bluuebunny/crossref_metadata_2025 huggingface dataset:
SARS-COV-2 RBD Oral Vaccine Boosted by Mucosal Immune Adjuvant LTB26 via DCs and B Cells Activation in Mice
Authors: Ma Yongping , Shi Qinlin , Wang Qiujuan , Chen Sijing , Gan Sijie , Fang Changyin , Shen Yanxi , Jiang Min , Lin Tao , Song Fangzhou
Published: April 2020

Although several SARS-COV-2 vaccines have been approved, no one oral live vaccine is available. Here, an oral SARS-COV-2 RBD live vaccine containing LTB26 adjuvant has been developed. BALB/c mice are oral vaccinated with attenuatedSalmonella typhimuriumSL7207 containing pcDNA3.1-LTB26RBD or pcDNA3.1-RBD plasmids. The result shows that the high level of RBD specific antibody is produced in pcDNA3.1- LTB26RBD treatment. The mechanism indicates that LTB26 enhances RBD antibody production by significantly upregulating the activity of MHC II+DCs and CD19+CD45+B cells. LTB26 mutant is derived from heat-labile enterotoxin B subunit (LTB) wild type ofEscherichia coliwith enhanced immune adjuvanticity. Based on the pre-experiment result that SL7207 interferes the function of LTB26, the purified LTB26 was mixed with purified human rotavirus VP8 antigen to explore the mechanism of adjuvant. The results suggests that LTB26 enhances mucosal immune responses via increased of BCR and MHC II+expression. Furthermore, LTB26 promotes both Th1 and Th2 cell mediated immunity. Therefore, LTB26 maybe a potent adjuvant for mucosal vaccine development in view of the safety of LTB26 than LT toxin.
Inhibition of nonsense-mediated decay rescues functional p53β/γ isoforms in MDM2-amplified cancers
Authors: Gudikote Jayanthi P. , Cascone Tina , Poteete Alissa , Sitthideatphaiboon Piyada , Wu Qiuyu , Morikawa Naoto , Zhang Fahao , Peng Shaohua , Tong Pan , Li Lerong , Shen Li , Nilsson Monique , Jones Phillip , Sulman Erik P. , Wang Jing , Bourdon Jean-Christophe , Johnson Faye M. , Heymach John V.
Published: April 2020

Common mechanisms for p53 loss in cancer include expression of MDM2 or the human papilloma virus (HPV)-encoded E6 protein which both mediate degradation of wild-type (WT) p53 (p53α). Here, we show that two alternatively-spliced, functional, truncated isoforms of p53 (p53β and p53γ, containing exons 1-9 of the p53 gene) can be markedly upregulated by pharmacologic or genetic inhibition of nonsense mediated decay (NMD), a regulator of aberrant mRNA stability. These isoforms lack the MDM2 binding domain and hence have reduced susceptibility to MDM2-mediated degradation. In MDM2-overexpressing cells bearing wildtypeTP53gene, NMD blockade increased p53β/γ expression and p53 pathway activation, enhanced radiosensitivity, and inhibited tumor growth. A similar pattern was observed in HPV+cancer cells and in cancer cells with p53 mutations downstream of exon 9. These results identify a novel therapeutic strategy for restoration of p53 function in tumors rendered p53 deficient through MDM2 overexpression, HPV infection, or certain p53 mutations.
Invasion and maintenance of meiotic drivers in populations of ascomycete fungi
Authors: Martinossi-Allibert Ivain , Veller Carl , Ament-Velásquez S. Lorena , Vogan Aaron A. , Rueffler Claus , Johannesson Hanna
Published: April 2020

Meiotic drivers are selfish genetic elements that are able to become over-represented among the products of meiosis. This transmission advantage makes it possible for them to spread in a population even when they impose fitness costs on their host organisms. Whether a meiotic driver can invade a population, and subsequently reach fixation or coexist in a stable polymorphism, depends on the one hand on the biology of the host organism, including its life-cycle, mating system, and population structure, and on the other hand on the specific fitness effects of the driving allele on the host. Here, we present a population genetic model for spore killing, a type of drive specific to fungi. We show how ploidy level, rate of selfing, and efficiency of spore killing affect the invasion probability of a driving allele and the conditions for its stable coexistence with the non-driving allele. Our model can be adapted to different fungal life-cycles, and is applied here to two well-studied genera of filamentous ascomycetes known to harbor spore killing elements,NeurosporaandPodospora. We discuss our results in the light of recent empirical findings for these two systems.
Influence of historical and human factors on genetic structure and diversity patterns in peripheral populations: implications for the conservation of Moroccan trout
Authors: Perea S , Al Amouri M , Gonzalez EG , Alcaraz L , Yahyaoui A , Doadrio I
Published: April 2020

The brown trouts.l.has been the focus of numerous phylogeographic and conservation studies due to its socioeconomic importance, its marked genetic and phenotypic differentiation and its broad distribution range. Especially interesting evolutionary patterns are observed for populations occupying peripheral areas of a distribution range, such as in the case of the highly isolated trout populations in Morocco.

Continuous stocking programs may conceal natural genetic patterns, making it challenging to discern evolutionary patterns. In Morocco, trout stocking programs have been implemented to increase the genetic diversity of native populations by pooling fish of different origins in the Ras el Ma hatchery (Azrou region) and then stocking them in the different basins. In this study, phylogenetic and phylogeographic patterns, as well as genetic structure and diversity, of Moroccan trout populations were analyzed to evaluate the impact of continuous fish stocking on evolutionary processes in order to better distinguish between natural and human-mediated patterns.

