Application of the iPLUS non-coding sequence in improving biopharmaceuticals production.

The biotechnological landscape has witnessed significant growth in biological therapeutics particularly in the field of recombinant protein production. Here we investigate the function of 3'UTR cis-regulatory elements in increasing mRNA and protein levels in different biological therapeutics and model systems, spanning from monoclonal antibodies to mRNA vaccines. We explore the regulatory function of iPLUS - a universal sequence capable of consistently augmenting recombinant protein levels. By incorporating iPLUS in a vector to express a monoclonal antibody used in immunotherapy, in a mammalian cell line used by the industry (ExpiCHO), trastuzumab production increases by 2-fold. As yeast Pichia pastoris is widely used in the manufacture of industrial enzymes and pharmaceuticals, we then used iPLUS in tandem (3x) and iPLUSv2 (a variant of iPLUS) to provide proof-of-concept data that it increases the production of a reporter protein more than 100-fold. As iPLUS functions by also increasing mRNA levels, we hypothesize that these sequences could be used as an asset in the mRNA vaccine industry. In fact, by including iPLUSv2 downstream of Spike we were able to double its production. Moreover, the same effect was observed when we introduced iPLUSv2 downstream of MAGEC2, a tumor-specific antigen tested for cancer mRNA vaccines. Taken together, our study provides data (TLR4) showing that iPLUS may be used as a valuable asset in a variety of systems used by the biotech and biopharmaceutical industry. Our results underscore the critical role of non-coding sequences in controlling gene expression, offering a promising avenue to accelerate, enhance, and cost-effectively optimize biopharmaceutical production processes.

No Evidence that Selection on Synonymous Codon Usage Affects Patterns of Protein Evolution in Bacteria.

Bias in synonymous codon usage has been reported across all kingdoms of life. Evidence suggests that codon usage bias is often driven by selective pressures, typically for translational efficiency. These selective pressures have been shown to depress the rate at which synonymous sites evolve. We hypothesize that selection on synonymous codon use could also slow the rate of protein evolution if a non-synonymous mutation changes the codon from being preferred to unpreferred. We test this hypothesis by looking at patterns of protein evolution using polymorphism and substitution data in two bacterial species, Escherichia coli and Streptococcus pneumoniae. We find no evidence that non-synonymous mutations that change a codon from being unpreferred to preferred are more common than the opposite. Overall, selection on codon bias seems to have little influence over non-synonymous polymorphism or substitution patterns.

Erythema elevatum diutinum in a patient with rheumatoid arthritis.

Erythema elevatum diutinum (EED) is a rare cutaneous neutrophilic vasculitis with many associated diseases reported in the literature. We report a 65-year-old woman with painful and itchy lesions on her elbows, hands, knees, and foot for a year. Histopathologic examination confirmed the diagnosis of erythema elevatum diutinum and treatment with dapsone produced significant clinical improvement within few weeks. Erythema elevatum diutinum is a rare disease that should be considered in patients with violaceous nodular plaques located over the extensor regions of the limbs. Knowledge of this unusual pathology and its association helps to avoid misdiagnosis and late treatment.

Strong evidence for the adaptive walk model of gene evolution in Drosophila and Arabidopsis.

Understanding the dynamics of species adaptation to their environments has long been a central focus of the study of evolution. Theories of adaptation propose that populations evolve by "walking" in a fitness landscape. This "adaptive walk" is characterised by a pattern of diminishing returns, where populations further away from their fitness optimum take larger steps than those closer to their optimal conditions. Hence, we expect young genes to evolve faster and experience mutations with stronger fitness effects than older genes because they are further away from their fitness optimum. Testing this hypothesis, however, constitutes an arduous task. Young genes are small, encode proteins with a higher degree of intrinsic disorder, are expressed at lower levels, and are involved in species-specific adaptations. Since all these factors lead to increased protein evolutionary rates, they could be masking the effect of gene age. While controlling for these factors, we used population genomic data sets of Arabidopsis and Drosophila and estimated the rate of adaptive substitutions across genes from different phylostrata. We found that a gene's evolutionary age significantly impacts the molecular rate of adaptation. Moreover, we observed that substitutions in young genes tend to have larger physicochemical effects. Our study, therefore, provides strong evidence that molecular evolution follows an adaptive walk model across a large evolutionary timescale.

Changing Population Size in McDonald-Kreitman Style Analyses: Artifactual Correlations and Adaptive Evolution between Humans and Chimpanzees.

