bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA Methylation Atlas of the Mouse Brain at Single-Cell Resolution
Authors: Liu Hanqing , Zhou Jingtian , Tian Wei , Luo Chongyuan , Bartlett Anna , Aldridge Andrew , Lucero Jacinta , Osteen Julia K. , Nery Joseph R. , Chen Huaming , Rivkin Angeline , Castanon Rosa G , Clock Ben , Li Yang Eric , Hou Xiaomeng , Poirion Olivier B. , Preissl Sebastian , O’Connor Carolyn , Boggeman Lara , Fitzpatrick Conor , Nunn Michael , Mukamel Eran A. , Zhang Zhuzhu , Callaway Edward M. , Ren Bing , Dixon Jesse R. , Behrens M. Margarita , Ecker Joseph R.
Published: May 2020

Mammalian brain cells are remarkably diverse in gene expression, anatomy, and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. We carried out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single nucleus DNA methylation sequencing to profile 110,294 nuclei from 45 regions of the mouse cortex, hippocampus, striatum, pallidum, and olfactory areas. We identified 161 cell clusters with distinct spatial locations and projection targets. We constructed taxonomies of these epigenetic types, annotated with signature genes, regulatory elements, and transcription factors. These features indicate the potential regulatory landscape supporting the assignment of putative cell types, and reveal repetitive usage of regulators in excitatory and inhibitory cells for determining subtypes. The DNA methylation landscape of excitatory neurons in the cortex and hippocampus varied continuously along spatial gradients. Using this deep dataset, an artificial neural network model was constructed that precisely predicts single neuron cell-type identity and brain area spatial location. Integration of high-resolution DNA methylomes with single-nucleus chromatin accessibility data allowed prediction of high-confidence enhancer-gene interactions for all identified cell types, which were subsequently validated by cell-type-specific chromatin conformation capture experiments. By combining multi-omic datasets (DNA methylation, chromatin contacts, and open chromatin) from single nuclei and annotating the regulatory genome of hundreds of cell types in the mouse brain, our DNA methylation atlas establishes the epigenetic basis for neuronal diversity and spatial organization throughout the mouse brain.
Excitatory GABAergic modulation of calyx terminals in the vestibular sensory end organ
Authors: Ramakrishna Yugandhar , Sadeghi Soroush G.
Published: May 2020

GABAergic sources have been identified in the vestibular sensory neuroepithelium, mainly in the supporting cells. However, existence of GABA receptors or any possible GABAergic effects on vestibular nerve afferents has not been investigated. The current study was conducted to determine whether activation of GABA-B receptors affects calyx afferent terminals in the central region of the cristae of the semicircular canals in rats. We used patch clamp recording in P13 – P18 Sprague-Dawley rats of either sex. Application of GABA-B receptor agonist baclofen inhibited voltage activated outward potassium currents. This effect was blocked by selective GABA-B receptor antagonist CGP 35348. Antagonists of small (SK) and large (BK) current potassium channels resulted in an almost complete block of baclofen effect. The remaining baclofen effect was due to inhibition of voltage gated calcium channels and was blocked by cadmium chloride. Furthermore, baclofen had no effect in the absence of calcium in the extracellular fluid. Inhibition of potassium currents by GABA-B activation resulted in an excitatory effect on calyx terminal action potential firing. While in the control condition calyces could only fire a single action potential during step depolarizations, in the presence of baclofen they fired continuously during steps and a few even showed spontaneous discharge. We also found a decrease in threshold for action potential generation and a decrease in first spike latency during step depolarization. These results provide the first evidence for the presence of GABA-B receptors on calyx terminals, show that their activation results in an unusual excitatory effect and that GABA inputs could be used to modulate calyx response properties.
The heart microbiome of insectivorous bats from Central and South Eastern Europe
Authors: Corduneanu Alexandra , Mihalca Andrei Daniel , Sándor Attila D. , Hornok Sándor , Malmberg Maja , Viso Natalia Pin , Bongcam-Rudloff Erik
Published: May 2020

