bluuebunny/crossref_metadata_2025 huggingface dataset:
AmyCo: the Amyloidoses Collection
Authors: Nastou Katerina C , Nasi Georgia I , Tsiolaki Paraskevi L , Litou Zoi I , Iconomidou Vassiliki A
Published: November 2018

Amyloid fibrils are formed when soluble proteins misfold into highly ordered insoluble fibrillar aggregates and affect various organs and tissues. The deposition of amyloid fibrils is the main hallmark of a group of disorders, called amyloidoses. Curiously, fibril deposition has been also recorded as a complication in a number of other pathological conditions, including well-known neurodegenerative or endocrine diseases. To date, amyloidoses are roughly classified, owing to their tremendous heterogeneity. In this work, we introduce AmyCo, a freely available collection of amyloidoses and clinical disorders related to amyloid deposition. AmyCo classifies 74 diseases associated with amyloid deposition into two distinct categories, namely 1) amyloidosis and 2) clinical conditions associated with amyloidosis. Each database entry is annotated with the major protein component (causative protein), other components of amyloid deposits and affected tissues or organs. Database entries are also supplemented with appropriate detailed annotation and are referenced to ICD-10, MeSH, OMIM, PubMed, AmyPro and UniProtKB databases. To our knowledge, AmyCo is the largest repository containing information about amyloidoses and diseases related to amyloid deposition. The AmyCo web interface is available at http://bioinformatics.biol.uoa.gr/amyco.
First estimation of the scale of canonical 5’ splice site GT>GC mutations generating wild-type transcripts and their medical genetic implications
Authors: Lin Jin-Huan , Tang Xin-Ying , Boulling Arnaud , Zou Wen-Bin , Masson Emmanuelle , Fichou Yann , Raud Loann , Tertre Marlène Le , Deng Shun-Jiang , Berlivet Isabelle , Ka Chandran , Mort Matthew , Hayden Matthew , Gac Gerald Le , Cooper David N. , Li Zhao-Shen , Férec Claude , Liao Zhuan , Chen Jian-Min
Published: November 2018

It has long been known that canonical 5’ splice site (5’SS) GT>GC mutations may be compatible with normal splicing. However, to date, the true scale of canonical 5’SS GT>GC mutations generating wild-type transcripts, both in the context of the frequency of such mutations and the level of wild-type transcripts generated from the mutation alleles, remain unknown. Herein, combining data derived from a meta-analysis of 45 informative disease-causing 5’SS GT>GC mutations (from 42 genes) and a cell culture-based full-length gene splicing assay of 103 5’SS GT>GC mutations (from 30 genes), we estimate that ∼15-18% of the canonical GT 5’SSs are capable of generating between 1 and 84% normal transcripts as a consequence of the substitution of GT by GC. We further demonstrate that the canonical 5’SSs whose substitutions of GT by GC generated normal transcripts show stronger complementarity to the 5’ end of U1 snRNA than those sites whose substitutions of GT by GC did not lead to the generation of normal transcripts. We also observed a correlation between the generation of wild-type transcripts and a milder than expected clinical phenotype but found that none of the available splicing prediction tools were able to accurately predict the functional impact of 5’SS GT>GC mutations. Our findings imply that 5’SS GT>GC mutations may not invariably cause human disease but should also help to improve our understanding of the evolutionary processes that accompanied GT>GC subtype switching of U2-type introns in mammals.
Colistin kills bacteria by targeting lipopolysaccharide in the cytoplasmic membrane
Authors: Sabnis Akshay , Hagart Katheryn L. H. , Klöckner Anna , Becce Michele , Evans Lindsay E. , Furniss R. Christopher D. , Mavridou Despoina A. I. , Murphy Ronan , Stevens Molly M. , Davies Jane C. , Larrouy-Maumus Gerald J. , Clarke Thomas B. , Edwards Andrew M.
Published: November 2018

Colistin is an antibiotic of last resort, but has poor efficacy and resistance is a growing problem. Whilst it is well established that colistin disrupts the bacterial outer membrane by selectively targeting lipopolysaccharide (LPS), it was unclear how this led to bacterial killing. We discovered that MCR-1 mediated colistin resistance is due to modified LPS at the cytoplasmic rather than outer membrane. In doing so, we also demonstrated that colistin exerts bactericidal activity by targeting LPS in the cytoplasmic membrane. We then exploited this information to devise a new therapeutic approach. Using the LPS transport inhibitor murepavadin, we were able to cause LPS accumulation in the cytoplasmic membrane, which resulted in increased susceptibility to colistin in vitro and improved treatment efficacy in vivo. These findings reveal new insight into the mechanism by which colistin kills bacteria, providing the foundations for novel approaches to enhance therapeutic outcomes.
SyntrophusConductive Pili Demonstrate that Common Hydrogen-Donating Syntrophs can have a Direct Electron Transfer Option
Authors: Walker David J.F. , Nevin Kelly P. , Holmes Dawn E. , Rotaru Amelia-Elena , Ward Joy E. , Woodard Trevor L. , Zhu Jiaxin , Ueki Toshiyuki , Nonnenmann Stephen S. , McInerney Michael J. , Lovley Derek R.
Published: November 2018

