bluuebunny/crossref_metadata_2025 huggingface dataset:
Gene expression noise produces cell-to-cell heterogeneity in eukaryotic homologous recombination rate
Authors: Liu Jian , François Jean-Marie , Capp Jean-Pascal
Published: March 2019

Variation in gene expression among genetically identical individual cells (called gene expression noise) directly contributes to phenotypic diversity. Whether such variation can impact genome stability and lead to variation in genotype remains poorly explored. We addressed this question by investigating whether noise in the expression of genes affecting homologous recombination (HR) activity either directly (RAD52) or indirectly (RAD27) confers cell-to-cell heterogeneity in HR rate inSaccharomyces cerevisiae. Using cell sorting to isolate subpopulations with various expression levels, we show that spontaneous HR rate is highly heterogeneous from cell-to-cell in clonal populations depending on the cellular amount of proteins affecting HR activity. Phleomycin-induced HR is even more heterogeneous, showing thatRAD27expression noise strongly affects the rate of recombination from cell-to-cell. Strong variations in HR rate between subpopulations are not correlated to strong changes in cell cycle stage. Moreover, this heterogeneity occurs even when simultaneously sorting cells at equal expression level of another gene involved in DNA damage response (BMH1) that is upregulated by DNA damage, showing that the initiating DNA damage is not responsible for the observed heterogeneity in HR rate. Thus gene expression noise seems mainly responsible for this phenomenon. Finally, HR rate non-linearly scales with Rad27 levels showing that total amount of HR cannot be explained solely by the time- or population-averaged Rad27 expression. Altogether, our data reveal interplay between heterogeneity at the gene expression and genetic levels in the production of phenotypic diversity with evolutionary consequences from microbial to cancer cell populations.
Biodiversity lost: The phylogenetic relationships of a complete mitochondrial DNA genome sequenced from the extinct wolf population of Sicily
Authors: Reale Stefano , Randi Ettore , Bonanno Floriana , Cumbo Valentina , Sammarco Ignazio , Spinnato Antonio , Seminara Salvatore
Published: March 2019

Using next-generation sequencing, we obtained for the first time a complete mitochondrial DNA genome from a museum specimen of the extinct wolf (Canis lupus) population of the island of Sicily (Italy). Phylogenetic analyses showed that this genome, which was aligned with a number of historical and extant complete wolf and dog mtDNAs sampled worldwide, was closely related to an Italian wolf mtDNA genome (TN93 andp-distances = 0.0012), five to seven times shorter than divergence among Sicilian and any other known wolf mtDNA genomes (distance range = 0.0050 – 0.0070). Sicilian and Italian haplotypes joined a basal clade belonging to the mtDNA haplogroup-2 of ancient western European wolf populations (Pilot et al. 2010). Bayesian calibration of divergence times indicated that this clade coalesced at MRCA = 13.400 years (with 95% HPD = 4000 – 21.230 years). These mtDNA findings suggest that wolves probably colonized Sicily from southern Italy towards the end of the last Pleistocene glacial maximum, when the Strait of Messina was almost totally dry. Additional mtDNA and genomic data will further clarify the origin and population dynamics before the extinction of wolves in Sicily.
Joint modelling of diffusion MRI and microscopy
Authors: Howard Amy FD , Mollink Jeroen , Kleinnijenhuis Michiel , Pallebage-Gamarallage Menuka , Bastiani Matteo , Cottaar Michiel , Miller Karla L , Jbabdi Saad
Published: March 2019

The combination of diffusion MRI with microscopy provides unique opportunities to study microstructural features of tissue, particularly when acquired in the same sample. Microscopy is frequently used to validate diffusion MRI microstructure models, addressing the indirect nature of dMRI signals. Typically, these modalities are analysed separately, and microscopy is taken as a gold standard against which dMRI-derived parameters are validated. Here we propose an alternative approach in which we combine diffusion MRI and microscopy data obtained from the same tissue sample to drive a single, joint model. This simultaneous analysis allows us to take advantage of the breadth of information provided by complementary data acquired from different modalities. By applying this framework to a spherical-deconvolution analysis, we are able to overcome a known degeneracy between fibre dispersion and radial diffusion. Spherical-deconvolution based approaches typically estimate a global fibre response function to determine the fibre orientation distribution in each voxel. However, the assumption of a ‘brain-wide’ fibre response function may be challenged if the diffusion characteristics of white matter vary across the brain. Using a generative joint dMRI-histology model, we demonstrate that the fibre response function is dependent on local anatomy, and that current spherical-deconvolution based models may be overestimating dispersion and underestimating the number of distinct fibre populations per voxel.
Cancer-type specific aneuploidies hard-wire chromosome-wide gene expression patterns of their tissue of origin
Authors: Auslander Noam , Heselmeyer-Haddad Kerstin , Patkar Sushant , Hirsch Daniela , Camps Jordi , Brown Markus , Bronder Daniel , Chen Wei-Dong , Lokanga Rachel , Wangsa Darawalee , Wangsa Danny , Hu Yue , Lischka Annette , Braun Rüdiger , Emons Georg , Ghadimi B. Michael , Gaedcke Jochen , Grade Marian , Montagna Cristina , Lazebnik Yuri , Difilippantonio Michael J. , Habermann Jens K. , Auer Gert , Ruppin Eytan , Ried Thomas
Published: March 2019