Host associated microbiome not only may affect the individual health-status or provide insights into the species- or group specific bacterial communities but may act as early warning signs in the assessment of zoonotic reservoirs, offering clues to predict, prevent and control possible episodes of emerging zoonoses. Bats may be carriers and reservoirs of multiple pathogens such as viruses, bacteria and parasites, showing in the same time robust immunity against many of them. The microbiota plays a fundamental role on the induction, training and function of the host immune system and the immune system has largely evolved in order to maintain the symbiotic relationship of the host with these diverse microbes. Thus, expanding our knowledge on bat-associated microbiome it can be usefully in understanding bats’ outstanding immune capacities. The aim of this study was to investigate the presence of different bacterial communities in heart tissue of insectivorous bats,Nyctalus noctula, Pipistrellus pipistrellusandRhinoplophus hipposideros, from Central and Eastern Europe using high-throughput sequencing of variable regions of the 16S rRNA. In addition, species-specific PCRs were used to validate the presence of the vector-borne pathogensBartonellaspp. andRickettsiaspp. In this study we identified a wide variety of bacterial groups, with the most abundant phyla being Proteobacteria and Firmicutes. The results showed that at individual level, the year or location had no effect on the diversity and composition of the microbiome, however host species determined both structure and abundance of the bacterial community. We report the presence of vector-borne bacteriaBartonellaspp. in samples ofN. noctulaand indications ofRickettsiaspp. inR. hipposideros. Our results provide a first insight into the bacterial community found in heart tissue of bats from Central and South Eastern Europe.
Grain Fe and Zn Contents Linked SSR Markers Based Genetic Diversity Reveal Perspective for Marker Assisted Biofortification Breeding in Rice
Authors: Raza Qasim , Riaz Awais , Saher Hira , Bibi Ayesha , Ali Syed Sultan , Sabar Muhammad
Published: May 2020

Rice is critical for sustainable food and nutritional security; however, nominal micronutrient quantities in grains aggravate malnutrition in rice-eating poor populations. Here, we assessed genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence repeat (SSR) markers in 56 fine and coarse grain rice accessions of different geographical origin. Aromatic fine gain accessions contained relatively higher Fe and Zn contents in brown rice (BR) than coarse grain accessions. Genotyping with 24 SSR markers identified 21 polymorphic markers, among which seventeen demonstrated higher gene diversity and polymorphism information content (PIC) values, strongly indicating that markers used in current research were moderate to highly informative for evaluating genetic diversity. Population structure, principal coordinate and phylogenetic analyses classified studied rice accessions into two fine grain specific and one fine and coarse grain admixture subpopulations. Single marker analysis recognized four ZnBR and single FeBR significant marker-trait associations (MTAs), contributing 15.41–39.72% in total observed phenotypic variance. Furthermore, high grain Fe and Zn contents linked marker alleles from significant MTAs were also identified. Collectively, these results indicate availability of wide genetic diversity in rice germplasm and perspective for marker-assisted biofortification breeding.
Transposable Elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita
Authors: Kozlowski Djampa KL , Hassanaly-Goulamhoussen Rahim , Rocha Martine Da , Koutsovoulos Georgios D , Bailly-Bechet Marc , Danchin Etienne GJ
Published: May 2020

Abstract

Despite reproducing without sexual recombination, the root-knot nematode Meloidogyne incognita is adaptive and versatile. Indeed, this species displays a global distribution, is able to parasitize a large range of plants and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability without sex remain poorly known and only low variation at the single nucleotide polymorphism level have been observed so far across different geographical isolates with distinct ranges of compatible hosts. Hence, other mechanisms than the accumulation of point mutations are probably involved in the genomic dynamics and plasticity necessary for adaptability. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M. incognita. Here, we have annotated the TE content of M. incognita, analyzed the statistical properties of this TE content, and used population genomics approach to estimate the mobility of these TEs across 12 geographical isolates, presenting phenotypic variations. The TE content is more abundant in DNA transposons and the distribution of TE copies identity to their consensuses sequence suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed variations across the different isolates. Compared to the M. incognita reference genome, we detected the insertion of some TEs either within genic regions or in the upstream regulatory regions. These predicted TEs insertions might thus have a functional impact. We validated by PCR the insertion of some of these TEs, confirming TE movements probably play a role in the genome plasticity with possible functional impacts.
Intact nucleosomal context enables chromodomain reader MRG15 to distinguish H3K36me3 from -me2
Authors: Faulkner Sarah , Couturier Antony M. , Josephson Brian , Watts Tom , Davis Benjamin G. , Esashi Fumiko
Published: May 2020

A wealth ofin vivoevidence demonstrates the physiological importance of histone H3 trimethylation at lysine 36 (H3K36me3), to which chromodomain-containing proteins, such as MRG15, bind preferentially compared to their dimethyl (H3K36me2) counterparts. However,in vitrostudies using isolated H3 peptides have failed to recapitulate a causal interaction. Here, we show that MRG15 can clearly discriminate between synthetic, fully intact model nucleosomes containing H3K36me2 and H3K36me3. MRG15 docking studies, along with experimental observations and nucleosome structure analysis suggest a model where the H3K36 side chain is sequestered in intact nucleosomes via a hydrogen bonding interaction with the DNA backbone, which is abrogated when the third methyl group is added to form H3K36me3. Hence, this mechanism provides a ‘methyl-switch’ for contextdependent reader selectivity. These results highlight the importance of such intra-chromatin interactions in understanding epigenetic regulation, a feature which is absent in commonly-used peptide or histone-only models.
YTHDF2 is essential for spermatogenesis and fertility through mediating a wave of transcript transition during spermatogonial differentiation
Authors: Zhao Xin-Xi , Lin Zhen , Fan Yong , Zhang Yu-Jie , Li Fei , Hong Tong , Feng Hua , Tong Ming-Han , Wang Ning-Ling , Kuang Yan-Ping , Lyu Qi-Feng
Published: May 2020

