bluuebunny/crossref_metadata_2025 huggingface dataset:
Screening assay using an epigenetic modulator library identifies I10 that promotes melanin synthesis in B16/F10 melanoma cells
Authors: Hwang Yun Jeong , Boo Yong Chool
Published: April 2020

Skin pigmentation is affected by genetic, epigenetic and many other factors, and contributes to human beauty and health. Recent studies reported that certain epigenetic modulators altered the gene expression of enzymes involved in melanin synthesis, suggesting that those drugs may be potentially useful in treating skin hyper‐ or hypo‐pigment disorders. The aim of the present study is to find a drug candidate from an epigenetic drug library that can promote melanin synthesis in cells. Each drug was examined for the stimulatory effects on melanin synthesis in B16F10 murine melanoma cells. Of 141 drugs tested, I10 was selected because it most effectively stimulated melanin synthesis. Like forskolin, an adenylate cyclase activator, I10 increased the mRNA and protein levels of tyrosinase enzyme, the rate‐limiting enzyme involved in melanin synthetic pathway. However, unlike forskolin, I10 did not stimulate the expression of microphthalmia‐associated transcription factor (MITF), a key regulator of melanin synthesis. Although much further research is needed, this current study suggests that I10 may promote cellular melanin synthesis through a mechanism that is distinct from that of forskolin, and it may be a new drug candidate for the treatment of skin hypo‐pigmentation disorders such as vitiligo.

Support or Funding Information

This work was supported by a National Research Foundation of Korea (NRF) grant funded by the Korea government (Ministry of Science and ICT) (No. 2019R1I1A2A01045132).
The role of NEGR1 in the formation of lipid droplets
Authors: An Dayoung , Joo Yeonhee , Kim Hyejin
Published: April 2020

Neuronal growth regulator 1 (NEGR1) is a membrane raft‐associated protein, which has been spotlighted as a new locus related to human obesity. We previously identified that NEGR1 interact with Niemann‐Pick diseases, type C2 (NPC2) that plays a key role in intracellular cholesterol trafficking, suggesting a new role of NEGR1 in the intracellular lipid transport. In this study, we report that the level of lipid droplets (LD) reduced in NEGR1‐overexpressiong 3T3L‐1 cells compared to vector‐transfected controls. Moreover, we observed that the intracellular LD level was higher in primary adipocytes obtained from NEGR1−/− mice than those from wild‐type mice. In addition, the expression level of LD‐associated protein, perilipin‐2/ADRP, increased in white adipose tissues of NEGR1‐deficient mice, although we could not detect any direct interaction between NEGR1 and ADRP proteins. Altogether, we suggest that NEGR1 is involved in LD formation possibly by regulating the intracellular lipid trafficking.

Support or Funding Information

Korea research foundation
Pharmacokinetics of a potent soluble epoxide hydrolase inhibitor in three formulations
Authors: YANG JUN , Wagner Karen , Wan Debin , Hwang Sung-Hee , McReynolds Cindy B. , Hammock Bruce D.
Published: April 2020

Inhibition of soluble epoxide hydrolase (sEHI) was shown to be potent to reduce the inflammation, lower the blood pressure in hypertension and is being developed for indication of chronic pain treatment. Guiding by in vitro potency screening, pharmacokinetics and in vivo efficacy studies, a potent sEHI (EC5026) is optimized for the followed clinical trials. Besides its own properties, formulation method is an important factor to be considered to reach ideal exposure time span and concentration in vivo, therefore for the efficacy in vivo.

Here, we compared three different formulation methods: PEG mixtures, hot melt extrusion (HME), spray‐dried dispersion (SDD) for EC5026 by comparing the pharmacokinetics in Sprague Dawley rats. A sensitive UHPLC/MS/MS method was developed to measure the concentration of EC 5026 in the blood of rats after oral dosing at 3mg/Kg as a single dose. The pharmacokinetics parameters including Cmax, Tmax, AUC were calculated using non‐compartment modeling analysis. The result shows that three different formulations have similar pharmacokinetics properties with the highest Cmax in SDD (1,557 ng/mL) followed by HME (1,432 ng/mL) and PEG mixture (1,329 ng/mL). Tmax are all about the same at 2.5 and 3 hour respectively. The T1/2s are between 75–90 hours.

