bluuebunny/crossref_metadata_2025 huggingface dataset:
The phylogenetic placement of Australian Linderniaceae and implications for generic taxonomy
Authors: Biffin Ed , Barker W. R. (Bill) , Wannan Bruce , Liang Yi-Shuo
Published: July 2018

The taxonomy of Linderniaceae has been considered difficult, particularly in the establishment of a stable generic framework. The prevailing approach in Australia and globally has been to adopt a broad concept of Lindernia encompassing several segregates that have at various times been recognised as genera or subgeneric taxa. A recent global conspectus drawing on molecular phylogeny returned Lindernia to a narrower circumscription and also retained several long-recognised and more recently established genera. It included a polyphyletic Vandellia, encompassing many Australian species previously accepted as belonging in Lindernia. Here, we test these generic concepts using the phylogenetic analysis of plastid matK DNA sequences, including representatives of Australian Linderniaceae. We propose a generic taxonomy that resolves existing polyphyly and balances the need for name changes against the information conveyed by generic names. Our concept of Lindernia recognises three monophyletic subgenera. Evidence is insufficient to determine whether Micranthemum should be subsumed in Lindernia or remains a close ally with a sister relationship to it. In light of our findings, we return most of the Australian species to Lindernia; we also establish for the first time: Lindernia subg. Ilysanthes (Raf.) Wannan, W.R.Barker & Y.S.Liang, based on Ilysanthes Raf.; a replacement name Yamazakia W.R.Barker, Y.S.Liang & Wannan for Tittmannia Rchb. nom. rej., with consequential combinations Y. viscosa (Hornem.) W.R.Barker, Y.S.Liang & Wannan, based on Gratiola viscosa Hornem. and Y. pusilla W.R.Barker, Y.S.Liang & Wannan, based on Gratiola pusilla Willd.; and, in expanding Torenia, the combination Tor. anagallis (Burm.f.) Wannan, W.R.Barker & Y.S.Liang, based on Ruellia anagallis Burm.f.
Characters of the inferior ovary of Myrteae (Myrtaceae) and their implication in the evolutionary history of the tribe
Authors: Harthman Vanessa de C. , de Souza Luiz A. , Lucas Eve J.
Published: July 2018

Myrtaceae is commonly known to have an inferior ovary of appendicular, receptacular or mixed origin. Other characters of the ovary, such as the number of carpels, number of locules, vascularisation pattern, number of ovules, placentation and presence of compitum have also been of interest to researchers aiming to better understand the evolutionary history of the tribe. In the present study, aspects of the structure of the inferior ovary of 21 species of Myrteae are analysed and reviewed as potential characters for better understanding the evolutionary history of Myrteae. Flower buds were embedded in historesin and paraplast and sectioned transversely and longitudinally with a rotary microtome. Results suggested that most species have an inferior ovary of appendicular origin and that a compitum, or compitum tissue, is present in all species analysed, differing only in the degree of development. Number of carpels and locules vary, with most species having two locules. Vascular supply is transeptal and axial, the latter being the most common condition in the investigated species. Data presented here enhance current evolutionary understanding of the tribe and its history. Results indicated that the inferior ovary of ancestral Myrteae may has had an appendicular origin, that the presence and nature of the compitum may have a positive effect on fertilisation efficiency and a relationship with number of ovules and that transepetal vascular supply may be taxonomically useful to define large groups such as Pimenta and Eugenia.
Reliable analysis of volatile compounds from small samples of Eucalyptus magnificata (Myrtaceae)
Authors: Collins Timothy L. , Andrew Rose L. , Greatrex Ben W. , Bruhl Jeremy J.
Published: July 2018

Phytochemistry is a source of data for plant systematics. This tool has much more value if herbarium specimens can be used without major damage and if results are comparable with fresh samples. A modified method for the solvent extraction of eucalypt leaf oils for phytochemical analysis and chemotaxonomy studies, including historical herbarium samples by gas chromatography–mass spectrometry (GC-MS), has been statistically assessed using Eucalyptus magnificata L.A.S.Johnson & K.D.Hill leaves. Leaf sample size was reduced by a factor of 250 to minimise damage to herbarium specimens, reduce solvent volume and simplify preparation of solvent extract before analysis. Leaf sampling treatments assessed the effects of the number of leaves and post-harvest air-drying on variation in components in the solvent extract. The results showed no statistically significant effect of leaf mass or the number of leaves used in GC-MS analyses on the precision of the measurements, but a significant difference among treatments for some oil constituents, particularly 1,8-cineole. Most differences in terpenoid concentration were due to variation among plants rather than extraction treatments. Extracts from air-dried herbarium leaves up to 44 years old were directly comparable with those from fresh leaves. Solvent extraction in 2 mL GC-MS vials of ~0.5 cm2 (16 mg) of leaf material, using fragments of fresh or air-dried leaves, drastically reduced sample and solvent volumes and showed that sampling from E. magnificata herbarium specimens for chemotaxonomy and chemotyping is a valid method, enabling broader sampling with much lower costs than for traditional fieldwork collections.
Rapid diffusion-state switching underlies stable cytoplasmic gradients in the
Caenorhabditis elegans
zygote
Authors: Wu Youjun , Han Bingjie , Li Younan , Munro Edwin , Odde David J. , Griffin Erik E.
Published: July 2018