Two mitochondrial and nine microsatellite markers were analyzed for all populations along the entire distribution range of brown trout in Morocco. Phylogenetic and phylogeographic analyses rendered two highly divergent evolutionary lineages, one comprising populations in the Drâa Basin and a second grouping the remaining Moroccan populations. Divergence of the Drâa lineage occurred during the Upper Pliocene, whilst differentiation within the second lineage coincided with the onset of the Pleistocene.

Genetic structuring among populations was evident. Nevertheless, populations exhibiting higher levels of genetic diversity were those affected by human-mediated processes, making it difficult to associate this diversity with natural processes. In fact, highly geographically isolated, not stocked populations showed the lowest values of genetic diversity. Although stocking management may increase the genetic diversity of these populations, it could also lead to the loss of local adaptive genotypes. Hence, current trout conservation programs should be revised.
Developing snakebite risk model using venomous snake habitat suitability as an indicating factor: An application of species distribution models in public health research
Authors: Yousefi Masoud , Kafash Anooshe , Khani Ali , Nabati Nima
Published: April 2020

Snakebite envenoming is an important public health problem in Iran, despite its risk not being quantified. This study aims to use venomous snakes’ habitat suitability as an indicator of snakebite risk, to identify high-priority areas for snakebite management across the country. Thus, an ensemble approach using five distribution modeling methods: Generalized Boosted Models, Generalized Additive Models, Maximum Entropy Modeling Generalized Linear Models, and Random Forest was applied to produce a spatial snakebite risk model for Iran. To achieve this, four venomous snakes’ habitat suitability (Macrovipera lebetina, Echis carinatus, Pseudocerastes persicusandNaja oxiana) were modeled and then multiplied. These medically important snakes are responsible for the most snakebite incidents in Iran. Multiplying habitat suitability models of the four snakes showed that the northeast of Iran (west of Khorasan-e-Razavi province) has the highest snakebite risk in the country. In addition, villages that were at risk of envenoming from the four snakes were identified. Results revealed that 51,112 villages are at risk of envenoming fromM. lebetina, 30,339 fromE. carinatus, 51,657 fromP. persicusand 12,124 fromN. oxiana. This paper demonstrates application of species distribution modeling in public health research and identified potential snakebite risk areas in Iran by using venomous snakes’ habitat suitability models as an indicating factor. Results of this study can be used in snakebite and human–snake conflict management in Iran. We recommend increasing public awareness of snakebite envenoming and education of local people in areas which identified with the highest snakebite risk.
Situation of antibiotic resistance in Bangladesh and its association with resistance genes for horizontal transfer
Authors: Safain Kazi Sarjana , Bhuyan Golam Sarower , Tasnim Sadia , Hasib Saad Hassan , Sultana Rosy , Islam Mohammad Sazzadul , Mahmud-Un-Nabi Mohammad Al , Sarker Suprovath Kumar , Noor Farjana Akther , Rahat Asifuzzaman , Bhuiyan Md Abdul Majid , Islam Md Tarikul , Manzoor Farhana , Anwar Sajid , Leung Daniel , Qadri Syed Saleheen , Qadri Firdausi , Mannoor Kaiissar
Published: April 2020

The study investigated the spectrum of antibiotic resistance and the associated genes for aminoglycoside, macrolide and ESBL class of antibiotics using clinical isolates. A total of 430 preserved bacterial strains (Acinetobacter baumannii, n= 20; Pseudomonas aeruginosa, n= 26; Klebsiella pneumoniae, n= 42; E. coli , n= 85; Staphylococcus aureus, n= 84; Salmonella Typhi, n= 82; Enterococcus spp., n= 27; Streptococcus pneumoniae, n= 36 and CNS, n = 28) were examined. The strains were isolated from patients admitted to various tertiary hospitals of Dhaka city between 2015 and 2019 with either acute respiratory infections, wound infections, typhoid fever or diarrhea. The isolates were reconfirmed by appropriate microbiological and biochemical methods. Antimicrobial susceptibility tests were done using Kirby–Bauer disk diffusion approach. PCR amplification using resistance gene-specific primers for aminoglycoside, macrolide and ESBL class of antibiotics was done and the amplified products were confirmed by Sanger sequencing. Of the total isolates, 53% came out as MDR with 96.6% of E. coli and 90% of Staphylococcus aureus. There was a year-wise gradual increase of MDR isolates from 2015-2018 and by 2019 the increase in MDR isolates became almost 2-fold compared to 2015. Among the five ESBL genes investigated, CTXM-1 came out as the most prevalent (63%) followed by NDM-1 (22%) and E. coli isolates were the predominant reservoir of these genes. ErmB (55%) was the most frequently detected macrolide resistance gene, whereas aac ( 6 ) -Ib (35.44%) was the most prevalent aminoglycoside resistance gene and these genes were most prevalent in E. coli and P. aeruginosa isolates, respectively. CTXM-1 and ErmB (16.66%) were the most frequent partners of coexistence followed by CTXM-1 and aac ( 3 ) -II.
Ectodomain shedding of L-selectin by ADAM17 in canine neutrophils
Authors: Snyder Kristin M. , McAloney Camille , Montel Joshua S. , Modiano Jaime F. , Walcheck Bruce
Published: April 2020