It is known that methods to estimate the rate of adaptive evolution, which are based on the McDonald-Kreitman test, can be biased by changes in effective population size. Here, we demonstrate theoretically that changes in population size can also generate an artifactual correlation between the rate of adaptive evolution and any factor that is correlated to the strength of selection acting against deleterious mutations. In this context, we have investigated whether several site-level factors influence the rate of adaptive evolution in the divergence of humans and chimpanzees, two species that have been inferred to have undergone population size contraction since they diverged. We find that the rate of adaptive evolution, relative to the rate of mutation, is higher for more exposed amino acids, lower for amino acid pairs that are more dissimilar in terms of their polarity, volume, and lower for amino acid pairs that are subject to stronger purifying selection, as measured by the ratio of the numbers of nonsynonymous to synonymous polymorphisms (pN/pS). All of these correlations are opposite to the artifactual correlations expected under contracting population size. We therefore conclude that these correlations are genuine.

Evolutionary history of two cryptic species of northern African jerboas.

BACKGROUND: Climatic variation and geologic change both play significant roles in shaping species distributions, thus affecting their evolutionary history. In Sahara-Sahel, climatic oscillations shifted the desert extent during the Pliocene-Pleistocene interval, triggering the diversification of several species. Here, we investigated how these biogeographical and ecological events have shaped patterns of genetic diversity and divergence in African Jerboas, desert specialist rodents. We focused on two sister and cryptic species, Jaculus jaculus and J. hirtipes, where we (1) evaluated their genetic differentiation, (2) reconstructed their evolutionary and demographic history; (3) tested the level of gene flow between them, and (4) assessed their ecological niche divergence. RESULTS: The analyses based on 231 individuals sampled throughout North Africa, 8 sequence fragments (one mitochondrial and seven single copy nuclear DNA, including two candidate genes for fur coloration: MC1R and Agouti), 6 microsatellite markers and ecological modelling revealed: (1) two distinct genetic lineages with overlapping distributions, in agreement with their classification as different species, J. jaculus and J. hirtipes, with (2) low levels of gene flow and strong species divergence, (3) high haplotypic diversity without evident geographic structure within species, and (4) a low level of large-scale ecological divergence between the two taxa, suggesting species micro-habitat specialization. CONCLUSIONS: Overall, our results suggest a speciation event that occurred during the Pliocene-Pleistocene transition. The contemporary distribution of genetic variation suggests ongoing population expansions. Despite the largely overlapping distributions at a macrogeographic scale, our genetic results suggest that the two species remain reproductively isolated, as only negligible levels of gene flow were observed. The overlapping ecological preferences at a macro-geographic scale and the ecological divergence at the micro-habitat scale suggest that local adaptation may have played a crucial role in the speciation process of these species.

A Population Genomics Lexicon.

Population genomics is a growing field stemming from soon a 100 years of developments in population genetics. Here, we summarize the main concepts and terminology underlying both theoretical and empirical statistical population genomics studies. We provide the reader with pointers toward the original literature as well as methodological and historical reviews.

The Impact of Protein Architecture on Adaptive Evolution.

Adaptive mutations play an important role in molecular evolution. However, the frequency and nature of these mutations at the intramolecular level are poorly understood. To address this, we analyzed the impact of protein architecture on the rate of adaptive substitutions, aiming to understand how protein biophysics influences fitness and adaptation. Using Drosophila melanogaster and Arabidopsis thaliana population genomics data, we fitted models of distribution of fitness effects and estimated the rate of adaptive amino-acid substitutions both at the protein and amino-acid residue level. We performed a comprehensive analysis covering genome, gene, and protein structure, by exploring a multitude of factors with a plausible impact on the rate of adaptive evolution, such as intron number, protein length, secondary structure, relative solvent accessibility, intrinsic protein disorder, chaperone affinity, gene expression, protein function, and protein-protein interactions. We found that the relative solvent accessibility is a major determinant of adaptive evolution, with most adaptive mutations occurring at the surface of proteins. Moreover, we observe that the rate of adaptive substitutions differs between protein functional classes, with genes encoding for protein biosynthesis and degradation signaling exhibiting the fastest rates of protein adaptation. Overall, our results suggest that adaptive evolution in proteins is mainly driven by intermolecular interactions, with host-pathogen coevolution likely playing a major role.

Psoriasiform keratosis - case report.

Psoriasiform Keratosis is a rare clinic entity. The etiopathogenesis remains unknown and the disease is characterized by a solitary, scaly or keratotic papule, or plaque mainly located on the extremities. Histopathological features closely resemble those of psoriasis. We report the case of a 70-year-old woman presenting a solitary and asymptomatic keratotic plaque, located on the back of the left leg, unresponsive to topical corticosteroids. We performed an excisional biopsy and histopathology was consistent with psoriasiform keratosis.