Significance

Intracellular concentration gradients regulate essential processes including the organization of the mitotic spindle, cytokinesis, and cell polarity. Unlike tissue-scale gradients, little is known about how intracellular gradients form. We used single-particle tracking to characterize the behaviors of individual molecules that sculpt gradients in the cytoplasm of the
Caenorhabditis elegans
zygote. Our findings suggest that MEX-5 and PIE-1 rapidly switch between fast- and slow-diffusing states with kinetics that vary along the axis of the cell. As a consequence, slow-diffusing MEX-5 and PIE-1 particles are highly polarized, giving rise to their respective gradients. Using mathematical modeling, we show that rapid diffusion-state switching can quickly pattern gradients across a range of temporal and spatial scales.
Enhancing antibody-dependent cell-mediated cytotoxicity: a strategy for improving antibody-based immunotherapy
Authors: Zahavi David , AlDeghaither Dalal , O’Connell Allison , Weiner Louis M
Published: July 2018

The targeting of surface antigens expressed on tumor cells by monoclonal antibodies (mAbs) has revolutionized cancer therapeutics. One mechanism of action of antibody-based immunotherapy is the activation of immune effector cells to mediate antibody-dependent cell-mediated cytotoxicity (ADCC). This review will summarize the process of ADCC, its important role in the efficacy of mAb therapy, how to measure it, and finally future strategies for antibody design that can take advantage of it to improve clinical performance.
Numerical Analysis of Bifurcation Angles and Branch Patterns in Intracranial Aneurysm Formation
Authors: Sasaki Tetsuo , Kakizawa Yukinari , Yoshino Masato , Fujii Yasuhiro , Yoroi Ikumi , Ichikawa Yozo , Horiuchi Tetsuyoshi , Hongo Kazuhiro
Published: July 2018

BACKGROUND

Hemodynamic factors, especially wall shear stress (WSS), are generally thought to play an important role in intracranial aneurysm (IA) formation. IAs frequently occur at bifurcation apices, where the vessels are exposed to the impact of WSS.

OBJECTIVE

To elucidate the relationship between bifurcation geometry and WSS for IA formation.

METHODS

Twenty-one bifurcation models varying in branch angles and branch diameters were made with 3-dimensional computer-aided design software. In all models, the value of maximum WSS (WSSMAX), the area of high WSS (AREA), and the magnitude of wall shear force over AREA (

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) were investigated by the steady-flow simulation of computational fluid dynamics.

RESULTS

On the basis of statistical analysis, WSSMAX tended to be high when the bifurcation angle and/or branch diameter was small. AREA and

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significantly increase as the bifurcation and/or the branch angle became larger.

CONCLUSION

The magnitude of WSS strongly correlated with bifurcation geometry. In addition to high WSS, AREA and

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were thought to affect IA formation. Observed bifurcation geometry may predict IA formation. Large branch angles and small branch may increase the risk of IA formation.
Henry David Thoreau
Authors: Robinson David M.
Published: July 2018

Henry David Thoreau (b. 1817–d. 1862) is best known as the author of Walden (1854), a pivotal work in American nature writing, and “Civil Disobedience” (1849), an influential call to resist war and slavery. Soon after graduating from Harvard College in 1836, Thoreau was befriended by Ralph Waldo Emerson, whose Nature (1836) depicted the natural world as a book of spiritual and ethical wisdom. Emerson encouraged Thoreau’s writing and journal keeping, and provided space on his property near Walden Pond for a writing retreat. The book that Thoreau wrote there, A Week on the Concord and Merrimack Rivers (1849), was a disappointing commercial failure. However, Thoreau’s effort to explain his experiment in solitude to his Concord neighbors yielded Walden, a literary masterpiece. Walden presented not only a moving description of a life close to nature as the seasons move through the year, but also a scalding critique of social institutions, conventional politics, and the deadness of conformist life. The writing of Walden, completed after Thoreau’s 1847 return to Concord, was an extended process in which Thoreau worked through seven drafts. Midway through the composition, in the early 1850s, Thoreau underwent an intellectual reorientation that can be described as a conversion from poet-philosopher to naturalist-scientist. He devoted effort to his Journal as a record of nature observation during his daily hikes. The gathering and organization of the particular facts of natural history gradually became his principal task until his death in 1862. His developing naturalist sensibility is evident in essays such as “Walking,” “Wild Apples,” and “Autumnal Tints.” These works retained his descriptive craft and vital prose style, and demonstrated his observational practice in the natural world. These essays were published in the early 1860s, but other projects such as Wild Fruits and his seasonal “Kalendar” of Concord remained unfinished. These and other works have been brought to life by recent research and scholarly editing of his surviving manuscripts. The recent discovery that Thoreau’s seasonal records could serve as a source for the scientific measurement of climate change has brought a new attention to the value of his later natural history investigations, showing him as a naturalist fully in step with the developments of 19th-century science. Thoreau’s antislavery fervor increased as the Civil War approached, and he followed the publication of “Civil Disobedience” with political essays characterized by an ardent condemnation of slavery and an impassioned defense of abolitionist John Brown.
Evolutionary Ecology of Communities
Authors: Cavender-Bares Jeannine , Kothari Shan , Pearse Will
Published: July 2018

