RNA Regulatory Networks 2.0.

The central role of RNA molecules in cell biology has been an expanding subject of study since the proposal of the "RNA world" hypothesis 60 years ago [...].

Recovery of ß-galactosidase produced by Kluyveromyces lactis by ion-exchange chromatography: Influence of pH and ionic strength parameters.

The use of ß-galactosidase in food products has been a major focus of the industry. Therefore, the development of efficient and inexpensive methodologies to purify it is essential. Thus, this study aimed to recover the enzyme ß-galactosidase (ß-gal) by ion-exchange chromatography in a fixed-bed column. Batch adsorption tests were performed using four types of adsorbents. The ß-gal adsorption capacity in batch mode using Streamline DEAE resin presented the best performance, with a retention capacity of 18.77 ± 0.14 U/g at pH 6.0. A 22 experimental design was applied to optimize the ß-gal recovery using an AKTA Start system, evaluating the ionic strength and the pH as process parameters. The results showed that ionic strength exerted a greater influence on fold purification (FP). The ß-gal fraction in elution using 0.1-0.4 M of NaCl showed a yield of 51.65 ± 0.17% and FP of 2.00 ± 0.43. Electrophoresis confirmed the ß-gal recovery, where an evident band with a molecular weight between 60 and 120 kDa was observed. These results point to the recovery of a stable ß-gal of K. lactis with potential industrial applications.

Structural Insights into Carboxylic Polyester-Degrading Enzymes and Their Functional Depolymerizing Neighbors.

Esters are organic compounds widely represented in cellular structures and metabolism, originated by the condensation of organic acids and alcohols. Esterification reactions are also used by chemical industries for the production of synthetic plastic polymers. Polyester plastics are an increasing source of environmental pollution due to their intrinsic stability and limited recycling efforts. Bioremediation of polyesters based on the use of specific microbial enzymes is an interesting alternative to the current methods for the valorization of used plastics. Microbial esterases are promising catalysts for the biodegradation of polyesters that can be engineered to improve their biochemical properties. In this work, we analyzed the structure-activity relationships in microbial esterases, with special focus on the recently described plastic-degrading enzymes isolated from marine microorganisms and their structural homologs. Our analysis, based on structure-alignment, molecular docking, coevolution of amino acids and surface electrostatics determined the specific characteristics of some polyester hydrolases that could be related with their efficiency in the degradation of aromatic polyesters, such as phthalates.

Kinetic study and characterization of surfactin production by Bacillus subtilis UFPEDA 438 using sugarcane molasses as carbon source.

The present study evaluated the surfactin production by Bacillus subtilis UFPEDA 438 using sugarcane molasses as a substrate. The effects of the cultivation conditions (temperature, agitation and aeration ratio) on the biosurfactant production and kinetic parameters were investigated. Characteristics of the biosurfactant were obtained after analyses of the emulsification index (EI) and critical micellar concentration (CMC) of the fermentation broth. The results showed that in relation to the product its formation kinetics is strongly affected by operational conditions. It was also observed that surfactin production can be partially dependent or fully independent on microbial growth. The maximum values of surfactin concentration (199.45 ± 0.13 mg/L) and productivity (8,187 mg/L.h) were obtained in the culture under cultivation time of 24 h, temperature of 36 °C, agitation of 100 rpm and aeration ratio of 0.4. Under optimal conditions, the fermentation broth achieved good emulsification capacity (EI >40%) and CMC value of 20.73 mg/L. The results revealed that Bacillus subtilis UFPEDA 438 is a good producer of biosurfactant and that sugarcane molasses is a viable substrate for the production of surfactin.

Use of plasmids for expression of proteins from the genus Leishmania in Escherichia coli: current state and perspectives.

