bluuebunny/crossref_metadata_2025 huggingface dataset:
Nesterenkonia salmonea sp. nov. and Nesterenkonia sphaerica sp. nov., isolated from the Southern Atlantic Ocean
Authors: Zhang Gaiyun , Wang Lina , Xie Fuquan , Pei Shengxiang , Jiang Li
Published: November 2019

Two Gram-positive, aerobic, non-motile and non-spore-forming actinobacteria, strains GY074Tand GY239T, were isolated from deep-sea sediment of the Southern Atlantic Ocean. The results of phylogenetic analysis of 16S rRNA gene sequences placed both isolates within the genusNesterenkonia, and showed a sequence similarity of 98.3 % between the two strains and similarites of 94.3–97.2 % with respect toNesterenkoniaspecies with validly published names. Based on whole-genome sequences, the values ofin silicoDNA–DNA hybridization and the average nucleotide identity between strains GY074Tand GY239Twere 21.2 and 78.1 %, respectively, less than the proposed cut-off level for species delineation, i.e. 70 and 95 %. For both strains, the major cellular fatty acids were anteiso-C17 : 0and anteiso-C15 : 0, and the major menaquinones were MK-7, MK-8 and MK-9. The major polar lipid contents of the two strains were similar with phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol and an unidentified glycolipid. The genomic DNA G+C contents of strains GY074Tand GY239Twere 61.1 and 64.2 mol%, respectively. On the basis of the phylogenetic analysis and physiological and chemotaxonomic data, the isolates represent two novel species of the genusNesterenkonia, for which the namesNesterenkonia salmoneasp. nov. (type strain GY074T=KCTC 39639T=MCCC 1A11256T) andNesterenkonia sphaericasp. nov. (type strain GY239T=KCTC 39640T=MCCC 1A10688T) are proposed.
수확 후 온도 처리에 따른 방울토마토의 저장 중 품질 변화
Authors: Park Kyung Min , Kim Hyo Jin , Kim Sang Seoup , Lee Sang Bong , Jeong Mooncheol , Park Kee Jai , Koo Minseon
Published: November 2019

Heat accumulation in the field accelerates softening and shortens the shelf life of cherry tomatoes. The purpose of this study was to investigate the effect of temperature treatment after harvest on the postharvest quality and microbial communities of cherry tomatoes. Regarding fruit quality properties, a 10℃ treatment after harvest caused a delay in increasing weight loss, firmness, electrolyte leakage and decay rate. After the temperature treatment, an approximately 1-2 log reduction on total viable cells, fungi, Enterobacteriaceae and coliforms was observed in the 10℃ treatment group compared with those at 20 and 30℃. However, total viable cells and decay rate remarkably increased at 10℃ treatment after 26 days. The microbial communities of cherry tomatoes in intitial day after temperature treatment were composed mainly of Staphylococcus xylosus or Bacillus pumilus. During storage, the relative abundance of Staphylococcus xylosus and Bacillus pumilus decreased while Pseudomonas fluorescens, Rahnella aquatilis and Leuconostoc mesenteroid increased during late storage. The rapid increase of total aerobic cells and decay rate in the 10℃ treatment group may be associated with a marked increase in Pseudomonas fluorescens. The results from this study demonstrate the effectiveness of pre-cooling to suppress the softening and indicate an impact on microbial community composition and dynamics during storage.
Effect of squid hydrolysate and squid powder on the quality characteristics of dried noodles with squid
Authors: Jang Mi-Soon , Park Ji-In , Jeong Yeon Gyeom , Shim Kil Bo
Published: November 2019

This study aimed the quality characteristics of dried noodles with squid (SDN) using squid enzyme hydrolysate and steamed and dried squid powder (SP) to obtain basic data for developing SDN with excellent taste, flavor and nutritive value. Since commercially available squid enzyme hydrolysates containing protease NP (P-NP) display high values of protein yield, °brix, and degree of hydrolysis, P-NP was used herein for squid hydrolysis. SP obtained through steaming for 20-30 min at 100℃ and then drying (50-65℃) to obtain a high yield of unsaturated fatty acids and free amino acids. SDN were prepared using 0, 5, 10, 15 and 20% SP and 45% SH on a wheat-flour basis. The SDN had higher crude protein and crude lipid contents than the control(not treated with SH and SP). The L value was lower in the SDN than in the control, while the a and b values significantly increased with an increase in SP content (p<0.05). Cooking properties (including weight, volume, and water absorption) and turbidity were significantly enhanced in the SDN rather than the control (p<0.05). The taurine content of SDN increased with an increase in SP content (p<0.05). The odor intensity significantly increased in the SDN rather than the control (p<0.05). The present results indicate that it is possible to prepare SDN in consideration of the health and flavor preference of consumers.
High production of GABA in Pyrus ussuriensis Maximowicz fruit extract by mixed fermentation of lactic acid bacteria
Authors: Choe Ji-Yeon , Lee Sam-Pin
Published: November 2019

