bluuebunny/crossref_metadata_2025 huggingface dataset:
Perspectives From Systems Biology to Improve Knowledge of Leishmania Drug Resistance
Authors: Horácio Elvira Cynthia Alves , Hickson Jéssica , Murta Silvane Maria Fonseca , Ruiz Jeronimo Conceição , Nahum Laila Alves
Published: April 2021

Neglected Tropical Diseases include a broad range of pathogens, hosts, and vectors, which represent evolving complex systems. Leishmaniasis, caused by different Leishmania species and transmitted to humans by sandflies, are among such diseases. Leishmania and other Trypanosomatidae display some peculiar features, which make them a complex system to study. Leishmaniasis chemotherapy is limited due to high toxicity of available drugs, long-term treatment protocols, and occurrence of drug resistant parasite strains. Systems biology studies the interactions and behavior of complex biological processes and may improve knowledge of Leishmania drug resistance. System-level studies to understand Leishmania biology have been challenging mainly because of its unusual molecular features. Networks integrating the biochemical and biological pathways involved in drug resistance have been reported in literature. Antioxidant defense enzymes have been identified as potential drug targets against leishmaniasis. These and other biomarkers might be studied from the perspective of systems biology and systems parasitology opening new frontiers for drug development and treatment of leishmaniasis and other diseases. Our main goals include: 1) Summarize current advances in Leishmania research focused on chemotherapy and drug resistance. 2) Share our viewpoint on the application of systems biology to Leishmania studies. 3) Provide insights and directions for future investigation.
Designing (for) Urban Food Webs
Authors: Felson Alexander J. , Ellison Aaron M.
Published: April 2021

Interest is growing in designing resilient and ecologically rich urban environments that provide social and ecological benefits. Regenerative and biocentric designs fostering urban ecological habitats including food webs that provide ecosystem services for people and wildlife increasingly are being sought. However, the intentional design of urban landscapes for food webs remains in an early stage with few precedents and many challenges. In this paper, we explore the potential to design (for) urban food webs through collaborations between designers and ecologists. We start by examining the ecology and management of Jamaica Bay in New York City as a case study of an anthropogenic landscape where ecosystems are degraded and the integrity of extant food webs are intertwined with human agency. A subsequent design competition focusing on ecological design and management of this large-scale landscape for animal habitat and ecosystem services for people illustrates how designers approach this anthropogenic landscape. This case study reveals that both designing urban landscapes for food webs and directly designing and manipulating urban food webs are complicated and challenging to achieve and maintain, but they have the potential to increase ecological health of, and enhance ecosystem services in, urban environments. We identify opportunities to capitalize on species interactions across trophic structures and to introduce managed niches in biologically engineered urban systems. The design competition reveals an opportunity to approach urban landscapes and ecological systems creatively through a proactive design process that includes a carefully crafted collaborative approach to constructing ecologically functioning landscapes that can integrate societal demands. As designers increasingly seek to build, adapt, and manage urban environments effectively, it will be critical to resolve the contradictions and challenges associated with human needs, ecosystem dynamics, and interacting assemblages of species. Ecologists and designers are still discovering and experimenting with designing (for) urban food webs and fostering species interactions within them. We recommend generating prototypes of urban food webs through a learning-by-doing approach in urban development projects. Design and implementation of urban food webs also can lead to research opportunities involving monitoring and experiments that identify and solve challenges of food-web construction while supporting and encouraging ongoing management.
Habitat Quality Determines Dispersal Decisions and Fitness in a Beetle – Fungus Mutualism
Authors: Nuotclà Jon Andreja , Diehl Janina Marie Christin , Taborsky Michael
Published: April 2021

Delayed dispersal of sexually mature offspring is a fundamental component of cooperative breeding. In ambrosia beetles, female offspring temporarily remain in their natal nest and refrain from reproduction, instead investing in alloparental care. Previous work has demonstrated a link between helping behaviour and the increased need for pathogen defence, arising from their close association with fungal cultivars. In the ambrosia beetle Xyleborinus saxesenii, mature female offspring can effectively fight pathogen infections and manage the microbial composition within the nest by adjusting the frequency of different hygienic and nest maintenance behaviours. This suggests a potential to respond flexibly to the ecology of their nest, which calls for a better understanding of the connection between behaviour and the microbial community thriving within their nests. Here, we studied the significance of the mutualistic fungus garden composition for the beetles’ nest ecology and fitness by experimentally varying substrate quality. We found that the vertically transmitted ambrosia fungus garden is composed of at least two fungus mutualist species and a wide variety of other microbes varying in their relative abundance. This is strongly affected by the moisture content of the substrate, which in nature depends on the age and type of wood. We found that the mutualist fungi complement each other in terms of dryness-resistance, allowing the beetles to utilise a broad range of substrates over prolonged time during which the wood gradually desiccates. Under suboptimal humidity conditions, the interaction between host and multiple fungus species has important ramifications for the behaviour of philopatric helpers, including their alloparental investment, sibling cannibalism and the timing of dispersal. Rearing five generations of beetles consecutively in dry substrate resulted in transgenerational effects on philopatry and alloparental care, probably mediated through the dominance of a particular fungus species that was driven by the experimental habitat condition. Interestingly, the nests of these selection lines produced much more offspring after five generations than any first-generation nest, which may have reflected increased egg laying by non-dispersing daughters. Our study highlights the importance of considering the interactions between the microbial community and their insect hosts for understanding social evolution in cooperatively breeding beetles.
MSCs and Inflammatory Cells Crosstalk in Regenerative Medicine: Concerted Actions for Optimized Resolution Driven by Energy Metabolism
Authors: Planat-Benard Valerie , Varin Audrey , Casteilla Louis
Published: April 2021

