sanitarios del Hospital Clínico Universitario de Valencia, e identificar las variables asociadas. Participaron 228 profesionales que cumplimentaron en mayo de 2020 una encuesta online elaborada ad hoc. Los profesionales sanitarios experimentaron síntomas de estrés (32%), depresión (26%), ansiedad (14%) y recuerdos intrusos (7,5%). Se observó mayor frecuencia de tristeza y ansiedad en mujeres y en profesionales que habían presentado síntomas de Covid-19. La categoría profesional con síntomas emocionales más frecuentes fue el de auxiliar de enfermería, y para estrés también enfermeros y residentes. Las unidades con mayor afectación fueron las de primera línea. Las variables psicológicas que se asociaron negativamente con la frecuencia de todas las manifestaciones sintomáticas fueron: autocuidado, autoestima, resiliencia y uso de estrategias de afrontamiento activas, junto a autoeficacia y apoyo social para estrés y depresión. Pese a las limitaciones del estudio, los resultados pueden contribuir a orientar programas preventivos para profesionales sanitarios en futuras crisis sanitarias.

The aim of this study was to explore the emotional impact of Covid-19 on healthcare professionals at the Clinical and University Hospital of Valencia (Spain), and to identify the associated variables. A total of 228 professionals completed an ad hoc online survey in May 2020. The healthcare professionals experienced symptoms of stress (32%), depression (26%), anxiety (14%) and intrusive memories (7.5%). A higher frequency of sadness and anxiety was observed in women and in professionals who had presented Covid-19 symptoms. The professional category with the most frequent emotional symptoms was that of auxiliary nurses, and for stress also nurses and residents. The most affected were the first line units. The psychological variables that were negatively associated with the frequency of all symptomatic manifestations were: self-care, self-esteem, resilience and use of active coping strategies, together with self-efficacy and social support for stress and depression. Despite the limitations of the study, the results may contribute to guide preventive programs for health professionals in future health crises.

Nonstandard RNA/RNA interactions likely enhance folding and stability of segmented ribosomes.

The ribosome is the molecular factory that catalyzes all coded protein synthesis in extant organisms. Eukaryotic ribosomes are typically assembled out of four rRNAs; namely, 5S, 5.8S, 18S, and 28S. However, the 28S rRNA of some trypanosomatid organisms has been found to be segmented into six independent rRNAs of different sizes. The two largest segments have multiple sites where they jointly form stems comprised of standard base pairs that can hold them together. However, such regions of interaction are not observed among the four smaller RNAs. Early reports suggested that trypanosomatid segmented ribosome assembly was essentially achieved thanks to their association with rProteins. However, examination of cryo-EM ribosomal structures from Trypanosoma brucei, Leishmania donovani, and Trypanosoma cruzi reveals several long-range nonstandard RNA/RNA interactions. Most of these interactions are clusters of individual hydrogen bonds and so are not readily predictable. However, taken as a whole, they represent significant stabilizing energy that likely facilitates rRNA assembly and the overall stability of the segmented ribosomes. In the context of origin of life studies, the current results provide a better understanding of the true nature of RNA sequence space and what might be possible without an RNA replicase.

The Peptidyl Transferase Center: a Window to the Past.

In his 2001 article, "Translation: in retrospect and prospect," the late Carl Woese made a prescient observation that there was a need for the then-current view of translation to be "reformulated to become an all-embracing perspective about which 21st century Biology can develop" (RNA 7:1055-1067, 2001, https://doi.org/10.1017/s1355838201010615). The quest to decipher the origins of life and the road to the genetic code are both inextricably linked with the history of the ribosome. After over 60 years of research, significant progress in our understanding of how ribosomes work has been made. Particularly attractive is a model in which the ribosome may facilitate an ∼180° rotation of the CCA end of the tRNA from the A-site to the P-site while the acceptor stem of the tRNA would then undergo a translation from the A-site to the P-site. However, the central question of how the ribosome originated remains unresolved. Along the path from a primitive RNA world or an RNA-peptide world to a proto-ribosome world, the advent of the peptidyl transferase activity would have been a seminal event. This functionality is now housed within a local region of the large-subunit (LSU) rRNA, namely, the peptidyl transferase center (PTC). The PTC is responsible for peptide bond formation during protein synthesis and is usually considered to be the oldest part of the modern ribosome. What is frequently overlooked is that by examining the origins of the PTC itself, one is likely going back even further in time. In this regard, it has been proposed that the modern PTC originated from the association of two smaller RNAs that were once independent and now comprise a pseudosymmetric region in the modern PTC. Could such an association have survived? Recent studies have shown that the extant PTC is largely depleted of ribosomal protein interactions. It is other elements like metallic ion coordination and nonstandard base/base interactions that would have had to stabilize the association of RNAs. Here, we present a detailed review of the literature focused on the nature of the extant PTC and its proposed ancestor, the proto-ribosome.