γ-Aminobutyric acid (GABA) was produced by the sequential fermentation of the fruit extract of Pyrus ussuriensis Maximowicz (PFE) with two strains of lactic acid bacteria. The soluble solid content of the PFE was 5.25 oBrix and it also displayed a high potassium content of 127.6 mg/100 g. The first lactic acid fermentation of PFE was performed with Leuconostoc citreum S5 at 25℃ for 2 days. Subsequently, the second lactic acid fermentation was carried out with the first fermented PFE fortified with 3% monosodium ʟ-glutamate (MSG) by Lacobacillus plantarum EJ2014 at 30℃ for 5 days. During the first fermentation, the pH of the PFE medium decreased from 4.42 to 4.19 and the acidity increased from 0.28% to 1.03%. After the second fermentation, pH was 4.64 and acidity was 1.23%. The viable cell counts of Lc. citreum S5 and L. plantarum EJ2014 were 7.94 log CFU/mL and 9.18 log CFU/mL, respectively. The amount of the reducing sugar in PFE increased during the first fermentation period and was nearly consumed during the 2nd fermentation. Notably, MSG was successfully converted into 1.78% of GABA during the second fermentation. In conclusion, high yield for production of GABA was achieved by a novel mixed fermentation of lactic acid bacteria, which highlights PFE as a functional food material.
Effect of red beet (Beta vulgaris L.) powder addition on physicochemical and microbial characteristics of tofu
Authors: Lee Kyo-Yeon , Kim Ah-Na , Rahman M. Shafiur , Choi Sung-Gil
Published: November 2019

This study aimed to investigate the enhancing effects of a specified amount of red beet (Beta vulgaris L.) powder on the quality of tofu over existing ones. Thereafter, physicochemical characteristics and microbial safety were compared between tofu prepared addition of red beet powder (RBP) at different concentrations (0.5-2%) and tofu without RBP. No significant differences in sample yield were observed (p>0.05) and, the brix degree and lightness of tofu significantly decreased with an increase in the RBP concentration (p<0.05). Texture analysis revealed that incorporation of RBP significantly increased the hardness of tofu (p<0.05), while the cohesiveness, springiness, and chewiness were not significantly altered. Furthermore, total phenolic content and antioxidant activity of RBP-incorporated tofu were significantly greater than those of untreated tofu on the DPPH radical scavenging assay, ABTS radical scavenging assay, and ferric reducing antioxidant power assay (p<0.05). In the case of microbial safety, RBP-incorporated tofu contained significantly fewer aerobic bacteria and yeast during storage than tofu without RBP (p<0.05). These results suggest that RBP incorporation in tofu increasees its functional quality and shelf-life.
Antioxidant and antibacterial activities of hot water and enzyme extracts from plants containing tannin pigments
Authors: Suh Hwa-Jin , Kim Yeon-Soon , Park Sanggyu , Park Shin
Published: November 2019

The purpose of this study was to investigate the antioxidant and antibacterial activities of hot water and enzyme extracts obtained from plants containing tannin pigments. The antioxidant activities were confirmed by analysis of the total phenolic content, determination of the DPPH and ABTS+ radical scavenging activities and lipid peroxidation experiments. The antibacterial activities were verified using disc diffusion methods against Escherichia coli and Listeria grayi. The IC50 values representing the DPPH radical scavenging activities of the hot water extracts were determined to be 9.4 to 21.5 μg/mL, while the IC50 values of the enzyme extracts were 3.7 to 6.58 μg/mL. It was confirmed that both extracts exhibited a good antioxidant activity comparable to that of ascorbic acid (i.e., 10.5 μg/mL), which is commonly employed for comparison. In addition, the TPC and ABTS+ radical scavenging activities were also significant, and lipid peroxidation experiments demonstrated ≥50% suppression compared to the negative control. Furthermore, the enzyme extracts showed a higher level of activity than the hot water extracts, and the presence of greater quantities of tannin-containing polyphenols in enzyme extracts ensures a high activity even when low extraction temperatures are employed. These results clearly indicate that tannin-containing plant extracts may play an important role in suppressing the free radicals produced by oxidative stress in living organisms, and therefore could exhibit potential for application as new biological materials following additional in-depth research.
Antioxidant and antimicrobial activities of polyphenols isolated from unripe apples (Malus pumila cv. Hongro)
Authors: Choi Ji-Hye , Chung Shin-Kyo
Published: November 2019

Unripe apples are discarded due to thinning out or falling in orchards, however they are abundant in functional ingredients. In this study, polyphenols were efficiently enzymatically extracted and isolated from unripe apples. Enzymatic extraction of polyphenols over 12 hours followed using Viscozyme L with an enzyme concentration of 2%(v/w) based on the total phenolic content. In order to isolate the polyphenols, extracts of unripe apples were eluted with water, 25, 50, 75 and 100% ethanol using Diaion HP-20 gel column chromatography. Polyphenol compounds of each fraction were analyzed by high performance liquid chromatography (HPLC), with the 50% ethanol fraction containing the most polyphenols (387.88 μg/mL of caffeic acid, 226.34 μg/mL of p-coumaric acid, and 187.33 μg/mL of phloridzin). The 50% ethanol fraction also contained the most antioxidants (total penolic and flavonoid content; p<0.05). Antioxidant assays using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, 2,2’-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging activity and ferric ion reducing antioxidant power (FRAP) activity exhibited the highest activities in the 50% ethanol fraction (p<0.05). Antimicrobial activities were also assessed as being highest in 50% ethanol fraction (p<0.05). The 50% ethanol fraction of unripe apple enzyme extracts can be used as a functional polyphenol material to improve the utilization of unripe apple.
Comparison of mineral contents of popular fruit and vegetable varieties in korea
Authors: Lee Sun-kyung , Ji Soo-Hyun , Lee You-Seok , Jo Gyeong-Suk , Kang Jeong-Hwa
Published: November 2019