The results above indicates all three formulations are proper for decent exposure of EC5026 with AUC from 6759–8516 ng/mL hr. The similarity among these three formulations allow the translation to the clinical trials using the new formulations (HME/SDD) from the preclinical studies with PEG mixture.

Support or Funding Information

Support or Funding InformationThis work was supported in part by NIEHS grant R35 ES030443, NIEHS Superfund Basic Research Program grant P42 ES04699.
Phaeohyphomycosis caused by Diaporthe phaseolorum in an immunocompetent patient in Thailand: a case report
Authors: Laosakul Kulwadee , Youngchim Sirida , Chuamanochan Mati , Rujiwetpongstorn Rujira , Tovanabutra Napatra , Chiewchanvit Siri
Published: April 2020

Phaeohyphomycosis is caused by a large, heterogeneous group of darkly pigmented fungi. It is an infrequent infection in humans. However, the prevalence has been increasing in recent years especially in immunocompromised patients. Diaporthe phaseolorum is a common black fungal pathogen of plants, which rarely causes human infection. We report the first case of cutaneous infection caused by Diaporthe phaseolorum in an immunocompetent host and the first in Asia. Although, the review of the literature revealed two previous cases of cutaneous infection caused by this organism, both of them were in immunocompromised hosts. A slow-growing asymptomatic nodule was the major clinical feature. Histopathological examination showed granulomatous inflammation and pigmented septate hyphae and yeast-like cells. The fungal isolation was identified by morphological characteristics and DNA sequencing. The lesion was resolved after complete surgical excision and oral fluconazole for two months. This report highlights the potential role of Diaporthe phaseolorum as an emerging cause of infection in immunocompetent patients.
Expression of an alcohol dehydrogenase gene in a heterotrophic bacterium induces carbon dioxide-dependent high-yield growth under oligotrophic conditions
Authors: Inaba Shinnosuke , Sakai Hironori , Kato Hiromi , Horiuchi Takayuki , Yano Hirokazu , Ohtsubo Yoshiyuki , Tsuda Masataka , Nagata Yuji
Published: April 2020

Sphingobium japonicum

strain UT26, whose γ-hexachlorocyclohexane-degrading ability has been studied in detail, is a typical aerobic and heterotrophic bacterium that needs organic carbon sources for its growth, and cannot grow on a minimal salt agar medium prepared without adding any organic carbon sources. Here, we isolated a mutant of UT26 with the ability to grow to visible state on such an oligotrophic medium from a transposon-induced mutant library. This high-yield growth under oligotrophic conditions (HYGO) phenotype was CO2-dependent and accompanied with CO2 incorporation. In the HYGO mutant, a transposon was inserted just upstream of the putative Zn-dependent alcohol dehydrogenase (ADH) gene (adhX) so that the adhX gene was constitutively expressed, probably by the transposon-derived promoter. The adhX-deletion mutant (UT26DAX) harbouring a plasmid carrying the adhX gene under the control of a constitutive promoter exhibited the HYGO phenotype. Moreover, the HYGO mutants spontaneously emerged among the UT26-derived hypermutator strain cells, and adhX was highly expressed in these HYGO mutants, while no HYGO mutant appeared among UT26DAX-derived hypermutator strain cells, indicating the necessity of adhX for the HYGO phenotype. His-tagged AdhX that was expressed in

