Amino acid usage and protein expression levels in the flatworm Schistosoma mansoni

Schistosoma mansoni is a parasitic flatworm that causes a human disease called schistosomiasis, or bilharzia. At the genomic level, S. mansoni is AT-rich, but has some compositional heterogeneity. Indeed, some regions of its genome are GC-rich, mainly in the regions located near the extreme ends of the chromosomes. Recently, we showed that, despite the strong bias towards A/T ending codons, highly expressed genes tend to use GC-rich codons. Here, we address the following question: are highly expressed sequences biased in their amino acid frequencies? Our analyses show that these sequences in S. mansoni, as in species ranging from bacteria to human, are strongly biased in nucleotide composition. Highly expressed genes tend to use GC-rich codons (in the first and second codon positions), which code the energetically cheapest amino acids. Therefore, we conclude that amino acid usage, at least in highly expressed genes, is strongly shaped by natural selection to avoid energetically expensive residues. Whether this is an adaptation to the parasitic way of life of S. mansoni, is unclear since the same pattern occurs in free-living species.

Main Factors Shaping Amino Acid Usage Across Evolution

The standard genetic code determines that in most species, including viruses, there are 20 amino acids that are coded by 61 codons, while the other three codons are stop triplets. Considering the whole proteome each species features its own amino acid frequencies, given the slow rate of change, closely related species display similar GC content and amino acids usage. In contrast, distantly related species display different amino acid frequencies. Furthermore, within certain multicellular species, as mammals, intragenomic differences in the usage of amino acids are evident. In this communication, we shall summarize some of the most prominent and well-established factors that determine the differences found in the amino acid usage, both across evolution and intragenomically.

One-year monitoring SARS-CoV-2 RNA surface contamination in hospitals reveals no correlation with organic material and negative pressure as a limiting factor for contamination

Understanding transmission routes of SARS-CoV-2 is crucial to establish effective interventions in healthcare institutions. Although the role of surface contamination in SARS-CoV-2 transmission has been controversial, fomites have been proposed as a contributing factor. Longitudinal studies about SARS-CoV-2 surface contamination in hospitals with different infrastructure (presence or absence of negative pressure systems) are needed to improve our understanding of their effectiveness on patient healthcare and to advance our knowledge about the viral spread. We performed a one-year longitudinal study to evaluate surface contamination with SARS-CoV-2 RNA in reference hospitals. These hospitals have to admit all COVID-19 patients from public health services that require hospitalization. Surfaces samples were molecular tested for SARS-CoV-2 RNA presence considering three factors: the dirtiness by measuring organic material, the circulation of a high transmissibility variant, and the presence or absence of negative pressure systems in hospitalized patients' rooms. Our results show that: (i) There is no correlation between the amount of organic material dirtiness and SARS-CoV-2 RNA detected on surfaces; (ii) SARS-CoV-2 high transmissible Gamma variant introduction significantly increased surface contamination; (iii) the hospital with negative pressure systems was associated with lower levels of SARS-CoV-2 surface contamination and, iv) most environmental samples recovered from contaminated surfaces were assigned as non-infectious. This study provides data gathered for one year about the surface contamination with SARS-CoV-2 RNA sampling hospital settings. Our results suggest that spatial dynamics of SARS-CoV-2 RNA contamination varies according with the type of SARS-CoV-2 genetic variant and the presence of negative pressure systems. In addition, we showed that there is no correlation between the amount of organic material dirtiness and the quantity of viral RNA detected in hospital settings. Our findings suggest that SARS CoV-2 RNA surface contamination monitoring might be useful for the understanding of SARS-CoV-2 dissemination with impact on hospital management and public health policies. This is of special relevance for the Latin-American region where ICU rooms with negative pressure are insufficient.

An overview of dinucleotide and codon usage in all viruses

Viruses are, by far, the most abundant biological entities on earth. They are found in all known ecological niches and are the causative agents of many important diseases in plants and animals. From an evolutionary point of view, since viruses do not share any orthologous genes, there is a general consensus that they are polyphyletic; that is, they do not have a common ancestor. This means that they appeared several times during the course of evolution. For their life cycle, they are always obligate parasites of a free cellular life form, which can be bacteria, archaea, or eukaryotes. More complexity is added to these entities by the fact that their genetic material can be DNA or RNA (double- or single-stranded) or retrotranscribed. Given these features, we wondered if some general rules can be inferred when studying two basic genomic signatures-dinucleotides and codon usage-analyzing all available complete and non-redundant viral sequences. In spite of the obviously biased sample of sequences available, some general features appear to emerge.

RFPDR: a random forest approach for plant disease resistance protein prediction

Background

Plant innate immunity relies on a broad repertoire of receptor proteins that can detect pathogens and trigger an effective defense response. Bioinformatic tools based on conserved domain and sequence similarity are within the most popular strategies for protein identification and characterization. However, the multi-domain nature, high sequence diversity and complex evolutionary history of disease resistance (DR) proteins make their prediction a real challenge. Here we present RFPDR, which pioneers the application of Random Forest (RF) for Plant DR protein prediction.

