bluuebunny/crossref_metadata_2025_split huggingface dataset:
Both Determinants of Allosteric and Active Sites Responsible for Catalytic Activity of Delta 12 Fatty Acid Desaturase by Domain Swapping
Authors: Shi Haisu , Tian Jinlong , Wu Chen , Li Mo , An Feiyu , Wu Rina , Shao Junhua , Zheng Yan , Luo Xue , Tao Dongbing , Chen Xu , Pi Yuzhen , Zhao Chunyan , Yue Xiqing , Wu Junrui 
Published: October 2019

AbstractCheese lacks essential fatty acids (EFAs). Delta 12 fatty acid desaturase (FADS12) is a critical enzyme required for EFA biosynthesis in fermentation of the predominant strains of cheese. Previously, we identified theFADS12gene and characterized its function for the first time inGeotrichum candidum, a dominant strain used to manufacture soft cheese with white rind. In this study, we analyzed the molecular mechanism ofFADS12function by swapping domains fromMortierella alpinaandG. candidumthat had, respectively, high and low oleic acid conversion rates. The results revealed three regions that are essential to this process, including regions from the end of the second transmembrane domain to the beginning of the third transmembrane domain, from the end of the third transmembrane domain to the beginning of the fourth transmembrane domain, and from the 30-amino acid from the end of the sixth transmembrane domain to the C-terminal end region. Based on our domain swapping analyses, nine pairs of amino acids including H112, S118, H156, Q161, K301, R306, E307, A309 and S323 in MaFADS12 (K123, A129, N167, M172, T302, D307, I308, E310 and D324 in GcFADS12) were identified as having a significantly effect onFADS12catalytic efficiency, and linoleic acid and its analogues (12,13-cyclopropenoid fatty acid) were found to inhibit the catalytic activity ofFADS12and related recombinant enzymes. Furthermore, the molecular mechanism ofFADS12inhibition was analyzed. The results revealed two allosteric domains, including one domain from the N-terminal region to the beginning of the first transmembrane domain and another from the 31stamino acid from the end of the sixth transmembrane domain to the C terminus. Y4 and F398 amino acid residues fromMaFADS12and eight pairs of amino acids including G56, L60, L344, G10, Q13, S24, K326 and L344 in MaFADS12 (while Y66, F70, F345, F20, Y23, Y34, F327 and F345 in GcFADS12) played a pivotal role inFADS12inhibition. Finally, we found that both allosteric and active sites were responsible for the catalytic activity ofFADS12at various temperatures, pH, and times. This study offers a solid theoretical basis to develop preconditioning methods to increase the rate at whichGcFADS12converts oleic and linoleic acids to produce higher levels of EFAs in cheese.
Paracrine control of α-cell glucagon exocytosis is compromised in human type-2 diabetes
Authors: Omar-Hmeadi Muhmmad , Lund Per-Eric , Gandasi Nikhil R , Tengholm Anders , Barg Sebastian 
Published: October 2019

AbstractGlucagon is secreted from pancreatic α-cells to activate gluconeogenesis and other pathways that raise blood glucose during hypoglycemia. Glucose-dependent regulation of glucagon secretion involves both α-cell-intrinsic mechanisms and paracrine control through insulin and somatostatin. In type-2 diabetes (T2D) inadequately high glucagon levels contribute to hyperglycemia. To understand these disease-associated changes at the cellular level, and to isolate intrinsic and paracrine effects, we analyzed glucagon granule exocytosis and membrane excitability in isolated α-cells from 56 non-diabetic (ND) and 15 T2D human donors. High resolution imaging showed that glucagon granule exocytosis had a U-shaped sensitivity to glucose, with the slowest rate around 7 mM glucose, and accelerated rates at <5 and >10 mM glucose. Exocytosis was reduced in T2D α-cells, but their glucose sensitivity remained intact and there were no changes in voltage-dependent ion currents or granule trafficking. Instead, α-cells from T2D donors were markedly insensitive to somatostatin and insulin, which rapidly inhibited exocytosis and electrical activity in ND cells. Thus, intrinsic mechanisms do not inhibit glucagon secretion at hyperglycemia, and elevated glucagon levels in human T2D reflect an insensitivity of α-cells to paracrine inhibition.
Single-molecule imaging reveals control of parental histone recycling by free histones during DNA replication
Authors: Gruszka Dominika T. , Xie Sherry , Kimura Hiroshi , Yardimci Hasan 
Published: October 2019

