bluuebunny/crossref_metadata_2025 huggingface dataset:
Lipid Desaturation Regulates the Balance between Self-renewal and Differentiation in Mouse Blastocyst-derived Stem Cells
Authors: Thomas Mannully Chanchal , Bruck-Haimson Reut , Zacharia Anish , Orih Paul , Shehadeh Alaa , Saidemberg Daniel , Kogan Natalya M , Alfandary Sivan , Serruya Raphael , Dagan Arie , Petit Isabelle , Moussaieff Arieh
Published: August 2022

Stem cells are defined by their ability to self-renew and to differentiate, both shown in multiple studies to be regulated by metabolic processes. To decipher metabolic signatures of self-renewal in blastocyst-derived stem cells, we compared early differentiating embryonic stem cells (ESCs) and their extra-embryonic counterparts - trophoblast (T)SCs to their self-renewing counterparts. A metabolomics analysis pointed to the desaturation of fatty acyl chains as a metabolic signature of differentiating blastocyst-derived SCs via the upregulation of delta-6 desaturase (D6D; FADS2) and delta-5 desaturase (D5D; FADS1), key enzymes in the biosynthesis of polyunsaturated fatty acids (PUFAs). The inhibition of D6D or D5D by specific inhibitors or SiRNA retained stemness in ESCs and TSCs, and attenuated endoplasmic reticulum (ER) stress-related apoptosis. D6D inhibition upregulated stearoyl-CoA desaturase-1 (Scd1) in ESCs, essential to maintain ER homeostasis. In TSCs, however, D6D inhibition downregulated Scd1. TSCs show higherScd1mRNA expression and high levels of monounsaturated fatty acyl chain products in comparison to ESCs. Addition of oleic acid – the product of Scd1 (essential for ESCs), to culture medium, was detrimental to TSCs. Interestingly, TSCs express a high molecular mass variant of Scd1 protein, hardly expressed by ESCs. Taken together, our data point to lipid desaturation as a metabolic regulator of the balance between differentiation and self-renewal of ESCs and TSCs. They point to lipid polydesaturation as a driver of differentiation in both cell types. In contrast, mono unsaturated fatty acids (MUFAs), known to be essential for ESCs are detrimental to TSCs.
Novel Smartphone Based Free Flap Monitoring Tool Using Machine Learning
Authors: Provenzano Destie , Chandawarkar Akash , Caterson Edward
Published: August 2022

Free flap monitoring is important to ensure early detection of arterial or venous failure to facilitate salvage. Our prior research has shown ability to magnify skin change as a result of skin changes. This study was undertaken to test the feasibility of detecting venous and arterial occlusion using a smartphone camera and pattern recognition (a simplistic implementation of a machine learning algorithm). Bilateral hands of seven patients were video recorded with various tourniquet pressures on one hand simulating no occlusion, venous occlusion, and arterial occlusion with the other hand as internal control. Video data resolved at an average iPhone camera quality of 33 fps was processed using the sci-kit learn library in Python to detect changes in color frequency between frames and then compared to the control hand. Comparing the test hand to the control hand allowed for the depiction of the “delta” that was sensitive enough to detect changes on a video without any additional augmentation. The average rate of change in red pixels between video frames was noticeably different compared to control for both arterial occlusion (1.06x greater) and venous occlusion (1.07x greater). A graphical representation depicted a clear relationship while an individual was undergoing occlusion (Fig 1). Our smartphone video capture and analysis facilitates visualization of skin perfusion and can distinguish between states of no occlusion, arterial occlusion, and venous occlusion. This study shows promise for the use of inexpensive smartphone monitoring in a clinical setting for accurate free flap monitoring.
Integrate multiscale module kernel for disease-gene discovery in biological networks
Authors: Xiang Ju , Meng Xiangmao , Zheng Ruiqing , Li Min
Published: August 2022

Biomedical data mining is very important for the research of complex diseases, and disease-gene discovery is one of the most representative topics in this field. Multiscale module structure (MMS) that widely exists in biological networks can provide useful insight for disease research. However, how to effectively mine information in MMS to enhance the ability of disease-gene discovery is challenging. Thus, we propose a type of novel hybrid methods (HyMSMK) for disease-gene discovery by integrating multiscale module kernel (MSMK) derived from multiscale module profile (MSMP). We extract MSMP with local to global structural information from comprehensive human protein interactome by multiscale modularity optimization with exponential sampling, and construct MSMK by using the MSMP as a feature matrix, combining with the relative information content of features and kernel sparsification. Then, we present several fusion strategies integrating MSMK, including a probabilistic model for rank aggregation. By a series of experiments, we study the effect of the fusion strategies and kernel sparsification on HyMSMK, and demonstrate that HyMSMK outperforms the state-of-art network-based algorithms. These results confirm that MSMK is particularly helpful for disease-gene discovery, and the kernel sparsification can improve HyMSMK in storage space and computing speed. This may provide useful insights for the study and application of MMS.
“I see salt everywhere”: A qualitative examination of the utility of arts-based participatory workshops to study noncommunicable diseases in Tanzania and Malawi
Authors: Bissett Maria , Gray Cindy M , Abdulla Sharifa , Bunn Christopher , Crampin Amelia C , Dillip Angel , Gill Jason MR , Kaare Heri C , Kalima Sharon , Kambalu Elson , Lwanda John , Makoye Herbert F , Mtema Otiyela , Perry Mia , Strachan Zoë , Todd Helen , Mtenga Sally M
Published: August 2022

