Psycholinguistic and emotion analysis of cryptocurrency discourse on X platform

This paper provides an extensive examination of a sizable dataset of English tweets focusing on nine widely recognized cryptocurrencies, specifically Cardano, Binance, Bitcoin, Dogecoin, Ethereum, Fantom, Matic, Shiba, and Ripple. Our goal was to conduct a psycholinguistic and emotional analysis of social media content associated with these cryptocurrencies. Such analysis can enable researchers and experts dealing with cryptocurrencies to make more informed decisions. Our work involved comparing linguistic characteristics across the diverse digital coins, shedding light on the distinctive linguistic patterns emerging in each coin's community. To achieve this, we utilized advanced text analysis techniques. Additionally, this work unveiled an understanding of the interplay between these digital assets. By examining which coin pairs are mentioned together most frequently in the dataset, we established co-mentions among different cryptocurrencies. To ensure the reliability of our findings, we initially gathered a total of 832,559 tweets from X. These tweets underwent a rigorous preprocessing stage, resulting in a refined dataset of 115,899 tweets that were used for our analysis. Overall, our research offers valuable perception into the linguistic nuances of various digital coins' online communities and provides a deeper understanding of their interactions in the cryptocurrency space.

Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling

Loss of H2A-H2B histone dimers is a hallmark of actively transcribed genes, but how the cellular machinery functions in the context of noncanonical nucleosomal particles remains largely elusive. In this work, we report the structural mechanism for adenosine 5'-triphosphate-dependent chromatin remodeling of hexasomes by the INO80 complex. We show how INO80 recognizes noncanonical DNA and histone features of hexasomes that emerge from the loss of H2A-H2B. A large structural rearrangement switches the catalytic core of INO80 into a distinct, spin-rotated mode of remodeling while its nuclear actin module remains tethered to long stretches of unwrapped linker DNA. Direct sensing of an exposed H3-H4 histone interface activates INO80, independently of the H2A-H2B acidic patch. Our findings reveal how the loss of H2A-H2B grants remodelers access to a different, yet unexplored layer of energy-driven chromatin regulation.

Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level

Single-stranded breaks (SSBs) are the most frequent DNA lesions threatening genomic integrity. A highly kinked DNA structure in complex with human PARP-1 domains led to the proposal that SSB sensing in Eukaryotes relies on dynamics of both the broken DNA double helix and PARP-1's multi-domain organization. Here, we directly probe this process at the single-molecule level. Quantitative smFRET and structural ensemble calculations reveal how PARP-1's N-terminal zinc fingers convert DNA SSBs from a largely unperturbed conformation, via an intermediate state into the highly kinked DNA conformation. Our data suggest an induced fit mechanism via a multi-domain assembly cascade that drives SSB sensing and stimulates an interplay with the scaffold protein XRCC1 orchestrating subsequent DNA repair events. Interestingly, a clinically used PARP-1 inhibitor Niraparib shifts the equilibrium towards the unkinked DNA conformation, whereas the inhibitor EB47 stabilizes the kinked state.

Thermodynamic Simulation of Environmental and Population Protection by Utilization of Technogenic Tailings of Enrichment

During mining, only 4-8% is converted to final products, and the rest is accumulated in landfills. There is a lack of research on the study of various patterns and mechanisms of the formation of cement clinker minerals during the simultaneous distillation of zinc. This paper presents studies of thermodynamic stimulation of environmental and population protection by utilization of technogenic enrichment waste as secondary raw materials for clinker production and zinc extraction. In particular, a comparison of the Gibbs energy (ΔG) of clinker formation under standard chemical equations and under non-standard chemical equations is given. According to the results of the study, using thermodynamic simulation, the temperature intervals of mineral formation, the dependence of the Gibbs energy on temperature (ΔG_T°), and the approximation equations were found; it was established that the presence of zinc ferrite contributes to the intensification of the formation of clinker minerals and the extraction of Zn to gas.