Leishmaniosis is caused by the protozoa of the genus Leishmania with a wide spectrum of clinical and epidemiological manifestations which are characterized into four clinical groups: cutaneous, mucocutaneous, diffuse cutaneous, and visceral. American visceral leishmaniosis (AVL) or visceral leishmaniosis (VL) has been known as the most severe form of the disease. However, despite the growing number of people exposed to the infection risk and the great effort done by the scientific community worldwide to significantly increase the knowledge about these diseases, there is no vaccine capable of preventing VL in humans. In this short review, we present some of the plasmids used for the expression of recombinant protein by Escherichia coli strains used mainly for the second generation of vaccines for leishmaniosis. It can be emphasized that currently, these vectors and hosts play an important role in developing vaccine strategies against the disease. Indeed, use of the E. coli BL21 (DE) strain is remarkable mainly due to its characteristics for being a stable protein producer as well as the use of histidine tags for antigen purification. KEY POINTS: • Plasmid vectors and E. coli will continue being important for studies about leishmaniosis. • Protein purification exploiting histidine tags is a key technique.

Interspecies Communication in Holobionts by Non-Coding RNA Exchange.

Complex organisms are associations of different cells that coexist and collaborate creating a living consortium, the holobiont. The relationships between the holobiont members are essential for proper homeostasis of the organisms, and they are founded on the establishment of complex inter-connections between all the cells. Non-coding RNAs are regulatory molecules that can also act as communication signals between cells, being involved in either homeostasis or dysbiosis of the holobionts. Eukaryotic and prokaryotic cells can transmit signals via non-coding RNAs while using specific extracellular conveyors that travel to the target cell and can be translated into a regulatory response by dedicated molecular machinery. Within holobionts, non-coding RNA regulatory signaling is involved in symbiotic and pathogenic relationships among the cells. This review analyzes current knowledge regarding the role of non-coding RNAs in cell-to-cell communication, with a special focus on the signaling between cells in multi-organism consortia.

Potential of "coalho" cheese whey as lactose source for ß-galactosidase and ethanol co-production by Kluyveromyces spp. yeasts.

The present study evaluated the co-production of ß-galactosidase and ethanol by Kluyveromyces marxianus ATCC 36907 and Kluyveromyces lactis NRRL Y-8279 using as carbon source the lactose found on "coalho" cheese whey. Cheese whey was subjected to partial deproteinization, and physicochemical parameters were assessed. Cultivations were carried out in an shaker to evaluate two carbon/nitrogen (C:N) ratios. The best C:N ratio (1.5:1) was carried to 1.5-L bioreactor cultivation in order to increase co-production yields. The stability of ß-galactosidase was assessed against different temperatures and pH, and in the presence of metal ions. Concerning the co-production of ß-galactosidase and ethanol, K. lactis proved to be more efficient in both the C:N ratios, reaching 21.09 U·mL-1 of activity and 7.10 g·L-1 of ethanol in 16 h. This study describes the development of a viable and value-adding biotechnological process using a regional cheese by-product from Northeast Brazil for co-production of biomolecules of industrial interest.

Conspicuous Plumage Does Not Increase Predation Risk: A Continent-Wide Test Using Model Songbirds.

The forces shaping female plumage color have long been debated but remain unresolved. Females may benefit from conspicuous colors but are also expected to suffer costs. Predation is one potential cost, but few studies have explicitly investigated the relationship between predation risk and coloration. The fairy-wrens show pronounced variation in female coloration and reside in a wide variety of habitats across Australasia. Species with more conspicuous females are found in denser habitats, suggesting that conspicuousness in open habitat increases vulnerability to predators. To test this, we measured attack rates on 3-D-printed models mimicking conspicuously colored males and females and dull females in eight different fairy-wren habitats across Australia. Attack rates were higher in open habitats and at higher latitudes. Contrary to our predictions, dull female models were attacked at similar rates to the conspicuous models. Further, the probability of attack in open habitats increased more for both types of female models than for the conspicuous male model. Across models, the degree of contrast (chromatic and achromatic) to environmental backgrounds was unrelated to predation rate. These findings do not support the long-standing hypothesis that conspicuous plumage, in isolation, is costly due to increased attraction of predators. Our results indicate that conspicuousness interacts with other factors in driving the evolution of plumage coloration.

Simultaneous removal of dihydroxybenzenes and toxicity reduction by Penicillium chrysogenum var. halophenolicum under saline conditions.