Mesenchymal stromal cells (MSCs) are currently widely used in cell based therapy regarding to their remarkable efficacy in controlling the inflammatory status in patients. Despite recent progress and encouraging results, inconstant therapeutic benefits are reported suggesting that significant breakthroughs in the understanding of MSCs immunomodulatory mechanisms of action remains to be investigated and certainly apprehended from original point of view. This review will focus on the recent findings regarding MSCs close relationship with the innate immune compartment, i.e. granulocytes and myeloid cells. The review will also consider the intercellular mechanism of communication involved, such as factor secretion, cell-cell contact, extracellular vesicles, mitochondria transfer and efferocytosis. Immune-like-properties of MSCs supporting part of their therapeutic effect in the clinical setting will be discussed, as well as their potentials (immunomodulatory, anti-bacterial, anti-inflammatory, anti-oxidant defenses and metabolic adaptation…) and effects mediated, such as cell polarization, differentiation, death and survival on various immune and tissue cell targets determinant in triggering tissue regeneration. Their metabolic properties in term of sensing, reacting and producing metabolites influencing tissue inflammation will be highlighted. The review will finally open to discussion how ongoing scientific advances on MSCs could be efficiently translated to clinic in chronic and age-related inflammatory diseases and the current limits and gaps that remain to be overcome to achieving tissue regeneration and rejuvenation.
Identification of Silkworm Hemocyte Subsets and Analysis of Their Response to Baculovirus Infection Based on Single-Cell RNA Sequencing
Authors: Feng Min , Xia Junming , Fei Shigang , Peng Ruoxuan , Wang Xiong , Zhou Yaohong , Wang Pengwei , Swevers Luc , Sun Jingchen
Published: April 2021

A wide range of hemocyte types exist in insects but a full definition of the different subclasses is not yet established. The current knowledge of the classification of silkworm hemocytes mainly comes from morphology rather than specific markers, so our understanding of the detailed classification, hemocyte lineage and functions of silkworm hemocytes is very incomplete. Bombyx mori nucleopolyhedrovirus (BmNPV) is a representative member of the baculoviruses and a major pathogen that specifically infects silkworms (Bombyx mori) and causes serious losses in sericulture industry. Here, we performed single-cell RNA sequencing (scRNA-seq) of hemocytes in BmNPV and mock-infected larvae to comprehensively identify silkworm hemocyte subsets and determined specific molecular and cellular characteristics in each hemocyte subset before and after viral infectmadion. A total of 20 cell clusters and their potential marker genes were identified in silkworm hemocytes. All of the hemocyte clusters were infected by BmNPV at 3 days after inoculation. Interestingly, BmNPV infection can cause great changes in the distribution of hemocyte types. The cells appearing in the infection group mainly belong to prohemocytes (PR), while plasmatocytes (PL) and granulocytes (GR) are very much reduced. Furthermore, we found that BmNPV infection suppresses the RNA interference (RNAi) and immune response in the major hemocyte types. In summary, our results revealed the diversity of silkworm hemocytes and provided a rich resource of gene expression profiles for a systems-level understanding of their functions in the uninfected condition and as a response to BmNPV.
Using the Red Band Difference Algorithm to Detect and Monitor a Karenia spp. Bloom Off the South Coast of Ireland, June 2019
Authors: Jordan Catherine , Cusack Caroline , Tomlinson Michelle C. , Meredith Andrew , McGeady Ryan , Salas Rafael , Gregory Clynton , Croot Peter L.
Published: April 2021

During the months of May, June, July and August 2019 the Red Band Difference algorithm was tested over Irish waters to assess its suitability for the Irish harmful algal bloom alert system. Over the 4 weeks of June an extensive localised surface phytoplankton bloom formed in the Celtic Sea, south of Ireland. Satellite imagery from the Sentinel-3a’s Ocean and Land Colour Instrument, processed using the Red Band Difference algorithm detected the bloom in surface shelf waters and helped monitor its movement. Daily satellite images indicated that the bloom appeared at the sea surface on the 2nd June 2019 and peaked in size and surface abundance in offshore shelf waters within 4 weeks, remnants remained at the surface into July. A particle tracking approach was used to replicate oceanic circulation patterns in the vicinity of the observed algal bloom and estimate its trajectory. The initial horizontal distribution of particles in the tracking model were based on a satellite imagery polygon of the bloom when it first appeared in surface waters. Good agreement was observed between satellite imagery of the bloom and the particle tracking model. In situ sampling efforts from a research cruise and the national inshore phytoplankton monitoring programme confirmed that Karenia mikimotoi was the causative organism of the bloom. This pilot study shows great potential to use the Red Band Difference algorithm in the existing Irish harmful algal bloom alert system. In addition, satellite ocean colour data combined with particle tracking model estimates can be a useful tool to monitor high biomass harmful algal bloom forming species, such as Karenia mikimotoi, in surface coastal waters around Ireland and elsewhere.
Variable Species Responses to Experimental Stony Coral Tissue Loss Disease (SCTLD) Exposure
Authors: Meiling Sonora S. , Muller Erinn M. , Lasseigne Danielle , Rossin Ashley , Veglia Alex J. , MacKnight Nicholas , Dimos Bradford , Huntley Naomi , Correa Adrienne M. S. , Smith Tyler Burton , Holstein Daniel M. , Mydlarz Laura D. , Apprill Amy , Brandt Marilyn E.
Published: April 2021

