bluuebunny/crossref_metadata_2025 huggingface dataset:
Perspectives on Mechanisms Supporting Neuronal Polarity From Small Animals to Humans
Authors: Wilson Carlos , Moyano Ana Lis , Cáceres Alfredo
Published: April 2022

Axon-dendrite formation is a crucial milestone in the life history of neurons. During this process, historically referred as “the establishment of polarity,” newborn neurons undergo biochemical, morphological and functional transformations to generate the axonal and dendritic domains, which are the basis of neuronal wiring and connectivity. Since the implementation of primary cultures of rat hippocampal neurons by Gary Banker and Max Cowan in 1977, the community of neurobiologists has made significant achievements in decoding signals that trigger axo-dendritic specification. External and internal cues able to switch on/off signaling pathways controlling gene expression, protein stability, the assembly of the polarity complex (i.e., PAR3-PAR6-aPKC), cytoskeleton remodeling and vesicle trafficking contribute to shape the morphology of neurons. Currently, the culture of hippocampal neurons coexists with alternative model systems to study neuronal polarization in several species, from single-cell to whole-organisms. For instance, in vivo approaches using C. elegans and D. melanogaster, as well as in situ imaging in rodents, have refined our knowledge by incorporating new variables in the polarity equation, such as the influence of the tissue, glia-neuron interactions and three-dimensional development. Nowadays, we have the unique opportunity of studying neurons differentiated from human induced pluripotent stem cells (hiPSCs), and test hypotheses previously originated in small animals and propose new ones perhaps specific for humans. Thus, this article will attempt to review critical mechanisms controlling polarization compiled over decades, highlighting points to be considered in new experimental systems, such as hiPSC neurons and human brain organoids.
The Dopamine Assisted Synthesis of MoO3/Carbon Electrodes With Enhanced Capacitance in Aqueous Electrolyte
Authors: Norouzi Nazgol , Omo-Lamai Darrell , Alimohammadi Farbod , Averianov Timofey , Kuang Jason , Yan Shan , Wang Lei , Stavitski Eli , Leshchev Denis , Takeuchi Kenneth J. , Takeuchi Esther S. , Marschilok Amy C. , Bock David C. , Pomerantseva Ekaterina
Published: April 2022

A capacitance increase phenomenon is observed for MoO3electrodes synthesizedviaa sol-gel process in the presence of dopamine hydrochloride (Dopa HCl) as compared to α-MoO3electrodes in 5M ZnCl2aqueous electrolyte. The synthesis approach is based on a hydrogen peroxide-initiated sol-gel reaction to which the Dopa HCl is added. The powder precursor (Dopa)xMoOy, is isolated from the metastable gel using freeze-drying. Hydrothermal treatment (HT) of the precursor results in the formation of MoO3accompanied by carbonization of the organic molecules; designated as HT-MoO3/C. HT of the precipitate formed in the absence of dopamine in the reaction produced α-MoO3, which was used as a reference material in this study (α-MoO3-ref). Scanning electron microscopy (SEM) images show a nanobelt morphology for both HT-MoO3/C and α-MoO3-ref powders, but with distinct differences in the shape of the nanobelts. The presence of carbonaceous content in the structure of HT-MoO3/C is confirmed by FTIR and Raman spectroscopy measurements. X-ray diffraction (XRD) and Rietveld refinement analysis demonstrate the presence of α-MoO3and h-MoO3phases in the structure of HT-MoO3/C. The increased specific capacitance delivered by the HT-MoO3/C electrode as compared to the α-MoO3-ref electrode in 5M ZnCl2electrolyte in a −0.25–0.70 V vs. Ag/AgCl potential window triggered a more detailed study in an expanded potential window. In the 5M ZnCl2electrolyte at a scan rate of 2 mV s−1, the HT-MoO3/C electrode shows a second cycle capacitance of 347.6 F g−1. The higher electrochemical performance of the HT-MoO3/C electrode can be attributed to the presence of carbon in its structure, which can facilitate electron transport. Our study provides a new route for further development of metal oxides for energy storage applications.
Microbiota Associated With Cholesteatoma Tissue in Chronic Suppurative Otitis Media
Authors: Frank Daniel N. , Magno Jose Pedrito M. , Velasco Karen Joyce S. , Bootpetch Tori C. , Salud Jacob Ephraim D. , David Kevin Jer V. , Miller Aaron L. , Yee Eljohn C. , Dulnuan Heather P. , Pyles Richard B. , Lacuata Jan Alexeis C. , Arbizo Jeric L. , Kofonow Jennifer M. , Guce Beatrice , Mendoza Kevin Michael D. , Robertson Charles E. , Ilustre Gabriel Martin S. , Chiong Alessandra Nadine E. , Lu Shi-Long , Tongol Erik A. , Sacayan Nicole D. , Yarza Talitha Karisse L. , Chiong Charlotte M. , Santos-Cortez Regie Lyn P.
Published: April 2022