This study investigated the mineral content of regularly consumed Korean produce in order to provide a basis for informed decisions regarding a balanced diet. Eleven minerals prevalent in the produce were analyzed by microwave digestion coupled with ICP-OES and ICP-MS. In general, vegetables showed a higher mineral content than fruits, with Daekwonseoneon peppers providing th highest values for P, K, and Mg among the 52 varieties of fruits and vegetables examined (79.57 mg/100 g, 638.59 mg/100 g and 37.30 mg/100 g, respectively). Among the 35 fruit varieties analyzed, Geumsil strawberries delivered the highest contents of Ca, P, Mg, Fe, Mn, and Mo (23.52 mg/100 g, 45.29 mg/100 g, 20.05 mg/100 g, 0.87 mg/100 g, 0.58 mg/100 g, 8.44 μg/100 g, respectively). High Ca and K contents were observed in grapes, particularly those of the Shine Muscat varieties (12.28 mg/100 g and 241.42 mg/100 g, respectively) and Jico tomato varieties contained the highest Na content (10.82 mg/100 g). Moreover, notable macro-mineral content was detected in nectarine (Cheonhong, Sunfre, and Fantasia) and baekdo (Cheonjungdo) peach varieties. Apples provided both macro-minerals autumn apples; Jahong, Arisoo, and Hongro and micro-minerals summer apple; SummerKing and Tsugaru with diverse mineral content in same varieties depending on the cultivation area. Based on our findings, a balanced diet containing the necessary contents of macro and micro-minerals can be easily achieved by varying the type and variety of regularly consumed produce.
Replicating Global Brain Connectivity as an Imaging Marker for Depression – Influence of Preprocessing Strategies and Randomized Placebo-Controlled Ketamine Treatment
Authors: Kraus Christoph , Mkrtchian Anahit , Kadriu Bashkim , Nugent Allison C. , Zarate Carlos A. , Evans Jennifer W.
Published: November 2019

Major depressive disorder (MDD) is associated with altered global brain connectivity (GBC), as assessed via resting state functional magnetic resonance imaging (rsfMRI). Previous studies found that antidepressant treatment with ketamine normalized aberrant GBC changes in the prefrontal and cingulate cortices, warranting further investigations of GBC as a putative imaging marker. However, the results were only obtained via global signal regression (GSR). This study is an independent replication of that analysis using a separate dataset. GBC was analyzed in 28 individuals with MDD and 22 healthy controls (HCs) at baseline, post-placebo, and post-ketamine. To investigate the effects of preprocessing, three distinct pipelines were used: 1) regression of white matter (WM)/cerebrospinal fluid (CSF) signals only (BASE); 2) WM/CSF+GSR (GSR); and 3) WM/CSF+physiological parameter regression (PHYSIO). Compared to PHYSIO and BASE regression, GSR reduced Fisher Z-scores (Fz-scores) in large clusters. PHYSIO did not resemble GBC preprocessed with GSR (GBCr). Reduced GBCr was observed in individuals with MDD at baseline in the anterior and medial cingulate cortices, as well as in the prefrontal cortex. Significant results were only found with GSR. Ketamine had no effect compared to baseline or placebo in either group. These results concur with several studies that used GSR to study GBC. Altered GBCr was observed in the cingulate and prefrontal cortices, but ketamine treatment had no effect. Further investigations are warranted into disease-specific components of global fMRI signals that may drive these results and of GBCr as a potential imaging marker in MDD.
DeePaN: A deep patient graph convolutional network integratingclinico-genomic evidence to stratify lung cancers benefiting from immunotherapy
Authors: Fang Chao , Xu Dong , Su Jing , Dry Jonathan R , Linghu Bolan
Published: November 2019

Immuno-oncology (IO) therapies have transformed the therapeutic landscape of non-small cell lung cancer (NSCLC). However, patient responses to IO are variable and influenced by a heterogeneous combination of health, immune and tumor factors. There is a pressing need to discover the distinct NSCLC subgroups that influence response. We have developed a deep patient graph convolutional network, we call “DeePaN”, to discover NSCLC complexity across data modalities impacting IO benefit. DeePaN employs high-dimensional data derived from both real world evidence (RWE) based electronic health records (EHRs) and genomics across 1,937 IO treated NSCLC patients. DeePaN demonstrated effectiveness to stratify patients into subgroups with significantly different (p-value of 2.2 × 10−11) overall survival of 20.35 months and 9.42 months post-IO therapy. Significant differences in IO outcome were not seen from multiple non-graph based unsupervised methods. Furthermore, we demonstrate that patient stratification from DeePaN has the potential to augment the emerging IO biomarker of tumor mutation burden (TMB). Characterization of the subgroups discovered by DeePaN indicates potential to inform IO therapeutic insight, including the enrichment of mutated KRAS and high blood monocyte count in the IO beneficial and IO non-beneficial subgroups, respectively. To the best of our knowledge, our work for the first time has proven the concept that graph based AI is feasible and can effectively integrate high-dimensional genomic and EHR data to meaningfully stratify cancer patients on distinct clinical outcomes, with potential to inform precision oncology.
Genomic signature of accelerated evolution in a saline-alkaline lake-dwelling Schizothoracine fish
Authors: Tong Chao , Li Miao
Published: November 2019