Syntrophic interspecies electron exchange is essential for the stable functioning of diverse anaerobic microbial communities. Hydrogen/formate interspecies electron transfer (HFIT), in which H2and/or formate function as diffusible electron carriers, has been considered to be the primary mechanism for electron sharing because most common syntrophs were thought to lack biochemical components, such as electrically conductive pili (e-pili), necessary for direct interspecies electron transfer (DIET). Here we report thatSyntrophus aciditrophicus, one of the most intensively studied microbial models for HFIT, produces e-pili and can grow via DIET. Pilin genes likely to yield e-pili were found in other genera of hydrogen/formate-producing syntrophs. The finding that DIET is a likely option for diverse syntrophs that are abundant in many anaerobic environments necessitates a reexamination of the paradigm that HFIT is the predominant mechanism for syntrophic electron exchange within anaerobic microbial communities of biogeochemical and practical significance.
Biofilm-associatedMycobacterium abscessuscells have altered antibiotic tolerance and surface glycolipids in Artificial Cystic Fibrosis Sputum Media
Authors: Hunt-Serracin Augusto Cesar , Parks Brian J. , Boll Joseph , Boutte Cara
Published: November 2018

Mycobacterium abscessus(Mab) is a biofilm-forming, multi-drug resistant, non-tuberculous mycobacterial (NTM) pathogen increasingly found in Cystic Fibrosis patients. Antibiotic treatment for these infections is often unsuccessful, partly due toMab’s high intrinsic antibiotic resistance. It is not clear whether antibiotic tolerance caused by biofilm formation also contributes to poor treatment outcomes. We studied the surface glycolipids and antibiotic tolerance ofMabbiofilms grown in Artificial Cystic Fibrosis Sputum (ACFS) media in order to determine how they are affected by nutrient conditions that mimic infection. We found thatMabdisplays more of the virulence lipid trehalose dimycolate when grown in ACFS compared to standard lab media. In ACFS media, biofilm-associated cells are more antibiotic tolerant than planktonic cells in the same well. This contrasts with standard lab medias, where biofilm and planktonic cells are both highly antibiotic tolerant. These results indicate thatMabcell physiology in biofilms depends on environmental factors, and that nutrient conditions found within Cystic Fibrosis infections could contribute to both increased virulence and antibiotic tolerance.
Robotic platform for microinjection into single cells in intact tissue
Authors: Shull Gabriella , Haffner Christiane , Huttner Wieland B. , Taverna Elena , Kodandaramaiah Suhasa B
Published: November 2018

Microinjection into single cells in intact tissue allows the delivery of membrane-impermeant molecules such as nucleic acids and proteins is a powerful technique to study and manipulate the behavior of these cells and, if applicable, their progeny. However, a high level of skill is required to perform such microinjection and is a low-throughput and low-yield process. The automation of microinjection into cells in intact tissue would empower an increasing number of researchers to perform these challenging experiments and could potentially open up new avenues of experimentation. We have developed the ‘Autoinjector’, a robot that utilizes images acquired from a microscope to guide a microinjection needle into tissue to deliver femtoliter volumes of liquids into single cells. The robotic operation enables microinjection of hundreds of cells within a single organotypic slice, resulting in an overall yield that is an order of magnitude greater than manual microinjection. We validated the performance of the Autoinjector by microinjecting both apical progenitors (APs) and newborn neurons in the embryonic mouse telencephalon, APs in the embryonic mouse hindbrain, and neurons in fetal human brain tissue. We demonstrate the capability of the Autoinjector to deliver exogenous mRNA into APs. Further, we used the Autoinjector to systematically study gap-junctional communication between neural progenitors in the embryonic mouse telencephalon and found that apical contact is a characteristic feature of the cells that are part of a gap junction-coupled cell cluster. The throughput and versatility of the Autoinjector will not only render microinjection a broadly accessible high-performance cell manipulation technique but will also provide a powerful new platform for bioengineering and biotechnology for performing single-cell analyses in intact tissue.
Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth
Authors: Chen Hung-Chang , Eling Nils , Martinez-Jimenez Celia Pilar , O’Brien Louise McNeill , Marioni John C. , Odom Duncan T. , la Roche Maike de
Published: November 2018

How age-associated decline of immune function leads to increased cancer incidence is poorly understood. Here, we have characterized the cellular composition of the γδ T cell pool in peripheral lymph nodes (pLNs) upon ageing. We found that ageing has minimal cell-intrinsic effects on function and global gene expression of γδ T cells, and TCRγδ diversity remained stable. However, ageing altered TCRδ chain usage and clonal structure of γδ T cell subsets. Importantly, IL-17-producing γδ17 T cells dominated the γδ T cell pool of aged mice - mainly due to the selective expansion of Vγ6+γδ17 T cells and augmented γδ17-polarisation of Vγ4+ T cells. Expansion of the γδ17 T cell compartment was supported by increased Interleukin-7 expression in the T cell zone of old mice. In a Lewis lung cancer model, pro-tumourigenic Vγ6+γδ17 T cells were exclusively activated in the tumour-draining LN and their infiltration into the tumour correlated with increased tumour size in aged mice. Thus, upon ageing, substantial compositional changes of γδ T cell pool in a dysregulated pLN microenvironment promote tumour growth.
FAM83D directs protein kinase CK1α to the mitotic spindle for proper spindle positioning
Authors: Fulcher Luke J. , He Zhengcheng , Mei Lin , Macartney Thomas J. , Wood Nicola T. , Prescott Alan R. , Whigham Arlene J. , Varghese Joby , Gourlay Robert , Ball Graeme , Clarke Rosemary , Campbell David G. , Maxwell Christopher A. , Sapkota Gopal P.
Published: November 2018