The burden of noncommunicable diseases (NCDs) including hypertension, diabetes and cancer, is rising in Sub-Saharan Africa countries like Tanzania and Malawi. This increase reflects complex interactions between diverse social, environmental, biological, and political factors. To intervene successfully, new approaches are therefore needed to understand how local knowledges and attitudes towards common NCDs influence health behaviours. This study compares the utility of using a novel arts-based participatory method and more traditional focus groups to generate new understandings of local knowledges, attitudes and behaviours towards NCDs and their risk factors. Single-gender arts-based participatory workshops and focus group discussions were conducted with local communities in Tanzania and Malawi. Thematic analysis compared workshop and focus group transcripts for depth of content and researcher-participant hierarchies. In addition, semiotic analysis examined the contribution of photographs of workshop activities to understanding participants’ experiences and beliefs about NCD risk factors. The arts-based participatory workshops produced in-depth, vivid, emotive narratives of participants’ beliefs about NCDs and their impact (e.g., “… it spreads all over your body and kills you - snake’s poison is similar to diabetes poison”), while the focus groups provided more basic accounts (e.g., “diabetes is a fast killer”). The workshops also empowered participants to navigate activities with autonomy, revealing their almost overwhelmingly negative beliefs about NCDs. However, enabling participants to direct the focus of workshop activities led to challenges, including the perpetuation of stigma (e.g., comparing smells associated with diabetes symptoms with sewage). Semiotic analysis of workshop photographs provided little additional insight beyond that gained from the transcripts. Arts-based participatory workshops are promising as a novel method to inform development of culturally relevant approaches to NCD prevention in Tanzania and Malawi. Future research should incorporate more structured opportunities for participant reflection during the workshops to minimise harm from any emerging stigma.
Integrative 4D-conformational mechanisms of single AdiC transporter molecules
Authors: Lewis John H. , Zhou Yufeng , Lu Zhe
Published: August 2022

To understand the mechanism of counter-transport of substrates by the amino-acid transporter AdiC, we used a state-of-the-art polarization-microscope to investigate conformation-specific changes of the emission polarization of a fluorophore attached to individual AdiC molecules. This capability enabled us to determine the lifetimes of two energetic states of each of AdiC’s four conformations in the absence and presence of its two natural substrates, totaling 24 states. From these lifetimes and relative state-to-state transition frequencies, we further determined 60 rate constants of all state transitions and the 4 KD values for the two substrates to interact with both sides of AdiC, quantitatively defining a 24-state model that satisfactorily predicts previously observed transporting behaviors of AdiC. Combining this temporal information and the existing structural information, we have successfully built a fully experiment-based integrative 4D-model to capture and exhibit the complex spatiotemporal mechanisms of a facilitated counter-transport of an amino acid and its metabolite. Thus, a combination of the present method and existing structural techniques serves as an effective means to help transition structural biology, which has thus far been highly successful in the investigation of individual static structures, to an integrative form of dynamic structural biology.
Diverse Strategies Utilized by Coronaviruses to Evade Antiviral Responses and Suppress Pyroptosis
Authors: Fu Xinyu , Xu Weilv , Yang Yang , Li Danyue , Shi Wen , Li Xinyue , Chen Nan , Lv Qian , Shi Yuhua , Xu Jidong , Yan Yuqi , Shi Fushan , Li Xiaoliang
Published: August 2022

Viral infection triggers inflammasome-mediated caspase-1 activation. Nevertheless, limited understanding exists regarding how viruses use the active caspase-1 to evade host immune response. Here, we use porcine epidemic diarrhea virus (PEDV) as a model of coronaviruses (CoVs) to illustrate the intricate regulation of CoVs to combat IFN-I signaling and pyroptosis. Our findings demonstrate that PEDV infection stabilizes caspase-1 expression via papain-like protease PLP2’s deubiquitinase activity and the enhanced stabilization of caspase-1 disrupts IFN-I signaling by cleaving RIG-I at D189 residue. 6-Thioguanine (6TG), a PLP2 inhibitor, plays a critical role in reversing the inhibitory effect of IFN-I via PLP2 and also inhibiting PEDV replication. Meanwhile, PLP2 can degrade GSDMD-p30 by removing its K27-linked ubiquitin chain at K275 to restrain pyroptosis. Papain-like proteases from other genera of CoVs (PDCoV and SARS-CoV-2) have the similar activity to degrade GSDMD-p30. We further demonstrate that SARS-CoV-2 N protein induced NLRP3 inflammasome activation also uses the active caspase-1 to counter IFN-I signaling by cleaving RIG-I. Therefore, our work unravels a novel antagonistic mechanism employed by CoVs to evade host antiviral response.
PhaeoEpiView: An epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum
Authors: Wu Yue , Timothée Chaumier , Manirakiza Eric , Veluchamy Alaguraj , Tirichine Leila
Published: August 2022

Motivation

Recent advances in DNA sequencing technologies in particular of long reads type greatly improved genomes assembly leading to discrepancies between both published annotations and epigenome tracks which did not keep pace with new assemblies. This comprises the availability of accurate resources which penalizes the progress in research.