Tibetan Plateau imposes extremely inhospitable environment on most wildlife. Besides the harsh aquatic environment including hypoxia and chronic cold, high salinity and alkalinity is an increasing threat to Tibetan endemic fishes. Previous genome-wide studies identified key genes contributed to highland fish adaptation to hypoxia and long-term cold, while our understanding of saline and alkaline adaptation in Tibetan fish remains limited. In this study, we performed a comparative genomics analysis in a saline lake-dwelling highland fish Gymnocypris przewalskii, aimed to identify candidate genes that contributed to saline and alkaline adaptation. We found elevated genome-wide rate of molecular evolution in G. przewalskii relative to lowland teleost fish species. In addition, we found nine genes encoding biological macromolecules associated with ion transport functions underwent accelerated evolution in G. przewalskii, which broadly expressed across kidney, gill, liver, spleen, brain and muscle tissues. Moreover, we found putative evidence of ion transport under selection were interacted by co-expression in G. przewalskii adaptation to high salinity and alkalinity environment of Lake Qinghai. Taken together, our comparative genomics study identified a set of rapidly evolving ion transport genes and transcriptomic signatures in Schizothoracine fish adaptation to saline and alkaline environment on the Tibetan Plateau.
The immunocytokine L19-TNF eradicates Sarcomas in combination with Chemotherapy agents or with immune check-point inhibitors
Authors: Corbellari Riccardo , Nadal Lisa , Villa Alessandra , Neri Dario , De Luca Roberto
Published: November 2019

Antibody-cytokine fusion proteins (also called “immunocytokines”) represent an emerging class of biopharmaceutical products, which are being considered for cancer immunotherapy. When used as single agents, pro-inflammatory immunocytokines are rarely capable of induce complete and durable cancer regression in mouse models and in patients. However, the combination treatment with conventional chemotherapy or with other immune-stimulatory agents typically increases the therapeutic efficacy of immunocytokines.

In this article, we describe combination treatments of a tumor-targeting antibody-cytokine fusion protein based on the L19 antibody (specific to a splice isoform of fibronectin) fused to murine tumor necrosis factor (TNF) with standard chemotherapy (dacarbazine, trabectedin or melphalan) or with an immune check-point inhibitor (anti-PD-1) in a BALB/c derived immunocompetent murine model of sarcoma (WEHI-164).

All combination treatments led to improved tumor remission compared to single agent treatments, suggesting that these combination partners may be suitable for further clinical development in sarcoma patients.
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
Authors: Tillu Vikas A. , Rae James , Gao Ya , Ariotti Nicholas , Floetenmeyer Matthias , Kovtun Oleksiy , McMahon Kerrie-Ann , Chaudhary Natasha , Parton Robert G. , Collins Brett M.
Published: November 2019

Caveolae are spherically shaped nanodomains of the plasma membrane, generated by cooperative assembly of caveolin and cavin proteins. Cavins are cytosolic peripheral membrane proteins with negatively charged intrinsically disordered regions (DR1-3) that flank positively charged α-helical regions (HR1 and HR2). Here we show that the three DR domains of Cavin1 are essential for caveola formation and dynamic trafficking of caveolae. Electrostatic interactions between DR and HR regions promote liquid-liquid phase separation behaviour of Cavin1 in vitro, assembly of Cavin1 oligomers in solution, generation of membrane curvature, association with caveolin-1 (CAV1), and Cavin1 recruitment to caveolae in cells. Removal of the first disordered region causes irreversible gel formation in vitro and results in aberrant caveola trafficking through the endosomal system. We propose a model for caveola assembly whereby fuzzy electrostatic interactions between Cavin1 and CAV1 proteins, combined with membrane lipid interactions, are required to generate membrane curvature and a metastable caveola coat.
An enzymatic assay to measure long-term adherence to pre-exposure prophylaxis and antiretroviral therapy
Authors: Olanrewaju Ayokunle O. , Sullivan Benjamin P. , Zhang Jane Y. , Bender Andrew T. , Sevenler Derin , Lo Tiffany J. , Fernandez-Suarez Marta , Drain Paul K. , Posner Jonathan D.
Published: November 2019

Poor adherence to pre-exposure prophylaxis (PrEP) and antiretroviral therapy (ART) can lead to human immunodeficiency virus (HIV) acquisition and emergence of drug resistant infections, respectively. Measurement of antiviral drug levels provides objective adherence information that may help prevent adverse health outcomes. Gold standard drug-level measurement by liquid chromatography/mass spectrometry is centralized, heavily instrumented, and expensive and is thus unsuitable and unavailable for routine use in clinical settings. We developed the REverse TranscrIptase Chain Termination (RESTRICT) assay as a rapid and accessible measurement of drug levels indicative of long-term adherence to PrEP and ART. The assay uses designer single stranded DNA templates and intercalating fluorescent dyes to measure complementary DNA (cDNA) formation by reverse transcriptase in the presence of nucleotide reverse transcriptase inhibitor drugs. We developed a probabilistic model for the RESTRICT assay by calculating the likelihood of incorporation of inhibitors into cDNA as a function of the relative concentrations of inhibitors and nucleotides. We validated the model by carrying out the RESTRICT assay using aqueous solutions of tenofovir diphosphate (TFV-DP), a measure of long-term adherence to PrEP and ART. We used dilution in water as a simple sample preparation strategy to detect TFV-DP spiked into blood. The RESTRICT assay accurately distinguishes TFV-DP drug levels within the clinical range for adherence and has the potential to be a useful test to identify patients with poor adherence to ART and PrEP.
Sensory Neurons Innervate Peripheral Lymph Nodes and Locally Regulate Gene Expression in Postsynaptic Endothelium, Stromal Cells, and Innate Leukocytes
Authors: Huang Siyi , Ziegler Carly G. K. , Austin John , Mannoun Najat , Vukovic Marko , Ordovas-Montanes Jose , Shalek Alex K. , von Andrian Ulrich H.
Published: November 2019