Otitis media (OM), defined as infection or inflammation of the middle ear (ME), remains a major public health problem worldwide. Cholesteatoma is a non-cancerous, cyst-like lesion in the ME that may be acquired due to chronic OM and cause disabling complications. Surgery is required for treatment, with high rates of recurrence. Current antibiotic treatments have been largely targeted to previous culturable bacteria, which may lead to antibiotic resistance or treatment failures. For this study, our goal was to determine the microbiota of cholesteatoma tissue in comparison with other ME tissues in patients with long-standing chronic OM. ME samples including cholesteatoma, granulation tissue, ME mucosa and discharge were collected from patients undergoing tympanomastoidectomy surgery for chronic OM. Bacteria were profiled by 16S rRNA gene sequencing in 103 ME samples from 53 patients. Respiratory viruses were also screened in 115 specimens from 45 patients. Differences in bacterial profiles (beta-diversity) and the relative abundances of individual taxa were observed between cholesteatoma and ME sample-types. Additionally, patient age was associated with differences in overall microbiota composition while numerous individual taxa were differentially abundant across age quartiles. No viruses were identified in screened ME samples. Biodiversity was moderately lower in cholesteatoma and ME discharge compared to ME mucosal tissues. We also present overall bacterial profiles of ME tissues by sample-type, age, cholesteatoma diagnosis and quinolone use, including prevalent bacterial taxa. Our findings will be useful for fine-tuning treatment protocols for cholesteatoma and chronic OM in settings with limited health care resources.
The Fungal Gut Microbiome Exhibits Reduced Diversity and Increased Relative Abundance of Ascomycota in Severe COVID-19 Illness and Distinct Interconnected Communities in SARS-CoV-2 Positive Patients
Authors: Reinold Johanna , Farahpour Farnoush , Schoerding Ann-Kathrin , Fehring Christian , Dolff Sebastian , Konik Margarethe , Korth Johannes , van Baal Lukas , Buer Jan , Witzke Oliver , Westendorf Astrid M. , Kehrmann Jan
Published: April 2022

Clinical and experimental studies indicate that the bacterial and fungal gut microbiota modulates immune responses in distant organs including the lungs. Immune dysregulation is associated with severe SARS-CoV-2 infection, and several groups have observed gut bacterial dysbiosis in SARS-CoV-2 infected patients, while the fungal gut microbiota remains poorly defined in these patients. We analyzed the fungal gut microbiome from rectal swabs taken prior to anti-infective treatment in 30 SARS-CoV-2 positive (21 non-severe COVID-19 and 9 developing severe/critical COVID-19 patients) and 23 SARS-CoV-2 negative patients by ITS2-sequencing. Pronounced but distinct interconnected fungal communities distinguished SARS-CoV-2 positive and negative patients. Fungal gut microbiota in severe/critical COVID-19 illness was characterized by a reduced diversity, richness and evenness and by an increase of the relative abundance of the Ascomycota phylum compared with non-severe COVID-19 illness. A dominance of a single fungal species with a relative abundance of >75% was a frequent feature in severe/critical COVID-19. The dominating fungal species were highly variable between patients even within the groups. Several fungal taxa were depleted in patients with severe/critical COVID-19.The distinct compositional changes of the fungal gut microbiome in SARS-CoV-2 infection, especially in severe COVID-19 illness, illuminate the necessity of a broader approach to investigate whether the differences in the fungal gut microbiome are consequences of SARS-CoV-2 infection or a predisposing factor for critical illness.
Lactate Dehydrogenase as a Potential Therapeutic Drug Target to Control Babesia bigemina
Authors: He Lan , Bastos Reginaldo G. , Yu Long , Laughery Jacob M. , Suarez Carlos E.
Published: April 2022

Babesia bigemina is a tick-borne apicomplexan hemoprotozoan responsible for bovine babesiosis. The current drugs used for bovine babesiosis treatment have several drawbacks, including toxicity, the lack of effectiveness to clear the parasite, and potential to develop resistance. Identifying compounds that target essential and unique parasite metabolic pathways is a rational approach toward finding alternative drug treatments. Based on the genome sequence and transcriptomics analysis, it can be inferred that anaerobic glycolysis is the dominant adenosine triphosphate (ATP) supply for Babesia, and lactate dehydrogenase (LDH) is one of the essential enzymes in this pathway. Furthermore, the Babesia LDH sequence is distinct from its bovine homologue and thus a potential chemotherapeutic target that would result in decreasing the ATP supply to the parasite but not to the host. Gossypol is a known efficient specific inhibitor of LDH in the sensu stricto B. bovis and the sensu lato B. microti, among other related parasites, but no such data are currently available in the sensu stricto B. bigemina parasites. Hereby, we show that the LDH amino acid sequence is highly conserved among sensu stricto but not in sensu lato Babesia spp. A predictive structural analysis of B. bigemina LDH showed the conservation of the key amino acids involved in the binding to gossypol compared to B. bovis. Gossypol has a significant (P < 0.0001) inhibitory effect on the in vitro growth of B. bigemina, with IC50 of 43.97 mM after 72 h of treatment. The maximum IC (IC98) was observed at 60 mM gossypol. However, a significant effect on the viability of cattle PBMC was observed when the cells were cultured with 60 mM (IC98) gossypol compared with DMSO-exposed control cells. Interestingly, B. bigemina cultured at 3% oxygen expresses significantly higher levels of LDH and is more resistant to gossypol than the parasites maintained at ambient conditions containing ~20% oxygen. Altogether, the results suggest the potential of gossypol as an effective drug against B. bigemina infection, but the risk of host toxicity at therapeutic doses should be further evaluated in in vivo studies.
Museum Exhibitions of Fossil Specimens Into Commercial Products: Unexpected Outflow of 3D Models due to Unwritten Image Policies
Authors: Matsui Kumiko , Kimura Yuri
Published: April 2022