The adhesion protein L-selectin (CD62L) is expressed at high levels by circulating neutrophils and has a critical role in initiating their recruitment at sites of inflammation. L-selectin expression is rapidly downregulated upon neutrophil activation by various stimuli through a proteolytic process referred to as ectodomain shedding, which regulates L-selectin’s binding avidity and neutrophil recruitment. In humans and mice, L-selectin shedding is primarily mediated by ADAM17 (a disintegrin and metalloproteinase 17). L-selectin expression is also rapidly downregulated by canine neutrophils upon their activation; however, the role of ADAM17 in this process has not been previously investigated. We show that a highly selective inhibitor of ADAM17, but not an inhibitor of its most closely related family member ADAM10, effectively blocked L-selectin downregulation from the surface of canine neutrophils following their activation. The ADAM17 inhibitors did not block the rapid upregulation of the CD18 integrin Mac-1 (CD11b/CD18), showing that they did not broadly impair neutrophil activation. To directly examine the expression of ADAM17, we used several anti-human ADAM17 mAbs. Many did not stain canine neutrophils; however, the ADAM17 function-blocking mAbs MEDI3622 and D1(A12) did stain and also blocked L-selectin downregulation. Taken together, our findings provide the first direct evidence that ADAM17 is a primary sheddase of canine L-selectin, which may serve as an important therapeutic target to prevent neutrophil dysfunction during conditions of excessive inflammation, such as sepsis.
First Detection of PathogenicEscherichia coliIsolates Associated With Donkey Foals’ Diarrhea in Northern China
Authors: Wen-qiang Liu , Nan Xia , Jing-wen Zhang , Ren-hu Wang , Gui-miao Jiang
Published: April 2020

Objective

The aim of this study was to identify the biological features, influence factor and Genome-wide properties of pathogenic donkeyEscherichia coli(DEC) isolates associated with severe diarrhea in Northern China.

Methods

The isolation and identification of DEC isolates were carried out by the conventional isolation、automatic biochemical analysis system、serotype identification、16S rRNA test、animal challenge and antibiotics sensitivity examination. The main virulence factors were identified by PCR. The complete genomic re-sequence and frame-sequence were analyzed.

Results

216 strains of DEC were isolated from diarrhea samples, conforming to the bacterial morphology and biochemical characteristics ofE.coli. The average size of the pure culture was 329.4 nm×223.5 nm. Agglutination test showed that O78 (117/179, 65.4%) was the dominant serotype and ETEC(130/216, 60.1%) was the dominant pathogenic type. Noticeable pathogenic were observed in 9 of 10 (90%) randomly selected DEC isolates caused the death of test mice (100%, 5/5) within 6h∼48h, 1 of 10 (10%) isolates caused the death of test mice (40%, 2/5) within 72h. Our data confirmed that DEC plays an etiology role in dirarrea/death case of donkey foal. Antibiotics sensitivity test showed significant susceptibility to DEC isolates were concentrated in Nor、EFT、ENR、CIP and AMK,while the isolates with severe antibiotic resistance was AM、TE、APR、FFC、RL and CN. Multi-drug resistance was also observed. A total of 15 virulence gene fragments were determined from DEC(n=30) including OMPA (73%), safD (77%), traTa (73%), STa(67%), EAST1 (67%), astA (63%), kspII (60%), irp2 (73%), iucD (57%), eaeA (57%), VAT (47%), iss (33%), cva (27%), ETT2 (73%) and K88 (60%) respectively. More than 10 virulence genes from 9 of 30(30%) DEC strains were detected, while 6 of 30(20%) DEC strains detected 6 virulence factors. phylogenetic evolutionary tree of 16S rRNA gene from different isolates shows some variability. The original data volume obtained from the genome re-sequencing of DEC La18 was 2.55G and Genome framework sequencing was carried out to demonstrate the predicted functions and evolutionary direction and genetic relationships with other animalE.coli.

Conclusions

These findings provide firstly fundamental data that might be useful in further study of the role of DEC and provide a new understanding of the hazards of traditionalcolibacillosisdue to the appear of new production models.
Combined single-cell gene and isoform expression analysis in haematopoietic stem and progenitor cells
Authors: Mincarelli Laura , Uzun Vladimir , Rushworth Stuart A. , Haerty Wilfried , Macaulay Iain C.
Published: April 2020

Single-cell RNA sequencing (scRNA-seq) enables gene expression profiling and characterization of novel cell types within heterogeneous cell populations. However, most approaches cannot detect alternatively spliced transcripts, which can profoundly shape cell phenotype by generating functionally distinct proteins from the same gene. Here, we integrate short- and long-read scRNA-seq of hematopoietic stem and progenitor cells to characterize changes in cell type abundance, gene and isoform expression during differentiation and ageing.
Protein manipulation using single copies of short peptide tags in cultured cells and inDrosophila melanogaster
Authors: Vigano M. Alessandra , Ell Clara-Maria , Kustermann Manuela MM , Aguilar Gustavo , Matsuda Shinya , Zhao Ning , Stasevich Timothy J , Pyrowolakis George , Affolter Markus
Published: April 2020