Immune responses within barrier tissues are regulated, in part, by nociceptors, specialized peripheral sensory neurons that detect noxious stimuli. Previous work has shown that nociceptor ablation not only alters local responses to immune challenge at peripheral sites, but also within draining lymph nodes (LNs). The mechanisms and significance of nociceptor-dependent modulation of LN function are unknown. Indeed, although sympathetic innervation of LNs is well documented, it has been unclear whether the LN parenchyma itself is innervated by sensory neurons. Here, using a combination of high-resolution imaging, retrograde viral tracing, single-cell transcriptomics (scRNA-seq), and optogenetics, we identified and functionally tested a sensory neuro-immune circuit that is preferentially located in the outermost cortex of skin-draining LNs. Transcriptomic profiling revealed that there are at least four discrete subsets of sensory neurons that innervate LNs with a predominance of peptidergic nociceptors, and an innervation pattern that is distinct from that in the surrounding skin. To uncover potential LN-resident communication partners for LN-innervating sensory neurons, we employed scRNA-seq to generate a draft atlas of all murine LN cells and, based on receptor-ligand expression patterns, nominated candidate target populations among stromal and immune cells. Using selective optogenetic stimulation of LN-innervating sensory axons, we directly experimentally tested our inferred connections. Acute neuronal activation triggered rapid transcriptional changes preferentially within our top-ranked putative interacting partners, principally endothelium and other nodal stroma cells, as well as several innate leukocyte populations. Thus, LNs are monitored by a unique population of sensory neurons that possesses immunomodulatory potential.
Genetically encoded phase contrast agents for digital holographic microscopy
Authors: Farhadi Arash , Bedrossian Manuel , Lee Justin , Ho Gabrielle H. , Shapiro Mikhail G. , Nadeau Jay
Published: November 2019

Quantitative phase imaging and digital holographic microscopy have shown great promise for visualizing the motion, structure and physiology of microorganisms and mammalian cells in three dimensions. However, these imaging techniques currently lack molecular contrast agents analogous to the fluorescent dyes and proteins that have revolutionized fluorescence microscopy. Here we introduce the first genetically encodable phase contrast agents based on gas vesicles, a unique class of air-filled protein nanostructures derived from buoyant microbes. The relatively low index of refraction of the air-filled core of gas vesicles results in optical phase advancement relative to aqueous media, making them a “positive” phase contrast agent easily distinguished from organelles, dyes, or microminerals. We demonstrate this capability by identifying and tracking the motion of gas vesicles and gas vesicle-expressing bacteria using digital holographic microscopy, and by imaging the uptake of engineered gas vesicles by mammalian cells. These results give phase imaging a biomolecular contrast agent, greatly expanding the capabilities of this powerful technology for three-dimensional biological imaging.
The Consequences of Egg Adaptation in the H3N2 Component to the Immunogenicity of Live Attenuated Influenza Vaccine
Authors: Goldhill Daniel H. , Lindsey Benjamin , Kugathasan Ruthiran , Garza Zandra Felix , Jagne Ya Jankey , Sallah Hadijatou Jane , Goderski Gabriel , van Tol Sophie , Höschler Katja , Meijer Adam , Barclay Wendy S. , de Silva Thushan I.
Published: November 2019

Adaptation in egg-passaged vaccine strains may cause reduced vaccine effectiveness due to altered antigenicity of the influenza haemagglutinin. We tested whether egg adaptation modified serum and mucosal antibody responses to the A(H3N2) component in the Live Attenuated Influenza Vaccine (LAIV). Twice as many children seroconverted to an egg-adapted H3N2 than the equivalent wildtype strain. Seroconversion to the wildtype strain was greater in children seronegative pre-LAIV, whereas higher mucosal IgA responses to wildtype antigen were observed if seropositive prior to vaccination. Sequencing of virus from nasopharyngeal swabs from 7 days post-LAIV showed low sequence diversity and no reversion of egg-adaptive mutations.
Vibrio deploys Type 2 secreted lipase to esterify cholesterol with host fatty acids and mediate cell egress
Authors: de Souza Santos Marcela , Chimalapati Suneeta , Ray Ann , Lee Wan-Ru , Rivera-Cancel Giomar , Lafrance Alexander , Vale Gonçalo , Pawłowski Krzysztof , Mitsche Matt , McDonald Jeffrey G , Liou Jen , Orth Kim
Published: November 2019

Pathogens find diverse niches for survival inside host cells where replication occurs in a relatively protected environment. Vibrio parahaemolyticus, a facultative intracellular pathogen, uses its type 3 secretion system 2 (T3SS2) to invade and replicate inside host cells. However, after extensive analysis, the T3SS2 pathogenicity island appeared to lack a mechanism for egress of this bacterium from the invaded host cell. Using a combination of cell biology, microbial genetics and lipid biochemistry, we found that VPA0226, a constitutively secreted lipase, is required for escape of Vibrio parahaemolyticus from host cells. Remarkably, this lipase must be delivered into the host cytoplasm where it preferentially uses fatty acids associated with innate immune response (i.e. arachidonic acid, 20:4) to esterify cholesterol, weakening the plasma membrane and allowing egress of the bacteria. This study reveals the resourcefulness of microbes and the interplay between virulence systems to evolve an ingenious scheme for survival and escape.