The concerted action of many protein kinases helps orchestrate the error-free progression through mitosis of mammalian cells. The roles and regulation of some prominent mitotic kinases, such as cyclin-dependent kinases, are well-established. However, these and other known mitotic kinases alone cannot account for the extent of protein phosphorylation that has been reported during mammalian mitosis. Here we demonstrate that CK1α, of the casein kinase 1 family of protein kinases, localises to the spindle and is required for proper spindle-positioning and timely cell division. CK1α is recruited to the spindle by FAM83D, and cells devoid ofFAM83D, or those harbouring CK1α-binding-deficientFAM83DF283A/F283Aknockin mutation, display pronounced spindle-positioning defects, and a prolonged mitosis. RestoringFAM83Dat the endogenous locus inFAM83D-/-cells, or artificially delivering CK1α to the spindle inFAM83DF283A/F283Acells, rescues these defects. These findings implicate CK1α as new mitotic kinase that orchestrates the kinetics and orientation of cell division.
The Range of Cooperativity Modulates Actin Binding Protein Cluster Size Density and Dynamics
Authors: Goff T. Le , Michelot A.
Published: November 2018

The actin cytoskeleton is composed of multiple networks which are specialized for several processes such as cell motility or cell division. Each of these networks are composed of organized actin microfilaments which are decorated with specific sets of actin binding proteins (ABPs). The molecular mechanisms guiding ABPs to specific actin networks are still poorly understood, but cooperativity, the mechanism by which the binding of an ABP is positively influenced by proximal bound ABPs, plays a crucial role in generating locally dense stretches of ABPs. Cooperative binding is characterized by its amplitude, but also by the range at which its effects are propagated along an actin filament through long-range allosteric interactions. The range of these allosteric effects is still debated, but is likely to be significant at the lengthscale of actin filaments in cells. Here, we investigated how cooperativity influences the clustering of ABPs, using a stochastic computational model of binding of ABPs to actin filaments. The model reproduces the formation of ABP clusters observed experimentally at the single filament scale, and provides a theoretical estimation of the range of cooperativity for proteins such as ADF/cofilin. We found that both the amplitude and the spatial range of cooperativity dramatically impact the properties of clustering. However, the parameters of cooperativity modulate differently the rate of assembly, size and dynamics of the ABP clusters, suggesting that cooperativity is an efficient mechanism to regulate precisely the recruitment of ABPs in cells. This work provides a more general framework for future understanding of how actin networks acquire distinct and specific protein compositions from a common cytoplasm.
Neural circuit robustness to acute, global physiological perturbations
Authors: Ratliff Jacob , Marder Eve , O’Leary Timothy
Published: November 2018

Neural function depends on underlying physiological processes that are highly sensitive to physical variables such as temperature. However, some robustness to perturbations in these variables manifests at the circuit level, suggesting that circuit properties are organized to tolerate consistent changes in underlying parameters. We show that a crustacean pacemaker circuit is robust to two global perturbations - temperature and pH - that differentially alter circuit properties. Consistent with high variability in underlying circuit parameters, we find that the critical temperatures and pH values where circuit activity breaks down vary widely across animals. Despite variability in critical points the network state transitions at these critical points are consistent, implying that qualitative circuit dynamics are preserved across animals, in spite of high quantitative parameter variability. Surprisingly, robustness perturbations in pH only moderately affect temperature robustness. Thus, robustness to a global perturbation does not necessarily imply sensitivity to other global perturbations.
Ergodicity analysis and antithetic integral control of a class of stochastic reaction networks with delays
Authors: Briat Corentin , Khammash Mustafa
Published: November 2018

Delays are important phenomena arising in a wide variety of real world systems, including biological ones, because of diffusion/propagation effects or as simplifying modeling elements. We propose here to consider delayed stochastic reaction networks, a class of networks that has been relatively few studied until now. The difficulty in analyzing them resides in the fact that their state-space is infinite-dimensional. We demonstrate here that by restricting the delays to be phase-type distributed, one can represent the associated delayed reaction network as a reaction network with finite-dimensional state-space. This can be achieved by suitably adding chemical species and reactions to the delay-free network following a simple algorithm which is fully characterized. Since phase-type distributions are dense in the set of probability distributions, they can approximate any distribution arbitrarily closely and this makes their consideration only a bit restrictive. As the state-space remains finite-dimensional, usual tools developed for non-delayed reaction network directly apply. In particular, we prove, for unimolecular mass-action reaction networks, that the delayed stochastic reaction network is ergodic if and only if the delay-free network is ergodic as well. Bimolecular reactions are more difficult to consider but slightly stronger analogous results are nevertheless obtained. These results demonstrate that delays have little to no harm to the ergodicity property of reaction networks as long as the delays are phase-type distributed, and this holds regardless the complexity of their distribution. We also prove that the presence of those delays adds convolution terms in the moment equation but does not change the value of the stationary means compared to the delay-free case. The covariance, however, is influenced by the presence of the delays. Finally, the control of a certain class of delayed stochastic reaction network using a delayed antithetic integral controller is considered. It is proven that this controller achieves its goal provided that the delay-free network satisfy the conditions of ergodicity and output-controllability.
Intracellular pH controls Wnt signaling downstream of glycolysis in the vertebrate embryo
Authors: Oginuma Masayuki , Harima Yukiko , Xiong Fengzhu , Pourquié Olivier
Published: November 2018