The dihydroxybenzenes are widely found in wastewater and usually more than one of these aromatic compounds co-exist as pollutants of water resources. The current study investigated and compared the removal efficiency of hydroquinone, catechol and resorcinol in binary substrate systems under saline conditions by Penicillium chrysogenum var. halophenolicum, to clarify the potential of this fungal strain to degrade these aromatic compounds. Since P. chrysogenum is a known penicillin producer, biosynthetic penicillin genes were examined and antibiotic was quantified in mono and binary dihydroxybenzene systems to elucidate the carbon flux of dihydroxybenzenes metabolism in the P. chrysogenum var. halophenolicum to the secondary metabolism. In binary substrate systems, the three assayed dihydroxybenzene compounds were found to be co-metabolized by fungal strain. The fungal strain preferentially degraded hydroquinone and catechol. Resorcinol was degraded slower and supports higher antibiotic titers than either catechol or hydroquinone. Dihydroxybenzenes were faster removed in mixtures compared to mono substrate systems, except for the case of hydroquinone. In this context, the expression of penicillin biosynthetic gene cluster was not related to the removal of dihydroxybenzenes. Penicillin production was triggered simultaneously or after dihydroxybenzene degradation, but penicillin yields, under these conditions, did not compromise dihydroxybenzene biological treatment. To investigate the decrease in dihydroxybenzenes toxicity due to the fungal activity, viability tests with human colon cancer cells (HCT116) and DNA damage by alkaline comet assays were performed. For all the conditions assays, a decrease in saline medium toxicity was observed, indicating its potential as detoxification agent.

Noncoding Transcriptional Landscape in Human Aging.

Aging is a universal phenomenon in metazoans, characterized by a general decline of the organism physiology associated with an increased risk of mortality and morbidity. Aging of an organism correlates with a decline in function of its cells, as shown for muscle, immune, and neuronal cells. As the DNA content of most cells within an organism remains largely identical throughout the life span, age-associated transcriptional changes must be achieved by epigenetic mechanisms. However, how aging may impact on the epigenetic state of cells is only beginning to be understood. In light of a growing number of studies demonstrating that noncoding RNAs can provide molecular signals that regulate expression of protein-coding genes and define epigenetic states of cells, we hypothesize that noncoding RNAs could play a direct role in inducing age-associated profiles of gene expression. In this context, the role of long noncoding RNAs (lncRNAs) as regulators of gene expression might be important for the overall transcriptional landscape observed in aged human cells. The possible functions of lncRNAs and other noncoding RNAs, and their roles in the regulation of aging-related cellular pathways will be analyzed.

Prevalence and prognostic impact of anemia and iron deficiency in patients hospitalized in an internal medicine ward: The PRO-IRON study.

OBJECTIVES: To assess prevalence, predictive factors, and prognostic impact on in-hospital mortality of anemia, iron deficiency anemia (IDA), iron deficiency with or without anemia (ID), and iron deficiency without anemia (IDWA) in patients admitted to an internal medicine ward. METHODS: This 1-year prospective study collected data on demographics, medical history, and blood tests in 771 consecutive patients on admission. RESULTS: Most patients were ≥65 years old (80%) and had hypertension (63%), moderate chronic kidney disease (CKD) (43%), and heart failure (41%). Prevalence of anemia, IDA, ID, and IDWA was 67%, 41%, 58%, and 18%, respectively. Anemia was independently associated with age ≥65 years (OR 1.76, 95% CI 1.15-2.70), active cancer (OR 2.44, 95% CI 1.42-4.39), and moderate CKD (OR 1.65, 95% CI 1.12-2.43). ID was independently associated with female gender (OR 2.29, 95% CI 1.64-3.22), heart failure (OR 1.65, 95% CI 1.16-2.37), and moderate CKD (OR 2.95, 95% CI 2.04-4.30). Incidence of in-hospital mortality was 21% and independently associated with anemia (RR 1.82, 95% CI 1.21-2.74). CONCLUSIONS: Anemia and iron deficiency were highly prevalent in internal medicine patients. As anemia negatively impacts on in-hospital mortality, awareness should be raised for effective diagnosis and management of these comorbidities in hospitalized patients.