Most carcinomas have characteristic chromosomal aneuploidies specific to the tissue of tumor origin. The reason for this specificity is unknown. As aneuploidies directly affect gene expression, we hypothesized that cancer-type specific aneuploidies, which emerge at early stages of tumor evolution, confer adaptive advantages to the physiological requirements of the tissue of origin. To test this hypothesis, we compared chromosomal aneuploidies reported in the TCGA database to chromosome arm-wide gene expression levels of normal tissues from the GTEx database. We find that cancer-type specific chromosomal aneuploidies mirror differential gene expression levels specific to the respective normal tissues which cannot be explained by copy number alterations of resident cancer driver genes. We propose that cancer-type specific aneuploidies “hard-wire” chromosome arm-wide gene expression levels present in normal tissues, favoring clonal expansion and tumorigenesis.

One sentence summary

The clonal evolution of cancer is initiated by tissue-specific transcriptional requirements
Human-level recognition of blast cells in acute myeloid leukemia with convolutional neural networks
Authors: Matek Christian , Schwarz Simone , Spiekermann Karsten , Marr Carsten
Published: March 2019

Reliable recognition of malignant white blood cells is a key step in the diagnosis of hematologic malignancies such as Acute Myeloid Leukemia. Microscopic morphological examination of blood cells is usually performed by trained human examiners, making the process tedious, time-consuming and hard to standardise.

We compile an annotated image dataset of over 18,000 white blood cells, use it to train a convolutional neural network for leukocyte classification, and evaluate the network’s performance. The network classifies the most important cell types with high accuracy. It also allows us to decide two clinically relevant questions with human-level performance, namely (i) if a given cell has blast character, and (ii) if it belongs to the cell types normally present in non-pathological blood smears.

Our approach holds the potential to be used as a classification aid for examining much larger numbers of cells in a smear than can usually be done by a human expert. This will allow clinicians to recognize malignant cell populations with lower prevalence at an earlier stage of the disease.
Likelihood-free nested sampling for biochemical reaction networks
Authors: Mikelson Jan , Khammash Mustafa
Published: March 2019

The development of mechanistic models of biological systems is a central part of Systems Biology. One major challenge in developing these models is the accurate inference of the model parameters. In the past years, nested sampling methods have gained an increasing amount of attention in the Systems Biology community. Some of the rather attractive features of these methods include that they are easily parallelizable and give an estimation of the variance of the final Bayesian evidence estimate from a single run. Still, the applicability of these methods is limited as they require the likelihood to be available and thus cannot be applied to stochastic systems with intractable likelihoods. In this paper, we present a likelihood-free nested sampling formulation that gives an unbiased estimator of the Bayesian evidence as well as samples from the posterior. Unlike most common nested sampling schemes we propose to use the information about the samples from the final prior volume to aid in the approximation of the Bayesian evidence and show how this allows us to formulate a lower bound on the variance of the obtained estimator. We proceed and use this lower bound to formulate a novel termination criterion for nested sampling approaches. We illustrate how our approach is applied to several realistically sized models with simulated data as well as recently published biological data. The presented method provides a viable alternative to other likelihood-free inference schemes such as Sequential Monte Carlo or Approximate Bayesian Computations methods. We also provide an intuitive and performative C++ implementation of our method.
μECoG Recordings Through a Thinned Skull
Authors: Brodnick Sarah K. , Ness Jared P. , Richner Thomas J. , Thongpang Sanitta , Novello Joseph , Hayat Mohammed , Cheng Kevin P , Krugner-Higby Lisa , Suminski Aaron J. , Ludwig Kip A. , Williams Justin C.
Published: March 2019

The studies described in this paper for the first time characterize the acute and chronic performance of optically transparent thin-film µECoG grids implanted on a thinned skull as both an electrophysiological complement to existing thinned skull preparation for optical recordings/manipulations, and a less invasive alternative to epidural or subdurally placed µECoG arrays. In a longitudinal chronic study, µECoG grids placed on top of a thinned skull maintain impedances comparable to epidurally placed µECoG grids that are stable for periods of at least one month. Optogenetic activation of cortex is also reliably demonstrated through the optically transparent ECoG grids acutely placed on the thinned skull. Finally, spatially distinct electrophysiological recordings were evident on µECoG electrodes placed on a thinned skull separated by 500-750µm, as assessed by stimulation evoked responses using optogenetic activation of cortex as well as invasive and epidermal stimulation of the sciatic and median nerve at chronic time points. Neural signals were collected through a thinned skull in multiple species, demonstrating potential utility in neuroscience research applications such as in vivo imaging, optogenetics, calcium imaging, and neurovascular coupling.
Multi-omics Integrative Analysis of Acute and Relapsing Malaria in a Non-Human Primate Model ofP. vivaxinfection
Authors: Tang Yan , Joyner Chester J , Cordy Regina J ,   Malaria Host-Pathogen Interaction Center (MaHPIC), Galinski Mary R , Lamb Tracey J , Styczynski Mark P.
Published: March 2019

