bluuebunny/crossref_metadata_2025 huggingface dataset:
Mild traumatic brain injury/ concussion initiates an atypical astrocyte response caused by blood-brain barrier dysfunction
Authors: Heithoff Benjamin P. , George Kijana K. , Shandra Oleksii , Robel Stefanie
Published: May 2021

Mild traumatic brain injury/ concussion (mTBI) account for 70-90% of all reported TBI cases and cause long lasting neurological consequences in 10 to 40% of patients. Recent clinical studies revealed increased blood-brain barrier (BBB) permeability in mTBI patients, which correlated with secondary damage after mTBI. However, the cascade of cellular events initiated by exposure to blood-borne factors resulting in sustained damage are not fully resolved. We previously reported that astrocytes respond atypically to mTBI rapidly downregulating many proteins essential to their homeostatic function while classic scar formation does not occur. Here, we tested the hypothesis that mTBI -induced BBB damage causes atypical astrocytes through exposure to blood-borne factors. Using a mTBI mouse model, 2-photon imaging, an endothelial cell-specific genetic ablation approach, and serum-free primary astrocyte cultures, we demonstrated that areas with atypical astrocytes coincide with BBB damage and that exposure of astrocytes to plasma proteins is sufficient to initiate downregulation of astrocyte homeostatic proteins. While mTBI resulted in frequent impairment of both physical and metabolic BBB properties and leakage of small-sized blood-borne factors, deposition of the coagulation factor fibrinogen or vessel rupture were rare. Surprisingly, even months after mTBI BBB repair did not occur in areas with atypical astrocytes. Together, these findings implicate that even relatively small BBB disturbances are sustained long-term and render nearby astrocytes dysfunctional, likely at the cost of neuronal health and function.
The outward Shaker channel OsK5.2 is beneficial to the plant salt tolerance through its role in K+ translocation and its control of leaf transpiration
Authors: Zhou Jing , Nguyen Thanh Hao , Luu Doan Trung , Sentenac Hervé , Véry Anne-Aliénor
Published: May 2021

High soil salinity constitutes a major environmental constraint to crop production worldwide, and the identification of genetic determinants of plant salt tolerance is awaited by breeders. While the leaf K+ to Na+ homeostasis is considered as key parameter of plant salt tolerance, the underlying mechanisms are not fully identified. Especially, the contribution of K+ channels to this homeostasis has been scarcely examined. Here, we show, using a reverse genetics approach, that the outwardly-rectifying K+ channel OsK5.2, involved in K+ translocation to the shoot and K+ release by guard cells for stomatal closure, is a strong determinant of rice salt tolerance. Upon saline treatment, OsK5.2 function in xylem sap K+ load was maintained, and even transiently increased, in roots. OsK5.2 selectively handled K+ in roots and was not involved in xylem sap Na+ load. In shoots, OsK5.2 expression was up-regulated from the onset of the saline treatment, enabling fast reduction of stomatal aperture, decreased transpirational water flow and therefore decreased trans-plant Na+ flux and reduced leaf Na+ accumulation. Thus, the OsK5.2 functions allowed shoot K+ nutrition while minimizing arrival of Na+, and appeared highly beneficial to the leaf K+ to Na+ homeostasis, the avoidance of salt toxicity and plant growth maintaining.
Contribution of metal transporters of the ABC, ZIP, and NRAMP families to manganese uptake and infective endocarditis virulence in Streptococcus sanguinis
Authors: Puccio Tanya , Kunka Karina S. , Kitten Todd
Published: May 2021

Streptococcus sanguinis is an important cause of infective endocarditis. In strain SK36, the ABC-family manganese transporter, SsaACB, is essential for virulence. We have now identified a ZIP-family protein, TmpA, as a secondary manganese transporter. A tmpA mutant had no phenotype, but a ΔssaACB ΔtmpA mutant was far more attenuated for serum growth and somewhat more attenuated for virulence in a rabbit model than its ΔssaACB parent. The growth of both mutants was restored by supplemental manganese, but the ΔssaACB ΔtmpA mutant required twenty-fold more and accumulated less. Although ZIP-family proteins are known for zinc and iron transport, TmpA-mediated transport of either metal was minimal. In contrast to ssaACB and tmpA, which appear ubiquitous in S. sanguinis, a mntH gene encoding an NRAMP-family transporter has been identified in relatively few strains, including VMC66. As in SK36, deletion of ssaACB greatly diminished VMC66 endocarditis virulence and serum growth, and deletion of tmpA from this mutant diminished virulence further. Virulence was not significantly altered by deletion of mntH from either VMC66 or its ΔssaACB mutant. This and the accompanying paper together suggest that SsaACB is of primary importance for endocarditis virulence while secondary transporters TmpA and MntH contribute to growth under differing conditions.
High-throughput, multiplex microfluidic test strip for the determination of antibiotic susceptibility in uropathogenic E. coli with smartphone detection
Authors: Needs Sarah H. , Rafaque Zara , Imtiaz Wajiha , Ray Partha , Andrews Simon , Edwards Alexander D.
Published: May 2021