Escherichia coli

and purified to homogeneity showed ADH activity towards methanol and other alcohols. Mutagenesis analysis of the adhX gene indicated a correlation between the ADH activity and the HYGO phenotype. These results demonstrated that the constitutive expression of an adhX-encoding protein with ADH activity in UT26 leads to the CO2-dependent HYGO phenotype. Identical or nearly identical adhX orthologues were found in other sphingomonad strains, and most of them were located on plasmids, suggesting that the adhX-mediated HYGO phenotype may be an important adaptation strategy to oligotrophic environments among sphingomonads.
Breastfeeding of Infants Born to Mothers with COVID-19: A Rapid Review
Authors: Yang Nan , Che Siyi , Zhang Jingyi , Wang Xia , Tang Yuyi , Wang Jianjian , Huang Liping , Wang Chenglin , Zhang Hairong , Baskota Muna , Ma Yanfang , Zhou Qi , Luo Xufei , Yang Shu , Feng Xixi , Li Weiguo , Fukuoka Toshio , Ahn Hyeong Sik , Lee Myeong Soo , Luo Zhengxiu , Liu Enmei , Chen Yaolong
Published: April 2020

Background

Existing recommendations on whether mothers with COVID-19 should continue breastfeeding are still conflicting. We aimed to conduct a rapid review of mother-to-child transmission of COVID-19 during breastfeeding.

Methods

We systematically searched Medline, Embase, Web of Science, Cochrane library, China Biology Medicine disc, China National Knowledge Infrastructure, Wanfang, and preprint articles up to March 2020. We included studies relevant to transmission through milk and respiratory droplets during breastfeeding of mothers with COVID-19, SARS, MERS and influenza. Two reviewers independently screened studies for eligibility, extracted data, assessed risk of bias and used GRADE to assess certainty of evidence.

Results

A total of 4481 records were identified in our literature search. Six studies (five case reports and one case series) involving 58 mothers (16 mothers with COVID-19, 42 mothers with influenza) and their infants proved eligible. Five case reports showed that the viral nucleic acid tests for all thirteen collected samples of breast milk from mothers with COVID-19 were negative. A case series of 42 influenza infected postpartum mothers taking precautions (hand hygiene and wearing masks) before breastfeeding showed that no neonates were infected with influenza during one-month of follow-up.

Conclusions

The current evidence indicates that SARS-CoV-2 viral nucleic acid has not been detected in breast milk. The benefits of breastfeeding may outweigh the risk of SARS-CoV-2 infection in infants. Mothers with COVID-19 should take appropriate precautions to reduce the risk of transmission via droplets and close contact during breastfeeding.
An automatic and efficient pulmonary nodule detection system based on multi-model ensemble
Authors: Chen Jian , Wang Wenlei , Ju Bin , Jiang Jing , Zhang Liying , He Huilin , Zhang Xuanxuan , Shen Yuqiang
Published: April 2020

Accurate pulmonary nodule detection plays an important role in early screening of lung cancer. Although there are many presented CAD systems based on deep learning for pulmonary nodule detection, these methods still have some problems in clinical use. The improvement of false negatives rate of tiny nodules, the reduction of false alarms and the optimization of time consumption are some of them that need to be solved as soon as possible. In view of the above problems, in this paper, we first propose a novel full convolution segmentation framework for lung cavity extraction in preprocessing stage to solve the time consumption problem of the existing pulmonary nodule detection systems. Furthermore, a 2D-NestedUNet segmentation network and a 3D-RPN detection network is stacked to get the high recall and low false positive rate on nodule candidate extraction, especially the recall of tiny nodules. Finally, a false positive reduction method based on multi-model ensemble is proposed for the further classification of nodule candidates. Our methods are evaluated on several public datasets, LUNA16, LNDb and ChestCT2019, which demonstrated the superior performance of our CAD system.
Efficient high throughput SARS-CoV-2 testing to detect asymptomatic carriers
Authors: Shental Noam , Levy Shlomia , Wuvshet Vered , Skorniakov Shosh , Shemer-Avni Yonat , Porgador Angel , Hertz Tomer
Published: April 2020