Recent innovations and cost reductions in photogrammetry-based 3D modeling have enabled museum visitors to create 3D models based on photographs exhibited in galleries without breaking museum policies. While several museums make 3D museum data available on sharing platforms, museum visitors publish unofficial 3D data belonging to museum exhibits using a photogrammetry-based approach. This study shows that photogrammetry-based 3D models can be generated without breaking conventional photo policies (i.e., no use of flash and tripods) and that museum visitors can create commercial products based on these models. 3D models certainly enhance scientific value and promote broader and deeper interests in the natural sciences; however, the rights of owners of museum pieces are ambiguous with regard to the dissemination of unofficial data. This also makes information attributable to the original specimen unclear, which can potentially lead to revenue loss. We propose a set of best practices for museum photo policies covering the data use of visitor-generated 3D models of displayed objects.
Study on Self-Excited Oscillation Suppression of Supersonic Inlet Based on Parallel Cavity
Authors: Cai FeiChao , Huang Xing
Published: April 2022

Aiming at the problem of self-excited oscillation in a supersonic inlet, the oscillation suppression of parallel cavities in a shock system is studied. Based on the shock dynamic model, the theoretical calculation model of parallel cavity under dynamic shock is established, and the effects of cavity volume and oscillation frequency on shock oscillation flow field parameters are analyzed. On this basis, an integrated numerical model including cavity and inlet and outflow fields is established, and the effects of cavity on the inlet flow field parameter distribution and parameter oscillation are compared by using unsteady numerical calculation algorithm. The theoretical calculation results show that the parallel cavity can reduce the amplitude of flow field pressure oscillation, and increasing the cavity volume is beneficial to suppress parameter oscillation. The unsteady numerical calculation of three groups of working conditions shows that the cavity changes the amplitude of parameter oscillation, and the high amplitude frequency point also decreases compared to the model without cavity. Through the alternating change of pressure between the channel and cavity during the movement of the shock wave, the cavity gas filling and overflow dampen the shock wave forward and pressure change of the mainstream, so as to suppress the self-excited oscillation.
Price Volatility of Hogs and Tracing of the Event in China: Based on CEEMDAN Method
Authors: Lv Xi , Tu Guoping , Li Heng
Published: April 2022

Since May 2018, the price of this hog cycle has increased by 196%, and the absolute price and its volatility are far beyond history. The violent fluctuation of hog prices seriously affects the sustainable development of the hog industry. This work uses the monthly data of hog prices from January 2010 to July 2021 to carry out an empirical analysis to examine the characteristics of the fluctuations and its influencing factors and employs CEEMADN to perform multi-scale feature decomposition on the price of hogs in China. Then, this study adopts the fine-to-coarse recombination algorithm to reconstruct components. Finally, the Bai–Perron structural breakpoint test is performed on the reconstructed components to find the basis for important events that affect the price fluctuation of hogs. Results show that the low-frequency components representing important regulatory policies and the trend components representing long-term development trends play a major role in the price trend of hogs. There are four structural breakpoints in the low-frequency components, indicating that the country’s regulatory policies for African swine fever, land and environmental problems, and tight supply and demand can effectively increase the hog production capacity and stabilize the hog market.
Effect on Soil Properties and Crop Yields to Long-Term Application of Superabsorbent Polymer and Manure
Authors: Yang Yonghui , Wu Jicheng , Du Yan-Lei , Gao Cuimin , Tang Darrell W. S. , van der Ploeg Martine
Published: April 2022

Intensive farming leads to soil degradation, and poses a serious threat to agricultural yield sustainability and soil ecology. Superabsorbent polymer (SAP) and organic manure (OM) are amendments that can remediate the soil, and improve soil structure and soil pore characteristics, thereby enhancing soil quality and promoting crop growth. These benefits may be enhanced through long-term continuous application of the amendments. X-ray computed tomography (CT) was used to determine the number, connectivity, and locations of pores (160–1,000 μm, >1,000 µm) in the soil at depths of 0–100 cm. Soil organic carbon content, proportion of water-stable macroaggregates (>0.25 mm) (WSM), soil bulk density, field water capacity, available water content, wilting point content, and saturated hydraulic conductivity were also determined. Compared to the control, long-term SAP and OM treatments significantly increased the number of 160–1,000 µm and >1,000 µm soil pores (5–20 cm depths), >1,000 µm and >160 µm soil porosity (at 0–20 cm depths), total organic carbon (10–20 cm and 40–50 cm), field water capacity (0–20 cm), available water content (0–20 cm), wilting point (10–30 cm), saturated water content (10–70 cm), saturated hydraulic conductivity (0–90 cm), and WSM (0–30 cm and 40–50 cm) while decreasing the soil bulk density (0–70 cm). Compared to OM, SAP had greater beneficial effects on the total organic carbon, soil field water capacity, available water content, saturated water content, saturated hydraulic conductivity, and WSM in soil at 0–20 cm depth. The improvements to soil quality resulted in an increase in the yields of wheat and maize. Therefore, although SAP and OM were both effective at improving soil properties and increasing the economic yield of wheat and maize, the effectiveness of SAP was greater than that of OM.
Plant Water Stress Reduces Aphid Performance: Exploring Mechanisms Driven by Water Stress Intensity
Authors: Kansman Jessica T. , Basu Saumik , Casteel Clare L. , Crowder David W. , Lee Benjamin W. , Nihranz Chad T. , Finke Deborah L.
Published: April 2022