Antibiotic resistance in urinary tract infections is a major global challenge and improved cost-effective and high throughput antibiotic susceptibility tests (AST) are urgently needed to inform correct antibiotic selection. We evaluated a high throughput microfluidic test strip for AST and minimum inhibitory concentration (MIC) determination in 20 urinary pathogenic E. coli (UPEC) isolates using six commonly prescribed or therapeutically beneficial antibiotics. The microfluidic MIC performs broth microdilution in 1 microliter volume capillaries, 100 X smaller than standard broth microdilution. Each test strip contains 10 parallel capillaries which are dipped into a single well of a 96 well plate, significantly increasing throughput over a microtitre plate. When tested with clinical UPEC isolates at standardised inoculum density, these devices gave 100% essential agreement (+/- 1 doubling dilution of antibiotic) to the gold standard microplate broth microdilution method described by CLSI. Although for some antibiotic/isolate combinations an earlier endpoint readout reduced accuracy, MIC test strips read at a 6h endpoint still gave 69 – 100 % essential agreement depending on the antibiotic. Growth could be detected significantly earlier than 6h, but with a trade-off between speed vs accuracy. These high-throughput, multiplexed test strips could be used to increase throughput and give faster results than microplates while retaining the core broth microdilution methodology of gold standard techniques for AST and MIC determination.
Regulation of osteoblast autophagy based on PI3K/AKT/mTOR signaling pathway study on the effect of β-ecdysterone on fracture healing
Authors: Tang Yanghua , Mo Yafeng , Xin Dawei , Xiong Zhenfei , Zeng Linru , Luo Gan
Published: May 2021

Purpose

To investigate the effects of β-ecdysterone on fracture healing and the underlying mechanism.

Methods

MTT assay was used to detect the cell viability and alkaline phosphatase (ALP) activity was measured using a commercial kit. AO/PI and flow cytometry assays were used to determine the state of apoptosis of osteoblasts. The expression level of RunX2, ATG7 and LC3 was evaluated by qRT-PCR and Western blot assays. X-ray and HE staining were conducted on the fractured femur to evaluate the pathological state. Immunohistochemical assay was used to detect the expression level of Beclin-1 and immunofluorescence assay was used to measure the expression level of LC3 in the fractured femurs. Western blot was utilized to determine the expression level of PI3K, p-AKT1, AKT1, p-mTOR, mTOR, p-p70S6K, and p70S6K.

Results

The ALP activity and expression of RunX2 in fractured osteoblasts were significantly suppressed by 3-methyladenine and elevated by rapamycin, 60, and 80 μM β-ecdysterone. The apoptotic state of fractured osteoblasts was enhanced by 3-methyladenine and alleviated by rapamycin, 60, and 80 μM β-ecdysterone. The state of autophagy both in fractured osteoblasts and femurs was inhibited by 3-methyladenine and facilitated by rapamycin and β-ecdysterone. Compared to control, Garrett score in 3-methyladenine group was significantly decreased and promoted in rapamycin and β-ecdysterone groups, accompanied by ameliorated pathological state. Lastly, the PI3K/AKT/mTOR pathway both in fractured osteoblasts and femurs was activated by 3-methyladenine and inhibited by rapamycin and β-ecdysterone.

Conclusion

β-ecdysterone might facilitate fracture healing by activating autophagy through suppressing PI3K/AKT/mTOR signal pathway.
In-Cell Sensitivity-Enhanced NMR of Intact Living Mammalian Cells
Authors: Ghosh Rupam , Xiao Yiling , Kragelj Jaka , Frederick Kendra K.
Published: May 2021

NMR has the resolution and specificity to determine atomic-level protein structures of isotopically-labeled proteins in complex environments and, with the sensitivity gains conferred by dynamic nuclear polarization (DNP), NMR has the sensitivity to detect proteins at their endogenous concentrations. However, DNP sensitivity enhancements are critically dependent on experimental conditions and sample composition. While some of these conditions are theoretically compatible with cellular viability, the effects of others on cellular sample integrity are unknown. Uncertainty about the integrity of cellular samples limits the utility of experimental outputs. Using several measures, we establish conditions that support DNP enhancements that can enable detection of micromolar concentrations of proteins in experimentally tractable times that are compatible with cellular viability. Taken together, we establish DNP assisted MAS NMR as a technique for structural investigations of biomolecules in intact viable cells that can be phenotyped both before and after NMR experiments.

Classification

Biophysics and Structural Biology
Development and applications of sialoglycan-recognizing probes (SGRPs) with defined specificities: exploring the dynamic mammalian sialoglycome
Authors: Srivastava Saurabh , Verhagen Andrea , Sasmal Aniruddha , Wasik Brian R. , Diaz Sandra , Yu Hai , Bensing Barbara A. , Khan Naazneen , Khedri Zahra , Secrest Patrick , Sullam Paul , Varki Nissi , Chen Xi , Parrish Colin R. , Varki Ajit
Published: May 2021

