We have developed a computational method based on polyploid phasing of long sequence reads to resolve collapsed regions of segmental duplications within genome assemblies. Segmental Duplication ...Assembler (SDA; https://github.com/mvollger/SDA ) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs. We apply it to single-molecule, real-time sequence data from three human genomes and recover 33-79 megabase pairs (Mb) of duplications in which approximately half of the loci are diverged (<99.8%) compared to the reference genome. We show that the corresponding sequence is highly accurate (>99.9%) and that the diverged sequence corresponds to copy-number-variable paralogs that are absent from the human reference genome. Our method can be applied to other complex genomes to resolve the last gene-rich gaps, improve duplicate gene annotation, and better understand copy-number-variant genetic diversity at the base-pair level.
Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines ...the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing
with continuous long-read or high-fidelity
sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value > 40) and highly contiguous (contig N50 > 23 Mbp) with low switch error rates (0.17%), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.
Bacteria can adversely affect the quality of drainage released from mine waste by catalyzing the oxidation of sulfide minerals and thereby accelerating the release of acidity and metals. However, the ...microbiological and geochemical controls on drainage quality from unsaturated and geochemically heterogeneous waste rock remain poorly understood. Here, we identified coexisting neutrophilic and acidophilic bacteria in different types of waste rock, indicating that robust endemic consortia are sustained within pore-scale microenvironments. Subsequently, natural weathering was simulated in laboratory column experiments with waste rock that contained either in-situ microbial consortia or suppressed populations with up to 1000 times smaller abundance and reduced phenotypic diversity after heating and drying. Drainage from waste rock with in-situ populations was up to two pH units lower and contained up to 16 times more sulfate and heavy metals compared to drainage from waste rock bearing treated populations, indicating significantly higher sulfide-oxidation rates. The drainage chemistry was further affected by sorption and formation of secondary-mineral phases (e.g., gypsum and hydroxy-carbonates). This study provides direct evidence for the existence of diverse microbial communities in waste rock and their important catalytic role on weathering rates, and illustrates the mutual controls of microbiology and geochemistry on waste-rock drainage quality.
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•Integrated approach to study microbial and geochemical controls on drainage quality.•Characterization of microbial abundance and community structures in waste rock.•Waste-rock weathering under simulated field conditions using column experiments•Demonstration of microbial catalysis of waste-rock weathering•Discrete secondary minerals and adsorption affect waste-rock drainage quality.
Inversions play an important role in disease and evolution but are difficult to characterize because their breakpoints map to large repeats. We increased by sixfold the number (n = 1,069) of ...previously reported great ape inversions by using single-cell DNA template strand and long-read sequencing. We find that the X chromosome is most enriched (2.5-fold) for inversions, on the basis of its size and duplication content. There is an excess of differentially expressed primate genes near the breakpoints of large (>100 kilobases (kb)) inversions but not smaller events. We show that when great ape lineage-specific duplications emerge, they preferentially (approximately 75%) occur in an inverted orientation compared to that at their ancestral locus. We construct megabase-pair scale haplotypes for individual chromosomes and identify 23 genomic regions that have recurrently toggled between a direct and an inverted state over 15 million years. The direct orientation is most frequently the derived state for human polymorphisms that predispose to recurrent copy number variants associated with neurodevelopmental disease.
The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation
. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed ...without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes
and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome.
The pathogenic fungus Cryptococcus neoformans must overcome iron limitation to cause disease in mammalian hosts. Previously, we reported a screen for insertion mutants with poor growth on haem as the ...sole iron source. In this study, we characterised one such mutant and found that the defective gene encoded a Vam6/Vps39/TRAP1 domain‐containing protein required for robust growth on haem, an important iron source in host tissue. We designated this protein Vps3 based on reciprocal best matches with the corresponding protein in Saccharomyces cerevisiae. C. neoformans encodes a second Vam6/Vps39/TRAP1 domain‐containing protein designated Vam6/Vlp1, and we found that this protein is also required for robust growth on haem as well as on inorganic iron sources. This protein is predicted to be a component of the homotypic fusion and vacuole protein sorting complex involved in endocytosis. Further characterisation of the vam6Δ and vps3Δ mutants revealed perturbed trafficking of iron acquisition functions (e.g., the high affinity iron permease Cft1) and impaired processing of the transcription factor Rim101, a regulator of haem and iron acquisition. The vps3Δ and vam6Δ mutants also had pleiotropic phenotypes including loss of virulence in a mouse model of cryptococcosis, reduced virulence factor elaboration and increased susceptibility to stress, indicating pleiotropic roles for Vps3 and Vam6 beyond haem use in C. neoformans.
Take Aways
Two Vam6/Vps39/TRAP1‐domain proteins, Vps3 and Vam6, support the growth of Cryptococcus neoformans on haem.
Loss of Vps3 and Vam6 influences the trafficking and expression of iron uptake proteins.