Stony coral tissue loss disease (SCTLD) was initially documented in Florida in 2014 and outbreaks with similar characteristics have since appeared in disparate areas throughout the northern Caribbean, causing significant declines in coral communities. SCTLD is characterized by focal or multifocal lesions of denuded skeleton caused by rapid tissue loss and affects at least 22 reef-building species of Caribbean corals. A tissue-loss disease consistent with the case definition of SCTLD was first observed in the U.S. Virgin Islands (USVI) in January of 2019 off the south shore of St. Thomas at Flat Cay. The objective of the present study was to characterize species susceptibility to the disease present in St. Thomas in a controlled laboratory transmission experiment. Fragments of six species of corals (Colpophyllia natans, Montastraea cavernosa, Orbicella annularis, Porites astreoides, Pseudodiploria strigosa, and Siderastrea siderea) were simultaneously incubated with (but did not physically contact) SCTLD-affected colonies of Diploria labyrinthiformis and monitored for lesion appearance over an 8 day experimental period. Paired fragments from each corresponding coral genotype were equivalently exposed to apparently healthy colonies of D. labyrinthiformis to serve as controls; none of these fragments developed lesions throughout the experiment. When tissue-loss lesions appeared and progressed in a disease treatment, the affected coral fragment, and its corresponding control genet, were removed and preserved for future analysis. Based on measures including disease prevalence and incidence, relative risk of lesion development, and lesion progression rates, O. annularis, C. natans, and S. siderea showed the greatest susceptibility to SCTLD in the USVI. These species exhibited earlier average development of lesions, higher relative risk of lesion development, greater lesion prevalence, and faster lesion progression rates compared with the other species, some of which are considered to be more susceptible based on field observations (e.g., P. strigosa). The average transmission rate in the present study was comparable to tank studies in Florida, even though disease donor species differed. Our findings suggest that the tissue loss disease affecting reefs of the USVI has a similar epizootiology to that observed in other regions, particularly Florida.
Early Visual Saliency Based on Isolated Optimal Features
Authors: Castellotti Serena , Montagnini Anna , Del Viva Maria Michela
Published: April 2021

Under fast viewing conditions, the visual system extracts salient and simplified representations of complex visual scenes. Saccadic eye movements optimize such visual analysis through the dynamic sampling of the most informative and salient regions in the scene. However, a general definition of saliency, as well as its role for natural active vision, is still a matter for discussion. Following the general idea that visual saliency may be based on the amount of local information, a recent constrained maximum-entropy model of early vision, applied to natural images, extracts a set of local optimal information-carriers, as candidate salient features. These optimal features proved to be more informative than others in fast vision, when embedded in simplified sketches of natural images. In the present study, for the first time, these features were presented in isolation, to investigate whether they can be visually more salient than other non-optimal features, even in the absence of any meaningful global arrangement (contour, line, etc.). In four psychophysics experiments, fast discriminability of a compound of optimal features (target) in comparison with a similar compound of non-optimal features (distractor) was measured as a function of their number and contrast. Results showed that the saliency predictions from the constrained maximum-entropy model are well verified in the data, even when the optimal features are presented in smaller numbers or at lower contrast. In the eye movements experiment, the target and the distractor compounds were presented in the periphery at different angles. Participants were asked to perform a simple choice-saccade task. Results showed that saccades can select informative optimal features spatially interleaved with non-optimal features even at the shortest latencies. Saccades’ choice accuracy and landing position precision improved with SNR. In conclusion, the optimal features predicted by the reference model, turn out to be more salient than others, despite the lack of any clues coming from a global meaningful structure, suggesting that they get preferential treatment during fast image analysis. Also, peripheral fast visual processing of these informative local features is able to guide gaze orientation. We speculate that active vision is efficiently adapted to maximize information in natural visual scenes.
Tissue-Dependent Variation Profiles of Tea Quality-Related Metabolites in New Shoots of Tea Accessions
Authors: Yamashita Hiroto , Katai Hideyuki , Ohnishi Toshiyuki , Morita Akio , Panda Sanjib Kumar , Ikka Takashi
Published: April 2021