The dynamic and reversible regulation roles of m6A modification, and the characterization of m6A readers have provided new insights into spermatogenesis at post-transcriptional level. YTHDF2 has been reported to recognize and mediate the m6A-containing transcripts decay during the mouse oocyte mature, embryonic stem cell differentiation, neural development, and zebrafish maternal-to-zygotic transition. However, the roles of YTHDF2 in mammalian spermatogenesis are uncertain. Here, we generated germ cell-specificYthdf2mutants (Ythdf2-vKO) at a C57BL/6J background, and demonstrated that YTHDF2 was essential for mouse spermatogenesis and fertility.Ythdf2-vKOprovided oligoasthenoteratozoospermia (OAT) phenotype with increased apoptosis in germ cells. High-throughput RNA-seq of the testis tissue showed the failure of the degradation of a wave of YTHDF2 target mRNA. Interestingly, RNA-seq analysis combined with our previous single-cell transcriptomics data of mouse spermatogenesis pointed out the failure of a wave of transcript transition during the spermatogenesis ofYthdf2-vKO, which was confirmed by gene expression analysis of diplotene spermatocytes and round spermatids obtained through fluorescence-activated cell sorting using qPCR. Our study demonstrates the fundamental role of YTHDF2 during mouse spermatogenesis and provides a potential candidate for the diagnosis of male infertility with OAT syndrome.

Author summary

Male infertility is becoming a worldwide health problem. Male gamete is generated through spermatogenesis, which is a complicated developmental process with dynamic transcriptome changes. RNA m6A modification has been reported as the most prominently internal mRNA modification, which control the tune of gene expression through mRNA splicing, export, translation and decay. RNA m6A modification is catalyzed by “writers”, and could be removed by “erasers”. The m6A modification enzymes are reported to play important roles during spermatogenesis. Given that the biological function of m6A modification are mediated through its “readers”, its readers might be proposed to be involved in the regulation of spermatogenesis. YTHDF2, as a reader of m6A modification, has been reported to mediate the m6A-containing transcripts decay. To explore the roles of YTHDF2 in spermatogenesis, we used germ cell-specific mutation strategy to knock out the mouseYthdf2. The mutants provided oligoasthenoteratozoospermia phenotype. Our study demonstrate that YTHDF2 is essential for mouse spermatogenesis. YTHDF2 could be a potential candidate for the diagnosis of oligoasthenoteratozoospermia syndrome.
Optimization of human papillomavirus-based pseudovirus techniques for efficient gene transfer
Authors: Gilson Timra D. , Gibson Ryan T. , Androphy Elliot J.
Published: May 2020

Human papillomavirus (HPV) L1 and L2 capsid proteins self-assemble into virions capable of efficiently packaging either its 8 kilobase genome or non-viral DNA. The ability of HPV capsids to package non-viral DNA makes these a useful tool for delivering plasmids to study proteins of interest in a variety of cell types. We describe optimization of current methods and present new protocols for using HPV capsids to deliver non-viral DNA thereby providing an alternative to DNA transfection. Using keratinocyte generated extracellular matrices can enhance infection efficiency in keratinocytes, hepatocytes and neuronal cells. Furthermore, we describe a suspension-based efficient technique for infecting different cell types.
The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold
Authors: Steckelberg Anna-Lena , Vicens Quentin , Costantino David A. , Nix Jay C. , Kieft Jeffrey S.
Published: May 2020

Exonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5’ to 3’ exonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.
Complementary and divergent roles for Ctage5 and Tango1 in zebrafish
Authors: Clark Eric M. , Link Brian A.
Published: May 2020

Coat protein complex II (COPII) factors mediate cargo export from the endoplasmic reticulum (ER), but bulky collagens and lipoproteins are too large for traditional COPII vesicles. Mammalian CTAGE5 and TANGO1 have been well characterized individually as specialized cargo receptors at the ER that function with COPII coats to facilitate trafficking of bulky cargoes. Here, we present a genetic interaction study in zebrafish of deletions inctage5,tango1, or both to investigate their potential distinct and complimentary functions. We found that Ctage5 and Tango1 have different roles related to organogenesis, collagen versus lipoprotein trafficking, stress-pathway activation, and survival. While deletion of bothctage5andtango1compounded phenotype severity, deletion of either factor alone revealed novel tissue specific defects in the building of heart, muscle, lens, and intestine, in addition to the previously described roles in the development of neural and cartilage tissues. Together, our results suggest that Ctage5 and Tango1 have overlapping, but also divergent roles in tissue development and homeostasis.