Formation of the body of vertebrate embryos proceeds sequentially by posterior addition of tissues. While this process depends on aerobic glycolysis acting upstream of Wnt signaling in tail bud cells, the molecular details of this regulation are unknown. Here we used chicken embryos and human tail bud-like cells differentiatedin vitrofrom iPS cells to show that glycolysis acts by increasing the intracellular pH (pHi) of tail bud cells. This promotes β-catenin acetylation leading to Wnt signaling activation and the choice of a mesodermal fate at the expense of the neural fate in tail bud precursors. Our data suggest that by increasing the pHi of tail bud cells, aerobic glycolysis creates a favorable chemical environment for non-enzymatic acetylation of β-catenin, ultimately triggering Wnt signaling.
Defining developmental diversification of diencephalon neurons through single-cell gene expression profiling
Authors: Guo Qiuxia , Li James Y. H.
Published: November 2018

The embryonic diencephalon gives rise to diverse neuronal cell types, which form complex integration centers and intricate relay stations of the vertebrate forebrain. Prior anecdotal gene expression studies suggest several developmental compartments within the developing diencephalon. In the current study, we utilized single-cell RNA sequencing to profile transcriptomes of dissociated cells from the diencephalon of E12.5 mouse embryos. Through analysis of unbiased transcriptional data, we identified the divergence of different progenitors, intermediate progenitors, and emerging neuronal cell types. After mapping the identified cell groups to their spatial origins, we were able to characterize the molecular features across different cell types and cell states, arising from various diencephalic compartments. Furthermore, we reconstructed the developmental trajectory of different cell lineages within the diencephalon. This allowed the identification of the genetic cascades and gene regulatory networks underlying the progression of the cell cycle, neurogenesis, and cellular diversification. The analysis provides new insights into the molecular mechanism underlying the specification and amplification of thalamic progenitor cells. In addition, the single-cell-resolved trajectories not only confirm a close relationship between the rostral thalamus and prethalamus, but also uncover an unexpected close relationship between the caudal thalamus, epithalamus and rostral pretectum. Our data provide a useful resource for the systematic study of cell heterogeneity and differentiation kinetics within the developing diencephalon.
Ribozyme-Mediated, Multiplex CRISPR Gene Editing and CRISPRi in Plasmodium yoelii
Authors: Walker Michael P. , Lindner Scott E.
Published: November 2018

Functional characterization of genes in Plasmodium parasites often relies on genetic manipulations to disrupt or modify a gene-of-interest. However, these approaches are limited by the time required to generate transgenic parasites for P. falciparum and the availability of a single drug selectable marker for P. yoelii. In both cases, there remains a risk of disrupting native gene regulatory elements with the introduction of exogenous sequences. To address these limitations, we have developed CRISPR-RGR, a SpCas9-based gene editing system for Plasmodium that utilizes a Ribozyme-Guide-Ribozyme (RGR) sgRNA expression strategy. Using this system with P. yoelii, we demonstrate that both gene disruptions and coding sequence insertions are efficiently generated, producing marker-free and scar-free parasites with homology arms as short as 80-100bp. Moreover, we find that the common practice of using one sgRNA can produce both unintended plasmid integration and the desired locus replacement editing events, while the use of two sgRNAs results in only locus replacement editing. Lastly, we show that CRISPR-RGR can be used for CRISPR interference (CRISPRi) by binding dCas9 to targets in the gene control region of a gene-of-interest, resulting in a modest reduction in gene expression. This robust and flexible system should open the door for in-depth and efficient genetic characterizations in both rodent- and human-infectious Plasmodium species.

Importance

Plasmodium parasites, the causative agent of malaria, still pose an enormous threat to public health worldwide. Gaining additional insight into the biology of the parasite is essential for generating an effective vaccine and identifying novel drug targets. To this end, CRISPR/Cas9 tools have been developed to more efficiently interrogate the Plasmodium genome than is possible with conventional reverse genetics approaches. Here, we describe CRISPR-RGR as an addition to the CRISPR/Cas9 toolbox for the rodent-infectious Plasmodium parasites. By using multiple ribozyme-flanked single guide RNAs expressed from RNA polymerase II promoters, transgenic parasites can be rapidly generated as designed without leaving selectable markers. Moreover, CRISPR-RGR can be adapted for use as a CRISPR interference (CRISPRi) system to alter gene expression without genome modification. Together, CRISPR-RGR for gene editing and CRISPRi application can hasten investigations into the biology and vulnerabilities of the malaria parasite.
Beat-Relevant Signals in Auditory Cortical Responses to Musical Excerpts
Authors: Rajendran Vani G. , Harper Nicol S. , Schnupp Jan W. H.
Published: November 2018

