Integration of CTCF loops, methylome, and transcriptome in differentiating LUHMES as a model for imprinting dynamics of the 15q11-q13 locus in human neurons.

Human cell line models, including the neuronal precursor line LUHMES, are important for investigating developmental transcriptional dynamics within imprinted regions, particularly the 15q11-q13 Angelman (AS) and Prader-Willi (PWS) syndrome locus. AS results from loss of maternal UBE3A in neurons, where the paternal allele is silenced by a convergent antisense transcript UBE3A-ATS, a lncRNA that terminates at PWAR1 in non-neurons. qRT-PCR analysis confirmed the exclusive and progressive increase in UBE3A-ATS in differentiating LUHMES neurons, validating their use for studying UBE3A silencing. Genome-wide transcriptome analyses revealed changes to 11 834 genes during neuronal differentiation, including the upregulation of most genes within the 15q11-q13 locus. To identify dynamic changes in chromatin loops linked to transcriptional activity, we performed a HiChIP validated by 4C, which identified two neuron-specific CTCF loops between MAGEL2-SNRPN and PWAR1-UBE3A. To determine if allele-specific differentially methylated regions (DMR) may be associated with CTCF loop anchors, whole genome long-read nanopore sequencing was performed. We identified a paternally hypomethylated DMR near the SNRPN upstream loop anchor exclusive to neurons and a paternally hypermethylated DMR near the PWAR1 CTCF anchor exclusive to undifferentiated cells, consistent with increases in neuronal transcription. Additionally, DMRs near CTCF loop anchors were observed in both cell types, indicative of allele-specific differences in chromatin loops regulating imprinted transcription. These results provide an integrated view of the 15q11-q13 epigenetic landscape during LUHMES neuronal differentiation, underscoring the complex interplay of transcription, chromatin looping, and DNA methylation. They also provide insights for future therapeutic approaches for AS and PWS.

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.

Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first telomere-to-telomere human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Although derived from highly accurate sequences, evaluation revealed evidence of small errors and structural misassemblies in the initial draft assembly. To correct these errors, we designed a new repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly quality value from 70.2 to 73.9 measured from PacBio high-fidelity and Illumina k-mers. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both high-fidelity and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies.

Telomere-to-telomere assembly of a complete human X chromosome.

After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end to end, and hundreds of unresolved gaps persist1,2. Here we present a human genome assembly that surpasses the continuity of GRCh382, along with a gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome3, we reconstructed the centromeric satellite DNA array (approximately 3.1 Mb) and closed the 29 remaining gaps in the current reference, including new sequences from the human pseudoautosomal regions and from cancer-testis ampliconic gene families (CT-X and GAGE). These sequences will be integrated into future human reference genome releases. In addition, the complete chromosome X, combined with the ultra-long nanopore data, allowed us to map methylation patterns across complex tandem repeats and satellite arrays. Our results demonstrate that finishing the entire human genome is now within reach, and the data presented here will facilitate ongoing efforts to complete the other human chromosomes.

La Resolución 1325: Mujeres, Paz y Seguridad en las Operaciones de Mantenimiento de la Paz / The Resolution 1325: Women, Peace, and Security in the Peacekeeping Operations / Resolução 1325: mulheres, paz e segurança nas Operações de Manutenção da Paz

Resumen Este artículo analiza la incorporación de la Resolución 1325 del Consejo de Seguridad de Naciones Unidas y sus Resoluciones Complementarias -las que conforman la Agenda Mujeres, Paz y Seguridad- en las Resoluciones que crearon las Operaciones de Mantenimiento de la Paz desde el año 2000 en adelante, que justamente son creadas por el mismo Organismo. Teóricamente, se proponen tres estadios de análisis: la mujer como sujeto de protección, la mujer como sujeto de pacificación y la promoción de la perspectiva de género, basándose en el contenido de la Agenda Mujeres, Paz y Seguridad. Tales estadios se aplican en las Resoluciones seleccionadas por medio de un análisis de texto. Las conclusiones evidencian falencias en la incorporación de la Resolución 1325 y sus Resoluciones Complementarias, instrumentos promovidos desde el propio Consejo de Seguridad de Naciones Unidas, junto con mostrar la existencia de una variabilidad en la forma como se incorporaron estos estadios de análisis en la selección de casos.

Abstract This article analyzes the incorporation of Resolution 1325 of the United Nations Security Council and it's Complementary Resolutions -that compose the Women, Peace, and Security Agenda- in the Resolutions that have created the Peacekeeping Operations from the year 2000 onwards, which are just created by the same Organization. Theoretically three concepts of analysis are proposed: the woman as subject of protection, the woman as subject of pacification, and the promotion of the gender perspective, based on the content of the Women, Peace, and Security Agenda. Such concepts are applied in the Resolutions selected by means of a text analysis. The conclusions show weaknesses in the incorporation of Resolution 1325 and it's Complementary Resolutions, instruments promoted by the United Nations Security Council itself, together with the existence of variability in the way in which these stages of analysis were incorporated into the selection of cases.

