Publications by authors named "Jochen Hecht"

Hi-C and capture Hi-C (CHi-C) both leverage paired-end sequencing of chimeric fragments to gauge the strength of interactions based on the total number of paired-end reads mapped to a common pair of restriction fragments. Mapped paired-end reads can have four relative orientations, depending on the genomic positions and strands of the two reads. We assigned one paired-end read orientation to each of the four possible re-ligations that can occur between two given restriction fragments.

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Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome (chrY). Native DNA was sequenced on a MinION Oxford Nanopore Technologies sequencing device to generate genome assemblies for seven major chrY human haplogroups. We analyzed and compared the chrY enrichment of sequencing data obtained using two different selective sequencing approaches: adaptive sampling and flow cytometry chromosome sorting.

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The endoparasitic crustacean Sacculina carcini (Cirripedia: Rhizocephala) has a much simpler morphology than conventional filter-feeding barnacles, reflecting its parasitic lifestyle. To investigate the molecular basis of its refined developmental program, we produced a draft genome sequence for comparison with the genomes of nonparasitic barnacles and characterized the transcriptomes of internal and external tissues. The comparison of clusters of orthologous genes revealed the depletion of multiple gene families but also several unanticipated expansions compared to non-parasitic crustaceans.

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  • Post-transplant lymphoproliferative disorder is a serious condition that arises in transplant patients due to weak T cell responses against the Epstein-Barr virus (EBV), often exacerbated by immunosuppressive medication.
  • The study aimed to analyze T cells and lymphoblastoid cell lines from kidney transplant recipients to better understand their responses to various immunosuppressants, revealing differing impacts on T cell function and proliferation.
  • Findings suggest that adjusting immunosuppression—particularly using mTOR inhibitors and reducing certain drugs like calcineurin inhibitors—could enhance antiviral immunity while still preventing organ rejection in patients at risk for EBV-related complications.
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  • This study provides the first comprehensive catalog of chimpanzee genetic diversity using non-invasive samples collected from 48 sites in Africa, focusing on chromosome 21.
  • The research reveals clear genetic differences among the four recognized chimpanzee subspecies and indicates unexpected local genetic exchanges, while also mapping patterns of population isolation, migration, and connectivity.
  • Unlike humans, chimpanzees lack a history of long-distance migrations, which may affect their cultural transmission, and the study introduces a precise geolocation method for identifying the origins of confiscated chimpanzees.
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  • Scientists wanted to find out what causes a serious disease that affects many body systems and causes fat loss.
  • They studied 5 people with this disease using special genetic testing and other advanced techniques to learn more about how their cells work.
  • They discovered that all 5 people had a specific genetic change, which led to different levels of health and symptoms, and they found a new type of illness that helps explain these differences.
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The relevance of the human oral microbiome to our understanding of human health has grown in recent years as microbiome studies continue to develop. Given the links of the oral cavity with the digestive, respiratory and circulatory systems, the composition of the oral microbiome is relevant beyond just oral health, impacting systemic processes across the body. However, we still have a very limited understanding about intrinsic and extrinsic factors that shape the composition of the healthy oral microbiome.

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We aimed to assess the duration of nasopharyngeal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA persistence in adults self-confined at home after acute infection; and to identify the associations of SARS-CoV-2 persistence with respiratory virus co-detection and infection transmission. A cross-sectional intra-household study was conducted in metropolitan Barcelona (Spain) during the time period of April to June 2020. Every adult who was the first family member reported as SARS-CoV-2-positive by reverse transcription polymerase chain reaction (RT-PCR) as well as their household child contacts had nasopharyngeal swabs tested by a targeted SARS-CoV-2 RT-PCR and a multiplex viral respiratory panel after a 15 day minimum time lag.

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In mouse development, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes; however, the molecular mechanisms of this specificity remain unclear. Here, we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.

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: Cystic fibrosis (CF) is an autosomal genetic disease, associated with the production of excessively thick mucosa and with life-threatening chronic lung infections. The microbiota of the oral cavity can act as a reservoir or as a barrier for infectious microorganisms that can colonize the lungs. However, the specific composition of the oral microbiome in CF is poorly understood.

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We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms.