Cellular development and specialized cellular functions are regulated processes which rely on highly dynamic molecular interactions among proteins, distributed in all cell compartments. Analysis of these interactions and their mechanisms of action has been one of the main topics in cellular and developmental research over the last fifty years. Studying and understanding the functions of proteins of interest (POIs) has been mostly achieved by their alteration at the genetic level and the analysis of the phenotypic changes generated by these alterations. Although genetic and reverse genetic technologies contributed to the vast majority of information and knowledge we have gathered so far, targeting specific interactions of POIs in a time- and space-controlled manner or analyzing the role of POIs in dynamic cellular processes such as cell migration or cell division would require more direct approaches. The recent development of specific protein binders, which can be expressed and function intracellularly, together with several improvements in synthetic biology techniques, have contributed to the creation of a new toolbox for direct protein manipulations. We selected a number of short tag epitopes for which protein binders from different scaffolds have been developed and tested whether these tags can be bound by the corresponding protein binders in living cells when they are inserted in a single copy in a POI. We indeed find that in all cases, a single copy of a short tag allows protein binding and manipulation. UsingDrosophila, we also find that single short tags can be recognized and allow degradation and relocalization of POIsin vivo.
Trade-Offs between Speed, Accuracy, and Dissipation in tRNAIleAminoacylation
Authors: Yu Qiwei , Mallory Joel D. , Kolomeisky Anatoly B. , Ling Jiqiang , Igoshin Oleg A.
Published: April 2020

Living systems maintain a high fidelity in information processing through kinetic proofreading, a mechanism to preferentially remove incorrect substrates at the cost of energy dissipation and slower speed. Proofreading mechanisms must balance their demand for higher speed, fewer errors, and lower dissipation, but it is unclear how rates of individual reaction steps are evolutionary tuned to balance these needs, especially when multiple proofreading mechanisms are present. Here, using a discrete-state stochastic model, we analyze the optimization strategies inEscherichia coliisoleucyl-tRNA synthetase. Surprisingly, this enzyme adopts an economic proofreading strategy and improves speed and dissipation as long as the error is tolerable. Through global parameter sampling, we reveal a fundamental dissipation-error relation that bounds the enzyme’s optimal performance and explains the importance of the post-transfer editing mechanism. The proximity of native system parameters to this bound demonstrates the importance of energy dissipation as an evolutionary force affecting fitness.

Graphical TOC Entry
Impact of Advanced Maternal Age on Physiologic Adaptations to Pregnancy in Vervet Monkeys
Authors: Plant Maren , Armstrong Cecilia , Ruggiero Alistaire , Sherrill Chrissy , Uberseder Beth , Jeffries Rachel , Nevarez Justin , Jorgensen Matthew J. , Kavanagh Kylie , Quinn Matthew A.
Published: April 2020

Context

The trend to delay pregnancy in the United States has resulted in the number of advanced maternal age (AMA) pregnancies to also increase. In humans, AMA is associated with a variety of pregnancy-related pathologies such as preeclampsia (PE). While AMA is known to be a factor which contributes to the development of pregnancy-induced diseases, the molecular and cellular mechanisms giving rise to this phenomenon are still very limited. This is due in part to lack of a pre-clinical model which has physiologic relevance to human pregnancy while also allowing control of environmental and genetic variability inherent in human studies.

Objective

To determine potential physiologic relevance of the vervet/African green monkey (Chlorocebus aethiops sabaeus)as a pre-clinical model to study the effects of AMA on adaptations to pregnancy.

Design

Thirteen age-diverse pregnant vervet monkeys (3-16 y.o.) were utilized to measure third trimester blood pressure (BP), complete blood count, iron measurements and hormone levels.

Results

Significant associations were observed between third trimester diastolic BP and maternal age. Furthermore, the presence of leukocytosis with enhanced circulating neutrophils was observed in AMA mothers compared to younger mothers. Moreover, we observed a negative relationship between maternal age and estradiol, progesterone and cortisol levels. Finally, offspring born to AMA mothers displayed a postnatal growth retardation phenotype.

Conclusions

These studies demonstrate physiologic impairment in the adaptation to pregnancy in AMA vervet/African green monkeys. Our data indicate the vervet/African green monkey may serve as a useful pre-clinical model and tool for deciphering pathological mediators of maternal disease in AMA pregnancy.
MicroRNA arm switching regulated by uridylation
Authors: Kim Haedong , Kim Jimi , Yu Sha , Lee Young-Yoon , Park Junseong , Choi Ran Joo , Yoon Seon-Jin , Kang Seok-Gu , Kim V. Narry
Published: April 2020

Strand selection is a critical step in microRNA (miRNA) biogenesis. Although the dominant strand may alter depending on cellular contexts, the molecular mechanism and physiological significance of such alternative strand selection (or “arm switching”) remain elusive. Here we find mir-324 as one of the strongly regulated miRNAs by arm switching, and identify terminal uridylyl transferases TUT4 and TUT7 as the key regulators. Uridylation of pre-mir-324 by TUT4/7 re-positions DICER on the pre-miRNA and shifts the cleavage site. This alternative processing produces a duplex with a different terminus, from which the 3′ strand (3p) is selected instead of the 5′ strand (5p). In glioblastoma, the TUT4/7 and 3p levels are upregulated while the 5p level is reduced. Manipulation of the strand ratio is sufficient to impair glioblastoma cell proliferation. This study uncovers a role of uridylation as a molecular switch in alternative strand selection and implicates its therapeutic potential.
Gamete-specific expression of TALE class HD genes activates the diploid sporophyte program inMarchantia polymorpha
Authors: Dierschke Tom , Flores-Sandoval Eduardo , Rast-Somssich Madlen I. , Althoff Felix , Zachgo Sabine , Bowman John L.
Published: April 2020

