bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of the re-extraction process of ethanol from catechin components from Korean green tea extract
Authors: Jo In-Hee , Kim Myung-Kyoo , Jang Suh-Yoon , Kim Na-Ra , Lee Won-Young
Published: March 2020

The purpose of this study was to determine the optimum re-extraction conditions of ethanol from catechin in Korean green tea (Camellia sinensis L.) using response surface methodology (RSM). The experiments were carried out according to a five level and two variable central composite design (CCD). The two independent variables were solvent ratio to sample content (1, 4, 7, 10, 13 mL/g) and extraction temperature (-20, -10, 0, 10, 20℃) on the dependent variables including yield, epigallocatechin (EGC), epicathchin (EC), epigallocatechingallate (EGCG), epicatechingallate (ECG), total catechin and caffeine. ANOVA results showed that Coefficients of determination (R2) of estimated models for dependent variables were ranged from 0.9054~0.9778, while R2 of caffeine were estimated 0.8770. The optimum ranges for the maximized extraction including yield, EGC, EC, EGCG, ECG, caffeine and total catechin were 4.5~7.5 mL/g in ratio of ethanol to sample and -8~8℃ in extraction temperature. The actual values of yield, EGC, EC, EGCG, ECG, caffeine and total catechin, respectively, at the optimized conditions were 35.02%, 13.31%, 3.978%, 19.11%, 4.29%, 5.30% and 40.68%
Changes in approximate composition, antioxidant activity and melatonin content of rapeseed during germination
Authors: Kim Seok Joong
Published: March 2020

The changes of approximate composition, antioxidant activity and melatonin content in rapeseed were monitored during 10 days germination to choose the optimum sprouts with beneficial functionalities. The moisture content of seeds increased from 3.23% to 17.50% during 10 days germination period, while ash content was similar (4.03~4.91%). The fat content was reduced from 38.18% to 22.65%, however, protein content increased from 21.43% to 26.72%. The carbohydrate content increased from 32.71% to 35.84% at 8th day. The reducing sugar and fiber contents reached 10.47% and 15.12% at 6th day from 4.04% and 12.82%, respectively. Eighth day sprouts contained highest level of polyphenol (gallic acid equivalent, 19.2 g/kg). Germination increased antioxidant activities (trolox equivalent, mmol/kg) of seeds with slight difference depending on assay. That is, antioxidant activity was highest at 6th day in DPPH radical scavenging (55.9), 10th day both in ABTS radical scavenging (71.6) and Fe(III) reducing (125.3), and 4th day in peroxy radical scavenging (116.7) assay. Melatonin content of seeds (0.85 μg/kg) also increased and reached up to 14.93 μg/kg at 6th day. In conclusion, germination more than 4 days raised antioxidant activity of seeds highly, and 6th day sprouts had additional benefit in terms of melatonin, reducing sugar and crude fiber contents.
Beauty activity of extracts from Saurus chinensis by ultra-fine ground
Authors: Park HyeJin , Park Ki-Tae , Hong Shin-Hyub , Kim Na-Hyun , Park Mi-Jeong , Hong Eun-Jin , Ahn Dong-Hyun , An Bong-Jeun , Cho Young-Je
Published: March 2020

In this study, beauty food activities were determined for extracts of Saurus chinensis as functional beauty food. Tyrosinase inhibitory effect was increased as more 4 folds by ultra-fine grind technology than normal grind technology in ethanol extracts from Saurus chinensis. A ultra-fine ground technology was used to increase the extraction yield for bioactive compounds from medicinal plants. Tyrosinase inhibitory activity, which is related to skin-whitening, was confirmed to be 100% for ethanol extracts at 1,000 ppm of phenolics. Anti-wrinkle activity was determined showing 30% of inhibition effect at above 1,000 ppm phenolic concentration. The elastase inhibitory activity of water and ethanol extracts from ultra-fine ground Saurus chinensis showed higher inhibition activity than compared to extracts from normal ground Saurus chinensis. Astringent activity in ethanol extracts was determined showing over 70% at 250 ppm of phenolics. Based on these results, Saurus chinensis extracts can be used as a functional beauty food and cosmetic with whitening, anti-wrinkle and pore contraction effects.
Changes in quality characteristics of sliced garlic with different freezing conditions during storage
Authors: Kim Seok-Young , Kim Hee-Sun , Kim Jin-Se , Han Gwi-Jung
Published: March 2020

This study was performed to evaluate the effect of different freezing conditions and storage periods on physicochemical and microbial characteristics of garlic. Garlics were washed, dried, sliced to 0.3 cm then packed in LDPE+LLDPE film bags. They were treated with still-air freezing at -20°C (SAF20), -40°C (SAF40) and immersed-liquid freezing at -40°C (ILF40). Frozen garlics were stored under frozen storage conditions for 7 months at -20°C and quality characteristics were measured monthly during the frozen storage. Freezing rate of garlic was the fastest in ILF 40 (10 min), SAF40 (40 min) and SAF20 (1,600 min) sequentially. In ILF40, drip loss, cutting force, total aerobic bacteria count and pH were the lowest, whereas pyruvic acid and allicin content were the highest (p<0.05) during frozen storage, these results were the most similar characteristics with the fresh garlic. During frozen storage, drip loss, color difference and total organic acid content were significantly fluctuated in SAF20 (p<0.05), while they were not changed in ILF40. Overall, total aerobic bacteria count and pH decreased, cutting force, pyruvic acid and allicin content remained unchanged in all groups. In conclusion, the optimal freezing conditions for garlic with the least quality changes was considered to be ILF40 (immersed liquid freezing), keeping quality characteristics up to 7 months by freezing storage.
Chemical compositions and antioxidant activities depending on cultivation methods and various parts of yuza
Authors: Lee Jong Eun , Kim Kyung Mi , Kim Jin Sook , Kim Gi Chang , Choi Song Yi , Kim Sang Bum
Published: March 2020