HR-Bac, a toolbox based on homologous recombination for expression, screening and production of multiprotein complexes using the baculovirus expression system

The Baculovirus/insect cell expression system is a powerful technology for reconstitution of eukaryotic macromolecular assemblies. Most multigene expression platforms rely on Tn7-mediated transposition for transferring the expression cassette into the baculoviral genome. This allows a rigorous characterization of recombinant bacmids but involves multiple steps, a limitation when many constructs are to be tested. For parallel expression screening and potential high throughput applications, we have established an open source multigene-expression toolbox exploiting homologous recombination, thus reducing the recombinant baculovirus generation to a single-step procedure and shortening the time from cloning to protein production to 2 weeks. The HR-bac toolbox is composed of a set of engineered bacmids expressing a fluorescent marker to monitor virus propagation and a library of transfer vectors. They contain single or dual expression cassettes bearing different affinity tags and their design facilitates the mix and match utilization of expression units from Multibac constructs. The overall cost of virus generation with HR-bac toolbox is relatively low as the preparation of linearized baculoviral DNA only requires standard reagents. Various multiprotein assemblies (nuclear hormone receptor heterodimers, the P-TEFb or the ternary CAK kinase complex associated with the XPD TFIIH subunit) are used as model systems to validate the toolbox presented.

Processing of Waste from Enrichment with the Production of Cement Clinker and the Extraction of Zinc

This paper presents studies on the processing of enrichment tailings as a component of a raw mixture in order to obtain cement clinker, with simultaneous distillation of zinc. Thermodynamic studies were carried out in the temperature range of 600–1600 °C using the software application “HSC Chemistry 6” developed by the metallurgical company Outokumpu (Finland). As a result of the conducted studies, we found that zinc contributes to the intensification of mineral formation of cement clinker. In particular, it was found that the formation of belite is possible in the temperature range from 990.7 to 1500 °C with Gibbs energy values of −0.01 and −323.8 kJ (which is better than the standard process by −11.4 kJ), respectively; the formation of alite is possible in the temperature range from 982.9 to 1500 °C with Gibbs energy values of −0.05 and −402.1 kJ (better than the standard process by −11.4 kJ), respectively; the formation of tricalcium aluminate is thermodynamically possible in the temperature range from 600 °C at ΔG_T^o = −893.8 kJ to 1500 °C at ΔG_T^o = −1899.3 kJ (better than the standard process by −1570.1 kJ), respectively; and the formation of four calcium aluminoferrite is possible in the temperature range from 600 °C at ΔG_T^o = −898.9 kJ to 1500 °C at ΔG_T^o = −1959.3 kJ (better than the standard process by −1570.2 kJ), respectively, with simultaneous distillation of zinc into a gaseous state for its further capture.

Association of cardiovascular risk factors with biological age

Funding Acknowledgements

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): National Academy of Medical Sciences of Ukraine

Background

Identifying reliable biomarkers of early ageing is an important goal for the prevention of cardiovascular disease (CVD).  Chronological age  (CA) is an essential risk factor for age-related disease including CVD. Biological age (BA) may be a more accurate metric for the risk of CVD and prediction of early vascular ageing, atherosclerosis. Available data allow us to judge the relationship of early ageing with all-cause mortality, healthspan and CVD. There is a hypothesis that BA can be used into models of risk prediction and stratification of CVD for personalized treatment.

Purpose

to determine the relationship between BA and factors of risk CVD in patients of different ages without clinical manifestations CVD.

Methods

We selected 102 patients aged 31–60 years with moderate cardiovascular risk without clinical symptoms of CVD. The patients did not receive regular drug therapy. Consenting subjects had a physical assessment, anthropometric measurements, electrocardiogram recording, blood sampling for laboratory analyses, including analysis of telomerase activity, telomere length in leukocytes and  buccal epithelium by a polymerase chain reaction in real-time. The SCORE scale was used for evaluation of the 10-year risk of fatal stroke and fatal myocardial infarction. In addition, 40 control individuals aged 31–60 years (20 men and 20 women), were also included in the study. BA was determined by 3 methods: PhenoAge, Voitenko’s method and Gorelkin-Pinhasov’s method. Multiple logistic regression analysis was used to develop a prediction of the early ageing model.