Ecological communities are composed of interacting or potentially interacting organisms. Communities do not evolve per se; rather, they shift in composition, diversity, and structure through time. The assembly of local communities is influenced by both regional factors and local processes, each of which can influence evolutionary patterns and processes within those communities. We start by discussing early ecological and evolutionary debates on the nature of communities and then consider regional-historical perspectives codified by later researchers. We then consider recent research on the phylogenetic structure of communities, considering the myriad local and long-term biogeographic and macroevolutionary processes that can affect it. On shorter evolutionary timescales, we briefly treat the literature in community genetics and eco-evolutionary dynamics, which shows how community interactions can exert evolutionary pressures that then have further consequences at the community and ecosystem scales. In these sections, we mostly draw from studies on plant communities, but we also consider trophic interactions, particularly plant-insect interactions, and animal community guilds, such as Anolis lizards and dragonflies. We discuss the importance of an evolutionary perspective on communities for understanding ecosystem processes, and its relevance for conservation and restoration. Finally, we discuss seminal methods to examine the consequences of evolutionary processes for community assembly.
Improved analytical model for the mass distribution in S-type galaxies
Authors: Lipovka Anton A
Published: July 2018

We propose a potential function that describes the gravitational potential of a spiral galaxy. We suggest a corresponding density distribution function which is simpler and more convenient for calculation when compared, for example, with the Miyamoto–Nagai (MN) one. The density distribution functions corresponding to MN and to our potential are compared for the Galaxy. Convenient analytical expressions for the corresponding rotation curves and the total baryon mass of a galaxy are suggested.
Upregulation of microRNA‐351 exerts protective effects during sepsis by ameliorating skeletal muscle wasting through the Tead‐4‐mediated blockade of the Hippo signaling pathway
Authors: Zhang Li‐Na , Tian Hui , Zhou Xiu‐Li , Tian Suo‐Chen , Zhang Xi‐Hong , Wu Tie‐Jun
Published: July 2018

Sepsis‐induced skeletal muscle wasting may lead to various severe clinical consequences. Understanding molecular mechanisms of the regulation of the loss of skeletal muscle mass in septic patients remains a significant clinical challenge. The current study was conducted to establish septic mouse models to explore the relationship between microRNA (miR)‐351 and the transcription element apical (TEA) domain transcription factor (Tead)‐4 gene and to investigate its effects on the skeletal muscle through mediating the Hippo signaling pathway in mice with acute sepsis. A total of 60 mice were collected to establish mouse models of acute sepsis. The positive expression rate of Tead‐4 and the apoptotic index (AI) were measured. A dual‐luciferase reporter gene assay was conducted to verify the targeting relationship between miR‐351 and Tead‐4. Furthermore, the muscle fiber diameter (MFD) and area (MFA) and the content of 3‐methylhistidine (3‐MH) and tyrosine (Tyr) were assessed. The expression levels of miR‐351, p38‐MAPK, Yes‐associated protein, Tead‐4, B‐cell lymphoma X protein (Bax), and Caspase‐3 were determined with quantitative RT‐PCR and Western blot analysis. Finally, cell viability, apoptosis, and levels of inflammatory factors, including IL‐1β, IL‐6, IGF‐1, TNF‐α, and monocyte chemoattractant protein‐1 were detected by 3‐(4, 5‐dimethylthiazol‐2‐yl)‐2, 5‐diphenyltetrazolium bromide assay, flow cytometry, and ELISA. Initially, Tead‐4 protein expression was higher in skeletal muscle tissues of mice with acute sepsis. Tead‐4 was identified to negatively regulate miR‐351. Upregulation of miR‐351 increased MFA and MFD, muscle weight water content, Bcl‐2 expression levels, and cell viability. Up‐regulation of miR‐351 reduced AI; 3‐MH and Tyr content; positive expression of Tead‐4 protein; the expression levels of p38‐MAPK, Yap, Tead‐4, Bax, and Caspase‐3; apoptosis; and inflammatory responses. The current study demonstrated that up‐regulation of miR‐351 inhibits the degradation of skeletal muscle protein and the atrophy of skeletal muscle in mice with acute sepsis by targeting Tead‐4 through suppression of the Hippo signaling pathway. Thus, miR‐351 overexpression may be a future therapeutic strategy for acute sepsis.—Zhang, L.‐N., Tian, H., Zhou, X.‐L., Tian, S.‐C., Zhang, X.‐H., Wu, T.‐J. Upregulation of microRNA‐351 exerts protective effects during sepsis by ameliorating skeletal muscle wasting through the Tead‐4‐mediated blockade of the Hippo signaling pathway. FASEB J. 32, 6934–6947 (2018). www.fasebj.org
H+- and Na+-elicited swift changes of the microtubule system in the biflagellated green algaChlamydomonas
Authors: Liu Yi , Visetsouk Mike , Mynlieff Michelle , Qin Hongmin , Lechtreck Karl F. , Yang Pinfen
Published: July 2018

The microtubule cytoskeletal system is integral to diverse cellular processes. Although microtubules are known for dynamic instability, the system is tightly controlled in typical interphase animal cells. In contrast, diverse evidence suggests that the system is mercurial in the unicellular fresh water green alga,Chlamydomonas, but intense autofluorescence from photosynthesis pigments has hindered the investigation. By expressing a bright fluorescent reporter protein at the endogenous level, we demonstrate in real time discreet sweeping changes in algal microtubules elicited by fluctuation of intracellular H+and Na+. These results suggest disparate sensitivity of this vital yet delicate system in diverse organisms; and illuminate how pH may drive crucial cellular processes; how plants respond to, and perhaps sense stresses; and how many species could be susceptible to accelerated changes in global environments.
Sensory Over-Responsivity: Parent Report, Direct Assessment Measures, and Neural Architecture
Authors: Tavassoli Teresa , Brandes-Aitken Anne , Chu Robyn , Porter Lisa , Schoen Sarah , Miller Lucy Jane , Gerdes Molly Rae , Owen Julia , Mukherjee Pratik , Marco Elysa J.
Published: July 2018

Background

Sensory processing differences are common across neurodevelopmental disorders. Thus, reliable measures are needed to understand biologic underpinnings of these differences. This study aims to define a scoring methodology specific to tactile (TOR) and auditory (AOR) over-responsivity. Second, using MRI Diffusion Tensor Imaging, we seek to determine whether children with AOR show measurable differences in their white matter integrity.