Glycans that are abundantly displayed on vertebrate cell surface and secreted molecules are often capped with terminal sialic acids (Sias). These diverse 9-carbon-backbone monosaccharides are involved in numerous intrinsic biological processes. They also interact with commensals and pathogens, while undergoing dynamic changes in time and space, often influenced by environmental conditions. However, most of this sialoglycan complexity and variation remains poorly characterized by conventional techniques, which often tend to destroy or overlook crucial aspects of Sia diversity and/or fail to elucidate native structures in biological systems i.e., in the intact sialome. To date, in situ detection and analysis of sialoglycans has largely relied on the use of plant lectins, sialidases or antibodies, whose preferences (with certain exceptions) are limited and/or uncertain. We took advantage of naturally-evolved microbial molecules (bacterial adhesins, toxin subunits and viral hemagglutinin-esterases) that recognize sialoglycans with defined specificity to delineate 9 classes of Sialoglycan Recognizing Probes (SGRPs: SGRP1–SGRP9) that can be used to explore mammalian sialome changes in a simple and systematic manner, using techniques common in most laboratories. SGRP candidates with specificity defined by sialoglycan microarray studies were engineered as tagged probes, each with a corresponding non-binding mutant probe as a simple and reliable negative control. The optimized panel of SGRPs can be used in methods commonly available in most bioscience labs, such as ELISA, Western Blot, flow cytometry and histochemistry. To demonstrate the utility of this approach, we provide examples of sialoglycome differences in tissues from C57BL/6 wild type mice and human-like Cmah−/− mice.
Differential transcriptomic response ofAnopheles arabiensistoPlasmodium vivaxandPlasmodium falciparuminfection
Authors: Tsapi Majoline Tchioffo , Kornobis Etienne , Puchot Nicolas , English Solomon , Proux Caroline , Goupeyou-Youmsi Jessy , Sakuntabhai Anavaj , Marie-Agnes-Dillies  , Milijaona Randrianarivelojosia , Girod Romain , Ndiath Mamadou Ousmane , Bourgouin Catherine
Published: May 2021

Plasmodium vivaxmalaria is now recognized as the second most dangerous parasitic threat to human health with the regular decrease ofPlasmodium falciparumworldwide over recent decades. A very limited numbers of studies address the interaction ofP. vivaxwith itsAnophelesmosquito vectors. Those studies were conducted inP. vivaxendemic countries withP.vivaxlocal major vectors for which limited genomic and genetic tools are available. Despite the presence ofP. vivaxin several African countries and increasing reports on its occurrence in many others, there is virtually no data on the molecular responses ofAnopheles arabiensis,a major African mosquito vector, toP. vivax, which limits the development of further “mosquito-targeted” interventions aimed at reducingP. vivaxtransmission. Taking advantage of the situation of Madagascar whereP. falciparum,P. vivaxandAn. arabiensisare present, we explore the molecular responses ofAn. arabiensistowards these two human malaria parasites. RNA sequencing on RNAs isolated from mosquito midguts dissected at the early stage of infection (24 hours) was performed using mosquitoes fed on the blood ofP. vivaxandP. falciparumgametocyte carriers in a field station. From ade novoassembly ofAn. arabiensismidgut total RNA transcriptome, the comparative analysis revealed that a greater number of genes were differentially expressed in the mosquito midgut in response toP. vivax(209) than toP. falciparum(81). Among these, 15 common genes were identified to be significantly expressed in mosquito midgut 24 hours after ingestingP. vivaxandP. falciparumgametocytes, including immune responsive genes and genes involved in amino-acid detoxification pathways. Importantly, working with both wild mosquitoes and field circulating parasites, our analysis revealed a strong mosquito genotype by parasite genotype interaction. Our study also identified 51 putative long non-coding RNAs differentially expressed inAn. arabiensismosquito infected midgut. Among these, several mapped to the publishedAn. arabiensisgenome at genes coding immune responsive genes such as gambicin 1, leucine-rich repeat containing genes, either on sense or antisense strands.

This study constitutes the first comparison ofAn. arabiensismolecular interaction withP. vivaxandP. falciparum, investigating both coding and long non-coding RNAs for the identification of potential transcripts, that could lead to the development of novel approaches to simultaneously block the transmission ofvivaxandfalciparummalaria.
Elucidating Tumor-stromal Metabolic Crosstalk in Colorectal Cancer through Integration of Constraint-Based Models and LC-MS Metabolomics
Authors: Wang Junmin , Delfarah Alireza , Gelbach Patrick , Fong Emma , Macklin Paul , Mumenthaler Shannon M. , Graham Nicholas A. , Finley Stacey
Published: May 2021

Colorectal cancer (CRC) is a major cause of morbidity and mortality in the United States. Tumor-stromal metabolic crosstalk in the tumor microenvironment promotes CRC development and progression, but exactly how stromal cells, in particular cancer-associated fibroblasts (CAFs), affect the metabolism of tumor cells remains unknown. Here we take a data-driven approach to investigate the metabolic interactions between CRC cells and CAFs, integrating constraint-based modeling and metabolomic profiling. Using metabolomics data, we perform unsteady-state parsimonious flux balance analysis to infer flux distributions for central carbon metabolism in CRC cells treated with or without CAF-conditioned media. We find that CAFs reprogram CRC metabolism through stimulation of glycolysis, the oxidative arm of the pentose phosphate pathway (PPP), and glutaminolysis as well as inhibition of the tricarboxylic acid cycle. To identify potential therapeutic targets, we simulate enzyme knockouts and find that inhibiting the hexokinase and glucose-6-phosphate dehydrogenase reactions exploits the CAF-induced dependence of CRC cells on glycolysis and oxidative PPP. Our work gives mechanistic insights into the metabolic interactions between CRC cells and CAFs and provides a framework for testing hypotheses towards CRC-targeted therapies.
Chimeric RNA:DNA Donorguide Improves HDR in vitro and in vivo
Authors: Simone Brandon W. , Lee Han B. , Daby Camden L. , Restrepo-Castillo Santiago , Martínez-Gálvez Gabriel , Ata Hirotaka , Gendron William A.C. , Clark Karl J. , Ekker Stephen C.
Published: May 2021