Results

Here, we used the latest improved telomere to telomere assembly of the model pennate diatom Phaeodactylum tricornutum to lift over the gene models from Phatr3, a previously annotated reference genome. We used the lifted genome annotation including genes and transposable elements to map the epigenome landscape, namely DNA methylation and post translational modifications of histones providing the community with PhaeoEpiView, a browser that allows the visualization of epigenome data as well as transcripts on an updated reference genome to better understand the biological significance of the mapped data on contiguous genome rather than a fragmented one. We updated previously published histone marks with a more accurate mapping using monoclonal antibodies instead of polyclonal and deeper sequencing. PhaeoEpiView will be continuously updated with the newly published epigenomic data making it the largest and richest epigenome browser of any stramenopile. We expect that PhaeoEpiView will be a standard tool for the coming era of molecular environmental studies where epigenetics holds a place of choice.

Availability

PhaeoEpiView is available at: https://PhaeoEpiView.univ-nantes.fr
Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning
Authors: Kick Daniel R. , Wallace Jason G. , Schnable James C. , Kolkman Judith M. , Alaca Barış , Beissinger Timothy M. , Ertl David , Flint-Garcia Sherry , Gage Joseph L. , Hirsch Candice N. , Knoll Joseph E. , de Leon Natalia , Lima Dayane C. , Moreta Danilo , Singh Maninder P. , Weldekidan Teclemariam , Washburn Jacob D.
Published: August 2022

Accurate prediction of the phenotypic outcomes produced by different combinations of genotypes, environments, and management interventions remains a key goal in biology with direct applications to agriculture, research, and conservation. The past decades have seen an expansion of new methods applied towards this goal. Here we predict maize yield using deep neural networks, compare the efficacy of two model development methods, and contextualize model performance using linear models, which are the conventional method for this task, and machine learning models We examine the usefulness of incorporating interactions between disparate data types. We find a deep learning model with interactions has the best average performance. Optimizing submodules for each datatype improved model performance relative to optimizing the whole model for all data types at once. Examining the effect of interactions in the best performing model revealed that including interactions altered the model’s sensitivity to weather and management features, including a reduction of the importance scores for timepoints expected to have limited physiological basis for influencing yield – those at the extreme end of the season, nearly 200 days post planting. Based on these results, deep learning provides a promising avenue for phenotypic prediction of complex traits in complex environments and a potential mechanism to better understand the influence of environmental and genetic factors.
In Silico Proteomics Approach Towards the Identification of Potential Novel Drug Targets Against Cryptococcus gattii
Authors: Robin Tanjin Barketullah , Rani Nurul Amin , Ahmed Nadim , Prome Anindita Ash , Bappy Md. Nazmul Islam , Ahmed Foeaz
Published: August 2022

Cryptococcosis is a condition caused by inhaling Cryptococcus gattii, the tiny fungus from the environment. It is thought that the pathogen C. gattii is clinically more virulent than C. neoformans and could be a vicious agent in coming decades. It can enter the host’s brain and harm human peripheral blood mononuclear cells’ DNA (PBMCs). It is vital to investigate potential alternative medications to treat this disease since global antifungal resistance preventing Cryptococci infections is on the rise, leading to treatment failure. In order to find effective novel drug targets for C. gattii, a comprehensive novel approach has been used in conjunction with in silico analysis. Among 6561 proteins of C. gattii we have found three druggable proteins (XP 003194316.1, XP 003197297.1, XP 003197520.1) after completing a series of steps including exclusion of paralogs, human homologs, non-essential and human microbiome homologs proteins. These three proteins are involved in pathogen specific pathways, and can be targeted for drugs to eliminate the pathogen from the host. The subcellular locations and their interactions with a high number of proteins also demonstrate their eligibility as potential drug targets. We have approached their secondary, tertiary model and docked them with 21 potential antifungal plant metabolites. From the molecular docking analysis, we found Amentoflavone, Baicalin, Rutin and Viniferin to be the most effective drugs to stop such proteins because of their increased binding affinity. Correspondingly, the drugs showed proper ADME properties and also analyzed to be safe (Figure 9, Table 6). Moreover, these potential drugs can successfully be used in the treatment of Cryptococcosis caused by the fungus Cryptococcus gattii. In vivo trail is highly recommended for further prospection.
Cannabis sativa oxylipin biosynthesis: Genome-wide characterization of lipoxygenase, allene oxide synthase, allene oxide cyclase, hydroperoxide lyase, and 12-oxo-phytodienoic acid reductase gene families
Authors: Borrego Eli J. , Robertson Mariah , Taylor James , Espinoza Elida
Published: August 2022

Cannabis sativa is a global multi-billion-dollar cash crop with numerous industrial uses, including in medicine and recreation where its value is largely owed to the production of pharmacological and psychoactive metabolites known as cannabinoids. Often underappreciated in this role, the lipoxygenase (LOX)-derived green leaf volatiles (GLVs), also known as the scent of cut grass, are the hypothetical origin of hexanoic acid, the initial substrate for cannabinoid biosynthesis. The LOX pathway is best known as the primary source of plant oxylipins, molecules analogous to the eicosanoids from mammalian systems. These molecules are chemically and functionally diverse group of fatty acid-derived signals that govern nearly all biological processes including plant defense and development. The interaction between oxylipin and cannabinoid biosynthetic pathways remains to be explored.