The COVID-19 pandemic is rapidly spreading throughout the world. Recent reports suggest that 10-30% of SARS-CoV-2 infected patients are asymptomatic. Other studies report that some subjects have significant viral shedding prior to symptom onset. Since both asymptomatic and pre-symptomatic subjects can spread the disease, identifying such individuals is critical for effective control of the SARS-CoV-2 pandemic. Therefore, there is an urgent need to increase diagnostic testing capabilities in order to also screen asymptomatic carriers. In fact, such tests will be routinely required until a vaccine is developed. Yet, a major bottleneck of managing the COVID-19 pandemic in many countries is diagnostic testing, due to limited laboratory capabilities as well as limited access to genome-extraction and Polymerase Chain Reaction (PCR) reagents. We developed P-BEST - a method for Pooling-Based Efficient SARS-CoV-2 Testing, using a non-adaptive group-testing approach, which significantly reduces the number of tests required to identify all positive subjects within a large set of samples. Instead of testing each sample separately, samples are pooled into groups and each pool is tested for SARS-CoV-2 using the standard clinically approved PCR-based diagnostic assay. Each sample is part of multiple pools, using a combinatorial pooling strategy based on compressed sensing designed for maximizing the ability to identify all positive individuals. We evaluated P-BEST using leftover samples that were previously clinically tested for COVID-19. In our current proof-of-concept study we pooled 384 patient samples into 48 pools providing an 8-fold increase in testing efficiency. Five sets of 384 samples, containing 1-5 positive carriers were screened and all positive carriers in each set were correctly identified. P-BEST provides an efficient and easy-to-implement solution for increasing testing capacity that will work with any clinically approved genome-extraction and PCR-based diagnostic methodologies.
Comparative Evaluation of cobas Influenza A/B & RSV and Simplexa Flu A/B & RSV for Rapid Detection of Influenza and Respiratory Syncytial Viruses
Authors: Hur Kyu-Hwa , Sung Heungsup , Kim Mi-Na
Published: April 2020

We compared two molecular point-of-care tests, the cobas Influenza A/B & RSV (cobas Liat) and the Simplexa Flu A/B & RSV (Simplexa). A total of 236 respiratory specimens from patients referred for respiratory viruses testing were retrospectively evaluated; 53 specimens tested positive for each of Flu A, Flu B, and RSV, and 77 specimens tested negative based on the results of the reference method, i.e. the Seegene Allplex Respiratory Panel 1/2/3 (Seegene, Seoul, Korea). The turnaround time (TAT) was 20 min per specimen for cobas Liat and 78 min per eight specimens for Simplexa. The numbers of invalid results were one (0.4%) in cobas Liat and 10 (4.2%) in Simplexa (p < 0.05). All results were consistent with those of the reference method in cobas Liat. The sensitivity and specificity for Flu A, Flu B and RSV A were 100% with Simplexa. However, the sensitivity for RSV B was 80.0% with Simplexa, which was significantly lower than that of cobas Liat (p < 0.05). Comparison of the cycle threshold (Ct) values for RSV with Simplexa and the reference method showed the correlation as continuous variables (p < 0.001) with a higher propensity for obtaining Ct values with Simplexa, the exception being the six false negative results; their Ct values were more than 30 in the reference method. Cobas Liat showed high sensitivity for the detection of RSV B with rapid TAT, and a good workflow efficiency.
Quantitative form and fit of N95 filtering facepiece respirators are retained and coronavirus surrogate is inactivated after heat treatments
Authors: Massey Travis , Borucki Monica , Paik Samuel , Fuhrer Kyle , Bora Mihail , Kane Staci , Haque Razi , Baxamusa Salmaan
Published: April 2020