Musical beat perception is widely regarded as a high-level ability involving widespread coordination across brain areas, but how low-level auditory processing must necessarily shape these dynamics, and therefore perception, remains unexplored. Previous cross-species work suggested that beat perception in simple rhythmic noise bursts is shaped by neural transients in the ascending sensory pathway. Here, we found that low-level processes even substantially explain the emergence of beat in real music. Firing rates in the rat auditory cortex in response to twenty musical excerpts were on average higher on the beat than off the beat tapped by human listeners. This “neural emphasis” distinguished the perceived beat from alternative interpretations, was predictive of the degree of consensus across listeners, and was accounted for by a spectrotemporal receptive field model. These findings indicate that low-level auditory processing may have a stronger influence on the location and clarity of the beat in music than previously thought.
Single-Trial Decoding of Scalp EEG Under Natural Conditions
Authors: Tuckute Greta , Hansen Sofie Therese , Pedersen Nicolai , Steenstrup Dea , Hansen Lars Kai
Published: November 2018

There is significant current interest in decoding mental states from electro-encephalography (EEG) recordings. EEG signals are subject-specific, sensitive to disturbances, and have a low signal-to-noise ratio, which has been mitigated by the use of laboratory-grade EEG acquisition equipment under highly controlled conditions. In the present study, we investigate single-trial decoding of natural, complex stimuli based on scalp EEG acquired with a portable, 32 dry-electrode sensor system in a typical office setting. We probe generalizability by a leave-one-subject-out cross-validation approach. We demonstrate that Support Vector Machine (SVM) classifiers trained on a relatively small set of de-noised (averaged) pseudo-trials perform on par with classifiers trained on a large set of noisy single-trial samples. For visualization of EEG signatures exploited by SVM classifiers, we propose a novel method for computing sensitivity maps of EEG-based SVM classifiers. Moreover, we apply the NPAIRS resampling framework for estimation of map uncertainty and show that effect sizes of sensitivity maps for classifiers trained on small samples of de-noised data and large samples of noisy data are similar. Finally, we demonstrate that the average pseudo-trial classifier can successfully predict the class of single trials from withheld subjects, which allows for fast classifier training, parameter optimization and unbiased performance evaluation in machine learning approaches for brain decoding.
Activity or Connectivity? Evaluating neurofeedback training in Huntington’s disease
Authors: Papoutsi Marina , Magerkurth Joerg , Josephs Oliver , Pépés Sophia E , Ibitoye Temi , Reilmann Ralf , Hunt Nigel , Payne Edwin , Weiskopf Nikolaus , Langbehn Douglas , Rees Geraint , Tabrizi Sarah J
Published: November 2018

Non-invasive methods, such as neurofeedback training (NFT), could support cognitive symptom management in Huntington’s disease (HD) by targeting brain regions whose function is impaired. The aim of our single-blind, sham-controlled study was to collect rigorous evidence regarding the feasibility of NFT in HD by examining two different methods, activity and connectivity real-time fMRI NFT. Thirty-two HD gene-carriers completed 16 runs of NFT training, using an optimized real-time fMRI protocol. Participants were randomized into four groups, two treatment groups, one receiving neurofeedback derived from the activity of the Supplementary Motor Area (SMA), and another receiving neurofeedback based on the correlation of SMA and left striatum activity (connectivity NFT), and two sham control groups, matched to each of the treatment groups. We examined differences between the groups during NFT training sessions and after training at follow-up sessions. Transfer of training was measured by measuring the participants’ ability to upregulate NFT target levels without feedback (near transfer), as well as by examining change in objective, a-priori defined, behavioural measures of cognitive and psychomotor function (far transfer) before and at 2 months after training. We found that the treatment group had significantly higher NFT target levels during the training sessions compared to the control group. However, we did not find robust evidence of better transfer in the treatment group compared to controls, or a difference between the two NFT methods. We also did not find evidence in support of a relationship between change in cognitive and psychomotor function and NFT learning success. We conclude that although there is evidence that NFT can be used to guide participants to regulate the activity and connectivity of specific regions in the brain, evidence regarding transfer of learning and clinical benefit was not robust. Although the intervention is non-invasive, given the costs and absence of reliable evidence of clinical benefit, we cannot recommend real-time fMRI NFT as a potential intervention in HD.
Vernonia Amygdalina Del (Bitter Leaf) extract ameliorates isoniazid (INH) induced liver injury in Swiss Albino Mice
Authors: Tilaye Gebreselassie Addisu , Zerihun Muluken Fekadie , Chuffa Kasaw Adane , Arayaselassie Mahelet , Seifu Daniel
Published: November 2018