This study was conducted to investigate the quality properties depending on the cultivation methods (general, organic, pesticide-free) of yuza and its various parts (peel, pulp, seed). The contents of hesperidin were the highest in yuza feel grown by pesticide-free method (13.23 mg/g). The contents of naringin presented a higher content in the peel, especially which of the general (4.62 mg/g) showed the highest value. Vitamin C analysis showed the highest content in the peel, significantly varied according to the cultivation method and various parts (p<0.05). Vitamin C value was significantly highest in organic peel, which was 770.02 mg/100 g, whereas among the peel, the pulp and the seed were it the lowest in the seed. The content of total polyphenols were the highest in general peel (0.85 mg/g). Flavonoid content of pesticide-free seed was significantly higher than those of the other yuja samples which was 0.89 mg/g (p<0.05). The DPPH radical scavenging activity was relatively more active in the peel among the above-mentioned three parts, especially the pesticide-free peel was most active, which was 73.94%. The ABTS radical scavenging activity of organic peel was significantly active among the samples, which was 84.47% (p<0.05). Based on these results, it can be said that yuja has variety of useful components in the pulp and the seed as well as the peel: and thus it’s hight recommended to develop more varied yuja products.
Changes of useful components and biological activities of Solanum nigrum Linne fruit according to different harvest time
Authors: Choi Seongkyu , Yun Kyeong-Won , Kim Yong-Doo , Jin Seong-Woo , Kim Kyung-Je , Kang Kyeong-Yun , Koh Young-Woo , Im Seung-bin , Jeong Sang-Wook , Seo Kyoung-Sun
Published: March 2020

In this study, we investigated the variation in free sugars, organic acids, antioxidant activity and anti-inflammatory effect of Solanum nigrum Linne fruits according to harvest time. Four kinds of free sugars (fructose, glucose, sucrose, maltose) were detected in S. nigrum fruit, and the free sugar contents varied significantly with harvest time. Organic acid content of S. nigrum fruit showed the highest in malic acid and acetic acid, and the highest content of total organic acids was found in S. nigrum fruit harvested on October 18th and October 25th. For the total polyphenol content, S. nigrum fruit harvested on October 18th was the highest. The strongest DPPH and ABTS radical scavenging activity was showed in S. nigrum fruit harvested on October 11th and October 18th. The anti-inflammatory activity and antioxidant effects were the highest in the ethanol extract from S. nigrum fruit collected on October 18th and October 11th. Thus, it seems the best to harvest of S. nigrum fruit harvested on October 11th and October 18th.
Antioxidant activities of soymilk added with green tea and rosemary extract
Authors: Ryu Ji-yeon , Song YeonWoo , Moon Jeong Yong , Jun Neung-Jae , Cho Somi Kim
Published: March 2020

The objective of this study was to compare antioxidant activities of green tea, rosemary, lemon and bamboo leaves extracts using three different extraction methods (80% ethanol sonication extraction, distilled water autoclave extraction, distilled water extraction at room temperature). As a result, green tea and rosemary extracts showed relatively high antioxidant activities compared with those of lemon and bamboo leaves. These green tea and rosemary extracts were subsequently added to soymilk and their mixtures were examined for antioxidant activities. Soymilk added with 10% green tea distilled water autoclave extracts and distilled water at room temperature extracts showed relatively high DPPH, 85.09±2.26%, 84.38±1.97%, and ABTS radical scavenging activities, 73.43±2.78%, 81.34±4.78%, respectively. On the other hand, soymilk added with 10% rosemary distilled water autoclave extracts showed remarkably higher DPPH radical scavenging activity while their ABTS radical scavenging ability was similar to that of non-added soymilk. In conclusion, our results suggest that the addition of green tea distilled water autoclave extracts, distilled water at room temperature extracts and rosemary distilled water autoclave extracts to soymilk could contribute to the development of added value soymilk products with increased antioxidant activities.
Radical scavenging and α-glucosidase inhibitory effects of Mongolian Iris bungei extract
Authors: Jeong Yun Hee , Jeong Gyeong Han , Kim Tae Hoon
Published: March 2020

In a continuing screening of selected medicinal plants native to Mongolia, the antioxidant and α-glucosidase inhibitory activities of methanol extract of Iris bungei were investigated. After extraction with 80% of methanol, the methanol fraction was further extracted with n-hexane, EtOAc and n-BuOH in order to obtain four different solvent-soluble fractions, namely n-hexane-soluble, EtOAc-soluble, n-BuOH-soluble and H2O residue. The antioxidant properties were evaluated by radical scavenging assay using 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS+) radicals. The anti-diabetic efficacy of I. bungei extract was investigated by α-glucosidase assay. All tested samples showed dose-dependent radical scavenging and α-glucosidase inhibitory activities. Among the tested extracts, the EtOAc-soluble fractions showed the greatest radical scavenging activity and α-glucosidase inhibitory properties among other solvent-soluble fractions. This result suggested that there was a significant relationship between the total phenolic content and biological efficacy. Thus, I. bungei extract might be considered as a new potential source of natural antioxidant and as a α-glucosidase inhibitory source. A more systematic investigation of this biomass sill be performed for further investigation of activity against antioxidative and anti-diabetic effects.
Effect of particle size of naked oat flours on physicochemical and antioxidant property
Authors: Jun Hyun-Il , Yoo Sun-Hee , Song Geun-Seoup , Kim Young-Soo
Published: March 2020