Introducing small genetic changes to study specific mutations or reverting clinical mutations to wild type has been an area of interest in precision genomics for several years. In fact, it has been found that nearly 90% of all human pathogenic mutations are caused by small genetic variations, and the methods to efficiently and precisely correct these errors are critically important. One common way to make these small DNA changes is to provide a single stranded DNA (ssDNA) donor containing the desired alteration together with a targeted double-strand break (DSB) at the genomic target. The donor is typically flanked by regions of homology that are often ~30-100bp in length to leverage the homology directed repair (HDR) pathway. Coupling a ssDNA donor with a CRISPR-Cas9 to produce a targeted DSB is one of the most streamlined approaches to introduce small changes. However, in many cell types this approach results in a low rate of incorporation of the desired alteration and has undesired imprecise repair at the 5’ or 3’ junction due to artifacts of the DNA repair process. We herein report a technology that couples the spatial temporal localization of an ssDNA repair template and leverages the nucleic acid components of the CRISPR-Cas9 system. We show that by direct fusion of an ssDNA template to the trans activating RNA (tracrRNA) to generate an RNA-DNA chimera, termed Donorguide, we recover precise integration of genetic alterations, with both increased integration rates and decreased imprecision at the 5’ or 3’ junctions relative to an ssODN donor in vitro in HEK293T cells as well as in vivo in zebrafish. Further, we show that this technology can be used to enhance gene conversion with other gene editing tools such as TALENs.
Integration and comparison of multi-omics profiles of NGLY1 deficiency plasma and cellular models to identify clinically relevant molecular phenotypes
Authors: Chen Songjie , Wang Guangwen , Shen Xiaotao , Hornburg Daniel , Rego Shannon , Hoffman Rene , Nevins Stephanie , Cheng Xun , Snyder Michael
Published: May 2021

NGLY1 (N-glycanase 1) deficiency is a rare congenital recessive disorder of protein deglycosylation unaddressed by the current standard of care. Using combined metabolomics and proteomics profiling, we show that NGLY1 deficiency activates the immune response and disturbs lipid metabolism, biogenic amine synthesis, and glutathione metabolism. These alterations were also observed in NGLY1 deficient patient-derived induced pluripotent stem cells (iPSCs) and differentiated neural progenitor cells (NPCs), which serve as personalized cellular models of the disease. These findings provide molecular insight into the pathophysiology of NGLY1 deficiency and suggest potential therapeutic strategies.
Seeing beyond the target: Leveraging off-target reads in targeted clinical tumor sequencing to identify prognostic biomarkers
Authors: Mangul Serghei , Brito Jaqueline J , Groha Stefan , Zaitlen Noah , Gusev Alexander
Published: May 2021

Clinical tumor sequencing is rapidly becoming a standard component of clinical care, providing essential information for selecting amongst treatment options and providing prognostic value. Here we develop a robust and scalable software platform (SBT: Seeing Beyond the Target) that mines discarded components of clinical sequences to produce estimates of a rich set of omics features including rDNA and mtDNA copy number, microbial species abundance, and T and B cell receptor sequences. We validate the accuracy of SBT via comparison to multimodal data from the TCGA and apply SBT to a tumor panel cohort of 2,920 lung adenocarcinomas to identify associations of clinical value. We replicated known associations of somatic events in TP53 with changes in rDNA (p=0.012); as well as diversity of BCR and TCR repertoires with the biopsy site (p=2.5×10−6, p<10−20). We observed striking differences in EGFR mutant lung cancers versus wild-type, including higher rDNA copy number and lower immune repertoire diversity. Integrating clinical outcomes, we identified significant prognostic associations with overall survival, including SBT estimates of 5S rDNA (p=1.9×10−4, hazard ratio = 1.22) and TCR diversity (p=2.7×10−3, hazard ratio=1.77). Both novel survival associations replicated in 1,302 breast carcinoma and 1,651 colorectal cancer tumors. We anticipate that feature estimates derived by SBT will yield novel biomarker hypotheses and open research opportunities in existing and emerging clinical tumor sequencing cohorts.
Structural basis of polyamine transport by human ATP13A2 (PARK9)
Authors: Sim Sue Im , von Bülow Sören , Hummer Gerhard , Park Eunyong
Published: May 2021

Polyamines are small, organic polycations that are ubiquitous and essential to all forms of life. Currently, how polyamines are transported across membranes is not understood. Recent studies have suggested that ATP13A2 and its close homologs, collectively known as P5B-ATPases, are polyamine transporters at endo-/lysosomes. Loss-of-function mutations of ATP13A2 in humans cause hereditary early-onset Parkinson’s disease. To understand the polyamine transport mechanism of ATP13A2, we determined high-resolution cryo-EM structures of human ATP13A2 in five distinct conformational intermediates, which together represent a near-complete transport cycle of ATP13A2. The structural basis of the polyamine specificity was revealed by an endogenous polyamine molecule bound to a narrow, elongated cavity within the transmembrane domain. The structures show an atypical transport path for a water-soluble substrate, where polyamines may exit within the cytosolic leaflet of the membrane. Our study provides important mechanistic insights into polyamine transport and a framework to understand functions and mechanisms of P5B-ATPases.