Systems-scale analysis of multiple layers of molecular and cellular data has significant potential for providing novel insights into malaria pathology and immunity. We present here a unique longitudinal multi-omics dataset encompassingMacaca mulattablood and bone marrow responses to infection byPlasmodium cynomolgi, a non-human primate (NHP) parasite species used to modelP. vivaxmalaria acute and relapsing infections in humans. We analyzed relationships across multiple biological layers using a mutual information-based machine learning approach to integrate heterogeneous longitudinal datasets and constructed an atlas of multi-omics relatedness networks (MORNs). Using this technique, we were able to detect signatures that defined both acute and relapsing infections. Importantly, relapse infections could be distinguished from both acutely-infected and uninfected NHP, suggesting that the host-parasite interactions during relapses are unique compared to acutePlasmodiuminfections. To our knowledge, this is the first report of large-scale, longitudinal multi-omics analysis of malaria in any system. This dataset, along with the method used to analyze it, provides a unique resource for the malaria research community and demonstrates the power of longitudinal infection study designs, NHP model systems and integrative multi-omics analyses.
A molecular model for self-assembly of synaptonemal complex protein SYCE3
Authors: Dunne Orla M , Davies Owen R
Published: March 2019

The synaptonemal complex (SC) is a supramolecular protein assembly that mediates homologous chromosome synapsis during meiosis. This zipper-like structure assembles in a continuous manner between homologous chromosome axes, enforcing a 100-nm separation along their entire length, and providing the necessary three-dimensional framework for crossover formation. The mammalian SC is formed of eight components - SYCP1-3, SYCE1-3, TEX12 and SIX6OS1 - arranged in transverse and longitudinal structures. These largely α-helical coiled-coil proteins undergo heterotypic interactions, coupled with recursive self-assembly of SYCP1, SYCE2-TEX12, and SYCP2-SYCP3, to achieve the vast supramolecular structure of the SC. Here, we report a novel self-assembly mechanism of SC central element component SYCE3, identified through multi-angle light scattering and small-angle X-ray scattering. SYCE3 adopts a dimeric four-helical bundle structure that acts as the building block for concentration-dependent self-assembly into a series of discrete higher order oligomers. This is achieved through staggered lateral interactions between self-assembly surfaces of SYCE3 dimers, and their end-on interaction through intermolecular domain-swap between dimer folds. These mechanisms combine to achieve potentially limitless SYCE3 assembly, which particularly favours formation of dodecamers of three laterally associated domain-swap tetramers. Our findings extend the family of self-assembling proteins within the SC and provide novel means for structural stabilisation of the SC central element.
mTORC1 In the Orbitofrontal Cortex Promotes Habitual Alcohol Seeking
Authors: Morisot Nadege , Berger Anthony L. , Phamluong Khanhky , Laguesse Sophie , Moffat Jeffrey J. , Ron Dorit
Published: March 2019

The mammalian target of rapamycin complex 1 (mTORCl) plays an important role in dendritic translation, synaptic plasticity, and learning and memory. We previously showed that heavy alcohol use activates mTORC1 in the orbitofrontal cortex (OFC) of rodents. Here, we set out to determine the consequences of alcohol-dependent mTORC1 activation in the OFC. We found that although inhibition of mTORC1 in the OFC does not alter rat alcohol intake per se, it attenuates alcohol seeking. We then tested whether mTORC1 in the OFC is required for goal-directed or habitual alcohol seeking. To do so, rats were trained self-administer alcohol under a random ratio (RR) or a random interval (RI) schedule of reinforcement, which biases toward goal-directed or habitual responding, respectively, and tested whether mTORC1 inhibition alters lever presses following alcohol devaluation. We found that pharmacological inhibition of mTORC1 or knockdown of the adaptor protein, Raptor, did not affect goal-directed alcohol responding but restored sensitivity to devaluation in RI-trained rats. In contrast, habitual responding for sucrose was unaltered by mTORC1 inhibition. These data suggest that mTORC1 in the OFC drives alcohol habit. We then elucidate the mechanism by which mTORC1 is activated by alcohol, and found that the recruitment of GluN2B during alcohol withdrawal stimulates mTORC1 in OFC cFos-positive neurons. Finally, we show that inhibition of GluN2B in the OFC attenuates both alcohol seeking and habitual responding for alcohol. Together, our data suggest that alcohol withdrawal promotes an NMDAR-dependent activation of mTORC1 which in turn drives habitual alcohol seeking.
Longshot: accurate variant calling in diploid genomes using single-molecule long read sequencing
Authors: Edge Peter , Bansal Vikas
Published: March 2019