Resumo Este artigo analisa a incorporação da Resolução 1325 do Conselho de Segurança das Nações Unidas e suas Resoluções Complementares - as que compõem a Agenda de Mulheres, Paz e Segurança- nas Resoluções que criaram as Operações da Manutenção da Paz a partir do ano 2000, que são criados apenas pela mesma agência. Teoricamente, três etapas de análise são propostas: a mulher como sujeito de proteção, a mulher como sujeito de pacificação e a promoção da perspectiva de gênero, com base no conteúdo da Agenda da Mulher de Paz e Segurança. Tais estágios são aplicados nas Resoluções selecionadas por meio de uma análise de texto. As conclusões mostram fragilidade na incorporação da Resolução 1325 e suas Resoluções Complementares, nos instrumentos promovidos pelo próprio Conselho de Segurança das Nações Unidas, além de mostrar a existência de uma variabilidade na forma como essas etapas de analise foram Incorporadas Na Seleção De Casos.

Global effect of the lack of inorganic polyphosphate in the extremophilic archaeon Sulfolobus solfataricus: A proteomic approach.

Inorganic polyphosphates (polyP) are present in all living cells and several important functions have been described for them. They are involved in the response to stress conditions, such as nutrient depletion, oxidative stress and toxic metals amongst others. A recombinant strain of Sulfolobus solfataricus unable to accumulate polyP was designed by the overexpression of its endogenous ppx gene. The overall impact of the lack of polyP on this S. solfataricus polyP (-) strain was analyzed by using quantitative proteomics (isotope-coded protein label, ICPL). Stress-related proteins, such as peroxiredoxins and heat shock proteins, proteins involved in metabolism and several others were produced at higher levels in the ppx expression strain. The polyP deficient strain showed an increased copper sensitivity and an earlier transcriptional up-regulation of copA gene coding for the P-type copper-exporting ATPase. This implies a complementary function of both copper resistance systems. These results strongly suggests that the lack of polyP makes this hyperthermophilic archaeon more sensitive to toxic conditions, such as an exposure to metals or other harmful stimuli, emphasizing the importance of this inorganic phosphate polymers in the adaptations to live in the environmental conditions in which thermoacidophilic archaea thrive. SIGNIFICANCE: Inorganic polyphosphate (polyP) are ubiquitous molecules with many functions in living organisms. Few studies related to these polymers have been made in archaea. The construction of a polyP deficient recombinant strain of Sulfolobus solfataricus allowed the study of the global changes in the proteome of this thermoacidophilic archaeon in the absence of polyP compared with the wild type strain. The results obtained using quantitative proteomics suggest an important participation of polyP in the oxidative stress response of the cells and as having a possible metabolic role in the cell, as previously described in bacteria. The polyP deficient strain also showed an increased copper sensitivity and an earlier transcriptional up-regulation of copA, implying a complementary role of both copper resistance systems.

Acroqueratoelastoidosis de costa: presentación de un caso con lesiones en pabellón auricular / Coastal acrokeratoelastoidosis: presentation of a case with lesions in both auricular pavilions

La acroqueratoelastoidosis de Costa es una genodermatosis rara, caracterizada por la presencia de múltiples pápulas queratósicas, pequeñas y firmes, en los márgenes laterales de palmas y plantas. Es-tas lesiones estacionarias y asintomáticas aparecen generalmente en la pubertad. Se desconoce su prevalencia. Es de herencia autosómica dominante con expresividad variable. La histología combina hiperqueratosis y acantosis, sin embargo, el hallazgo más importante es la elastorrexis. No se aconseja tratamiento en la mayoría de los pacienes. Se reporta el caso de una paciente de 61 años, sin antecedentes familiares de esta condición, que consulta por aparición en la adolescencia de lesiones hiperqueratósicas asintomáticas en márgenes laterales de ambas manos y lesiones similares en ambos pabellones auriculares.

Acrokeratoelastoidosis is a rare genodermatosis, characterized by the presence of multiple kerato-tic papules, small and firm, on the lateral margins of palms and soles. These stationary and asymptomatic lesions usually appear at puberty. Its pre-valence is unknown. It is of autosomal dominant inheritance with variable expressivity. Histology combines hyperkeratosis and acanthosis, howe-ver, the most important finding is elastorhexis. Treatment is not advised in most patients. We report the case of a 61-year-old female patient, with no family history of this condition, who consulted for appearance in adolescence of as-ymptomatic hyperkeratotic lesions in the lateral margins of both hands and similar lesions in both auricular pavilions.

