bluuebunny/crossref_metadata_2025 huggingface dataset:
Loss of a subunit of vacuolar ATPase identifies unexpected biological signatures of reduced organelle acidificationin vivo
Authors: Lore Pottie , Wouter Van Gool , Michiel Vanhooydonck , Franz-Georg Hanisch , Geert Goeminne , Andreja Rajkovic , Paul Coucke , Patrick Sips , Bert Callewaert
Published: December 2020

The inability to maintain a strictly regulated endo(lyso)somal acidic pH through the proton-pumping action of the vacuolar-ATPases has been associated with various human diseases including heritable connective tissue disorders, neurodegenerative diseases and cancer. Multiple studies have investigated the pleiotropic effects of reduced acidificationin vitro, but the mechanisms elicited by impaired endo(lyso)somal acidificationin vivoremain poorly understood. Here, we show that loss ofatp6v1e1bin zebrafish leads to early mortality, associated with craniofacial dysmorphisms, vascular anomalies, cardiac dysfunction, hypotonia and epidermal structural defects, reminiscent of the phenotypic manifestations in cutis laxa patients carrying a defect in theATP6V1E1gene. Mechanistically, we found thatin vivogenetic depletion ofatp6v1e1bleads to N-glycosylation defects and reduced maturation of endosomal and lysosomal vesicles, but retains the hypoxia-mediated response. In order to gain further insights into the processes affected by aberrant organelle acidification, we performed an untargeted analysis of the transcriptome and metabolome in earlyatp6v1e1b-deficient larvae. We report multiple affected pathways including but not limited to oxidative phosphorylation, sphingolipid and fatty acid metabolism with profound defects in mitochondrial respiration. Taken together, our results identify new complex biological effects of reduced organelle acidificationin vivo, which likely contribute to the multisystemic manifestations observed in disorders caused by v-ATPase deficiency.
Can citizen science analysis of camera trap data be used to study reproduction? Lessons from Snapshot Serengeti program
Authors: Lucie Thel , Simon Chamaillé-Jammes , Léa Keurinck , Maxime Catala , Craig Packer , Huebner Sarah E. , Christophe Bonenfant
Published: December 2020

Ecologists increasingly rely on camera-trap data to estimate biological parameters such as population abundance. Because of the huge amount of data, the assistance of non-scientists is often sought after, but an assessment of the data quality is necessary. We tested whether volunteers data from one of the largest citizen science projects - Snapshot Serengeti - could be used to study breeding phenology. We tested whether the presence of juveniles (less than one or 12 months old) of species in the Serengeti: topi, kongoni, Grant’s gazelle, could be reliably detected by the “naive” volunteers vs. trained observers. We expected a positive correlation between the proportion of volunteers identifying juveniles and their effective presence within photographs, assessed by the trained observers.

The agreement between the trained observers was good (Fleiss’ κ > 0.61 for juveniles of less than one and 12 month(s) old), suggesting that morphological criteria can be used to determine age. The relationship between the proportion of volunteers detecting juveniles less than a month old and their actual presence plateaued at 0.45 for Grant’s gazelle, reached 0.70 for topi and 0.56 for kongoni. The same relationships were much stronger for juveniles younger than 12 months, reaching 1 for topi and kongoni. The absence of individuals < one month and the presence of juveniles < 12 months could be reliably assumed, respectively, when no volunteer and when all volunteers reported a presence of a young. In contrast, the presence of very young individuals and the absence of juveniles appeared more difficult to ascertain from volunteers’ classification, given how the classification task was presented to them.

Volunteers’ classification allows a moderately accurate but quick sorting of photograph with/without juveniles. We discuss the limitations of using citizen science camera-traps data to study breeding phenology, and the options to improve the detection of juveniles.
Lyophilized yeast powder for adjuvant free thermostable vaccine delivery
Authors: Kumar Ravinder , Kharbikar Bhushan N.
Published: December 2020

Thermolabile nature of commercially available vaccines necessitates their storage, transportation and dissemination under refrigerated condition. Maintenance of continuous cold chain at every step increases the final cost of vaccines. Any breach in the cold chain, even for a short duration results in the need to discard the vaccine. As a result, there is a pressing need for the development of thermostable vaccines. In this proof of concept study, we showed thatE. colicurli-GFP fusion protein remains stable in freeze-dried yeast powder for more than a 13 and 6 months when stored at 30 °C and 37 °C respectively. Stability of the heterologous protein remains unaffected during the process of heat-inactivation and lyophilization. The mass of lyophilized yeast powder remains almost unchanged during the entire period of storage. Expressed protein remains intact even after two cycles of freeze and thaws. The protease deficient strain appears ideal for the development of whole recombinant yeast-based vaccines. The cellular abundance of expressed antigen in dry powder after a year was comparable to freshly lyophilized cells. SEM microscopy showed the intact nature of cells in powdered form even after a year of storage at 30 °C. Observation made in this study showed that freeze-dry yeast powder can play a vital role in the development of thermostable vaccines.
Hypothalamic glucocorticoid receptor in CRF neurons is essential for HPA axis habituation to repeated stressor
Authors: Dournes Carine , Dine Julien , Lopez Juan-Pablo , Brivio Elena , Anderzhanova Elmira , Roeh Simone , Kuehne Claudia , Holzapfel Maria , Huettl Rosa-Eva , Stoffel Rainer , Tietze Lisa , Eggert Carola , Schieven Marcel , Jakovcevski Mira , Deussing Jan M. , Chen Alon
Published: December 2020

