bluuebunny/crossref_metadata_2025 huggingface dataset:
Crucial role of ppGpp in the resilience ofEscherichia colito growth disruption
Authors: Patacq Clément , Chaudet Nicolas , Letisse Fabien
Published: September 2020

Bacteria grow in constantly changing environments that can suddenly become completely deleted in essential nutrients. The stringent response, a rewiring of the cellular metabolism mediated by the alarmone (p)ppGpp, plays a crucial role in adjusting bacterial growth to the severity of the nutritional insult. The ability of (p)ppGpp to trigger a slowdown of cell growth or induce bacterial dormancy has been widely investigated. However, little is known about the role of (p)ppGpp in promoting growth recovery after severe growth inhibition. In this study, we performed a time-resolved analysis of (p)ppGpp metabolism inEscherichia colias it recovered from a sudden slowdown in growth. Results show thatE. colirecovers by itself from the growth disruption provoked by the addition of serine hydroxamate, the serine analogue that we used to induce the stringent response. Growth inhibition was accompanied by a severe disturbance of metabolic activity and more surprisingly, by a transient overflow of valine and alanine. Our data also show that ppGpp is crucial for growth recovery since in the absence of ppGpp,E. coli’s growth recovery was slower. In contrast, an increased concentration of pppGpp was found to have no significant effect on growth recovery. Interestingly, the observed decrease in intracellular ppGpp levels in the recovery phase correlated with bacterial growth and the main effect involved was identified as growth dilution rather than active degradative process. This report thus significantly expands our knowledge of (p)ppGpp metabolism inE. coliphysiology.

IMPORTANCE

The capacity of microbes to resist and overcome environmental insults, know as resilience, allows them to survive in changing environments but also to resist antibiotic and biocide treatments, immune system responses. Although the role of the stringent response in bacterial resilience to nutritional insults has been well studied, little is known about its importance in the ability of the bacteria to not just resist but also recover from these disturbances. To address this important question, we investigated growth disruption resilience in the model bacteriumEscherichia coliand its dependency on the stringent response alarmone (p)ppGpp by quantifying ppGpp and pppGpp levels as growth was disrupted and then recovered. Our findings may thus contribute to understanding how ppGpp improvesE. coli’s resilience to nutritional stress and other environmental insults.
Community pharmacists’ knowledge and preparedness to participate in the fight against Coronavirus disease 2019 (COVID-19) in Zambia
Authors: Hangoma Jimmy Mapenzi , Mudenda Steward , Mwenechanya Mpande Mukumbwa , Kalungia Aubrey Chichoni
Published: September 2020

Background

Coronavirus disease (COVID-19) pandemic has severely strained healthcare systems globally. Community pharmacists remain vital health professionals with unique roles in responding to symptoms, supplying medicines, and providing health promotion in the communities where they serve. The purpose of this study was to assess the level of knowledge and preparedness of community pharmacists in Zambia as frontline workers in curbing COVID-19.

Method

This descriptive cross-sectional survey was conducted among 300 registered community pharmacists in Zambia. A self-administered online questionnaire was used to collect the data. Descriptive statistics were used to analyse the data using the Statistical Package for Social Sciences version 23.

Results

From a total of 393 community pharmacists, 300 participated in the study indicating a response rate of 76.3%. 97% of the pharmacists knew the common signs and symptoms of COVID-19, 83% knew the national guidelines for screening criteria, and 93% were aware that a suspected case of COVID-19 presenting to the community pharmacy needed to be alerted to the national response team. Only 59% knew they needed to self-isolate and self-report should they experience symptoms of COVID-19. 85% stated that personal protective equipment was inadequate in the pharmacies they operated from. 60% of the pharmacists were prepared to participate in the frontline fight against COVID-19.

Conclusion

Community pharmacists in Zambia are knowledgeable about COVID-19 signs and symptoms, including the technical guidelines on the screening and detection of suspected cases. Community pharmacists are prepared to participate in the frontline fight against the COVID-19 pandemic in Zambia.
Social multipliers and the Covid-19 epidemic: Analysis through constrained maximum entropy modeling
Authors: Foley Duncan K.
Published: September 2020

Social multipliers occur when individual actions influence other individual actions so as to lead to amplified aggregate effects. Epidemic infections offer a dramatic example of this phenomenon since individual actions such as social distancing and masking that have small effects on individuals’ risk can have very large effects in reducing risk when they are widely adopted. This paper uses the info-metric method of constrained maximum entropy modeling to estimate the impact of social multiplier effects in the Covid-19 epidemic with a model that infers the length of infection, the rate of mortality, the base infection factor, and reductions in the infection factor due to changes in social behavior from data on daily infections and deaths. When the model takes account of the rate of reporting of infections, it can produce three rather different scenarios of epidemic dynamics, which have marginally different posterior probabilities: one in which reporting is very low, under 10% and the estimated infection is correspondingly large, and immunity effects play a significant role in stabilizing the epidemic; a second in which reporting is on the order of 25% and the model estimates a significant portion of the population as having inherent immunity to the infection; and a third where reporting rates are close to 100%, and the epidemic is controlled mostly by changes in social behavior. These qualitatively different scenarios reflect the limited data the method can extract information from in this case.
Rats strategically manage learning during perceptual decision making
Authors: Masís Javier , Chapman Travis , Rhee Juliana Y. , Cox David D. , Saxe Andrew M.
Published: September 2020