Highlights

Cryo-EM structures of human ATP13A2 in five distinct conformations at 2.5–3.7 Å resolutions.

Unique features of ATP13A2 in comparison to other P-type ATPases.

Structure of the substrate-binding pocket of ATP13A2 and the molecular basis of polyamine binding.

Conformational changes along the transport cycle and proposed model for polyamine transport.
A Role for Synaptonemal Complex in Meiotic Mismatch Repair
Authors: Voelkel-Meiman Karen , Oke Ashwini , Feil Arden , Shames Alexander , Fung Jennifer , MacQueen Amy
Published: May 2021

During meiosis a large subset of interhomolog recombination repair intermediates form within the physical context of the synaptonemal complex (SC), a protein-rich structure assembled at the interface of aligned homologous chromosomes. However, the functional relationship between SC structure and homologous recombination remains poorly defined. In prior work we determined that tripartite SC is dispensable for recombination in S. cerevisiae; SC central element proteins Ecm11 and Gmc2 instead limit the number of recombination events. Here we report that while dispensable for recombination per se, SC central element proteins influence the processing of interhomolog recombination intermediates in a manner that minimizes errors in mismatch correction. Failure to correct mis-paired bases within heteroduplex at meiotic recombination sites leads to genotypically sectored colonies (post meiotic segregation events) arising from mitotic proliferation of mismatch-containing spores. We discovered an increase in post-meiotic segregation at the THR1 locus in cells lacking Ecm11 or Gmc2, or in the SC-deficient but crossover recombination-proficient zip1[Δ21-163] mutant. High-throughput sequencing of octad meiotic products revealed a genome-wide increase in recombination events with uncorrected mismatches in ecm11 mutants relative to wild type. Meiotic cells missing Ecm11 also display longer gene conversion tracts, but tract length alone does not account for the higher frequency of uncorrected mismatches. Interestingly, the per-nucleotide mismatch frequency is elevated in ecm11 mutants when analyzing all gene conversion tracts, but is similar between wild type and ecm11 if one considers only those events with uncorrected mismatches. Our data suggest that a subset of recombination events is similarly susceptible to mismatch repair errors in both wild type and ecm11 strains, but in ecm11 mutants many more recombination events fall into this inefficient repair category. Finally, we observe elevated post-meiotic segregation at THR1 in mutants with a dual deficiency in MutSγ-mediated crossover recombination and SC assembly, but not in the mlh3 mutant, which lacks MutSγ crossovers but has abundant SC. We propose that SC structure promotes efficient mismatch repair of joint molecule recombination intermediates resolved via both MutSγ-associated and MutSγ-independent pathways, and is the molecular basis for elevated post-meiotic segregation in both MutSγ crossover-proficient (ecm11, gmc2) and MutSγ crossover-deficient (msh4, zip3) strains.
A Longitudinal Study of Antimicrobial Resistance inEnterococcusspp. Isolated from a Beef Processing Plant and Retail Ground Beef
Authors: Holman Devin B. , Klima Cassidy L. , Gzyl Katherine E. , Zaheer Rahat , Service Cara , Jones Tineke H. , McAllister Tim A.
Published: May 2021

Antimicrobial use in food-producing animals has come under increasing scrutiny due to its potential association with antimicrobial resistance (AMR). Monitoring of AMR in indicator microorganisms such asEnterococcusspp. in meat production facilities and retail meat products can provide important information on the dynamics and prevalence of AMR in these environments. In this study, swabs or samples were obtained from various locations in a commercial beef packing operation (n = 600 total) and from retail ground beef (n = 60) over a 19-month period. All samples/swabs were enriched forEnterococcusspp. and suspected enterococci isolates were identified using species-specific PCR primers.Enterococcus faecaliswas the most frequently isolated species followed byEnterococcus hirae,which was found mostly on hides and ground beef.Enterococcus faecium(n = 9) andE.faecalis(n = 120) isolates were further characterized for antimicrobial resistance and resistant genes due to the clinical significance of these species. Twenty-one unique AMR profiles were identified, with 90% of isolates resistant to at least two antimicrobials, and two that were resistant to nine antimicrobials. Tetracycline resistance was observed most often inE.faecalis(28.8%) and was likely mediated bytet(M). Genomic analysis of selectedE.faecalisandE.faeciumisolates revealed that many of the isolates in this study clustered with other publicly available genomes from ground beef, suggesting that these strains are well adapted to the beef packaging environment.