Methods

This study includes children with AOR and TOR from a mixed neurodevelopmental disorders cohort including autism and sensory processing dysfunction (n= 176) as well as neurotypical children (n= 128). We established cut-off scores for over-responsivity using the parent report: Short Sensory Profile (SSP), and the direct assessment: Sensory Processing-Three Dimensions:Assessment (SP-3D:A). Group comparisons, based on AOR phenotype, were then conducted comparing the white matter fractional anisotropy in 23 regions of interest.

Results

Using the direct assessment, 31% of the children with neurodevelopmental disorders had AOR and 27% had TOR. The Inter-test-agreement between SSP and SP-3D:A for AOR was 65% and TOR was 50%. Children with AOR had three white matter tracts showing decreased fractional anisotropy relative to children without AOR.

Conclusions

This study identified cut scores for AOR and TOR using the SSP parent report and SP-3D:A observation. A combination of questionnaire and direct observation measures should be used in clinical and research settings. The SSP parent report and SP-3D:A direct observation ratings overlapped moderately for sensory related behaviors. Based on these initial structural neuroimaging results, we suggest a putative neural network may contribute to AOR.
Genomics ofCryptococcus neoformans
Authors: Ashton PM , Thanh LT , Trieu PH , Van Anh D , Trinh NM , Beardsley J , Kibengo F , Chierakul W , Dance DAB , Hung LQ , Chau NVV , Tung NLN , Chan AK , Thwaites GE , Lalloo DG , Anscombe C , Nhat LTH , Perfect J , Dougan G , Baker S , Harris S , Day JN
Published: July 2018

C. neoformansvar.grubii(C. neoformans) is an environmentally acquired pathogen causing 181 000 HIV-associated deaths each year. We used whole genome sequencing (WGS) to characterise 699 isolates, primarilyC. neoformansfrom HIV-infected patients, from 5 countries in Asia and Africa. We found that 91% of our clinical isolates belonged to one of three highly clonal sub-clades of VNIa, which we have termed VNIa-4, VNIa-5 and VNIa-93. Parsimony analysis revealed frequent, long distance transmissions ofC. neoformans; international transmissions took place on 13% of VNIa-4 branches, and intercontinental transmissions on 7% of VNIa-93 branches. The median length of within sub-clade internal branches was 3-6 SNPs, while terminal branches were 44.5-77.5 SNPs. The short median internal branches were partly driven by the large number (12-15% of internal branches) of polytomies in the within-sub-clade trees. To simultaneously explain our observation of no apparent molecular clock, short internal branches and frequent polytomies we hypothesise thatC. neoformansVNIa spends much of its time in the environment in a quiescent state, while, when it is sampled, it has almost always undergone an extended period of growth. Infections with VNIa-93 were associated with a significantly reduced risk of death by 10 weeks compared with infections with VNIa-4 (Hazard Ratio = 0.45, p = 0.003). We detected a recombination in the mitochondrial sequence of VNIa-5, suggesting that mitochondria could be involved in the propensity of this sub-clade to infect HIV-uninfected patients. These data highlight the insight into the biology and epidemiology of pathogenic fungi which can be gained from WGS data.
Assessing the impact of taxon resolution on network structure, with implication for comparative ecology
Authors: Hemprich-Bennett David R. , Oliveira Hernani F. M. , Le Comber Steven C. , Rossiter Stephen J. , Clare Elizabeth L.
Published: July 2018

Constructing networks has become an indispensable approach in understanding how different taxa interact. However, methodologies vary widely among studies, potentially limiting our ability to meaningfully compare results. In particular, how network architecture is influenced by the extent to which nodes are resolved to either taxa or taxonomic units is poorly understood. To address this, here we collate nine datasets of ecological interactions, from both observations and DNA metabarcoding, and construct networks under a range of commonly-used node resolutions. We demonstrate that small changes in node resolution can cause wide variation in almost all key metric values, including robustness and nestedness. Moreover, relative values of metrics such as robustness were seen to fluctuate continuously with node resolution, thereby potentially confounding comparisons of networks, as well as interpretations concerning their constituent ecological interactions. These findings highlight the need for care when comparing networks, especially where these differ with respect to node resolution.

Statement of authorship

DRHB, SJR and ELC conceived of the project, DRHB facilitated fieldwork in Malaysia, DRHB, HFMO and ELC undertook field collections, DRHB, SCLC and HFMO analysed the data, and DRHB wrote the manuscript with input from all authors.