Balancing the speed and accuracy of decisions is crucial for survival, but how organisms manage this trade-off during learning is largely unknown. Here, we track this trade-off during perceptual learning in rats and simulated agents. At the start of learning, rats chose long reaction times that did not optimize instantaneous reward rate, but by the end of learning chose near-optimal reaction times. To understand this behavior, we analyzed learning dynamics in a recurrent neural network model of the task. The model reveals a fundamental trade-off between instantaneous reward rate and perceptual learning speed, putting the goals of learning quickly and accruing immediate reward in tension. We find that the rats’ strategy of long initial responses can dramatically expedite learning, yielding higher total reward over task engagement. Our results demonstrate that prioritizing learning can be advantageous from a total reward perspective, and suggest that rats engage in cognitive control of learning.
Efficient Spline Regression for Neural Spiking Data
Authors: Sarmashghi Mehrad , Jadhav Shantanu P , Eden Uri
Published: September 2020

Point process generalized linear models (GLMs) provide a powerful tool for characterizing the coding properties of neural populations. Spline basis functions are often used in point process GLMs, when the relationship between the spiking and driving signals are nonlinear, but common choices for the structure of these spline bases often lead to loss of statistical power and numerical instability when the signals that influence spiking are bounded above or below. In particular, history dependent spike train models often suffer these issues at times immediately following a previous spike. This can make inferences related to refractoriness and bursting activity more challenging. Here, we propose a modified set of spline basis functions that assumes a flat derivative at the endpoints and show that this limits the uncertainty and numerical issues associated with cardinal splines. We illustrate the application of this modified basis to the problem of simultaneously estimating the place field and history dependent properties of a set of neurons from the CA1 region of rat hippocampus, and compare it with the other commonly used basis functions. We have made code available in MATLAB to implement spike train regression using these modified basis functions.
SuperPlotsOfData – a web app for the transparent display and quantitative comparison of continuous data from discrete conditions
Authors: Goedhart Joachim
Published: September 2020

Plots and charts are graphical tools that make data intelligible and digestible by humans. But the oversimplification of data by only plotting the statistical summaries conflicts with the transparent communication of results. Therefore, plotting of all data is generally encouraged and this can be achieved by using a dotplot for discrete conditions. Dotplots, however, often fail to communicate whether the data are from different technical or biological replicates. The superplot has been proposed to improve the communication of experimental design and results. To simplify the plotting of data from discrete conditions as a superplot, the SuperPlotsOfData web app was generated. The tool offers easy and open access to state-of-the-art data visualization. In addition, it incorporates recent innovations in data visualization and analysis, including raindcloud plots and estimation statistics. The free, open-source webtool can be accessed at:https://huygens.science.uva.nl/SuperPlotsOfData/

Abstract Figure
Drought tolerance ofHakeaspecies (Proteaceae) from a range of biomes and life-histories predicted by climatic niche
Authors: Oyanoghafo Osazee O. , O’ Brien Corey , Choat Brendan , Tissue David , Rymer Paul D.
Published: September 2020

Extreme drought conditions across the globe are impacting biodiversity with serious implications for the persistence of native species. However, quantitative data on drought tolerance is not available for diverse flora to inform conservation management. We quantified physiological drought tolerance in the diverse Hakea genus (Proteaceae) to test predictions based on climatic-origin, life history and functional traits. We sampled terminal branches of replicate plants of 16 species in a common garden. Xylem cavitation was induced in branches under varying water potential (tension) in a centrifuge and the tension generating 50% loss of conductivity (stem P50) was characterized as a metric for drought tolerance. The same branches were used to estimate plant functional traits, including wood density, specific leaf area, and Huber value (sap flow area to leaf area ratio). There was significant variation in stem P50 among species, which was negatively associated with the species climate-origin (rainfall and aridity). Drought tolerance did not differ among life histories; however, a drought avoidance strategy with terete leaf form and greater Huber value may be important for species to colonize and persist in the arid biome. Our findings will contribute to future prediction of species vulnerability to drought and adaptive management under climate change.
Phenotypic and clonal stability of antigen-inexperienced memory-like T cells across the genetic background, hygienic status, and aging
Authors: Moudra Alena , Niederlova Veronika , Novotny Jiri , Schmiedova Lucie , Kubovciak Jan , Matejkova Tereza , Drobek Ales , Pribikova Michaela , Stopkova Romana , Cizkova Dagmar , Neuwirth Ales , Michalik Juraj , Krizova Katerina , Hudcovic Tomas , Kolar Michal , Kozakova Hana , Kreisinger Jakub , Stopka Pavel , Stepanek Ondrej
Published: September 2020

