Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.

Bulk and single-cell DNA sequencing has enabled reconstructing clonal substructures of somatic tissues from frequency and cooccurrence patterns of somatic variants. However, approaches to characterize phenotypic variations between clones are not established. Here we present cardelino (https://github.com/single-cell-genetics/cardelino), a computational method for inferring the clonal tree configuration and the clone of origin of individual cells assayed using single-cell RNA-seq (scRNA-seq). Cardelino flexibly integrates information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. We apply cardelino to a published cancer dataset and to newly generated matched scRNA-seq and exome-seq data from 32 human dermal fibroblast lines, identifying hundreds of differentially expressed genes between cells from different somatic clones. These genes are frequently enriched for cell cycle and proliferation pathways, indicating a role for cell division genes in somatic evolution in healthy skin.

Phosphorus deprivation affects composition and spatial distribution of membrane lipids in legume nodules.

In legumes, symbiotic nitrogen (N) fixation (SNF) occurs in specialized organs called nodules after successful interactions between legume hosts and rhizobia. In a nodule, N-fixing rhizobia are surrounded by symbiosome membranes, through which the exchange of nutrients and ammonium occurs between bacteria and the host legume. Phosphorus (P) is an essential macronutrient, and N2-fixing legumes have a higher requirement for P than legumes grown on mineral N. As in the previous studies, in P deficiency, barrel medic (Medicago truncatula) plants had impaired SNF activity, reduced growth, and accumulated less phosphate in leaves, roots, and nodules compared with the plants grown in P sufficient conditions. Membrane lipids in M. truncatula tissues were assessed using electrospray ionization-mass spectrometry. Galactolipids were found to increase in P deficiency, with declines in phospholipids (PL), especially in leaves. Lower PL losses were found in roots and nodules. Subsequently, matrix-assisted laser desorption/ionization-mass spectrometry imaging was used to spatially map the distribution of the positively charged phosphatidylcholine (PC) species in nodules in both P-replete and P-deficient conditions. Our results reveal heterogeneous distribution of several PC species in nodules, with homogeneous distribution of other PC classes. In P poor conditions, some PC species distributions were observed to change. The results suggest that specific PC species may be differentially important in diverse nodule zones and cell types, and that membrane lipid remodeling during P stress is not uniform across the nodule.

Linkage of the Nit1C gene cluster to bacterial cyanide assimilation as a nitrogen source.

A genetic linkage between a conserved gene cluster (Nit1C) and the ability of bacteria to utilize cyanide as the sole nitrogen source was demonstrated for nine different bacterial species. These included three strains whose cyanide nutritional ability has formerly been documented (Pseudomonas fluorescens Pf11764, Pseudomonas putida BCN3 and Klebsiella pneumoniae BCN33), and six not previously known to have this ability [Burkholderia (Paraburkholderia) xenovorans LB400, Paraburkholderia phymatum STM815, Paraburkholderia phytofirmans PsJN, Cupriavidus (Ralstonia) eutropha H16, Gluconoacetobacter diazotrophicus PA1 5 and Methylobacterium extorquens AM1]. For all bacteria, growth on or exposure to cyanide led to the induction of the canonical nitrilase (NitC) linked to the gene cluster, and in the case of Pf11764 in particular, transcript levels of cluster genes (nitBCDEFGH) were raised, and a nitC knock-out mutant failed to grow. Further studies demonstrated that the highly conserved nitB gene product was also significantly elevated. Collectively, these findings provide strong evidence for a genetic linkage between Nit1C and bacterial growth on cyanide, supporting use of the term cyanotrophy in describing what may represent a new nutritional paradigm in microbiology. A broader search of Nit1C genes in presently available genomes revealed its presence in 270 different bacteria, all contained within the domain Bacteria, including Gram-positive Firmicutes and Actinobacteria, and Gram-negative Proteobacteria and Cyanobacteria. Absence of the cluster in the Archaea is congruent with events that may have led to the inception of Nit1C occurring coincidentally with the first appearance of cyanogenic species on Earth, dating back 400-500 million years.

Quasi-epitaxial growth of [Ru(bpy)3 ](2+) by confinement in clay nanoplatelets yields polarized emission.