Data Accessibility Statement

All data used in this analysis will be archived in Dryad and made available by DOI. Specific analysis scripts are available on GitHub with links given in the manuscript.
MeCP2 isoform e1 mutant mice recapitulate motor and metabolic phenotypes of Rett syndrome
Authors: LaSalle Janine M.
Published: July 2018

Mutations in the X-linked geneMECP2cause the majority of Rett syndrome (RTT) cases. Two differentially spliced isoforms of exons 1 and 2 (MeCP2-e1 and MeCP2-e2) contribute to the diverse functions of MeCP2, but only mutations in exon 1, not exon 2, are observed in RTT. We previously described an isoform-specific MeCP2-e1 deficient male mouse model of a human RTT mutation that lacks MeCP2-e1 while preserving expression of MeCP2-e2. However, RTT patients are heterozygous females that exhibit delayed and progressive symptom onset beginning in late infancy, including neurologic as well as metabolic, immune, respiratory, and gastrointestinal phenotypes. Consequently, we conducted a longitudinal assessment of symptom development in MeCP2-e1 mutant females and males. A delayed and progressive onset of motor impairments was observed in both female and male MeCP2-e1 mutant mice, including hind limb clasping and motor deficits in gait and balance. Because these motor impairments were significantly impacted by age-dependent increases in body weight, we also investigated metabolic phenotypes at an early stage of disease progression. Both male and female MeCP2-e1 mutants exhibited significantly increased body fat compared to sex-matched wild-type littermates prior to weight differences.Mecp2e1-/ymales exhibited significant metabolic phenotypes of hypoactivity, decreased energy expenditure, increased respiratory exchange ratio (RER), but decreased food intake compared to wildtype. Untargeted analysis of lipid metabolites demonstrated a distinguishable profile in MeCP2-e1 female mutant liver characterized by increased triglycerides. Together these results demonstrate that MeCP2-e1 mutation in mice of both sexes recapitulate early and progressive metabolic and motor phenotypes of human RTT.
Enhancing Percolation in Phosphatic Clay Using Diatoms under Laboratory Conditions
Authors: Horton Melba D. , Vital Dieff , Defino Paul , Spaulding Sarah , Albarelli Gary
Published: July 2018

Clay settling areas are large impoundments brought about by phosphate mining with water-holding capacity that renders it very poor for agriculture and crop production. This study aims to enhance water percolation in phosphatic clay using porous diatom frustules under laboratory conditions. Phosphatic clay collected from settling areas was brought to the laboratory for the experiment. Diatom frustules were purchased commercially and dry samples of the diatom,Didymospheniawere provided by the University of Colorado-Boulder. Oven-dried clay was mixed with diatom frustules into 125 mL centrifuge tubes following a 1:1 volume ratio as experimental set-ups while pure phosphatic clay was used as control. Deionized water was poured into each set-up and the percentage of unpercolated water overlying the sediment, water retained in the sediment particles, water that percolated and passed through the hole of the centrifuge tube were monitored for 48 hours. Results showed that the addition of diatom frustules enhances the percolation of water in the sediment mixture especially those withDidymospheniafrustules. However, this mixture also showed higher percentage of water retained in the sediment particles which could be attributed to the high carbon and organic content brought about by the presence of stalks which is a major component of this species morphology. Considering howDidymospheniadisturbs freshwater habitats, proper management may render it useful for the mitigation of clay settling areas in the land environment. The implication of this on crop production remains to be explored and furtherin situexperimentations need to be conducted.

IMPORTANCE

Clay settling areas abound in places where phosphate mining is conducted. The very fine particles and the chemical property of this phosphatic clay allows it to hold water more than normal clay sediments making the area unstable and less suitable for agricultural use. Studies show that mitigative measures to enhance surface drainage is very costly leaving most areas barren and unused. Diatoms are unicellular algae in various size and shapes with silicified cell walls that are porous and are ubiquitous in aquatic environments. The significance of our research is being able to demonstrate the potential use of diatoms, most especially the genusDidymospheniawhich is regarded as an environmental threat to some habitats, in mitigating the drainage problem in clay settling areas by mixing phosphatic clay with diatom frustules. This process is cost-effective and more importantly provides utilization of a resource that is regarded as nuisance in freshwater environments.
Utilisation of the Prestwick Chemical Library®to identify drugs that inhibit the growth of Mycobacteria
Authors: Kanvatirth Panchali , Jeeves Rose E. , Bacon Joanna , Besra Gurdyal S. , Alderwick Luke J.
Published: July 2018

Tuberculosis (TB) is an infectious bacterial disease that kills approximately 1.3 million people every year. Despite global efforts to reduce both the incidence and mortality associated with TB, the emergence of drug resistant strains has slowed any progress made towards combating the spread of this deadly disease. The current TB drug regimen is inadequate, takes months to complete and poses significant challenges when administering to patients suffering from drug resistant TB. New treatments that are faster, simpler and more affordable are urgently required. Arguably, a good strategy to discover new drugs is to start with an old drug. Here, we have screened a library of 1200 FDA approved drugs from the Prestwick Chemical library®using a GFP microplate assay. Drugs were screened against GFP expressing strains ofMycobacterium smegmatisandMycobacterium bovisBCG as surrogates forMycobacterium tuberculosis,the causative agent of TB in humans. We identified several classes of drugs that displayed antimycobacterial activity against bothM. smegmatisandM. bovisBCG, however each organism also displayed some selectivity towards certain drug classes. Variant analysis of whole genomes sequenced for resistant mutants raised to florfenicol, vanoxerine and pentamidine highlight new pathways that could be exploited in drug repurposing programmes.
Drosophilakinesin-8 stabilises the kinetochore-microtubule interaction
Authors: Edzuka Tomoya , Goshima Gohta
Published: July 2018