In this genetic study Ctage5 and Tango1 endoplasmic reticulum cargo receptors were investigated togetherin vivofor the first time. Cell differentiation, survival, trafficking, and stress pathway activation were investigated.
An incoherent feedforward loop interprets NFκB/RelA dynamics to determine TNF-induced necroptosis decisions
Authors: Metzig Marie Oliver , Tang Ying , Mitchell Simon , Taylor Brooks , Foreman Robert , Wollman Roy , Hoffmann Alexander
Published: May 2020

Balancing cell death is essential to maintain healthy tissue homeostasis and prevent disease. Tumor necrosis factor (TNF) not only activates nuclear factor κB (NFκB), which coordinates the cellular response to inflammation, but may also trigger necroptosis, a pro-inflammatory form of cell death. Whether TNF-induced NFκB cross-regulates TNF-induced necroptosis fate decisions is unclear. Live-cell microscopy and model-aided analysis of death kinetics identified a molecular circuit that interprets TNF-induced NFκB/RelA dynamics to control necroptosis decisions. Inducible expression of TNFAIP3/A20 forms an incoherent feedforward loop to interfere with the RIPK3-containing necrosome complex and protect a fraction of cells from transient, but not long-term TNF exposure. Furthermore, dysregulated NFκB dynamics often associated with disease diminish TNF-induced necroptosis. Our results suggest that TNF’s dual roles in either coordinating cellular responses to inflammation, or further amplifying inflammation are determined by a dynamic NFκB-A20-RIPK3 circuit, that could be targeted to treat inflammation and cancer.
B1 and B2 B cells are characterized by distinct CpG modification states at DNMT3A-maintained enhancers
Authors: Mahajan Vinay S. , Mattoo Hamid , Sun Na , Viswanadham Vinayak , Yuen Grace J. , Allard-Chamard Hugues , Ahmad Maimuna , Murphy Samuel JH , Cariappa Annaiah , Tuncay Yesim , Pillai Shiv
Published: May 2020

We show that DNA methylation is a layered process in B lymphocytes. An underlying foundational methylome is stably established during B lineage commitment and overlaid with a DNMT3A-maintained dynamic methylome which is sculpted in distinct ways in B1 and B2 B cells during B cell development. An engineered loss of DNMT3A after commitment to the B lineage unmasks a foundational methylome that is shared in both B1 and B2 sub-lineages. The dynamic methylome is comprised of novel enhancers whose methylation state is maintained by DNMT3A but can be modulated in strikingly different ways in B1 and B2 B cells. During B1 B cell development, the dynamic methylome undergoes a prominent programmed demethylation event that is not observed during B2 B cell development. The methylation pattern of the dynamic methylome is determined by the coincident recruitment of DNMT3A and TET enzymes and it regulates the developmental expression of B1 and B2 lineage-specific genes.
Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis
Authors: Xu Chaoyi , Fischer Douglas K. , Rankovic Sanela , Li Wen , Dick Rob , Runge Brent , Zadorozhnyi Roman , Ahn Jinwoo , Aiken Christopher , Polenova Tatyana , Engelman Alan N. , Ambrose Zandrea , Rousso Itay , Perilla Juan R.
Published: May 2020

Reverse transcription, an essential event in the HIV-1 lifecycle, requires deoxynucleotide triphosphates (dNTPs) to fuel DNA synthesis, thus requiring penetration of dNTPs into the viral core. The central cavity of the capsid protein (CA) hexamer reveals itself as a plausible channel that allows the passage of dNTPs into assembled capsids. Nevertheless, the molecular mechanism of nucleotide import into the capsid remains unknown. Employing all-atom molecular dynamics simulations, we established that cooperative binding between nucleotides inside a CA hexamer cavity results in energetically-favorable conditions for passive translocation of dNTPs into the HIV-1 capsid. Furthermore, binding of the host cell metabolite inositol hexakisphosphate (IP6) enhances dNTP import, while binding of synthesized molecules like benzenehexacarboxylic acid (BHC) inhibits it. The enhancing effect on reverse transcription by IP6and the consequences of interactions between CA and nucleotides were corroborated using atomic force microscopy, transmission electron microscopy, and virological assays. Collectively, our results provide an atomistic description of the permeability of the HIV-1 capsid to small molecules and reveal a novel mechanism for the involvement of metabolites in HIV-1 capsid stabilization, nucleotide import and reverse transcription.
Temporal Dysbiosis of Infant Nasal Microbiota Relative to Respiratory Syncytial Virus Infection
Authors: Grier Alex , Gill Ann L. , Kessler Haeja A. , Corbett Anthony , Bandyopadhyay Sanjukta , Java James , Holden-Wiltse Jeanne , Falsey Ann R. , Topham David J. , Mariani Thomas J. , Caserta Mary T. , Walsh Edward E. , Gill Steven R.
Published: May 2020

Rationale

Respiratory Syncytial Virus (RSV) infection is a leading cause of infant respiratory disease and hospitalization. Infant airway microbiota occupying the nasopharynx have been associated with respiratory disease risk and severity. The extent to which interactions between RSV and microbiota occur in the airway, and their impact on respiratory disease severity and infection susceptibility, are not well understood.