Re-use of filtering facepiece respirators (FFRs, commonly referred to as N95s) normally meant for single use only is becoming common in healthcare facilities due to shortages caused by the COVID19 pandemic. Here we report that mouse hepatitis virus (MHV) initially seeded on FFR filter material is inactivated (6 log reduction as measured by 50% tissue culture infective dose (TCID50)) after dry heating at 75 ºC for 30 minutes. We also find that the quantitative fit of FFRs after heat treatment at this temperature, under dry conditions or at 90% relative humidity, is not affected by single or ten heating cycles. Previous studies have reported that the filtration efficiency of FFR filters is not negatively impacted by these heating conditions. These results suggest that thermal inactivation of coronaviruses is a potentially rapid and widely deployable method to re-use N95 FFRs in emergency situations where re-using FFRs is a necessity and broad-spectrum sterilization is unavailable. However, we also found that a heat source that emits radiation (e.g., an exposed heating element) results in rapid qualitative degradation of the FFR. Finally, we discuss differences in the results reported here and other recent studies investing heat as a means to recycle FFRs and suggest that overall wear time and donning/doffing cycles are important factors that need to be considered.
Epidemiology, clinical course, and outcomes of critically ill adults with COVID-19 in New York City: a prospective cohort study
Authors: Cummings Matthew J. , Baldwin Matthew R. , Abrams Darryl , Jacobson Samuel D. , Meyer Benjamin J. , Balough Elizabeth M. , Aaron Justin G. , Claassen Jan , Rabbani LeRoy E. , Hastie Jonathan , Hochman Beth R. , Salazar-Schicchi John , Yip Natalie H. , Brodie Daniel , O’Donnell Max R.
Published: April 2020

Background

Nearly 30,000 patients with coronavirus disease-2019 (COVID-19) have been hospitalized in New York City as of April 14th, 2020. Data on the epidemiology, clinical course, and outcomes of critically ill patients with COVID-19 in this setting are needed.

Methods

We prospectively collected clinical, biomarker, and treatment data on critically ill adults with laboratory-confirmed-COVID-19 admitted to two hospitals in northern Manhattan between March 2nd and April 1st, 2020. The primary outcome was in-hospital mortality.

Secondary outcomes included frequency and duration of invasive mechanical ventilation, frequency of vasopressor use and renal-replacement-therapy, and time to clinical deterioration following hospital admission. The relationship between clinical risk factors, biomarkers, and in-hospital mortality was modeled using Cox-proportional-hazards regression. Each patient had at least 14 days of observation.

Results

Of 1,150 adults hospitalized with COVID-19 during the study period, 257 (22%) were critically ill. The median age was 62 years (interquartile range [IQR] 51-72); 170 (66%) were male. Two-hundred twelve (82%) had at least one chronic illness, the most common of which were hypertension (63%; 162/257) and diabetes mellitus (36%; 92/257). One-hundred-thirty-eight patients (54%) were obese, and 13 (5%) were healthcare workers. As of April 14th, 2020, in-hospital mortality was 33% (86/257); 47% (122/257) of patients remained hospitalized. Two-hundred-one (79%) patients received invasive mechanical ventilation (median 13 days [IQR 9-17]), and 54% (138/257) and 29% (75/257) required vasopressors and renal-replacement-therapy, respectively. The median time to clinical deterioration following hospital admission was 3 days (IQR 1-6). Older age, hypertension, chronic lung disease, and higher concentrations of interleukin-6 and d-dimer at admission were independently associated with in-hospital mortality.