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  • The oral cavity contains a diverse microbiome, and research has shown that individuals with Down syndrome (DS) display unique oral health characteristics, including a lower rate of cavities but a higher prevalence of gum diseases.
  • A study using a Citizen-Science approach involved analyzing the oral microbiomes of 27 people with DS and matched controls to understand these differences better.
  • The findings indicated that individuals with DS have a lower salivary pH and less diverse oral microbiomes, suggesting potential links to oral health issues, but further research is needed to confirm these relationships.
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Chemotherapy has direct toxic effects on cancer cells; however, long-term cancer control and complete remission are likely to involve CD8 T cell immune responses. To study the role of CD8 T cell infiltration in the success of chemotherapy, we examined patients with muscle invasive bladder cancer (MIBC) who were categorized on the basis of the response to neoadjuvant chemotherapy (NAC). We identified the intratumoral CXCR3 chemokine system (ligands and receptor splice variants) as a critical component for tumor eradication upon NAC in MIBC.

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Background: At the COVID-19 spring 2020 pandemic peak in Spain, prevalence of SARS-CoV-2 infection in a cohort of 578 randomly selected health care workers (HCWs) from Hospital Clínic de Barcelona was 11.2%.

Methods: A follow-up survey 1 month later (April-May 2020) measured infection by rRT-PCR and IgM, IgA, and IgG to the receptor-binding domain of the spike protein by Luminex.

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  • * Out of 578 participants, 9.3% tested positive for antibodies, with a cumulative infection rate of 11.2%, indicating a significant portion had undiagnosed cases.
  • * The findings suggest a relatively low level of seroprevalence among HCW during the epidemic peak, highlighting the need for regular COVID-19 testing in healthcare settings.
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Psoriasis is a very common chronic inflammatory skin disease characterized by epidermal thickening and scaling resulting from keratinocyte hyperproliferation and impaired differentiation. Pathomechanistic studies in psoriasis are often limited by using whole skin tissue biopsies, neglecting their stratification and cellular diversity. This study aimed at characterizing epidermal alterations in psoriasis at the level of keratinocyte populations.

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Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions. The analysis is based on counts of chimeric read pairs that map to interacting regions of the genome. However, the processing and quality control presents a number of unique challenges.

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Reactivation of the BK polyomavirus is known to lead to severe complications in kidney transplant patients. The current treatment strategy relies on decreasing the immunosuppression to allow the immune system to clear the virus. Recently, we demonstrated a clear association between the resolution of BKV reactivation and reconstitution of BKV-specific CD4 T-cells.

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Influenza vaccination is a common approach to prevent seasonal and pandemic influenza. Pre-existing antibodies against close viral strains might impair antibody formation against previously unseen strains-a process called original antigenic sin. The role of this pre-existing cellular immunity in this process is, despite some hints from animal models, not clear.

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Chromosomal rearrangements and specific aneuploidy patterns are initiating events and define subgroups in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Here we analyzed 250 BCP-ALL cases and identified a novel subgroup ('PAX5-plus', n = 19) by distinct DNA methylation and gene expression profiles. All patients in this subgroup harbored mutations in the B-lineage transcription factor PAX5, with p.

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Background: Target enrichment combined with chromosome conformation capturing methodologies such as capture Hi-C (CHC) can be used to investigate spatial layouts of genomic regions with high resolution and at scalable costs. A common application of CHC is the investigation of regulatory elements that are in contact with promoters, but CHC can be used for a range of other applications. Therefore, probe design for CHC needs to be adapted to experimental needs, but no flexible tool is currently available for this purpose.

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Background: The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral microbiome of 1500 adolescents around Spain and its relationships with lifestyle, diet, hygiene, and socioeconomic and environmental parameters.

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Connective tissues support organs and play crucial roles in development, homeostasis and fibrosis, yet our understanding of their formation is still limited. To gain insight into the molecular mechanisms of connective tissue specification, we selected five zinc-finger transcription factors - OSR1, OSR2, EGR1, KLF2 and KLF4 - based on their expression patterns and/or known involvement in connective tissue subtype differentiation. RNA-seq and ChIP-seq profiling of chick limb micromass cultures revealed a set of common genes regulated by all five transcription factors, which we describe as a connective tissue core expression set.

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Osteogenesis Imperfecta (OI) is a clinically and genetically heterogeneous disorder. Although differential diagnosis is greatly facilitated by next generation sequencing, its availability can vary considerably. In this study, we compared targeted gene panel or exome sequencing with clinical scoring and grouping in a cohort of 50 OI index patients recruited by a single Indian clinical center in an unselected fashion.

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