Impact Statement

Considering the course of a pathogen’s evolution, there appears to be interplay between secretion systems, providing unique, synergistic mechanisms to support a successful lifestyle for possibly pathogenesis, symbiosis and/or parasitosis.
Aire-dependent genes undergo Clp1-mediated 3’UTR shortening associated with higher transcript stability in the thymus
Authors: Guyon Clotilde , Jmari Nada , Padonou Francine , Li Yen-Chin , Ucar Olga , Fujikado Noriyuki , Coulpier Fanny , Blanchet Christophe , Root David E. , Giraud Matthieu
Published: November 2019

The ability of the immune system to avoid autoimmune disease relies on tolerization of thymocytes to self-antigens whose expression and presentation by thymic medullary epithelial cells (mTECs) is controlled predominantly by Aire at the transcriptional level and possibly regulated at other unrecognized levels. Aire-sensitive gene expression is influenced by several molecular factors, some of which belong to the 3’end processing complex, suggesting they might impact transcript stability and levels through an effect on 3’UTR shortening. We discovered that Aire-sensitive genes display a pronounced preference for short-3’UTR transcript isoforms in mTECs, a feature preceding Aire’s expression and correlated with the preferential selection of proximal polyA sites by the 3’end processing complex. Through an RNAi screen and generation of a lentigenic mouse, we found that one factor, Clp1, promotes 3’UTR shortening associated with higher transcript stability and expression of Aire-sensitive genes, revealing a post-transcriptional level of control of Aire-activated expression in mTECs.
A deregulated stress response underlies distinct INF2 associated disease profiles
Authors: Bayraktar S. , Nehrig J. , Menis E. , Karli K. , Janning A. , Struk T. , Halbritter J. , Michgehl U. , Krahn M.P. , Schuberth C.E. , Pavenstädt H.P. , Wedlich-Söldner R.
Published: November 2019

Monogenic diseases provide favorable opportunities to elucidate the molecular mechanisms of disease progression and improve medical diagnostics. However, the complex interplay between genetic and environmental factors in disease etiologies makes it difficult to discern the mechanistic links between different alleles of a single locus and their associated pathophysiologies. Here we systematically characterize a large panel (>50) of autosomal dominant mutants of the actin regulator inverted formin 2 (INF2) that have been reported to cause the podocytic kidney disease focal segmental glomerulosclerosis (FSGS) and the neurological disorder Charcot Marie-Tooth disease (CMT). We found that INF2 mutations lead to deregulated activation of the formin and a constitutive stress response in cultured cells, primary patient cells and Drosophila nephrocytes. Using quantitative live-cell imaging we were able to identify distinct subsets of INF2 variants that exhibit varying degrees of activation. Furthermore, we could clearly distinguish between INF2 mutations that were linked exclusively to FSGS from those that caused a combination of FSGS and CMT. Our results indicate that cellular profiling of disease-associated mutations can contribute substantially to sequence-based phenotype predictions.
Metabolic signatures of regulation by phosphorylation and acetylation
Authors: Smith Kirk , Shen Fangzhou , Lee Ho Joon , Chandrasekaran Sriram
Published: November 2019

Acetylation and phosphorylation are highly conserved post-translational modifications (PTMs) that regulate cellular metabolism, yet how metabolic control is shared between these PTMs is unknown. Here we analyze transcriptome, proteome, acetylome, and phosphoproteome datasets inE.coli,S.cerevisiae, and mammalian cells across diverse conditions using CAROM, a new approach that uses genome-scale metabolic networks and machine-learning to classify regulation by PTMs. We built a single machine-learning model that accurately distinguished reactions controlled by each PTM in a condition across all three organisms based on reaction attributes (AUC>0.8). Our model uncovered enzymes regulated by phosphorylation during a mammalian cell-cycle, which we validate using phosphoproteomics. Interpreting the machine-learning model using game-theory uncovered enzyme properties including network connectivity, essentiality, and condition-specific factors such as maximum flux that differentiate regulation by phosphorylation from acetylation. The conserved and predictable partitioning of metabolic regulation identified here between these PTMs can enable rational engineering of regulatory circuits.

Graphical Abstract
Mechanical Suppression of Breast Cancer Cell Invasion and Paracrine Signaling Requires Nucleo-Cytoskeletal Connectivity
Authors: Yi Xin , Wright Laura E. , Pagnotti Gabriel M. , Uzer Gunes , Powell Katherine M. , Wallace Joseph , Sankar Uma , Rubin Clinton T. , Mohammad Khalid , Guise Theresa A. , Thompson William R.
Published: November 2019

Exercise benefits the musculoskeletal system and reduces the effects of cancer. The beneficial effects of exercise are multifactorial, where metabolic changes and tissue adaptation influence outcomes. Mechanical signals, a principal component of exercise, are anabolic to the musculoskeletal system and restrict cancer progression. We examined the mechanisms through which cancer cells sense and respond to mechanical signals. Low-magnitude, high-frequency signals were applied to human breast cancer cells in the form of low-intensity vibration (LIV). LIV decreased invasion through matrix and impaired secretion of osteolytic factors PTHLH, IL-11, and RANKL. Furthermore, paracrine signals from mechanically stimulated cancer cells, reduced osteoclast differentiation resorptive capacity. Physically disconnecting the nucleus by knockdown of SUN1 and SUN2 impaired the ability of LIV to suppress invasion and production of osteolytic factors. LIV also increased cell stiffness; an effect dependent on an intact LINC complex. These data show that mechanical signals alter the metastatic potential of human breast cancer cells, where the nucleus serves as a mechanosensory apparatus to alter cell structure and intercellular signaling.
Backstepping mechanism of kinesin-1
Authors: Toleikis Algirdas , Carter Nicholas J. , Cross Robert A.
Published: November 2019

