bluuebunny/crossref_metadata_2025_split huggingface dataset:
New non-bilaterian transcriptomes provide novel insights into the evolution of coralskeletomes
Authors: Conci Nicola , Wörheide Gert , Vargas Sergio 
Published: April 2019

AbstractA general feature of animalskeletomesis the co-presence of taxonomically widespread and lineage-specific proteins that actively regulate the biomineralization process. Among cnidarians, the skeletomes of scleractinian corals have been shown to follow this trend, however in this group distribution and phylogenetic analyses of biomineralization-related genes have been often based on limited numbers of species, with other anthozoan calcifiers such as octocorals, being overlooked. Wede-novosequenced the transcriptomes of four soft-coral species characterized by different calcification strategies (aragonite skeletonvs. calcitic sclerites) and data-mined published non-bilaterian transcriptomic resources to construct a taxonomically comprehensive sequence database to map the distribution of scleractinian and octocoralskeletomecomponents. At the large scale, no protein showed a ‘Cnidaria+Placozoa’ or ‘Cnidaria+Ctenophora’ distribution, while some were found in cnidarians and Porifera. Within Scleractinia and Octocorallia, we expanded the distribution for several taxonomically restricted genes (TRGs) and propose an alternative evolutionary scenario, involving an early single biomineralization-recruitment event, for galaxinsensu stricto. Additionally, we show that the enrichment of acidic residues within skeletogenic proteins did not occur at the Corallimorpharia-Scleractinia transition, but appears to be associated with protein secretion in the organic matrix. Finally, the distribution of octocoral calcification-related proteins appears independent of skeleton mineralogy (i.e. aragonite/calcite) with no differences on the proportion of shared skeletogenic proteins between scleractinians and aragonitic or calcitic octocorals. This points toskeletomehomogeneity within but not between groups of calcifying cnidarians, although some proteins like galaxins and SCRiP-3a could represent instances of commonality.
A Ssd1 homolog impacts trehalose and chitin biosynthesis and contributes to virulence inAspergillus fumigatus
Authors: Thammahong Arsa , Dhingra Sourabh , Bultman Katherine M. , Kerkaert Joshua , Cramer Robert A. 
Published: April 2019

AbstractRegulation of fungal cell wall biosynthesis is critical to maintain cell wall integrity in the face of dynamic fungal infection microenvironments. In this study, we observe that a yeastssd1homolog,ssdA,in the filamentous fungusAspergillus fumigatusis involved in trehalose and cell wall homeostasis. AnssdAnull mutant strain exhibited an increase in trehalose levels and a reduction in colony growth rate. Over-expression ofssdAin contrast perturbed trehalose biosynthesis and reduced conidia germination rates. ThessdAnull mutant strain was more resistant to cell wall perturbing agents while over-expression ofssdApromoted increased sensitivity. Over-expression ofssdAsignificantly increased chitin levels and both loss and over-expression ofssdAaltered sub-cellular localization of the class V chitin synthase CsmA. Strikingly, over-expression ofssdAabolished adherence to abiotic surfaces and severely attenuated the virulence ofA. fumigatusin a murine model of invasive pulmonary aspergillosis. In contrast, despite the severein vitrofitness defects observed upon loss ofssdA,neither surface adherence or murine survival was impacted. In conclusion,A. fumigatusSsdA plays a critical role in cell wall homeostasis that alters fungal-host interactions.ImportanceLife threatening infections caused by the filamentous fungusAspergillus fumigatusare increasing along with a rise in fungal strains resistant to contemporary antifungal therapies. The fungal cell wall and the associated carbohydrates required for its synthesis and maintenance are attractive drug targets given that many genes encoding proteins involved in cell wall biosynthesis and integrity are absent in humans. Importantly, genes and associated cell wall biosynthesis and homeostasis regulatory pathways remain to be fully defined inA. fumigatus.In this study, we identify SsdA, a model yeast Ssd1p homolog, as an important component of trehalose and fungal cell wall biosynthesis inA. fumigatusthat consequently impacts fungal virulence in animal models of infection.
An integrated one-step assay combining thermal lysis and loop-mediated isothermal DNA amplification (LAMP) in 30 min fromE. coliandM. smegmatiscells on a paper substrate
Authors: Naik Priyanka , Jaitpal Siddhant , Shetty Prasad , Paul Debjani 
Published: April 2019