Loss of Vps3 or Vam6 eliminates the ability of C. neoformans to cause disease in a mouse model of cryptococcosis.
The pathogenic fungus Cryptococcus neoformans must overcome iron limitation to cause disease in mammalian hosts. Two Vam6/Vps39/TRAP1 domain‐containing proteins, Vps3 and Vam6, are required for robust growth on haem as well as proper regulation of iron homeostasis. Two independent deletion mutants for each gene, or double mutants lacking both genes, are unable to cause disease in a mouse inhalation model of cryptococcosis.
Objective
Patients with incurable cancer should receive general palliative care according to their needs, as provided through collaboration between hospital departments, municipalities, and general ...practices and as outlined in national guidelines. However, the implementation of general palliative care in Denmark has been inadequate. This study aimed to investigate the healthcare professionals' (HCPs') perceptions on barriers to and facilitators of the implementation of the Danish National Guideline (NG) for general palliative care.
Methods
This descriptive, qualitative study was guided by the Consolidated Framework for Implementation Research (CFIR). Qualitative focus group and individual interviews were conducted with 23 HCPs. The interview guide, coding, analysis, and reporting of findings were developed within the CFIR framework.
Results
The main barriers to implementing NG were as follows: lack of knowledge about the NG, lack of an implementation plan, and insufficient communication and collaboration across sectors. Important facilitators were as follows: HCP motivation to meet palliative care needs, HCPs with special functions taking responsibility for incorporating NG into local guidelines, and the role of district nurses specialised in palliative care as opinion leaders providing security and continuity for the HCPs working in palliative care.
Conclusions
To address the needs of patients with incurable cancer, greater efforts are required on implementing general palliative care. Although HCPs in our setting were motivated to improve NG implementation, financial resources and strategies are necessary to ensure sufficient knowledge uptake and accommodate identified barriers in order to translate the NG into practice.
Purpose
During the COVID-19 pandemic, teleconsultations have increasingly been used to reduce physical contact and thus risk of infection. This study investigated how patients with cancer experienced ...the COVID-19 pandemic and how they perceived the change from in-person consultations to telephone consultations in an oncology outpatient clinic. The aim was to provide insights that could optimize the future use of teleconsultations in cancer care.
Methods
This qualitative study included 15 patients with colorectal, breast, gynecological, lung, or prostate cancer treated at the outpatient clinic at the Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Denmark in June or July 2020. Data were collected through semi-structured individual interviews and analyzed by thematic analysis.
Results
Patients with cancer experienced social, psychological, and organizational consequences of the COVID-19 pandemic related to their cancer care. Not all patients were comfortable with telephone consultations. Six themes were identified: (1) double burden as a consequence of simultaneous cancer and the COVID-19 pandemic, (2) parameters for patient satisfaction with telephone consultations, (3) the importance of relatives attending consultations, (4) loss of information and nuances during telephone consultations, (5) the impact of physicians’ language and communicative skills during telephone consultations, and (6) patients’ suggestions for future telephone consultations.
Conclusion
Beyond the COVID-19 pandemic, it is important that hospitals offering teleconsultations involve patients’ preferences, consider for which patients and consultations the solution is suitable, which technology to use, how to prepare patients and relatives, and how to provide physicians with the necessary communicative skills.
During the COVID-19 pandemic, teleconsultations (TC) have been increasingly used in cancer care as an alternative to outpatient visits. We aimed to examine patient-related and cancer-specific ...characteristics associated with experiences with TC among patients with cancer during the COVID-19 pandemic.
This population-based survey included patients with breast, lung, gastrointestinal, urological, and gynaecological cancers with appointments in the outpatient clinics, Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Denmark in March and April 2020. Age- and sex-adjusted logistic regression analyses were used to study associations of sociodemographics, cancer and general health, anxiety, and health literacy with patients' experiences of TC in regards to being comfortable with TC, confident that the doctor could provide information or assess symptoms/side effects and the perceived outcome of TC.
Of the 2119 patients with cancer receiving the electronic survey, 1160 (55%) participated. Two thirds of patients (68%) had consultations with a doctor changed to TC. Being male, aged 65-79 years, and having TC for test results were statistically significantly associated with more comfort, confidence, and perceived better outcome of TC. Having breast cancer, anxiety, low health literacy, or TC for a follow-up consultation were statistically significantly associated with less positive experiences with TC. Living alone, short education, disability pension, and comorbidity were statistically significantly associated with anxiety and low health literacy.
Most patients reported positive experiences with TC, but in particular patients with anxiety and low health literacy, who were also the patients with fewest socioeconomic and health resources, felt less comfortable and confident with and were more likely to perceive the outcome negatively from this form of consultation. TC may be suitable for increasing integration into standard cancer care but it should be carefully planned to meet patients' different information needs in order not to increase social inequality in cancer.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
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