This study was carried out to investigate the effect of particle size of naked oat flour (NOF) on physicochemical property and antioxidant activity. The NOF was passed through 250 μm and 160 μm size sieves to obtain three fractions (fraction A: 250 μm or more, fraction B: 160-250 μm, and fraction C: 160 μm or less). Moisture, crude protein, crude fat, and crude ash contents of NOF were 8.4, 15.7, 10.0, and 1.8%, respectively, and these contents were increased as the particle size of NOF decreased. The mineral and free amino acid contents of NOF also had a similar tendency. The contents of total starch, amylose, starch damage, total dietary fiber, β-glucan, total phenolics, and flavonoids in NOF were 56.4%, 21.4%, 11.7%, 11.0%, 4.7%, 237.8 μg/g and 90.9 μg/g, respectively. As the particle size of NOF decreased, total starch, amylose, and starch damage contents increased, whereas total dietary fiber, β-glucan, total phenolic and flavonoid contents decreased. Also, three antioxidant activities of NOF were closely correlated with their total phenolics and flavonoids contents, showing high correlation coefficient values (R2=0.87 and 0.81, respectively).
Immunomodulatory effects of β-1,3/1,6-glucan and lactic acid bacteria in LP-BM5 murine leukemia viruses-induced murine acquired immune deficiency syndrome
Authors: Kim Min-Soo , Kim JoongSu , Ryu Min Jung , Kim Ki hong , Hwang Kwontack
Published: March 2020

In this study, β-1,3/1,6-glucan, lactic acid bacteria, and β-1,3/1,6-glucan+lactic acid bacteria were tested for 10 weeks using an immunodeficient animal model infected with LP-BM5 murine AIDS virus On the immune activity. Cytokines production, plasma immunoglobulin concentration, T cell and B cell proliferation were measured. As a result, the T cell proliferative capacity which was weakened by immunization with LP-BM5 murine AIDS virus increased significantly T cell proliferative capacity compared with the red ginseng control group. B cell proliferative capacity was significantly higher than the infected control group. Increased B cell proliferation was reduced. In the cytokine production, IL-2, IL-12 and IL-15 in the Th1-type cytokine increased the secretion of IL-2, IL-12 and IL-15 compared to the infected control. The proliferative capacity of the treated group was higher than that of the mixed treatment group. TNF-α was significantly decreased compared with the infected control group. The IL-4, IL-6 and IL-10 levels were significantly inhibited in the infected control group and the Th1/Th2 type cytokine expression was regulated by immunohistochemistry. IgE, IgA, and IgG levels were significantly lower in the immunoglobulin secretion assay than in the control. As a result, the immunomodulatory effect of β-1,3/1,6-glucan+lactic acid bacteria was confirmed by mixing with LP-BM5 murine AIDS virus-infected immunodeficient animal model.
Improvement of colitis preventive effects of Gochujang by addition of Lactobacillus plantarum on C57BL/6 mice
Authors: Park Eui-Seong , Heo Ju-Hee , Lim Yaung-Iee , Ju Jaehyun , Park Kun-Young
Published: March 2020

Gochujang, a traditional Korean food, is fermented by mixing red pepper powder, various grain, meju and salt. Changes in the kind of ingredients and fermentation method could increase health functionalities. In this study, in vivo anti-colitis effects of gochujang prepared with mixed grains, bamboo salt baked 3 times and meju starters on DSS-induced colitis in C57BL/6 mice were studied. We prepared gochujang prepared with mixed grains (MG), bamboo salt, and Aspergillus oryzae (A) and Baccillus subtilis (B) mixed starters (MG-AB) and gochujang prepared with MG, bamboo salt and A, B and Lactobacillus plantarum (L) mixed starters (MG-ABL). MG-AB and MG-ABL significantly increased body weight and colon length compared to the control (p<0.05). MG-ABL showed significantly decreased interleukin-6 (IL-6) expression in serum compared to the control and MG-AB group (p<0.05). MG-ABL also regulated mRNA and protein levels of pro-apoptotic Bcl-2-associated X protein (Bax) and anti-apoptotic B-cell lymphoma-2 (Bcl-2) in the mice colon tissue (p<0.05). Therefore, MG-ABL exhibited the increased anticolitis effects by inhibiting damage of colon tissue, probably by regulating a pro-inflammatory cytokine of IL-6 and regulated apoptosis related genes. These results indicated that gochujang changed with good ingredients and starters had colitis preventive effects and might be due to active compounds in mixed grain and bamboo salt, and produced by L during the fermentation of gochujang.
Study on the storage stability of the white internal organs using natural materials
Authors: Han Ye-Jin , Ku Su-Kyung , Kim Tae-Kyung , Sung Jung-Min , Kim Young-Boong , Choi Yun-Sang
Published: March 2020