Eukaryotic life cycles alternate between haploid and diploid phases and in phylogenetically diverse unicellular eukaryotes, expression of paralogous homeodomain genes in the two gametes directs the haploid-to-diploid transition. In the unicellular Chlorophyte algaChlamydomonasKNOX and BELL TALE-homeodomain genes mediate the transition. Here we demonstrate that in the liverwortMarchantia polymorphapaternal (sperm) expression three of the five phylogenetically diverse BELL genes, MpBELL234, and maternal (egg) expression of MpKNOX1mediate the haploid-to-diploid transition. Loss-of-function alleles of either result in zygotic or early embryonic arrest. In land plants both the haploid gametophyte and diploid sporophyte are complex multicellular organisms. Expression of MpKNOX1and two other paralogs, MpBELL1and MpKNOX2, during sporophyte development is consistent with a later role in patterning the sporophyte. These results indicate that the ancestral mechanism to activate diploid gene expression was retained in early diverging land plants and subsequently co-opted during evolution of the diploid sporophyte body.
Concerted action of kinesins KIF5B and KIF13B promotes efficient secretory vesicle transport to microtubule plus ends
Authors: Serra-Marques Andrea , Martin Maud , Katrukha Eugene A. , Grigoriev Ilya , Peeters Cathelijn A.E. , Liu Qingyang , Hooikaas Peter Jan , Yao Yao , Solianova Veronika , Smal Ihor , Pedersen Lotte B. , Meijering Erik , Kapitein Lukas C. , Akhmanova Anna
Published: April 2020

Intracellular transport relies on multiple kinesins, but it is poorly understood which kinesins are present on particular cargos, what their contributions are and whether they act simultaneously on the same cargo. Here, we show that Rab6-positive secretory vesicles are transported from the Golgi apparatus to the cell periphery by kinesin-1 KIF5B and kinesin-3 KIF13B, which determine the location of secretion events. KIF5B plays a dominant role, whereas KIF13B helps Rab6 vesicles to reach freshly polymerized microtubule ends, to which KIF5B binds poorly, likely because its cofactors, MAP7-family proteins, are slow in populating these ends. Sub-pixel localization demonstrated that during microtubule plus-end directed transport, both kinesins localize to the vesicle front and can be engaged on the same vesicle. When vesicles reverse direction, KIF13B relocates to the middle of the vesicle, while KIF5B shifts to the back, suggesting that KIF5B but not KIF13B undergoes a tug-of-war with a minus-end directed motor.
Punishment history biases corticothalamic responses to motivationally-significant stimuli
Authors: Lucantonio Federica , Su Zhixiao , Chang Anna J. , Bari Bilal A. , Cohen Jeremiah Y.
Published: April 2020

Making predictions about future rewards or punishments is fundamental to adaptive behavior. These processes are influenced by prior experience. For example, prior exposure to aversive stimuli or stressors changes behavioral responses to negative- and positive-value predictive cues. Here, we demonstrate a role for medial prefrontal cortex (mPFC) neurons projecting to the paraventricular nucleus of the thalamus (PVT; mPFC→PVT) in this process. We found that a history of punishments negatively biased behavioral responses to motivationally-relevant stimuli in mice and that this negative bias was associated with hyperactivity in mPFC→PVT neurons during exposure to those cues. Furthermore, artificially mimicking this hyperactive response with selective optogenetic excitation of the same pathway recapitulated the punishmentinduced negative behavioral bias. Together, our results highlight how information flow within the mPFC→PVT circuit is critical for making predictions about imminent motivationally-relevant outcomes as a function of prior experience.
Single-cell RNA sequencing deconvolutes thein vivoheterogeneity of human bone marrow-derived mesenchymal stem cells
Authors: Wang Zun , Li Xiaohua , Yang Junxiao , Gong Yun , Zhang Huixi , Qiu Xiang , Liu Ying , Zhou Cui , Chen Yu , Greenbaum Jonathan , Cheng Liang , Hu Yihe , Xie Jie , Yang Xucheng , Li Yusheng , Schiller Martin R. , Tan Lijun , Tang Si-Yuan , Shen Hui , Xiao Hong-Mei , Deng Hong-Wen
Published: April 2020

Bone marrow-derived mesenchymal stem cells (BM-MSCs) are multipotent stromal cells, which have a critical role in the maintenance of skeletal tissues such as bone, cartilage, and the fat found in bone marrow. In addition to providing microenvironmental support for hematopoietic processes, BM-MSCs can differentiate into various mesodermal lineages including osteoblast/osteocyte, chondrocyte, and adipocyte cells that are crucial for bone metabolism. While BM-MSCs have high cell-to-cell heterogeneity in gene expression, the cell subtypes that contribute to this heterogeneityin vivoin humans have not been characterized. To investigate the transcriptional diversity of BM-MSCs, we applied single-cell RNA sequencing (scRNA-seq) on freshly isolated CD271+BM-derived mononuclear cells (BM-MNCs) from two human subjects. We successfully identified LEPRhiCD45lowBM-MSCs within the CD271+BM-MNC population, and further codified the BM-MSCs into distinct subpopulations corresponding to the osteogenic, chondrogenic, and adipogenic differentiation trajectories, as well as terminal-stage quiescent cells. Biological functional annotations of transcriptomes suggest that osteoblast precursors may induce angiogenesis coupled with osteogenesis, and chondrocyte precursors may have the potential to differentiate into myocytes. We discovered transcripts for several cluster of differentiation (CD) markers that were highly expressed (e.g., CD167b, CD91, CD130 and CD118) or absent (e.g., CD74, CD217, CD148 and CD68) in BM-MSCs and could be novel markers for human BM-MSC purification. This study is the first systematicin vivodissection of human BM-MSCs cell subtypes at the single-cell resolution, revealing insight into the extent of their cellular heterogeneity and bone homeostasis.
Single-dimensional human brain signals for two-dimensional economic choice options
Authors: Seak Leo Chi U , Volkmann Konstantin , Pastor-Bernier Alexandre , Grabenhorst Fabian , Schultz Wolfram
Published: April 2020