Architecture design of a reinforcement environment for learning sign languages.

Different fields such as linguistics, teaching, and computing have demonstrated special interest in the study of sign languages (SL). However, the processes of teaching and learning these languages turn complex since it is unusual to find people teaching these languages that are fluent in both SL and the native language of the students. The teachings from deaf individuals become unique. Nonetheless, it is important for the student to lean on supportive mechanisms while being in the process of learning an SL. Bidirectional communication between deaf and hearing people through SL is a hot topic to achieve a higher level of inclusion. However, all the processes that convey teaching and learning SL turn difficult and complex since it is unusual to find SL teachers that are fluent also in the native language of the students, making it harder to provide computer teaching tools for different SL. Moreover, the main aspects that a second language learner of an SL finds difficult are phonology, non-manual components, and the use of space (the latter two are specific to SL, not to spoken languages). This proposal appears to be the first of the kind to favor the Costa Rican Sign Language (LESCO, for its Spanish acronym), as well as any other SL. Our research focus stands on reinforcing the learning process of final-user hearing people through a modular architectural design of a learning environment, relying on the concept of phonological proximity within a graphical tool with a high degree of usability. The aim of incorporating phonological proximity is to assist individuals in learning signs with similar handshapes. This architecture separates the logic and processing aspects from those associated with the access and generation of data, which makes it portable to other SL in the future. The methodology used consisted of defining 26 phonological parameters (13 for each hand), thus characterizing each sign appropriately. Then, a similarity formula was applied to compare each pair of signs. With these pre-calculations, the tool displays each sign and its top ten most similar signs. A SUS usability test and an open qualitative question were applied, as well as a numerical evaluation to a group of learners, to validate the proposal. In order to reach our research aims, we have analyzed previous work on proposals for teaching tools meant for the student to practice SL, as well as previous work on the importance of phonological proximity in this teaching process. This previous work justifies the necessity of our proposal, whose benefits have been proved through the experimentation conducted by different users on the usability and usefulness of the tool. To meet these needs, homonymous words (signs with the same starting handshape) and paronyms (signs with highly similar handshape), have been included to explore their impact on learning. It allows the possibility to apply the same perspective of our existing line of research to other SL in the future.

Quiste de colédoco con sintomatología obstructiva en embarazada / Common bile duct cyst with obstructive symptoms in a pregnant woman

Los quistes de colédoco son poco comunes, en los países occidentales se ha reportado una incidencia de 1 por cada 100 mil nacidos vivos. En países asiáticos, esta incidencia es mayor, 1 por 100 nacidos vivos. Son usualmente diagnosticados durante la infancia y en el 25 % de los pacientes se presentan durante su vida adulta. Es inusual que se presenten durante el embarazo, sobre todo, que se manifieste durante el primer trimestre. Se realizó un informe de caso con presentación inusual del cuadro clínico no causal, de una embarazada en su primer trimestre con sintomatología obstructiva, evolucionando a colangitis. se realizan exámenes de gabinete como ultrasonografía abdominal y exámenes de laboratorio revelando obstrucción, además de realizarse colangioresonancia y ultrasonografía endoscópica dando como resultado quiste de colédoco tipo 1C, se realiza drenaje. Posteriormente al alta hospitalaria, la paciente presenta nuevamente cuadro de colangitis, se realiza drenaje endoscópico, sin embargo, presenta aborto

Choledochal cysts are rare, in western countries an incidence of 1 per 100,000 live births has been reported. In Asian countries, this incidence is higher 1 per 100 live births. They are usually diagnosed during childhood and in 25 % of patients they present during their adult life. It is unusual for them to occur during pregnancy, especially during the first trimester. A case report was made with an unusual presentation of the non-causal clinical picture, of a pregnant woman in her first trimester with obstructive symptoms, evolving to cholangitis. Cabinet examinations such as abdominal ultrasonography are performed, resulting in type 1C common bile duct cyst. Drainage is performed After discharge from the hospital, the patient presents again with cholangitis, endoscopic drainage is performed, however, she has abortion

Aflatoxin M1 in Nicaraguan and locally made hard white cheeses marketed in El Salvador.