Unzippers, resolvers and sensors: a structural and functional biochemistry tale of RNA helicases.

The centrality of RNA within the biological world is an irrefutable fact that currently attracts increasing attention from the scientific community. The panoply of functional RNAs requires the existence of specific biological caretakers, RNA helicases, devoted to maintain the proper folding of those molecules, resolving unstable structures. However, evolution has taken advantage of the specific position and characteristics of RNA helicases to develop new functions for these proteins, which are at the interface of the basic processes for transference of information from DNA to proteins. RNA helicases are involved in many biologically relevant processes, not only as RNA chaperones, but also as signal transducers, scaffolds of molecular complexes, and regulatory elements. Structural biology studies during the last decade, founded in X-ray crystallography, have characterized in detail several RNA-helicases. This comprehensive review summarizes the structural knowledge accumulated in the last two decades within this family of proteins, with special emphasis on the structure-function relationships of the most widely-studied families of RNA helicases: the DEAD-box, RIG-I-like and viral NS3 classes.

A comprehensive SARS-CoV-2 and COVID-19 review, Part 2: host extracellular to systemic effects of SARS-CoV-2 infection.

COVID-19, the disease caused by SARS-CoV-2, has caused significant morbidity and mortality worldwide. The betacoronavirus continues to evolve with global health implications as we race to learn more to curb its transmission, evolution, and sequelae. The focus of this review, the second of a three-part series, is on the biological effects of the SARS-CoV-2 virus on post-acute disease in the context of tissue and organ adaptations and damage. We highlight the current knowledge and describe how virological, animal, and clinical studies have shed light on the mechanisms driving the varied clinical diagnoses and observations of COVID-19 patients. Moreover, we describe how investigations into SARS-CoV-2 effects have informed the understanding of viral pathogenesis and provide innovative pathways for future research on the mechanisms of viral diseases.

Transcriptomic Analysis of Acetaminophen Biodegradation by Penicillium chrysogenum var. halophenolicum and Insights into Energy and Stress Response Pathways.

(1) Background: Acetaminophen (APAP), an active component of many analgesic and antipyretic drugs, is one of the most concerning trace contaminants in the environment and is considered as an emergent pollutant of marine and aquatic ecosystems. Despite its biodegradability, APAP has become a recalcitrant compound due to the growth of the global population, the ease of availability, and the inefficient wastewater treatment applied. (2) Methods: In this study, we used a transcriptomic approach to obtain functional and metabolic insights about the metabolization of APAP by a phenol-degrading fungal strain, Penicillium chrysogenum var. halophenolicum. (3) Results: We determined that the transcriptomic profile exhibited by the fungal strain during APAP degradation was very dynamic, being characterized by an abundance of dysregulated transcripts which were proportional to the drug metabolization. Using a systems biology approach, we also inferred the protein functional interaction networks that could be related to APAP degradation. We proposed the involvement of intracellular and extracellular enzymes, such as amidases, cytochrome P450, laccases, and extradiol-dioxygenases, among others. (4) Conclusions: Our data suggested that the fungus could metabolize APAP via a complex metabolic pathway, generating nontoxic metabolites, which demonstrated its potential in the bioremediation of this drug.

Biogenesis and mechanism of action of small non-coding RNAs: insights from the point of view of structural biology.

Non-coding RNAs are dominant in the genomic output of the higher organisms being not simply occasional transcripts with idiosyncratic functions, but constituting an extensive regulatory network. Among all the species of non-coding RNAs, small non-coding RNAs (miRNAs, siRNAs and piRNAs) have been shown to be in the core of the regulatory machinery of all the genomic output in eukaryotic cells. Small non-coding RNAs are produced by several pathways containing specialized enzymes that process RNA transcripts. The mechanism of action of these molecules is also ensured by a group of effector proteins that are commonly engaged within high molecular weight protein-RNA complexes. In the last decade, the contribution of structural biology has been essential to the dissection of the molecular mechanisms involved in the biosynthesis and function of small non-coding RNAs.