Short abstract

Habituation of the hypothalamic-pituitary-adrenal (HPA) axis to repeated homotypic stressors is crucial for the organism’s well-being. Many physiological and psychological disorders are associated with HPA axis dysfunction. Here, we show that glucocorticoid receptors in CRF neurons of the hypothalamic paraventricular nucleus are essential for HPA habituation. By increasing inhibitory tone onto CRF neurons, glucocorticoid receptors led to essential cellular modulation and hypothalamic-pituitary-adrenal axis activation dampening, when re-exposed to the same stressor.
Clade GR and Clade GH Isolates in Asia Show Highest Amount of SNPs
Authors: Sengupta Antara , Hassan Sk. Sarif , Choudhury Pabitra Pal
Published: December 2020

Clades are monophyletic groups composed of a common ancestor and all its lineal descendants. As the propensity of virulence of a disease depends upon the type of clade the virus belongs to and it causes different fatality rates of disease in different countries, so the clade-wise analysis of SARS-CoV-2 isolates collected from different countries can illuminate the actual evolutionary relationships between them. In this study, 1566 SARS-CoV-2 genome sequences across ten Asian countries are collected, clustered, and characterized based on the clade they belong to. The isolates are compared to the Wuhan reference sequence (Accession no:MN996528.1) to identify the mutations that occurred at different protein regions. Structural changes in amino acids due to mutations lead to functional instability of the proteins. Detailed clade-wise functional assessments are carried out to quantify the stability and vulnerability of the mutations occurring in SARS-CoV-2 genomes which can shade light on personalized prevention and treatment of the disease and encourage towards the invention of clade-specific vaccines.
Reduced listener-speaker neural coupling underlies speech understanding difficulty in older adults
Authors: Liu Lanfang , Li Hehui , Ding Xiaowei , Zhou Qi , Gao Dingguo , Lu Chunming , Ding Guosheng
Published: December 2020

An increasing body of studies have highlighted the importance of listener-speaker neural coupling in successful speech communication. How this mechanism may change with normal aging and the association of this change with age-related decline in speech understanding remain unexplored. In this study, we scanned with fMRI a young and an older speaker telling real-life stories, and then played the audio recordings to groups of young (N = 28, aged 19-27y) and older adults (N = 27, aged 58-75y) during scanning, respectively. The older listeners understood the story worse than the young, and the advancing age of the older listeners was associated with poorer speech understanding. Compared to the young listener-speaker dyads, the older dyads exhibited weaker neural couplings in both linguistic and extra-linguistic areas. Moreover, within the older group, the listener’s age was negatively correlated with the overall strength of interbrain coupling, which in turn was associated with poorer speech understanding. These results reveal the deficits of older adults in achieving neural alignment with other brains, which may underlie the age-related decline in speech understanding.
The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions
Authors: Pichon Xavier , Moissoglu Konstadinos , Coleno Emeline , Wang Tianhong , Imbert Arthur , Peter Marion , Chouaib Racha , Walter Thomas , Mueller Florian , Zibara Kazem , Bertrand Edouard , Mili Stavroula
Published: December 2020

RNA localization and local translation are important for numerous cellular functions. In mammals, a class of mRNAs localize to cytoplasmic protrusions in an APC-dependent manner, with roles during cell migration. Here, we investigated this localization mechanism. We found that the KIF1C motor interacts with APC-dependent mRNAs and is required for their localization. Live cell imaging revealed rapid, active transport of single mRNAs over long distances that requires both microtubules and KIF1C. Two color imaging directly showed single mRNAs transported by single KIF1C motors, with the 3’UTR being sufficient to trigger KIF1C-dependent RNA transport and localization. Moreover, KIF1C remained associated with peripheral, multimeric RNA clusters and was required for their formation. These results reveal an RNA transport pathway in mammalian cells, in which the KIF1C motor has a dual role both in transporting RNAs and in promoting their clustering within cytoplasmic protrusions. Interestingly, KIF1C also transports its own mRNA suggesting a possible feedback loop acting at the level of mRNA transport.
Topical heterogeneity in affective touch: Does it impact body image?
Authors: Cazzato Valentina , Sacchetti Sofia , Shin Shelby , Makdani Adarsh , Trotter Paula Diane , McGlone Francis
Published: December 2020