Objectives

To characterize associations between the nasal microbiota and RSV infection before, during, and after infants’ first respiratory illness.

Methods

Nasal 16S rRNA microbial community profiling of two cohorts of infants in the first year of life: 1) a cross-sectional cohort of 89 RSV infected infants sampled during illness and 102 population matched healthy controls, and 2) an individually matched longitudinal cohort of 12 infants who developed RSV infection and 12 who did not, sampled at time points before, during, and after infection.

Measurements and Main Results

We identified 12 taxa significantly associated with RSV infection. All 12 were differentially abundant during infection, with seven differentially abundant prior to infection, and eight differentially abundant after infection. Eight of these taxa were associated with disease severity. Nasal microbiota composition was more discriminative of healthy vs. infected than of disease severity.

Conclusions

Our findings elucidate the chronology of nasal microbiota dysbiosis and suggest an altered developmental trajectory associated with first-time RSV infection. Microbial temporal dynamics reveal indicators of disease risk, correlates of illness and severity, and the impact of RSV infection on microbiota composition. Identified taxa represent appealing targets for additional translationally-oriented research.
Role of combined cell membrane and wall mechanical properties regulated by polarity signals in cell budding
Authors: Tsai Kevin , Britton Samuel , Nematbakhsh Ali , Zandi Roya , Chen Weitao , Alber Mark
Published: May 2020

The budding yeast,Saccharomyces cerevisiae, is a prime biological model to study mechanisms underlying asymmetric growth. Previous studies have shown that, prior to yeast bud emergence, polarization of a conserved small GTPase, Cdc42, must be established. Additionally, hydrolase changes the mechanical properties of the cell wall and plasma membrane with the periplasm between them (cell surface). However, how the surface mechanical properties in the emerging bud are different from the properties of the mother cell and their role in bud formation are not well understood. We hypothesize that the polarized chemical signal alters the local dimensionless ratio of stretching to bending stiffness of the cell surface of the emerging yeast bud. To test this hypothesis, a novel three-dimensional coarse-grained particle-based model has been developed which describes inhomogeneous mechanical properties of the cell surface. Model simulations suggest that regulation of the dimensionless ratio of stretching to bending stiffness of the cell surface is necessary to initiate bud formation. Furthermore, model simulations predict that bud shape depends strongly on the experimentally observed molecular distribution of the polarized signaling molecule Cdc42, while the neck shape of the emerging bud is strongly impacted by the properties of the chitin and septin ring. This 3D model of asymmetric cell growth can also be used for studying viral budding and other vegetative reproduction processes performed via budding.
Multiplex CRISPRi-Cas9 silencing of planktonic and stage-specific biofilm genes inEnterococcus faecalis
Authors: Afonina Irina , Ong June , Chua Jerome , Lu Timothy , Kline Kimberly A.
Published: May 2020

Enterococcus faecalisis an opportunistic pathogen, which can cause multidrug-resistant life-threatening infections. Gaining a complete understanding of enterococcal pathogenesis is a crucial step in identifying a strategy to effectively treat enterococcal infections. However, bacterial pathogenesis is a complex process often involving a combination of genes and multi-level regulation. Compared to established knockout methodologies, CRISPRi approaches enable rapid and efficient silencing of genes to interrogate gene products and pathways involved in pathogenesis. As opposed to traditional gene inactivation approaches, CRISPRi can also be quickly repurposed for multiplexing or used to study essential genes. Here we have developed a novel dual-vector nisin-inducible CRISPRi system inE. faecalisthat can efficiently silence via both non-template and template strand targeting. Since nisin-controlled gene expression system is functional in various Gram-positive bacteria, the developed CRISPRi tool can be extended to other genera. This system can be applied to study essential genes, genes involved in antimicrobial resistance, and genes involved in biofilm formation and persistence. The system is robust, and can be scaled up for high-throughput screens or combinatorial targeting. This tool substantially enhances our ability to study enterococcal biology and pathogenesis, host-bacteria interactions, and inter-species communication.