Short-read sequencing technologies such as Illumina enable the accurate detection of single nucleotide variants (SNVs) and short insertion/deletion variants in human genomes but are unable to provide information about haplotypes and variants in repetitive regions of the genome. Single-molecule sequencing technologies such as Pacific Biosciences and Oxford Nanopore generate long reads (≥ 10 kb in length) that can potentially address these limitations of short reads. However, the high error rate of SMS reads makes it challenging to detect small-scale variants in diploid genomes. We introduce a variant calling method, Longshot, that leverages the haplotype information present in SMS reads to enable the accurate detection and phasing of single nucleotide variants in diploid genomes. Using whole-genome Pacific Biosciences data for multiple human individuals, we demonstrate that Longshot achieves very high accuracy for SNV detection (precision ≥0.992 and recall ≥0.96) that is significantly better than existing variant calling methods. Longshot can also call SNVs with good accuracy using whole-genome Oxford Nanopore data. Finally, we demonstrate that it enables the discovery of variants in duplicated regions of the genome that cannot be mapped using short reads. Longshot is freely available at https://github.com/pjedge/longshot.
Salmonellagenomic island 3 is an integrative and conjugative element and contributes to copper and arsenic resistance ofSalmonella enterica
Authors: Arai Nobuo , Sekizuka Tsuyoshi , Tamamura Yukino , Kusumoto Masahiro , Hinenoya Atsushi , Yamasaki Shinji , Iwata Taketoshi , Watanabe-Yanai Ayako , Kuroda Makoto , Akiba Masato
Published: March 2019

Salmonellagenomic island 3 (SGI3) was first described as a chromosomal island inSalmonella4,[5],12:i:-, a monophasic variant ofSalmonella entericasubsp.entericaserovar Typhimurium. The SGI3 DNA sequence detected fromSalmonella4,[5],12:i:-isolated in Japan was identical to that of a previously reported one across entire length of 81 kb. SGI3 consists of 86 open reading frames, including a copper homeostasis and silver resistance island (CHASRI) and an arsenic resistance operon in addition to genes related to conjugative transfer and DNA replication or partitioning, suggesting that the island is a mobile genetic element. We successfully selected transconjugants that acquired SGI3 after filter mating experiments using theS. entericaserovars Typhimurium, Heidelberg, Hadar, Newport, Cerro, and Thompson as recipients. Southern blot analysis using I-CeuI-digested genomic DNA demonstrated that SGI3 was integrated into a chromosomal fragment of the transconjugants. PCR and sequencing analysis demonstrated that SGI3 was inserted into the 3′ end of the tRNA genespheVorpheR. The length of the target site was 52 or 55 bp, and a 55-bpattIsequence indicating generation of the circular form of SGI3 was also detected. The transconjugants had a higher MIC against CuSO4compared with the recipient strains under anaerobic conditions. Resistance was defined by thecusgene cluster in the CHASRI. The transconjugants also had distinctly higher MICs against Na2HAsO4compared with recipient strains under aerobic conditions. These findings clearly demonstrate that SGI3 is an integrative and conjugative element and contributes to the copper and arsenic resistance ofS. enterica.
Snow is an important control of plant community functional composition
Authors: Happonen Konsta , Aalto Juha , Kemppinen Julia , Niittynen Pekka , Virkkala Anna-Maria , Luoto Miska
Published: March 2019

The functional composition of plant communities is a critical modulator of climate change impacts on ecosystems, but it is not a simple function of regional climate. In the Arctic tundra, where climate change is proceeding the most rapidly, communities have not shifted their trait composition as predicted by spatial temperature-trait relationships. Important causal pathways are thus missing from models of trait composition change. Here, we study causes of plant community functional variation in a tundra landscape. We consider the community weighted means of plant vegetative height, as well as two traits related to the leaf economic spectrum. Specifically, we model their responses to locally measured summer air temperature, snow conditions, and soil resource levels. For each of the traits we also quantify the importance of intraspecific trait variation (ITV) for between-community functional differences and trait-environment matching. Our study shows that in a tundra landscape 1) snow is the most influential abiotic variable affecting functional composition, 2) vegetation height is under weak local environmental control, whereas leaf economics is under strong local environmental control, 3) the relative magnitude of ITV differs between traits, and 4) ITV is not very consequential for community-level trait-environment relationships.
ANCESTRAL PERSISTENCE OF VESTIBULO-SPINAL REFLEXES IN AXIAL MUSCLES IN HUMANS
Authors: Guillaud Etienne , Faure Céline , Doat Emilie , Bouyer Laurent , Guehl Dominique , Cazalets Jean-René
Published: March 2019

Accurate control of the trunk is essential for maintaining balance in an upright subject. Most studies addressing vestibulo-spinal reflexes have investigated the role of the lower limbs, while limited attention has been paid to the back muscles. To address this issue, we challenged the persistence of vestibular evoked myogenic potentials (VEMPs) in back muscles in situations in which the leg muscle responses were modulated. Nineteen subjects were submitted to galvanic vestibular stimulations (GVS). Body sway and VEMPs were recorded in the paraspinal and limb muscles. During treadmill locomotion, the VEMPS in the lower limbs were observed only during the stance phase, whereas the axial VEMPs were observed during all phases. In upright standing subjects, slight head contact was sufficient to abolish the VEMPs in the lower limbs, while the VEMPs remained present in the paraspinal muscles. Similarly, during parabolic flight-induced microgravity, the VEMPs in the lower limb muscles were suppressed, while those in the axial muscles persisted despite the absence of gravitational information from the otolithic system. Our results depict a differentiated control mechanism of axial and appendicular muscles when a perturbation is detected by vestibular inputs. The persistent feature of axial myogenic adjustments suggests that a hard-wired reflex is functionally efficient to maintain posture. By contrast, the ankle responses to perturbations occur only when the accompanying sensory feedback is congruent, challenging the balance task and gravity. Overall, this study using GVS in microgravity is the first to present an approach delineating feed-forward vestibular control in the absence of all feedback.
Wnt activator FOXB2 drives prostate cancer neuroendocrine differentiation
Authors: Moparthi Lavanya , Pizzolato Giulia , Koch Stefan
Published: March 2019