Kinesin-1 is an ATP-driven molecular motor that transports cellular cargo along microtubules. At low loads, kinesin-1 almost always steps forwards, towards microtubule plus ends, but at higher loads, it can also step backwards. Backsteps are usually 8 nm, but can be larger. These larger backwards events of 16 nm, 24 nm or more are thought to be slips rather than steps, because they are too fast to consist of multiple, tightly-coupled 8 nm steps. Here we propose that not just these larger backsteps, but all kinesin-1 backsteps, are slips. We show firstly that kinesin waits before forward steps for less time than before backsteps and detachments; secondly that kinesin waits for the same amount of time before backsteps and detachments and thirdly that by varying the microtubule type we can change the ratio of backsteps to detachments, without affecting forward stepping. Our findings indicate that backsteps and detachments originate from the same state and that this state arises later in the mechanochemical cycle than the state that gives rise to forward steps. To explain our data, we propose that in each cycle of ATP turnover, forward kinesin steps can only occur before Pi release, whilst backslips and detachments can only occur after Pi release. In the scheme we propose, Pi release gates access to a weak binding K.ADP-K.ADP state that can slip back along the microtubule, re-engage, release ADP and try again to take an ATP-driven forward step. We predict that this rescued detachment pathway is key to maintaining kinesin processivity under load.

Significance statement

Kinesin-1 molecular motors are ATP-driven walking machines that typically step forward, towards microtubule plus ends. But they can also step backwards, especially at high load. Backsteps are currently thought to occur by directional reversal of forwards walking. To the contrary, we propose here that kinesin backsteps are not steps, but slips. We show that backwards translocations originate from a different and later state in the kinesin mechanism than the state that generates forward steps. To explain this, we propose that following ATP binding, kinesin molecules that fail to step forward within a load-dependent time window convert to a state that can slip back, rebind to the microtubule, and try again to step forward.
Covert spatial attention speeds target individuation
Authors: Foster Joshua J. , Bsales Emma M. , Awh Edward
Published: November 2019

Covert spatial attention has long been thought to speed visual processing. Psychophysics studies have shown that target information accrues faster at attended locations than at unattended locations. However, with behavioral evidence alone, it is difficult to determine whether attention speeds visual processing of the target, or subsequent post-perceptual stages of processing (e.g. decision making and response selection). Moreover, while many studies have shown that that attention can boost the amplitude of visually-evoked neural responses, no effect has been observed on the latency of those neural responses. Here, we offer new evidence that may reconcile the neural and behavioral findings. Our study focused on the N2pc, an EEG marker of visual selection that has been linked with object individuation – the formation of an object representation that is distinct from the background and from other objects. In two experiments, we manipulated whether or not covert attention was precisely deployed to the location of an impending search target. We found that the target-evoked N2pc onset approximately 20 ms earlier when the target location was cued than when it was not cued. Thus, although attention may not speed the earliest stages of sensory processing, attention does speed the critical transition between raw sensory encoding and the formation of individuated object representations.

Significance Statement

Covert spatial attention improves processing at attended locations. Past behavioral studies have shown that information about visual targets accrues faster at attended than at unattended locations. However, it has remained unclear whether attention speeds perceptual analysis or subsequent post-perceptual stages of processing. Here we present robust evidence that attention speeds the N2pc, an electrophysiological signal that indexes the formation of individuated object representations. Our findings show that attention speeds a relatively early stage of perceptual processing, while also elucidating the specific perceptual process that is speeded.
Suramin potently inhibits binding of the mammalian high mobility group protein AT-hook 2 to DNA
Authors: Su Linjia , Bryan Nadezda , Battista Sabrina , Freitas Juliano , Garabedian Alyssa , D’Alessio Federica , Romano Miriam , Falanga Fabiana , Fusco Alfredo , Kos Lidia , Chambers Jeremy , Fernandez-Lima Francisco , Chapagain Prem P. , Vasile Stefan , Smith Layton , Leng Fenfei
Published: November 2019

The mammalian high mobility group protein AT-hook 2 (HMGA2) is a multi-functional DNA-binding protein which plays important roles in tumorigenesis and adipogenesis. Previous results showed that HMGA2 is a potential therapeutic target of anticancer and anti-obesity drugs by inhibiting its DNA-binding activities. Here we report the development of a miniaturized, automated AlphaScreen high throughput screening (HTS) assay to identify inhibitors targeting HMGA2-DNA interactions. After screening the LOPAC1280 compound library, we discovered that suramin, a negatively charged antiparasitic drug potently inhibits the HMGA2-DNA interaction. Our results also show that the inhibition is through suramin binding to the AT-hooks of HMGA2, therefore blocking its DNA binding capacity. Furthermore, we demonstrate that suramin can induce brain tumor stem cells differentiation into cells with neurite-like structures, a process triggered by disrupting HMGA2-DNA interactions. Since suramin has strong antitumor and anti-metastasis activities, our discovery suggests that HMGA2 and HMGA2-like proteins may be the cellular target of this century-old drug.
Molecular and Circuit Architecture of Social Hierarchy
Authors: Nelson Adam C. , Kapoor Vikrant , Vaughn Eric , Gnanasegaram Jeshurun A. , Rubinstein Nimrod D. , Murthy Venkatesh N , Dulac Catherine
Published: November 2019