IMPORTANCE

Enterococcus faecaliscauses multidrug resistant life-threatening infections, and is often co-isolated with other pathogenic bacteria from polymicrobial biofilm-associated infections. Genetic tools to dissect complex interactions in mixed microbial communities are largely limited to transposon mutagenesis and traditional time- and labour-intensive allelic exchange methods. Built upon streptococcal dCas9, we developed an easily-modifiable, inducible CRISPRi system forE. faecalisthat can efficiently silence single and multiple genes. This system can silence genes involved in biofilm formation, antibiotic resistance, and can be used to interrogate gene essentiality. Uniquely, this tool is optimized to study genes important for biofilm initiation, maturation, and maintenance, and can be used to perturb pre-formed biofilms. This system will be valuable to rapidly and efficiently investigate a wide range of aspects of complex enterococcal biology.
Characterising the Diffusion of Biological Nanoparticles on Fluid and Elastic Membranes
Authors: Debets V.E. , Janssen L.M.C. , Šarić A.
Published: May 2020

Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes.
Pathogenic variants in KPTN gene identified by clinical whole-genome sequencing
Authors: Thiffault Isabelle , Atherton Andrea , Heese Bryce A. , T. Abdelmoity Ahmed , Pawar Kailash , Farrow Emily , Zellmer Lee , Miller Neil , Soden Sarah , Saunders Carol
Published: May 2020

Status epilepticus is not rare in critically ill intensive care unit patients, but its diagnosis is often delayed or missed. The mortality for convulsive status epilepticus is dependent on the underlying aetiologies and the age of the patients and thus varies from study to study. In this context, effective molecular diagnosis in a pediatric patient with a genetically heterogeneous phenotype is essential. Homozygous or compound heterozygous variants in KPTN have been recently associated with a syndrome typified by macrocephaly, neurodevelopmental delay, and seizures. We describe a comprehensive investigation of a 9-yr-old male patient who was admitted to the intensive care unit, with focal epilepsy, static encephalopathy, autism spectrum disorder, and macrocephaly of unknown etiology, who died of status epilepticus. Clinical whole-genome sequencing revealed compound heterozygous variants in the KPTN gene. The first variant is a previously characterized 18-bp in-frame duplication (c.714_731dup) in exon 8, resulting in the protein change p.Met241_Gln246dup. The second variant, c.394 + 1G > A, affects the splice junction of exon 3. These results are consistent with a diagnosis of autosomal recessive KPTN-related disease. This is the fourth clinical report for KPTN deficiency, providing further evidence of a wider range of severity.
Redetermination and new description of the crystal structure of vanthoffite, Na6Mg(SO4)4
Authors: Balić-Žunić Tonči , Pamato Martha G. , Nestola Fabrizio
Published: May 2020

The crystal structure of vanthoffite {hexasodium magnesium tetrakis[sulfate(VI)]}, Na6Mg(SO4)4, was solved in the year 1964 on a synthetic sample [Fischer & Hellner (1964).Acta Cryst.17, 1613]. Here we report a redetermination of its crystal structure on a mineral sample with improved precision. It was refined in the space groupP21/cfrom a crystal originating from Surtsey, Iceland. The unique Mg (site symmetry \overline{1}) and the two S atoms are in usual, only slightly distorted octahedral and tetrahedral coordinations, respectively. The three independent Na atoms are in a distorted octahedral coordination (1×) and distorted 7-coordinations intermediate between a `split octahedron' and a pentagonal bipyramid (2×). [MgO6] coordination polyhedra interchange with one half of the sulfate tetrahedra in <011> chains forming a (100) meshed layer, with dimers formed by edge-sharing [NaO7] polyhedra filling the interchain spaces. The other [NaO7] polyhedra are organized in a parallel layer formed by [010] and [001] chains united through edge sharing and bonds to the remaining half of sulfate groups and to [NaO6] octahedra. The two types of layers interconnect through tight bonding, which explains the lack of morphological characteristics typical of layered structures.
Comparison of total phenolic content and antioxidant activities in selected coloured plants
Authors: Wong Pei Yun , Tan Seok Tyug
Published: May 2020

Purpose

Literature has consistently reported that coloured plants are rich in dietary bioactive compounds. Therefore, this study aims to compare the total phenolic content and antioxidant activities in selected coloured plants (blue butterfly pea flower, roselle calyx, yellow bell pepper and purple sweet potato).

Design/methodology/approach

Total Phenolic Content (TPC) was determined using Folin–Ciocalteu assay, while antioxidant activities were evaluated using 2,2-dophenyl-1-picryl-hydrazyl-hydrate (DPPH) radical scavenging, Ferric Reducing Antioxidant Power (FRAP) and Trolox Equivalent Antioxidant Capacity (TEAC) assays.

Findings

TPC was reported from 273.15 ± 19.57 µg GAE/g DW (blue butterfly pea flower extract) to 363.10 ± 7.94 µg GAE/g DW (roselle calyx extract). Antioxidant activities as determined by DPPH assay ranged from 17.26 ± 0.06% (purple sweet potato extract) to 83.38 ± 1.04% (yellow bell pepper extract); while for FRAP assay was 4.92 ± 0.18 mg Fe (II)/g DW (purple sweet potato extract) to 128.33 ± 11.59 mg Fe (II)/g DW (roselle calyx extract). On the other hand, TEAC values were in the range of 15.26 ± 2.83 µg Trolox/g DW (roselle calyx extract) to 364.27 ± 7.14 µg Trolox/g DW (blue butterfly pea flower extract). A significant moderate positive correlation was observed between TPC and DPPH (r = 0.562) as well as TPC and FRAP (r = 0.686).