The purpose of this study was to investigate the ability of natural antioxidants as stabilizers for meat by-products to prevent lipid oxidation. The white internal organs were evaluated using different treatments: no antioxidant (control), ascorbic acid (T1), Artemisiacapillaris Thunb. (T2), Opuntia (T3), Schisandra chinensis (T4), and Saururuschinensis (Lour.) Baill (T5). Antioxidant activities were analyzed by measuring DPPH contents, superoxide anion radical levels, nitrate scavenging activities, and total polyphenol contents. T1 and T2 showed higher antioxidant activities and total polyphenol contents (p<0.05). Additionally, changes in physicochemical properties (pH, color, volatile basic nitrogen [VBN], and thiobarbituric acid reactive substances [TBARS]) and microbiological aspects in white internal organs processed with antioxidants were investigated. As storage time increased, the CIE a* and b* values of the white internal organs processed with natural antioxidants were decreased (p<0.05), and CIE L* values were low, particularly for the T3 sample relative to that in the control. Moreover, the pH, VBN, and TBARS values of samples T2–T5 were increased after 7 days of storage, but showed low values compared with those of the control (p<0.05). Moreover, compared with the control group, the treatments showed antimicrobial effects. Our results indicated that these natural antioxidants could be used as lipid oxidation stabilizers of meat by-products during storage and that Artemisiacapillaris Thunb. and Opuntia may have applications as natural antioxidants in the meat by-product industry.
Physicochemical characteristics of Sengmaksan added with Liriope platyphylla roasted for different times
Authors: Kim Gyeong-Wha , Kang Min-Jung , Kang Jae-Ran , Shin Jung-Hye
Published: March 2020

This study investigates, the physicochemical characteristics of Sengmaksan (SM) prepared with Liriope platyphylla (LP) that had been roasted for different times (0, 30, 60, and 90 min, denoted as S-0, S-30, S-60, and S-90, respectively) The Hunter’s color values such as lightness (L), redness (a), and yellowness (b) were the highest in S-0, while the lowest was found in S-90. The amount of soluble solid and reducing sugar content of S-60 were higher than the others. None of the samples exhibit significant differences in, their pH and acidity. The total content of phenolic compounds increased with the LP roasting time, but the total flavonoid and total anthocyanin contents of the SM decreased at the same time. The total ginsenoside (Ro, Rb2, Re, Rf, Rg1, Rg2, Rg3, Rh1, and Rh2) content did not show significant differences. The DPPH and ABTS radical scavenging activities increased according to the concentration, as well as with the LP roasting time. The ferric reducing antioxidant power (FRAP) showed trends similar to the radical scavenging activity, but it was more sensitive to the LP roasting time. From these results, the active ingredient in S-60 was higher, and the antioxidant activities of SM increased along with the roasting time of LP.
The anti-oxidant, whitening and anti-wrinkle effects of Castanea crenata inner shell extracts processed by enzyme treatment and pressurized extraction
Authors: Gu Yul Ri , Kim Ju Hyeon , Hong Joo-Heon
Published: March 2020

In this study, the anti-oxidant, whitening, and anti-wrinkle effects of Castanea crenata inner shell extracts processed by enzyme treatment and pressurized extraction were investigated. The Castanea crenata inner shell was first hydrolyzed using celluclast, viscozyme, or hemicellulase. Then, it was subjected to pressure extraction for different durations (30, 60, and 120 min). The yields of the Castanea crenata inner shell extracts processed by different enzyme treatments followed by pressurized extraction for different times are in the range of 12.42-29.80%. The total polyphenol, flavonoid, and tannin contents of the C30m (celluclast enzyme and autoclave extracts at 30 min) extract were 15.48, 10.82, and 15.82 g/100 g, respectively. The total sugar content of the H120m(hemicellulase enzyme and autoclave extracts at 120 min) extract is 61.07 g/100 g. The 1,1-diphenyl-2-pycrylhydrazyl (DPPH) and 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging activities of the C30m extract at 1,000 μg/mL are 89.20, and 81.96%, respectively. The superoxide radical scavenging and ferric-reducing antioxidant power of the C30m extract at 1,000 μg/mL are 67.63% and 1,324.79 μM, respectively. Further, the tyrosinase and elastase inhibition activity of the C30m extract at 1,000 μg/mL are 61.32, and 61.06%, respectively. Our results indicate that the Castanea crenata inner shell extracts processed by enzyme treatment followed by pressurized extraction could have beneficial effects on facial skin and they should be considered for use in new functional cosmetics.
Optimization of formation of the ginsenoside Rg3 in
black ginseng steamed with acetic acid solution
Authors: Lee Gee-Dong
Published: March 2020

This study aimed to obtain high quality black ginseng with a high content of the
ginsenoside Rg3 and melanoidins and low benzopyrene content via nine
steaming-drying cycles. The steaming-drying of ginseng was carried out at low
pH, and the heat treatment conditions were set to gradually decrease. The
steaming-drying conditions were evaluated using response surface methodology.
The coefficients of determination (R2) of the models were
0.8926–0.9744 (p<0.05) for the dependent parameters. The response surface
for the intensity of the brown color of the black ginseng showed a maximum point
at which the brown color intensity was 3.39 (OD at 420 nm) at a mean steaming
time of 155.25 min and a mean drying temperature of 57.56°C. The response
surface for the ginsenoside Rg3 content of black ginseng showed a
saddle point with a maximum ginsenoside Rg3 content of 6.26 mg/g at a
mean steaming time of 177.72 min and a mean drying temperature of
65.46°C. However, the response surface for the benzopyrene content of
black ginseng showed a maximum point, with the lowest benzopyrene content of
0.22 μg/kg occurring at a mean steaming time of 60.97 min and a mean
drying temperature of 56.42°C. The optimal conditions were determined to
be a mean steaming time of 175 min and at a mean drying temperature of
68°C; black ginseng manufactured using these conditions yielded a brown
color intensity of 2.72 and a Rg3 content of 6.20 mg/g, with a low
benzopyrene content of 0.29 μg/kg.
Molecular stratification of endometrioid ovarian carcinoma predicts clinical outcome
Authors: Hollis Robert L , Thomson John P , Stanley Barbara , Churchman Michael , Meynert Alison M , Rye Tzyvia , Bartos Clare , Iida Yasushi , Croy Ian , Mackean Melanie , Nussey Fiona , Okamoto Aikou , Semple Colin A , Gourley Charlie , Herrington C. Simon
Published: March 2020