Kinesin-8 is required for proper chromosome alignment in a variety of animal and yeast cell types. However, how this conserved motor protein controls chromosome alignment remains unclear, as multiple biochemical activities, including inconsistent ones between studies, have been identified for this motor family. Here, we show thatDrosophilakinesin-8 Klp67A possesses both microtubule (MT) plus-end-stabilising and ‐destabilising activities in addition to commonly observed MT plus-end-directed motility and tubulin-binding activityin vitro, and is required for stable kinetochore-MT attachment during prometaphase in S2 cells In the absence of kinesin-8Klp67A, abnormally-long MTs interact in an “end-on” fashion with kinetochores at normal frequency. However, the interaction was not stable and, once-attached, MTs were frequently detached. This phenotype was rescued by ectopic expression of MT plus-end-stabilising factor CLASP, but not by artificial shortening of MTs. These results suggest that MT-stabilising activity of kinesin-8Klp67Ais critical for stable kinetochore-MT attachment. Finally, human kinesin-8KIF18Awas also shown important to ensure proper MT attachment.
“DoC-feeling”: a new behavioural tool to help diagnose the Minimally Conscious State
Authors: Hermann Bertrand , Goudard Gwen , Courcoux Karine , Valente Mélanie , Labat Sebastien , Despois Lucienne , Bourmaleau Julie , Richard-Gilis Louise , Faugeras Frédéric , Demeret Sophie , Sitt Jacobo D , Naccache Lionel , Rohaut Benjamin
Published: July 2018

Objectives

The clinical distinction between vegetative state/unresponsive wakefulness syndrome (UWS) and minimally conscious state (MCS) is a key step to elaborate a prognosis and formulate an appropriate medical plan for any patient suffering from disorders of consciousness (DoC). However, this assessment is often challenging and may require specialized expertise. In this study, we hypothesized that pooling subjective reports of the level of consciousness of a given patient across several nursing staff members can be used to clinically detect MCS.

Setting and Participants

Patients referred for consciousness assessment were prospectively screened. MCS (target condition) was defined according to the best Coma Recovery Scale-Revised score (CRS-R) obtained from expert physicians (reference standard). “DoC-feeling” score consisted in the median value of multiple ratings of patient’s behavior observation pooled from multiple staff members during a week of hospitalisation (index test). Individual ratings were collected at the end of each shift using a 100mm visual analog scale, blinded from the reference standard. Diagnostic accuracy was evaluated using area under the receiver operating characteristic curve (AUC), sensitivity and specificity metrics.

Results

692 ratings performed by 83 nursing staff members were collected from 47 patients. Twenty patients were in a UWS and 27 in a MCS. DoC-feeling scores obtained by pooling all individual ratings obtained for a given patient were significantly greater in MCS than in UWS patients (59.2 mm [IQR: 27.3-77.3] vs. 7.2 mm [IQR: 2.4-11.4]; p<0.001) yielding an AUC of 0.92 (95%CI: 0.84-0.99).

Conclusions

DoC-feeling capitalizes on the expertise of nursing staff to evaluate patients’ consciousness. Together with the CRS-R as well as with brain imaging, DoC-feeling might improve diagnostic and prognostic accuracy of DoC patients.

Strengths and limitations of this study

We designed a new behavioural tool called “DoC-feeling” to help face the clinical challenge of the detection of Minimally Conscious State in patients suffering from disorders of consciousness (DoC)

“DoC-feeling score” quantifies nursing staff’s subjective perception of patient’s consciousness by pooling multiple assessments obtained from multiple caregivers (“wisdom of the crowds”)

This score which requires no particular training showed a very good accuracy when compared to the gold standard (repeated expert clinical assessment using the Coma Recovery Scale – Revised (CRS-R))

A validation in a separate cohort would help to determine its place in consciousness assessment

This score should be tested not only against the CRS-R but also against brain-imaging techniques to test for its capacity to detect covert signs of consciousness
CHD8 Regulates Cellular Homeostasis and Neuronal Function Genes Across Multiple Models of CHD8 Haploinsufficiency
Authors: Wade A. Ayanna , Lim Kenneth , Catta-Preta Rinaldo , Nord Alex S.
Published: July 2018

The packaging of DNA into chromatin determines the transcriptional potential of cells and is central to eukaryotic gene regulation. Recent sequencing of patient mutations has linked de novo loss-of-function mutations to chromatin remodeling factors with specific, causal roles in neurodevelopmental disorders. Characterizing cellular and molecular phenotypes arising from haploinsufficiency of chromatin remodeling factors could reveal convergent mechanisms of pathology. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeling factor gene and has among the highest de novo loss-of-function mutations rates in patients with autism spectrum disorder (ASD). Mutations to CHD8 are expected to drive neurodevelopmental pathology through global disruptions to gene expression and chromatin state, however, mechanisms associated with CHD8 function have yet to be fully elucidated. We analyzed published transcriptomic and epigenomic data across CHD8 in vitro and in vivo knockdown and knockout models to identify convergent mechanisms of gene regulation by CHD8. We found reproducible high-affinity interactions of CHD8 near promoters of genes necessary for basic cell functions and gene regulation, especially chromatin organization and RNA processing genes. Overlap between CHD8 interaction and differential expression suggests that reduced dosage of CHD8 directly relates to decreased expression of these genes. In addition, genes important for neuronal development and function showed consistent dysregulation, though there was a reduced rate and decreased affinity for CHD8 interactions near these genes. This meta-analysis verifies CHD8 as a critical regulator of gene expression and reveals a consistent set of high affinity CHD8 interaction targets observed across human and mouse in vivo and in vitro studies. Our findings highlight novel core functions of CHD8 and indicate direct and downstream gene regulatory impacts that are likely to be associated with neuropathology underlying CHD8-associated neurodevelopmental disorder.
Dynamic recruitment of single RNAs to processing bodies depends on RNA functionality
Authors: Pitchiaya Sethuramasundaram , Mourao Marcio D.A. , Jalihal Ameya , Xiao Lanbo , Jiang Xia , Chinnaiyan Arul M. , Schnell Santiago , Walter Nils G.
Published: July 2018