Aflatoxin M1 is a carcinogenic and genotoxic metabolite of Aflatoxins present in food contaminated by fungi for lactating cattle, it is excreted through milk and when used to make cheese, the toxin will also be transferred to the dairy. The contamination of unripened hard white cheese with AFM1 seems to vary according to the season of the year, possibly due to the change of foodstuff, from fresh pasture in the rainy season to dried foods in the dry season and vice versa. This research determined both the prevalence and contents of AFM1 in cheeses of local and Nicaraguan origin marketed in El Salvador, as well as the changes occurred according to the season and the association between levels of AFM1 with meteorological parameters. The significantly higher prevalence of AFM1 contamination in both local cheeses and Nicaraguans, was found in the dry season and the lowest in the rainy season (41 % vs. 20 %; 31 % vs. 0%, respectively), the same trend was observed in AFM1 contents (0.076 vs. 0.036 µg/kg; 0.050 vs. 0.021 µg/kg, respectively). A significant association was demonstrated between levels of AFM1 with the averages of accumulated rainfall and relative humidity according to the sampled season. The prevalence of AFM1 in cheeses indicate that El Salvador and Nicaragua are endemic to dairy contamination by that mycotoxin. Seasonal variation may be due to a lack of rainfall, that promotes the growth of aflatoxigenic fungi in the crops of raw materials, which will be used for feedstuff intended for dairy cattle, thus, the consumption of contaminated food will cause the temporary increase of AFM1 in milk and their derivatives.

Further Characterization of the Pseudo-Symmetrical Ribosomal Region.

The peptidyl transferase center of the modern ribosome has been found to encompass an area of twofold pseudosymmetry (SymR). This observation strongly suggests that the very core of the ribosome arose from a dimerization event between two modest-sized RNAs. It was previously shown that at least four non-standard interactions exist between the two halves of SymR. Herein, we verify that the structure of the SymR is highly conserved with respect to both ribosome transition state and phylogenetic diversity. These comparisons also reveal two additional sites of interaction between the two halves of SymR and refine our understanding of the previously known interactions. In addition, the possible role that magnesium may have in the coordination, stabilization, association, and evolutionary history of the two halves (A-region and P-region) was examined. Together, the results identify a likely site where structural elements and Mg2+ ions may have facilitated the ligation of two aboriginal RNAs into a single unit.

Susceptibility of Caligus rogercresseyi collected from the native fish species Eleginops maclovinus (Cuvier) to antiparasitics applied by immersion.

A major challenge for Chilean salmon farming is infestation by the ectoparasite Caligus rogercresseyi. In addition, there is evidence that a loss of chemotherapeutic treatment efficacy against important fish pathogens is occurring in salmon farming, including antiparasitic efficacy. Currently, there are known techniques that allow the determination of the susceptibility profile of parasites to antiparasitic treatment. However, there is scarce information about both threshold values and categorization of antiparasitic susceptibility for C. rogercresseyi. Bioassay technique allowed the determination of both mean values and the natural variation of EC50%, which were contrasted with available susceptibility thresholds. Results allowed to determine that parasites from the native fish host, Eleginops maclovinus, are susceptible to azamethiphos, deltamethrin and cypermethrin treatments, showing a high susceptibility profile to antiparasitics.

On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes.

Compared with the large corpus of published work devoted to the study of the origin and early development of anabolism, little attention has been given to the discussion of the early evolution of catabolism in spite of its significance. In the present study, we have used comparative genomics to explore the evolution and phylogenetic distribution of the enzymes that catalyze the extant catabolic pathways of the monosaccharides glucose and ribose, as well as those of the nucleobases adenine, guanine, cytosine, uracil, and thymine. Based on the oxygen dependence of the enzymes, their conservation, and evolution, we speculate on the relative antiquity of the pathways. Our results allow us to suggest which catabolic pathways and enzymes may have already been present in the last common ancestor. We conclude that the enzymatic degradations of ribose, as well as those of purines adenine and guanine, are among the most ancient catabolic pathways which can be traced by protein-based methodologies.

Marchiafava-Bignami's Disease, as Etiologic Diagnosis of Athetosis.

The Marchiafava-Bignami disease, characterized by demyelination and necrosis of the corpus callosum, has typically been associated with chronic alcohol intake, and clinically has various symptoms and signs. However, several cases have been reported without alcohol association, and these - according to several publications - have some common points, such as preference for female, related to malnutrition, and radiological involvement of the splenium of the corpus callosum. We report a case of a patient with the characteristics described above and whose clinical manifestation was Athetosis. The authors associate this manifestation with the somatotopic distribution of the corpus callosum, and contribute to the etiologic diagnosis of Athetosis as a manifestation of the Marchiafava-Bignami disease, which has not been reported in the medical literature according to our review of the database.