SUMMARYFaithful replication of chromatin domains during cell division is fundamental to eukaryotic development. During replication, nucleosomes are disrupted ahead of the replication fork, followed by their rapid reassembly on daughter strands from the pool of recycled parental and newly synthesized histones. Here, we use single-molecule imaging and replication assays in Xenopus laevis egg extracts to determine the outcome of replication fork encounters with nucleosomes. Contrary to current models, the majority of parental histones are evicted from the DNA, with histone recycling, nucleosome sliding and replication fork stalling also occurring but at lower frequencies. The anticipated local histone transfer only becomes dominant upon depletion of free histones from extracts. Our studies provide the first direct evidence that parental histones remain in close proximity to their original locus during recycling and reveal that provision of excess histones results in impaired histone recycling, which has the potential to affect epigenetic memory.
Novel repellents for the blood-sucking insectsRhodnius prolixusandTriatoma infestans, vectors of Chagas disease
Authors: Ramírez Melanie , Ortiz Mario I. , Guerenstein Pablo , Molina Jorge 
Published: October 2019

AbstractBackgroundStudying the behavioral response of blood-sucking, disease-vector insects to potentially repellent volatile compounds could shed light on the development of new control strategies. Volatiles released by human facial skin microbiota play different roles in the host-seeking behavior of triatomines. We assessed the repellency effect of such compounds of bacterial origin onTriatoma infestansandRhodnius prolixus, two important vectors of Chagas disease in Latin America.MethodsUsing an exposure device, insects were presented to human odor alone (negative control) and in the presence of three individual tested compounds (2-mercaptoethanol, dimethyl sulfide and 2-phenylethanol, which was only tested inR. prolixus) and the gold-standard repellent NN-diethyl-3-methylbenzamide–DEET (positive control). We quantified the time the insects spent in the proximity of the host and performed nonparametric statistical tests to determine if any of the compounds evaluated affected the behavior of the insect.ResultsWe found volatiles that significantly reduced the time spent in the proximity of the host. These were 2-phenylethanol and 2-mercaptoethanol forR. prolixus, and dimethyl sulfide and 2-mercaptoethanol forT. infestans. Such an effect was also observed in both species when DEET was presented, although only at the higher doses tested.ConclusionsThe new repellents modulated the behavior of two Chagas disease vectors belonging to two different triatomine tribes, and this was achieved using a dose up to three orders of magnitude lower than that needed to evoke the same effect with DEET. Future efforts in understanding deeply the mechanism of action of repellent compounds such as 2-mercaptoethanol, as well as an assessment of their temporal and spatial repellent properties, could lead to the development of novel control strategies for insect vectors refractory to DEET.
Allium roseum L. extract inhibits amyloid beta aggregation and toxicity involved in Alzheimer’s disease
Authors: Boubakri Abdelbasset , Leri Manuela , Bucciantini Monica , Najjaa Hanen , Ben Arfa Abdelkarim , Stefani Massimo , Neffati Mohamed 
Published: October 2019

ABSTRACTAllium roseum is an important medicinal and aromatic plant, specific to the North African flora and a rich source of important nutrients and bioactive molecules including flavonoids and organosulfur compounds whose biological activities and pharmacological properties are well known. In the present study, the inhibition of amyloid beta protein toxicity by the ethanolic extract of this plant is investigated for the first time. Preliminary biochemical analyses identified kæmpferol and Luteolin-7-o-glucoside as the more abundant phenolic compounds. The effects of A. roseum extract (ARE) on amyloid beta-42 (Aβ42) aggregation and aggregate cytotoxicity, were investigated by biophysical (ThT assay, Dynamic light scattering and transmission electron microscopy) and cellular assays (cytotoxicity, aggregate immunolocalization, ROS measurement and intracellular Ca2+ imaging). The biophysical data suggest that ARE affects the structure of Aβ42 peptide, inhibits its polymerization, and interferes with the path of fibrillogenesis. The data with cultured cells shows that ARE reduces Aß42 aggregate toxicity by inhibiting aggregate binding to the cell membrane and by decreasing both oxidative stress and intracellular Ca2+. Accordingly, ARE could act as a neuroprotective factor against Aβ aggregate toxicity in Alzheimer’s disease.
Feasibility of real-time in vivo89Zr-DFO-labeled CAR T-cell trafficking using PET imaging
Authors: Lee Suk Hyun , Soh Hyunsu , Chung Jin Hwa , Cho Eun Hyae , Lee Sang Joo , Ju Ji-Min , Shin Joong Hyuk , Kim Hyori , Oh Seung Jun , Lee Sang-Jin , Chung Junho , Kim Seog-Young , Ryu Jin-Sook 
Published: October 2019