Several metabolites define tea quality in new tea shoots composed of leaf and stem. To improve tea quality for breeding, it is important to understand the tissue-dependent genetic mechanisms and metabolic network responsible for the profile of tea quality-related metabolites. We analyzed the volatiles and specialized metabolites as the tea quality-related metabolites in leaves and stems of new shoots in 30 tea accessions to understand the tissue variation and network between tea quality-related metabolites. Our results provided the tissue-dependent variation network in the tea quality-related metabolites, including volatiles in new leaves and stems in tea accessions. Each volatile content in tea accessions showed the coefficient of variation ranging from 58.7 to 221.9% and 54.2 to 318.3% in new leaves and new stems, respectively. The accumulation pattern of tea quality-related metabolites in new leaves and stems varied depending on the accession. When comparing tea genetic populations, the profile of tea quality-related metabolites of new leaves, but not new stems, was the key to distinguishing tea genetic populations by chemical indicators. We described the network between tea quality-related metabolites, especially the dense network in new leaves. These results also will provide the key information for metabolic engineering and the selection of breeding materials in tea plants based on the tea quality-related metabolites and aid in understanding their molecular mechanisms and network of metabolic variation.
Expression of Myoglobin in Normal and Cancer Brain Tissues: Correlation With Hypoxia Markers
Authors: Elsherbiny Marwa E. , Shaaban Mohammed , El-Tohamy Rana , Elkholi Islam E. , Hammam Olfat Ali , Magdy Mona , Allalunis-Turner Joan , Emara Marwan
Published: April 2021

Background

Myoglobin (MB) is increasingly recognized as a key player in cancer growth and metastasis. Low oxygen tensions, commonly associated with highly aggressive and recurrent cancers, have been shown to regulate its expression in several cancers such as lung, neck, prostate and breast cancer. However, it is not yet known whether it contributes to the growth and spread of brain cancers especially Glioblastoma multiforme (GBM).

Methods

Here we investigate the expression of MB, and its correlation with the hypoxia markers carbonic anhydrase IX (CAIX) and lactate dehydrogenase A (LDHA), in human tissue microarrays of multiple organ tumors, brain tumors, and GBM tumors, and their respective cancer-adjacent normal tissues. Correlation between MB protein expression and tumor grade was also assessed.

Results

We show that MB protein is expressed in a wide variety of cancers, benign tumors, cancer-adjacent normal tissues, hyperplastic tissue samples and normal brain tissue, and low oxygen tensions modulate MB protein expression in different brain cancers, including GBM. Enhanced nuclear LDHA immune-reactivity in GBM was also observed. Finally, we report for the first time a positive correlation between MB expression and brain tumor grade.

Conclusion

Our data suggest that hypoxia regulate MB expression in different brain cancers (including GBM) and that its expression is associated with a more aggressive phenotype as indicated by the positive correlation with the brain tumor grade. Additionally, a role for nuclear LDHA in promoting aggressive tumor phenotype is also suggested based on enhanced nuclear expression which was observed only in GBM.
Cognitive Effects and Depression Associated With Taxane-Based Chemotherapy in Breast Cancer Survivors: A Meta-Analysis
Authors: Ibrahim Eiman Y. , Domenicano Ilaria , Nyhan Kate , Elfil Mohamed , Mougalian Sarah S. , Cartmel Brenda , Ehrlich Barbara E.
Published: April 2021

Purpose: This meta-analysis provides a longitudinal assessment of depression and cognitive impairment induced by taxane-based chemotherapy in women with breast cancer after 6 months of treatment. We highlighted the incidence and prevalence, the cognitive pattern in neuropsychological studies, and the relationship between chemotherapy-induced cognitive impairment and different risk factors. We estimated the effect sizes on each cognitive domain and differentiated effect sizes by each method of comparison of effects (i.e., baseline data, or control groups).

Methods: The databases MEDLINE and Embase were searched for publications about taxane-related cognitive changes in patients with breast cancer published from 1980 to 2019. Cross-sectional and self-reported outcomes studies were excluded except for the depression item. Included studies were assessed for risk of bias with the Newcastle–Ottawa Scale. We estimated effect sizes for each cognitive domain and differentiated effect sizes by each method of comparison of effects. The review is reported in compliance with the PRISMA Statement; it was registered prospectively in PROSPERO as CRD42020163255.

Results: Eleven studies meeting the criteria were analyzed, which resulted in a sample of 1,057 patients with breast cancer who received chemotherapy including 820 patients (77%) who received taxane-based chemotherapy. Attention and concentration, depression, and executive function domains had significant chemotherapy-induced impairment across all comparison types. Statistically significant improvement was found in language and verbal memory when comparing chemotherapy patients' test scores with baseline or matched controls. Taxane-based chemotherapy had a non-significant effect on processing speed, visual memory, visuospatial, and motor function domains.