The Wnt signaling pathway is of paramount importance for development and disease. However, the tissue-specific regulation of Wnt pathway activity remains incompletely understood. Here we identify FOXB2, an uncharacterized forkhead box family transcription factor, as a potent activator of Wnt signaling in normal and cancer cells. Mechanistically, FOXB2 induces the non-classical Wnt ligand WNT7B, which increases TCF/LEF-dependent transcription without activating LRP6 or β-catenin. Proximity ligation and RNA interference identified YAP1, JUN, and DDX5 as transcriptional co-regulators required for FOXB2-dependent Wnt activation. Although FOXB2 expression is limited in adults, it is induced in select cancers, particularly advanced prostate cancer. RNA-seq data analysis suggests that FOXB2/WNT7B expression in prostate cancer is associated with a transcriptional program that favors neuronal differentiation and decreases recurrence-free survival. Consistently, FOXB2 is induced during neuroendocrine transformation of LNCaP prostate carcinoma cells, and conversely, FOXB2 overexpression is sufficient to induce their differentiation. Our results suggest that FOXB2 is a tissue-specific Wnt enhancer that promotes prostate cancer malignant transformation.
Protein secondary structure determines the temporal relationship between folding and disulfide formation
Authors: Robinson Philip J , Kanemura Shingo , Cao Xiaofei , Bulleid Neil J
Published: March 2019

How and when disulfides form in proteins during their folding is a fundamental question in cell biology. Two models describe the relationship between disulfide formation and folding, the folded precursor model, in which formation of nascent structure occurs prior to the disulfides and the quasi-stochastic model where disulfides form prior to complete domain folding. Here we investigate oxidative folding within a cellular milieu of three structurally diverse substrates in order to understand the folding mechanisms required to achieve correct cysteine coupling. We use a eukaryotic translation system in which we can manipulate the redox conditions and produce stalled translation intermediates representative of different stages of translocation. We identify different disulfide bonded isomers by non-reducing SDS-PAGE. Using this approach, we determined whether each substrate followed a folding driven or disulfide driven mechanism. Our results demonstrate that the folding model is substrate-dependent with disulfides forming prior to complete domain folding in a domain lacking secondary structure, whereas disulfide formation was absent at this stage in proteins with defined structural elements. In addition, we demonstrate the presence and rearrangement of non-native disulfides specifically in substrates following the quasi-stochastic model. These findings demonstrate why non-native disulfides are prevented from forming in proteins with well-defined secondary structure.

Significance statement

A third of human proteins contain structural elements called disulfide bonds that are often crucial for stability and function. Disulfides form between cysteines in the specialised environment of the endoplasmic reticulum (ER), during the complex process of protein folding. Many proteins contain multiple cysteines that can potentially form correct or incorrect cysteine pairings. To investigate how correct disulfide pairs are formed in a biological context, we developed an experimental approach to assess disulfide formation and rearrangement as proteins enter the ER. We found that a protein domain with atypical secondary structure undergoes disulfide orchestrated folding as it enters the ER and is prone to incorrect disulfide formation. In contrast, proteins with defined secondary structure form folding dependent, native disulfides. These findings show how different mechanisms of disulfide formation can be rationalised from structural features of the folding domains.
‘Candidatus Phytoplasma platensis’, a novel taxon associated with daisy (Bellis perennis) virescence and related diseases in South America
Authors: Fernández Franco Daniel , Galdeano Ernestina , Conci Luis Rogelio
Published: March 2019