Antigen-inexperienced memory-like T (AIMT) cells are functionally unique T cells representing one of the two largest subsets of murine CD8+T cells. However, differences between laboratory inbred strains, insufficient data from germ-free mice, a complete lack of data from feral mice, and unclear relationship between AIMT cells formation during aging represent major barriers for better understanding of their biology. We performed a thorough characterization of AIMT cells from mice of different genetic background, age, and hygienic status by flow cytometry and multi-omics approaches including analyses of gene expression, TCR repertoire, and microbial colonization. Our data showed that AIMT cells are steadily present in mice independently of their genetic background and hygienic status. Despite differences in their gene expression profiles, young and aged AIMT cells originate from identical clones. We identified that CD122 discriminates two major subsets of AIMT cells in a strain-independent manner. Whereas thymic CD122LOWAIMT cells (innate memory) prevail only in young animals with high thymic IL-4 production, peripheral CD122HIGHAIMT cells (virtual memory) dominate in aged mice. Co-housing with feral mice changed the bacterial colonization of laboratory strains, but had only minimal effects on the CD8+T-cell compartment including AIMT cells.
CENP-A chromatin prevents replication stress at centromeres to avoid structural aneuploidy
Authors: Giunta Simona , Hervé Solène , White Ryan R. , Wilhelm Therese , Dumont Marie , Scelfo Andrea , Gamba Riccardo , Wong Cheng Kit , Rancati Giulia , Smogorzewska Agata , Funabiki Hironori , Fachinetti Daniele
Published: September 2020

Chromosome segregation relies on centromeres, yet their repetitive DNA is often prone to aberrant rearrangements under pathological conditions. Factors that maintain centromere integrity to prevent centromere-associated chromosome translocations are unknown. Here, we demonstrate the importance of the centromere-specific histone H3 variant CENP-A in safeguarding DNA replication of alpha-satellite repeats to prevent structural aneuploidy. Rapid removal of CENP-A in S-phase, but not other cell cycle stages, caused accumulation of R-loops with increased centromeric transcripts, and interfered with replication fork progression. Replication without CENP-A causes recombination at alpha-satellites in an R-loop-dependent manner, unfinished replication and anaphase bridges. In turn, chromosome breakage and translocations arise specifically at centromeric regions. Our findings provide insights into how specialized centromeric chromatin maintains the integrity of transcribed noncoding repetitive DNA during S-phase.

Abstract Figure
Research on the Influence of Different Temperature Conditions on the Microbial Community in Anearobic-Anoxic-Oxic process on the Plateau
Authors: Huang Decai , Zong Yongchen , Zhang Ning , Li Yuanwei , Hao Kaiyue
Published: September 2020

In order to further understand the influence of different temperature conditions in the low temperature range on the microbial community structure in the Anearobic-Anoxic-Oxic waste water treatment process on the plateau, four temperature conditions were designed in the research, including 25°C, 20°C, 15°C and 10°C. Each working condition lasted three days. Activated sludge from anaerobic tank, anoxic tank and oxic tank under each working condition was analyzed based on the 16S rRNA high-throughput sequencing technology. The result shows that the plateau temperature conditions have little influence on the level abundance of phylum. Under all conditions, Bacteroidetes, Proteobacteria and Actinobacteria are the main phyla. The abundance of nitrifying bacterium and phosphorus removal bacteria rose in the first three conditions and fell at 10 °C. The abundance of Denitrification bacteria and Nitrite oxidizing bacteria was significantly higher than that of Ammonia oxidation bacteria and Azotobacter bacteria and Phosphorus-accumulating Organisms(PAO) had an overall advantage over Glycogen-accumulating Organisms (GAO) throughout the research.
Identification of novel differentially expressed zooxanthellal genes fromAiptasia-Symbiodiniumendosymbiosis through SDS-based RNA purification
Authors: Chen Bo-Nien , Song Paching , Chen Ming-Chyuan , Hong Ming-Chang
Published: September 2020

Endosymbiosis between dinoflagellates and cnidarian hosts first occurred more than 200 million years ago; however, symbiosis-specific genes and cellular processes involved in the establishment, maintenance, and breakdown of endosymbiosis remain unclear. Therefore, this study aimed to identify the zooxanthellal genes associated with the aforementioned biological processes during endosymbiosis inAiptasia-Symbiodiniumendosymbionts. Here, zooxanthellae isolates were treated with 0.02% SDS to decrease potential host RNA contamination and to enhance the identification of novel symbiosis/nonsymbiosis-associated differentially expressed zooxanthellal genes through suppressive subtractive hybridization (SSH) and next-generation sequencing (NGS) methods. Consequently, among 214 symbiosis-specific transcripts identified herein that displayed identity to only 5.6% of host-derived transcripts, 64% were well-known functional genes. In the nonsymbiotic stage, 181 differentially expressed transcripts were identified, of which 64.1% belonged to well-known functional genes. BLAST revealed that 8 categories of cellular processes were significantly induced in symbiotic or nonsymbiotic zooxanthellae. Together with the results of quantitative analysis, the results revealed that photosynthesis, flagellate biosynthesis and motility, stress-induced responses, cell wall biosynthesis, starch synthesis and transport, lipid biosynthesis and metabolism, host/symbiont immune response, intercellular communication, cell growth, and cell cycle regulation were the major cellular processes occurring in symbiotic/nonsymbiotic stages. The present results provide insights into the mechanisms involved in regulating the different physiological processes in symbiotic/nonsymbiotic zooxanthellae and may guide future studies.
An important role of the interplay betweenBdnftranscription and histone acetylation in epileptogenesis
Authors: Walczak Agnieszka , Czaban Iwona , Skupien Anna , Pels Katarzyna K. , Szczepankiewicz Andrzej A. , Krawczyk Katarzyna , Ruszczycki Błażej , Wilczynski Grzegorz M. , Dzwonek Joanna , Magalska Adriana
Published: September 2020