Conclusions: The occurrence of chemotherapy-induced cognitive impairment 6 months or more after the course of treatment in people with breast cancer is frequent in the domains of attention, executive function, and depression. Other domains appear stable or improve with time after treatment cessation.
Chaperonin-Containing TCP1 Complex (CCT) Promotes Breast Cancer Growth Through Correlations With Key Cell Cycle Regulators
Authors: Ghozlan Heba , Showalter Adrian , Lee Eunkyung , Zhu Xiang , Khaled Annette R.
Published: April 2021

Uncontrolled proliferation as a result of dysregulated cell cycling is one of the hallmarks of cancer. Therapeutically targeting pathways that control the cell cycle would improve patient outcomes. However, the development of drug resistance and a limited number of inhibitors that target multiple cell cycle modulators are challenges that impede stopping the deregulated growth that leads to malignancy. To advance the discovery of new druggable targets for cell cycle inhibition, we investigated the role of Chaperonin-Containing TCP1 (CCT or TRiC) in breast cancer cells. CCT, a type II chaperonin, is a multi-subunit protein-folding complex that interacts with many oncoproteins and mutant tumor suppressors. CCT subunits are highly expressed in a number of cancers, including breast cancer. We found that expression of one of the CCT subunits, CCT2, inversely correlates with breast cancer patient survival and is subject to copy number alterations through genomic amplification. To investigate a role for CCT2 in the regulation of the cell cycle, we expressed an exogenous CCT2-FLAG construct in T47D and MCF7 luminal A breast cancer cells and examined cell proliferation under conditions of two-dimensional (2D) monolayer and three-dimensional (3D) spheroid cultures. Exogenous CCT2 increased the proliferation of cancer cells, resulting in larger and multiple spheroids as compared to control cells. CCT2-expressing cells were also able to undergo spheroid growth reversal, re-attaching, and resuming growth in 2D cultures. Such cells gained anchorage-independent growth. CCT2 expression in cells correlated with increased expression of MYC, especially in spheroid cultures, and other cell cycle regulators like CCND1 and CDK2, indicative of a novel activity that could contribute to the increase in cell growth. Statistically significant correlations between CCT2, MYC, and CCND1 were shown. Since CCT2 is located on chromosome 12q15, an amplicon frequently found in soft tissue cancers as well as breast cancer, CCT2 may have the basic characteristics of an oncogene. Our findings suggest that CCT2 could be an essential driver of cell division that may be a node through which pathways involving MYC, cyclin D1 and other proliferative factors could converge. Hence the therapeutic inhibition of CCT2 may have the potential to achieve multi-target inhibition, overcoming the limitations associated with single agent inhibitors.
Suitability of Placental Blood Samples of Newborns for Pre-Transfusion Testing
Authors: Alissa Rana , Williams Patty D. , Baker Erika L. , Hipp Jennifer A. , Saremian Jinous , Aysola Agnes E.
Published: April 2021

Objective: To show concordance between heel stick and placental blood sample pairs for newborns' pre-transfusion testing and to validate placental blood's tube and gel methodology.

Methods: Placental samples were collected for pre-transfusion testing at birth from 78 singleton and twin newborns admitted to our Mother–Baby Unit to compare with the results of heel stick samples taken from same newborns. Gestational age ≥35 weeks, weight ≥2,000 g. The study was approved by the Institutional Review Board (IRB). Informed consent was obtained from newborn parents. ABO blood group, Rhesus factor (Rh), direct antiglobulin test (DAT), and antibody screen were performed. Ortho ProVue Analyzer was used for tube and gel methods. McNemar's test for paired categorical data was performed.

Results: One hundred percent concordance in 78 pairs for ABO and Rh. Seventy-four pairs were tested for antibodies, 72 were both negative, 1 was both positive, and 1 gave discordant result. Ninety-nine percent concordance, p = 0.999. Sixty-five pairs were both DAT negative, seven were both DAT positive, and six gave discordant results. Ninety-two percent concordance, p = 0.68. Placental blood gave identical results comparing tube with gel methods.

Conclusions: Placental blood is suitable for pre-transfusion testing and can replace heel sticks. Placental blood tube and gel methods are validated.
Xuebijing Protects Against Septic Acute Liver Injury Based on Regulation of GSK-3β Pathway
Authors: Cao Liping , Li Zhenghong , Ren Yi , Wang Mengmeng , Yang Zhizhou , Zhang Wei , Han Xiaoqin , Yao Mengya , Sun Zhaorui , Nie Shinan
Published: April 2021

Xuebijing (XBJ), the only drug approved for the sepsis and multiple organ dysfunction, and its protective effects against acute liver injury (ALI) and its mechanism. The aim of this study was to evaluate the protective effect of XBJ on cecal ligation and perforation (CLP)-induced mouse ALI model and LPS-induced RAW264.7 cell ALI model. Mice were pretreated with XBJ before the CLP model was established, and serum and liver tissues were collected at the end of the experiment to assess the levels of inflammatory factors and liver injury. Results showed that XBJ pretreatment reduced liver/body weight, aspartate aminotransferase (AST) and alanine aminotransferase (ALT) activities in serum, and inhibited levels of pro-inflammatory factors in serum. Cells were treatment with XBJ and modeled by LPS modeling increased cell viability in the XBJ-treated group compared to the model group and XBJ also decreased serum pro-inflammatory factors in a dose-dependent manner. Western blot detected that XBJ also up-regulated the phosphorylated levels of glycogen synthase kinase-3β (p-GSK-3β) and cAMP-response element-binding protein (p-CREB) and down-regulated the phosphorylated level of nuclear factor kappa-B (p-NF-κB) in liver and cell. After overexpression of GSK-3β in cells, the mechanism was further investigated using CO-IP analysis. The binding of p-NF-κB and p-CREB to CREB-binding protein (CBP) was increased and decreased, respectively, indicating that GSK-3β regulated inflammation by regulating the binding of p-NF-κB and p-CREB to CBP. The present studies suggested that the hepatoprotective effect of XBJ may be through up-regulation of GSK-3β (Ser9) and increasing the binding of p-CREB to CBP, thereby alleviating the inflammatory response.
Reconfigurable THz Metamaterial Filter Based on Binary Response for Information Processing System
Authors: Ahamed Eistiak , Tamim Ahmed Mahfuz , Faruque Mohammad Rashed Iqbal , Sifat Rasheduzzaman , Islam Mohammad Tariqul
Published: April 2021