AbstractIntroductionChimeric antigen receptor (CAR) T-cells have been developed recently, producing impressive outcomes in patients with hematologic malignancies. However, there is no standardized method for cell trafficking and in vivo CAR T-cell monitoring. We assessed the feasibility of real-time in vivo89Zr-p-Isothiocyanatobenzyl-desferrioxamine (Df-Bz-NCS, DFO) labeled CAR T-cell trafficking using positron emission tomography (PET).ResultsThe 89Zr-DFO radiolabeling efficiency of Jurkat/CAR and human peripheral blood mononuclear cells (hPBMC)/CAR T-cells was 70–79%, and cell radiolabeling activity was 98.1–103.6 kBq/106 cells. Cell viability after radiolabeling was >95%. Compared with unlabeled cells, cell proliferation was not significantly different during the early period after injection; however, the proliferative capacity decreased over time (p = 0.02, day 7 after labeling). IL-2 or IFN-γ secretion was not significantly different between unlabeled and labeled CAR T-cells. PET/magnetic resonance images in the xenograft model showed that most of the 89Zr-DFO-labeled Jurkat/CAR T-cells were distributed in the lung (24.4% ± 3.4%ID) and liver (22.9% ± 5.6%ID) by 1 hour after injection. The cells gradually migrated from lung to the liver and spleen by day 1, and remained stably until day 7 (on day 7: lung 3.9% ± 0.3%ID, liver 36.4% ± 2.7%ID, spleen 1.4% ± 0.3%ID). No significant accumulation of labeled cells was identified in tumors. A similar pattern was observed in ex vivo biodistributions on day 7 (lung 3.0% ± 1.0%ID, liver 19.8% ± 2.2%ID, spleen 2.3% ± 1.7%ID). 89Zr-DFO-labeled hPBMC/CAR T-cells showed the similar distribution on serial PET images as Jurkat/CAR T-cells. The distribution of CAR T-cells was cross-confirmed by flow cytometry, Alu polymerase chain reaction, and immunohistochemistry.ConclusionUsing PET imaging of 89Zr-DFO-labeled CAR T-cells, real time in vivo cell trafficking is feasible. It can be used to investigate cellular kinetics, initial in vivo biodistribution, and the safety profile in future CAR T-cell development.
Non-canonical autophagy in dendritic cells restricts cross-presentation and anti-tumor immunity
Authors: Sil Payel , Zhao Fei , Muse Ginger W. , Wong Sing-Wai , Kolb Joseph P. , DeGraff Laura Miller , Tucker Charles J. , Scappini Erica , Snyder Annelise G. , Grimm Sara , Oberst Andrew , Martinez Jennifer 
Published: October 2019

SummaryMajor Histocompatibility Complex I (MHC-I) molecules classically present peptides derived from endogenous antigens, but exogenous antigens can also gain access to the MHC-I machinery in dendritic cells (DCs), which can activate antigen-specific CD8+T cells. This process, termed cross-presentation, can be triggered by the uptake of dying autologous cells, including tumor cells, by DCs. The molecular mechanisms that underlie efficient cross-presentation remain largely uncharacterized, and an improved understanding of these mechanisms might reveal novel strategies for anti-tumor therapies. Rubicon (RUBCN) is a molecule required for LC3-associated phagocytosis (LAP), but dispensable for canonical autophagy, and mice lacking this protein develop an autoimmune inflammatory pathology with age. Here, we demonstrate thatRubcn-deficient DCs have increased retention of engulfed cellular cargo in immature phagosomes resulting in increased phagosome-to-cytosol escape and antigen access to proteasome-mediated degradation. As a result, mice selectively lackingRubcnin DCs mount stronger tumor antigen-specific CD8+T cell responses and exhibit decreased tumor burden compared to wild type littermates. These findings identify LAP as a key regulator of cross-presentation and suggest that targeting RUBCN might represent a novel strategy for anti-tumor therapy.
Defining the DmsA Signal Sequence Interaction with DmsD And TatBC
Authors: Ghosh Deepanjan , Ramasamy Sureshkumar 
Published: October 2019