Recent evidence suggests that altered responses to affective touch - a pleasant interoceptive stimulus associated with activation of the C-Tactile (CT) system, may contribute to the aetiology and maintenance of mental conditions characterised by body image disturbances (e.g., Anorexia Nervosa). Here, we investigated whether tactile pleasantness and intensity differ across body sites, and if individual differences in dysmorphic appearance concerns and body awareness might be associated to touch perceptions across body sites. To this end, we measured perceived pleasantness and intensity of gentle, dynamic stroking touches applied to the palm, forearm, face, abdomen and back of 30 female participants (mean age: 25.87±1.17yrs) using CT-optimal (3 cm/s) and non-CT optimal (0.3 and 30 cm/s) stroking touch. As expected, participants rated CT-targeted touch as more pleasant compared to the two non-CT optimal stroking touch at all body sites. Nevertheless, CT-targeted touch applied to the abdomen elicited the lowest pleasantness ratings compared to all other body sites and to the two non-CT optimal stroking touch. Individual differences in body awareness and dysmorphic concerns significantly predicted preference for CT-optimal over non-CT optimal stroking touch applied to the forearm and the back. These findings begin to elucidate the link between CT sensitivity, dysmorphic appearance concerns and body awareness, which may have implications for future research looking to inform early interventions. Addressing impaired processing of affective interoceptive stimuli, such as CT-targeted touch, may be the key to current treatment approaches available for those populations at risk of disorders characterised by body image disturbance.
Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms
Authors: Rosenthal Sun Hee , Gerasimova Anna , Ma Charles , Li Hai-Rong , Grupe Andrew , Chong Hansook , Acab Allan , Smolgovsky Alla , Owen Renius , Elzinga Christopher , Chen Rebecca , Sugganth Daniel , Freitas Tracey , Graham Jennifer , Champion Kristen , Bhattacharya Anindya , Racke Frederick , Lacbawan Felicitas
Published: December 2020

Identification of genomic mutations by molecular testing plays an important role in diagnosis, prognosis, and treatment of myeloid neoplasms. Next-generation sequencing (NGS) is an efficient method for simultaneous detection of clinically significant genomic mutations with high sensitivity. However, due to lack of standard NGS protocols, the application of NGS for hematologic malignancies into clinical settings remains limited. We report development and validation of a 48-gene NGS panel for molecular profiling of myeloid neoplasms including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Target regions were captured by hybridization with complementary biotinylated DNA baits, and NGS was performed on an Illumina NextSeq500 instrument. A bioinformatics pipeline that was developed in-house was used to detect single nucleotide variations (SNVs), insertions/deletions (indels), andFLT3internal tandem duplications (FLT3-ITD). An analytical validation study was performed on 184 unique specimens for variants with allele frequencies ≥5%. Variants identified by the 48-gene panel were compared to those identified by a 35-gene hematologic neoplasms panel using an additional 137 unique specimens. The developed assay was applied to a large cohort (n=2,053) of patients with suspected myeloid neoplasms. Analytical validation yielded 99.6% sensitivity (95% CI: 98.9-99.9%) and 100% specificity (95% CI: 100%). Concordance of variants detected by the 2 tested panels was 100%. Among patients with suspected myeloid neoplasms (n=2,053), 54.5% patients harbored at least one clinically significant mutation: 77% in AML patients, 48% in MDS, and 45% in MPN. Together, these findings demonstrate that the assay can identify mutations associated with diagnosis, prognosis, and treatment options of myeloid neoplasms.
Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar)
Authors: Brown Ryan , Moore Lindsey , Mani Amir , Patel Sonal , Salinas Irene
Published: December 2020

The microbial communities that live in symbiosis with the mucosal surfaces of animals provide the host with defense strategies against pathogens. These microbial communities are largely shaped by the environment and the host genetics. Triploid Atlantic salmon (Salmo salar) are being considered for aquaculture as they are reproductively sterile and thus cannot contaminate the natural gene pool. It has not been previously investigated how the microbiome of triploid salmon compares to that of their diploid counterparts. In this study, we compare the steady-state skin and gill microbiome of both diploid and triploid salmon, and determine the effects of salmonid alphavirus 3 experimental infection on their microbial composition. Our results show limited differences in the skin-associated microbiome between triploid and diploid salmon, irrespective of infection. In the gills, we observed a high incidence of the bacterial pathogenCandidatus Branchiomonas, with higher abundance in diploid compared to triploid control fish. Diploid salmon infected with SAV3 showed greater histopathological signs of epitheliocystis compared to controls, a phenomenon not observed in triploid fish. Our results indicate that ploidy can affect the alpha diversity of the gills but not the skin-associated microbial community. Importantly, during a natural outbreak ofBranchiomonas sp. the gill microbiome of diploid Atlantic salmon became significantly more dominated by this pathogen than in triploid animals. Thus, our results suggest that ploidy may play a role on Atlantic salmon gill health and provide insights into co-infection with SAV3 andC. Branchiomonasin Atlantic salmon.
Association between toothbrushing and non-alcoholic fatty liver disease
Authors: Kim Ji-Youn , Park Yong-Moon , Lee Gyu-Na , Song Hyun Chul , Ahn Yu-Bae , Han Kyungdo , Ko Seung-Hyun
Published: December 2020