Light-matter interactions between the metallic and dielectric layers along with the controlling of electromagnetic waves can create a way to develop micro-devices and moderate the functionalities for advanced applications. This study describes a new controlling technique of the plasmatic electron packet based on an electric split-ring resonator (eSRR). All numerical experiments were performed using an advanced CST electromagnetic package. The proposed metamaterial tunneled structure in this study operates using terahertz (THz) frequency spectrum as an efficient digital processing filter. The array combination of the tunneled structure consisted of three individual unit cells. Moreover, the two engineered metallic arms added to the tunneled structure exhibited two peak resonances and one passband frequency region. A large evanescent field was produced to enhance the wave-metal interactions with the presence of a metal-dielectric micro-tunnel. The intensity of the electromagnetic wave-metal interactions was encoded to binary 0 and 1 for information encoding purposes. As a result, the reconfigurable micro-unit cell metamaterial tunneled structure was able to effectively control the electric field and allow electron packets to be digitally encoded for the information processing system.
Overexpression of the HDA15 Gene Confers Resistance to Salt Stress by the Induction of NCED3, an ABA Biosynthesis Enzyme
Authors: Truong Hai An , Lee Seokjin , Trịnh Cao Son , Lee Won Je , Chung Eui-Hwan , Hong Suk-Whan , Lee Hojoung
Published: April 2021

Salt stress constitutes a major form of abiotic stress in plants. Histone modification plays an important role in stress tolerance, with particular reference to salt stress resistance. In the current study, we found that HDA15 overexpression confers salt stress resistance to young seedling stages of transgenic plants. Furthermore, salt stress induces HDA15 overexpression. Transcription levels of stress-responsive genes were increased in transgenic plants overexpressing HDA15 (HDA15 OE). NCED3, an abscisic acid (ABA) biosynthetic gene, which is highly upregulated in HDA15 transgenic plants, enhanced the accumulation of ABA, which promotes adaptation to salt stress. ABA homeostasis in HDA15 OE plants is maintained by the induction of CYP707As, which optimize endogenous ABA levels. Lastly, we found that the double-mutant HDA15 OE/hy5 ko plants are sensitive to salt stress, indicating that interaction between HDA15 and ELONGATED HYPOCOTYL 5 (HY5) is crucial to salt stress tolerance shown by HDA15 OE plants. Thus, our findings indicate that HDA15 is crucial to salt stress tolerance in Arabidopsis.
Production of Betacyanins in Transgenic Nicotiana tabacum Increases Tolerance to Salinity
Authors: Zhou Yanfei , Karl Tanja , Lewis David H. , McGhie Tony K. , Arathoon Steve , Davies Kevin M. , Ryan Ken G. , Gould Kevin S. , Schwinn Kathy E.
Published: April 2021

Although red betalain pigments (betacyanins) have been associated with salinity tolerance in some halophytes like Disphyma australe, efforts to determine whether they have a causal role and the underlying mechanisms have been hampered by a lack of a model system. To address this, we engineered betalain-producing Nicotiana tabacum, by the introduction of three betalain biosynthetic genes. The plants were violet-red due to the accumulation of three betacyanins: betanin, isobetanin, and betanidin. Under salt stress, betacyanic seedlings had increased survivability and leaves of mature plants had higher photochemical quantum yields of photosystem II (Fv/Fm) and faster photosynthetic recovery after saturating light treatment. Under salt stress, compared to controls betacyanic leaf disks had no loss of carotenoids, a slower rate of chlorophyll degradation, and higher Fv/Fm values. Furthermore, simulation of betacyanin pigmentation by using a red filter cover improved Fv/Fm value of green tissue under salt stress. Our results confirm a direct causal role of betacyanins in plant salinity tolerance and indicate a key mechanism is photoprotection. A role in delaying leaf senescence was also indicated, and the enhanced antioxidant capability of the betacyanic leaves suggested a potential contribution to scavenging reactive oxygen species. The study can inform the development of novel biotechnological approaches to improving agricultural productivity in saline-affected areas.
Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Tara Oceans
Authors: Pierella Karlusich Juan José , Bowler Chris , Biswas Haimanti
Published: April 2021

Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO2 to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO2, which is vital information toward modeling their response to future CO2 levels. The Tara Oceans expeditions generated molecular data coupled with in situ biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO2 variability. The current study investigates the interlink between the environmental variability of CO2 and other physicochemical parameters with the gene and transcript copy numbers of five key enzymes of diatom CO2 concentration mechanisms (CCMs): Rubisco activase and carbonic anhydrase (CA) as part of the physical pathway, together with phosphoenolpyruvate carboxylase, phosphoenolpyruvate carboxykinase, and malic enzyme as part of the potential C4 biochemical pathway. Toward this aim, we mined >200 metagenomes and >220 metatranscriptomes generated from samples of the surface layer of 66 globally distributed sampling sites and corresponding to the four main size fractions in which diatoms can be found: 0.8–5 μm, 5–20 μm, 20–180 μm, and 180–2,000 μm. Our analyses revealed that the transcripts for the enzymes of the putative C4 biochemical CCM did not in general display co-occurring profiles. The transcripts for CAs were the most abundant, with an order of magnitude higher values than the other enzymes, thus implying the importance of physical CCMs in diatom natural communities. Among the different classes of this enzyme, the most prevalent was the recently characterized iota class. Consequently, very little information is available from natural diatom assemblages about the distribution of this class. Biogeographic distributions for all the enzymes show different abundance hotspots according to the size fraction, pointing to the influence of cell size and aggregation in CCMs. Environmental correlations showed a complex pattern of responses to CO2 levels, total phytoplankton biomass, temperature, and nutrient concentrations. In conclusion, we propose that biophysical CCMs are prevalent in natural diatom communities.
Cultivating the Interpersonal Domain: Compassion in the Supervisor-Doctoral Student Relationship
Authors: Lundgren Oskar , Osika Walter
Published: April 2021

The long-term and complex supervisor-doctoral student relationship is often characterised by tension and frictions. In higher education research, models, and interventions that take the potential beneficial interpersonal effects of compassion into account seem to be scarce. Hence, the aim of this study was to conceptualise the potential role compassion could have in the cultivation of an affiliative and sustainable supervisor-doctoral student relationship. The concept of compassion was investigated and analysed in relation to a contemporary model of supervisor behaviours. Furthermore, a systematic literature search in the scientific databases PubMed, PsychInfo, ScienceDirect, and Google Scholar was performed. The conceptual analysis revealed that the interpersonal domain, in which compassion could afford a shared sense of warmth, is neglected in previous definitions. Furthermore, the integration of compassion into a model of adaptive supervisor behaviour indicates a strong case for a salutary role for compassion in the supervisor-doctoral student relationship. However, the literature review showed that empirical data are lacking, and more studies are needed. The role of compassion deserves to be investigated empirically in this particular interpersonal context.
Boundary Loss-Based 2.5D Fully Convolutional Neural Networks Approach for Segmentation: A Case Study of the Liver and Tumor on Computed Tomography
Authors: Han Yuexing , Li Xiaolong , Wang Bing , Wang Lu
Published: April 2021

Image segmentation plays an important role in the field of image processing, helping to understand images and recognize objects. However, most existing methods are often unable to effectively explore the spatial information in 3D image segmentation, and they neglect the information from the contours and boundaries of the observed objects. In addition, shape boundaries can help to locate the positions of the observed objects, but most of the existing loss functions neglect the information from the boundaries. To overcome these shortcomings, this paper presents a new cascaded 2.5D fully convolutional networks (FCNs) learning framework to segment 3D medical images. A new boundary loss that incorporates distance, area, and boundary information is also proposed for the cascaded FCNs to learning more boundary and contour features from the 3D medical images. Moreover, an effective post-processing method is developed to further improve the segmentation accuracy. We verified the proposed method on LITS and 3DIRCADb datasets that include the liver and tumors. The experimental results show that the performance of the proposed method is better than existing methods with a Dice Per Case score of 74.5% for tumor segmentation, indicating the effectiveness of the proposed method.
The Effects of Plant Growth-Promoting Bacteria with Biostimulant Features on the Growth of a Local Onion Cultivar and a Commercial Zucchini Variety
Authors: Novello Giorgia , Cesaro Patrizia , Bona Elisa , Massa Nadia , Gosetti Fabio , Scarafoni Alessio , Todeschini Valeria , Berta Graziella , Lingua Guido , Gamalero Elisa
Published: April 2021

The reduction of chemical inputs due to fertilizer and pesticide applications is a target shared both by farmers and consumers in order to minimize the side effects for human and environmental health. Among the possible strategies, the use of biostimulants has become increasingly important as demonstrated by the fast growth of their global market and by the increased rate of registration of new products. In this work, we assessed the effects of five bacterial strains (Pseudomonas fluorescens Pf4, P. putida S1Pf1, P. protegens Pf7, P. migulae 8R6, and Pseudomonas sp. 5Vm1K), which were chosen according to their previously reported plant growth promotion traits and their positive effects on fruit/seed nutrient contents, on a local onion cultivar and on zucchini. The possible variations induced by the inoculation with the bacterial strains on the onion nutritional components were also evaluated. Inoculation resulted in significant growth stimulation and improvement of the mineral concentration of the onion bulb, induced particularly by 5Vm1K and S1Pf1, and in different effects on the flowering of the zucchini plants according to the bacterial strain. The present study provides new information regarding the activity of the five plant growth-promoting bacteria (PGPB) strains on onion and zucchini, two plant species rarely considered by the scientific literature despite their economic relevance.
Central Acting Hsp10 Regulates Mitochondrial Function, Fatty Acid Metabolism, and Insulin Sensitivity in the Hypothalamus
Authors: Wardelmann Kristina , Rath Michaela , Castro José Pedro , Blümel Sabine , Schell Mareike , Hauffe Robert , Schumacher Fabian , Flore Tanina , Ritter Katrin , Wernitz Andreas , Hosoi Toru , Ozawa Koichiro , Kleuser Burkhard , Weiß Jürgen , Schürmann Annette , Kleinridders André
Published: April 2021

