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.

Beyond the Pericapsular Nerve Group (PENG) Block: A Narrative Review.

The pericapsular nerve group block shows promising results in providing pain relief with a potential motor-sparing effect in hip fracture patients. In this narrative review, we analyze the published articles, and we describe the structures achieved when performing the block. We conducted a literature search to identify the articles performing the pericapsular nerve group block, in the adult or paediatric population, from November 1, 2018, to May 15, 2021. Of the 68 selected articles, 38 were considered eligible, including 1 double-blinded randomized comparative trial, 4 observational studies, and 33 case series and case reports. The technique was described in both acute and chronic pain settings, mainly performed as single shot. All studies described effective analgesia. Quadriceps weakness was experienced in some patients. It has been described as easy to perform and has a low rate of complications. It lacks, however, adequately powered randomized controlled trials to assess its clinical value and efficacy.

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.

Ultrasonography-guided anterior approach for axillary nerve blockade: An anatomical study.

Combined ultrasound (US)-guided blockade of the suprascapular and axillary nerves (ANs) has been proposed as an alternative to interscalene blockade for pain control in shoulder joint pathology or postsurgical care. This technique could help avoid respiratory complications and/or almost total upper limb palsy. Nowadays, the AN blockade is mostly performed using an in-plane caudal-to-cephalic approach from the posterior surface of the shoulder, reaching the nerve immediately after it exits the neurovascular quadrangular space (part of the spatium axillare). Despite precluding most respiratory complications, this approach has not made postsurgical pain relief any better than an interscalene blockade, probably because articular branches of the AN are not blocked.Cephalic-to-caudal methylene blue injections were placed in the first segment of the AN of six Thiel-embalmed cadavers using an US-guided anterior approach in order to compare the distribution with that produced by a posterior approach to the contralateral AN in the same cadaver. Another 21 formalin-fixed cadavers were bilaterally dissected to identify the articular branches of the AN.We found a good spread of the dye on the AN and a constant relationship of this nerve with the subscapularis muscle. The dye reached the musculocutaneous nerve, which also contributes to shoulder joint innervation. We describe the anatomical landmarks for an ultrasonography-guided anterior AN blockade and hypothesize that this anterior approach will provide better pain control than the posterior approach owing to complete blocking of the joint nerve. Clin. Anat. 33:488-499, 2020. © 2019 Wiley Periodicals, Inc.

Chronotype-Dependent Changes in Sleep Habits Associated with Dim Light Melatonin Onset in the Antarctic Summer.

Dim light melatonin onset (DLMO) is the most reliable measure of human central circadian timing. Its modulation by light exposure and chronotype has been scarcely approached. We evaluated the impact of light changes on the interaction between melatonin, sleep, and chronotype in university students (n = 12) between the Antarctic summer (10 days) and the autumn equinox in Montevideo, Uruguay (10 days). Circadian preferences were tested by validated questionnaires. A Morningness-Eveningness Questionnaire average value (47 ± 8.01) was used to separate late and early participants. Daylight exposure (measured by actimetry) was significantly higher in Antarctica versus Montevideo in both sensitive time windows (the morning phase-advancing and the evening phase-delaying). Melatonin was measured in hourly saliva samples (18-24 h) collected in dim light conditions (<30 lx) during the last night of each study period. Early and late participants were exposed to similar amounts of light in both sites and time windows, but only early participants were significantly more exposed during the late evening in Antarctica. Late participants advanced their DLMO with no changes in sleep onset time in Antarctica, while early participants delayed their DLMO and sleep onset time. This different susceptibility to respond to light may be explained by a subtle difference in evening light exposure between chronotypes.

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.

Host influence in the genomic composition of flaviviruses: A multivariate approach.

Flaviviruses present substantial differences in their host range and transmissibility. We studied the evolution of base composition, dinucleotide biases, codon usage and amino acid frequencies in the genus Flavivirus within a phylogenetic framework by principal components analysis. There is a mutual interplay between the evolutionary history of flaviviruses and their respective vectors and/or hosts. Hosts associated to distinct phylogenetic groups may be driving flaviviruses at different pace and through various sequence landscapes, as can be seen for viruses associated with Aedes or Culex spp., although phylogenetic inertia cannot be ruled out. In some cases, viruses face even opposite forces. For instance, in tick-borne flaviviruses, while vertebrate hosts exert pressure to deplete their CpG, tick vectors drive them to exhibit GC-rich codons. Within a vertebrate environment, natural selection appears to be acting on the viral genome to overcome the immune system. On the other side, within an arthropod environment, mutational biases seem to be the dominant forces.

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.

Variabilidade espacial da produtividade de milho irrigado e sua correlação com variáveis explicativas de planta / Spatial variability of grain yield of irrigated corn and its correlation with explanatory plant variables

RESUMO: Em decorrência da instabilidade da produtividade das principais culturas associada ao déficit hídrico, tem se tornado cada vez mais frequente a necessidade do uso de tecnologias como a irrigação e a agricultura de precisão (AP). O presente trabalho objetivou avaliar a variabilidade espacial da produtividade de grãos de milho e sua correlação com variáveis explicativas de planta em área irrigada. O estudo foi conduzido nas safras agrícolas 2010/2011 e 2011/2012, em área de 35ha, manejada em sistema plantio direto e irrigação por pivô central. Os componentes de produtividade e a produtividade de grãos foram avaliados seguindo uma malha amostral de 100x100m. A produtividade de grãos e a maior parte dos componentes de produtividade apresentaram baixa dispersão dos dados, condicionando a normalidade dos dados. A produtividade de grãos, mesmo com a irrigação, apresentou elevada variabilidade espacial. Na análise de trilha, verificaram-se altos coeficientes de determinação dos componentes de produtividade com a produtividade de grãos.

ABSTRACT: Due to yield instability of main crops associated to drought, the use of technologies such irrigation and precision agriculture (PA) have been recently adopted in large scale. This study had the objective to assess the spatial variability of corn yield and its correlation with explanatory plant variables in an irrigated field. The study was carried out during the growing seasons 2010/2011 and 2011/2012, in an area of 35ha managed under no-till and center-pivot irrigation. Corn yield and yield components were evaluated following a sampling grid of 100x100m. Grain yield and most yield components showed low dispersion data, resulting in data normality. Even under irrigation, corn yield showed high spatial variability. In path analysis, it was found high determination coefficients of corn yield with yield components.