Brain-Derived Neurotrophic Factor is one of the most important trophic proteins in the brain. The role of this growth factor in neuronal plasticity, in health and disease, has been extensively studied. However, mechanisms of epigenetic regulation ofBdnfgene expression in epilepsy are still elusive. In our previous work, using a rat model of neuronal activation upon kainate-induced seizures, we observed a repositioning ofBdnfalleles from the nuclear periphery towards the nuclear center. This change ofBdnfintranuclear position was associated with transcriptional gene activity.

In the present study, using the same neuronal activation model, we analyzed the relation between the percentage of theBdnfallele at the nuclear periphery and clinical and morphological traits of epilepsy. We observed that the decrease of the percentage of theBdnfallele at the nuclear periphery correlates with stronger mossy fiber sprouting - an aberrant form of excitatory circuits formation. Moreover, usingin vitrohippocampal cultures we showed thatBdnfrepositioning is a consequence of the transcriptional activity. Inhibition of RNA polymerase II activity in primary cultured neurons with Actinomycin D completely blockedBdnfgene transcription and repositioning observed after neuronal excitation. Interestingly, we observed that histone deacetylases inhibition with Trichostatin A induced a slight increase ofBdnfgene transcription and its repositioning even in the absence of neuronal excitation. Presented results provide novel insight into the role of BDNF in epileptogenesis. Moreover, they strengthen the statement that this particular gene is a good candidate to search for a new generation of antiepileptic therapies.
Disulfiram inhibitsM. tuberculosisgrowth by altering methionine pool, redox status and host-immune response
Authors: Chaudhary Deepika , Marzuki Mardiana , Lee Andrea , Bouzeyen Rania , Singh Avantika , Gosain Tannu Priya , Kidwai Saqib , Grady Courtney , Tsotetsi Kholiswa , Chawla Kiran , Shihui Foo , Lum Josephine , Gupta Sonu Kumar , Agarwal Nisheeth , Tsenova Liana , Kumar Yashwant , Lee Bernett , Kumar Pradeep , Thakur Krishan Gopal , Singh Ramandeep , Singhal Amit
Published: September 2020

Methionine biosynthetic pathway, essential for the growth ofMycobacterium tuberculosis(Mtb) in the host, represents an attractive target for the development of novel anti-tuberculars. Here, we have biochemically characterized homoserine acetyl transferase (HSAT viz. MetA) ofMtb, which catalyses the first committed step of methionine and S-adenosylmethionine (SAM) biosynthesis. High-throughput screening of a 2300 compound library resulted in identification of thiram, an anti-fungal organosulfur compound, as the most potent MetA inhibitor. Further analysis of thiram analogs led to the identification of orally bioavailable disulfiram (DIS, an anti-alcoholism FDA approved drug) as a novel inhibitor of MetA. Both thiram and DIS restricted the growth of drug-sensitive and drug-resistantMtbstrains in a bactericidal manner. ThermoFlour assay demonstrated direct binding of DIS with MetA. Metabolomic and transcriptomic studies showed DIS mediated perturbation of methionine and redox homeostasis, respectively, inMtb. In concordance, the effect of DIS onMtbgrowth was partially rescued by supplementation with either L-methionine as well as N-acetyl cysteine, suggesting a multi-target killing mechanism. InMtb-infected mice, DIS administration restricted bacterial growth, increased efficacy of isoniazid, ameliorated lung pathology, modulated lung immune cell landscape and protective immune response. Taken together, our results demonstrate that DIS can be repurposed for designing an effective anti-tubercular therapy.
Energy-dependent protein folding: modeling how a protein folding machine may work
Authors: Sahakyan Harutyun K. , Nazaryan Karen B. , Mushegian Arcady R. , Sorokina Irina N.
Published: September 2020

Proteins fold robustly and reproducibly in vivo, but many cannot fold in vitro in isolation from cellular components. The pathways to proteins’ native conformations, either in vitro or in vivo, remain largely unknown. The slow progress in recapitulating protein folding pathways in silico may be an indication of the fundamental deficiencies in our understanding of folding as it occurs in nature. Here we consider the possibility that protein folding in living cells may not be driven solely by the decrease in Gibbs free energy and propose that protein folding in vivo should be modeled as an active energy-dependent process. The mechanism of action of such protein folding machine might include direct manipulation of the peptide backbone. To show the feasibility of a protein folding machine, we conducted molecular dynamics simulations that were augmented by the application of mechanical force to rotate the C-terminal amino acid while simultaneously limiting the N-terminal amino acid movements. Remarkably, the introduction of this simple manipulation of peptide backbones to the standard molecular dynamics simulation indeed facilitated the formation of native structures in five diverse alpha-helical peptides. Such effect may play a role during co-translational protein folding in vivo: considering the rotating motion of the tRNA 3’-end in the peptidyltransferase center of the ribosome, it is possible that this motion might introduce rotation to the nascent peptide and influence the peptide’s folding pathway in a way similar to what was observed in our simulations.
Calibration of consonant perception to room reverberation
Authors: Vlahou Eleni , Ueno Kanako , Shinn-Cunningham Barbara G. , Kopčo Norbert
Published: September 2020