Mitochondria are critical for hypothalamic function and regulators of metabolism. Hypothalamic mitochondrial dysfunction with decreased mitochondrial chaperone expression is present in type 2 diabetes (T2D). Recently, we demonstrated that a dysregulated mitochondrial stress response (MSR) with reduced chaperone expression in the hypothalamus is an early event in obesity development due to insufficient insulin signaling. Although insulin activates this response and improves metabolism, the metabolic impact of one of its members, the mitochondrial chaperone heat shock protein 10 (Hsp10), is unknown. Thus, we hypothesized that a reduction of Hsp10 in hypothalamic neurons will impair mitochondrial function and impact brain insulin action. Therefore, we investigated the role of chaperone Hsp10 by introducing a lentiviral-mediated Hsp10 knockdown (KD) in the hypothalamic cell line CLU-183 and in the arcuate nucleus (ARC) of C57BL/6N male mice. We analyzed mitochondrial function and insulin signaling utilizing qPCR, Western blot, XF96 Analyzer, immunohistochemistry, and microscopy techniques. We show that Hsp10 expression is reduced in T2D mice brains and regulated by leptin in vitro. Hsp10 KD in hypothalamic cells induced mitochondrial dysfunction with altered fatty acid metabolism and increased mitochondria-specific oxidative stress resulting in neuronal insulin resistance. Consequently, the reduction of Hsp10 in the ARC of C57BL/6N mice caused hypothalamic insulin resistance with acute liver insulin resistance.
Feasibility Assessment of an Encapsulated Longevity Spinach (Gynura procumbens L.) Extract Plant in Indonesia
Authors: Tristantini Dewi , Setiawan Heri , Santoso Leon Lukhas
Published: April 2021

The rise of globalization in recent years has favored the adoption of unhealthy lifestyles for many people, increasing their likelihood of diseases with silent symptoms. Longevity spinach (Gynura procumbens L.) is a medicinal plant that has strong phenolic compounds which could act as natural antioxidants to reduce the chance of contracting severe silent diseases. This study was focused on the feasibility of an affordable herbal supplement manufacturing plant using longevity spinach with a water solvent. Production simulation was carried out using SuperPro Designer v.9.0, and an estimated annual production of 26,082 bottles was analyzed based on several economic parameters. The production process for herbal supplements from longevity spinach extract consisted of leaf-washing, drying, and grinding, as well as active compound extraction from leaves with water, filtration, evaporation, freeze-drying, and encapsulation. For 30 encapsulated herbal supplements, prices started from USD 22.8/bottle, and the designed production plant was economically feasible (PBP = ±17 months, IRR = 91.65%, and NPV = USD 3,972,653.13). It can be concluded that encapsulated longevity spinach water extract could become an affordable herbal supplement, with feasible manufacturing for further investment activity.
The Use of the ROS Scavenger Cysteine as a Surface Ligand of Metal Nanoclusters and Its Bactericidal Elimination Effect
Authors: Krisnawati Dyah Ika , Hsu Po-Hsuan , Lin Yu-Hsiang , Alimansur Moh , Atmojo Didik Susetiyanto , Rahmawati Elfi Quyumi , Rahayu Dwi , Khafid Muhamad , Lu Ssu-Chiao , Kuo Tsung-Rong
Published: April 2021

The bactericidal effects of fluorescent metal nanoclusters have impeded their bacterial bioimaging applications due to the reactive oxygen species (ROS) generation that is induced by the nanoclusters in bacteria to cause bacterial death. Herein, an ROS scavenger of cysteine was exploited as a surface ligand to prepare cysteine-conjugated gold nanoclusters (Cys–AuNCs) and cysteine-conjugated silver nanoclusters (Cys–AgNCs) using a facile hydrothermal approach. The structural and optical characterizations demonstrated successful syntheses of Cys–AuNCs and Cys–AgNCs. With the same weight concentration, the bactericidal effect increased in the order of Cys–AuNCs, Cys–AgNCs, and silver nanoparticles (AgNPs), according to the results of the bacterial growth curves. Furthermore, based on the results of the standard colony-counting method, the Cys–AuNCs revealed the best biocompatibility compared to those of the Cys–AgNCs and AgNPs in Escherichia coli (E. coli). The superior biocompatibility of the Cys–AuNCs can be attributed to the use of the ligand of cysteine as an ROS scavenger to reduce ROS in E. coli. Electron paramagnetic resonance (EPR) analyses indicated that the use of the ROS scavenger cysteine as the surface ligand of the Cys–AuNCs eliminated the ROS production induced by the Cys–AuNCs in E. coli. The biocompatible Cys–AuNCs were also confirmed as a fluorescent probe using confocal microscopy. Highly biocompatible Cys–AuNCs could be a potential fluorescent probe in the application of bacterial bioimaging.