Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts.

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 96 samples within 4 hours. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day. We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. The presented strategy has high sample stability and should be considered as an option for SARS-CoV-2 testing in large populations.

HLA-B*51 and its main subtypes in Brazilian patients with Behçet's disease.

OBJECTIVES: This study aimed to evaluate the frequency of HLA-B*51 and its subtypes in Brazilian patients with Behçet's disease (BD) and healthy controls (HC) and to assess possible associations with disease manifestations. METHODS: A cross-sectional study with sequential BD patients and HC. HLAB*51 presence was determined by sequence-specific polymerase chain reaction (SSP-PCR) and HLA-B*51 subtypes by the Sanger sequencing method. RESULTS: Eighty-three BD patients and 258 HC were evaluated. HLA-B*51 was found in 30.1% of DB patients and in 15.5% of HC (p=0.003). The most prevalent subtypes in DB patients were HLA-B*51:01 (60.0%), HLA-B*51:08 (20.0%), HLA-B*51:22 (8.0%), HLAB* 51:29 (8.0%) and HLA-B*51:02 (4.0%), while HLA-B*51:01 (77.5%) and HLA-B*51:55 (7.5%) were the most prevalent in HC. HLA-B*51 was less frequently found in patients with neurologic involvement (8.0% vs. 29.3%; p=0.034) while HLAB*51:01 was more observed in patients with ocular involvement (93.3% vs. 60.3%; p=0.014). No BD patient with neurologic or vascular involvement presented HLA-B*51:01. HLAB*51:08 was more frequent in patients with vascular manifestations (60.0% vs. 15.4%; p=0.012). In multivariate analysis, HLA-B*51 was an independent risk factor for BD (OR=2.410; 95%CI: 1.332-4.361; p=0.004) and HLA-B*51:08 had an independent association with vascular manifestations of BD (OR = 14.843; 95%CI: 1.550 - 142.115; p=0.019). CONCLUSIONS: The prevalence of HLAB*51 is higher in Brazilian BD patients compared to HC, and it is a risk factor for BD. The HLA-B*51:08 subtype was independently associated with vascular manifestations of BD.

Aberrant patterns of X chromosome inactivation in a new line of human embryonic stem cells established in physiological oxygen concentrations.

One of the differences between murine and human embryonic stem cells (ESCs) is the epigenetic state of the X chromosomes in female lines. Murine ESCs (mESCs) present two transcriptionally active Xs that will undergo the dosage compensation process of XCI upon differentiation, whereas most human ESCs (hESCs) spontaneously inactivate one X while keeping their pluripotency. Whether this reflects differences in embryonic development of mice and humans, or distinct culture requirements for the two kinds of pluripotent cells is not known. Recently it has been shown that hESCs established in physiological oxygen levels are in a stable pre-XCI state equivalent to that of mESCs, suggesting that culture in low oxygen concentration is enough to preserve that epigenetic state of the X chromosomes. Here we describe the establishment of two new lines of hESCs under physiological oxygen level and the characterization of the XCI state in the 46,XX line BR-5. We show that a fraction of undifferentiated cells present XIST RNA accumulation and single H3K27me foci, characteristic of the inactive X. Moreover, analysis of allele specific gene expression suggests that pluripotent BR-5 cells present completely skewed XCI. Our data indicate that physiological levels of oxygen are not sufficient for the stabilization of the pre-XCI state in hESCs.

Establishment of new lines of human embryonic stem cells: evolution of the methodology.

Although since 1998 more than 1,200 different hESC lines have been established worldwide, there is still a recognized interest in the establishment of new lines of hESC, particularly from HLA types and ethnic groups underrepresented among the currently available lines. The methodology of hESC derivation has evolved significantly since the initial derivations using human LIF (hLIF) for maintenance of pluripotency. However, there are still a number of alternative strategies for the different steps involved in establishing a new line of hESC. We have analyzed the different strategies/parameters used between 1998 and 2010 for the derivation of the 375 hESC lines able to form teratomas in immunocompromised mice deposited in two international stem cell registries. Here we describe some trends in the methodology for establishing hESC lines, discussing the developments in the field. Nevertheless, we describe a much greater heterogeneity of strategies for hESCs derivation than what is used for murine ESC lines, indicating that optimum conditions have not been identified yet, and thus, hESC establishment is still an evolving field of research.

A survey of parameters involved in the establishment of new lines of human embryonic stem cells.

Since the derivation of the first human embryonic stem cell (hESC) lines by Thomson and coworkers in 1998, more than 1,200 different hESC lines have been established worldwide. Nevertheless, there is still a recognized interest in the establishment of new lines of hESC, particularly from HLA types and ethnic groups currently underrepresented among the available lines. The methodology of hESC derivation has evolved significantly since 1998, when human LIF (hLIF) was used for maintenance of pluripotency. However, there are a number of different strategies for the several steps involved in establishing a new line of hESC. Here we make a survey of the most relevant parameters used between 1998 and 2010 for the derivation of the 375 hESC lines deposited in two international stem cell registries, and able to form teratomas in immunocompromised mice. Although we identify some trends in the methodology for establishing hESC lines, our data reveal a much greater heterogeneity of strategies than what is used for derivation of murine ESC lines, indicating that optimum conditions have not been consolidated yet, and thus, hESC establishment is still an evolving field of research.