Results

The comparing patients of the control and main groups of the same CA shows, that patients with CVD risk have significantly higher BA, higher levels of proatherogenic lipids and shorter telomere length of the buccal epithelium. It was determined that body mass index, blood pressure, glucose levels are associated with an increase in BA in the main and the control groups. The increase of BA in the control group was associated with smoking, telomere length and telomerase activity and the level of antioxidant protection, in patients of the main group premature aging was associated with impaired lipid metabolism.

Conclusion

The biomarkers of biological aging can have benefits of the early identification of persons who age "faster" than others. The possibility of measuring biological aging can allow the assessment of health status at a time when there are still no symptoms, and interventions are more likely to be effective.

Atomic structure of the SAGA complex and it's interaction with TBP

The transcription of eukaryotic protein genes is controlled by a plethora of proteins which act together in multi-component complexes to facilitate the DNA dependent RNA polymerase II (Pol II) enzyme to bind to the transcription start site and to generate messenger RNA from the gene's coding sequence. The protein that guides the transcription machinery to the exact transcription start site is called TATA-box Binding Protein, or TBP. TBP is part of two large protein complexes involved in Pol II transcription, TFIID and SAGA. The two complexes share several subunits implicated in the interaction with TBP and contain proteins with structural elements highly homologous to nucleosomal histones. Despite the intensive study of transcription initiation, the mode of interaction of TBP with these complexes and its release upon DNA binding was elusive. In this study we demonstrate the quasi-atomic model of SAGA in complex with TBP. The structure reveals the intricate network of interactions that coordinate the different functional domains of SAGA and resolves a deformed octamer of histone-fold domains at the core of SAGA. This deformed octamer is precisely tuned to establish a peripheral site for TBP binding, where it is protected by steric hindrance against the binding of spurious DNA. Complementary biochemical analysis points to a mechanism for TBP delivery and release from SAGA that requires the general transcription factor TFIIA and whose efficiency correlates with the affinity of DNA to TBP.As the TBP binding machinery is highly similar in TFIID and SAGA, we demonstrated a universal mechanism of how TBP is delivered to gene promoters during transcription initiation.

Hemodynamic and metabolic disorders in obese patients with resistant hypertension

 

Resistant hypertension (RH) is an important cause of cardiovascular morbidity and mortality. Both true and pseudo-resistant arterial hypertension (AH) represent a big problem not only in blood pressure (BP) control, but also in those possible adverse cardiovascular events, the development of which is associated with failure to achieve target BP levels.

The aim of the study was to establish the features of hemodynamic and metabolic parameters in obese patients with true and pseudo-resistant AH.

Material and methods

The study included 200 patients with uncontrolled AH and obesity. Patients were initially prescribed dual antihypertensive therapy. Those patients who did not reach target BP levels after 3 months on dual therapy were additionally assigned a third antihypertensive drug. Of the 98 patients who were assigned triple therapy, 48 patients did not reach target BP (27 patients had pseudo-resistant and 21 patients had true resistant AH). These patients were additionally prescribed a fourth antihypertensive drug (spironolactone). The effectiveness of the treatment was evaluated 6 months after the start of antihypertensive therapy.

Results

After 6 months of therapy, patients with RH had higher body mass index (BMI) and higher BP levels compared to patients without this condition. Patients with RH also had more pronounced cardiovascular remodeling, higher levels of triglycerides, insulin, HbA1c, more pronounced insulin resistant (IR), which was confirmed by greater HOMA-IR, greater imbalance of adipokines, proinflamation activity and higher activity of the renin-angiotensin-aldosterone system (RAAS). A comparative assessment of pseudo-resistance and true resistance showed that patients with true resistance differed from pseudo-resistant patients with significantly lower BMI (p=0.02). In addition, in the absence of differences in BP levels, cardiovascular remodeling, lipid and carbohydrate profiles, patients with true resistance had significantly higher levels of aldosterone (p=0.04), higher activity of oxidative stress (malonic dialdehyde, p=0.01 and diene conjugates, p=0.03), a lower level of total antioxidant protection (p=0.00), a higher level of adiponectin (p=0.00), and a lower level of leptin (p=0.00), compared with pseudo-resistant patients.