Endometrioid ovarian carcinoma (EnOC) is an under-investigated type of ovarian carcinoma. Here, we report the largest genomic study of EnOCs to date, performing whole exome sequencing of 112 cases following rigorous pathological assessment. High frequencies of mutation were detected in CTNNB1(43%), PIK3CA(43%), ARID1A(36%), PTEN(29%), TP53(26%) and SOX8(19%), a novel target of recurrent mutation in EnOC. POLE and mismatch repair protein-encoding genes were mutated at lower frequency (6%, 18%) with significant co-occurrence. A molecular taxonomy was constructed using a novel algorithm (PRISTINE), identifying clinically distinct EnOC subtypes: TP53m cases demonstrated greater genomic complexity, were frequently FIGO stage III/IV at diagnosis (48%) and incompletely debulked (44%), and demonstrated inferior survival; conversely, CTNNB1m cases demonstrated low complexity and excellent clinical outcome, were predominantly stage I/II at diagnosis (89%) and completely resected (87%). Tumour complexity provides further resolution within the TP53wt/CTNNB1wt group. Moreover, we identify the WNT, MAPK/RAS and PI3K pathways as good candidate targets for molecular therapeutics in EnOC.
Mouse-specific but infection-unspecific IgM repertoire fingerprint following viral infection
Authors: Yermanos Alexander , Kräutler Nike Julia , Pedrioli Alessandro , Menzel Ulrike , Greiff Victor , Stadler Tanja , Oxenius Annette , Reddy Sai T.
Published: March 2020

Antibody repertoire sequencing provides a molecular fingerprint of current and past pathogens encountered by the immune system. Most repertoire studies in humans require measuring the B cell response in the blood, resulting in a large bias to the IgM isotype. The extent to which the circulating IgM antibody repertoire correlates to lymphoid tissue-resident B cells in the setting of viral infection remains largely uncharacterized. Therefore, we compared the IgM repertoires from both blood and bone marrow (BM) plasma cells (PCs) following acute or chronic lymphocytic choriomeningitis virus (LCMV) infection in mice. Despite previously reported serum alterations between acute and chronic infection, IgM repertoire signatures based on clonal diversity metrics, public clones, network and phylogenetic analysis were largely unable to distinguish infection cohorts. Our findings, however, revealed mouse-specific congruence between the blood and PC repertoires irrespective of infection status. Our study reveals that IgM repertoire analyses may be unsuitable for providing a fingerprint of current or previous immune challenges.
Understanding phase-amplitude coupling from bispectral analysis
Authors: Zandvoort Coen S. , Nolte Guido
Published: March 2020

Two measures of cross-frequency coupling (CFC) are Phase-Amplitude Coupling (PAC) and bicoherence. The estimation of PAC with meaningful bandwidth for the high frequency amplitude is crucial in order to avoid misinterpretations. While recommendations on the bandwidth of PAC’s amplitude component exist, there is no consensus yet. Here, we show that the earlier recommendations on filter settings lead to estimates which are smeared in the frequency domain, which makes it difficult to distinguish higher harmonics from other types of CFC. We also show that smearing can be avoided with a different choice of filter settings by theoretically relating PAC to bicoherence. To illustrate this, PAC estimates of simulations and empirical data are compared to bispectral analyses. We used simulations replicated from an earlier study and empirical data from human electro-encephalography and rat local field potentials. PAC’s amplitude component was estimated using a bandwidth with a ratio of (1) 2:1, (2) 1:1, or (3) 0.5:1 relative to the frequency of the phase component. For both simulated and empirical data, PAC was smeared over a broad frequency range and not present when the estimates comprised a 2:1- and 0.5:1-ratio, respectively. In contrast, the 1:1-ratio accurately avoids smearing and results in clear signals of CFC. Bicoherence estimates, which do not smear across frequencies by construction, were found to be essentially identical to PAC calculated with the recommended frequency setting.
Adaptable pulsatile flow generated by quantitative imaging of stem-cell derived cardiomyocytes for disease modeling
Authors: Qian Tongcheng , Gil Daniel A. , Guzman Emmanuel Contreras , Gastfriend Benjamin D. , Tweed Kelsey E. , Palecek Sean P. , Skala Melissa C.
Published: March 2020

Endothelial cells (EC)in vivoare continuously exposed to a mechanical microenvironment from blood flow, and fluidic shear stress plays an important role in EC behavior. New approaches to generate physiologically and pathologically relevant pulsatile flows are needed to understand EC behavior under different shear stress regimes. Here, we demonstrate an adaptable pump (Adapt-Pump) platform for generating pulsatile flows via quantitative imaging of human pluripotent stem cell-derived cardiac spheroids (CS). Pulsatile flows generated from the Adapt-Pump system can recapitulate unique CS contraction characteristics, accurately model responses to clinically relevant drugs, and simulate CS contraction changes in response to fluidic mechanical stimulation. We discovered that ECs differentiated under a long QT syndrome derived pathological pulsatile flow exhibit abnormal EC monolayer organization. This Adapt-Pump platform provides a powerful tool for modeling the cardiovascular system and improving our understanding of EC behavior under different mechanical microenvironments.
Versatile Method to measure locomotion
Authors: Barwell Taylor , Raina Sehaj , Seroude Laurent
Published: March 2020