Psoriasiform Keratosis - Case report

Psoriasiform Keratosis is a rare clinic entity. The etiopathogenesis remains unknown and the disease is characterized by a solitary, scaly or keratotic papule, or plaque mainly located on the extremities. Histopathological features closely resemble those of psoriasis. We report the case of a 70-year-old woman presenting a solitary and asymptomatic keratotic plaque, located on the back of the left leg, unresponsive to topical corticosteroids. We performed an excisional biopsy and histopathology was consistent with psoriasiform keratosis.

[SwapINN: analytic study about prescription swaps at pharmacies]. / DCIsão: estudo analítico sobre a substituição de prescrições nas farmácias.

INTRODUCTION: In order to cut spending, compulsory INN prescription was suggested in Portugal during 2012. This instigated discussion among stakeholders in the matter. The authors studied prescription-dispensing dynamics in a real population. OBJECTIVES: To determine the percentage of swapped prescriptions; to assess factors associated with the swap; to analyse justifications for doing so; to quantify the cost difference for patients and the National Health Service. MATERIAL AND METHODS: Analytic study. Convenience sample consisting of all prescriptions from a Primary Health Care unit, from the 19th to the 23rd December 2011. Third day follow-up, using phone call interviews. Software: Excel and SPSS. TESTS: Chi-square and Mann-Whitney, SL = 0.05. RESULTS: Total of 255 prescriptions. Majority prescribed to women (62%), mean age of 52, four years of school education and for acute situations. A percentage of 31% of prescribed drugs were swapped. The swaps had no statistical relation with age, sex or literacy of the patient, nor with the prescriber or pharmacy. Swapping of prescribed drugs for chronic situations was lower (p < 0.001), as well as for original brand prescriptions (p < 0.001). Anti-infectious and anti-allergic were the most swapped groups (p = 0.009). Seventy-two percent of users were not aware of the swap. Regarding the swapped drugs, users paid on average 79% more than what was originally prescribed, and the National Health Service 5% more. DISCUSSION/CONCLUSION: The authors found changes in 31% of the prescriptions, with higher costs for both users and National Health Service. Selection, information and registration bias were considered. With compulsory INN prescriptions, we suggest regular analysis of prescription-dispensing dynamics, based on the available national data.

Introdução: A prescrição obrigatória por DCI foi imposta em 2012, para redução de custos do SNS e motivou discussão entre as partes envolvidas. Estudámos, numa população real, a dinâmica prescrição-dispensa de medicamentos.Objetivos: Determinar a percentagem de prescrições substituídas; avaliar os fatores associados à substituição; identificar as respetivas justificações; quantificar os diferenciais dos custos para utente e Serviço Nacional de Saúde.Material e Métodos: Estudo analítico. Amostra de conveniência constituída pelos medicamentos prescritos de uma unidade de saúde, de 19 a 23 de Dezembro de 2011. Três dias depois, os utentes foram entrevistados telefonicamente. Software: Excel® e SPSS®. Testes: Qui-quadrado e Mann-Whitney; n.s. = 0,05.Resultados: Total de 255 prescrições. A maioria foi efetuada a mulheres (62%), idade média 52 anos, 4 anos de escolaridade (33%) e para situações agudas (53%). Foram substituídas 31% das prescrições, sem relação com idade, sexo ou escolaridade, nem com o médico prescritor ou farmácia. Os medicamentos prescritos para situações crónicas foram menos substituídos (p < 0,001), assim como as prescrições de marca (p < 0,001). Os anti-infeciosos e anti-alérgicos foram os grupos com mais substituições (p = 0,009). Os utentes não se aperceberam da substituição em 72% dos casos. Nos casos de substituição, o utente pagou, em média, mais 79% que o prescrito e o Serviço Nacional de Saúde 5%.Discussão/Conclusão: Verificou-se substituição de 31% das prescrições, com mais custos para utente e Serviço Nacional de Saúde. Consideramos possível viés de seleção, informação e registo. Sendo agora obrigatória a prescrição por DCI, sugerimos a análise regular, a nível nacional, com base nas aplicações informáticas em uso, da prescrição e respetiva dispensa.

Pyoderma gangrenosum in a newborn--case report.

Pyoderma gangrenosum is a rare, inflammatory, chronic and recurrent disease of unknown etiology, characterized by noninfectious, necrotizing and painful cutaneous ulcers. Usually it affects adults aged between 25 and 54 years old and rarely children (less than 4%), in which it mainly affects the head, face, buttocks, genital and perianal region. The disease presents a quick response to systemic corticosteroids. We report a case of a newborn with hemorrhagic and necrotic ulcers, distributed in the abdomen, buttocks and genital region with rapid and effective response to oral prednisone.