Purpose

We examined how consonant perception is affected by a preceding speech carrier simulated in the same or a different room, for a broad range of consonants. Carrier room, carrier length, and carrier length/target room uncertainty were manipulated. A phonetic feature analysis tested which phonetic categories are most influenced by the acoustic context of the carrier.

Method

Two experiments were performed, each with 9 participants. Targets consisted of vowel-consonant (VC) syllables presented in one of 2 strongly reverberant rooms, preceded by a VC carrier presented either in the same room, a different reverberant room, or an anechoic room. In Experiment 1 the carrier length and the target room randomly varied from trial to trial while in Experiment 2 they were fixed within blocks of trials.

Results

Compared to the no-carrier condition, a consistent carrier provided only a small advantage for consonant perception, whereas inconsistent carriers disrupted performance significantly. For a different-room carrier, carrier length had an effect; performance dropped significantly in the 2-VC compared to the 4-VC carrier length. The only effect of carrier uncertainty was an overall drop in performance. Phonetic analysis showed that an inconsistent carrier significantly degraded identification of the manner of articulation, especially for stop consonants, and, in one of the rooms, also of voicing.

Conclusions

Calibration of consonant perception to strong reverberation is exhibited through disruptions in perception when the room is switched. The strength of calibration varies across different consonants and phonetic features, as well as across rooms and durations of exposure to a given room.
Patterns of roost site use by Asian hornbills and implications for seed dispersal
Authors: Naniwadekar Rohit , Rathore Akanksha , Shukla Ushma , Datta Aparajita
Published: September 2020

Animals spend a significant amount of time roosting. Therefore, understanding roosting patterns and the processes that influence roosting behaviour and roost site choice is essential. Hornbills exhibit interesting roosting patterns with some species roosting communally in large flocks. They are important seed dispersers and patterns of roost site use can have a significant influence on seed dispersal distributions and thereby on plant recruitment. We documented roost site use by four Great Hornbills (Buceros bicornis) and one Wreathed Hornbill (Rhyticeros undulatus) at a site in north-east India using GPS telemetry. We examined the influence of riverine habitats, nests and foraging range on roost selection. We determined the proportion of seeds that hornbills disperse at roosts and the dispersal distances of seeds dispersed at roosts from the source trees. Through telemetry, we found that roosts of Great Hornbills were generally in forested habitats. Our telemetry data showed that Wreathed Hornbill roosts were close to the river. These results were corroborated by observational data from roost sites where we had regular detections of relatively large flocks of Wreathed Hornbills and occasionally Great Hornbills. The roost sites were not close to the nest sites and were generally within the 95% kernel density diurnal activity ranges. Hornbills dispersed a small proportion of seeds at roost sites. Seeds dispersed at roost sites had almost twice the dispersal distances compared to those dispersed at non-roost sites. This study highlights variation in roost site pattern across individual hornbills and its implications for seed dispersal.
An Assistive Computer Vision Tool to Automatically Detect Changes in Fish Behavior In Response to Ambient Odor
Authors: Banerjee Sreya , Alvey Lauren , Brown Paula , Yue Sophie , Li Lei , Scheirer Walter J.
Published: September 2020

The analysis of fish behavior in response to odor stimulation is a crucial component of the general study of cross-modal sensory integration in vertebrates. In zebrafish, the centrifugal pathway runs between the olfactory bulb and the neural retina, originating at the terminalis neuron in the olfactory bulb. Any changes in the ambient odor of a fish’s environment warrants a change in visual sensitivity and can trigger mating-like behavior in males due to increased GnRH signaling in the terminalis neuron. Behavioral experiments to study this phenomenon are commonly conducted in a controlled environment where a video of the fish is recorded over time before and after the application of chemicals to the water. Given the subtleties of behavioral change, trained biologists are currently required to annotate such videos as part of a study. This process of manually analyzing the videos is time-consuming, requires multiple experts to avoid human error/bias and cannot be easily crowdsourced on the Internet. Machine learning algorithms from computer vision, on the other hand, have proven to be effective for video annotation tasks because they are fast, accurate, and, if designed properly, can be less biased than humans. In this work, we propose to automate the entire process of analyzing videos of behavior changes in zebrafish by using tools from computer vision, relying on minimal expert supervision. The overall objective of this work is to create a generalized tool to predict animal behaviors from videos using state-of-the-art deep learning models, with the dual goal of advancing understanding in biology and engineering a more robust and powerful artificial information processing system for biologists.
Root growth responses to mechanical impedance are regulated by a network of ROS, ethylene and auxin signalling in Arabidopsis
Authors: Jacobsen Amy G.R. , Xu Jian , Topping Jennifer F. , Lindsey Keith
Published: September 2020

The growth and development of root systems, essential for plant performance, is influenced by mechanical properties of the substrate in which the plants grow. Mechanical impedance, such as by compacted soil, can reduce root elongation and limit crop productivity.