Developing sensors in the domains of food safety, soil analysis, water quality monitoring and healthcare often requires distinguishing between different species of bacteria. The most rapid, sensitive and specific method to identify bacteria is by analysing their DNA sequence, which comprises of disinfection and lysis of bacterial cells, amplification of the isolated DNA and detection of the amplified sequence. Seamless integration of these assays on a paper substrate remains a big challenge in paperfluidic nucleic acid analyis. Combining lysis and isothermal amplification in a single reaction step is difficult because the porosity of paper and the presence of cell debris following lysis reduces the efficiency of DNA amplification. On the other hand, extracting and purifying the DNA after lysis to improve the amplification efficiency involves addition of chemical reagents, one or more wash steps and manual intervention. This problem is even more complex for mycobacteria as its thick cell wall structure impedes lysis and the high GC-content of the genome requires careful optimization of enzymatic denaturation during isothermal amplification. Here we successfully combine thermal lysis and loop-mediated isothermal amplification (LAMP) into a single reaction step on paper without the need for any intermediate intervention. We demonstrate our integrated assay by amplifying DNA from 100 CFU/mL ofEscherichia coli(MG1655) andMycobacterium smegmatis(mc2155) cells in 30 min on a paper substrate. We also confirm thatE. coliandM. smegmatiscan be completely disinfected on paper by heating at 60 °C for 5 min and 15 min respectively, making this assay safe and suitable for incorporation into diverse paperfluidic sensors for field use.Electronic Supplementary Information (ESI) is available.
A likelihood method for estimating present-day human contamination in ancient DNA samples using low-depth haploid chromosome data
Authors: Moreno-Mayar J. Víctor , Korneliussen Thorfinn Sand , Albrechtsen Anders , Dalal Jyoti , Renaud Gabriel , Nielsen Rasmus , Malaspinas Anna-Sapfo 
Published: April 2019

1AbstractMotivationThe presence of present-day human contaminating DNA fragments is one of the challenges defining ancient DNA (aDNA) research. This is especially relevant to the ancient human DNA field where it is difficult to distinguish endogenous molecules from human contaminants due to their genetic similarity. Recently, with the advent of high-throughput sequencing and new aDNA protocols, hundreds of ancient human genomes have become available. Contamination in those genomes has been measured with computational methods often developed specifically for these empirical studies. Consequently, some of these methods have not been implemented and tested while few are aimed at low-depth data, a common feature in aDNA datasets.ResultsWe develop a new X-chromosome-based maximum likelihood method for estimating present-day human contamination in low-depth sequencing data. We implement our method for general use, assess its performance under conditions typical of ancient human DNA research, and compare it to previous nuclear data-based methods through extensive simulations. For low-depth data, we show that existing methods can produce unusable estimates or substantially underestimate contamination. In contrast, our method provides accurate estimates for a depth of coverage as low as 0.5× on the X-chromosome when contamination is below 25%. Moreover, our method still yields meaningful estimates in very challenging situations, i.e., when the contaminant and the target come from closely related populations or with increased error rates. With a running time below five minutes, our method is applicable to large scale aDNA genomic studies.Availability and implementationThe method is implemented in C++ and R and is freely available in https://github.com/sapfo/contaminationX.Contactmorenomayar@gmail.com, annasapfo.malaspinas@unil.ch.
Dual-matrix 3D culture system as a biomimetic model of epithelial tissues
Authors: Bogorodskaya Diana , McLane Joshua S. , Ligon Lee A. 
Published: April 2019