Drought alters plant traits in ways that affect herbivore performance. However, we lack a comprehensive understanding of the plant-derived mechanisms that mediate insect responses to drought. Water stress occurs along gradients of intensity, and the impacts of drought intensity on plant-insect interactions is understudied. Here, we assessed aphid performance on wheat plants exposed to a gradient of water stress and measured plant nutrients and phytohormones that may mediate aphid response to drought. We show that water stress reduced aphid performance, and the negative effect grew stronger as the magnitude of water stress increased. The plant response to water limitation was not consistent across the stress gradient and was reliant on the trait measured. Water limitation did not affect whole-plant nitrogen; however, water limitation did reduce amino acid concentration and increase sugars, but only under high stress intensity. The phytohormones abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA), and the expression of their associated gene transcripts, were also differentially affected by water stress intensity. In well-watered conditions, aphid feeding increased concentrations of the defense-related hormones SA and JA over time; however, any amount of water limitation prevented aphid induction of JA. Although aphids may experience a reprieve from JA-related defenses in stressed conditions, SA levels remain high in response to aphid feeding, indicating aphids are still vulnerable to SA-related defenses. Any level of water stress also increased the expression of a callose-associated gene transcript, a physical defense that impairs feeding. Thus, poor aphid performance on mildly-stressed plants was correlated with increased plant defenses, whereas poor performance on highly-stressed plants was correlated with stronger plant defense induction and reduced plant nutritional quality. Understanding the mechanisms driving aphid and plant performance under water stress conditions can improve our ability to predict how aphid populations will respond to climate change.
Identification of a Solute Carrier Family-Based Signature for Predicting Overall Survival in Osteosarcoma
Authors: Zheng Di , Wei Zhun , Guo Weichun
Published: April 2022

Given the important role of SLC family in essential physiological processes including nutrient uptake, ion transport, and waste removal, and that their dysregulation was found in distinct forms of cancer, here we identified a novel gene signature of SLC family for patient risk stratification in osteosarcoma. Gene expression data and relevant clinical materials of osteosarcoma samples were retrieved from The Cancer Genome Atlas (TCGA) database. Prognosis-related SLC genes were identified by performing univariate Cox regression analysis and were utilized to construct a four-SLC gene signature in osteosarcoma. It allowed patients to be classified into high- and low-risk groups, and Kaplan-Meier survival analysis in the training, testing, entire, and external GSE21257 cohorts suggested that the overall survival of patients in high-risk group was consistently worse than that in low-risk group, suggesting the promising accuracy and generalizability of the SLC-based signature in predicting the prognosis of patients with osteosarcoma. Moreover, univariate and multivariate Cox regression analyses indicated that the derived risk score was the only independent prognostic factor for osteosarcoma patients in TCGA and GSE21257 cohorts. Besides, a prognostic nomogram comprising the derived risk score and clinical features including gender and age was developed for clinical decision-making. Functional enrichment analyses of the differentially expressed genes between high- and low-risk group revealed that immune-related biological processes and pathways were significantly enriched. Estimation of tumor immune microenvironment using ESTIMATE algorithm revealed that patients with lower risk score had higher stromal, immune, and ESTIMATE score, and lower tumor purity. ssGSEA analyses indicated that the scores of various immune subpopulations including CD8+ T cells, DCs, and TIL were lower in high-risk group than these in low-risk group in both cohorts. As for the related immune functions, the scores of APC co-inhibition, CCR, check-point, T cell co-stimulation, and Type II IFN response were lower in high-risk group than these in low-risk group in both cohorts. In all, we identified a novel prognostic signature based on four SLC family genes that accurately predicted overall survival in osteosarcoma patients. Furthermore, the signature is linked to differences in immunological status and immune cell infiltrations in the tumor microenvironment.
PI3K Signaling in Dendritic Cells Aggravates DSS-Induced Colitis
Authors: Kuttke Mario , Hromadová Dominika , Yildirim Ceren , Brunner Julia S. , Vogel Andrea , Paar Hannah , Peters Sophie , Weber Maria , Hofmann Melanie , Kerndl Martina , Kieler Markus , Datler Hannes , Musiejovsky Laszlo , Salzmann Manuel , Lang Michaela , Soukup Klara , Halfmann Angela , Sharif Omar , Schabbauer Gernot
Published: April 2022

Aberrant innate immune responses to the gut microbiota are causally involved in the pathogenesis of inflammatory bowel diseases (IBD). The exact triggers and main signaling pathways activating innate immune cells and how they modulate adaptive immunity in IBD is still not completely understood. Here, we report that the PI3K/PTEN signaling pathway in dendritic cells enhances IL-6 production in a model of DSS-induced colitis. This results in exacerbated Th1 cell responses and increased mortality in DC-specific PTEN knockout (PTENΔDC) animals. Depletion of the gut microbiota using antibiotics as well as blocking IL-6R signaling rescued mortality in PTENΔDC mice, whereas adoptive transfer of Flt3L-derived PTEN-/- DCs into WT recipients exacerbated DSS-induced colitis and increased mortality. Taken together, we show that the PI3K signaling pathway in dendritic cells contributes to disease pathology by promoting IL-6 mediated Th1 responses.
IL-33 and IL-10 Serum Levels Increase in MCI Patients Following Homotaurine Treatment
Authors: Toppi Elisa , Sireno Laura , Lembo Micaela , Banaj Nerisa , Messina Beatrice , Golesorkhtafti Sedigheh , Spalletta Gianfranco , Bossù Paola
Published: April 2022