Non-alcoholic fatty liver disease (NAFLD) is considered the hepatic manifestation of metabolic syndrome. Periodontitis, as chronic inflammatory destructive disease, is associated metabolic syndomes bidirectionally. Toothbrushing is an essential and important way to manage periodontitis through mechanical removal of biofilm at periodontal tissue. We aimed to assess the association between toothbrushing frequency and the prevalent NAFLD in nationally representative Korean adults. Among adults aged 19 years and older who participated in the Korea National Health and Nutrition Examination Survey in 2010, a total of 6,352 subjects were analyzed. NAFLD was defined as fatty liver index ≥60. Multiple logistic regression analysis was used to estimate multivariable-adjusted odds ratios (ORs) and 95% confidence intervals (CIs). An inverse association between toothbrushing frequency and NAFLD was found. The adjusted ORs (95% CIs) of NALFD was 0.56 (0.35 - 0.90) in the group who performed toothbrushing ≥ 3 per day compared to the group that performed toothbrushing ≤ 1 per day. For those with toothbrushing frequency ≤1 per day, the adjusted OR (95% CIs) of NAFLD was 2.27 (1.22-4.23) in smokers and 4.55 (1.98 – 10.44) in subjects with diabetes mellitus (DM), compared to those without the disease and with toothbrushing frequency ≥2 per day, respectively. Our results indicate that higher frequency of toothbrushing is inversely associated with NAFLD. As a modifiable oral habit, regular toothbrushing may be recommended to lower risk of NAFLD, especially in high risk groups such as smokers and diabetic patients.
Human major infections: tuberculosis, treponematoses, leprosy – a paleopathological perspective of their evolution
Authors: Henneberg Maciej , Holloway-Kew Kara , Lucas Teghan
Published: December 2020

Objective

The key to evolution is reproduction. Pathogens can either kill the human host or can invade the host without causing death, thus ensuring their own survival, reproduction and spread. Tuberculosis, treponematoses and leprosy are widespread chronic infectious diseases whereby the host is not immediately killed. These diseases are examples of the co-evolution of host and pathogen. They can be well studied as the paleopathological record is extensive, spanning over 200 human generations.

Methods

The paleopathology of each disease has been well documented in the form of published synthetic analyses recording each known case and case frequencies in the samples they were derived from. Here the data from these synthetic analyses were re-analysed to show changes in the prevalence of each disease over time. A total of 69,379 skeletons are included in this study.

Results

There was ultimately a decline in the prevalence of each disease over time, this decline was statistically significant (Chi-squared, p<0.001). A trend may start with the increase in the disease’s prevalence before the prevalence declines, in tuberculosis the decline is monotonic.

Conclusions

Increase in skeletal changes resulting from the respective diseases appears in the initial period of host-disease contact, followed by a decline resulting from co-adaptation that is mutually beneficial for the disease (spread and maintenance of pathogen) and host (less pathological reactions to the infection). Eventually either the host may become immune or tolerant, or the pathogen tends to be commensalic rather than parasitic.
Characterization of genetic diversity and population structure withinStaphylococcus chromogenesby multilocus sequence typing
Authors: Huebner Rebeca , Mugabi Robert , Hetesy Gabriella , Fox Lawrence , De Vliegher Sarne , De Visscher Anneleen , Barlow John W , Sensabaugh George
Published: December 2020

Staphylococcus chromogenesis a common skin commensal in cattle and has been identified as a frequent cause of bovine mastitis and intramammary infections. To better understand the extent of strain diversity within this species and to facilitate study of strain variation as a factor in pathogenicity, we have developed a seven locus Multilocus Sequence Typing (MLST) scheme. The scheme was tested on 120 isolates collected from three geographic locations, Vermont and Washington State in the United States and Belgium. A total of 46 sequence types (STs) were identified with most of the STs being location specific. The utility of the typing scheme is indicated by a discrimination power of 95.6% for all isolates and greater than 90% for isolates from each of the three locations. Phylogenetic analysis placed 39 of the 46 STs into single core group consistent with a common genetic lineage; the STs in this group differ by less than 0.5% at the nucleotide sequence level. Most of the diversification in this lineage group can be attributed to mutation; recombination plays a limited role. This lineage group includes two clusters of single nucleotide variants in starburst configurations indicative of recent clonal expansion; nearly 50% of the isolates sampled in this study are in these two clusters. The remaining seven STs were set apart from the core group by having alleles with highly variable sequences at one or more loci. Recombination had a higher impact than mutation in the diversification of these outlier STs. Alleles with hypervariable sequences were detected at five of the seven loci used in the MLST scheme; the average sequence distances between the hypervariable alleles and the common core alleles ranged from 12 to 34 nucleotides. The extent of these sequence differences suggests the hypervariable alleles may be remnants of an ancestral genotype.
A dynamic spike threshold with correlated noise predicts observed patterns of negative interval correlations in neuronal spike trains
Authors: Sidhu Robin S. , Johnson Erik C. , Jones Douglas L. , Ratnam Rama
Published: December 2020