Liver plays a central role in the metabolism of drugs. Drug clearance and transformation exposes liver to toxic injury. Antitubercular drugs have been found to be hepatotoxic and potentially lead to drug-induced liver injury. Isoniazid is one of the most hepatotoxic first line antitubercular drugs. Conventional drugs used in the treatment of liver disease are often inadequate and a search for supplementation or alternative drugs for the treatment of hepatic damage is indispensible. Therefore our study aims to investigate the hepatoprotective potential of Vernonia Amygdalina Del (bitter leaf) extract against Isoniazid-induced liver injury in Swiss Albino Mice. Treatment of Mice orally with Vernonia Amygdalina Del extract at dose of 250mg/kg and 375 mg/kg significantly lowered (P<0.05) the serum level of liver enzymes in Isoniazid pretreated mice. The hepatoptotective activity of the extract found to be comparable with the standard drug, Silymarin (100 mg/kg, P.o.). Moreover, treatment with the extract significantly alleviated Isoniazid induced hepatic injury as supported by the photomicrographs of liver section of mice. The data shows aqueous Vernonia Amygdalina Del extract has a very promising hepatoprotective potential against isoniazid-induced liver injury.
Hi-C detects novel structural variants in HL-60 and HL-60/S4 cell lines
Authors: Jacobson Elsie C. , Grand Ralph S. , Perry Jo K. , Vickers Mark H. , Olins Ada L. , Olins Donald E. , O’Sullivan Justin M.
Published: November 2018

Cancer cell lines often have large structural variants (SVs) that evolve over time. There are many reported differences in large scale SVs between HL-60 and HL-60/S4, two cell lines derived from the same acute myeloid leukemia sample. However, the stability and variability of inter- and intra-chromosomal structural variants between different sources of the same cell line is unknown. Here, we used Hi-C and RNA-seq to identify and compare large SVs in HL-60 and HL-60/S4 cell lines. Comparisons with previously published karyotypes identified novel SVs in both cell lines. Hi-C was used to characterize the known expansion centered on the MYC locus. The MYC expansion was integrated into known locations in HL-60/S4, and a novel location (chr4) in HL-60. The HL-60 cell line has more within-line structural variation than the HL-60/S4 derivative cell line. Collectively we demonstrate the usefulness of Hi-C and with RNA-seq data for the identification and characterization of SVs.
Highly efficient multiplex human T cell engineering without double-strand breaks using Cas9 base editors
Authors: Webber Beau R. , Lonetree Cara-lin , Kluesner Mitchell G. , Johnson Matthew J. , Pomeroy Emily J. , Diers Miechaleen D. , Lahr Walker S. , Draper Garrett , Slipek Nicholas J. , Lovendahl Klaus N. , McElroy Amber , Gordon Wendy R. , Osborn Mark J. , Moriarity Branden S.
Published: November 2018

Chimeric antigen receptor engineered T cell (CAR-T) immunotherapy has shown efficacy against a subset of hematological malignancies1,2, yet its autologous nature and ineffectiveness against epithelial and solid cancers limit widespread application. To overcome these limitations, targeted nucleases have been used to disrupt checkpoint inhibitors and genes involved in alloreactivity3–6. However, the production of allogeneic, “off-the-shelf” T cells with enhanced function requires multiplex genome editing strategies that risk off-target effects, chromosomal rearrangements, and genotoxicity due to simultaneous double-strand break (DSB) induction at multiple loci7–10. Moreover, it has been well documented that DSBs are toxic lesions that can drive genetic instability11,12. Alternatively, CRISPR/Cas9 base editors afford programmable enzymatic nucleotide conversion at targeted loci without induction of DSBs13,14. We reasoned this technology could be used to knockout gene function in human T cells while minimizing safety concerns associated with current nuclease platforms. Through systematic reagent and dose optimization, we demonstrate highly efficient multiplex base editing and consequent protein knockout in primary human T cells at loci relevant to the generation of allogeneic CAR-T cells including the T cell receptor α constant (TRAC) locus, β-2 microglobulin (B2M), and programmed cell death 1 (PDCD1). Multiplex base edited T cells equipped with a CD19 CAR killed target cells more efficiently; and importantly, both DSB induction and translocation frequency were greatly reduced compared to cells engineered with Cas9 nuclease. Collectively, our results establish a novel multiplex gene editing platform to enhance both the safety and efficacy of engineered T cell-based immunotherapies.
Identification of common molecular biomarker signatures in blood and brain of Alzheimer’s disease
Authors: Rahman Md. Rezanur , Islam Tania , Shahjaman Md. , Quinn Julian M.W. , Holsinger R. M. Damian , Moni Mohammad Ali
Published: November 2018

Background

Alzheimers disease (AD) is a progressive neurodegenerative disease characterized by memory loss and confusion. Neuroimaging and cerebrospinal fluid-based early detection is limited in sensitivity and specificity as well as by cost. Therefore, detecting AD from blood cell analysis could improve early diagnosis and treatment of the disease. The present study aimed to identify blood cell transcripts that reflect brain expression levels of factors linked to AD progression.

Methods

We analyzed blood cell and brain microarray gene expression datasets from NCBI-GEO for AD association and expression in blood and brain. We also used eQTL and epigenetics data to identify AD-related genes that were regulated similarly in blood and brain.