Microenvironmental influence on microtumour infiltration patterns: 3D-mathematical modelling supported by in vitro studies.

Mathematical modelling approaches have become increasingly abundant in cancer research. Tumour infiltration extent and its spatial organization depend both on the tumour type and stage and on the bio-physicochemical characteristics of the microenvironment. This sets a complex scenario that often requires a multidisciplinary and individually adjusted approach. The ultimate goal of this work is to present an experimental/numerical combined method for the development of a three-dimensional mathematical model with the ability to reproduce the growth and infiltration patterns of a given avascular microtumour in response to different microenvironmental conditions. The model is based on a diffusion-convection reaction equation that considers logistic proliferation, volumetric growth, a rim of proliferative cells at the tumour surface, and invasion with diffusive and convective components. The parameter values of the model were fitted to experimental results while radial velocity and diffusion coefficients were made spatially variable in a case-specific way through the introduction of a shape function and a diffusion-limited-aggregation (DLA)-derived fractal matrix, respectively, according to the infiltration pattern observed. The in vitro model consists of multicellular tumour spheroids (MTSs) of an epithelial mammary tumour cell line (LM3) immersed in a collagen I gel matrix with a standard culture medium ("naive" matrix) or a conditioned medium from adipocytes or preadipocytes ("conditioned" matrix). It was experimentally determined that both adipocyte and preadipocyte conditioned media had the ability to change the MTS infiltration pattern from collective and laminar to an individual and atomized one. Numerical simulations were able to adequately reproduce qualitatively and quantitatively both kinds of infiltration patterns, which were determined by area quantification, analysis of fractal dimensions and lacunarity, and Bland-Altman analysis. These results suggest that the combined approach presented here could be established as a new framework with interesting potential applications at both the basic and clinical levels in the oncology area.

Ántrax cutáneo, último brote diagnosticado en Chile / Cutaneous anthrax, the last outbreak diagnosed in Chile

Resumen El ántrax, es una zoonosis causada por una bacteria generadora de esporas, llamada Bacillus anthracis. En forma natural tiene una distribución global, con una predilección en zonas agrícolas con pocas normativas de sanidad pública veterinaria. El contagio humano ocurre por el consumo de carnes de animales enfermos, por contacto a través de una puerta de entrada en la piel o por la inhalación de esporas de productos derivados del animal afectado (lana, cuero, huesos). La infección en los seres humanos compromete con mayor frecuencia la piel, seguido por el tracto gastrointestinal y los pulmones. El control de la enfermedad se basa en la prevención, de allí la importancia de la vigilancia en la detección de casos y brotes. Presentamos el último brote de ántrax cutáneo diagnosticado en Chile con descripción de dos primeros casos clínicos del brote.

Anthrax is a zoonosis caused by a spore-forming bacterium, called Bacillus anthracis. Naturally it is of global distribution, with a predilection in agricultural zones with few norms of public veterinary health. Human contagion occurs through the consumption of diseased animal's meat or through a doorway into the skin or through the spores inhalation of products derived from the affected animal (wool, leather, bones). The most frequent infection in humans occurs in the skin, followed by the gastrointestinal tract and lungs. We present the last outbreak of cutaneous anthrax diagnosed in Chile with a description of the first two clinical cases of the outbreak. Control disease is based on prevention, hence the importance of surveillance in detecting cases and outbreaks.

N-acetylcysteine inhibits kinase phosphorylation during 3T3-L1 adipocyte differentiation.

OBJECTIVES: Reports investigating the effects of antioxidants on obesity have provided contradictory results. We have previously demonstrated that treatment with the antioxidant N-acetylcysteine (NAC) inhibits cellular triglyceride (Tg) accumulation as well as total cellular monoamine oxidase A (MAOA) expression in 3T3-L1 mature adipocytes (Calzadilla et al., Redox Rep. 2013;210-218). Here we analyzed the role of NAC on adipogenic differentiation pathway. METHODS: Assays were conducted using 3T3-L1 preadipocytes (undifferentiated cells: CC), which are capable of differentiating into mature adipocytes (differentiated cells: DC). We studied the effects of different doses of NAC (0.01 or 1 mM) on DC, to evaluate cellular expression of phospho-JNK½ (pJNK½), phospho-ERK½ (pERK½) and, mitochondrial expression of citrate synthase, fumarate hydratase and MAOA. RESULTS: Following the differentiation of preadipocytes, an increase in the expression levels of pJNK½ and pERK½ was observed, together with mitotic clonal expansion (MCE). We found that both doses of NAC decreased the expression of pJNK½ and pERK½. Consistent with these results, NAC significantly inhibited MCE and modified the expression of different mitochondrial proteins. DISCUSSION: Our results suggested that NAC could inhibit Tg and mitochondrial protein expression by preventing both MCE and kinase phosphorylation.