To understand better the mechanisms involved in plant root responses to mechanical impedance stress, we investigated changes in the root transcriptome and hormone signalling responses of Arabidopsis to artificial root barrier systemsin vitro.

We demonstrate that upon encountering a barrier, reduced Arabidopsis root growth and the characteristic ‘step-like’ growth pattern is due to a reduction in cell elongation associated with changes in signalling gene expression. Data from RNA-sequencing combined with reporter line and mutant studies identified essential roles for reactive oxygen species, ethylene and auxin signalling during the barrier response.

We propose a model in which early responses to mechanical impedance include reactive oxygen signalling that is followed by integrated auxin and ethylene responses to mediate root growth changes. Inhibition of ethylene responses allows improved growth in response to root impedance, a result that may inform future crop breeding programmes.
miR-125-chinmopathway regulates dietary restriction dependent enhancement of lifespan inDrosophila
Authors: Pandey Manish , Bansal Sakshi , Bar Sudipta , Sokol Nicholas S. , Tennessen Jason M. , Kapahi Pankaj , Chawla Geetanjali
Published: September 2020

Dietary restriction (DR) extends healthy lifespan in diverse species. Age and nutrient-related changes in the abundance of microRNAs (miRNAs) and their processing factors have been linked to organismal longevity. However, the mechanisms by which they modulate lifespan and the tissue-specific role of miRNA mediated networks in DR dependent enhancement of lifespan remains largely unexplored. We show that two neuronally enriched and highly conserved microRNAs,miR-125andlet-7mediate the DR response inDrosophila melanogaster. Functional characterization ofmiR-125demonstrates its role in neurons while its targetchinmoacts both in neurons and the fat body to modulate fat metabolism and longevity. Proteomic analysis revealed that Chinmo exerts its DR effects by regulating expression ofFATP, CG2017, CG9577, CG17554, CG5009, CG8778, CG9527andFASN1. Our findings identifymiR-125as a conserved effector of DR pathway and open up the avenue for this small RNA molecule and its downstream effectors to be considered as potential drug candidates for treatment of late-onset diseases and biomarkers for healthy aging in humans.
Many are called but few are chosen – Multiple clonal origins greatly elevate the functional heterogeneity of tumors
Authors: Chen Bingjie , Wu Xianrui , Ruan Yongsen , Zhang Yulin , Wen HJ , Lan Ping , Wu Chung-I
Published: September 2020

Each tumor is usually accepted to be of a single origin from a progenitor cell. The shared evolutionary paths impose a limit on the nature of genetic diversity of the tumor. However, there are also numerous stem cell niches with independent proliferation potentials. To reconcile the contrasting perspectives, we propose a model whereby each tumor is of multiple clonal origins but the most proliferative one would eclipse other minor clones. The detection of the minor clones would entail an extreme scheme of large-number but small-volume sampling. In two cases of colon tumors so sampled, one indeed has 13 independent clones of disparate sizes and even the smaller clones have tens of thousands of cells dispersed non-locally. The other, much larger, tumor has only one prevailing clone that engulfs two tiny patches of minor clones. In both cases, the expanding clone spawns a hierarchy of subclones that resemble vassal states on its wake of expansion. The timing of metastasis can also be mapped to the precise stage of the clonal expansion. In conclusion, multiple independent clones, likely common but difficult to detect, can greatly elevate the non-neutral diversity within a tumor. This much-elevated diversity has many theoretical and clinical implications.
Tet2 Controls β cells Responses to Inflammation in Type 1 Diabetes
Authors: Rui Jinxiu , Deng Songyan , Ponath Gerald , Kursawe Romy , Lawlor Nathan , Sumida Tomokazu , Levine-Ritterman Maya , Perdigoto Ana Luisa , Stitzel Michael L. , Pitt David , Lu Jun , Herold Kevan C.
Published: September 2020

β cells may participate and contribute to their own demise during Type 1 diabetes (T1D). We identified a novel role of Tet2 in regulating immune killing of β cells. Tet2 is induced in murine and human β cells with inflammation but its expression is reduced in surviving β cells. Tet2-KO mice that receive WT bone marrow transplants develop insulitis but not diabetes and islet infiltrates do not eliminate β cells even though immune cells from the mice can transfer diabetes to NOD/scidrecipients. Tet2-KO β cells show reduced expression of inflammatory genes, associated with closed transcription factor binding sites. Tet2-KO recipients are protected from transfer of disease by diabetogenic immune cells. We conclude that Tet2 regulates pathologic interactions between β cells and immune cells and controls intrinsic protective pathways. Modulating TET2 may enable survival of β cells or their replacements in the setting of pathologic immune cells.
Phospho-islands and the evolution of phosphorylated amino acids in mammals
Authors: Moldovan Mikhail A. , Gelfand Mikhail S.
Published: September 2020

Background

Protein phosphorylation is the best studied post-translational modification strongly influencing protein function. Phosphorylated amino acids not only differ in physico-chemical properties from non-phosphorylated counterparts, but also exhibit different evolutionary patterns, tending to mutate to and originate from negatively charged amino acids. The distribution of phosphosites along protein sequences is non-uniform, as phosphosites tend to cluster, forming so-called phospho-islands.