A nano confinement strategy is presented to control the spatial orientation and emission polarization of phosphorescent metal complexes. Through nano-confinement of the phosphorescent metal complex [Ru(bpy)3 ](2+) by attaching it to anionic clay nanoplatelets, it is possible to simultaneously lock the spatial orientation of the complex and fix its emission polarization. This quasi-epitaxial approach may provide a future work strategy directed at light emitting diodes and lasers.

A single-cell atlas enables mapping of homeostatic cellular shifts in the adult human breast.

Here we use single-cell RNA sequencing to compile a human breast cell atlas assembled from 55 donors that had undergone reduction mammoplasties or risk reduction mastectomies. From more than 800,000 cells we identified 41 cell subclusters across the epithelial, immune and stromal compartments. The contribution of these different clusters varied according to the natural history of the tissue. Age, parity and germline mutations, known to modulate the risk of developing breast cancer, affected the homeostatic cellular state of the breast in different ways. We found that immune cells from BRCA1 or BRCA2 carriers had a distinct gene expression signature indicative of potential immune exhaustion, which was validated by immunohistochemistry. This suggests that immune-escape mechanisms could manifest in non-cancerous tissues very early during tumor initiation. This atlas is a rich resource that can be used to inform novel approaches for early detection and prevention of breast cancer.

Nanoplatelets of sodium hectorite showing aspect ratios of ≈20,000 and superior purity.

Applying a combination of melt synthesis followed by long-term annealing a fluorohectorite is obtained which is unique with respect to homogeneity, purity, and particle size. Counterintuitively, the hectorite undergoes a disorder-to-order transition upon swelling to the level of the bilayer hydrate. Alkylammonium-exchanged samples show at any chain length only a single basal spacing corroborating a nicely homogeneous layer charge density. Its intracrystalline reactivity improves greatly upon annealing, making it capable to spontaneously and completely disintegrate into single clay lamellae of 1 nm thickness. Realizing exceptional aspect ratios of around 20,000 upon delamination, this synthetic clay will offer unprecedented potential as functional filler in highly transparent nanocomposites with superior gas barrier and mechanical properties.

Metal artefact reduction from dental hardware in carotid CT angiography using iterative reconstructions.

PURPOSE: To determine the value of a metal artefact reduction (MAR) algorithm with iterative reconstructions for dental hardware in carotid CT angiography. METHODS: Twenty-four patients (six of which were women; mean age 70 ± 12 years) with dental hardware undergoing carotid CT angiography were included. Datasets were reconstructed with filtered back projection (FBP) and using a MAR algorithm employing normalisation and an iterative frequency-split (IFS) approach. Three blinded, independent readers measured CT attenuation values and evaluated image quality and degrees of artefacts using axial images, multi-planar reformations (MPRs) and maximal intensity projections (MIP) of the carotid arteries. RESULTS: CT attenuation values of the internal carotid artery on images with metal artefacts were significantly higher in FBP (324 ± 104HU) datasets compared with those reconstructed with IFS (278 ± 114HU; P < 0.001) and with FBP on images without metal artefacts (293 ± 106HU; P = 0.006). Quality of IFS images was rated significantly higher on axial, MPR and MIP images (P < 0.05, each), and readers found significantly less artefacts impairing the diagnostic confidence of the internal carotid artery (P < 0.05, each). CONCLUSION: The MAR algorithm with the IFS approach allowed for a significant reduction of artefacts from dental hardware in carotid CT angiography, hereby increasing image quality and improving the accuracy of CT attenuation measurements. KEY POINTS: • CT angiography of the neck has proven value for evaluating carotid disease • Neck CT angiography images are often degraded by artefacts from dental implants • A metal artefact reduction algorithm with iterative reconstruction reduces artefacts significantly • Visualisation of the internal carotid artery is improved.

Draft genome sequence of the cyanide-utilizing bacterium Pseudomonas fluorescens strain NCIMB 11764.

We report here the 6.97-Mb draft genome sequence of Pseudomonas fluorescens strain NCIMB 11764, which is capable of growth on cyanide as the sole nitrogen source. The draft genome sequence allowed the discovery of several genes implicated in enzymatic cyanide turnover and provided additional information contributing to a better understanding of this organism's unique cyanotrophic ability. This is the first sequenced genome of a cyanide-assimilating bacterium.