Conclusions

Patients with resistant hypertension differed from hypertensive obese patients without resistance with higher BMI and BP, higher levels of triglycerides, insulin, HbA1c, more pronounced IR, cardiovascular remodeling, imbalance of oxidative stress - antioxidant protection system, higher proinflammatory and RAAS activity. Patients with true resistance differed from pseudo-resistant patients with significantly lower BMI, higher aldosterone levels, more pronounced imbalance of the system of oxidative stress - antioxidant protection and less pronounced adipokines imbalance.

Funding Acknowledgement

Type of funding source: None

[INFLUENCE OF ALCOHOL CONSUMPTION TO THE FIRSTLY DIAGNOSED LUNG TUBERCULOSIS AND TREATMENT EFFICIENCY]

The study of the clinical and laboratory dynamics after an intensive phase of treatment in patients with firstly diagnosed pulmonary tuberculosis (FDTB) with alcohol consumption, and the development of a method for predicting the effectiveness of treatment. Examined 109 men with FDTB aged 20 to 50 years. Depending on the level of alcohol consumption, 3 groups of patients were formed. Patients of each group divided into two subgroups depending on the treatment regimen. The highest response to antioxidant therapy had indicators of phagocytic and enzymatic activity of neutrophils and endogenous intoxication. The dynamics of a decrease in all indicators of oxidative stress in groups 1 and 2 was higher in patients who additionally received antioxidants. The positive effects of group 3 was less. The models of prediction the positive dynamics level in the treatment of patients depending on the scheme therapy received have been developed. Predictors of treatment efficacy for patients with FDTB and alcohol intake with standard therapy are baseline alcohol consumption level, phagocytic index, and blood lymphocyte count. When prescribing antioxidants to a standard therapy regimen - initial level of alcohol consumption and phagocytic number. The degree of alcohol consumption is a common determinant of treatment effectiveness, regardless of treatment regimen.

A study of lexical function detection with word2vec and supervised machine learning

In this work, we report the results of our experiments on the task of distinguishing the semantics of verb-noun collocations in a Spanish corpus. This semantics was represented by four lexical functions of the Meaning-Text Theory. Each lexical function specifies a certain universal semantic concept found in any natural language. Knowledge of collocation and its semantic content is important for natural language processing, as collocation comprises the restrictions on how words can be used together. We experimented with word2vec embeddings and six supervised machine learning methods most commonly used in a wide range of natural language processing tasks. Our objective was to study the ability of word2vec embeddings to represent the context of collocations in a way that could discriminate among lexical functions. A difference from previous work with word embeddings is that we trained word2vec on a lemmatized corpus after stopwords elimination, supposing that such vectors would capture a more accurate semantic characterization. The experiments were performed on a collection of 1,131 Excelsior newspaper issues. As the experimental results showed, word2vec representation of collocations outperformed the classical bag-of-words context representation implemented in a vector space model and fed into the same supervised learning methods.

[MEDICAL AND SOCIAL CHARACTERISTICS OF PATIENTS WITH TUBERCULOSIS IN THE CONTEXT OF ALCOHOL CONSUMPTION]

The objective of the research was to study the clinical data of patients with firstly diagnosed pulmonary tuberculosis (FDTB) and different levels of alcohol consumption. The study involved 102 patients with FDTB and alcohol consumption. According to the results of the AUDIT questionnaire, patients were divided into three groups. Group 1 - persons who scored 0-7 points according to the test results, group 2 - 8-15 points and group 3 - 16 points or more. The results of the study showed that patients of group 3 are more socially deprived. Alcohol abuse in patients with tuberculosis was significantly more often (p<0.05) associated with late detection of active tuberculosis, the severity of respiratory complaints, a higher involved of lung tissue in patological process according to the results of x-ray examinations, a tendency to form multiple cavities and a greater massiveness of bacterial excretion compared to groups of low-drinkers and moderate use of alcohol. Patients with FDTB who consume alcohol with a health hazard and abuse alcohol have a decrease in social adaptation and prevalence of common forms of tuberculosis with massive bacterial excretion. The fact they are more likely to develop progressive forms of the disease is a serious public health problem. Therefore, special attention aimed at the prevention of tuberculosis in this cohort of patients is necessary and justified.