Degradation of 2,4-dichlorophenoxyacetic acid by a halotolerant strain of Penicillium chrysogenum: antibiotic production.

The extensive use of pesticides in agriculture has prompted intensive research on chemical and biological methods in order to protect contamination of water and soil resources. In this paper the degradation of the pesticide 2,4-dichlorophenoxyacetic acid by a Penicillium chrysogenum strain previously isolated from a salt mine was studied in batch cultures. Co-degradation of 2,4-dichlorophenoxyacetic acid with additives such as sugar and intermediates of pesticide metabolism was also investigated. Penicillium chrysogenum in solid medium was able to grow at concentrations up to 1000 mg/L of 2,4-dichlorophenoxyacetic acid (2,4-D) with sucrose. Meanwhile, supplementation of the solid medium with glucose and lactose led to fungal growth at concentrations up to 500 mg/L of herbicide. Batch cultures of 2,4-D at 100 mg/L were developed under aerobic conditions with the addition of glucose, lactose and sucrose, showing sucrose as the best additional carbon source. The 2,4-D removal was quantified by liquid chromatography. The fungus was able to use 2,4-D as the sole carbon and energy source under 0%, 2% and 5.9% NaCl. The greatest 2,4-D degradation efficiency was found using alpha-ketoglutarate and ascorbic acid as co-substrates under 2% NaCl at pH 7. Penicillin production was evaluated in submerged cultures by bioassay, and higher amounts of beta-lactam antibiotic were produced when the herbicide was alone. Taking into account the ability of P. chrysogenum CLONA2 to degrade aromatic compounds, this strain could be an interesting tool for 2,4-D herbicide remediation in saline environments.

A Structural View of miRNA Biogenesis and Function.

Micro-RNAs (miRNAs) are a class of non-coding RNAs (ncRNAs) that act as post-transcriptional regulators of gene expression. Since their discovery in 1993, they have been the subject of deep study due to their involvement in many important biological processes. Compared with other ncRNAs, miRNAs are generated from devoted transcriptional units which are processed by a specific set of endonucleases. The contribution of structural biology methods for understanding miRNA biogenesis and function has been essential for the dissection of their roles in cell biology and human disease. In this review, we summarize the application of structural biology for the characterization of the molecular players involved in miRNA biogenesis (processors and effectors), starting from the X-ray crystallography methods to the more recent cryo-electron microscopy protocols.

The interplay between lncRNAs, RNA-binding proteins and viral genome during SARS-CoV-2 infection reveals strong connections with regulatory events involved in RNA metabolism and immune response.

Rationale: Viral infections are complex processes based on an intricate network of molecular interactions. The infectious agent hijacks components of the cellular machinery for its profit, circumventing the natural defense mechanisms triggered by the infected cell. The successful completion of the replicative viral cycle within a cell depends on the function of viral components versus the cellular defenses. Non-coding RNAs (ncRNAs) are important cellular modulators, either promoting or preventing the progression of viral infections. Among these ncRNAs, the long non-coding RNA (lncRNA) family is especially relevant due to their intrinsic functional properties and ubiquitous biological roles. Specific lncRNAs have been recently characterized as modulators of the cellular response during infection of human host cells by single stranded RNA viruses. However, the role of host lncRNAs in the infection by human RNA coronaviruses such as SARS-CoV-2 remains uncharacterized. Methods: In the present work, we have performed a transcriptomic study of a cohort of patients with different SARS-CoV-2 viral load and analyzed the involvement of lncRNAs in supporting regulatory networks based on their interaction with RNA-binding proteins (RBPs). Results: Our results revealed the existence of a SARS-CoV-2 infection-dependent pattern of transcriptional up-regulation in which specific lncRNAs are an integral component. To determine the role of these lncRNAs, we performed a functional correlation analysis complemented with the study of the validated interactions between lncRNAs and RBPs. This combination of in silico functional association studies and experimental evidence allowed us to identify a lncRNA signature composed of six elements - NRIR, BISPR, MIR155HG, FMR1-IT1, USP30-AS1, and U62317.2 - associated with the regulation of SARS-CoV-2 infection. Conclusions: We propose a competition mechanism between the viral RNA genome and the regulatory lncRNAs in the sequestering of specific RBPs that modulates the interferon response and the regulation of RNA surveillance by nonsense-mediated decay (NMD).