A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours.

Human cerebral cancers are known to contain cell types resembling the varying stages of neural development. However, the basis of this association remains unclear. Here, we map the development of mouse cerebrum across the developmental time-course, from embryonic day 12.5 to postnatal day 365, performing single-cell transcriptomics on >100,000 cells. By comparing this reference atlas to single-cell data from >100 glial tumours of the adult and paediatric human cerebrum, we find that tumour cells have an expression signature that overlaps with temporally restricted, embryonic radial glial precursors (RGPs) and their immediate sublineages. Further, we demonstrate that prenatal transformation of RGPs in a genetic mouse model gives rise to adult cerebral tumours that show an embryonic/juvenile RGP identity. Together, these findings implicate the acquisition of embryonic-like states in the genesis of adult glioma, providing insight into the origins of human glioma, and identifying specific developmental cell types for therapeutic targeting.

Human branching cholangiocyte organoids recapitulate functional bile duct formation.

Human cholangiocyte organoids show great promise for regenerative therapies and in vitro modeling of bile duct development and diseases. However, the cystic organoids lack the branching morphology of intrahepatic bile ducts (IHBDs). Here, we report establishing human branching cholangiocyte organoid (BRCO) cultures. BRCOs self-organize into complex tubular structures resembling the IHBD architecture. Single-cell transcriptomics and functional analysis showed high similarity to primary cholangiocytes, and importantly, the branching growth mimics aspects of tubular development and is dependent on JAG1/NOTCH2 signaling. When applied to cholangiocarcinoma tumor organoids, the morphology changes to an in vitro morphology like primary tumors. Moreover, these branching cholangiocarcinoma organoids (BRCCAOs) better match the transcriptomic profile of primary tumors and showed increased chemoresistance to gemcitabine and cisplatin. In conclusion, BRCOs recapitulate a complex process of branching morphogenesis in vitro. This provides an improved model to study tubular formation, bile duct functionality, and associated biliary diseases.

Characterization of the Nit6803 nitrilase homolog from the cyanotroph Pseudomonas fluorescens NCIMB 11764.

We report the purification and characterization of a nitrilase (E.C. 3.5.5.1) (Nit11764) essential for the assimilation of cyanide as the sole nitrogen source by the cyanotroph, Pseudomonas fluorescens NCIMB 11764. Nit11764, is a member of a family of homologous proteins (nitrile_sll0784) for which the genes typically reside in a conserved seven-gene cluster known as Nit1C. The physical properties and substrate specificity of Nit11764 resemble those of Nit6803, the current reference protein for the family, and the only true nitrilase that has been crystallized. The substrate binding pocket of the two enzymes places the substrate in direct proximity to the active site nucleophile (C160) and conserved catalytic triad (Glu44, Lys126). The two enzymes exhibit a similar substrate profile, however, for Nit11764, cinnamonitrile, was found to be an even better substrate than fumaronitrile the best substrate previously identified for Nit6803. A higher affinity for cinnamonitrile (Km 1.27 mM) compared to fumaronitrile (Km 8.57 mM) is consistent with docking studies predicting a more favorable interaction with hydrophobic residues lining the binding pocket. By comparison, 3,4-dimethoxycinnamonitrile was a poorer substrate the substituted methoxyl groups apparently hindering entry into the binding pocket. in situ 1H NMR studies revealed that only one of the two nitrile substituents in the dinitrile, fumaronitrile, was attacked yielding trans-3-cyanoacrylate (plus ammonia) as a product. The essentiality of Nit11764 for cyanotrophy remains uncertain given that cyanide itself is a poor substrate and the catalytic efficiencies for even the best of nitrile substrates (~5 × 103 M-1 s-1) is less than stellar.

Freshwater monitoring by nanopore sequencing.

While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.