Structure of SAGA and mechanism of TBP deposition on gene promoters

SAGA (Spt-Ada-Gcn5-acetyltransferase) is a 19-subunit complex that stimulates transcription via two chromatin-modifying enzymatic modules and by delivering the TATA box binding protein (TBP) to nucleate the pre-initiation complex on DNA, a pivotal event in the expression of protein-encoding genes¹. Here we present the structure of yeast SAGA with bound TBP. The core of the complex is resolved at 3.5 Å resolution (0.143 Fourier shell correlation). The structure reveals the intricate network of interactions that coordinate the different functional domains of SAGA and resolves an octamer of histone-fold domains at the core of SAGA. This deformed octamer deviates considerably from the symmetrical analogue in the nucleosome and is precisely tuned to establish a peripheral site for TBP, where steric hindrance represses binding of spurious DNA. Complementary biochemical analysis points to a mechanism for TBP delivery and release from SAGA that requires transcription factor IIA and whose efficiency correlates with the affinity of DNA to TBP. We provide the foundations for understanding the specific delivery of TBP to gene promoters and the multiple roles of SAGA in regulating gene expression.

Comparative analysis of functional changes indicators in the body of students with different teaching of physical culture lessons

Based on the position of psychological theory of activity, the question of the need to improve the functional state of students in universities is actualized. On the basis of the ascertaining experiment, the most informative functional test was identified, which characterizes the adaptive mechanisms of the organism. Taking into account the practice of introducing extracurricular activities into physical education of university students, a comparative analysis of the index of functional changes in the organism of students engaged in different ratios of educational process organization forms is carried out.

TFIIH: A multi-subunit complex at the cross-roads of transcription and DNA repair

Transcription factor IIH (TFIIH) is a multiprotein complex involved in both eukaryotic transcription and DNA repair, revealing a tight connection between these two processes. Composed of 10 subunits, it can be resolved into a 7-subunits core complex with the XPB translocase and the XPD helicase, and the 3-subunits kinase complex CAK, which also exists as a free complex with a distinct function. Initially identified as basal transcription factor, TFIIH also participates in transcription regulation and plays a key role in nucleotide excision repair (NER) for opening DNA at damaged sites, lesion verification and recruitment of additional repair factors. Our understanding of TFIIH function in eukaryotic cells has greatly benefited from studies of the genetic rare diseases xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD), that are not only characterized by cancer and aging predispositions but also by neurological and developmental defects. Although much remains unknown about TFIIH function, significant progresses have been done regarding the structure of the complex, the functions of its catalytic subunits and the multiple roles of the regulatory core-TFIIH subunits. This review provides a non-exhaustive survey of key discoveries on the structure and function of this pivotal factor, which can be considered as a promising target for therapeutic strategies.

Molecular structure of promoter-bound yeast TFIID

Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe.

Transcription preinitiation complex assembly begins with the recognition of the gene promoter by the TATA-box Binding Protein-containing TFIID complex. Here the authors present a Cryo-EM structure of promoter-bound yeast TFIID complex, providing a detailed view of its subunit organization and promoter DNA contacts.