Resorcinol degradation by a Penicillium chrysogenum strain under osmotic stress: mono and binary substrate matrices with phenol.

A phenol-degrading Penicillium chrysogenum strain previously isolated from a salt mine was able to grow at 1,000 mg l(-1) of resorcinol on solid medium. The aerobic degradation of resorcinol by P. chrysogenum CLONA2 was studied in batch cultures in minimal mineral medium with 58.5 g l(-1) of sodium chloride using resorcinol as the sole carbon source. The fungal strain showed the ability to degrade up to 250 mg l(-1) of resorcinol. Resorcinol and phenol efficiency degradation by P. chrysogenum CLONA2 was compared. This strain removes phenol faster than resorcinol. When phenol and resorcinol were in binary substrate matrices, phenol enhanced resorcinol degradation, and organic load decreased with respect to the mono substrate matrices. The acute toxicity of phenol and resorcinol, individually and in combination, to Artemia franciscana larvae has been verified before and after the bioremediation process with P. chrysogenum CLONA2. The remediation process was effective in mono and binary substrate systems.

Atrial fibrillation and thromboembolic risk: what is the extent of adherence to guidelines in clinical practice?

BACKGROUND: Atrial fibrillation (AF) is the most common cardiac rhythm disorder in clinical practice, with a growing prevalence in recent decades. Through the use of thromboembolic risk scores it is possible to adjust thromboprophylaxis to individual risk. The aim of this study was to evaluate the conformity of antithrombotic therapy prescribed at hospital discharge with the guidelines in patients with AF and its influence on long-term morbidity and mortality. METHODS: We performed a retrospective analysis, based on medical records and phone interview, of consecutive patients admitted to an internal medicine department over a one-year period with a diagnosis of AF or atrial flutter--ICD-9-CM 427.31/32. We determined individual thromboembolic risk in accordance with the ACC/AHA/ESC risk categories, and assessed conformity of antithrombotic therapy with the guidelines. Independent predictors of long-term (378 +/- 241 days) mortality and mortality or readmission were identified by multivariate analysis. RESULTS: The study population consisted of 174 patients with a diagnosis of AF, 59.8% (104) female, mean age 77 +/- 10 years. Hypertension (65.7%) and heart failure (61.3%) were the most prevalent comorbidities. Most patients (82.7%) were stratified as high thromboembolic risk and the remainder as moderate risk. The antithrombotic therapy prescribed at hospital discharge was documented in 155 patients, 126 (81.3%) with high thromboembolic risk. Of the latter group of patients, oral anticoagulation (OAC) was prescribed in 65 (51.6%) and proposed but contraindicated in 24 (19.0%). In patients with moderate thromboembolic risk, therapeutic options were divided between OAC (69.0%), antiplatelet therapy (17.2%) and no thromboprophylaxis (13.8%). Overall there was discordance between the therapy instituted and the guidelines in 25.8% of patients. Age 85 years or over was the only independent predictor of death (HR 1.92; 95% CI 0.94-3.91), while OAC (HR 0.43; 95% CI 0.27-0.70) and male gender (HR 0.58; 95% CI 0.36-0.94) were independent protective factors against death or hospital readmission. CONCLUSIONS: In this study, patients admitted with AF were mainly elderly, women and with high thromboembolic risk. The prescription rate of OAC in patients at high risk was lower than recommended in the guidelines, which were not followed in a quarter of patients. The main therapeutic option in cases of moderate risk was OAC. OAC use was the only modifiable factor able to improve prognosis of patients with AF, and it is thus crucial to ensure adherence to the guidelines in daily clinical practice.