Conclusions

Critical illness among patients hospitalized with COVID-19 in New York City is common and associated with a high frequency of invasive mechanical ventilation, extra-pulmonary organ dysfunction, and substantial in-hospital mortality.
Mandatory social distancing associated with increased doubling time: an example using hyperlocal data
Authors: Ebell Mark H. , Bagwell-Adams Grace
Published: April 2020

In a hyperlocal analysis of doubling time of COVID-19, we found that a county that implemented mandatory social distancing and other measures to reduce spread of infection saw an earlier increase in doubling time than surrounding counties.
A novel USP30 inhibitor recapitulates genetic loss of USP30 and sets the trigger for PINK1-PARKIN amplification of mitochondrial ubiquitylation
Authors: Rusilowicz-Jones Emma , Jardine Jane , Kallinos Andreas , Pinto-Fernandez Adan , Guenther Franziska , Giurrandino Mariacarmela , Barone Francesco G. , McCarron Katy , Burke Christopher J. , Murad Alejandro , Martinez Aitor , Marcassa Elena , Gersch Malte , Buckmelter Alex , Kayser-Bricker Katherine J. , Lamoliatte Frederic , Gajbhiye Akshada , Davis Simon , Scott Hannah C. , Murphy Emma , England Katherine , Mortiboys Heather , Komander David , Trost Matthias , Kessler Benedikt M. , Ioannidis Stephanos , Ahlijanian Michael , Urbé Sylvie , Clague Michael J.
Published: April 2020

The mitochondrial deubiquitylase USP30 negatively regulates the selective autophagy of damaged mitochondria. It has been proposed as an actionable target to alleviate the loss of function of the mitophagy pathway governed by the Parkinson’s Disease associated genes PINK1 and PRKN. We present the characterisation of a N-cyano pyrrolidine derived compound, FT3967385, with high selectivity for USP30. The compound is well tolerated with no loss of total mitochondrial mass. We demonstrate that ubiquitylation of TOM20, a component of the outer mitochondrial membrane import machinery that directly interacts with USP30, represents a robust biomarker for both USP30 loss and inhibition. We have conducted proteomics analyses on a SHSY5Y neuroblastoma cell line model to directly compare the effects of genetic loss of USP30 with selective inhibition in an unbiased fashion. We have thereby identified a subset of ubiquitylation events consequent to mitochondrial depolarisation that are USP30 sensitive. Within responsive elements of the ubiquitylome, several components of the outer mitochondrial membrane transport (TOM) complex are most prominent. Thus, our data support a model whereby USP30 can regulate the availability of ubiquitin at the specific site of mitochondrial PINK1 accumulation following membrane depolarisation. In this model, USP30 deubiquitylation of TOM complex components dampens the trigger for the Parkin-dependent amplification of mitochondrial ubiquitylation leading to mitophagy. Accordingly, PINK1 generation of phospho-Ser65 Ubiquitin proceeds more rapidly and to a greater extent in cells either lacking USP30 or subject to USP30 inhibition.
Rapid direct nucleic acid amplification test without RNA extraction for SARS-CoV-2 using a portable PCR thermocycler
Authors: Wee Soon Keong , Sivalingam Suppiah Paramalingam , Yap Eric Peng Huat
Published: April 2020

There is an ongoing worldwide coronavirus disease 2019 (Covid-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At present, confirmatory diagnosis is by reverse transcription polymerase chain reaction (RT-PCR), typically taking several hours and requiring a molecular laboratory to perform. There is an urgent need for rapid, simplified and cost-effective detection methods. We have developed and analytically validated a protocol for direct rapid extraction-free PCR (DIRECT-PCR) detection of SARS-CoV-2 without the need for nucleic acid purification. As few as 6 RNA copies per reaction of viral nucleocapsid (N) gene from respiratory samples such as sputum and nasal exudate can be detected directly using our one-step inhibitor-resistant assay. The performance of this assay was validated on a commercially available portable PCR thermocycler. Viral lysis, reverse transcription, amplification and detection are achieved in a single-tube homogeneous reaction within 36 minutes. This minimized hands-on time, reduces turnaround-time for sample-to-result and obviates the need for RNA purification reagents. It could enable wider use of Covid-19 testing for diagnosis, screening and research in countries and regions where laboratory capabilities are limiting.
Comparison of SARS-CoV2 N gene real-time RT-PCR targets and commercially available mastermixes
Authors: Brown Julianne R , O’Sullivan Denise , Pereira Rui PA , Whale Alexandra S , Busby Eloise , Huggett Jim , Harris Kathryn
Published: April 2020

We aim to test four one-step RT real-time mastermix options for use in SARS-CoV2 real-time PCR, with three primer/probe assays targeting the N gene. The lower limit of detection is determined using a SARS CoV2 N gene RNA transcript dilution series (to 1 copy/µl) and verified using 74 nose and throat swabs.