A phylogenetic approach to the early evolution of autotrophy: the case of the reverse TCA and the reductive acetyl-CoA pathways

In recent decades, a number of hypotheses on the autotrophic origin of life have been presented. These proposals invoke the emergence of reaction networks leading from CO or CO2 to the organic molecules required for life. It has also been suggested that the last (universal) common ancestor (LCA or LUCA) of all extant cell lineages was a chemolitho-autotrophic thermophilic anaerobe. The antiquity of some carbon fixation pathways, the phylogenetic basal distribution of some autotrophic organisms, and the catalytic properties of iron-sulfur minerals have been advanced in support of these ideas. Here we critically examine the phylogenetic distribution and evolution of enzymes that are essential for two of the most ancient autotrophic means of metabolism: the reductive tricarboxylic acid (rTCA) cycle and the reductive acetyl-CoA pathway. Phylogenetic analysis of citryl-CoA synthetase and of citryl-CoA lyase, key enzymatic components of the rTCA cycle, and of CO dehydrogenase/acetyl-CoA synthase, a key enzyme in the reductive acetyl-CoA pathway, revealed that all three enzymes have undergone major lateral transfer events and therefore cannot be used as proof of the LCA’s metabolic abilities nor as evidence of an autotrophic origin of life (AU)

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A phylogenetic approach to the early evolution of autotrophy: the case of the reverse TCA and the reductive acetyl-CoA pathways.

In recent decades, a number of hypotheses on the autotrophic origin of life have been presented. These proposals invoke the emergence of reaction networks leading from CO or CO2 to the organic molecules required for life. It has also been suggested that the last (universal) common ancestor (LCA or LUCA) of all extant cell lineages was a chemolitho-autotrophic thermophilic anaerobe. The antiquity of some carbon fixation pathways, the phylogenetic basal distribution of some autotrophic organisms, and the catalytic properties of iron-sulfur minerals have been advanced in support of these ideas. Here we critically examine the phylogenetic distribution and evolution of enzymes that are essential for two of the most ancient autotrophic means of metabolism: the reductive tricarboxylic acid (rTCA) cycle and the reductive acetyl-CoA pathway. Phylogenetic analysis of citryl-CoA synthetase and of citryl-CoA lyase, key enzymatic components of the rTCA cycle, and of CO dehydrogenase/acetyl-CoA synthase, a key enzyme in the reductive acetyl-CoA pathway, revealed that all three enzymes have undergone major lateral transfer events and therefore cannot be used as proof of the LCA's metabolic abilities nor as evidence of an autotrophic origin of life.

Nanometer scale pores similar in size to the entrance of the ribosomal exit cavity are a common feature of large RNAs.

The highly conserved peptidyl transferase center (PTC) of the ribosome contains an RNA pore that serves as the entrance to the exit tunnel. Analysis of available ribosome crystal structures has revealed the presence of multiple additional well-defined pores of comparable size in the ribosomal (rRNA) RNAs. These typically have dimensions of 1-2 nm, with a total area of ∼100 Å(2) or more, and most are associated with one or more ribosomal proteins. The PTC example and the other rRNA pores result from the packing of helices. However, in the non-PTC cases the nitrogenous bases do not protrude into the pore, thereby limiting the potential for hydrogen bonding within the pore. Instead, it is the RNA backbone that largely defines the pore likely resulting in a negatively charged environment. In many but not all cases, ribosomal proteins are associated with the pores to a greater or lesser extent. With the exception of the PTC case, the large subunit pores are not found in what are thought to be the evolutionarily oldest regions of the 23S rRNA. The unusual nature of the PTC pore may reflect a history of being created by hybridization between two or more RNAs early in evolution rather than simple folding of a single RNA. An initial survey of nonribosomal RNA crystal structures revealed additional pores, thereby showing that they are likely a general feature of RNA tertiary structure.

Metalloproteins and the pyrite-based origin of life: a critical assessment.

We critically examine the proposal by Wächtershäuser (Prokaryotes 1:275-283, 2006a, Philos Trans R Soc Lond B Biol Sci 361: 787-1808, 2006b) that putative transition metal binding sites in protein components of the translation machinery of hyperthermophiles provide evidence of a direct relationship with the FeS clusters of pyrite and thus indicate an autotrophic origin of life in volcanic environments. Analysis of completely sequenced cellular genomes of Bacteria, Archaea and Eucarya does not support the suggestion by Wächtershäuser (Prokaryotes 1:275-283, 2006a, Philos Trans R Soc Lond B Biol Sci 361: 787-1808, 2006b) that aminoacyl-tRNA synthetases and ribosomal proteins bear sequence signatures typical of strong covalent metal bonding whose absence in mesophilic species reveals a process of adaptation towards less extreme environments.