Many studies require the ability to quantify locomotor behavior over time. The list of tracking softwares and their capabilities are constantly growing. At the 2019 CanFly Conference we presented preliminary results from an investigation of the effects of expressing polyglutamine repeats in fly muscles on longevity, locomotion and protein aggregation and received a lot of inquiries about our protocol to measure locomotion and how to use the FlyTracker MatLab software. This report describes a versatile locomotion measuring device and custom MatLab scripts for the extraction and analysis, and compilation of FlyTracker data in a format compatible with spreadsheet softwares. The measurement and analysis of multiple genotypes and both sexes across age shows that this method yields reproducible results that confirm that normal aging is associated with a progressive decline in locomotion as indicated by increased immobility and reduced velocity.
Utilizing Quantum Biological Techniques on a Quantum Processing Unit for Improved Protein Binding Site Determination
Authors: Sandeep Samarth , Gupta Vaibhav , Keenan Torin
Published: March 2020

Iff Technologies has constructed a tool named Polar+ that can predict protein-to-protein binding sites on a given receptor protein that operates faster and at a higher quality than the prominent industry standards for protein binding, including Autodock Vina and SwissDock. The ability to provide this advantage comes from a new approach to biophysics, dubbed many-body biological quantum systems, that are modeled using quantum processing units and quantum algorithms. This paper provides both experimental and theoretical evidence behind the validity of the quantum biology approach to protein modeling, an overview of the first experimental work completed by Polar+, and a review of the results obtained.
Window of Opportunity for Mitigation to Prevent Overflow of ICU capacity in Chicago by COVID-19
Authors: Maslov Sergei , Goldenfeld Nigel
Published: March 2020

Executive Summary

We estimate the growth in demand for ICU beds in Chicago during the emerging COVID-19 epidemic, using state-of-the-art computer simulations calibrated for the SARS-CoV-2 virus. The questions we address are these:

Will the ICU capacity in Chicago be exceeded, and if so by how much?

Can strong mitigation strategies, such as lockdown or shelter in place order, prevent the overflow of capacity?

When should such strategies be implemented?

Our answers are as follows:

The ICU capacity may be exceeded by a large amount, probably by a factor of ten.

Strong mitigation can avert this emergency situation potentially, but even that will not work if implemented too late.

If the strong mitigation precedes April 1st, then the growth of COVID-19 can be controlled and the ICU capacity could be adequate. The earlier the strong mitigation is implemented, the greater the probability that it will be successful. After around April 1 2020, any strong mitigation will not avert the emergency situation. In Italy, the lockdown occurred too late and the number of deaths is still doubling every 2.3 days. It is difficult to be sure about the precise dates for this window of opportunity, due to the inherent uncertainties in computer simulation. But there is high confidence in the main conclusion that it exists and will soon be closed.

Our conclusion is that, being fully cognizant of the societal trade-offs, there is a rapidly closing window of opportunity to avert a worst-case scenario in Chicago, but only with strong mitigation/lockdown implemented in the next week at the latest. If this window is missed, the epidemic will get worse and then strong mitigation/lockdown will be required after all, but it will be too late.
Deletion of calcineurin from astrocytes reproduces proteome signature of Alzheimer’s disease and epilepsy and predisposes to seizures
Authors: Tapella Laura , Dematteis Giulia , Ruffinatti Federico Alessandro , Ponzoni Luisa , Fiordaliso Fabio , Corbelli Alessandro , Albanese Enrico , Pistolato Beatrice , Pagano Jessica , Barberis Elettra , Marengo Emilio , Balducci Claudia , Forloni Gianluigi , Verpelli Chiara , Sala Carlo , Distasi Carla , Sala Mariaelvina , Genazzani Armando A. , Manfredi Marcello , Lim Dmitry
Published: March 2020

In astrocytes, calcineurin (CaN) is involved in neuroinflammation and gliosis, while its role in healthy CNS or in early neuro-pathogenesis is poorly understood. Here we report that in astroglial CaN KO (ACN-KO) mice, at one month of age, proteome is deranged in hippocampus and cerebellum. Bioinformatic analysis reveals association with Alzheimer’s disease (AD) and epilepsy. We found significant overlap with the proteome of an AD mouse model and of human subjects with drug-resistant epilepsy. In Barnes maze ACN-KO mice learned the task but adopted serial search strategy. Strikingly, from five months of age ACN-KO mice develop spontaneous seizures with an inflammatory signature of epileptic brains. These results suggest that astroglial CaN KO impairs hippocampal connectivity, produces proteome features of neurological disorders and predisposes mice to seizures. We suggest that astroglial CaN may serve as a novel Ca2+-sensitive switch which regulates protein expression and homeostasis in the CNS.
Genes critical for development and differentiation of dopaminergic neurons are downregulated in Parkinson’s disease
Authors: Verma Aditi , Suresh Priya , Gnanabharathi Barathan , Hirsch Etienne C. , Ravindranath Vijayalakshmi
Published: March 2020