Homotaurine is a potential therapeutic compound for treatment of Alzheimer’s disease (AD), but its efficacy is still under investigation. Emerging data have shown that other than neuroprotective, homotaurine is endowed with anti-inflammatory activities, though with still unclear underlying mechanisms. Inflammation plays a critical role in the pathogenesis of AD and we previously suggested that homotaurine supplementation in patients with amnestic mild cognitive impairment (MCI) plays beneficial effects associated to a decrease in the circulating levels of the pro-inflammatory cytokine IL-18. Here we report that MCI patients supplemented with homotaurine for 12 months show elevated serum levels of IL-10 and IL-33, as compared to baseline, in addition to the described IL-18 decrease. Furthermore, we observed a significant positive correlation between IL-10 and IL-33 levels after treatment but not at the baseline, underlining the effectiveness of the compound in modulating both cytokines in an inter-related fashion and in regulating the pro/anti-inflammation balance. Furthermore, the elevation of both IL-10 and IL-33 is significantly associated with an improvement of episodic memory of treated patients, as measured by the Delayed Verbal Ray Test. In conclusion, our results confirm that homotaurine treatment exerts an overall anti-inflammatory action in MCI patients, based not only on the down-regulation of pro-inflammatory IL-18, but also on up-regulation of the anti-inflammatory IL-33 and IL-10 cytokines, which in turn are associated with an amelioration of patient’s cognitive functions. Future studies should be addressed to investigate the molecular mechanisms of homotaurine anti-inflammatory activity and its therapeutic exploitation in early AD.
A Protective HLA Extended Haplotype Outweighs the Major COVID-19 Risk Factor Inherited From Neanderthals in the Sardinian Population
Authors: Mocci Stefano , Littera Roberto , Tranquilli Stefania , Provenzano Aldesia , Mascia Alessia , Cannas Federica , Lai Sara , Giuressi Erika , Chessa Luchino , Angioni Goffredo , Campagna Marcello , Firinu Davide , Del Zompo Maria , La Nasa Giorgio , Perra Andrea , Giglio Sabrina
Published: April 2022

Sardinia has one of the lowest incidences of hospitalization and related mortality in Europe and yet a very high frequency of the Neanderthal risk locus variant on chromosome 3 (rs35044562), considered to be a major risk factor for a severe SARS-CoV-2 disease course. We evaluated 358 SARS-CoV-2 patients and 314 healthy Sardinian controls. One hundred and twenty patients were asymptomatic, 90 were pauci-symptomatic, 108 presented a moderate disease course and 40 were severely ill. All patients were analyzed for the Neanderthal-derived genetic variants reported as being protective (rs1156361) or causative (rs35044562) for severe illness. The β°39 C>T Thalassemia variant (rs11549407), HLA haplotypes, KIR genes, KIRs and their HLA class I ligand combinations were also investigated. Our findings revealed an increased risk for severe disease in Sardinian patients carrying the rs35044562 high risk variant [OR 5.32 (95% CI 2.53 - 12.01), p = 0.000]. Conversely, the protective effect of the HLA-A*02:01, B*18:01, DRB*03:01 three-loci extended haplotype in the Sardinian population was shown to efficiently contrast the high risk of a severe and devastating outcome of the infection predicted for carriers of the Neanderthal locus [OR 15.47 (95% CI 5.8 – 41.0), p < 0.0001]. This result suggests that the balance between risk and protective immunogenetic factors plays an important role in the evolution of COVID-19. A better understanding of these mechanisms may well turn out to be the biggest advantage in the race for the development of more efficient drugs and vaccines.
A Novel Approach to Using Seabed Geomorphology as a Predictor of Habitat Use in Highly Mobile Marine Predators: Implications for Ecology and Conservation
Authors: Wyles Hannah M. E. , Boehme Lars , Russell Debbie J. F. , Carter Matt I. D.
Published: April 2022

Understanding how marine predators find patchily distributed prey resources in a dynamic environment is key to identifying important ecological areas for ecosystem-level conservation management. However, the mechanisms underpinning important foraging areas often result from complex interactions between static and dynamic covariates (e.g. topography and currents). Modelling habitat associations with hydrodynamic processes is rarely useful when attempting to identify and characterise foraging areas across an individual’s foraging range. Investigating the influence of static habitat features on predator behaviour can provide a more tractable baseline understanding of habitat associations, upon which additional complexity can be added. Seabed gradient covariates (e.g. slope and aspect) are often used, yet such metrics are computed at singular user-defined resolutions, and provide limited ecological insight when used in isolation. Instead, categorising the seabed into geomorphological features may provide better characterisation of seabed structure. Here we explore the utility of a pattern recognition algorithm to delineate whole geomorphological features (“geomorphons”) on the seabed (e.g. valleys, ridges, footslopes) from bathymetry data, and examine the influence of geomorphology on marine predator habitat use. We demonstrate the potential application of this approach in a case study, examining the influence of geomorphons on the at-sea behaviour of a highly mobile predator inhabiting shelf seas: the grey seal (Halichoerus grypus). We analyse GPS tracking data from three seals tagged in the southern North Sea, an area with heterogeneous geomorphology. We use hidden Markov models (HMMs) to infer foraging and travelling behaviour and model the effect of different feature types on the probability of switching between states. All three seals showed an increased probability of transitioning from travelling to foraging when encountering slopes, footslopes and hollows, and foraging activity was concentrated at slopes on the fringes of the Dogger Bank. We hypothesise that such features may host prey aggregations, and/or lead to increased prey capture success. The results suggest the importance of such areas for grey seals in the southern North Sea, a region undergoing rapid and widespread anthropogenic habitat change. This method could be incorporated into future species distribution models to improve estimates of predator distribution, informing conservation management and marine spatial planning.
Antibiotic Treatment Ameliorates the Impact of Stony Coral Tissue Loss Disease (SCTLD) on Coral Communities
Authors: Forrester Graham E. , Arton Laura , Horton Argel , Nickles Katie , Forrester Linda M.
Published: April 2022