Despite their unique importance in this crop, there has not been a comprehensive investigation focusing on the genes responsible for oxylipin biosynthesis in any Cannabis species. This study documents the first genome-wide catalogue of the Cannabis sativa oxylipin biosynthetic genes and identified 21 LOX, five allene oxide synthases (AOS), three allene oxide cyclases (AOC), one hydroperoxide lyase (HPL), and five 12-oxo-phytodienoic acid reductases (OPR). Gene collinearity analysis found chromosomal regions containing several isoforms maintained across Cannabis, Arabidopsis, and tomato. Promoter, expression, weighted co-expression genetic network, and functional enrichment analysis provide evidence of tissue- and cultivar-specific transcription and roles for distinct isoforms in oxylipin and cannabinoid biosynthesis.

This knowledge facilitates future targeted approaches towards Cannabis crop improvement and for the manipulation of cannabinoid metabolism.
The Blood Proteome of Imminent Lung Cancer Diagnosis
Authors:   The Lung Cancer Cohort Consortium (LC3), Albanes Demetrius , Alcala Karine , Alcala Nicolas , Amos Christopher I. , Arslan Alan A. , Bassett Julie K. , Brennan Paul , Cai Qiuyin , Chen Chu , Feng Xiaoshuang , Freedman Neal , Guida Florence , Hung Rayjean J. , Hveem Kristian , Johansson Mikael , Johansson Mattias , Koh Woon-Puay , Langhammer Arnulf , Milne Roger L. , Muller David , Onwuka Justina , Sørgjerd Elin Pettersen , Robbins Hilary A. , Sesso Howard D. , Severi Gianluca , Shu Xiao-Ou , Sieri Sabina , Smith-Byrne Karl , Stevens Victoria , Tinker Lesley , Tjønneland Anne , Visvanathan Kala , Wang Ying , Wang Renwei , Weinstein Stephanie , Yuan Jian-Min , Zahed Hana , Zhang Xuehong , Zheng Wei
Published: August 2022

Identification of novel risk biomarkers may enhance early detection of smoking-related lung cancer. We measured 1,162 proteins in blood samples drawn at most three years before diagnosis in 731 smoking-matched case-control sets nested within six prospective cohorts from the US, Europe, Singapore, and Australia.

We identified 36 proteins with replicable associations with risk of imminent lung cancer diagnosis (all p<4×10-5). These included several documented tumor markers (e.g. CA-125/MUC-16 and CEACAM5/CEA) but most had not been previously reported. The 36 proteins included several growth factors (e.g. HGF, IGFBP-1, IGFP-2), tumor necrosis factor-receptors (e.g. TNFRSF6B, TNFRSF13B), and chemokines and cytokines (e.g. CXL17, GDF-15, SCF). The odds ratio per standard deviation ranged from 1.31 for IGFBP-1 (95% CI: 1.17-1.47) to 2.43 for CEACAM5 (95% CI: 2.04-2.89). We mapped the 36 proteins to the hallmarks of cancer and found that proliferative signaling, tumor-promoting inflammation, and activation of invasion and metastasis were most frequently implicated.

Statement of significance

After screening 1,162 proteins, we identified 36 markers of imminent smoking-related lung cancer diagnosis with a wide range of functions and relevance across the hallmarks of cancer. Forthcoming studies will address the extent to which these markers can discriminate future lung cancer cases and their utility for early detection.
Memory B cells and memory T cells induced by SARS-CoV-2 booster vaccination or infection show different dynamics and efficacy to the Omicron variant
Authors: Mise-Omata Setsuko , Ikeda Mari , Takeshita Masaru , Uwamino Yoshifumi , Wakui Masatoshi , Arai Tomoko , Yoshifuji Ayumi , Murano Kensaku , Siomi Haruhiko , Nakagawara Kensuke , Ohyagi Masaki , Ando Makoto , Hasegawa Naoki , Saya Hideyuki , Murata Mitsuru , Fukunaga Koichi , Namkoong Ho , Lu Xiuyuan , Yamasaki Sho , Yoshimura Akihiko
Published: August 2022

Although BNT162b2 vaccination was shown to prevent infection and reduce COVID-19 severity, and the persistence of immunological memory generated by the vaccination has not been well elucidated. We evaluated memory B and T cell responses to the SARS-CoV-2 spike protein before and after the third BNT162b2 booster. Although the antibody titer against the spike receptor-binding domain (RBD) decreased significantly 8 months after the second vaccination, the number of memory B cells continued to increase, while the number of memory T cells decreased slowly. Memory B and T cells from unvaccinated infected patients showed similar kinetics. After the third vaccination, the antibody titer increased to the level of the second vaccination, and memory B cells increased at significantly higher levels before the booster, while memory T cells recovered close to the second vaccination levels. In memory T cells, the frequency of CXCR5+CXCR3+CCR6- cTfh1 was positively correlated with RBD-specific antibody-secreting B cells. Furthermore, T cell-dependent antibody production from reactivated memory B cells in vitro was correlated to the Tfh-like cytokine levels. For the response to variant RBDs, although 60%-80% of memory B cells could bind to the Omicron RBD, their binding affinity was low, while memory T cells show an equal response to the Omicron spike. Thus, the persistent presence of memory B and T cells will quickly upregulate antibody production and T cell responses after Omicron strain infection, which prevents severe illness and death due to COVID-19.
Development of an amplicon nanopore sequencing strategy for detection of mutations conferring intermediate resistance to vancomycin in Staphylococcus aureus strains
Authors: Moller Abraham G. , Petit Robert A. , Davis Michelle H. , Read Timothy D.
Published: August 2022