ABSTRACTRecent years have seen an unprecedented rise in the use of 3D culture systems, both in fundamental research and in more translational settings such as drug testing and disease modeling. However, 3D cultures often remain underused by cell biology labs, both due to technical difficulties in system setup and inherent drawbacks of many of the common systems. Here we describe an easy to use, inexpensive and rapidly assembled 3D culture system, suitable for generation of both normal polarized epithelial cysts and in-situ tumor spheroids. This system allows for exploration of many questions of normal and cancer cell biology, including morphogenesis, epithelial polarization, cell motility, intra- and intercellular communication, invasion, metastasis, and tumor-stoma interaction. The 3D cultures are made up of a stiffness tunable, dual-matrix model that can incorporate co-culture of multiple cell types. The model allows for increased physiological relevance by mimicking the organization, ligand composition and stiffness presentin-vivo. The setup allows for a wide spectrum of manipulation, including removing cells from the system for DNA/protein expression, transfection and high-resolution imaging of live or fixed cells.
Macrophage-mediated immunoediting drives ductal carcinoma evolution: Space is the game changer
Authors: Gatenbee Chandler , West Jeffrey , Baker Annie M. , Guljar Nafia , Jones Louise , Graham Trevor A. , Robertson-Tessi Mark , Anderson Alexander R. A. 
Published: April 2019

ABSTRACTUnder normal conditions, the immune system is capable of rapidly detecting and eliminating potentially dangerous entities, including tumor cells. Due to intense selection pressure imposed by the immune response, tumor cells often evolve strategies to avoid elimination in a process known as immunoediting. It is less known how the evolutionary response to immune predation is altered by context. We explore the evolution of immune escape strategies in ductal cancers, a natural case in which to study evolution in different contexts: inside and outside of ducts. We highlight the role of macrophages as a source of “public goods,” releasing diffusible factors (reactive oxygen species and growth factors). Immunohistochemistry reveals differences between macrophage densities of invasive ductal carcinomas and non-invasive ductal carcinomasin situ. For the first time, immunohistochemistry (IHC) imaging data comparing DCIS to IDC were used to initialize mechanistic agent-based models of evolutionary dynamics. By using IHC to map the initial conditions of a growing tumor, we show that spatial competition and structure influence transient dynamics during invasion. These dynamics are context-dependent, a conclusion that may be missed from interpreting imaging or non-spatial modeling alone. Before invasion, the presence of macrophages correlate with shorter ductal breach times. After invasion, tumors may employ a “pioneer-engineer” strategy where pioneering immunoresistant cells on the tumor’s edge stimulate the release of M1-macrophage-derived reactive oxygen species, degrading surrounding stroma. Behind the invasive edge, the engineering immunosuppressive cells promote the release of M2-macrophage-derived growth factors, providing a long-term immune escape strategy. Together, mathematical modeling and image analysis highlight the crucial role tumor-associated macrophages play in immune escape and invasion, both inside and outside of ducts.
Latitudinal variation in circadian rhythmicity in Nasonia vitripennis
Authors: Paolucci Silvia , Benetta Elena Dalla , Salis Lucia , Doležel David , van de Zande Louis , Beukeboom Leo W. 
Published: April 2019

ABSTRACTMany physiological processes of living organisms show circadian rhythms, governed by an endogenous clock. This clock has a genetic basis and is entrained by external cues such as light and temperature. Other physiological processes exhibit seasonal rhythms, that are also responsive to light and temperature. We previously reported a natural latitudinal cline of photoperiodic diapause induction in the parasitic wasp Nasonia vitripennis in Europe and a correlated haplotype frequency for the circadian clock gene period (per). To evaluate if this correlation is reflected in circadian behaviour, we investigated circadian locomotor activity of seven populations from the cline. We found that the proportion of rhythmic males is higher than females in constant darkness, and that mating decreased rhythmicity of both sexes. Only for virgin females, the free running period (τ) increased weakly with latitude. Wasps from the most southern locality had an overall shorter free running rhythm and earlier onset, peak and offset of activity during the 24 h period, than wasps from the northernmost locality. We evaluate this variation in rhythmicity as a function of period haplotype frequencies in the populations and discuss its functional significance in the context of local adaptation.
Modern clinical Mycobacterium tuberculosis strains leverage type I IFN pathway for a pro-inflammatory response in the host
Authors: Shankaran Deepthi , Arumugam Prabhakar , Bothra Ankur , Gandotra Sheetal , Rao Vivek 
Published: April 2019