Social hierarchy is a common organizational structure of animal groups, in which an individual’s social status generates an adaptive behavioral state that facilitates interactions with other group members. Although generally stable, the social status of an animal can change, underscoring the plasticity of the underlying neural circuits. Here, we uncover the molecular and biophysical properties of a cortico-thalamic circuit that supports the emergence of hierarchy in mice. We established a robust behavioral paradigm to explore the establishment of hierarchy among groups of unfamiliar males, and identified the mediodorsal thalamus (MDT) and the caudal part of anterior cingulate area (cACC) as brain areas that are differentially activated between dominants and subordinates. Glutamatergic MDT neurons project to inhibitory parvalbumin interneurons of the cACC, and activity levels of both cell types control competitive performance. Synaptic inputs and excitability of MDT neurons undergo dramatic changes according to the animal social status, and single nucleus sequencing identified increased transcription of the voltage gated ion channelTrpm3in dominant mice, leading to enhanced excitatory transmission in the MDT-cACC circuit. Our data suggest a model in which cellular, molecular and biophysical plasticity in a thalamocortical circuit controls the expression of social status.
Sex identification of ancient pinnipeds using the dog genome
Authors: Bro-Jørgensen Maiken Hemme , Keighley Xénia , Ahlgren Hans , Scharff-Olsen Camilla Hjorth , Rosing-Asvid Aqqalu , Dietz Rune , Ferguson Steven H. , Gotfredsen Anne Birgitte , Jordan Peter , Glykou Aikaterini , Lidén Kerstin , Olsen Morten Tange
Published: November 2019

Determining the male and female representation in zooarchaeological material from hunted animal species is essential, to fully investigate the effects and means of prehistoric hunting practices, and may further provide valuable biological information on past animal life-history, behaviour and demography. However, the fragmented nature of the zooarchaeological record and a lack of clear diagnostic skeletal markers, often prevents such inference. Here, we test the usability of the dog nuclear genome (CanFam3.1) for sex identification of pinnipeds. First, a contemporary sample set (n=72) of ringed seals (Pusa hispida), with known sex was used to test the genetic sex identification method. By quantifying the proportion of X chromosome reads, as the chrX/chr1 ratio, the ratios clustered in two clearly distinguishable sex groups. Of the 72 individuals, 69 were identified to the accurate sex, which proves a high reliability of the genetic method. Second, random down sampling of a subset of the ringed seal samples to different read number, suggests at least 5000 DNA sequence reads mapped to the reference genome as the lower limit for which this method is applicable. Finally, applying this standard, sex identification was successfully carried out on a broad set of ancient pinniped samples, including walruses (Odobenus rosmarus), grey seals (Halichoerus grypus) and harp seals (Pagophilus groenlandicus), which all showed clearly distinct male and female chrX/chr1 ratio groups.
Development of microsatellite markers for the threatened speciesColeocephalocereus purpureus(Cactaceae) using next-generation sequencing
Authors: Fraga Daphne Amaral , de Carvalho Anderson Figueiredo , Santana Ricardo Souza , Machado Marlon Câmara , Lacorte Gustavo Augusto
Published: November 2019

Ten microsatellite loci were developed and validated for the endangered cactus speciesColeocephalocereus purpureus. The markers were obtained from sequences generated by whole genome shotgun sequencing approaches. A testing group of 36 specimens of the main grouping were genotyped and all described markers presented suitable outcomes to population genetic studies, showing polymorphic status forC. purpureustesting group with clean and reproducible amplification. No evidence for scoring errors, null alleles or linkage disequilibrium was detected. Number of alleles per locus ranged from 3 to 6 and expected heterozygosity ranged from 0.78 to 0.99. These new microsatellite loci are suitable to be used in future diversity and structure population studies ofC. purpureus.
The effect of proximity on the function and energy transfer capability of fluorescent protein pairs
Authors: Pope Jacob R. , Johnson Rachel L. , Jamieson W. David , Worthy Harley L , Kailasam Senthilkumar D. , Auhim Husam Sabah , Watkins Daniel W. , Rizkallah Pierre , Castell Oliver , Jones D. Dafydd
Published: November 2019

Fluorescent proteins (FPs) are commonly used in pairs to monitor dynamic biomolecular events through changes in their proximity via distance dependent processes such as Förster resonance energy transfer (FRET). Many FPs have a tendency to oligomerise, which is likely to be promoted through attachment to associating proteins through increases in local FP concentration. We show here that on association of FP pairs, the inherent function of the FPs can alter. Artificial dimers were constructed using a bioorthogonal Click chemistry approach that combined a commonly used green fluorescent protein (superfolder GFP) with itself, a yellow FP (Venus) or a red FP (mCherry). In each case dimerisation changes the inherent fluorescent properties, including FRET capability. The GFP homodimer demonstrated synergistic behaviour with the dimer being brighter than the sum of the two monomers. The structure of the GFP homodimer revealed that a water-rich interface is formed between the two monomers, with the chromophores being in close proximity with favourable transition dipole alignments. Dimerisation of GFP with Venus results in a complex displaying ∼86% FRET efficiency, which is significantly below the near 100% efficiency predicted. When GFP is complexed with mCherry, FRET and mCherry fluorescence itself is essentially lost. Thus, the simple assumptions used when monitoring interactions between proteins via FP FRET may not always hold true, especially under conditions whereby the protein-protein interactions promote FP interaction.

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