IMPORTANCE

Antimicrobial resistance (AMR) is a serious challenge facing the agricultural industry. Understanding the flow of antimicrobial resistant-bacteria through the beef fabrication process and into ground beef is an important step in identifying intervention points for reducing AMR. In this study we used enterococci as indicator bacteria for monitoring AMR in a commercial beef packaging facility and in retail ground beef over a 19-month period. Although washing of carcasses post-hide removal reduced the isolation frequency ofEnterococcusspp., a number of antimicrobial resistant-Enterococcus faecalisisolates were recovered from ground beef produced in the packaging plant. Genome analysis showed that severalE.faecalisisolates were genetically similar to publicly available isolates recovered from retail ground beef in the United States.
Structural basis for recognition of anti-migraine drug lasmiditan by the serotonin receptor 5-HT1F–G protein complex
Authors: Huang Sijie , Xu Peiyu , Tan Yangxia , You Chongzhao , Zhang Yumu , Jiang Yi , Xu H. Eric
Published: May 2021

Migraine headache has become global pandemics and is the number one reason of work day loss. The most common drugs for anti-migraine are the triptan class of drugs that are agonists for serotonin receptors 5-HT1B and 5-HT1D. However, these drugs have side effects related to vasoconstriction that could have fatal consequences of ischemic heart disease and myocardial infarction. Lasmiditan is a new generation of anti-migraine drug that selectively binds to the serotonin receptor 5-HT1F due to its advantage over the tripan class of anti-migraine drugs. Here we report the cryo-EM structure of the 5-HT1F in complex with Lasmiditan and the inhibitory G protein heterotrimer. The structure reveals the mechanism of 5-HT1F-selective activation by Lasmiditan and provides a template for rational design of anti-migraine drugs.
Genome of the giant panda roundworm illuminates its host shift and parasitic adaptation
Authors: Xie Yue , Wang Sen , Wu Shuangyang , Gao Shenghan , Meng Qingshu , Wang Chengdong , Lan Jingchao , Luo Li , Zhou Xuan , Xu Jing , Gu Xiaobin , He Ran , Yang Zijiang , Peng Xuerong , Hu Songnian , Yang Guangyou
Published: May 2021

Baylisascaris schroederi, a bamboo-feeding giant panda (Ailuropoda melanoleuca)-specific roundworm (ascaridoid) parasite, is the causative agent of baylisascariasis, which represents a leading reason for the mortality of wild giant panda populations and therefore poses a significant threat to giant panda conservation. Here we present a 293-Mb chromosome-level genome assembly ofB. schroederito inform its biology, including host adaptations. Comparative genomics revealed an evolutionary trajectory accompanied by host-shift events in ascaridoid parasite lineages after host separations, suggesting their potential transmissions and fast adaptations to hosts. Genomic and anatomical lines of evidence, including expansion and positive selection of genes related to cuticle and basal metabolisms, indicates thatB. schroederiundergoes specific adaptations to survive in the sharp-edged bamboo enriched gut of giant panda by structurally increasing its cuticle thickness and efficiently utilizing host nutrients during gut parasitism. Also, we characterized the secretome and predicted potential drug and vaccine targets for new interventions. Overall, this genome resource provides new insights into the host adaptation ofB. schroederito giant panda as well as the host-shift events in ascaridoid parasite lineages. These findings also add to our knowledge on the unique biology of the giant panda roundworm and aid the development of much-needed novel strategies for the control of baylisascariasis and thus the protection of giant panda populations.
Refining conformational ensembles of flexible proteins against small-angle X-ray scattering data
Authors: Pesce Francesco , Lindorff-Larsen Kresten
Published: May 2021

Intrinsically disordered proteins and flexible regions in multi-domain proteins display substantial conformational heterogeneity. Characterizing the conformational ensembles of these proteins in solution typically requires combining one or more biophysical techniques with computational modelling or simulations. Experimental data can either be used to assess the accuracy of a computational model or to refine the computational model to get a better agreement with the experimental data. In both cases, one generally needs a so-called forward model, i.e. an algorithm to calculate experimental observables from individual conformations or ensembles. In many cases, this involve one or more parameters that need to be set, and it is not always trivial to determine the optimal values or to understand the impact on the choice of parameters. For example, in the case of small-angle X-ray scattering (SAXS) experiments, many forward models include parameters that describe the contribution of the hydration layer and displaced solvent to the background-subtracted experimental data. Often, one also needs to fit a scale factor and a constant background for the SAXS data, but across the entire ensemble. Here, we present a protocol to dissect the effect of free-parameters on the calculated SAXS intensities, and to identify a reliable set of values. We have implemented this procedure in our Bayesian/Maximum Entropy framework for ensemble refinement, and demonstrate the results on four intrinsically disordered proteins and a three-domain protein connected by flexible linkers. Our results show that the resulting ensembles can depend on the parameters used for solvent effects, and suggests that these should be chosen carefully. We also find a set of parameters that work robustly across all proteins.

SIGNIFICANCE

The flexibility of a protein is often key to its biological function, yet understanding and characterizing its conformational heterogeneity is difficult. We here describe a robust protocol for combining small-angle X-ray scattering experiments with computational modelling to obtain a conformational ensemble. In particular, we focus on the contribution of protein hydration to the experiments and how this is included in modelling the data. Our resulting algorithm and software should make modelling intrinsically disordered proteins and multi-domain proteins more robust, thus aiding in understanding the relationship between protein dynamics and biological function.
Are plants in sown flower strips suitable for communities of wild bees? Pollination network approach in conservation biology
Authors: Hadrava Jiří , Talašová Anna , Straka Jakub , Benda Daniel , Kazda Jan , Klečka Jan
Published: May 2021

Drastic reductions of insect diversity and abundance are observed in the highly fragmented agricultural landscapes of central Europe. Declines of pollinators may have detrimental effects on the reproduction of wild insect-pollinated plants as well as the yield of crops. In order to mitigate such impacts, sown flower strips on arable land within Agri-Environment Climate Schemes (AECS) are supported across EU countries. However, it is not clear whether sown flower strips provide equivalent benefits to wild flower-visiting insects as semi-natural habitats.