We performed transcriptome analysis using RNA sequencing on substantia nigra pars compacta (SNpc) from mice after acute and chronic 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) treatment and Parkinson’s disease (PD) patients. Acute and chronic exposure to MPTP resulted in decreased expression of genes involved in sodium channel regulation. However, upregulation of pro-inflammatory pathways was seen after single dose but not after chronic MPTP treatment. Dopamine biosynthesis and synaptic vesicle recycling pathways were downregulated in PD patients and after chronic MPTP treatment in mice. Genes essential for midbrain development and determination of dopaminergic phenotype such as, LMX1B, FOXA1, RSPO2, KLHL1, EBF3, PITX3, RGS4, ALDH1A1, RET, FOXA2, EN1, DLK1, GFRA1, LMX1A, NR4A2, GAP43, SNCA, PBX1, and GRB10 were downregulated in human PD and overexpression of LMX1B rescued MPP+induced death in SH-SY5Y neurons. Downregulation of gene ensemble involved in development and differentiation of dopaminergic neurons indicate their critical involvement in pathogenesis and progression of human PD.
CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells
Authors: Kubo Naoki , Ishii Haruhiko , Xiong Xiong , Bianco Simona , Meitinger Franz , Hu Rong , Hocker James D. , Conte Mattia , Gorkin David , Yu Miao , Li Bin , Dixon Jesse R. , Hu Ming , Nicodemi Mario , Zhao Huimin , Ren Bing
Published: March 2020

Topologically associating domains (TAD) and insulated neighborhoods (INs) have been proposed to constrain enhancer-promoter communications to enable cell-type specific transcription programs, but recent studies show that disruption of TADs and INs resulted in relatively mild changes in gene expression profiles. To better understand the role of chromatin architecture in dynamic enhancer-promoter contacts and lineage-specific gene expression, we have utilized the auxin-inducible degron system to acutely deplete CTCF, a key factor involved in TADs and IN formation, in mouse embryonic stem cells (mESCs) and examined chromatin architecture and gene regulation during neural differentiation. We find that while CTCF depletion leads to global weakening of TAD boundaries and loss of INs, only a minor fraction of enhancer-promoter contacts are lost, affecting a small subset of genes. The CTCF-dependent enhancer-promoter contacts tend to be long-range, spanning hundreds of kilobases, and are established directly by CTCF binding to promoters. Disruption of CTCF binding at the promoter reduces enhancer-promoter contacts and transcription, while artificial tethering of CTCF to the promoter restores the enhancer-promoter contacts and gene activation. Genome-wide analysis of CTCF binding and gene expression across multiple mouse tissues suggests that CTCF-dependent promoter-enhancer contacts may regulate expression of additional mouse genes, particularly those expressed in the brain. Our results uncover both CTCF-dependent and independent enhancer-promoter contacts, and highlight a distinct role for CTCF in promoting enhancer-promoter contacts and gene activation in addition to its insulator function.
Myocardial injury is associated with in-hospital mortality of confirmed or suspected COVID-19 in Wuhan, China: A single center retrospective cohort study
Authors: Zhang Fan , Yang Deyan , Li Jing , Gao Peng , Chen Taibo , Cheng Zhongwei , Cheng Kangan , Fang Quan , Pan Wan , Yi Chunfeng , Fan Hongru , Wu Yonghong , Li Liwei , Fang Yong , Liu Juan , Tian Guowei , He Liqun
Published: March 2020

Background

Since December 2019, a cluster of coronavirus disease 2019 (COVID-19) occurred in Wuhan, Hubei Province, China and spread rapidly from China to other countries. In-hospital mortality are high in severe cases and cardiac injury characterized by elevated cardiac troponin are common among them. The mechanism of cardiac injury and the relationship between cardiac injury and in-hospital mortality remained unclear. Studies focused on cardiac injury in COVID-19 patients are scarce.

Objectives

To investigate the association between cardiac injury and in-hospital mortality of patients with confirmed or suspected COVID-19.

Methods

Demographic, clinical, treatment, and laboratory data of consecutive confirmed or suspected COVID-19 patients admitted in Wuhan No.1 Hospital from 25thDecember, 2019 to 15thFebruary, 2020 were extracted from electronic medical records and were retrospectively reviewed and analyzed. Univariate and multivariate Cox regression analysis were used to explore the risk factors associated with in-hospital death.

Results

A total of 110 patients with confirmed (n=80) or suspected (n=30) COVID-19 were screened and 48 patients (female 31.3%, mean age 70.58±13.38 year old) among them with high-sensitivity cardiac troponin I (hs-cTnI) test within 48 hours after admission were included, of whom 17 (17/48, 35.4%) died in hospital while 31 (31/48, 64.6%) were discharged or transferred to other hospital. High-sensitivity cardiac troponin I was elevated in 13 (13/48, 27.1%) patents. Multivariate Cox regression analysis showed pulse oximetry of oxygen saturation (SpO2) on admission (HR 0.704, 95% CI 0.546-0.909, per 1% decrease, p=0.007), elevated hs-cTnI (HR 10.902, 95% 1.279-92.927, p=0.029) and elevated d-dimer (HR 1.103, 95%CI 1.034-1.176, per 1mg/L increase, p=0.003) on admission were independently associated with in-hospital mortality.