Staphylococcus aureus is a major cause of bacteremia and other hospital-acquired infections. The cell-wall active antibiotic vancomycin is commonly used to treat both methicillin-resistant (MRSA) and sensitive (MSSA) infections, but vancomycin intermediate S. aureus (VISA) variants can arise through de novo mutations. Here we performed pilot experiments to develop a combined PCR/long-read sequencing-based method for detection of previously known VISA-causing mutations. We amplified 16 genes (walR, walK, rpoB, graR, graS, vraF, vraG, stpI, vraR, vraS, agrA, sarA, clpP, ccpA, prsA, and yvqF) known from prior studies to be associated with mutations responsible for VISA as 10 amplicons and sequenced amplicon pools as long-reads with Oxford Nanopore adapter ligation on Flongle flow cells. We then detected mutations by mapping reads against a parental consensus or known reference sequence and comparing called variants against a database of known VISA mutations from laboratory selection. There was high (>1000x) coverage of each amplicon in the pool, no relationship between amplicon length and coverage, and the ability to detect the causative mutation (walK 646C>G) in a VISA mutant derived from the USA300 strain (N384-3 from parental strain N384). Mixing mutant (N384-3) and parental (N384) DNA at various ratios from 0 to 1 mutant suggested a mutation detection threshold of roughly the average minor allele frequency of 6.5% at 95% confidence (two standard errors above mean mutation frequency). The study lays the groundwork for direct S. aureus antibiotic phenotype inference using rapid nanopore sequencing from clinical samples.

Importance

Bacteremia mortality is known to increase rapidly with time after infection, making rapid diagnostics and treatment necessary. Successful treatment depends on correct administration of antibiotics based on knowledge of strain antibiotic susceptibility. Staphylococcus aureus is a major causative agent of bacteremia and is also increasingly antibiotic resistant. In this work, we develop a method to improve detection of a complex, polygenic antibiotic resistance phenotype in S. aureus, vancomycin-intermediate resistance (VISA) through long-read genomic sequencing of amplicons representing genes most commonly mutated in VISA selection. This method both speeds up VISA determination relative to purely culture-based detection and incorporates the most comprehensive database of VISA genetic determinants known to date.
Antigenic characterization of the SARS-CoV-2 Omicron subvariant BA.2.75
Authors: Wang Qian , Iketani Sho , Li Zhiteng , Guo Yicheng , Yeh Andre Yanchen , Liu Michael , Yu Jian , Sheng Zizhang , Huang Yaoxing , Liu Lihong , Ho David D.
Published: August 2022

The SARS-CoV-2 Omicron subvariant BA.2.75 emerged recently and appears to be spreading rapidly. It has nine mutations in its spike compared to BA.2, raising concerns it may further evade vaccine-elicited and therapeutic antibodies. Here, we found BA.2.75 to be moderately more neutralization resistant to sera from vaccinated/boosted individuals than BA.2 (1.8-fold), similar to BA.2.12.1 (1.1-fold), but more neutralization sensitive than BA.4/5 (0.6-fold). Relative to BA.2, BA.2.75 showed heightened resistance to class 1 and class 3 monoclonal antibodies to the receptor-binding domain, while gaining sensitivity to class 2 antibodies. The resistance was largely conferred by the G446S and R460K mutations. Of note, BA.2.75 was slightly resistant (3.7-fold) to bebtelovimab, the only therapeutic antibody with potent activity against all Omicron subvariants. BA.2.75 also exhibited higher receptor binding affinity than other Omicron subvariants. BA.2.75 provides yet another example of the ongoing evolution of SARS-CoV-2 as it gains transmissibility while incrementally evading antibody neutralization.
Condensin reorganizes centromeric chromatin during mitotic entry into a bipartite structure stabilized by cohesin
Authors: Sacristan Carlos , Samejima Kumiko , Ruiz Lorena Andrade , Lambers Maaike L.A. , Buckle Adam , Brackley Chris A. , Robertson Daniel , Hori Tetsuya , Webb Shaun , Fukagawa Tatsuo , Gilbert Nick , Marenduzzo Davide , Earnshaw William C. , Kops Geert J.P.L.
Published: August 2022