Stony coral tissue loss disease has spread widely in the Caribbean and causes substantial changes to coral community composition because of its broad host range and high fatality rate. To reduce SCTLD impacts, intervention programs throughout the region have divers treating corals with antibiotics. We assessed the effect of antibiotic treatment in the British Virgin Islands by comparing coral communities at 13 treated sites to those at 13 untreated sites. The prevalence of white syndromes (assumed to be primarily SCTLD), the severity of white syndrome lesions, partial colony mortality and complete colony mortality all showed a qualitative pattern consistent with benefits of treatment: they were reduced at treated sites for species highly susceptible to SCTLD. In contrast, the prevalence and severity of lesions from other diseases, and other causes of tissue loss, were all unrelated to treatment. Re-ordering of rank abundance at the community-level was also consistent with a positive effect of treatment because rare, highly SCTLD-susceptible species increased slightly in relative cover at treated sites. Although there was limited statistical support for these responses individually, collectively the overall pattern of results indicates a modest beneficial effect of the intervention program for highly susceptible species. Diver-based intervention programs using antibiotics may thus be a viable part of management plans for STLD at the epidemic stage.
Cold Thermal Priming of Laminaria digitata (Laminariales, Phaeophyceae) Gametophytes Enhances Gametogenesis and Thermal Performance of Sporophytes
Authors: Gauci Clément , Bartsch Inka , Martins Neusa , Liesner Daniel
Published: April 2022

Thermal characteristics of kelp species have been studied in many ways, but potentially persistent effects of temperature across generations are yet poorly understood. In this context, the effect of thermal priming on fertility and growth of the N-Atlantic kelp speciesLaminaria digitatawas investigated within and across life cycle generations in a two-step common garden experiment. Using vegetative clonal gametophytes from cold (5°C) and warm (15°C) pre-experimental cultivation (3 years), we first quantified gametogenesis and recruitment over two weeks at a common temperature of 10°C. Then, recruited sporophytes were transferred to a temperature gradient spanning the tolerance range of the species from 0°C to 20°C. We hypothesized that a warm gametophyte pre-experimental cultivation promotes performance of sporophytes at warm temperatures and vice versa. Interestingly, gametogenesis speed and sporophyte recruitment were higher in gametophytes following cold compared to warm pre-experimental cultivation, which indicates carry-over effects of temperature within the gametophyte generation. Compared to warm pre-experimental cultivation of gametophytes, a cold pre-experimental cultivation enhanced growth of juvenileLaminaria digitatasporophytes by more than 69% at the extreme low and high temperatures of 0 and 20°C. This is the first evidence for a cross-generational effect between gametophyte parents and offspring sporophytes. As cold gametophyte cultivation increased the trait performance of gametogenesis, recruitment and thermal tolerance of juvenile sporophytes, priming of early life cycle stages may be used to increase resilience and productivity of kelps in marine forest restoration efforts and kelp mariculture.
Range-Wide Comparison of Gray Whale Body Condition Reveals Contrasting Sub-Population Health Characteristics and Vulnerability to Environmental Change
Authors: Torres Leigh G. , Bird Clara N. , Rodríguez-González Fabian , Christiansen Fredrik , Bejder Lars , Lemos Leila , Urban R Jorge , Swartz Steven , Willoughby Amy , Hewitt Joshua , Bierlich KC.
Published: April 2022

Climate change is a global phenomenon, yet impacts on resource availability to predators may be spatially and temporally diverse and asynchronous. As capital breeders, whales are dependent on dense, predictable prey resources during foraging seasons. An Unusual Mortality Event (UME) of Eastern North Pacific (ENP) gray whales (Eschrichtius robustus) was declared in 2019 due to a dramatic rise in stranded animals, many emaciated. Climate change impacts may have affected prey availability on the primary foraging grounds of ENP gray whales (~20,000 individuals) in the Arctic and sub-Arctic region and in coastal habitats between northern California, USA and British Columbia, Canada where a small sub-group of ENP whales called the Pacific Coast Feeding Group (PCFG; ~230 individuals) forages. To investigate variability of gray whale body condition relative to changing ocean conditions, we compare two datasets of gray whale aerial photogrammetry images collectedviaUnoccupied Aircraft Systems (UAS) on the ENP wintering grounds in San Ignacio Lagoon, Mexico (SIL; n=111) and on the PCFG feeding grounds in Oregon, USA (n=72) over the same three-year period (2017–2019). We document concurrent body condition improvement of PCFG whales in Oregon while body condition of whales in SIL declined. This result indicates that the UME may have affected ENP whales due to reduced energetic gain on some Arctic/sub-Arctic foraging grounds, while PCFG whales are recovering from poor prey conditions during the NE Pacific marine heatwave event of 2014–2016. Surprisingly, we found that PCFG whales in Oregon had significantly worse body condition than whales in SIL, even when accounting for year and phenology. We derive support for this unexpected findingviaphotogrammetry analysis of opportunistic aerial images of gray whales on Arctic foraging grounds (n=18) compared to PCFG whales in Oregon (n=30): the body condition of PCFG whales was significantly lower (t=2.96, p=0.005), which may cause PCFG whales to have reduced reproductive capacity or resilience to environmental perturbations compared to ENP whales. Overall, our study elucidates divergent gray whale body condition across sub-groups and time, and we demonstrate the value of UAS to effectively monitor and identify the physiological response of whales to climate change.
Prediction of the Central Indian Ocean Mode in S2S Models
Authors: Qin Jianhuang , Zhou Lei , Li Baosheng , Meng Ze
Published: April 2022