Originality/value

This study was the first to compare the total phenolic content and antioxidant activities in coloured plants. Findings derived from this study can be extended to the formulation of natural food colourants and nutraceuticals.
Relative export competitiveness of the Cambodian rice sector
Authors: Kea Sokvibol , Li Hua , Shahriar Saleh , Abdullahi Nazir Muhammad
Published: May 2020

Purpose

In this paper, the authors derive time-varying relative export competitiveness (REC) of the Cambodian rice sector from 1995 to 2018 and examine the key determinants of the REC.

Design/methodology/approach

Three different REC indexes are calculated in this paper. The authors also developed the relative symmetric export competitiveness (RSEC) index for calculation of comparative advantage. The short-run regression (SRR) model was applied for capturing the determinants of the REC.

Findings

The study results reveal that Cambodia's rice exports became relatively competitive over time. The key findings suggest the Cambodian REC was strengthened as a result of a successful implementation of rice policy and rectangular strategy. The benefits gained from EBA and BRI were found to be the factors contributed to the REC. The higher per capita income had a positive effect on the REC, while higher domestic prices reduced the REC in some phases of the sectoral development.

Research limitations/implications

Further research is needed in two directions. First, the future studies might focus on other agro-products of Cambodia. Second, the development of the crop-specific factor endowment (CFE) model to consider the effect of endowment factors on the REC could be preferred in light of the data availability.

Originality/value

The research enriches the literature on the agricultural trade and provides a basis for further studies. This work makes a few contributions. First, it is the first study on the REC analysis for the Cambodian rice sector. Second, the latest 24-year data sets were covered. Third, a wide range of comparisons of REC among the world's top rice exporters was provided following implications of the various economic policies and foreign policy strategies, such as RS, EBA and BRI.
Late!: 100% social
Authors: Villalobos Araya Rodrigo
Published: May 2020

Learning outcomes

The learning outcomes are designing an empresarial strategy and considering different business strategies and environment variables.

Case overview/synopsis

On November of 2015, Eduardo Castillo, General Manager of Late! (B Corporation) programed a directory reunion in which he had to pose a proposal of strategic expansion and growth for the company for future years. A fine of October 2015 publicly revealed the collusion of the two large conglomerates of tissue paper in the Chilean market, with this situation Eduardo took advantage of the discomfort of the consumers and looked alternative brands, he evaluates the launching of a new product: toilet paper Late!. Eduardo had to present at the board meeting the backgrounds to decide the expansion and the strategic growth of the company, taking advantage of the collusion case of the toilet paper or continue their successful project of bottled water.

Complexity academic level

This case focuses primarily on the processes of social enterprise for undergraduate or graduate courses in social entrepreneurship, business model innovation, sustainability, strategic management, emerging markets and business in Chile. Also, this case is also ideal to teach the “business model canvas” and “B Corp.”

Supplementary materials

Teaching Notes are available for educators only.

Subject code

CSS 11: Entrepreneurship.
Tadweer: improving municipal solid waste sustainability practices
Authors: Al Bloushi Badreya Gharib , Ahmad Syed Zamberi , Bani Mfarrej Manar Fawzi
Published: May 2020

Learning outcomes

To examine and create an ideal pathway model that can implement aiming to change the current improper practices in managing municipal solid waste (MSW) to sustainable practices. To acquire a better understanding of public participation and community culture helps in achieving the aim of reducing the amount of waste generation, sending less waste to landfill sites and encouraging the reuse and recycling of materials instead. To help students whom the awareness in the community regarding the importance of protecting the environment and acting in a civilization way has increased. To improve the MSW sustainability practices and enhance the waste sustainability practices together with energy and material conservation. To have more extensive knowledge and awareness of issues in waste management and some of the dilemmas managers of strategic and operations face.

Case overview/synopsis

Abu Dhabi’s center of waste management is known as Tadweer is a governmental entity under the Abu Dhabi Executive Council. Tadweer is responsible for managing every MSWs includes collecting, transferring, segregating, treating, recycling, reusing and tracking all kinds of wastes. CEO of Tadweer Dr Salem Alkabi called his team that manages various departments such as strategy, operations, projects and licensing. The meeting was to discuss Tadweer’s future directing and strategy for mismanagement of solid waste dumping into landﬁlls in Abu Dhabi. Dumping in landfills is the main challenge Tadweer faced. Mr. Abdulrahman Albloushi’s strategy and business development executive director of Tadweer highlighted to Alkaabi how Tadweer could improve the waste management practices to make it more sustainable. Furthermore, assisting the center gets more benefit from the waste s instead of losing this valuable waste into landfills. Consequently, Mr. Abdulrahman must grapple with some difficult questions: how much the effectiveness in collecting waste from where it generated and removing it out-of-sight?