Negative correlations in the sequential evolution of interspike intervals (ISIs) are a signature of memory in neuronal spike-trains. They provide coding benefits including firing-rate stabilization, improved detectability of weak sensory signals, and enhanced transmission of information by improving signal-to-noise ratio. Primary electrosensory afferent spike-trains in weakly electric fish fall into two categories based on the pattern of SCCs: non-bursting units have negative SCCs which remain negative but decay to zero with increasing lags (Type I SCCs), and bursting units have oscillatory (alternating sign) SCCs which damp to zero with increasing lags (Type II SCCs). Here, we predict and match observed ISI serial correlations in these afferents using a stochastic dynamic threshold model. We determine SCCs as a function of an arbitrary discrete noise correlation functionRk, wherekis a multiple of the mean ISI. The function permits forward and inverse calculations of SCCs. Both types of SCCs can be generated by adding colored noise to the spike threshold with Type I SCCs generated with slow noise and Type II SCCs generated with fast noise. We show that a first-order autoregressive (AR) process with a single parameter is sufficient to predict and accurately match both types of afferent SCCs, the type being determined by the sign of the AR parameter. The predicted and experimentally observed SCCs are in geometric progression. The theory predicts that the limiting sum of SCCs is −0.5 yielding a perfect DC-block in the power spectrum of the spike train. Observed SCCs from afferents have a limiting sum that is slightly larger at −0.475 ± 0.04 (mean ± s.d.). We conclude that the underlying process for generating ISIs may be a simple combination of low-order autoregressive (AR) processes, and discuss the results from the perspective of optimal coding.
Accurate detection and tracking of ants in indoor and outdoor environments
Authors: Wu Meihong , Cao Xiaoyan , Guo Shihui
Published: December 2020

Monitoring social insects’ activity is critical for biologists researching their group mechanism. Manually labelling individual insects in a video is labour-intensive. Automated tracking social insects is particularly challenging: (1) individuals are small and similar in appearance; (2) frequent interactions with each other cause severe and long-term occlusion. We propose a detection and tracking framework for ants by: (1) adopting a two-stage object detection framework using ResNet-50 as backbone and coding the position of regions of interest to locate ants accurately; (2) using the ResNet model to develop the appearance descriptors of ants; (3) constructing long-term appearance sequences and combining them with motion information to achieve online tracking. To validate our method, we build a video database of ant colony captured in both indoor and outdoor scenes. We achieve a state-of-the-art performance of 95.7% mMOTA and 81.1% mMOTP in indoor videos, 81.8% mMOTA and 81.9% mMOTP in outdoor videos. Our method runs 6-10 times faster than existing methods for insect tracking. The datasets and code are made publicly available, we aim to contribute to an automated tracking tool for biologists in relevant domains.

Author summary

The research on the group behavior of social insects is in great favor with biologists. But before analysis, each insect needs to be tracked separately in a video. Obviously, that is a time-consuming and labor-intensive work. In this manuscript, we introduce a detection and tracking framework that can automatically track the movement of ants in a video scene. The software first uses a residual network to detect the positions of ants, then learns the appearance descriptor of each ant as appearance information via another residual network. Furthermore, we obtain motion information of each ant by using the Kalman filter. Combining with appearance and motion information, we can accurately track every ant in the ant colony. We validate the performance of our framework using 4 indoor and 5 outdoor videos, including multiple ants. We invite interested readers to apply these methods using our freely available software.
Reconstitution of β-adrenergic regulation of CaV1.2: Rad-dependent and Rad-independent protein kinase A mechanisms
Authors: Katz Moshe , Subramaniam Suraj , Chomsky-Hecht Orna , Tsemakhovich Vladimir , Belkacemi Anouar , Flockerzi Veit , Klussmann Enno , Hirsch Joel A. , Weiss Sharon , Dascal Nathan
Published: December 2020

Introduction

Cardiac L-type voltage-gated CaV1.2 channels are crucial in physiological regulation of cardiac excitation-contraction coupling. Adrenergic modulation of CaV1.2 starts with activation of β-adrenergic receptors (AR) and culminates in protein kinase A (PKA) - induced increase of calcium influx through CaV1.2 channels. To date, this cascade has never been fully reconstituted in heterologous systems; even partial reconstitution proved challenging and controversial. A recent study identified Rad, a calcium channel inhibitory protein, as an essential component of the adrenergic signaling cascade. We corroborated this finding, further characterized, and fully reconstituted, the complete β-AR CaV1.2 modulation cascade in a heterologous expression system.

Objective

Our primary goal was to heterologously reconstitute the complete β-adrenergic cascade, and to investigate the role of Rad and additional molecular determinants in adrenergic regulation of cardiac CaV1.2.

Methods and Results

We utilized theXenopusoocyte heterologous expression system. We expressed CaV1.2 channel subunits, without or with Rad and β1-AR or β2-AR. To activate PKA, we injected cyclic AMP (cAMP) into the oocytes, or extracellularly applied isoproterenol (Iso) to stimulate β-AR. Whole-cell Ba2+currents served as readout. We find and distinguish between two distinct pathways of PKA modulation of CaV1.2: Rad-dependent (~80% of total) and Rad-independent. We separate the two mechanisms by showing distinct requirements for the cytosolic N- and distal C- termini of α1Cand for the CaVβ subunit. Finally, for the first time, we reconstitute the complete pathway using agonist activation of either β1-AR or β2-AR. The reconstituted system reproduces the known features of β-AR regulation in cardiomyocytes, such as a >2-fold increase in CaV1.2 current, a hyperpolarizing shift in activation curve, and a high constitutive activity of β2-AR.