Here, we apply plant-pollinator network approach to evaluate the function of sown flower strips for the communities of wild bees. We compared the structural characteristics and the robustness of plant-pollinator networks in sown flower strips and nearby semi-natural habitats. We also quantified the importance of individual plant species for bees based on simulations of plant-pollinator extinction cascades.

We found that assemblages of plants and pollinators were less diverse in sown flower strips than in semi-natural habitats, more generalized, and more nested. However, we did not find any significant differences in network robustness to plant-pollinator coextinctions. Further, simulations revealed a large variation in the functional importance among plant species from both habitats.

We conclude that although the analysis of network robustness suggested that plants in the sown flower strips and semi-natural habitats were functionally equivalent, this masked important differences among the two habitats. From the conservation point of view, semi-natural habitats were superior in supporting a more diverse community of solitary bees and bumblebees.
Automated segmentation of insect anatomy from micro-CT images using deep learning
Authors: Toulkeridou Evropi , Gutierrez Carlos Enrique , Baum Daniel , Doya Kenji , Economo Evan P.
Published: May 2021

Three-dimensional (3D) imaging, such as micro-computed tomography (micro-CT), is increasingly being used by organismal biologists for precise and comprehensive anatomical characterization. However, the segmentation of anatomical structures remains a bottleneck in research, often requiring tedious manual work. Here, we propose a pipeline for the fully-automated segmentation of anatomical structures in micro-CT images utilizing state-of-the-art deep learning methods, selecting the ant brain as a test case. We implemented the U-Net architecture for 2D image segmentation for our convolutional neural network (CNN), combined with pixel-island detection. For training and validation of the network, we assembled a dataset of semi-manually segmented brain images of 94 ant species. The trained network predicted the brain area in ant images fast and accurately; its performance tested on validation sets showed good agreement between the prediction and the target, scoring 80% Intersection over Union (IoU) and 90% Dice Coefficient (F1) accuracy. While manual segmentation usually takes many hours for each brain, the trained network takes only a few minutes. Furthermore, our network is generalizable for segmenting the whole neural system in full-body scans, and works in tests on distantly related and morphologically divergent insects (e.g., fruit flies). The latter suggest that methods like the one presented here generally apply across diverse taxa. Our method makes the construction of segmented maps and the morphological quantification of different species more efficient and scalable to large datasets, a step toward a big data approach to organismal anatomy.
Interpretable Deep Learning for Breast Cancer Cell Phenotyping Using Diffraction Images from Lens-Free Digital In-Line Holography
Authors: Song Tzu-Hsi , Cao Mengzhi , Min Jouha , Im Hyungsoon , Lee Hakho , Lee Kwonmoo
Published: May 2021

Lens-free digital in-line holography (LDIH) offers a wide field of view at micrometer-scale resolution, surpassing the capabilities of lens-based microscopes, making it a promising diagnostic tool for high-throughput cellular analysis. However, the complex nature of holograms renders them challenging for human interpretation, necessitating time- consuming computational processing to reconstruct object images. To address this, we present HoloNet, a novel deep learning architecture specifically designed for direct analysis of holographic images from LDIH in cellular phenotyping. HoloNet extracts both global features from diffraction patterns and local features from convolutional layers, achieving superior performance and interpretability compared to other deep learning methods. By leveraging raw holograms of breast cancer cells stained with well-known markers ER/PR and HER2, HoloNet demonstrates its effectiveness in classifying breast cancer cell types and quantifying molecular marker intensities. Furthermore, we introduce the feature-fusion HoloNet model, which extracts diffraction features associated with breast cancer cell types and their marker intensities. This hologram embedding approach allows for the identification of previously unknown subtypes of breast cancer cells, facilitating a comprehensive analysis of cell phenotype heterogeneity, leading to precise breast cancer diagnosis.
The satiating power of sustainability: the effect of package sustainability on perceived satiation of healthy food
Authors: Donato Carmela , Barone Ada Maria , Romani Simona
Published: May 2021

Purpose

This research investigates the influence of package sustainability on food satiation perception.

Design/methodology/approach

Research hypotheses were tested through three experimental studies.

Findings

Three experimental studies show that food quality is associated to higher perceived food satiation (preliminary study); that a food packaged in a sustainable package is perceived as more satiating than the same food packaged in a non-sustainable package and that this effect is explained by the higher perceived quality triggered by the presence of a sustainable package (Study 1); and that the positive relationship between higher perceived quality and perceived satiation is verified only for healthy but not for unhealthy foods (Study 2).

Originality/value

The present research advances knowledge on the highly debated issue of sustainable food packages. By proposing that consumers might perceive a healthy food presented in a sustainable package as more satiating, the authors show another extrinsic packaging cue modifying consumers' perception, namely package sustainability.
How to use spontaneous customer comments to identify nonlinear background of satisfaction with restaurant services
Authors: Tontini Gerson , Irgang Luís , Kroenke Adriana , Hadlich Ivan , Picolo Jaime Dagostim , Mikulic Josip
Published: May 2021

Purpose

The purpose of this study is to demonstrate how to use customer spontaneous comments to identify which aspects influence the overall customer satisfaction with restaurant services from a nonlinear perspective.