[OPTIMIZATION OF DIAGNOSIS OF PULMONARY HYPERTENSION SYNDROME IN PATIENTS WITH CHRONIC OBSTRUCTIVE PULMONARY DISEASE IN COMBINATION WITH ISCHEMIC HEART DISEASE]

Objective - to develop a new additional method for assessing the level of pulmonary artery pressure in patients with chronic obstructive lung obstruction (COPD) in combination with ischemic heart disease (IHD), which will improve the quality of early diagnosis of pulmonary hypertension syndrome in this category of patients. The study included 104 male patients diagnosed with COPD in combination with IHD. All patients were subjected to a comprehensive clinical examination, examination of the function of external respiration, ultra sound examination of the structural and functional state of the heart and blood vessels, determination of blood levels of factors of the systemic inflammatory response. Based on the data obtained from the study, it was assumed that the values of the smoking index (IC), the forced expiratory volumein 1 s (FEV1), the average volumetric rate of the forced vital capacity of the lungs (COC25-75), the content of the C-reactive protein in the plasma blood (CRP) can be prognostic markers for the formation of pulmonary hypertension in the comorbidity of COPD with IHD and a use ful model for determining mean pulmonary artery pressure. Calculation of mean pulmonary artery pressure in patients with COPD with and IHD contributes to anincrease in the effectivenes sofearly diagnosis of pulmonary hypertension syndrome, which inturn will help optimize the assessment of the prognosis and therapy of this contingent of patients.

The production of multiprotein complexes in insect cells using the baculovirus expression system

The production of a homogeneous protein sample in sufficient quantities is an essential prerequisite not only for structural investigations but represents also a rate-limiting step for many functional studies. In the cell, a large fraction of eukaryotic proteins exists as large multicomponent assemblies with many subunits, which act in concert to catalyze specific activities. Many of these complexes cannot be obtained from endogenous source material, so recombinant expression and reconstitution are then required to overcome this bottleneck. This chapter describes current strategies and protocols for the efficient production of multiprotein complexes in large quantities and of high quality, using the baculovirus/insect cell expression system.

Import of Nuclear DNA-Encoded RNAs into Mitochondria and Mitochondrial Translation

Targeting nuclear DNA-encoded tRNA into mitochondria is a quasi-ubiquitous process, found in a variety of species, although the mechanisms of this pathway seem to differ from one system to another. In all cases reported, this import concerns small non-coding RNAs and the vast majority of imported RNAs are transfer RNAs. If was commonly assumed that the main criterion to presume a tRNA to be imported is the absence of the corresponding gene in mitochondrial genome, in some cases the imported species seemed redundant in the organelle. By studying one of such "abnormal" situation in yeast S. cerevisiae, we discovered an original mechanism of conditional regulation of mitochondrial translation exploiting the RNA import pathway. Here, we provide an outline of the current state of RNA import in yeast and discuss the possible impact of the newly described mechanism of translational adaptation.

Identification of the Rps28 binding motif from yeast Edc3 involved in the autoregulatory feedback loop controlling RPS28B mRNA decay

In the yeast Saccharomyces cerevisiae, the Edc3 protein was previously reported to participate in the auto-regulatory feedback loop controlling the level of the RPS28B messenger RNA (mRNA). We show here that Edc3 binds directly and tightly to the globular core of Rps28 ribosomal protein. This binding occurs through a motif that is present exclusively in Edc3 proteins from yeast belonging to the Saccharomycetaceae phylum. Functional analyses indicate that the ability of Edc3 to interact with Rps28 is not required for its general function and for its role in the regulation of the YRA1 pre-mRNA decay. In contrast, this interaction appears to be exclusively required for the auto-regulatory mechanism controlling the RPS28B mRNA decay. These observations suggest a plausible model for the evolutionary appearance of a Rps28 binding motif in Edc3.

[Fat distribution and its relationship with genetic polymorphism in patients with nonalcoholic liver disease]

The article presents the results of research which demonstrated that the features of fat distribution in patients with non-alcoholic fatty liver disease (NAFLD), which depended on the sex and the activity of alanine transaminase. It is shown that carriers G allele rs6666089ADIPOR1 had significantly higher levels of visceral, subcutaneous adipose tissue and their relation and% liver fat in the compared with carriers A allele. The findings suggest that the development of more severe hepatic steatosis in carriers of GG genotype of rs6666089 ADIPOR1, confirming participation in the formation of ectopic fat NAFLD.