Many water-dwelling bacteria can cause severe diseases such as cholera, typhoid or leptospirosis. One way to prevent outbreaks is to test water sources to find out which species of microbes they contain, and at which levels. Traditionally, this involves taking a water sample, followed by growing a few species of 'indicator bacteria' that help to estimate whether the water is safe. An alternative technique, called metagenomics, has been available since the mid-2000s. It consists in reviewing (or 'sequencing') the genetic information of most of the bacteria present in the water, which allows scientists to spot harmful species. Both methods, however, require well-equipped laboratories with highly trained staff, making them challenging to use in remote areas. The MinION is a pocket-sized device that ­ when paired with a laptop or mobile phone ­ can sequence genetic information 'on the go'. It has already been harnessed during Ebola, Zika or SARS-CoV-2 epidemics to track the genetic information of viruses in patients and environmental samples. However, it is still difficult to use the MinION and other sequencers to monitor bacteria in water sources, partly because the genetic information of the microbes is highly fragmented during DNA extraction. To address this challenge, Urban, Holzer et al. set out to optimise hardware and software protocols so the MinION could be used to detect bacterial species present in rivers. The tests focussed on the River Cam in Cambridge, UK, a waterway which faces regular public health problems: local rowers and swimmers often contract waterborne infections, sometimes leading to river closures. For six months, Urban, Holzer et al. used the MinION to map out the bacteria present across nine river sites, assessing the diversity of species and the presence of disease-causing microbes in the water. In particular, the results showed that optimising the protocols made it possible to tell the difference between closely related species ­ an important feature since harmful and inoffensive bacteria can sometimes be genetically close. The data also revealed that the levels of harmful bacteria were highest downstream of urban river sections, near a water treatment plant and river barge moorings. Together, these findings demonstrate that optimising MinION protocols can turn this device into a useful tool to easily monitor water quality. Around the world, climate change, rising urbanisation and the intensification of agriculture all threaten water quality. In fact, access to clean water is one of the United Nations sustainable development goals for 2030. Using the guidelines developed by Urban, Holzer et al., communities could harness the MinION to monitor water quality in remote areas, offering a cost-effective, portable DNA analysis tool to protect populations against deadly diseases.

Homogeneous precipitation by formamide hydrolysis: synthesis, reversible hydration, and aqueous exfoliation of the layered double hydroxide (LDH) of Ni and Al.

Homogenous precipitation by formamide hydrolysis results in the formation of a formate-intercalated layered double hydroxide (LDH) of Ni(II) and Al(III). The formate-LDH is sensitive to the atmospheric humidity and reversibly exchanges its intercalated water with atmospheric moisture. The hydration/dehydration cycle is complete within a narrow range of 0-30% relative humidity with significant hysteresis and involves a randomly interstratified intermediate phase. When immersed in water, the formate ion grows its hydration sphere (osmotic swelling), eventually leading to the exfoliation of the metal hydroxide layers into lamellar particles having in-plane dimensions of 100-200 nm and a thickness of 9-12 nm. These nanoplatelets restack to thicker tactoids again upon evaporation of the dispersion. The intercalated formate ion can be exchanged with nitrate ions in solution but not with iodide ions. These observations have implications for many applications of LDHs in the area of carbon dioxide sorption and catalysis.

A cell atlas of human thymic development defines T cell repertoire formation.

The thymus provides a nurturing environment for the differentiation and selection of T cells, a process orchestrated by their interaction with multiple thymic cell types. We used single-cell RNA sequencing to create a cell census of the human thymus across the life span and to reconstruct T cell differentiation trajectories and T cell receptor (TCR) recombination kinetics. Using this approach, we identified and located in situ CD8αα+ T cell populations, thymic fibroblast subtypes, and activated dendritic cell states. In addition, we reveal a bias in TCR recombination and selection, which is attributed to genomic position and the kinetics of lineage commitment. Taken together, our data provide a comprehensive atlas of the human thymus across the life span with new insights into human T cell development.

Draft Genome Sequence of the Cyanotroph Pseudomonas monteilii BCN3.

We report here the first draft genome of Pseudomonas monteilii BCN3, a cyanotroph isolated from sewage sludge. The genome consists of approximately 6,029,517 bp with a G+C content of 61.89% and 5,369 annotated protein-coding genes.

In- vitro-activity of additive application of hydrogen peroxide in antimicrobial photodynamic therapy using LED in the blue spectrum against bacteria and biofilm associated with periodontal disease.