ABSTRACTHost phagocytes respond to infections by innate defense mechanisms through metabolic shuffling in order to restrict the invading pathogen. However, this very plasticity of the host provides an ideal platform for pathogen mediated manipulation. By employing the macrophage model of Mtb infection, we identify an important strategy employed by modern clinical lineages in regulating the host immune–metabolism axis. The potent ability of these strains to specifically elicit a strong and early macrophage type I IFN response (in contrast to the protracted response to ancient Mtb), was dependent on an increased ability to localize in acidified phagosomes; this higher transit via acidified compartments is important for stimulation of the DNA dependent signaling in infected macrophages. The augmented IFN signaling provided a positive regulatory loop for enhanced expression of the cellular oxysterol-CH25H which in turn facilitated higher levels of IL6 in macrophages infected with the modern Mtb strains. Requirement of type I IFN signaling in mycobacterial intracellular growth highlights another unique ability of Mtb to manipulate host cell physiology and proinflammatory responses.Significance StatementCo-evolution with humans has enabled the development of novel adaptive mechanisms for survival in host specific environments in the human TB pathogen-Mtb. We present one such mechanism of modern Mtb strains harnessing the type I IFN immune axis to regulate the host pro-inflammatory response. Our results highlight the use of host intracellular endosomal transit as a mechanism by these strains to ensure a strong type I IFN response in macrophages. We also demonstrate the ability of Mtb to regulate macrophage cholesterol metabolism in order to fine tune the host innate responses. These findings lay the foundation of the future development of a host axis directed intervention strategy against this pathogen.
Axonal Transport Of An Insulin-Like Peptide Mrna Promotes Stress Recovery InC. Elegans
Authors: Chandra Rashmi , Li Lisa , Husain Zahabiya , Mishra Shashwat , Alcedo Joy 
Published: April 2019

ABSTRACTAberrations in insulin or insulin-like peptide (ILP) signaling in the brain causes many neurological diseases. Here we report that mRNAs of specific ILPs are surprisingly mobilized to the axons ofC. elegansduring stress. Transport of the ILPins-6mRNA to axons facilitates recovery from stress, whereas loss of axonal mRNA delays recovery. In addition, the axonal traffic ofins-6mRNA is regulated by at least two opposing signals: one that depends on the insulin receptor DAF-2 and a kinesin-2 motor; and a second signal that is independent of DAF-2, but involves a kinesin-3 motor. While Golgi bodies that package nascent peptides, like ILPs, have not been previously found inC. elegansaxons, we show that axons of stressedC. eleganshave increased Golgi ready to package peptides for secretion. Thus, our findings present a mechanism that facilitates an animal’s rapid recovery from stress through axonal ILP mRNA mobilization.
Functional Mature Human Microglia Developed in Human iPSC Microglial Chimeric Mouse Brain
Authors: Xu Ranjie , Boreland Andrew J. , Li Xiaoxi , Posyton Anthony , Kwan Kelvin , Hart Ronald P. , Jiang Peng 
Published: April 2019

AbstractMicroglia, the brain-resident macrophages, exhibit highly dynamic functions in neurodevelopment and neurodegeneration. Human microglia possess unique features as compared to mouse microglia, but our understanding of human microglial functions is largely limited by an inability to obtain human microglia under homeostatic states. We developed a human pluripotent stem cell (hPSC)-based microglial chimeric mouse brain model by transplanting hPSC-derived primitive macrophage precursors into neonatal mouse brains. The engrafted human microglia widely disperse in the brain and replace mouse microglia in corpus callosum at 6 months post-transplantation. Single-cell RNA-sequencing of the microglial chimeric mouse brains reveals that xenografted hPSC-derived microglia largely retain human microglial identity, as they exhibit signature gene expression patterns consistent with physiological human microglia and recapitulate heterogeneity of adult human microglia. Importantly, the engrafted hPSC-derived microglia exhibit dynamic response to cuprizone-induced demyelination and species-specific transcriptomic differences in the expression of neurological disease-risk genes in microglia. This model will serve as a novel tool to study the role of human microglia in brain development and degeneration.
A post-translational modification signature defines changes in soluble tau correlating with oligomerization in early stage Alzheimer’s disease brain
Authors: Ercan-Herbst Ebru , Schöndorf David C. , Behrendt Annika , Klaus Bernd , Ramos Borja Gomez , Weber Christian , Ehrnhoefer Dagmar E. 
Published: April 2019