Conclusions

The adrenergic modulation of CaV1.2 is composed of two distinct pathways, Rad-independent and Rad-dependent. The latter contributes most of the β-AR-induced enhancement of CaV1.2 activity, crucially depends on CaVβ subunit, and is differently regulated by β1-AR and β2-AR. The reconstitution of the full β-AR cascade provides the means to address central unresolved issues related to roles of auxiliary proteins in the cascade, CaV1.2 isoforms, and will help to develop therapies for catecholamine-induced cardiac pathologies.
Complex history of aerobic respiration and phototrophy in the Chloroflexota class Anaerolineae revealed by high-quality draft genome ofCa. Roseilinea mizusawaensis AA3_104
Authors: Ward Lewis M. , Li-Hau Fátima , Kakegawa Takeshi , McGlynn Shawn E.
Published: December 2020

The candidate genus Roseilinea is a novel lineage in the Chloroflexota (formerly Chloroflexi or green nonsulfur bacteria) phylum known so far only from very incomplete metagenome-assembled genomes and preliminary enrichments. Roseilinea is notable for appearing capable of anoxygenic photoheterotrophy despite being only distantly related to well-known phototrophic Chloroflexota in the Chloroflexia class such asChloroflexusandRoseiflexus.Here, we present a high quality metagenome-assembled genome of a member of Roseilinea, greatly improving our understanding of the metabolic capacity and taxonomic assignment of this genus. These data allow us to confidently describe the genetic basis for photoheterotrophy in these organisms as well as propose a candidate family for these organisms,Ca.Roseilineaceae, within the Anaerolineae class of Chloroflexota.
Differential Requirements for the CENP-O Complex Reveal Parallel PLK1 Kinetochore Recruitment Pathways
Authors: Nguyen Alexandra L. , Fadel Marie Diane , Cheeseman Iain M.
Published: December 2020

Similar to other core biological processes, the vast majority of cell division components are essential for viability across human cell lines. However, genome-wide screens have identified a number of proteins that exhibit cell line-specific essentiality. Defining the behaviors of these proteins is critical to our understanding of complex biological processes. Here, we harness differential essentiality to reveal the contributions of the 4-subunit centromere-localized CENP-O complex, whose precise function has been difficult to define. Our results support a model in which the CENP-O complex and BUB1 act in parallel pathways to recruit a threshold level of PLK1 to mitotic kinetochores, ensuring accurate chromosome segregation. We demonstrate that targeted changes to either pathway sensitizes cells to the loss of the other component, resulting in cell-state dependent requirements. This approach also highlights the advantage of comparing phenotypes across diverse cell lines to define critical functional contributions and behaviors that could be exploited for the targeted treatment of disease.
Understanding the Evolutionary Games in NSCLC Microenvironment
Authors: Bhattacharya Ranjini , Velde Robert Vander , Marusyk Viktoriya , Desai Bina , Kaznatcheev Artem , Marusyk Andriy , Basanta David
Published: December 2020

While initially highly successful, targeted therapies eventually fail as populations of tumor cells evolve mechanisms of resistance, leading to resumption of tumor growth. Historically, cell-intrinsic mutational changes have been the major focus of experimental and clinical studies to decipher origins of therapy resistance. While the importance of these mutational changes is undeniable, a growing body of evidence suggests that non-cell autonomous interactions between sub-populations of tumor cells, as well as with non-tumor cells within tumor microenvironment, might have a profound impact on both short term sensitivity of cancer cells to therapies, as well as on the evolutionary dynamics of emergent resistance. In contrast to well established tools to interrogate the functional impact of cell-intrinsic mutational changes, methodologies to understand non-cell autonomous interactions are largely lacking.

Evolutionary Game Theory (EGT) is one of the main frameworks to understand the dynamics that drive frequency changes in interacting competing populations with different phenotypic strategies. However, despite a few notable exceptions, the use of EGT to understand evolutionary dynamics in the context of evolving tumors has been largely confined to theoretical studies. In order to apply EGT towards advancing our understanding of evolving tumor populations, we decided to focus on the context of the emergence of resistance to targeted therapies, directed against EML4-ALK fusion gene in lung cancers, as clinical responses to ALK inhibitors represent a poster child of limitations, posed by evolving resistance. To this end, we have examined competitive dynamics between differentially labelled therapy-naïve tumor cells, cells with cell-intrinsic resistance mechanisms, and cells with cell-extrinsic resistance, mediated by paracrine action of hepatocyte growth factor (HGF), withinin vitrogame assays in the presence or absence of front-line ALK inhibitor alectinib. We found that producers of HGF were the fittest in every pairwise game, while also supporting the proliferation of therapy-naïve cells. Both selective advantage of these producer cells and their impact on total population growth was a linearly increasing function of the initial frequency of producers until eventually reaching a plateau. Resistant cells did not significantly interact with the other two phenotypes. These results provide insights on reconciling selection driven emergence of subpopulations with cell non-cell autonomous resistance mechanisms, with lack of evidence of clonal dominance of these subpopulations. Further, our studies elucidate mechanisms for co-existence of multiple resistance strategies within evolving tumors. This manuscript serves as a technical report and will be followed up with a research paper in a different journal.
u-track 3D: measuring and interrogating dense particle dynamics in three dimensions
Authors: Roudot Philippe , Legant Wesley R. , Zou Qiongjing , Dean Kevin M. , Isogai Tadamoto , Welf Erik S. , David Ana F. , Gerlich Daniel W. , Fiolka Reto , Betzig Eric , Danuser Gaudenz
Published: December 2020