Bellis perennis virescence (BellVir) phytoplasma affects ornamental daisies in Argentina. It has been previously classified within the X-disease group, subgroup III-J, which is one of the most important and widely distributed in South America, affecting diverse plant hosts. In this study, we compared 16S rRNA, ribosomal proteins rpIV and rps3, secA and immunodominant proteins imp and idpA genes of BellVir phytoplasma with previously described ‘Candidatus Phytoplasma’ species. The 16S rRNA gene of strain BellVir shared less than 97.5% with all previously described ‘Ca. Phytoplasma’ taxa except for ‘Ca. Phytoplasma pruni’. According to the recommended rules for the description of novel taxa within ‘Ca. Phytoplasma’, it should be considered as ‘Ca. P. pruni’-related strain. However, multilocus analysis showed further molecular diversity that distinguished BellVir phytoplasma from ‘Ca. Phytoplasma pruni’. Besides, BellVir phytoplasma and 16SrIII-J related strains have a geographical distribution restricted to South America, where ‘Ca. P.pruni’ has not been detected. Two insect vectors have been reported to transmit 16SrIII-J phytoplasmas, which have not been found to transmit ‘Ca. Phytoplasma pruni’. Having a wide host range, they have not been detected in Prunus persica. Therefore, based on multilocus sequence analyses, specific vector transmission and geographical distribution, we propose the recognition of the novel phytoplasma species ‘Ca. Phytoplasma platensis’, within the X-disease clade, with Bellis perennis virescence phytoplasma as the reference strain.
Antimicrobial susceptibility and serotype distribution of Streptococcus agalactiae recto-vaginal colonizing isolates from pregnant women at a tertiary hospital in Pretoria, South Africa: an observational descriptive study
Authors: Said Mohamed , Dangor Yusuf , Mbelle Nontombi , Madhi Shabir A. , Kwatra Gaurav , Ismail Farzana
Published: March 2019

Introduction

Streptococcus agalactiae or Group B Streptococcus (GBS) is a significant cause of neonatal sepsis. Intrapartum antibiotic prophylaxis is recommended for pregnant women identified to be recto-vaginally colonised between 34-37 weeks gestational age to decrease the risk of invasive disease in their newborns. The aim of this study was to investigate serotype distribution and antimicrobial susceptibility patterns of GBS isolates cultured from recto-vaginal specimens during pregnancy.

Methods

Sixty-nine archived maternal colonizing isolates were tested against penicillin, erythromycin, clindamycin, vancomycin and levofloxacin. Minimum Inhibitory Concentration (MIC) testing was performed using the E-test method. Serotyping was performed by latex agglutination method.

Results

The most common serotypes detected were Ia (54%), III (20%), V (16%), II (6%), IV (2%) and Ib (1%), respectively. All isolates were fully susceptible to penicillin, vancomycin and levofloxacin. Eight (11%) and 50 (56%) isolates showed intermediate resistance to erythromycin and clindamycin respectively, and one isolate was resistant to erythromycin. MLSB phenomenon was noted in 3 (4%) of the isolates.

Conclusion

GBS colonizing isolates remain susceptible to penicillin and remains the drug of choice for intrapartum antibiotic prophylaxis and treatment of invasive disease in newbrons. Macrolides should only be used if clinically indicated due to the high prevalence of intermediate resistance. A hexavalent GBS vaccine currently under development would provide coverage for 100% of the isolates identified in this study.
Deconvolving multiplexed protease signatures with substrate reduction and activity clustering
Authors: Zhuang Qinwei , Holt Brandon Alexander , Kwong Gabriel A. , Qiu Peng
Published: March 2019

Proteases are pleiotropic, promiscuous enzymes that degrade proteins and peptides, which drive important processes in health and disease. The ability to quantify the activity of protease signatures by sampling with Massively Multiplexed Activity (MMA) libraries will provide unparalleled biological information. Under such a framework, a designed library of peptide substrates is exposed to a cocktail of proteases, the cleavage velocity of each substrate is measured, and individual protease activity levels are inferred from the data. Previous studies have developed individual protease sensors, but multiplexed substrate cleavage data becomes difficult to interpret as the number of cross-cutting proteases increases. Computational methods for parsing this data to estimate individual protease activities primarily use an extensive compendium of all possible protease-substrate combinations, which require impractical amounts of training data when scaling up to MMA libraries. Here we provide a computational method for estimating protease activities efficiently by reducing the number of substrates and clustering proteases with similar cleavage activities into families. This method is scalable and will enable the future use of MMA libraries with applications spanning therapeutic and diagnostic biotechnology.
A novel growth factor-dependent thermogenic brown adipocyte cell line from defined precursor cells
Authors: Kindler Dagmar , Sousa Isabel S , Schweizer Sabine , Lerch Sarah , Klingenspor Martin , Herzig Stephan , Vegiopoulos Alexandros
Published: March 2019

Molecular pathways regulating brown adipocyte formation and metabolism can be exploited as targets for the treatment of obesity and disorders of glucose and lipid metabolism such as type-2 diabetes. Investigations in this direction require adequate cell models for brown adipocytes and their precursors. We report the establishment of a novel clonal cell line derived from defined Lin−Sca1+ adipocyte precursors from murine interscapular brown fat. In contrast to most currently available lines, immortalization was achieved by serial passaging without viral or genetic manipulation. Instead, the media were supplemented with basic fibroblast growth factor, which was required for the maintenance of stable long-term growth and immature morphology. BATkl2 cells differentiated to adipocytes with high efficiency upon standard adipogenic induction independently of PPARg agonists and even at higher passage numbers. BATkl2 adipocytes showed readily detectable Uncoupling protein 1 (Ucp1) protein expression and acutely responded to norepinephrine with increased Ucp1 mRNA expression, lipolysis and uncoupled mitochondrial respiration. Highly efficient siRNA-mediated knockdown was demonstrated in the growth state as well as in differentiating adipocytes, whereas plasmid DNA transfection was achieved in immature cells. These features make the BATkl2 cell line an attractive brown (pre)-adipocyte cell model.
Generation of a High-Density Rat EST Map
Authors: Scheetz Todd E. , Raymond Michael R. , Nishimura Darryl Y. , McClain Ann , Roberts Chad , Birkett Clay , Gardiner Jack , Zhang Jie , Butters Nichole , Sun Christine , Kwitek-Black Anne , Jacob Howard , Casavant Thomas L. , Soares M. Bento , Sheffield Val C.
Published: March 2019