Cellular RNAs often colocalize with cytoplasmic, membrane-less ribonucleoprotein (RNP) granules enriched for RNA processing enzymes, termed processing bodies (PBs). Here, we track the dynamic localization of individual miRNAs, mRNAs and long non-coding RNAs (lncRNAs) to PBs using intracellular single-molecule fluorescence microscopy. We find that unused miRNAs stably bind to PBs, whereas functional miRNAs, repressed mRNAs and lncRNAs both transiently and stably localize within either the core or periphery of PBs, albeit to different extents. Consequently, translation potential and positioning of cis-regulatory elements significantly impact PB-localization dynamics of mRNAs. Using computational modeling and supporting experimental approaches we show that phase separation into large PBs attenuates mRNA silencing, suggesting that physiological mRNA turnover predominantly occurs outside of PBs. Instead, our data support a role for PBs in sequestering unused miRNAs to regulate their surveillance and provides a framework for investigating the dynamic assembly of RNP granules by phase separation at single-molecule resolution.
Determining the Mutation Bias of Favipiravir in Influenza Using Next-generation Sequencing
Authors: Goldhill Daniel H. , Langat Pinky , Xie Hongyao , Galiano Monica , Miah Shahjahan , Kellam Paul , Zambon Maria , Lackenby Angie , Barclay Wendy
Published: July 2018

Favipiravir is a broad spectrum antiviral drug that may be used to treat influenza. Previous research has identified that favipiravir likely acts as a mutagen but the precise mutation bias that favipiravir induces in influenza virus RNAs has not been described. Here, we use next-generation sequencing (NGS) with barcoding of individual RNA molecules to accurately and quantitatively detect favipiravir-induced mutations and to sample orders of magnitude more mutations than would be possible through Sanger sequencing. We demonstrate that favipiravir causes mutations and show that favipiravir primarily acts as a guanine analogue and secondarily as an adenine analogue resulting in the accumulation of transition mutations. We also use a standard NGS pipeline to show that the mutagenic effect of favipiravir can be measured by whole genome sequencing of virus.

Importance

New antiviral drugs are needed as a first line of defence in the event of a novel influenza pandemic. Favipiravir is a broad-spectrum antiviral which is effective against influenza. The exact mechanism of how favipiravir works to inhibit influenza is still unclear. We used next-generation sequencing (NGS) to demonstrate that favipiravir causes mutations in influenza RNA. The greater depth of NGS sequence information over traditional sequencing methods allowed us to precisely determine the bias of particular mutations caused by favipiravir. NGS can also be used in a standard diagnostic pipeline to show that favipiravir is acting on the virus by revealing the mutation bias pattern typical to the drug. Our work will aid in testing whether viruses are resistant to favipiravir and may help demonstrate the effect of
favipiravir on viruses in a clinical setting. This will be important if favipiravir is used during a future influenza pandemic.
Emergence of Multidrug-Resistant Uropathogens harboring ESBL, Carbapenem, Aminoglycosides and AmpC resistant genes from Northern India
Authors: Gajamer Varsha Rani , Bhattacharjee Amitabha , Paul Deepjyoti , Ingti Birson , Sarkar Arunabha , Kapil Jyotsna , Singh Ashish Kumar , Pradhan Nilu , Tiwari Hare Krishna
Published: July 2018

Extended-spectrum β-lactamase (ESBL) producing bacteria acts as a serious threat, and its co-existence with other antibiotic resistant gene makes the clinical scenario worse nowadays. Therefore in this study, we investigated the occurrence of ESBL genes coexisting with carbapenem, AmpC and aminoglycoside resistance gene in uropathogens. Out of 1516 urine samples, 454 showed significant bacteriuria with a prevalence rate of 29.94 %. Escherichia coli (n=340) were found to be the most predominant uropathogen followed by Klebsiella pneumoniae (n=92), Pseudomonas aeruginosa (n=10) and Proteus mirabilis (n=9). Among the total uropathogens, sixty-three ESBL-producers were identified which included blaCTX-M-15 (n=32), followed by blaCTX-M-15 + blaOXA-2 (n=15), blaCTX-M-15 + blaOXA-2 + blaTEM (n=6), blaOXA-2 (n=5), blaOXA-2 + blaSHV-76 (n=1), blaTEM+SHV-76 (n= 1) and blaTEM (n=1). All ESBL genes were found on plasmid incompatibility types: HI1, I1, FIA+FIB, FIA and Y and were horizontally transferable. Among 63 ESBL-producers, 59 isolates harboured carbapenem-resistant genes which included blaNDM-5 (n=48), blaNDM-5 + blaOXA-48 (n=5), blaNDM-5 + blaIMP (n=5) and blaNDM-5 + blaIMP + blaVIM (n=1). The ESBL producing uropathogens also harbored 16S rRNA methylase genes which included rmtB (n=9), rmtA (n=4), rmtC (n=1) and ArmA (n=1) followed by AmpC genes which includes CIT (n=8) and DHA-1 (n=1) genes. Imipenem and gentamicin were found to be more effective. We speculating, this is the first report showing the prevalence of multidrug-resistant uropathogens in this area demanding regular surveillance for such resistance mechanisms which will be useful for health personnel to treat ESBL infection and its co-existence with another antibiotic resistance gene.
Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole genome sequencing
Authors: Nordlund Jessica , Marincevic-Zuniga Yanara , Cavelier Lucia , Raine Amanda , Martin Tom , Lundmark Anders , Abrahamsson Jonas , Norén-Nyström Ulrika , Lönnerholm Gudmar , Syvänen Ann-Christine
Published: July 2018