Results

We identified 9 differentially expressed genes (DEG; AD versus controls) common to blood cells and brain (CNBD1, SUCLG2-AS1, CCDC65, PDE4D, MTMR1, C3, SLC6A15, LINC01806, and FRG1JP) and 18 genes (HSD17B1, GAS5, RPS5, VKORC1, GLE1, WDR1, RPL12, MORN1, RAD52, SDR39U1, NPHP4, MT1E, SORD, LINC00638, MCM3AP-AS1, GSDMD, RPS9, and GNL2) that were commonly dysregulated between AD blood and brain tissues using SNP and cis-eQTL data. This data revealed significant neurodegeneration-associated molecular pathways in the ribosomal and complement systems. Integration of these different analyses revealed dys-regulation of hub transcription factors (SREBF2, NR1H2, NR1H3, PRDM1, XBP1) and microRNAs (miR-518e, miR-518a-3p, miR-518b, miR-518c, miR-518d-3p and miR-518f) in AD. Several significant histone modification sites in DEGs were also identified.

Conclusion

We have identified new putative links between pathological processes in brain and transcripts in blood cells in AD subjects that may enable the use of blood to diagnose and monitor AD onset and progression.
YAP independently regulates cell size and population growth dynamics via non-cell autonomous mediators
Authors: Mugahid Douaa , Kalocsay Marian , Gruver Scott , Peshkin Leonid , Kirschner Marc W.
Published: November 2018

The Hippo pathway, in which changes at the cell surface and in the extracellular environment control the activity of a downstream transcription factor, known as YAP in mammalian cells and Yorkie in Drosophila, has recently taken center-stage as perhaps the most important pathway in metazoans for controlling organ size. In intact tissues YAP activity is inhibited and the organ does not overgrow. When the organ is damaged, YAP is active and necessary for growth and regeneration to occur. The exact process by which YAP drives organ and tissue growth is not fully understood, although it is known to affect both cell size and cell number. Since cell size and proliferation are highly interdependent in many cultured cell studies, we investigated the role of YAP in the simultaneous regulation of both cell size and number. Our experiments reveal that YAP controls both cell size and cell proliferation by independent circuits, and that it affects each process non-cell autonomously via extracellular mediators. We identify that CYR61, a known secreted YAP target, is the major regulator of the non-cell autonomous increase in cell number, but does not affect cell size. The molecular identity of the non-cell autonomously acting mediator of cell size is yet to be identified.
Network-based identification of genetic factors in Ageing, lifestyle and Type 2 Diabetes that Influence in the progression of Alzheimer’s disease
Authors: Chowdhury Utpala Nanda , Ahmad Shamim , Islam M. Babul , Huq Fazlul , Quinn Julian M.W. , Moni Mohammad Ali
Published: November 2018

Motivation

Alzheimer’s disease (AD) is currently incurable and the causative risk factors are still poorly understood, which impedes development of effective prevention and treatment strategies. We propose a network-based quantitative framework to reveal details of the complex interaction between the various genetic contributors to AD susceptibility. We analyzed gene expression microarray data from tissues affected by AD, advanced ageing, high alcohol consumption, type II diabetes, high body fat, high dietary fat, obesity, high dietary red meat intake, sedentary lifestyle, smoking, and control datasets. We developed genetic associations and diseasome networks for these factors and AD using the neighborhood-based benchmarking and multilayer network topology approaches.

Results

The study identified 484 genes differentially expressed between AD and controls. Among these, 27 genes showed elevated expression both in individuals in AD and in smoker datasets; similarly 21 were observed in AD and type II diabetes datasets and 12 for AD and sedentary lifestyle datsets. However, AD shared less than ten such elevated expression genes with other factors examined. 3 genes, namely HLA-DRB4, IGH and IGHA2 showed increased expression among the AD, type II diabetes and alcohol consumption datasets; 2 genes, IGHD and IGHG1, were commonly up-regulated among the AD, type II diabetes, alcohol consumption and sedentary lifestyle datasets. Protein-protein interaction networks identified 10 hub genes: CREBBP, PRKCB, ITGB1, GAD1, GNB5, PPP3CA, CABP1, SMARCA4, SNAP25 and GRIA1. Ontological and pathway analyses genes, including Online Mendelian Inheritance in Man (OMIM) and dbGaP databases were used for gold benchmark gene-disease associations to validate the significance of these putative target genes of AD progression.

Conclusion

Our network-based methodologies have uncovered molecular pathways that may influence AD development, suggesting novel mechanisms that contribute to AD risk and which may form the basis of new therapeutic and diagnostic approaches.

Contact

mohammad.moni@sydney.edu.au
Early Detection of Neurological Dysfunction Using Blood Cell Transcript Profiles
Authors: Moni Mohammad Ali , Rana Humayan Kabir , Islam M. Babul , Ahmed Md Bashir , Liò Pietro , Huq Fazlul , Quinn Julian M.W.
Published: November 2018

Identification of genes whose regulation of expression is similar in both brain and blood cells could enable monitoring of significant neurological traits and disorders by analysis of blood samples. We thus employed transcriptional analysis of pathologically affected tissues, using agnostic approaches to identify overlapping gene functions and integrating this transcriptomic information with expression quantitative trait loci (eQTL) data. Here, we estimate the correlation of genetic expression in the top-associated cis-eQTLs of brain tissue and blood cells in Parkinson’s (PD).