We have developed a high-density EST map of the rat, consisting of >11,000 ESTs. These ESTs were placed on a radiation hybrid framework map of genetic markers spanning all 20 rat autosomes, plus the X chromosome. The framework maps have a total size of ∼12,400 cR, giving an average correspondence of 240 kb/cR. The frameworks are all LOD 3 chromosomal maps consisting of 775 radiation-hybrid-mapped genetic markers and ESTs. To date, we have generated radiation-hybrid-mapping data for >14,000 novel ESTs identified by our Rat Gene Discovery and Mapping Project (http://ratEST.uiowa.edu), from which we have placed >11,000 on our framework maps. To minimize mapping errors, ESTs were mapped in duplicate and consensus RH vectors produced for use in the placement procedure. This EST map was then used to construct high-density comparative maps between rat and human and rat and mouse. These maps will be a useful resource for positional cloning of genes for rat models of human diseases and in the creation and verification of a tiling set of map order for the upcoming rat-genome sequencing.
A Novel Chromatin Immunoprecipitation and Array (CIA) Analysis Identifies a 460-kb CENP-A-Binding Neocentromere DNA
Authors: Lo Anthony W.I. , Magliano Dianna J. , Sibson Mandy C. , Kalitsis Paul , Craig Jeffrey M. , Choo K.H. Andy
Published: March 2019

Centromere protein A (CENP-A) is an essential histone H3-related protein that constitutes the specialized chromatin of an active centromere. It has been suggested that this protein plays a key role in the epigenetic marking and transformation of noncentromeric genomic DNA into functional neocentromeres. Neocentromeres have been identified on more than two-thirds of the human chromosomes, presumably involving different noncentromeric DNA sequences, but it is unclear whether some generalized sequence properties account for these neocentromeric sites. Using a novel method combining chromatin immunoprecipitation and genomic array hybridization, we have identified a 460-kb CENP-A-binding DNA domain of a neocentromere derived from the 20p12 region of an invdup (20p) human marker chromosome. Detailed sequence analysis indicates that this domain contains no centromeric α-satellite, classical satellites, or other known pericentric repetitive sequence motifs. Putative gene loci are detected, suggesting that their presence does not preclude neocentromere formation. The sequence is not significantly different from surrounding non-CENP-A-binding DNA in terms of the prevalence of various interspersed repeats and binding sites for DNA-interacting proteins (Topoisomerase II and High-Mobility-Group protein I). Notable variations include a higher AT content similar to that seen in human α-satellite DNA and a reduced prevalence of long terminal repeats (LTRs), short interspersed repeats (SINEs), and Alus. The significance of these features in neocentromerization is discussed.
DNA Transfection Mediated by Cationic Lipid Reagents
Authors: Kumar Priti , Nagarajan Arvindhan , Uchil Pradeep D.
Published: March 2019

Liposomal transfection reagents vary in their ability to transfect cell lines efficiently. Some are generalists, whereas others are best used with specific cell types. The nonliposomal FuGENE 6 and the cationic liposomal Lipofectamine 2000 are examples of reagents that can successfully transfect most adherent and suspension cell types (including several primary and hard-to-transfect cell types) with negligible toxicity and a minimal number of manipulations. Importantly, both reagents can be used to transfect cells in the presence of serum, minimizing the number of manipulations during the transfection procedure. We also provide an alternative protocol that uses the cationic lipid reagents Lipofectin and Transfectam.
Critical success factors for next generation technical education institutions
Authors: Kashiramka Smita , Sagar Mahim , Dubey Amlendu Kumar , Mehndiratta Amit , Sushil Sushil
Published: March 2019

Purpose

The purpose of this paper is to create a hierarchy of critical success factors affecting the higher technical education institutions, taking a case study of India. Using total interpretive structural modeling (TISM), the paper attempts to establish the inter-linkages among ten critical success factors for enhancing the performance of these institutions.

Design/methodology/approach

The paper employs Total Interpretive Structural Modeling (TISM) to understand the hierarchy of the factors and their interplay using response from 18 experts in the domain.

Findings

The findings reveal that autonomy and accountability coupled with availability of sustainable funds are the driving factors for the success of the institutions. Infrastructural facilities and establishment of centers of excellence act as amplification factors. Introduction of new programs and their accreditation, improvement in faculty quality, research output and improvement in performance of academically weak students emerge as process factors that drive the output factors, namely, academic performance and student placement.

Research limitations/implications

The major limitation of this study is the scope that was limited to 191 institutions, as mandated in the project.

Practical implications

This study has important implications for the institutions as well as the policy makers to channelize their focus and efforts on driving and amplification factors that would ultimately lead to enhanced performance of the next generation higher technical education institutions.