AbstractTau is a microtubule-binding protein that can receive various post-translational modifications (PTMs) including phosphorylation, methylation, acetylation, glycosylation, nitration, sumoylation and truncation. Hyperphosphorylation of tau is linked to its aggregation and the formation of neurofibrillary tangles (NFTs), which are a hallmark of Alzheimer’s disease (AD). While more than 70 phosphorylation sites have been detected previously on NFT tau, studies of oligomeric and detergent-soluble tau in human brains during the early stages of AD are lacking. Here we apply a comprehensive electrochemiluminescence ELISA assay to analyze twenty-five different PTM sites as well as tau oligomerization in control and sporadic AD brain. The samples were classified as Braak stages 0-I, II or III-IV, respectively, corresponding to the progression of microscopically detectable tau pathology throughout different brain regions. We find that soluble tau oligomers are strongly increased at Braak stages III-IV in all brain regions under investigation, including the temporal cortex, which does not contain NFTs at this stage of pathology. We additionally identified five phosphorylation sites that are specifically and consistently increased across the entorhinal cortex, hippocampus and temporal cortex in the same donors. Three of these sites correlate with tau oligomerization in all three brain regions, but do not overlap with the epitopes of phospho-sensitive antibodies commonly used for the immunohistochemical detection of NFTs. Our results thus suggest that soluble oligomers are characterized by a small set of specific phosphorylation events that differ from those dominating in mature NFTs and shed light on early PTM changes of tau during AD pathogenesis in human brains.
Drosophilafemale-specific brain neuron elicits persistent position- and direction-selective male-like social behaviors
Authors: Wu Yang , Bidaye Salil S. , Mahringer David 
Published: April 2019

SummaryLatent neural circuitry in the female brain encoding male-like mating behaviors has been revealed in both mice and flies. InDrosophila, a key component of this circuitry consists of thedoublesex-expressing pC1 neurons, which were deemed to exist in both sexes and function based on the amount of cells being activated. Here, we identify pC1-alpha, a female-specific subtype of pC1, as responsible for inducing persistent male-like social behaviors in females. We demonstrate that activation of a single pC1-alpha neuron is sufficient for such induction in a position- and direction-selective manner, and activity of pC1-alpha neurons as a whole is indispensable for maintaining normal sexual receptivity. These dual functions of pC1-alpha may require different neurotransmission, with acetylcholine specifically required for the former but not the latter. Our findings suggest that pC1-alpha may be the female counterpart of male P1 due to their shared similarities in morphology, lineage, and social promoting function.
Mycobacterium tuberculosis cording in the cytosol of live lymphatic endothelial cells
Authors: Lerner Thomas R. , Queval Christophe J. , Lai Rachel P. , Russell Matthew , Fearns Antony , Greenwood Daniel J. , Collinson Lucy , Wilkinson Robert J. , Gutierrez Maximiliano G. 
Published: April 2019

AbstractThe ability of Mycobacterium tuberculosis to form serpentine cords is intrinsically related to its virulence, but specifically how M. tuberculosis cording contributes to pathogenesis remains obscure. We show that several M. tuberculosis clinical isolates form intracellular cords in primary human lymphatic endothelial cells (hLEC) in vitro and also in the lymph nodes of patients with tuberculosis. We identified via RNA-seq a transcriptional programme in hLEC that activates cellular pro-survival and cytosolic surveillance of intracellular pathogens pathways. Consistent with this, cytosolic access of hLEC is required for intracellular M. tuberculosis cording; and cord formation is dependent on the M. tuberculosis ESX-1 type VII secretion system and the mycobacterial lipid PDIM. Finally, we show that M. tuberculosis cording is a novel size-dependent mechanism used by the pathogen to evade xenophagy in the cytosol of endothelial cells. These results provide a mechanism that explains the long-standing association between M. tuberculosis cording and virulence.