We introduced quantitative frameworks to reveal the complex relationship of various biasing genetic factors in PD, a neurodegenerative disease. We examined gene expression microarray and RNA-Seq datasets from human brain and blood tissues from PD-affected and control individuals. Differentially expressed genes (DEG) were identified for both brain and blood cells to determine common DEG overlaps. Based on neighborhood-based benchmarking and multilayer network topology aproaches we then developed genetic associations of factors with PD.

Overlapping DEG sets underwent gene enrichment using pathway analysis and gene ontology methods, which identified candidate common genes and pathways. We identified 12 significantly dysregulated genes shared by brain and blood cells, which were validated using dbGaP (gene SNP-disease linkage) database for gold-standard benchmarking of their significance in disease processes. Ontological and pathway analyses identified significant gene ontology and molecular pathways that indicate PD progression.

In sum, we found possible novel links between pathological processes in brain and blood cells by examining cell path-way commonalities, corroborating these associations using well validated datasets. This demonstrates that for brain-related pathologies combining gene expression analysis and blood cell cis-eQTL is a potentially powerful analytical approach. Thus, our methodologies facilitate data-driven approaches that can advance knowledge of disease mechanisms and may enable prediction of neurological dysfunction using blood cell transcript profiling.
On Using Local Ancestry to Characterize the Genetic Architecture of Human Phenotypes: Genetic Regulation of Gene Expression in Multiethnic or Admixed Populations as a Model
Authors: Zhong Yizhen , Perera Minoli , Gamazon Eric R.
Published: November 2018

Background

Understanding the nature of the genetic regulation of gene expression promises to advance our understanding of the genetic basis of disease. However, the methodological impact of use of local ancestry on high-dimensional omics analyses, including most prominently expression quantitative trait loci (eQTL) mapping and trait heritability estimation, in admixed populations remains critically underexplored.

Results

Here we develop a statistical framework that characterizes the relationships among the determinants of the genetic architecture of an important class of molecular traits. We estimate the trait variance explained by ancestry using local admixture relatedness between individuals. Using National Institute of General Medical Sciences (NIGMS) and Genotype-Tissue Expression (GTEx) datasets, we show that use of local ancestry can substantially improve eQTL mapping and heritability estimation and characterize the sparse versus polygenic component of gene expression in admixed and multiethnic populations respectively. Using simulations of diverse genetic architectures to estimate trait heritability and the level of confounding, we show improved accuracy given individual-level data and evaluate a summary statistics based approach. Furthermore, we provide a computationally efficient approach to local ancestry analysis in eQTL mapping while increasing control of type I and type II error over traditional approaches.

Conclusion

Our study has important methodological implications on genetic analysis of omics traits across a range of genomic contexts, from a single variant to a prioritized region to the entire genome. Our findings highlight the importance of using local ancestry to better characterize the heritability of complex traits and to more accurately map genetic associations.
Immunological Diversity with Similarity
Authors: Arora Rohit , Burke Harry M. , Arnaout Ramy
Published: November 2018

A diverse immune repertoire is considered a hallmark of good health, but measuring diversity requires a framework that incorporates not only sequences’ relative frequencies but also their functional similarity to each other. Using experimentally measured dissociation constants from over 1,300 antibody-antigen and T-cell receptor (TCR)-peptide pairs, we developed a framework for functional immunological diversity based on binding and applied it to nearly 400 high-throughput antibody and TCR repertoires to reveal patterns in immunological memory, infection, vaccination, and aging. We show that functional diversity adds information that is not captured by raw diversity, revealing signatures of e.g. clonal selection, and that unlike raw diversity, functional diversity is a robust measure that does not require correction for sampling error. Finally, we show that according to functional diversity, unlike raw diversity, individuals’ repertoires overlap substantially, indicating a definable ceiling for the functional diversity of human adaptive immunity. Similarity redefines diversity in complex systems.
Computational psychiatry 2.0 and implications for stress research
Authors: Pashkov Anton A. , Berebin Mikhail A.
Published: November 2018

Stress-related disorders are highly prevalent in modern society and pose significant challenge to human’s health. Being recently emerged branch of psychiatry, computational psychiatry is geared toward mathematical modeling of psychiatric disorders. Harnessing power of computer sciences and statistics may bridge the complex nature of psychiatric illnesses with hidden brain computational mechanisms. Stress represents an adaptive response to environmental threats but, while getting chronic, it leads to progressive deflection from homeostasis or result in buildup of allostatic load, providing researches with unique opportunity to track patterns of deviations from adaptive responding toward full-blown disease development. Computational psychiatry toolkit enables us to quantitatively assess the extent of such deviations, to explicitly test competing hypotheses which compare the models with real data for goodness-of-fit and, finally, to tethering these computational operations to structural or functional brain alterations as may be revealed by non-invasive neuroimaging and stimulation techniques.

It is worth noting that brain does not directly face environmental demands imposed on human or animal, but rather through detecting signals and acting out via bodily systems. Therefore, it is of critical importance to take homeostatic and allostatic mechanisms into account when considering sophisticated interactions between brain and body and how their partnership may result in establishment of stress-susceptible or resilient profiles.

In this article, with a particulate focus on brain-gut interactions, we outline several possible directions to widen the scope of application of computational approach in mental health care field trying to integrate computational psychiatry, psychosomatics and nutritional medicine