Originality/value

This paper is a part of pan India project carried out to assess the performance of higher technical education institutions in India.
Execution costs, investability, and actual foreign investment in emerging markets
Authors: Ahn Hee-Joon , Cai Jun , Cheung Yan-Leung
Published: March 2019

Purpose

This paper focuses on execution costs as liquidity measure. Execution costs are related to volatility and are an important component of a firm’s cost of capital. The purpose of this paper is to examine whether emerging market firms have lower execution costs when they face less restrictions on foreign investment and when they have more foreign shareholders.

Design/methodology/approach

The authors begin by documenting the cross-sectional behavior of execution costs. The authors then obtain preliminary evidence on the interaction between execution costs, the investability index and actual foreign investment. These results foreshadow those the authors obtain with the regression analysis. The ordinary least square results show that more investable firms have lower execution costs after the authors control for firm size, stock price, return volatility, industry effects and country effects. This evidence is very robust and highly significant. Direct foreign ownership (FO) in emerging market firms also appear to be associated with lower execution costs. The economic benefit from lowering the investability index on trade execution costs is highly significant.

Findings

Using a large cross-sectional sample from 23 emerging markets, the authors show that firms with more ex ante restrictions on FO, measured by the investability index, have lower execution costs, such as quoted spreads (QS) and effective spreads (ES), after the authors control for firm size, stock price, return volatility, industry factors and country effects. In addition, direct FO in emerging market firms appears to be associated with lower execution costs. However, ex ante restrictions on FO dominate the influence of direct FO. For a 0.5 increase in the investability index in the range of 0–1, the QS will be reduced by 17 percent of the mean QS, and the ES will be reduced by 12 percent of the mean ES from the sample stocks.

Originality/value

There are important differences between the approach and most of the financial liberalization studies. First, whereas most of the earlier studies are conducted at the level of country or market analysis, the investigation is at the level of individual stocks. Second, the authors focus on a cross-sectional association that avoids a criticism leveled at time series analyses. Over-time studies often use specific time points to represent financial liberalization watersheds. This approach can be misleading when financial liberalizations are viewed as processes that unfold over time. Third, the proxies for financial openness are available not only for individual firms across markets, but the authors also make a distinction between potential and actual foreign investment. The authors further categorize actual foreign investment into direct and indirect FO.
Augmentation of passive magnetic bearing performance by using air or iron intervals
Authors: Safaeian Reza , Heydari Hossein
Published: March 2019

Purpose

This paper aims to suggest the use of air or iron intervals between axially magnetized rings to increase the forces and stiffness of permanent magnet passive magnetic bearings (PMBs). The paper calculates the stiffness of such bearings through an analytical method and optimizes the dimensions of the magnets for achieving maximum stiffness.

Design/methodology/approach

For determining the magnetic fields distribution, forces and stiffness of the bearings, a 2D analytical method is used, based on the subdomain method. For the sake of generalization, all of the parameters are normalized and optimized for maximum normalized stiffness per magnet volume ratio.

Findings

The optimum sizes of the magnets as well as the optimum dimensions of the air or iron intervals are calculated in this paper. The optimum sizes of the magnets are around the air gap length and it is very difficult to realize them. Using iron intervals can improve the stiffness to the extremely high values in practical dimensions of the magnets.

Originality/value

This paper presents a novel configuration for improving the performance of PMBs with alternately axially magnetized rings.
Investigation of facilities management practices for providing feedback during the design development and review stages
Authors: Fatayer Fadi A. , Hassanain Mohammad A. , Abdallah Abdullatif , Al-Hammad Abdul-Mohsen
Published: March 2019

Purpose

The purpose of this paper is to investigate the current practices of the early facilities management (FM) involvement during the design development and review stages (DDRS), and recommend activities aimed at achieving better integration.

Design/methodology/approach

A comprehensive literature review was conducted to ascertain the challenges faced by the integrated design team (IDT) in the absence of the facilities managers’ review of design solutions, and underscore the significance of the early involvement of facilities managers during the DDRS. A questionnaire survey was then developed for collecting data on eight aspects of the current practices of early FM involvement during the DDRS. The questionnaire survey was administered to the FM departments of 13 long established, public universities in Saudi Arabia. Ten responses were obtained and analyzed.

Findings

The findings suggest that the early involvement of the FM department enhances the operation and maintenance of facilities. This has been measured through reductions in the number of architectural, structural, electrical, plumbing, heating, ventilating and air conditioning defects.

Practical implications

Recommendations were provided to facilitate the process of integrating the practices of two influential stakeholders of building projects. These recommendations encompass the need for maintainability considerations at the early schematic stage, the necessity of direct contact between the two parties and the necessity of facility managers’ increased familiarity of the design stage activities, among other recommendations. In this way, the study promotes the awareness of the significance of integrating FM with the IDT at the DDRS.

Originality/value

This study contributes to the literature and practice by presenting a detailed analysis of the integration process between the FM department and the IDT. Furthermore, the outcomes of the integration between the parties were measured to assess the effectiveness of the collaboration and highlight the possible areas of improvement.