Structural chromosomal rearrangements that may lead to in-frame gene-fusions represent a leading source of information for diagnosis, risk stratification, and prognosis in pediatric acute lymphoblastic leukemia (ALL). However, short-read whole genome sequencing (WGS) technologies struggle to accurately identify and phase such large-scale chromosomal aberrations in cancer genomes. We therefore evaluated linked-read WGS for detection of chromosomal rearrangements in an ALL cell line (REH) and primary samples of varying DNA quality from 12 patients diagnosed with ALL. We assessed the effect of input DNA quality on phased haplotype block size and the detectability of copy number aberrations (CNAs) and structural variants (SVs). Biobanked DNA isolated by standard column-based extraction methods was sufficient to detect chromosomal rearrangements even at low 10x sequencing coverage. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements and aneuploidy assessment. With use of haplotype information from the linked-reads, we also identified additional structural variants, such as a compound heterozygous deletion of ERG in a patient with the DUX4-IGH fusion gene. Thus, linked-read WGS allows detection of important pathogenic variants in ALL genomes at a resolution beyond that of traditional karyotyping or short-read WGS.
“Rapid Eye Movement sleep deprivation of rat generates ROS in the hepatocytes and makes them more susceptible to oxidative stress”
Authors: Pandey Atul , Kar Santosh K
Published: July 2018

Background

Rapid Eye Movement sleep deprivation (REMSD) of rats causes inflammation of the liver and apoptotic cell death of neurons and hepatocytes. Studies also suggest that REMSD are involved with muscle injury, cardiac injury and neurodegerative diseases.

Objective and methods

The aim of this research was to determine whether REMSD of rats would generate reactive oxygen species (ROS) and create oxidative stress in the hepatocytes. We selectively deprived the rats from REM sleep using the standard flower pot method.

Results

We observed that when rats were subjected to REMSD, the levels of ROS in the hepatocytes increased with the increase in the number of days of REMSD by ∼265%, but it returned towards normal levels after recovery sleep for 5 days (∼36%) compared to controls. Nitric oxide synthase (iNOS) gene and protein was found elevated in hepatocytes in response to REM sleep loss as confirmed by real time PCR and western blot analysis compared to controls. The level of nitric oxide (NO) also increased by ∼ 675% in the hepatocytes of REMSD rats as compared to that of control group of animals.

Discussion

We have analyzed the oxidative stress generated and potentiation of hepatocytes against oxidative stress in response to REMSD. Since, REM sleep is known to play an important role for survival of most animals and has important role in maintenance of body physiology. Hence, our findings that loss of REM sleep in hepatocytes of rats can affect the ROS levels and induce iNOS & NO circulation, while making them more susceptible to oxidative stress assumes significance.

Highlights of the study

We observed elevated levels of ROS in the hepatocytes of REM sleep deprived rats.

The hepatocytes of REMSD group of rats were found more susceptible to oxidative stress than that of control groups.

We found increased expression of iNOS gene and nitric oxide synthase protein in the hepatocytes of REMSD rats.

We observed that nitric oxide levels in the hepatocytes of REM sleep deprived rats increased positively with days of REMSD, but returned to its normal levels after 5 days of recovery sleep.
The flower pot method of REM sleep deprivation causes apoptotic cell death in the hepatocytes of rat
Authors: Pandey Atul , Kumar Devesh , Ray Gopesh , Kar Santosh
Published: July 2018

Introduction

The rapid eye movement sleep deprivation (REMSD) of rats relates with increased inflammations, acute phase response, oxidative damage, neuronal cell loss, and neurodegenerative diseases. Whereas, its role outside brain are not well studied. This study tried to explore the causal effect of REM sleep loss on hepatocytes.

Methods

We deprived the rats of REM sleep using standard flower pot method. We focused on liver to see the REMSD affects which controls most of the metabolic processes of the body.

Results

We report here that flower pot induced REMSD causes apoptotic cell death of hepatocytes (~10% by Annexin Assay & ~20% by TUNEL assay). This were further got alleviated up to extent after sleep recovery of 5 days (recovered approximately 8.0% by Annexin Assay & 14% by TUNEL assay). The gene expression and protein level profiling revealed the up-regulation of p53, Bax, Cytochrome c, Caspase 3, and Caspase 9. While, Bcl2 which is an anti-apoptotic protein were down-regulated in response to REMSD. Relentless recovery of 5 days affected the expression pattern of these genes/proteins.

Conclusions

Our study offer great pathological and physiological significance for sleep loss, by inferring the apoptotic cell-death in the hepatocytes of rat. This further signifies the functional and preventive role of REM sleep which is unique to mammals and avians with certain exceptions, as its loss can affect the natural well-being and survival of the individuals.

Highlights of the study

We observed significant apoptosis in the hepatocytes of REMSD group of rats.

Our expression analysis confirmed altered expression for genes p53, Bcl2, Bax, and Caspase-3 after REMSD.

Protein level analysis supported our gene expression results for p53, Bcl2, Bax, Caspase 3 and Caspase 9 after REMSD.

Sleep recovery improved the respective genes and protein expression levels towards normalcy, signifying the functional role of REM sleep.