The Structural Maintenance of Chromosomes (SMC) complexes cohesin and condensin establish the 3D organization of mitotic chromosomes1–3. Cohesin is essential to maintain sister chromatid pairing until anaphase onset4, while condensin is important for mitotic centromere structure and elastic resistance to spindle forces5–8. Both complexes are also important to form productive kinetochore-spindle attachments6, 8, 9. How condensin and cohesin work together to shape the mitotic centromere to ensure faithful chromosome segregation remains unclear. Here we show by super-resolution imaging, Capture-C analysis and polymer modeling that vertebrate centromeres are partitioned into two distinct condensin-dependent subdomains during mitosis. This bipartite sub-structure is found in human, mouse and chicken centromeres and also in human neocentromeres devoid of satellite repeats, and is therefore a fundamental feature of vertebrate centromere identity. Super-resolution imaging reveals that bipartite centromeres assemble bipartite kinetochores with each subdomain capable of binding a distinct microtubule bundle. Cohesin helps to link the centromere subdomains, limiting their separation in response to mitotic spindle forces. In its absence, separated bipartite kinetochores frequently engage in merotelic spindle attachments. Consistently, uncoupling of centromere subdomains is a common feature of lagging chromosomes in cancer cells. The two-domain structure of vertebrate regional centromeres described here incorporates architectural roles for both condensin and cohesin and may have implications for avoiding chromosomal instability in cancer cells.
Compensatory mutations reducing the fitness cost of plasmid carriage occur in plant rhizosphere communities
Authors: Bird Susannah M. , Ford Samuel , Thompson Catriona M. A. , Little Richard , Hall James P.J. , Jackson Robert W. , Malone Jacob , Harrison Ellie , Brockhurst Michael A.
Published: August 2022

Plasmids drive bacterial evolutionary innovation by transferring ecologically important functions between lineages, but acquiring a plasmid often comes at a fitness cost to the host cell. Compensatory mutations, which ameliorate the cost of plasmid carriage, promote plasmid maintenance in simplified laboratory media across diverse plasmid-host associations. Whether such compensatory evolution can occur in more complex communities inhabiting natural environmental niches where evolutionary paths may be more constrained is, however, unclear. Here we show a substantial fitness cost of carrying the large conjugative plasmid pQBR103 in Pseudomonas fluorescens in the plant rhizosphere. This plasmid fitness cost could be ameliorated by compensatory mutations affecting the chromosomal global regulatory system gacA/gacS, which arose rapidly in plant rhizosphere communities and were exclusive to plasmid carriers. These findings expand our understanding of the importance of compensatory evolution in plasmid dynamics beyond simplified lab media. Compensatory mutations contribute to plasmid survival in bacterial populations living within complex microbial communities in their natural environmental niche.
Dissection of Drosophila Wandering Larval Brains for Patch-Clamping Neurons
Authors: Fernandez-Chiappe Florencia , Muraro Nara I.
Published: August 2022

An enormous amount of neuroscientific knowledge has been gained from studying the larval stage of Drosophila. From an electrophysiological point of view, the larval neuromuscular junction has played an important role in this quest for knowledge, as it presents practical advantages such as accessibility and a stereotypic pattern. The physiological properties of larval central neurons have been less explored, with information regarding mainly a few identified motoneurons available to date. This protocol describes a quick and easy dissection of the brain of wandering third-instar Drosophila larvae to produce an ex vivo preparation in which central neurons can be patch-clamped. Immobilizing fresh and tiny tissues, such as larval brains, to perform successful patch-clamp recordings is a crucial step; here we explain in detail how this can be achieved using cyanoacrylate glue.
Gaining legitimacy or exploiting opportunities? MNCs’ response to the belt and road initiative in China
Authors: Lv Ping , Arnoldi Jakob , Villadsen Anders Ryom
Published: August 2022

Purpose

This study aims to investigate whether and why multinational corporations (MNCs) seek to reduce institutional costs of foreign direct investments (FDIs) by aligning with transnational political frameworks.

Design/methodology/approach

This study uses the Chinese Belt and Road Initiative (BRI) to test whether MNCs’ subsidiaries in China increase FDI into BRI-affiliated countries after the BRI’s launch. This study compares FDIs by Chinese subsidiaries of foreign MNCs in the year before and two years after the BRI’s announcement. Hypotheses are tested for two explanations of why foreign MNCs seek to exploit the BRI.

Findings

Investments into BRI-affiliated countries increased after the announcement of the BRI, and this increase is positively moderated by institutional distance between the MNC home country and the BRI-affiliated target country. This shows that the greater the institutional costs of investing in a BRI-affiliated country, the more responsive the MNCs’ Chinese subsidiary will be to the BRI.

Research limitations/implications

This study demonstrates that MNCs respond to transnational political frameworks. This study only studies the immediate response because the BRI is an infrastructure project. Better infrastructure will, over time, lead to more investments; however, the immediate response is due not to infrastructure but political structure.

Originality/value

The results show how MNCs use transnational political frameworks. The idea that MNCs can channel FDI through existing subsidiaries for this purpose has not previously been discussed in the literature.
The fog index in accounting research: contributions and challenges
Authors: Efretuei Ekaete , Hussainey Khaled
Published: August 2022

Purpose

The objective of this paper is to review the use of the fog index in accounting research.

Design/methodology/approach

This paper uses a systematic literature review (SLR) methodology with a sample of 126 accounting research articles. The review applies the theoretical framework of disclosure's stewardship, valuation and accountability roles to identify the contributions and challenges of using the fog index in accounting research.