Prediction of precipitation during the Indian summer monsoon (ISM) is a persistent scientific challenge. The central Indian Ocean (CIO) mode was proposed as a subseasonal climate mode over the tropical Indian Ocean, and it has a close relation with monsoon intraseasonal oscillations (MISO) during the ISM both in observations and simulations. In this study, the prediction skill of the CIO mode in the subseasonal-to-seasonal (S2S) air–sea coupled models is examined. The ECMWF and UKMO models display significantly higher skills for up to about 2 and 3 weeks, respectively, which are longer than other S2S models. The decline of the CIO mode prediction skill is due to the reduced signal of subseasonal zonal winds at 850 hPa over the tropical central Indian Ocean (especially along the equator; 5°S–5°N, 70°E–85°E). Therefore, a better simulation of tropical subseasonal zonal winds is required to improve the CIO mode prediction in models, and the improvement will benefit a better MISO simulation and a higher prediction skill during the ISM.
Kelp (Saccharina latissima) Mitigates Coastal Ocean Acidification and Increases the Growth of North Atlantic Bivalves in Lab Experiments and on an Oyster Farm
Authors: Young Craig S. , Sylvers Laine H. , Tomasetti Stephen J. , Lundstrom Andrew , Schenone Craig , Doall Michael H. , Gobler Christopher J.
Published: April 2022

Coastal zones can be focal points of acidification where the influx of atmospheric CO2 can be compounded by additional sources of acidity that may collectively impair calcifying organisms. While the photosynthetic action of macrophytes may buffer against coastal ocean acidification, such activity has not been well-studied, particularly among aquacultured seaweeds. Here, we report on field and laboratory experiments performed with North Atlantic populations of juvenile hard clams (Mercenaria mercenaria), eastern oysters (Crassostrea virginica), and blue mussels (Mytilus edulis) grown with and without increased CO2 and with and without North Atlantic kelp (Saccharina latissima) over a range of aquaculture densities (0.3 – 2 g L-1). In all laboratory experiments, exposure to elevated pCO2 (>1,800 µatm) resulted in significantly reduced shell- and/or tissue-based growth rates of bivalves relative to control conditions. This impairment was fully mitigated when bivalves were exposed to the same acidification source but also co-cultured with kelp. Saturation states of aragonite were transformed from undersaturated to saturated in the acidification treatments with kelp present, while the acidification treatments remained undersaturated. In a field experiment, oysters grown near aquacultured kelp were exposed to higher pH waters and experienced significantly faster shell and tissue based growth rates compared to individuals grown at sites away from kelp. Collectively, these results suggest that photosynthesis by S. latissima grown at densities associated with aquaculture increased pH and decreased pCO2, fostering a carbonate chemistry regime that maximized the growth of juvenile bivalves. As S. latissima has been shown to benefit from increased CO2, growing bivalves and kelp together under current or future acidification scenarios may be a synergistically beneficial integrated, multi-trophic aquaculture approach.
Building Block Analysis of ATIII Affinity Fractions of Heparins: Application to the ATIII Binding Capacity of Non-conventional 3-O-Sulfated Sequences
Authors: Mourier Pierre
Published: April 2022

In heparin, some 3-O-sulfated sequences do not meet the structural requirements of the ATIII binding pentasaccharide. These “non-conventional” sequences are the object of this study. In a previous paper (Mourier P. Heparinase digestion of 3-O-sulfated sequences: selective heparinase II digestion for separation and identification of binding sequences present in ATIII affinity fractions of bovine intestine heparins), we demonstrated that unsaturated 3-O-sulfated disaccharides detected in exhaustive heparin digests were specifically cleaved by heparinase I. Consequently, building blocks analyses of heparins using heparinases I+II+III digestion could be compared with experiments where only heparinase II is used. In these latter conditions of depolymerization, the 3-O-sulfated sequences digested into unsaturated 3-O-sulfated disaccharides with heparinases I+II+III, were heparinase II-resistant on their non-reducing side, resulting in longer new building blocks. These properties were used to study the structural neighborhood of these 3-O-sulfated moieties, which have still-undefined biological functions. In this part, heparinases I+II+III and heparinase II digestions of porcine mucosa, bovine mucosa and bovine lung heparins were compared in six fractions of increasing affinity for ATIII. Tagging of building blocks by reductive amination with sulfanilic acid was used. The distribution of 3-O-sulfated building blocks in the ATIII affinity fractions was used to examine the ATIII binding of these sequences.
SPP1 and CXCL9 Promote Non-alcoholic Steatohepatitis Progression Based on Bioinformatics Analysis and Experimental Studies
Authors: Wang Wen , Liu Xiaojing , Wei Peiyao , Ye Feng , Chen Yunru , Shi Lei , Zhang Xi , Li Jianzhou , Lin Shumei , Yang Xueliang
Published: April 2022

Background and Aims

Non-alcoholic fatty liver disease (NAFLD) is a major chronic liver disease worldwide, and non-alcoholic steatohepatitis (NASH) is one of its pathological subtypes. The pathogenesis of NASH has not yet been fully elucidated. The purpose of this study was to identify the hub genes and pathways involved in NASH using bioinformatics methods. The hub genes were confirmed in human and animal models.