AbstractRedox – enzyme maturation proteins (REMP) ensure co-factor loading and folding of proteins targeted to the twin-arginine translocation (Tat) pathway. The details of the interaction of a REMP with the corresponding signal sequence of its substrate are not well understood. Here, we demonstrate the features of the signal sequence for the Tat substrate DmsA (ssDmsA) responsible for complex formation with its REMP, DmsD, and with the Tat membrane complex TatB & TatC (TatBC). A heterologously expressed ssDmsA/DmsD complex forms two stochiometric populations corresponding to monomeric and dimeric forms of the complex. The monomeric complex has a higher affinity for the TatBC complex than the dimeric, which imply higher level regulation process to ensure the maturation of protein before translocation. Results from various binding studies yielded the shortest signal peptide required for ssDmsA/DmsA interaction and the region responsible for the TatBC interaction. Further experiments like alanine scanning in this peptide highlight the possible residues that are essential for this complex formation.
Dopamine 2 receptor signaling controls the daily burst in phagocytic activity in the mouse retinal pigment epithelium
Authors: Goyal Varunika , DeVera Christopher , Laurent Virginie , Sellers Jana , Chrenek Micah A. , Hicks David , Baba Kenkichi , Iuvone P. Michael , Tosini Gianluca 
Published: October 2019

AbstractPurposeA burst in phagocytosis of spent photoreceptor outer fragments by retinal pigment epithelium (RPE) is a rhythmic process occurring 1-2 hours after the onset of light. This phenomenon is considered crucial for the health of the photoreceptors and RPE. We have recently reported that dopamine, via dopamine 2 receptor (D2R), shifts the circadian rhythm in the RPE.MethodsHere, we first investigated the impact of the removal of D2R on the daily peak of phagocytosis by RPE and then we analyzed the function and morphology of retina and RPE in the absence of D2R.ResultsD2R KO mice do not show a daily burst of phagocytic activity after the onset of light. Also, in contrast to control, phosphorylation of FAK did not increase significantly in KO mice at ZT1. RNA sequencing revealed a total of 394 differentially expressed genes (DEGs) between ZT23 and ZT1 in the control mice, whereas in D2R KO mice, we detected 1054 DEGs. Pathway analysis of the gene expression data implicated integrin signaling to be one of the upregulated pathways in control but not in D2R KO mice. No difference in retinal thickness, visual function, or morphology of RPE cells was observed between WT and D2R KO mice at the age of 3 and 12 months.ConclusionsOur data suggest that removal of D2R prevents the burst in phagocytosis and a related increase in the phosphorylation of FAK after light onset. The pathway analysis points towards a putative role of D2R in controlling integrin signaling, which is known to play an important role in the control of the daily burst of phagocytosis by the RPE. Our data also indicate that the absence in the burst of phagocytic activity in the early morning does not produce any apparent deleterious effect on the retina or RPE up to one year of age.
FvLcp1, a type-D fungal LysM protein with Chitin-binding domains, is a secreted protein involved in host recognition and fumonisin production in Fusarium verticillioides - maize kernel interaction
Authors: Zhang Huan , Kim Man S. , Huang Jun , Yan Huijuan , Yang Tao , Song Linlin , Yu Wenying , Shim Won Bo 
Published: October 2019

SUMMARYFusarium verticillioides is one of the key maize ear rot pathogens and produces fumonisins, a group of mycotoxins detrimental to humans and animals. Unfortunately, our understanding on how this fungus interacts with maize kernels to trigger mycotoxin biosynthesis is very limited.We performed a systematic computational network-based analysis of large-scale F. verticillioides RNA-seq datasets to identify potential gene subnetwork modules that are associated with virulence and fumonisin regulation.Among the highly discriminative subnetwork modules, we identified a putative hub gene FvLCP1, which encodes a putative a type-D fungal LysM protein with a signal peptide, three LysM domains, and two chitin binding domains. FvLcp1 is a unique protein that harbors these domains amongst five representative Fusarium species.FvLcp1 is a secreted protein important for fumonisin production with LysM domain playing acritical role. Chitin-binding domain was essential for in vitro chitin binding.Using rice blast fungus, we learned that FvLcp1 accumulates in appressoria, a key infection structure, suggesting that FvLcp1 could be involved in host recognition and infection. Also, full length FvLcp1 was able to suppress the BAX triggered plant cell death in Nicotiana benthamiana.This is the first report where a unique type-D LysM secreted protein with chitin-binding domain in mycotoxigenic fungus F. verticillioides was shown to be potentially involved in suppressing host cell death and promoting fumonisins biosynthesis while the pathogen colonizes maize kernels.
Temperature shapes movement and habitat selection by a heat-sensitive ungulate
Authors: Alston Jesse M. , Joyce Michael J. , Merkle Jerod A. , Moen Ron A. 
Published: October 2019