Methods

A recently published collection of experimentally validated DR proteins was used as a positive dataset, while 10x10 nested datasets, ranging from 400-4,000 non-DR proteins, were used as negative datasets. A total of 9,631 features were extracted from each protein sequence, and included in a full dimension (FD) RFPDR model. Sequence selection was performed, to generate a reduced-dimension (RD) RFPDR model. Model performances were evaluated using an 80/20 (training/testing) partition, with 10-cross fold validation, and compared to baseline, sequence-based and state-of-the-art strategies. To gain some insights into the underlying biology, the most discriminatory sequence-based features in the RF classifier were identified.

Results and Discussion

RD-RFPDR showed to be sensitive (86.4 ± 4.0%) and specific (96.9 ± 1.5%) for identifying DR proteins, while robust to data imbalance. Its high performance and robustness, added to the fact that RD-RFPDR provides valuable information related to DR proteins underlying properties, make RD-RFPDR an interesting approach for DR protein prediction, complementing the state-of-the-art strategies.

Phylogenetic analysis of SARS-CoV-2 viruses circulating in the South American region: genetic relations and vaccine strain match

The pandemic of coronavirus disease 2019 (COVID-19) is caused by a novel member of the family Coronaviridae, now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent studies revealed the emergence of virus variants with substitutions in the spike and/or nucleocapsid and RNA-dependent RNA polymerase proteins that are partly responsible for enhanced transmission and reduced or escaped anti-SARS-CoV-2 antibodies that may reduce the efficacy of antibodies and vaccines against the first identified SARS-CoV-2 strains. In order to gain insight into the emergence and evolution of SARS-CoV-2 variants circulating in the South American region, a comprehensive phylogenetic study of SARS-CoV-2 variants circulating in this region was performed. The results of these studies revealed sharp increase in virus effective population size from March to April of 2020. At least 62 different genotypes were found to circulate in this region. Variants of concern (VOCs) Alpha, Beta, Gamma and Delta co-circulate in the region, together with variants of interest (VOIs) Lambda, Mu and Zeta. Most of SARS-CoV-2 variants circulating in the South American region belongs to B.1 genotypes and have substitutions in the spike and/or nucleocapsid and polymerase proteins that confer high transmissibility and/or immune resistance. 148 amino acid positions of the spike protein and 70 positions of the nucleocapsid were found to have substitutions in different variants isolated in the region by comparison with reference strain Wuhan-Hu-1. Significant differences in codon usage among spike genes of SARS-CoV-2 strains circulating in South America was found, which can be linked to SARS-CoV-2 genotypes.

Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts

The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.

An Evolutionary Insight into Zika Virus Strains Isolated in the Latin American Region

Zika virus (ZIKV) is an emerging pathogen member of the Flaviviridae family. ZIKV has spread rapidly in the Latin American region, causing hundreds of thousands of cases of ZIKV disease, as well as microcephaly in congenital infections. Detailed studies on the pattern of evolution of ZIKV strains have been extremely important to our understanding of viral survival, fitness, and evasion of the host’s immune system. For these reasons, we performed a comprehensive phylogenetic analysis of ZIKV strains recently isolated in the Americas. The results of these studies revealed evidence of diversification of ZIKV strains circulating in the Latin American region into at least five different genetic clusters. This diversification was also reflected in the different trends in dinucleotide bias and codon usage variation. Amino acid substitutions were found in E and prM proteins of the ZIKV strains isolated in this region, revealing the presence of novel genetic variants circulating in Latin America.

Recycling of polyurethanes from laboratory to industry, a journey towards the sustainability