[Relationship gene polymorphism adipor1 with cardiovascular risk in patients with nonalcoholic fatty liver disease]

The aim of the research was to study the link between the polymorphic gene ADIPOR1 and the development of cardiovascular risk in patients with non-alcoholic fatty liver disease (NAFLD). It was found that the carriers of the G allele ADIPOR1 rs 1342387, compared with the carriers of the A allele have a potentially higher degree of cardiovascular risk. NAFLD carriers of the G genotype ADIPOR1 observed proatherogenic lipid profile and a significant increase in the thickness of the intima-media. The results confirm the modulation of genetic factors in the implementation of cardiovascular risk in patients with NAFLD.

Selection of RNA aptamers imported into yeast and human mitochondria

In the yeast Saccharomyces cerevisiae, nuclear DNA-encoded is partially imported into mitochondria. We previously found that the synthetic transcripts of yeast tRNA(Lys) and a number of their mutant versions could be specifically internalized by isolated yeast and human mitochondria. The mitochondrial targeting of tRNA(Lys) in yeast was shown to depend on the cytosolic precursor of mitochondrial lysyl-tRNA synthetase and the glycolytic enzyme enolase. Here we applied the approach of in vitro selection (SELEX) to broaden the spectrum of importable tRNA-derived molecules. We found that RNAs selected for their import into isolated yeast mitochondria have lost the potential to acquire a classical tRNA-shape. Analysis of conformational rearrangements in the importable RNAs by in-gel fluorescence resonance energy transfer (FRET) approach permitted us to suggest that protein factor binding and subsequent import require formation of an alternative structure, different from a classic L-form tRNA model. We show that in the complex with targeting protein factor, enolase 2, tRK1 adopts a particular conformation characterized by bringing together the 3'-end and the TPsiC loop. This is a first evidence for implication of RNA secondary structure rearrangement in the mechanism of mitochondrial import selectivity. Based on these data, a set of small RNA molecules with significantly improved efficiency of import into yeast and human mitochondria was constructed, opening the possibility of creating a new mitochondrial vector system able to target therapeutic oligoribonucleotides into deficient human mitochondria.

Deleterious mutation in the mitochondrial arginyl-transfer RNA synthetase gene is associated with pontocerebellar hypoplasia

Homozygosity mapping was performed in a consanguineous Sephardic Jewish family with three patients who presented with severe infantile encephalopathy associated with pontocerebellar hypoplasia and multiple mitochondrial respiratory-chain defects. This resulted in the identification of an intronic mutation in RARS2, the gene encoding mitochondrial arginine-transfer RNA (tRNA) synthetase. The mutation was associated with the production of an abnormally short RARS2 transcript and a marked reduction of the mitochondrial tRNA(Arg) transcript in the patients' fibroblasts. We speculate that missplicing mutations in mitochondrial aminoacyl-tRNA synthethase genes preferentially affect the brain because of a tissue-specific vulnerability of the splicing machinery.

tRNA import into yeast mitochondria is regulated by the ubiquitin-proteasome system

In Saccharomyces cerevisiae, one of two cytosolic lysine-tRNAs is partially imported into mitochondria. We demonstrate that three components of the ubiquitin/26S proteasome system (UPS), Rpn13p, Rpn8p and Doa1p interact with the imported tRNA and with the essential factor of its mitochondrial targeting, pre-Msk1p. Genetic and biochemical assays demonstrate that UPS plays a dual regulatory role, since the overall inhibition of cellular proteasome activity reduces tRNA import, while specific depletion of Rpn13p or Doa1p increases it. This result suggests a functional link between UPS and tRNA mitochondrial import in yeast and indicates on the existence of negative and positive import regulators.