Particle tracking is a ubiquitous task in the study of dynamic molecular and cellular processes through microscopy. Light-sheet microscopy has opened a path to acquiring complete cell volumes for investigation in 3-dimensions (3D). However, hypothesis formulation and quantitative analysis have remained difficult due to fundamental challenges in the visualization and the verification of large and dense sets of 3D particle trajectories. Here we describe u-track 3D, a software package that addresses these two challenges. Building on the established framework of particle association in space and time implemented for 2D time-lapse sequences, we first report a complete and versatile pipeline for particle tracking in 3D. We then present the concept of dynamic region of interest (dynROI), which allows an experimenter to interact with dynamic 3D processes in 2D views amenable to visual inspection. Third, we present an estimator of trackability which defines a score for every trajectory, thereby overcoming the challenges of trajectory validation by visual inspection. With these combined strategies, u-track 3D provides a framework for the unbiased study of molecular processes in complex volumetric sequences.
SINE Retrotransposons Import Polyadenylation Signals to 3’UTRs in Dog (Canis familiaris)
Authors: Choi Jessica D. , Del Pinto Lelani A. , Sutter Nathan B.
Published: December 2020

Background

Messenger RNA 3’ untranslated regions (3’UTRs) control many aspects of gene expression and determine where the transcript will terminate. The polyadenylation signal (PAS) AAUAAA is a key regulator of transcript termination and this hexamer, or a similar sequence, is very frequently found within 30 bp of 3’UTR ends. Short interspersed element (SINE) retrotransposons are found throughout genomes in high copy number. When inserted into genes they can disrupt expression, alter splicing, or cause nuclear retention of mRNAs. The genomes of the domestic dog and other carnivores carry hundreds of thousands Can-SINEs, a tRNA-related SINE with transcription termination potential. Because of this we asked whether Can-SINEs may help terminate transcript in some dog genes.

Results

Dog 3’UTRs have several peaks of AATAAA PAS frequency within 40 bp of the 3’UTR end, including four bp-interval peaks at 28, 32, and 36 bp from the end. The periodicity is partly explained by TAAA(n) repeats within Can-SINE AT-rich tails. While density of antisense-oriented Can-SINEs in 3’UTRs is fairly constant with distances from 3’end, sense-oriented Can-SINEs are common at the 3’end but nearly absent farther upstream. There are nine Can-SINE sub-types in the dog genome and the consensus sequence sense strands (head to tail) all carry at least three PASs while antisense strands usually have none. We annotated all repeat-masked Can-SINE copies in the Boxer reference genome and found that the young SINEC_Cf type has a mode of 15 bp for target site duplications (TSDs). We find that all Can-SINE types favor integration at TSDs beginning with A(4). The count of AATAAA PASs differs significantly between sense and antisense-oriented retrotransposons in transcripts. Can-SINEs near 3’UTR ends are very likely to carry AATAAA on the mRNA sense strand while those farther upstream are not. We also identified loci where Can-SINE insertion has truncated or altered a dog 3’UTR compared to the human ortholog.

Conclusion

Dog Can-SINE activity has imported AATAAA PASs into gene transcripts and led to alteration of 3’UTRs. AATAAA sequences are selectively removed from Can-SINEs in introns and upstream 3’UTR regions but are retained at the far downstream end of 3’UTRs, which we infer reflects their role as termination sequences for these transcripts.
Lipid Droplets Promote Phase Separation of Ago2 to Accelerate Dicer1 Loss and Decelerate miRNA Activity in Lipid Exposed Hepatic Cells
Authors: Bandyopadhyay Diptankar , Basu Sudarshana , Mukherjee Ishita , Chakraborty Ritobrita , Mukherjee Kamalika , Chattopadhyay Krishnananda , Chakrabarti Saikat , Chakrabarti Partha , Bhattacharyya Suvendra N.
Published: December 2020

miR-122 is a liver specific miRNA that plays an important role in controlling metabolic homeostasis in mammalian liver cells. Interestingly, miR-122 on exposure to lipotoxic stress is reduced in liver cells. To fight stress, miRNA processor Dicer1 is depleted to cause reduced miR-122 production and the lowering of miRNA level ensures a better stress response in hepatocytes under lipotoxic stress. Interestingly, lipid droplets, formed in the liver cells on exposure to high fat, ensure cytoplasmic phase separation of Ago2 and prevent interaction of Ago2 with Dicer1. Lipid droplets bind miRNA and enhance miRNA-Ago2 uncoupling and Ago2 phase separation. Loss of interaction between Ago2 and Dicer1 eventually facilitates export and lowering of cellular Dicer1, a process also dependent on the endosomal maturation controller protein Alix, thereby ceasing pre-miRNA processing by Dicer1 in lipid exposed cells. Depletion of lipid droplets by downregulation of Perilipins with siRNAs resulted in a rescue of cellular Dicer1 level and Ago2-Dicer1 interaction. This is a novel mechanism that liver cells adopt to restrict cellular miRNA levels under stress condition. Thus, lipid droplets prevent cell death upon exposure to high fat by reducing intra and extracellular pool of miR-122 in hepatic tissue.
Optimized cryo-EM data acquisition workflow by sample thickness determination
Authors: Rheinberger Jan , Oostergetel Gert , Resch Guenter P , Paulino Cristina
Published: December 2020