Rewarding choice options typically contain multiple components, but neural signals in single brain voxels are scalar and primarily vary up or down. In a previous study, we had designed reward bundles that contained the same two milkshakes with independently set amounts; we had used psychophysics and rigorous economic concepts to estimate two-dimensional choice indifference curves (IC) that represented revealed stochastic preferences for these bundles in a systematic, integrated manner. All bundles on the same ICs were equally revealed preferred (and thus had same utility, as inferred from choice indifference); bundles on higher ICs (higher utility) were preferred to bundles on lower ICs (lower utility). In the current study, we used the established behavior for testing with functional magnetic resonance imaging (fMRI). We now demonstrate neural responses in reward-related brain structures of human female and male participants, including striatum, midbrain and medial orbitofrontal cortex that followed the characteristic pattern of ICs: similar responses along ICs (same utility despite different bundle composition), but monotonic change across ICs (different utility). Thus, these brain structures integrated multiple reward components into a scalar signal, well beyond the known subjective value coding of single-component rewards.

Significance Statement

Rewards have several components, like the taste and size of an apple, but it is unclear how each component contributes to the overall value of the reward. While choice indifference curves of economic theory provide behavioural approaches to this question, it is unclear whether brain responses capture the preference and utility integrated from multiple components. We report activations in striatum, midbrain and orbitofrontal cortex that follow choice indifference curves representing behavioral preferences over and above variations of individual reward components. In addition, the concept-driven approach encourages future studies on natural, multi-component rewards that are prone to irrational choice of normal and brain-damaged individuals.
Machine Learning and Optimal Control of Enzyme Activities to Preserve Solvent Capacity in the Cell
Authors: Britton Samuel , Alber Mark , Cannon William R.
Published: April 2020

Experimental measurements or computational model predictions of the post-translational regulation of enzymes needed in a metabolic pathway is a difficult problem. Consequently, regulation is mostly known only for well-studied reactions of central metabolism in various model organisms. In this study, we utilize two approaches to predict enzyme regulation policies and investigate the hypothesis that regulation is driven by the need to maintain the solvent capacity in the cell. The first predictive method uses a statistical thermodynamics and metabolic control theory framework while the second method is performed using a hybrid optimization-reinforcement learning approach. Efficient regulation schemes were learned from experimental data that either agree with theoretical calculations or result in a higher cell fitness using maximum useful work as a metric. Model predictions provide the following novel general principles: (1) the regulation itself causes the reactions to be much further from equilibrium instead of the common assumption that highly non-equilibrium reactions are the targets for regulation; (2) regulation is used to maintain the concentrations of both immediate and downstream product concentrations rather than to maintain a specific energy charge; and (3) the minimal regulation needed to maintain metabolite levels at physiological concentrations also results in the maximal energy production rate that can be obtained at physiological conditions. The resulting energy production rate is an emergent property of regulation which may be represented by a high value of the adenylate energy charge. In addition, the predictions demonstrate that the amount of regulation needed can be minimized if it is applied at the beginning or branch point of a pathway, in agreement with common notions. The approach is demonstrated for three pathways in the central metabolism ofE. coli(gluconeogenesis, glycolysis-TCA and Pentose Phosphate-TCA) that each require different regulation schemes. It is shown quantitatively that hexokinase, glucose 6-phosphate dehydrogenase and glyceraldehyde phosphate dehydrogenase, all branch points of pathways, play the largest roles in regulating central metabolism.
Data-driven reduction of dendritic morphologies with preserved dendro-somatic responses
Authors: Wybo Willem A.M. , Jordan Jakob , Ellenberger Benjamin , Mengual Ulisses M. , Nevian Thomas , Senn Walter
Published: April 2020

Dendrites shape information flow in neurons. Yet, there is little consensus on the level of spatial complexity at which they operate. We present a flexible and fast method to obtain simplified neuron models at any level of complexity. Through carefully chosen parameter fits, solvable in the least squares sense, we obtain optimal reduced compartmental models. We show that (back-propagating) action potentials, calcium-spikes and NMDA-spikes can all be reproduced with few compartments. We also investigate whether afferent spatial connectivity motifs admit simplification by ablating targeted branches and grouping the affected synapses onto the next proximal dendrite. We find that voltage in the remaining branches is reproduced if temporal conductance fluctuations stay below a limit that depends on the average difference in input impedance between the ablated branches and the next proximal dendrite. Further, our methodology fits reduced models directly from experimental data, without requiring morphological reconstructions. We provide a software toolbox that automatizes the simplification, eliminating a common hurdle towards including dendritic computations in network models.
Small Molecule Channels Harness Membrane Potential to Concentrate Potassium in trk1Δtrk2Δ Yeast
Authors: Hou Jennifer , Daniels Page N. , Burke Martin D.
Published: April 2020