Methods

Here, we have developed an HMM-based procedure for the identification of phospho-islands and studied the properties of the obtained phosphorylation clusters. To check robustness of evolutionary analysis, we consider different models for the reconstructions of ancestral phosphorylation states.

Results

Clustered phosphosites differ from individual phosphosites in several functional and evolutionary aspects including underrepresentation of phosphotyrosines, higher conservation, more frequent mutations to negatively charged amino acids. The spectrum of tissues, frequencies of specific phosphorylation contexts, and mutational patterns observed near clustered sites also are different.
Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde
Authors: Hamid Iman , Korunes Katharine , Beleza Sandra , Goldberg Amy
Published: September 2020

Humans have undergone large migrations over the past hundreds to thousands of years, exposing ourselves to new environments and selective pressures. Yet, evidence of ongoing or recent selection in humans is difficult to detect. Many of these migrations also resulted in gene flow between previously separated populations. These recently admixed populations provide unique opportunities to study rapid evolution in humans. Developing methods based on distributions of local ancestry, we demonstrate that this sort of genetic exchange has facilitated detectable adaptation to a malaria parasite in the admixed population of Cabo Verde within the last ∼20 generations. We estimate the selection coefficient is approximately 0.08, one of the highest inferred in humans. Notably, we show that this strong selection at a single locus has likely affected patterns of ancestry genome-wide, potentially biasing demographic inference. Our study provides evidence of adaptation in a human population on historical timescales.
Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering
Authors: Tompkins KJ , Houtti M , Litzau LA , Aird EJ , Everett BA , Nelson AT , Pornschloegl L , Limón-Swanson LK , Evans RL , Evans K , Shi K , Aihara H , Gordon WR
Published: September 2020

Replication initiator proteins (Reps) from the HUH-endonuclease superfamily process specific single-stranded DNA (ssDNA) sequences to initiate rolling circle/hairpin replication in viruses, such as crop ravaging geminiviruses and human disease causing parvoviruses. In biotechnology contexts, Reps are the basis for HUH-tag bioconjugation and a critical adeno-associated virus genome integration tool. We solved the first co-crystal structures of Reps complexed to ssDNA, revealing a key motif for conferring sequence specificity and for anchoring a bent DNA architecture. In combination, we developed a deep sequencing cleavage assay, termed HUH-seq, to interrogate subtleties in Rep specificity and demonstrate how differences can be exploited for multiplexed HUH-tagging. Together, our insights allowed engineering of only four amino acids in a Rep chimera to predictably alter sequence specificity. These results have important implications for modulating viral infections, developing Rep-based genomic integration tools, and enabling massively parallel HUH-tag barcoding and bioconjugation applications.
Pooled analysis of radiation hybrids identifies loci for growth and drug action in mammalian cells
Authors: Khan Arshad H. , Lin Andy , Wang Richard T. , Bloom Joshua S. , Lange Kenneth , Smith Desmond J.
Published: September 2020

Genetic screens in mammalian cells commonly focus on loss-of-function approaches. To evaluate the phenotypic consequences of extra gene copies, we used bulk segregant analysis (BSA) of radiation hybrid (RH) cells. We constructed six pools of RH cells, each consisting of ∼2500 independent clones, and placed the pools under selection in media with or without paclitaxel. Low pass sequencing identified 859 growth loci, 38 paclitaxel loci, 62 interaction loci, and three loci for mitochondrial abundance at genome-wide significance. Resolution was measured as ∼30 kb, close to single-gene. Divergent properties were displayed by the RH-BSA growth genes compared to those from loss-of-function screens, refuting the balance hypothesis. In addition, enhanced retention of human centromeres in the RH pools suggests a new approach to functional dissection of these chromosomal elements. Pooled analysis of RH cells showed high power and resolution and should be a useful addition to the mammalian genetic toolkit.
Successful thesis proposals in architecture and urban planning
Authors: Abdellatif Mahmoud , Abdellatif Reham
Published: September 2020

Purpose

The purpose of this research is to improve the understanding of what constitutes a successful thesis proposal (TP) and as such enhance the quality of the TP writing in architecture, planning and related disciplines.

Design/methodology/approach

Based on extended personal experience and a review of relevant literature, the authors proposed a conception of a successful TP comprising 13 standard components. The conception provides specific definition/s, attributes and success rules for each component. The conception was applied for 15 years on several batches of Saudi graduate students. The implications of the conception were assessed by a students' opinion survey. An expert inquiry of experienced academics from architectural schools in nine countries was applied to validate and improve the conception.