Materials and Methods

Three Gene Expression Omnibus (GEO) datasets (GSE48452, GSE58979, and GSE151158) of NASH patients and healthy controls were included in the study. We used GEO2R to identify differentially expressed genes (DEGs) between NASH patients and healthy controls. Functional enrichment analyses were then performed to explore the potential functions and pathways of the DEGs. In all DEGs, only two genes were highly expressed in NASH patients throughout the three datasets; these two genes, SPP1 and CXCL9, were further studied. Serum and liver tissues from NASH patients and healthy controls were collected. Serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels were measured in NASH patients and healthy controls. Liver tissues were stained with hematoxylin and eosin. Immunohistochemical staining was used to evaluate the expression levels of the two genes in liver tissues. Male C57BL/6J mice were fed a methionine choline-deficient (MCD) diet for 8 weeks, after which serum ALT and AST levels were measured and liver tissues were stained.

Results

SPP1 and CXCL9 were the hub genes detected in the three datasets. “Lipid metabolism,” “inflammatory response,” and “lymphocyte activation” were the most significant biological functions in GSE48452, GSE58979, and GSE151158, respectively. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the toll-like receptor signaling pathway was significantly enriched in NASH patients. Serum ALT and AST levels were significantly increased in NASH patients compared to healthy controls. Liver tissues had more serious steatosis, hepatocyte ballooning degeneration, and lobular inflammatory infiltration, and the expression of SPP1 and CXCL9 in liver cells was significantly upregulated in NASH patients compared to healthy controls. MCD diet mice were consistent with NASH patients.

Conclusion

SPP1 and CXCL9 may play important roles in NASH pathogenesis and could be potential therapeutic targets and biomarkers of NASH in the future. Further experimental studies are needed to confirm our results.
Whole-Genome Sequence Approach and Phylogenomic Stratification Improve the Association Analysis of Mutations With Patient Data in Influenza Surveillance
Authors: Van Poelvoorde Laura , Vanneste Kevin , De Keersmaecker Sigrid C. J. , Thomas Isabelle , Van Goethem Nina , Van Gucht Steven , Saelens Xavier , Roosens Nancy H. C.
Published: April 2022

Each year, seasonal influenza results in high mortality and morbidity. The current classification of circulating influenza viruses is mainly focused on the hemagglutinin gene. Whole-genome sequencing (WGS) enables tracking mutations across all influenza segments allowing a better understanding of the epidemiological effects of intra- and inter-seasonal evolutionary dynamics, and exploring potential associations between mutations across the viral genome and patient’s clinical data. In this study, mutations were identified in 253 Influenza A (H3N2) clinical isolates from the 2016-2017 influenza season in Belgium. As a proof of concept, available patient data were integrated with this genomic data, resulting in statistically significant associations that could be relevant to improve the vaccine and clinical management of infected patients. Several mutations were significantly associated with the sampling period. A new approach was proposed for exploring mutational effects in highly diverse Influenza A (H3N2) strains through considering the viral genetic background by using phylogenetic classification to stratify the samples. This resulted in several mutations that were significantly associated with patients suffering from renal insufficiency. This study demonstrates the usefulness of using WGS data for tracking mutations across the complete genome and linking these to patient data, and illustrates the importance of accounting for the viral genetic background in association studies. A limitation of this association study, especially when analyzing stratified groups, relates to the number of samples, especially in the context of national surveillance of small countries. Therefore, we investigated if international databases like GISAID may help to verify whether observed associations in the Belgium A (H3N2) samples, could be extrapolated to a global level. This work highlights the need to construct international databases with both information of viral genome sequences and patient data.
Temperature Rise Increases the Bioavailability of Marine Synechococcus-Derived Dissolved Organic Matter
Authors: Zhang Jiajie , Liu Jihua , Liu Daixi , Chen Xiao , Shi Quan , He Chen , Li Gang
Published: April 2022

Synechococcus is one group of main primary producers and plays a key role in oceanic carbon fixation and transformation. To explore how the temperature rise affects the bioavailability of Synechococcus-derived dissolved organic matter (SOM) and whether this effect would be altered by the involvement of heterotrophic bacteria, we compared the optical and molecular properties of the SOM of axenic Synechococcus sp. PCC7002 culture (Syn) to that with associated heterotrophic bacteria (SynB) under 15, 18, and 21°C growth temperatures at exponential and decay growth phases. Our results showed that the temperature rise increased the bioavailability of the SOM of both Syn and SynB cultures by lowering the proportion of the hydrogen-poor and double-bond structure-rich humus-like components and highly unsaturated substances, as indicated by the increase of spectral slope ratio (SR) and biological index (BIX) and decrease of humification index (HIX). Moreover, the involvement of heterotrophic bacteria modified the Synechococcus-derived SOM, together with its intracellular dissolved organic matter (DOM) excludes, lowering the SOM bioavailability. Our results indicated that the warming in climate change scenario may enhance the bioavailability of the Synechococcus-derived SOM although it may be tempered by the involvement of heterotrophic bacteria, providing an insight for preservation of the organic carbon pool in global oceans.