The recycling of any kind of plastic to convert it in valuable products is one of the main challenges of today's society. Besides, if the recycling process is itself green, then it would be a great achievement. This paper reviews the way covered from the first attempts of reusing the polyurethane (PU) scraps as a filler for cushions to the last chemical routes employing green recycling agents. Polyurethane is the 6th most used polymer all over the world with a production of 18 millions tons per year, which means a daily production of PU specialties greater than 1 million of cubic meters, equivalent to the volume of the Empire State Building. The thermostable nature of the majority of the polyurethanes specialties has made that the preferred solution for their recycling are the chemical recycling processes. Among them, glycolysis is the one that receives a greater attention from an industrial point of view, so this review puts the spotlight on it. However, the existing reviews in literature do not paid a special attention on glycolysis and only give a superficial description of the process. Nevertheless, in the present review, the scientific literature relative to glycolysis is completely reviewed, updated and ordered according the type of PU specialty recycled. Additionally, the other main chemical recycling processes are also revisited in a more extended and deeper way than in the previous approaches to this topic. Moreover, it is crucial to take into account that some of these technologies, which were described in the literature as promising technologies at laboratory scale are now commercial processes running at industrial scale. For that reason, it is essential to remark that the present review comprises not only a detailed state of art of the scientific literature on the subject, also includes a detailed revision of the past and running on pilot plants and industrial facilities, including several patents, which has never been covered in the current literature. Moreover, this review also describes the most recent studies employing crude glycerol (biodiesel subproduct) as an economic, sustainable and environmental friendly cleavage agent, which should lead the way to the industrial implantation of split-phase glycolysis in a near future, providing high quality recovered products, susceptible of replacing raw ones in the synthesis of new PU specialties. What is more, this review intends that any reader could know and understand the reactions involved in the polyurethane chemistry and recycling, the main polyurethanes types and the fundamentals of the recycling strategies in order to comprehend what are the advantages and drawbacks of each recycling process as starting point for looking for new advantageous alternatives from an environmental, technical and economic point of view. Broader context. This paper reviews the main advances in the polyurethane (PU) recycling field, from laboratory and academia processes to pilot plant and industrial scale ones, including the most relevant patents in the subject. Opposite to other common used plastics, PUs are not polymerization but condensation polymers, synthesized from polyols and isocyanates. The wide diversity of polyols and isocyanates allows the synthesis of numerous different compounds covering a huge range of applications. As a direct consequence of their commercial success, an increasing quantity of PU waste is being disposed by landfilling in the last decades. Such waste comprises not only post-consumer products but also scrap from slabstock manufacturing, which can reach the 10% of the total foam production. However, the massive enforcement of the environmental laws is pointing out a new route in the polymer waste removal sector based in the polymer recycling, and this fact has placed the research in waste treatment as one of the most prolific topics nowadays. In fact, polymer recycling processes have experienced a growing attention from the research and industrial worlds as a direct result of the enforcement of the environmental legislations. Hence, it is essential to develop new environmental sustainable recycling processes with the aim of conserving the natural resources, reducing the amount of waste disposed in landfills and enhancing the sustainability for forthcoming generation.

An Isochore-Like Structure in the Genome of the Flatworm Schistosoma mansoni

Eukaryotic genomes are compositionally heterogeneous, that is, composed by regions that differ in guanine-cytosine (GC) content (isochores). The most well documented case is that of vertebrates (mainly mammals) although it has been also noted among unicellular eukaryotes and invertebrates. In the human genome, regarded as a typical mammal, this heterogeneity is associated with several features. Specifically, genes located in GC-richest regions are the GC3-richest, display CpG islands and have shorter introns. Furthermore, these genes are more heavily expressed and tend to be located at the extremes of the chromosomes. Although the compositional heterogeneity seems to be widespread among eukaryotes, the associated properties noted in the human genome and other mammals have not been investigated in depth in other taxa Here we provide evidence that the genome of the parasitic flatworm Schistosoma mansoni is compositionally heterogeneous and exhibits an isochore-like structure, displaying some features associated, until now, only with the human and other vertebrate genomes, with the exception of gene concentration.

Transduction of an immortalized olfactory ensheathing glia cell line with the green fluorescent protein (GFP) gene: Evaluation of its neuroregenerative capacity as a proof of concept

Olfactory ensheathing glia (OEG) cells are known to foster axonal regeneration of central nervous system (CNS) neurons. Several lines of reversibly immortalized human OEG (ihOEG) have been previously established that enabled to develop models for their validation in vitro and in vivo. In this work, a constitutively GFP-expressing ihOEG cell line was obtained, and named Ts14-GFP. Ts14-GFP neuroregenerative ability was similar to that found for the parental line Ts14 and it can be assayed using in vivo transplantation experimental paradigms, after spinal cord or optic nerve damage. Additionally, we have engineered a low-regenerative ihOEG line, hTL2, using lentiviral transduction of the large T antigen from SV40 virus, denominated from now on Ts12. Ts12 can be used as a low regeneration control in these experiments.

Pharmacological inhibition of GSK-3 is not strictly correlated with a decrease in tyrosine phosphorylation of residues 216/279

Recent evidence suggests that intramolecular autophosphorylation is responsible for the tyrosine phosphorylation (pY) of residues 279 or 216 of glycogen synthase kinase-3 (GSK-3alpha or beta), an event that appears to play an important role in regulating this kinase. This provocative hypothesis was based on the capacity of certain nonselective GSK-3 inhibitors to alter both the activity of GSK-3 and its pY. Inhibitors of GSK-3 are not always capable of preventing this tyrosine phosphorylation, which may require an extended period of time. For example, although lithium chloride inhibits GSK-3 activity, this inhibition does not alter its pY content. Furthermore, even when GSK-3 activity is impaired, GSK-3 pY can still be modified by physiological or pharmacological agents. Taken together, these data indicate that GSK-3 kinase activity is not necessarily correlated with the extent of GSK-3 pY. We hypothesized that some as-yet-unidentified tyrosine kinases and phosphatases may also regulate this kinase.