Pyoderma gangrenosum in a newborn - case report / Pioderma gangrenoso em recem - nascido - relato de caso

Pyoderma gangrenosum is a rare, inflammatory, chronic and recurrent disease of unknown etiology, characterized by noninfectious, necrotizing and painful cutaneous ulcers. Usually it affects adults aged between 25 and 54 years old and rarely children (less than 4%), in which it mainly affects the head, face, buttocks, genital and perianal region. The disease presents a quick response to systemic corticosteroids. We report a case of a newborn with hemorrhagic and necrotic ulcers, distributed in the abdomen, buttocks and genital region with rapid and effective response to oral prednisone.

O Pioderma gangrenoso é uma doença inflamatória rara, crônica e recorrente, de etiopatogenia desconhecida, caracterizada por uma ulceração não-infecciosa, necrotizante e dolorosa da pele. Geralmente, afeta adultos na faixa de 25 a 54 anos e raramente crianças (menos de 4%), nestes acomete preferencialmente cabeça e face, nádegas, região perianal e genital. Apresenta rápida resposta à corticoterapia sistêmica. Relata-se um caso de recém-nascida com lesões ulceradas de pioderma gangrenoso de fundo hemorrágico e necrótico distribuídas em abdômen, região genital e glútea com resposta rápida e efetiva à prednisona oral.

Salmonella: the forgotten pathogen: health hazards of compliance with European bathing water legislation.

The increasing demands on recreational waters have made microbial contamination a matter of public and scientific concern. This study aimed to search for Salmonella spp. in waters classified according EU Directive 2006/7/EC, in order to assess associations between its prevalence and the concentration of the non-pathogenic new faecal indicators: Escherichia coli and intestinal enterococci. Although a statistically significant association was observed Salmonella was detected on beaches classified as "Good" (9.3%) and "Excellent" (14.4%) which compromises the idea that faecal indicators can be predictors of pathogens. Attending the high prevalence of Salmonella found (23.1%) it seemed important to improve the efficiency of the conventional analytical method (ISO 6340:1995), comparing its draft with SML-VIDAS Salmonella and two new chromogenic media: AES Salmonella Agar Plate (ASAP) and Simple Method Salmonella (SMS). ASAP showed the higher efficiency and can be recommended for a faster detection and presumptive identification of salmonellae in bathing waters.

A produçäo vocal do bebê: construçäo partilhada pela díade / Baby's vocal production: a dyadic shared construction

Investiga a produçäo vocal do bebê como produto que emerge, ao longo do tempo, da dinämica processual das negociaçöes entre os parceiros diádicos. Analisa os registros em video-cassete de uma díade mäe-bebê, durante os primeiros seis meses de vida em situaçäo natural. Estuda duas organizaçöes diádicas: face-a-face e mäe-objeto-bebê. Observa o uso proporcionalmente mais frequente de sons semelhantes a vogais nas organizaçöes face-a-face, näo ocorrendo naquelas mäe-objeto-bebê. Encontra uma relaçäo entre a utilizaçäo proporcionalmente superior do processo de especularidade e o aumento de sons semelhantes a vogais, apenas nas organizaçöes face-a-face. Propöe uma perspectiva teórica e metodológica que considera o desenvolvimento da comunicaçäo como um processo relacional/dialógico que constrói significados partilhados criando o novo. A emergência dos Ss e da própria comunicaçäo resulta desta dinâmica processual

A producao vocal do bebe: construcao partilhada pela diade

Este trabalho investigou a producao vocal do bebe como produto que emerge, ao longo do tempo, da dinamica processual das negociacoes entre os parceiros diadicos. Foram analisados os registros em video-cassete de uma diade mae-bebe, durante os primeiros seis meses de vida do bebe, em situacao natural. Duas organizacoes diadicas foram estudadas: face-a-face e mae-objeto-bebe. O uso proporcionalmente mais frequente de sons semelhantes a vogais foi observado nas organizacoes face-a-face, nao ocorrendo naquelas mae-objeto-bebe. Foi encontrada uma relacao entre a utilizacao proporcionalmente superior do processo de especularidade e o aumento de sons semelhantes a vogais, apenas nas organizacoes face-a-face. E proposta uma perspectiva teorica e metodologica que considera o desenvolvimento da comunicacao como um processo relacional/dialogico que constroi significados partilhados criando o novo. A emergencia dos sujeitos e da propria comunicacao resulta desta dinamica processual.