Evidence for an Adaptation Mechanism of Mitochondrial Translation via tRNA Import from the Cytosol

Although mitochondrial import of nuclear DNA-encoded RNAs is widely occurring, their functions in the organelles are not always understood. Mitochondrial function(s) of tRNA(Lys)(CUU), tRK1, targeted into Saccharomyces cerevisiae mitochondria was mysterious, since mitochondrial DNA-encoded tRNA(Lys)(UUU), tRK3, was hypothesized to decode both lysine codons, AAA and AAG. Mitochondrial targeting of tRK1 depends on the precursor of mitochondrial lysyl-tRNA synthetase, pre-Msk1p. Here we show that substitution of pre-Msk1p by its Ashbya gossypii ortholog results in a strain in which tRK3 is aminoacylated, while tRK1 is not imported. At elevated temperature, drop of tRK1 import inhibits mitochondrial translation of mRNAs containing AAG codons, which coincides with the impaired 2-thiolation of tRK3 anticodon wobble nucleotide. Restoration of tRK1 import cures the translational defect, suggesting the role of tRK1 in conditional adaptation of mitochondrial protein synthesis. In contrast with the known ways of organellar translation control, this mechanism exploits the RNA import pathway.

Targeting of tRNA into yeast and human mitochondria: the role of anticodon nucleotides

In vivo, yeast mitochondria import a single cytoplasmic tRNA, tRNA(CUU)Lys, while human mitochondria do not import any cytoplasmic tRNA. We have previously demonstrated that both yeast and human isolated mitochondria can specifically internalize tRNA(CUU)Lys, several of its mutant versions and some mutant versions of yeast cytosolic tRNA(UUU)Lys (not imported in vivo). Aminoacylation of tRNA(CUU)Lys by the cytoplasmic lysyl-tRNA synthetase was a prerequisite for its import. Here we are studying the influence of one-base replacements in the anticodon of tRNAs(Lys) on their aminoacylation, on binding to the precursor of the mitochondrial lysyl-tRNA synthetase (carrier protein directing the import), and on the efficiency of import into isolated yeast and human mitochondria. We show that the base U35 is the main identity element for the yeast cytoplasmic lysyl-tRNA synthetase. The single replacement that abolished import was C34G, while all the others only modulated the import efficiency. The need of aminoacylation for import and for interaction with the carrier protein was shown only for a subset of mutant versions, while the others could be recognized and internalized without aminoacylation or in misacylated forms.

Testing the efficiency of sensory coding with optimal stimulus ensembles

According to Barlow's seminal "efficient coding hypothesis," the coding strategy of sensory neurons should be matched to the statistics of stimuli that occur in an animal's natural habitat. Using an automatic search technique, we here test this hypothesis and identify stimulus ensembles that sensory neurons are optimized for. Focusing on grasshopper auditory receptor neurons, we find that their optimal stimulus ensembles differ from the natural environment, but largely overlap with a behaviorally important sub-ensemble of the natural sounds. This indicates that the receptors are optimized for peak rather than average performance. More generally, our results suggest that the coding strategies of sensory neurons are heavily influenced by differences in behavioral relevance among natural stimuli.

Import of nuclear encoded RNAs into yeast and human mitochondria: experimental approaches and possible biomedical applications

Mitochondria import from the cytoplasm the vast majority of proteins and some RNAs. Although there exists extended knowledge concerning the mechanisms of protein import, the import of RNA is poorly understood. It was almost exclusively studied on the model of tRNA import, in several protozoans, plants and yeast. Mammalian mitochondria, which do not import tRNAs naturally, are hypothesized to import other small RNA molecules from the cytoplasm. We studied tRNA import in the yeast system, both in vitro and in vivo, and applied similar approaches to study 5S rRNA import into human mitochondria. Despite the obvious divergence of RNA import systems suggested for different species, we find that in yeast and human cells this pathway involves similar mechanisms exploiting cytosolic proteins to target the RNA to the organelle and requiring the integrity of pre-protein import apparatus. The import pathway might be of interest from a biomedical point of view, to target into mitochondria RNAs that could suppress pathological mutations in mitochondrial DNA. Yeast represents a good model to elaborate such a gene therapy approach. We have described here the various approaches and protocols to study RNA import into mitochondria of yeast and human cells in vitro and in vivo.