Sample thickness is a known key parameter in cryo-electron microscopy (cryo-EM) and can affect the amount of high-resolution information retained in the image. Yet, common data acquisition approaches in single particle cryo-EM do not take it into account. Here, we demonstrate how the sample thickness can be determined before data acquisition, allowing to identify optimal regions and restrict automated data collection to images with preserved high-resolution details. This quality over quantity approach, almost entirely eliminates the time- and storage-consuming collection of suboptimal images, which are discarded after a recorded session or during early image processing due to lack of high-resolution information. It maximizes data collection efficiency and lowers the electron microscopy time required per dataset. This strategy is especially useful, if the speed of data collection is restricted by the microscope hardware and software, or if microscope access time, data transfer, data storage and computational power are a bottleneck.

Synopsis

Sample thickness is a key parameter in single particle cryo-electron microscopy. Determining sample thickness before data acquisition allows to target optimal areas and maximize data output quality of single particle cryo-electron microscopy sessions. Scripts and optimized workflows for EPU and SerialEM are presented and available as open-source.
LearnOBots: navigating through uncharted waters
Authors: Taimoor Sadaf
Published: December 2020

Learning outcomes

In the light of the case and the accompanying case questions, the students should understand the theoretical underpinnings of the Blue ocean strategy. Application and critical evaluation of analytical frameworks associated with the blue ocean strategy. Role of political, socio-cultural and technological factors undermining the success of any endeavor aimed at bringing about innovation in education in Pakistan. The critical balance that social enterprises need to develop between their commercial and social impact goals.

Case overview/synopsis

Founded in early 2014, LearnOBots was a young social enterprise spearheaded by Shamyl Bin Mansoor and Faisal Laghari. The venture aimed to provide science, technology, engineering, and mathematics-based, tech supported experiential learning to young kids, which would eventually help improve the educational standards in the country. This case presents the complex dilemma of an enterprise, which achieved market traction to its novel business idea but soon faced changing competitive dynamics that posed a challenge to the uncontested blue ocean strategy that the venture attempted to create. The case is a rich description of the idiosyncrasies that an innovative startup faces in emerging markets context. It gives an insight on the balancing act that social enterprises need to achieve between their business goals and social impact aspirations.

Complexity academic level

This case is geared toward undergraduate students enrolled in courses of strategy and entrepreneurship.

Supplementary materials

Teaching Notes are available for educators only.

Subject code

CSS 3: Entrepreneurship.
Influence of temperature and irradiance on the different solar PV panel technologies
Authors: Nadia Mars , Lassad Houcine , Abderrahmen Zaafouri , Abdelkader Chaari
Published: December 2020

Tunisia has high solar radiation levels, which makes it suitable for the installation of photovoltaic (PV) systems. The design of these kinds of systems is an important step because there are many crucial factors to assess the PV module efficiency such as temperature, module types and solar radiation.This paper aims to give an analysis of the most influencing factor for selecting location. In fact, after estimating the PV panel inclination, the solar radiation and the temperature in “Zarzis” (southeastern of Tunisia), a comparative analysis among the different PV panel types was given. Additionally, to find which technologies are suitable for the climate conditions of this area, it is important to compare the effect of temperature and solar radiation on their performances.
The effects of board size and board composition on CSR disclosure: a study of banking sectors in Bangladesh
Authors: Rouf Md. Abdur , Hossan Md. Alamgir
Published: December 2020

Purpose

The purpose of this study is to provide a profound understanding of the nature and extent of corporate social responsibility (CSR) disclosure in the annual report by the listed banking sectors in Bangladesh for examining the effect of board size and board composition on CSR disclosure.

Design/methodology/approach

The sample selected of all the 30 listed banks enlisted in the Dhaka Stock Exchange and the study used a content analysis approach. An ordinary least square regression model is fitted to the data for assessing the effect of independent variables on the total CSR disclosure score. An un-weighted approach has been used for this study.

Findings

The results of the study demonstrate that the extent of CSR disclosure of listed banks in Bangladesh varies from 11.11% to 73.33%, and on average, they report 45.37% and 43.44%, respectively. Moreover, the study observed a significant relationship between the proportion of female directors and CSR disclosure. Conversely, board size has been found no significant relationship with the CSR disclosure but the proportion of independent directors has been found a significant relationship with the CSR disclosure in the annual report by the listed banking sectors in Bangladesh.

Social implications

The study is expected to get a maximum scenario of CSR disclosure of banking sectors in Bangladesh. Government and other regulatory bodies can also get full information concerning CSR disclosure practices for formulating guidelines in this regard. If the Government of Bangladesh implicates the policies that the banks are to nominate a required number of female directors to boards, the consideration of the significant number of female directors and their power will be able to protect the interests of different stakeholder groups notably.

Originality/value

The study contributes to the CSR literature as it presents empirical evidence of the effects of board size and board composition on the CSR disclosure of banking sectors in developing countries such as Bangladesh.