Many protein ion channels harness membrane potential to move ions in opposition to their chemical gradient. Deficiencies of such proteins cause several human diseases, including cystic fibrosis, Bartter Syndrome Type II, and proximal renal tubular acidosis. Using yeast as a readily manipulated eukaryotic model system, we asked whether, in the context of a deficiency of such protein ion channel functionin vivo, small molecule channels could similarly harness membrane potential to concentrate ions. In yeast, Trk potassium transporters use membrane potential to move potassium ions from a compartment of relatively low concentration outside cells (∼15mM) to one of >10 times higher concentration inside (150-500mM). trk1Δtrk2Δ yeast are missing these potassium transporters and thus cannot concentrate potassium or grow in standard media. Here we show that potassium permeable, but not potassium selective, small molecule ion channels formed by the natural product amphotericin B can harness membrane potential to concentrate potassium in trk1Δtrk2Δ cells and thereby restore growth. This finding expands the list of potential human channelopathies that might be addressed by a molecular prosthetics approach.
Suppressing chemoresistance in lung cancer via dynamic phenotypic switching and intermittent therapy
Authors: Nam Arin , Mohanty Atish , Bhattacharya Supriyo , Kotnala Sourabh , Achuthan Srisairam , Hari Kishore , Nathan Anusha , Rangarajan Govindan , Massarelli Erminia , Levine Herbert , Jolly Mohit Kumar , Kulkarni Prakash , Salgia Ravi
Published: April 2020

A major challenge in cancer therapy is drug resistance, which is typically attributed to acquired mutations and tumor heterogeneity. However, emerging evidence suggests that dynamic cellular interactions and group behavior also contribute to drug resistance, although, the details of such mechanisms are poorly understood. Here, by combining real time cellular growth data with mathematical modeling, we showed that the cisplatin-sensitive and tolerant lung cancer cells when co-cultured in cisplatin-free and cisplatin-treated environments, exhibit drastically different group strategies in response to environmental changes. While tolerant cells exhibited a persister-like behaviour and were attenuated by sensitive cells, sensitive cells ‘learned’ to evade chemotherapy from tolerant cells when co-cultured. Further, tolerant cells could switch phenotypes to become sensitive, although high cisplatin concentrations suppressed this switching. Finally, switching cisplatin administration from continuous to intermittent suppressed the emergence of tolerant cells, suggesting that intermittent rather than continuous chemotherapy may result in better outcomes in lung cancer.
Autocrine insulin pathway signaling regulates actin dynamics in cell wound repair
Authors: Nakamura Mitsutoshi , Verboon Jeffrey M. , Allen Tessa E. , Abreu-Blanco Maria Teresa , Liu Raymond , Dominguez Andrew N.M. , Delrow Jeffrey J. , Parkhurst Susan M.
Published: April 2020

Cells are exposed to frequent mechanical and/or chemical stressors that can compromise the integrity of the plasma membrane and underlying cortical cytoskeleton. The molecular mechanisms driving the immediate repair response launched to restore the cell cortex and circumvent cell death are largely unknown. Using microarrays and drug-inhibition studies to assess gene expression, we find that initiation of cell wound repair in theDrosophilamodel is dependent on translation, whereas transcription is required for subsequent steps. We identified 253 genes whose expression is up-regulated (80) or down-regulated (173) in response to laser wounding. A subset of these genes were validated using RNAi knockdowns and exhibit aberrant actomyosin ring assembly and/or actin remodeling defects. Strikingly, we find that the canonical insulin signaling pathway controls actin dynamics through the actin regulators Girdin and Chickadee (profilin), and its disruption leads to abnormal wound repair. Our results provide new insight for understanding how cell wound repair proceeds in healthy individuals and those with diseases involving wound healing deficiencies.
Chromosome-scale assembly of the bread wheat genome,Triticum aestivum, reveals over 5700 new genes
Authors: Alonge Michael , Shumate Alaina , Puiu Daniela , Zimin Aleksey , Salzberg Steven L.
Published: April 2020

Bread wheat (Triticum aestivum)is a major food crop and an important plant system for agricultural genetics research. However, due to the complexity and size of its allohexaploid genome, genomic resources are limited compared to other major crops. The IWGSC recently published a reference genome and associated annotation (IWGSC v1.0, Chinese Spring) that has been widely adopted and utilized by the wheat community. Although this reference assembly represents all 3 wheat subgenomes at chromosome scale, it was derived from short reads, and thus is missing a substantial portion of the expected 16 gigabases of genomic sequence. We earlier published an independent wheat assembly (Triticum 3.1, Chinese Spring) that came much closer in length to the expected genome size, although it was only a contig-level assembly lacking gene annotations. Here, we describe a reference-guided effort to scaffold those contigs into chromosome-length pseudomolecules, add in any missing sequence that was unique to the IWGSC 1.0 assembly, and annotate the resulting pseudomolecules with genes. Our updated assembly, Triticum 4.0, contains 15.07 gigabases of non-gap sequence anchored to chromosomes, which is 1.2 gigabases more than the previous reference assembly. It includes 108,639 genes unambiguously localized to chromosomes, including over 2000 genes that were previously unplaced. We also discovered more than 5700 new genes, all of them duplications in the Chinese Spring genome that are missing from the IWGSC assembly and annotation. The Triticum 4.0 assembly and annotations are freely available atwww.ncbi.nlm.nih.gov/bioproject/PRJNA392179.
Sudden hyposmia as a prevalent symptom of COVID-19 infection
Authors: Marchese-Ragona Rosario , Ottaviano Giancarlo , Piero Nicolai , Vianello Andrea , Miryam Carecchio
Published: April 2020