Complexity academic level

This case study is designed for undergraduate and postgraduate students, and executive MBA students of business management programs, especially for waste management, environmental management and strategic management courses.

Supplementary materials

Teaching Notes are available upon request.

Subject code

CSS 4: Environmental management.
Sunshine Fastech Pvt. Ltd.: working capital financing decision
Authors: Mehta Bhoomi Ruchit
Published: May 2020

Learning outcomes

The learning outcomes of this paper is to understand the working capital finances offered by bank; comprehend application by the company, loan proposal and bank procedure for additional finance; compute, analyze and interpret financial statements of company and its peers; and assess various factors to be considered while taking loan sanctioning decisions.

Case overview/synopsis

Sunshine had expanded its business by starting in-house manufacturing of a few stages of production of fasteners. Sunshine was in urgent need of additional finance for working capital and had applied to Rajya Bank of India Ltd. (RBIL), requesting to enhance working capital finance limits and other changes. Ruchit Mehta, Relationship Manager of S.G. Highway Branch of RBIL have to assess this request and include his evaluations in the proposal, which he had to present to Assistant General Manager of RBIL.

Complexity academic level

MBA or related program in finance courses such as financial management, corporate finance, financial statement analysis, bank management/finance and training program on “credit management” for bank employees.

Supplementary materials

Teaching Notes are available for educators only.

Subject code

CSS 1: Accounting and Finance
Working with individuals who have experienced homelessness: Stresses and successes
Authors: Rogers Jim , George Thomas , Roberts Amanda
Published: May 2020

Purpose

Staff who work with vulnerable people with multiple needs are known to experience high levels of stress and burnout, as well as high levels of job satisfaction. This paper aims to explore the experiences of staff working in a project with individuals experiencing long-term homelessness in Lincolnshire.

Design/methodology/approach

An evaluation of a project working with individuals experiencing long-term homelessness included a focus group set up to explore the experiences and well-being of front line staff and managers. One-to-one interviews with staff were also held to provide more in-depth data about the experiences of individual staff members.

Findings

Six key themes were identified from the discussions with participants. Decision latitude and the ability to follow service users on person-centred journeys over long periods were positive aspects of the work which were highly valued and seemed to contribute to high levels of job satisfaction. Things which also made a positive contribution were elements of support provided by the employer and a number of personal coping strategies. Themes identified which had a negative impact on well-being related to high workloads and to the multiple and competing demands from service users and other agencies.

Originality/value

Few studies of any kind have explored the experiences and well-being of staff working in the frontline of homelessness services. This small-scale qualitative study provides a number of suggestions for further research with this population. Findings cannot be generalised but match those of other recent studies which suggest high levels of stress but little evidence of burnout, and that carefully developed workplace support mechanisms play a key role in maintaining commitment to the role and preventing burnout.
Facade inspections with drones–theoretical analysis and exploratory tests
Authors: Falorca Jorge Furtado , Lanzinha João Carlos Gonçalves
Published: May 2020

Purpose

This paper presents a reflection on the effectiveness of using drones in the technical inspection of building facades, as a practical alternative to more expensive and heavier conventional means. In order to verify this assumption qualitatively, a number of field tests are presented and discussed.

Design/methodology/approach

The first stage consisted of a literature review. The analysis initially investigated drone technology. Then, an insight into some general applications in Civil Engineering was compiled, focusing in particular on the Construction Industry (CI), as well as the scope of building envelope inspections. In the second stage, field tests with drones were performed and the resulting data was appraised in order to get facade pathologies diagnosis as accurate as possible.

Findings

Through this study, the adaptability and versatility of using drones were checked. Thus, it has been confirmed that drone technology is an effective and promising alternative methodology to support technical inspection and diagnosis of building envelope pathologies. In fact, drones seem to be a worthwhile tool for supporting certain Civil Engineering activities–particularly when displaying a multirotor configuration, loading high-definition (HD) cameras, for both stills photography and video.

Research limitations/implications

As the main goal of this approach was simply a qualitative assessment of evidence on the advantages of using drones compared with conventional means, other kinds of comparative analysis were not discussed in depth. However, this and other potential restrictive issues may represent an opportunity to push more developments. A deeper knowledge of data handling and clear procedures for the use of drones could be very valuable for the CI and for building envelope inspections.

Practical implications

In investigating this subject, this research can offer valuable input to enable a greater awareness of the use of drones in the technical inspection of buildings, particularly in hard-to-reach locations, to the detriment of conventional means. In these circumstances, this methodology can bring great benefits, particularly from an environmental impact point of view, since the resources used are much lower. In addition, a very reliable diagnosis can be achieved more quickly, and at a much lower cost.

Originality/value

The introduction of a standard for drone inspection practice is still at an early stage, with initial steps being taken in an apparently well-focused effort to achieve consolidation. Research studies of this kind may have an important role to play in drawing the stakeholders' attention to the benefits of using this technique, particularly for those working in the building usage phase.