Findings

Assessment of the proposed conception demonstrated several positive implications on students' knowledge, performance and outputs which illustrates its applicability in real life. Experts' validation of the conception and constructive remarks have enabled further improvements on the definitions, attributes and success rules of the TP components.

Research limitations/implications

The proposed TP conception with its 13 components is limited to standard problem-solving research and will differ in the case of other types such as hypothesis-based research.

Practical implications

The proposed conception is a useful directive and evaluative tool for writing and assessing thesis proposals for graduate students, academic advisors and examiners.

Social implications

The research contributes to improving the quality of thesis production process among the academic community in the built environment fields.

Originality/value

The paper is meant to alleviate the confusion and hardship caused by the absence of a consensus on what constitutes a successful TP in the fields of architecture, urban planning and related disciplines.
Perceived benefits and issues associated with COBie datasheet handling in the construction industry
Authors: Kumar Vishal , Teo Evelyn Ai Lin
Published: September 2020

Purpose

Until now, the usage and usability factors of Construction Operation Building information exchange (COBie) datasheet have remained largely overlooked. This oversight may be the potential factor in the lower adoption rates as well as the effective usage of COBie datasheet in the architecture, engineering and construction-facilities management industry. The purpose of this study is to investigate the benefits and key issues associated with COBie datasheet handling and identify the key technological solutions, which can help in mitigating the identified issues.

Design/methodology/approach

A literature review was conducted to identify the key benefits of using COBie and issues, which are associated with COBie datasheet handling. This paper has also designed a questionnaire based on a literature review and surveyed professionals who are well versed with handling COBie datasheet. Using responses, the issues are analyzed and discussed using non-parametric statistical analysis.

Findings

A total of 9 key benefits and 24 key issues categorized under three groups of usability issues, technical issues and organizational/other issues were identified. The results from the survey agree with all the key issues associated with COBie datasheet handling (with 86 responses). This research also proposes key ideas, that can help in mitigating these issues.

Originality/value

There is a paucity in published literature, which discusses in detail about the various issues associated with COBie datasheet handling. This research study aims to address this gap by identifying key issues by looking at the entire COBie data-capturing process holistically. Finding from this study can help professionals to understand these issues and develop appropriate technological solutions, which can make COBie data capturing and understanding easier. The findings could also assist in increasing the adoption rate of COBie, which could be achieved through mitigation of identified issues.
Towards sustainable tourism: an empirical investigation
Authors: Garg Prerna , Pandey Anoop
Published: September 2020

Purpose

Looking at the paucity of research examining behaviour in reference to sustainable tourism in India, the study aims to propose a framework for predicting the mediating role played by personal norms in determining the intention to adopt sustainable tourism in India.

Design/methodology/approach

The study is cross-sectional in nature and has gathered responses from 275 valid respondents with diverse socio-demographic profiles. EFA was conducted, followed by CFA and structural model analysis to test the hypothesized relationships.

Findings

The results indicate that all the hypotheses were found to be significant, thus confirming the direct and indirect effect of consumer knowledge and consumer perceived effectiveness on an intention to adopt sustainable tourism.

Research limitations/implications

The study has not just added a different perspective to sustainable tourism but has also attempted to capture the attention of all academicians and practitioners who have sidelined this relevant concept in Indian context.

Practical implications

Marketers aiming to alter tourist’s behaviour with respect to sustainability must understand that they need to redesign their strategies within the context of personal norms or values.

Originality/value

While some of the literature has attempted to explore the attitudinal dimension of environmentally conscious behaviour, there is much scope to examine the factors motivating the formation of intention towards sustainable tourism in Indian context. The confined use of constructs from value-belief-norm model and theory of planned behaviour in sustainable tourism, has led to the development of the proposed research framework in the study.
Illegal gold mining in Indonesia: structure and causes
Authors: Hasibuan Ongku P. , Tjakraatmadja Jann H. , Sunitiyoso Yos
Published: September 2020

Purpose

This study aims to understand the process, structure and determinants of persistent illegal gold mining in Indonesia.

Design/methodology/approach

An exploratory study included a literature review, field observations and in-depth interviews. Fieldwork was conducted at two mining locations in Kalimantan, Indonesia. Sixteen respondents representing key stakeholders: government, mining companies, mining associations and community, including illegal miners, were interviewed. The findings of the literature review were categorized as the push or pull factors within the topics, and field observations verified the literature review results regarding Indonesia. Interview data were analyzed using content analysis methods. A structural diagram of the actors and causal loop diagrams among the determinants of illegal gold mining was created and interpreted.

Findings

A complex activity process and structure were revealed involving a range of actors. Politicians, government officials and law enforcement authorities added the complexity to the structure. Six main determinants of persistent illegal gold mining emerged: financial, low entry barrier, regulations and policies, supporting resources availability, politics and power and psychosocial factors.

Practical implications

This study provides a deeper understanding for policymakers to consider when formulating policies on natural resources, and insights for mining companies to minimize conflicts with the community.

Originality/value

The study contributes to our knowledge of the complex structure and main determinants of illegal gold mining in Indonesia, which supports efforts to curtail this illegal activity.