Design/methodology/approach

The authors collected data from 399 spontaneous comments about a chain of fast-food restaurants in Brazil. The comments are freely available on the TripAdvisor portal and were extracted and classified according to seven dimensions related to the quality of services: tangibles, reliability, responsiveness, assurance, empathy, quality of the food and price. Next, the authors combine the critical incident technique (CIT) and the penalty-reward contrast analysis (PRCA) to investigate the nonlinear relationship between service quality assessment and overall customer satisfaction.

Findings

The method of integrating CIT with PRCA explains 64.7% of the variation in the customer's assessment of the services provided (RAdj2 = 0.647). This shows that spontaneous comments from customers are related to their overall satisfaction with the service provided. Besides, the findings suggest that consumers tend to comment more about positive than negative experiences regarding aspects related to food, attendants' empathy and service assurance, and more negative comments about aspects related to responsiveness and price. However, it was found that negative comments have a stronger influence on overall satisfaction than positive comments.

Originality/value

Using comments available for free on the Internet and evaluating how positive and negative comments can jointly influence customer satisfaction, the proposed methodology demonstrates how restaurants can use their customers' spontaneous comments to identify critical aspects to be managed and improved. To the best of authors’ knowledge, this is the first study presenting how restaurants can use customer spontaneous comments, freely available on the internet, to identify the relevance of different aspects of the services provided from a nonlinear perspective. In addition, the present study shows that although customers spontaneously tend to share more positive than negative comments about restaurant services, events related to negative experiences have a stronger influence on overall satisfaction.
Experimental validation of numerical simulations of free-surface flow within casting mould cavities
Authors: Bublík Ondřej , Lobovský Libor , Heidler Václav , Mandys Tomáš , Vimmr Jan
Published: May 2021

Purpose

The paper targets on providing new experimental data for validation of the well-established mathematical models within the framework of the lattice Boltzmann method (LBM), which are applied to problems of casting processes in complex mould cavities.

Design/methodology/approach

An experimental campaign aiming at the free-surface flow within a system of narrow channels is designed and executed under well-controlled laboratory conditions. An in-house lattice Boltzmann solver is implemented. Its algorithm is described in detail and its performance is tested thoroughly using both the newly recorded experimental data and well-known analytical benchmark tests.

Findings

The benchmark tests prove the ability of the implemented algorithm to provide a reliable solution when the surface tension effects become dominant. The convergence of the implemented method is assessed. The two new experimentally studied problems are resolved well by simulations using a coarse computational grid.

Originality/value

A detailed set of original experimental data for validation of computational schemes for simulations of free-surface gravity-driven flow within a system of narrow channels is presented.
Developing corporate social responsibility in financial services
Authors: Deigh Linda , Farquhar Jillian Dawes
Published: May 2021

Purpose

The purpose of this study is to contribute to the theory and practice of financial services marketing in sub-Saharan Africa (sSA) by investigating how financial service providers are developing corporate social responsibility (CSR) practices, in particular, seeking to uncover the involvement of stakeholders.

Design/methodology/approach

Following an interpretivist approach, the study uncovers fresh and context-rich insights through an analysis of a multiple case study consisting of retail banks in Ghana. Data consist of semi-structured interviews with senior managers and analysis of documents and archives.

Findings

The study uncovers three key CSR practices practised by the retail banks: giving, community and corporate reputation/brand with which their stakeholders are only to some extent involved. Banks not as yet drawing extensively on stakeholder resources for CSR practices.

Research limitations/implications

The study uses an inductive and in-depth approach to explore contextual insights into CSR, but with subsequent limitations on how far the findings can be extended.

Practical implications

The study offers outline for financial services marketing involving stakeholders in CSR.

Social implications

It discovers that banks acquire social capital through their CSR activities in the community.

Originality/value

The study contributes to financial services marketing theory and practice through an evidence-based framework uncovering the development of CSR through practices that as yet draw on stakeholder resources to a limited extent. Research suggests that CSR practices are dynamic and subject to a range of situational conditions.
Modeling the Big Data challenges in context of smart cities – an integrated fuzzy ISM-DEMATEL approach
Authors: Khan Mohd Imran , Khan Shahbaz , Khan Urfi , Haleem Abid
Published: May 2021

Purpose

Big Data can be utilised for efficient use of resources and to provide better services to the resident in order to enhance the delivery of urban services and create sustainable build environment. However, the adoption of Big Data faces many challenges at the implementation level. Therefore, the purpose of this paper is to identify the challenges towards the efficient application of Big Data in smart cities development and analyse the inter-relationships.

Design/methodology/approach

The 14 Big Data challenges are identified through the literature review and validated with the expert’s feedback. After that the inter-relationships among the identified challenges are developed using an integrated approach of fuzzy Interpretive Structural Modelling (fuzzy-ISM) and fuzzy Decision-Making Trial and Evaluation Laboratory (fuzzy-DEMATEL).

Findings

Evaluation of interrelationships among the challenges suggests that diverse population in smart cities and lack of infrastructure are the significant challenges that impede the integration of Big Data in the development of smart cities.

Research limitations/implications

This study will enable practitioners, policy planners involved in smart city projects in tackling the challenges in an optimised manner for the hindrance free and accelerated development of smart cities.

Originality/value

This research is an initial effort to develop an interpretive structural model of Big Data challenges for smart cities development which gives a clearer picture of how the identified challenges interact with each other.