BACKGROUND: Although antimicrobial photodynamic therapy (aPDT) has been shown to be efficient in killing planktonic periodontopathogenic bacteria, its activity on established biofilms is very limited. The aim of the present in-vitro study was to evaluate the potential effect of hydrogen peroxide as a pretreatment for aPDT. METHODS: aPDT consisting of riboflavin as photosensitizer and illumination by a LED lamp emitting in the blue spectrum for 30 s and 60 s (aPDT60) was combined with a pretreatment with 0.25% and 3% hydrogen peroxide. The antimicrobial activity of these treatments was determined against eight oral species (incl. Porphyromonas gingivalis and Tannerella forsythia) and against eight-species biofilms. Treatment of biofilms in an artificial pocket model included a mechanical removal of the biofilm. RESULTS: Against planktonic bacteria, pretreatment with hydrogen peroxide increased killing of planktonic bacteria, after aPDT60 no viable bacteria were detected in 7 of 8 strains. In biofilms formed on well-plates, aPDT60 reduced bacterial counts only by 0.53 log10 cfu, whereas reduction was closed to 4 log10 or higher when 3% hydrogen peroxide was used. When biofilms were treated in the periodontal-pocket model, reduction of cfu was less than 0.5 log10 after mechanical therapy or aPDT60 only, however no bacteria were detected after mechanical biofilm removal followed by the use 3% of hydrogen peroxide and aPDT60. CONCLUSIONS: aPDT using riboflavin and blue LED light applied after mechanical removal of biofilm and adjunctive 3% hydrogen peroxide solution appears to represent an alternative for antimicrobial periodontal therapy.

Intratumoral Genetic and Functional Heterogeneity in Pediatric Glioblastoma.

Pediatric glioblastoma (pGBM) is a lethal cancer with no effective therapies. To understand the mechanisms of tumor evolution in this cancer, we performed whole-genome sequencing with linked reads on longitudinally resected pGBM samples. Our analyses showed that all diagnostic and recurrent samples were collections of genetically diverse subclones. Clonal composition rapidly evolved at recurrence, with less than 8% of nonsynonymous single-nucleotide variants being shared in diagnostic-recurrent pairs. To track the origins of the mutational events observed in pGBM, we generated whole-genome datasets for two patients and their parents. These trios showed that genetic variants could be (i) somatic, (ii) inherited from a healthy parent, or (iii) de novo in the germlines of pGBM patients. Analysis of variant allele frequencies supported a model of tumor growth involving slow-cycling cancer stem cells that give rise to fast-proliferating progenitor-like cells and to nondividing cells. Interestingly, radiation and antimitotic chemotherapeutics did not increase overall tumor burden upon recurrence. These findings support an important role for slow-cycling stem cell populations in contributing to recurrences, because slow-cycling cell populations are expected to be less prone to genotoxic stress induced by these treatments and therefore would accumulate few mutations. Our results highlight the need for new targeted treatments that account for the complex functional hierarchies and genomic heterogeneity of pGBM. SIGNIFICANCE: This work challenges several assumptions regarding the genetic organization of pediatric GBM and highlights mutagenic programs that start during early prenatal development.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/9/2111/F1.large.jpg.

Successful remission of thrombotic thrombocytopenic purpura with rituximab in a patient with undifferentiated connective tissue disorder.

Thrombotic thrombocytopenic purpura (TTP) is rarely associated with undifferentiated connective tissue disorder. We present a patient with TTP, undifferentiated connective tissue disorder, and very high titer of anti-ribonucleoprotein antibodies. Her TTP did not respond to intravenous methylprednisolone and cyclophosphamide requiring her to remain dependent on plasmapheresis. Her disease remitted successfully after 4 doses of rituximab given at weekly intervals and she remained in continuous remission 6 months after therapy. We propose early and aggressive use of B-cell depletion therapy in TTP associated with autoimmune disorders.

Immune Cell Dynamics Unfolded by Single-Cell Technologies.

The single-cell revolution is paving the way towards the molecular characterisation of every cell type in the human body, revealing relationships between cell types and states at high resolution. Changes in cellular phenotypes are particularly prevalent in the immune system and can be observed in its continuous remodelling up to adulthood, response to disease and development of immunological memory. In this review, we delve into the world of cellular dynamics of the immune system. We discuss current single-cell experimental and computational approaches in this area, giving insights into plasticity and commitment of cell fates. Finally, we provide an outlook on upcoming technological developments and predict how these will improve our understanding of the immune system.