Findings

This paper shows that the primary contribution of the fog index to accounting research relates to the disclosure obfuscation hypothesis (e.g. whether management obfuscates narratives associated with earnings). It also finds that the challenge in using the fog index is in disentangling its measure of firm environmental complexity from narrative obfuscation. Regarding disclosure utility, there is limited evidence on the differential effects of complexity on investor types and whether the fog index findings are associated with narrative obfuscation or firm environmental complexity is driven by investor types.

Research limitations/implications

The authors develop a research database of fog index studies categorised based on contributions to disclosure obfuscation or disclosure utility, highlighting contributions to the stewardship, valuation and accountability roles of disclosures, which researchers can use to develop future studies.

Originality/value

This paper contributes to accounting literature by offering the first comprehensive review on the use of the fog index in accounting research. It offers researchers a consolidated review of the study of linguistic complexity of accounting information and disclosure functions using a theoretical framework that can inform regulators, policymakers and future researchers in designing future research/policy.
Averting the “resource curse phenomenon” through government effectiveness. Evidence from Ghana's natural gas production
Authors: Adabor Opoku
Published: August 2022

Purpose

The “resource curse phenomenon” has received a lot of attention from researchers; however, there has not been any sound explanation to back this phenomenon since the main reason why natural resource should restrain economic growth instead of boosting economic growth remains unanswered. This paper contributes to literature on “resource curse hypothesis” by examining the role of government effectiveness in influencing the impact of gas resource rent on economic growth.

Design/methodology/approach

The study adopted the Cobb-Douglass production and incorporated gas resource rent, institutional quality (government effectiveness), inflation and exchange rate as additional variables that influences total output (gross domestic product). The author estimated the empirical form of the Cobb-Douglass production using autoregressive distributed lag model (ARDL) and Toda and Yamamoto (1995) as the main estimation strategies while other time series approaches were used as a robustness check.

Findings

The estimates from the ARDL short-run and the long-run dynamics suggest that the direct impact of gas resource rent on economic growth was positive but not statistically significant. At the same time, the interacting of gas resource rent and government effectiveness showed a positive and statistically significant effect of nearly 0.4123 and 0.8724 on economic growth in the long run and short run, respectively. The results from the Toda and Yamamoto (1995) also indicated that economic growth has a strong influence on gas resource rent while government effectiveness drives economic growth and not vice versa.

Research limitations/implications

The findings from this study imply that government effectiveness plays a crucial role in averting the “resource curse phenomenon”. Hence, improving government effectiveness and efficiency through minimizing corruption among state institutions would be imperative in curbing the “resource curse phenomenon” in developing countries.

Originality/value

The influential role of government effectiveness on the relationship between gas resource rent on economic growth is examined.
CircFNDC3B knockdown restrains the progression of oesophageal squamous cell carcinoma through miR‐214‐3p/CDC25A axis
Authors: Wang Jiawei , Li Xiaolin , Duan Chao , Jia Yifei
Published: August 2022

Circular RNA (circRNAs) Fibronectin Type III Domain Containing 3B (FNDC3B) (circFNDC3B) has been revealed to be involved in the progression of oesophageal squamous cell carcinoma (ESCC). Hence, the potential regulatory network of circFNDC3B in ESCC was further investigated. Levels of genes and proteins were examined by qRT‐PCR and Western blot. In vitro assays were performed using colony formation assay, 5‐Ethynyl‐2′‐deoxyuridine (EdU) assay, flow cytometry, wound healing assay, and transwell assay. The target relationship between miR‐214‐3p and circFNDC3B or cell division cycle 25 homologue A (CDC25A) was verified by dual‐luciferase reporter and RIP assays. In vivo assay was carried out using the xenograft nude mice model. CircFNDC3B was highly expressed in ESCC, and high circFNDC3B expression was tightly associated with poor prognosis in ESCC patients. Functionally, circFNDC3B knockdown not only suppressed ESCC cell growth, migration and invasion in vitro, but hindered ESCC tumour growth in vivo. Mechanistically, circFNDC3B acted as a sponge for miR‐214‐3p to up‐regulate the expression of its target CDC25A. Rescue experiments showed that miR‐214‐3p inhibitor reversed the anticancer effects of circFNDC3B knockdown. Moreover, forced expression of miR‐214‐3p suppressed the malignant phenotypes mentioned above, while this condition was abolished by CDC25A overexpression. CircFNDC3B silencing restrains the tumorigenesis of oesophageal squamous cell carcinoma through miR‐214‐3p/CDC25A axis, which opens a new window to the development of novel therapeutic strategy for ESCC patients.
Life‐history traits of the endangered mud snail Batillaria multiformis in their northern limit population in Mutsu Bay, Japan
Authors: Kanaya Gen , Yamada Katsumasa , Itoh Hajime , Igarashi Takeshi
Published: August 2022