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has recently caused a pandemic that has involved Italy as the second worldwide nation in terms of infected patients and deaths. The clinical manifestation of Covid-19 ranges from asymptomatic carrier status to severe pneumonia. Asymptomatic individuals in Covid-19 are those who are carriers of the virus but do not show clinical symptoms and are able to transmit the disease in the same degree as symptomatic carriers. In order to contain contagions is of supreme importance to identify asymptomatic patients because this subpopulation is one of the main factors contributing to the spread of this disease. We report on six Italian patients with COVID-19 who presented sudden hyposmia as the only or most prominent disease manifestation, without upper or lower respiratory tract involvement or other major features of the disease. A supra-threshold olfaction test confirmed the hyposmia in all patients. The onset of hyposmia during a Covid-19 outbreak should be considered as a warning sign of an infection that requires a diagnostic test for Covid-19
The effect of adding oat flour on the nutritional and sensory quality of wheat bread
Authors: Krochmal-Marczak Barbara , Tobiasz-Salach Renata , Kaszuba Joanna
Published: April 2020

Purpose

Flour from oat grain is characterised by a high content of protein andβ-glucans, with a favourable amino acid composition and a substantial content of fat, including unsaturated fatty acids. Additives to bread that enrich its nutritional value can worsen physical properties. It is important to know how to develop recipes for healthy bread based on wheat flour, with the appropriate addition of oat flour. The purpose of this study was to determine the influence on the physical properties of bread made of wheat flour, following the addition of oat flour. The purpose was also to find a recipe for a new product with higher nutritional value, which would then be acceptable for consumers.

Design/methodology/approach

In addition to wheat flour, flour made of oat grains, obtained from the naked Nagus variety (hulless oat), was added. The flour was analysed for moisture, dry matter, proteins andβ-glucans, as well as total dietary fibre − soluble and insoluble. The dough was made with wheat flour according to a recipe, which included yeast, salt and water as well as extra oat flour in various proportions − 15, 25 and 30%, respectively. The bread was baked using a direct single-phase method developed by the Baking Institute in Berlin. Both the physicochemical and sensory evaluation were carried out on the bread.

Findings

The recipe for wheat bread that included 15% proportion of oat flour supplement was found to be the most acceptable in both the sensory (n = 30) and qualitative evaluation and would be suitable to produce nutritious bread. The use of 25% and 30% additions of oat flour resulted in a reduction in bread weight, volume and yield, which ultimately lead to an increase in overall baking losses.

Originality/value

This study proved that 15% oat flour could be used as an optimum addition for the production of wheat-oat bread. This bread may lead to a new assortment of bakery products with pro-health properties.
Exploring producers' motivations and challenges within a farmers' market
Authors: Michel-Villarreal Rosario , Vilalta-Perdomo Eliseo Luis , Hingley Martin
Published: April 2020

Purpose

The purpose of this study is to explore food producers' motivations and challenges whilst participating in short food supply chains (SFSCs). This paper compares findings with previous literature and investigates the topic in the context of producers' motivations.

Design/methodology/approach

The paper includes a literature review concerning producers' motivations to engage in SFSCs. A case study was designed to investigate motivations underlying producers' engagement in SFSCs, as well as the challenges that they face. Semi-structured interviews were conducted in a farmers' market located in Mexico. Thematic analysis is used to identify the principal issues for producers'. Propositions based on findings are presented.

Findings

Findings suggest that small, large, part-time and full-time producers are willing to engage with farmers' markets for diverse primary economic and non-economic motivations. Individual and collective challenges were also identified.

Originality/value

This research helps to explain producers' motivations and challenges within SFSCs in an under-researched context, namely a focus on producers' and in the Global South.
How do human resource management practices affect employee well-being? A mediated moderation model
Authors: Zhang Xinggui , Lin Zhibin , Liu Yizhu , Chen Xiao , Liu David Ming
Published: April 2020

Purpose

The study examines how human resource management practices (HRMPs) – including ability practice, motivation practice and opportunity practice – affect employee well-being (EWB) – including life well-being, job well-being and psychological well-being – in the Chinese cultural context.

Design/methodology/approach

A sample of 529 employees from various industries in China participated in the survey for this study. Data were analyzed using structural equation modeling.

Findings

The findings indicate that HRMPs have a significant positive effect on EWB. Specifically, practices based on ability, motivation and opportunity have a significant positive effect on job well-being, life well-being and psychological well-being, respectively. Integrity leadership moderates the impact of HRMPs on EWB. Organizational justice has a partial mediating effect on the relationship between HRMPs and EWB. Integrity leadership moderates the mediation effect of organizational justice in the relationship between HRMPs and EWB.

Practical implications

Human resource policies and practices need to create a fair organizational atmosphere, and managers implementing them must have integrity leadership. When selecting and promoting managers, organizations should pay attention to not only a candidate's ability but also his or her integrity.

Originality/value

This study uncovers how the important roles of organizational justice and integrity leadership act on the relationship between HRMPs and EWB, thus advancing our understanding of how HRMPs can effectively increase EWB.