Pluripotent reprogramming of fibroblasts by lentiviral mediated insertion of SOX2, C-MYC, and TCL-1A.

Reprogramming of somatic cells to pluripotency promises to boost cellular therapy. Most instances of direct reprogramming have been achieved by forced expression of defined exogenous factors using multiple viral vectors. The most used 4 transcription factors, octamer-binding transcription factor 4 (OCT4), (sex determining region Y)-box 2 (SOX2), Kruppel-like factor 4 (KLF4), and v-myc myelocytomatosis viral oncogene homolog (C-MYC), can induce pluripotency in mouse and human fibroblasts. Here, we report that forced expression of a new combination of transcription factors (T-cell leukemia/lymphoma protein 1A [TCL-1A], C-MYC, and SOX2) is sufficient to promote the reprogramming of human fibroblasts into pluripotent cells. These 3-factor pluripotent cells are similar to human embryonic stem cells in morphology, in the ability to differentiate into cells of the 3 embryonic layers, and at the level of global gene expression. Induced pluripotent human cells generated by a combination of other factors will be of great help for the understanding of reprogramming pathways. This, in turn, will allow us to better control cell-fate and apply this knowledge to cell therapy.

Random X inactivation and extensive mosaicism in human placenta revealed by analysis of allele-specific gene expression along the X chromosome.

Imprinted inactivation of the paternal X chromosome in marsupials is the primordial mechanism of dosage compensation for X-linked genes between females and males in Therians. In Eutherian mammals, X chromosome inactivation (XCI) evolved into a random process in cells from the embryo proper, where either the maternal or paternal X can be inactivated. However, species like mouse and bovine maintained imprinted XCI exclusively in extraembryonic tissues. The existence of imprinted XCI in humans remains controversial, with studies based on the analyses of only one or two X-linked genes in different extraembryonic tissues. Here we readdress this issue in human term placenta by performing a robust analysis of allele-specific expression of 22 X-linked genes, including XIST, using 27 SNPs in transcribed regions. We show that XCI is random in human placenta, and that this organ is arranged in relatively large patches of cells with either maternal or paternal inactive X. In addition, this analysis indicated heterogeneous maintenance of gene silencing along the inactive X, which combined with the extensive mosaicism found in placenta, can explain the lack of agreement among previous studies. Our results illustrate the differences of XCI mechanism between humans and mice, and highlight the importance of addressing the issue of imprinted XCI in other species in order to understand the evolution of dosage compensation in placental mammals.

Syphilis at the crossroad of phylogenetics and paleopathology.

The origin of syphilis is still controversial. Different research avenues explore its fascinating history. Here we employed a new integrative approach, where paleopathology and molecular analyses are combined. As an exercise to test the validity of this approach we examined different hypotheses on the origin of syphilis and other human diseases caused by treponemes (treponematoses). Initially, we constructed a worldwide map containing all accessible reports on palaeopathological evidences of treponematoses before Columbus's return to Europe. Then, we selected the oldest ones to calibrate the time of the most recent common ancestor of Treponema pallidum subsp. pallidum, T. pallidum subsp. endemicum and T. pallidum subsp. pertenue in phylogenetic analyses with 21 genetic regions of different T. pallidum strains previously reported. Finally, we estimated the treponemes' evolutionary rate to test three scenarios: A) if treponematoses accompanied human evolution since Homo erectus; B) if venereal syphilis arose very recently from less virulent strains caught in the New World about 500 years ago, and C) if it emerged in the Americas between 16,500 and 5,000 years ago. Two of the resulting evolutionary rates were unlikely and do not explain the existent osseous evidence. Thus, treponematoses, as we know them today, did not emerge with H. erectus, nor did venereal syphilis appear only five centuries ago. However, considering 16,500 years before present (yBP) as the time of the first colonization of the Americas, and approximately 5,000 yBP as the oldest probable evidence of venereal syphilis in the world, we could not entirely reject hypothesis C. We confirm that syphilis seems to have emerged in this time span, since the resulting evolutionary rate is compatible with those observed in other bacteria. In contrast, if the claims of precolumbian venereal syphilis outside the Americas are taken into account, the place of origin remains unsolved. Finally, the endeavor of joining paleopathology and phylogenetics proved to be a fruitful and promising approach for the study of infectious diseases.

Cativeiro Barroco: a escravidão urbana em Minas Gerais, Mariana e Ouro Preto na primeira metade do século XVIII / Barroc prison: urban slavery in Minas Gerais, Mariana and Ouro Preto in the first half of the XVIII century

Esta dissertação tem como tema o estudo da vida dos escravos 'ao ganho', na sociedade da área mineradora de Minas Gerais no século XVIII. O estudo da documentação sobre a repressão e normatização das ações dos escravos no espaço urbano, serviu para que podéssemos apreender os aspectos cotidianos da vida dos escravos urbanos como: origem, trabalho, sobrevivência, lazer e as estratégias para a alforria. No decorrer do trabalho concluímos pela especificidade do espaço urbano em Mariana e Vila Rica que, anteciparam as formações urbanas do século XIX e a consolidação das características da escravidão urbana e as várias estratégias desenvolvidas pelos escravos para organizar a sua vida, cultura e possibilidades de manumissão (AU).