Conclusions

Cardiac injury defined by hs-cTnI elevation and elevated d-dimer on admission were risk factors for in-hospital death, while higher SpO2could be seen as a protective factor, which could help clinicians to identify patients with adverse outcome at the early stage of COVID-19.
A microscopy-based kinetic analysis of yeast vacuolar protein sorting
Authors: Casler Jason C. , Glick Benjamin S.
Published: March 2020

The yeastSaccharomyces cerevisiaeis amenable to studying membrane traffic by live-cell fluorescence microscopy. We used this system to explore two aspects of cargo protein traffic through prevacuolar endosome (PVE) compartments to the vacuole. First, at what point during Golgi maturation does a biosynthetic vacuolar cargo depart from the maturing cisternae? To address this question, we modified a regulatable fluorescent secretory cargo by adding a vacuolar targeting signal. Traffic of the vacuolar cargo requires the GGA clathrin adaptors, which arrive during the early-to-late Golgi transition. Accordingly, the vacuolar cargo begins to exit the Golgi near the midpoint of maturation, significantly before exit of a secretory cargo. Second, how are cargoes delivered from PVE compartments to the vacuole? To address this question, we tracked biosynthetic and endocytic cargoes after they had accumulated in PVE compartments. The results imply that stable PVE compartments repeatedly deliver material to the vacuole by a kiss-and-run mechanism.
Dynamic Sex Chromosome Expression in Drosophila Male Germ Cells
Authors: Mahadevaraju Sharvani , Fear Justin M. , Akeju Miriam , Galletta Brian J. , Pinheiro Mara MLS. , Avelino Camila C. , Cabral-de-Mello Diogo C. , Conlon Katie , Dell’Orso Stafania , Demere Zelalem , Mansuria Kush , Mendonça Carolina A. , Palacios-Gimenez Octavio M. , Ross Eli , Savery Max , Yu Kevin , Smith Harold E. , Sartorelli Vittorio , Rusan Nasser M. , Vibranovski Maria D. , Matunis Erika , Oliver Brian
Published: March 2020

Sex chromosome gene content and expression is unusual. In many organisms the X and Y chromosomes are inactivated in spermatocytes, possibly as a defense mechanism against insertions into unpaired chromatin. In addition to current sex chromosomes, Drosophila has a small gene-poor X-chromosome relic (4th) that re-acquired autosomal status. Using single cell RNA-Seq, we demonstrate that the single X and pair of 4thchromosomes are specifically inactivated in primary spermatocytes. In contrast, genes on the single Y chromosome become maximally active in primary spermatocytes. Reduced X steady-state transcript levels are due to failed activation of RNA-Polymerase-II by phosphorylation of Serine 2 and 5.

One Sentence Summary

Sex chromosome expression during spermatogenesis at the single cell level
Mechanisms of up-regulation of Ubiquitin-Proteasome activity in the absence of NatA dependent N-terminal acetylation
Authors: Kats Ilia , Kschonsak Marc , Khmelinskii Anton , Armbruster Laura , Ruppert Thomas , Knop Michael
Published: March 2020

N-terminal acetylation is a prominent protein modification and inactivation of N-terminal acetyltransferases (NATs) cause protein homeostasis stress. Using multiplexed protein stability (MPS) profiling with linear ubiquitin fusions as reporters for the activity of the ubiquitin proteasome system (UPS) we observed increased UPS activity in NatA, but not NatB or NatC mutants. We find several mechanisms contributing to this behavior. First, NatA-mediated acetylation of the N-terminal ubiquitin independent degron regulates the abundance of Rpn4, the master regulator of the expression of proteasomal genes. Second, the abundance of several E3 ligases involved in degradation of UFD substrates is increased in cells lacking NatA. Finally, we identify the E3 ligase Tom1 as a novel chain elongating enzyme (E4) involved in the degradation of linear ubiquitin fusions via the formation of branched K11 and K29 ubiquitin chains, independently of the known E4 ligases involved in UFD, leading to enhanced ubiquitination of the UFD substrates.
Acute stressors experienced by layer breeders do not affect measures of stress and fear in their offspring
Authors: Peixoto Mariana R. L. V. , Karrow Niel A. , Newman Amy , Head Jessica , Widowski Tina M.
Published: March 2020

Stressors experienced by layer breeders during egg production can lead to changes in the egg hormone content, potentially impacting their offspring, the commercial layers. Genetic differences might also affect the offspring’s susceptibility to maternal experiences. In this study, we tested if maternal stress affects measures of stress and fear in five strains of layer breeders: commercial brown 1 & 2, commercial white 1 & 2 and a pure line White Leghorn. Each strain was equally separated into two groups: “Maternal Stress” (MS), where hens were subjected to a series of 8 consecutive days of acute psychological stressors, and “Control,” which received routine husbandry. Additional eggs from Control were injected either with corticosterone diluted in a vehicle solution (“CORT”) or just “Vehicle.” Stress- and fear-responses of the offspring were measured in a plasma corticosterone test and a combined human approach and novel object test. Both MS and CORT treatments failed to affect the measured endpoints in the offspring, but significant strain differences were found. The offspring of the white strains showed a higher physiological response compared to brown strains, but the White 2 offspring was consistently the least fearful strain in the behaviour tests. Our study found that the acute psychological stressors experienced by layer breeders did not affect the parameters tested in their offspring and that corticosterone does not seem to be the primary mediator of maternal stress in laying hens. This is highly important, as in poultry production, layer breeders are often subjected to short-term stressors. In addition, we successfully dissociated the physiological and behavioural parameters of stress response in laying hens, showing that increased concentrations of plasma corticosterone in response to stress is not directly associated with high levels of fear.
Mitochondrial Genome Sequence ofPhytophthora sansomeanaand Comparative Analysis ofPhytophthoraMitochondrial Genomes
Authors: Cai Guohong , Scofield Steven R.
Published: March 2020

Phytophthora sansomeanainfects soybean and causes root rot. It was recently separated from the species complexP. megasperma sensu lato.In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine otherPhytophthoraspecies. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthetase genes, 16 ribosomal proteins genes, atatCtranslocase gene, six conserved ORFs and a uniqueorf402.The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10Phytophthoraspecies revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3’ truncatedatp9gene was found inP. nicotianae.All 10Phytophthoraspecies, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny ofPhytophthoraspp.