As a citizen‐based research project in an elementary school, we examined the life‐history traits of the endangered mud snail Batillaria multiformis in Mutsu Bay, one of the species northernmost populations in Japan. The snails occurred widely in the intertidal zone in summer, but they were densely aggregated near the low‐tide line from autumn to winter. Shell lengths (SLs) ranged from 1.2 to 49.5 mm, and one to four or more size cohorts occurred in the population. Batillaria multiformis spawned from August to September, settled in autumn, and grew to 4–6 mm SL the following spring. The snails grew to 5–10, 10–15, 15–20, and 20–25 mm SL in the second to fifth autumns, respectively. The highest growth rates were from July to August, while shell growth stopped from September to April. The snails became sexually mature at least 4–10 years (24.1 to ca. 50 mm SL) after settlement, at which time shell growth stopped and a callus knob was formed. Batillaria multiformis in Mutsu Bay exhibited much larger shell sizes and delayed maturation compared to southern populations. Shell growth rates differed in the summers of 2014, 2015, and 2016 (+0.69, +1.11, and +4.59 mm SL 30‐d−1, respectively), corresponding to the mean sediment temperatures in August (22.8, 24.5, and 26.4°C, respectively). These results indicate that thermal conditions constitute an important determinant of annual shell growth in the northern limit population of B. multiformis. Ongoing climate change can lead to changes in life‐history traits of macroinvertebrates, including mud snails, particularly near their northern distribution limits.
The problem of power: Partial electrification in Northern Uganda
Authors: Nielsen Kirsten Milo , Eriksen Thomas Hylland
Published: August 2022

This article considers the relation between infrastructural development and precarious work in the context of the electrification of a village in Northern Uganda. The case of a welder illustrates how partial electrification creates precarious conditions for work and how flexibility and creativity are used to mitigate its effects. In looking beyond precarity at the strategies employed by small‐scale business owners in Northern Uganda, this article aims to shed light on how people relate to infrastructural realities and play an active role in shaping the affordances and impact of infrastructures in the Global South.
Textures of precarity: Repurposing in a Ugandan refugee settlement
Authors: Wainman Nicholas , Whyte Susan Reynolds , Meinert Lotte
Published: August 2022

Palabek Refugee Settlement in Northern Uganda hosts more than 40,000 refugees from South Sudan. They receive plots of land upon which they must build their own houses, as well as a few relief items and minimal food rations. The people who cross the border are not passive recipients of humanitarian aid. They creatively repurpose items often associated with precarity and helplessness in ways that challenge images of refugee victimhood. UNHCR tarpaulins are used in various projects, including video halls and churches. USAID cooking oil tins serve to make house doors that protect, bring privacy and give the owners status. These projects are not only opportunities for agency; they also offset the persistent waiting that often characterizes life in forced displacement.
Sous‐vide cooking endows a better microstructure for hairtail (Trichiurus lepturus) than traditional cooking: Mechanisms of moisture migration
Authors: Li Yuan , Li Cijian , Chen Meiyu , Liu Zunying , Zeng Mingyong , Hu Yaqin
Published: August 2022

Sous‐vide cooking is a highly praised method used to cook muscle foods because of its desired effect of providing better sensory properties by maintaining texture. In this study, we further explored the effect of water on texture by revealing the mechanisms of moisture migration. Low field nuclear magnetic resonance (LF‐NMR) showed that the nonflowing water in sous‐vide cooking hairtail was 2.36 ± 0.33% higher than that in traditional cooking. Magnetic resonance imaging (MRI) was used to clarify the law of moisture migration induced by temperature, and the moisture migration of the sous‐vide cooking hairtail was slower during the holding heating stage. The microstructure explained the change rules of the texture. The degree of change was consistent with the moisture migration level. Digitalizing analysis quantitatively verified the effect of sous‐vide cooking on the hairtail microstructure. The low moisture migration rate of sous‐vide cooking resulted in a less damaged microstructure of the hairtail, manifesting as a desirable texture.

Practical Application

LF‐NMR and MRI showed that sous‐vide hairtails exhibited a lower moisture migration rate. The holding heating stage only slightly changed the microstructure of the hairtail. The digitalizing analysis confirmed the moisture migration mechanisms. Heat‐induced protein denaturation was closely related to the water state.
A review of movement models in open population capture–recapture
Authors: Efford Murray G. , Schofield Matthew R.
Published: August 2022

Understanding rates of survival and recruitment is critical to population management, and capture–recapture methods of estimation are widely used. Spatial models allow for a spatial detection process and can include the movement of activity centres between sampling times. Movement is often treated as a random walk with the step length governed by a probability kernel. However, the movement component of open population spatially explicit capture–recapture models (open SECR) has evolved haphazardly and comparison among studies is difficult.

We review published studies, document suitable probability kernels and address the issues of scale and buffer dependence in open SECR by a combination of simulation and case studies on ovenbirdsSeiurus aurocapillaand tigersPanthera tigris.

Flexible 2‐parameter kernels, such as the bivariate ‐distribution, fit better than the popular bivariate normal and resulted in higher estimates of survival. We reconcile different parameterizations of the bivariate ‐distribution and identify a problem when the kernel is defined in terms of its margins.

Movement models failed to separate mortality and emigration in simulated data when the data were a random mixture of long and short movements. Our estimates of ovenbird survival were buffer‐dependent, and we interpret this as a sign that the data are inadequate for joint modelling of survival and movement. Estimates of tiger survival were more nearly asymptotic on buffer width.

We repeat the warning of earlier authors that movement models are effective for separating mortality and emigration only when the data span the range of movement. We appeal for more complete and consistent reporting of movement models and identify topics for future research.