AbstractContextWarmer weather caused by climate change poses increasingly serious threats to the persistence of many species, but animals can modify behavior to mitigate at least some of the threats posed by warmer temperatures. Identifying and characterizing how animals modify behavior to avoid the negative consequences of acute heat will be crucial for understanding how animals will respond to warmer temperatures in the future.ObjectivesWe studied the extent to which moose (Alces alces), a species known to be sensitive to heat, mitigates heat on hot summer days via multiple different behaviors: (1) reduced movement, (2) increased visitation to shade, (3) increased visitation to water, or (4) a combination of these behaviors.MethodsWe used GPS telemetry and a step-selection function to analyze movement and habitat selection by moose in northeastern Minnesota, USA.ResultsMoose reduced movement, used areas of the landscape with more shade, and traveled nearer to mixed forests and bogs during periods of heat. Moose used shade far more than water to ameliorate heat, and the most pronounced changes in behavior occurred between 15°C and 20°C.ConclusionsResearch characterizing the behaviors animals use to facilitate thermoregulation will aid conservation of heat-sensitive species in a warming world. The modeling framework presented in this study is a promising method for evaluating the influence of temperature on movement and habitat selection.
Metabolome-informed microbiome analysis refines metadata classifications and reveals unexpected medication transfer in captive cheetahs
Authors: Gauglitz Julia M. , Morton James T. , Tripathi Anupriya , Hansen Shalisa , Gaffney Michele , Carpenter Carolina , Weldon Kelly C. , Shah Riya , Parampil Amy , Fidgett Andrea , Swafford Austin D. , Knight Rob , Dorrestein Pieter C. 
Published: October 2019

Structured AbstractEven high-quality collection and reporting of study metadata in microbiome studies can lead to various forms of inadvertently missing or mischaracterized information that can alter the interpretation or outcome of the studies, especially with non-model organisms. Metabolomic profiling of fecal microbiome samples can provide empirical insight into unanticipated confounding factors that are not possible to obtain even from detailed care records. We illustrate this point using data from cheetahs from the San Diego Zoo Safari Park. The metabolomic characterization indicated that one cheetah had to be moved from the non-antibiotic-exposed to the antibiotic-exposed group. The detection of the antibiotic in this second cheetah was likely due to grooming interactions with the cheetah that was administered antibiotics. Similarly, because transit time for stool is variable, early fecal samples within the first few days of antibiotic prescription do not all contain detectable antibiotics. Therefore, the microbiome is not affected by the antibiotics at those time points. These insights significantly altered the way the samples were grouped for analysis (antibiotic vs no antibiotic), and the subsequent understanding of the effect of the antibiotics on the cheetah microbiome. Metabolomics also revealed information about numerous other medications, and provided unexpected dietary insights that in turn improved our understanding of the molecular patterns on the impact on the community microbial structure. These results suggest that untargeted metabolomics data provide empirical evidence to correct records of non-model organisms in captivity, although we also expect these methods will be appropriate for experimental conditions typical in human studies.ImportanceMetabolome-informed analyses can enhance ‘omics studies by enabling the correct partitioning of samples by identifying hidden confounders inadvertently misrepresented or omitted from carefully curated metadata. We demonstrate the utility of metabolomics in a study characterizing the microbiome associated with liver disease in cheetahs. Metabolome-informed reinterpretation of metagenome and metabolome profiles factored in an unexpected transfer of antibiotics preventing misinterpretation of the data. Our work suggests that untargeted metabolomics can be used to verify, augment, and correct sample metadata to support improved grouping of sample data for microbiome analyses, here for non-model organisms in captivity. However, the techniques also suggest a path forward for correcting clinical information in human studies to enable higher-precision analyses.