The N2 assay demonstrates the most sensitive detection of SARS-Cov-2 RNA. Three of the four mastermixes performed well, with the Takara One Step PrimeScript™ III RT-PCR Kit mastermix demonstrating improved performance at the lower limit of detection.
The crystal structure of nsp10-nsp16 heterodimer from SARS-CoV-2 in complex with S-adenosylmethionine
Authors: Rosas-Lemus Monica , Minasov George , Shuvalova Ludmilla , Inniss Nicole L. , Kiryukhina Olga , Wiersum Grant , Kim Youngchang , Jedrzejczak Robert , Maltseva Natalia I. , Endres Michael , Jaroszewski Lukasz , Godzik Adam , Joachimiak Andrzej , Satchell Karla J. F.
Published: April 2020

SARS-CoV-2 is a member of the coronaviridae family and is the etiological agent of the respiratory Coronavirus Disease 2019. The virus has spread rapidly around the world resulting in over two million cases and nearly 150,000 deaths as of April 17, 2020. Since no treatments or vaccines are available to treat COVID-19 and SARS-CoV-2, respiratory complications derived from the infections have overwhelmed healthcare systems around the world. This virus is related to SARS-CoV-1, the virus that caused the 2002-2004 outbreak of Severe Acute Respiratory Syndrome. In January 2020, the Center for Structural Genomics of Infectious Diseases implemented a structural genomics pipeline to solve the structures of proteins essential for coronavirus replication-transcription. Here we show the first structure of the SARS-CoV-2 nsp10-nsp16 2’-O-methyltransferase complex with S-adenosylmethionine at a resolution of 1.80 Å. This heterodimer complex is essential for capping viral mRNA transcripts for efficient translation and to evade immune surveillance.
The accumulation of colibactin intermediates does not affect the growth and morphology ofpks+Escherichia coli
Authors: Morales-Lozada Yermary , Gómez-Moreno Ramón , Báez-Bravo Gabriela , Robledo Iraida E. , Suazo-Dávila Dámaris , Cabrera Carlos R. , Baerga-Ortiz Abel
Published: April 2020

Colibactin is a natural product made by numerous strains ofE. colithat harbor thepksgenomic island. The deletion of one of the genes within thepks island,the peptidase clbP, has been found to disrupt the maturation of colibactin, thus promoting the accumulation in the periplasmic space of numerous biosynthesis intermediates, some of which have been characterized chemically. To date, no one has reported the effect of such an accumulation of intermediates on the cellular morphology of the producingE. colibacterium. In this report, we describe the scanning electron microscopy (SEM) images of numerous clinical isolates ofE. coliharboring thepks island, collected from Puerto Rico hospitals. We have observed that the wild type isolates that harbor thepks islanddisplay lesions on the bacterial envelope surface. These lesions are absent in isolates lacking thepks island. To determine whether this phenotype is associated with colibactin production, we deleted theclbPgene from the extraintestinal pathogenicE. colistrain IHE3034, thus disrupting its ability to make colibactin. The wild-type IHE3034 displayed a spherical shape with no envelope lesions, and was practically indistinguishable from the ΔclbPdeletion mutant. To our knowledge, this work provides the first SEM images of a pks deletion mutant.

Importance

Thepksgenomic island has been linked to the promotion of DNA damage and colorectal cancer, through the production of genotoxic compound colibactin in some strains ofE. coli.While much is known about the mechanism of colibactin toxicity once it enters the mammalian cell, the prior steps leading to colibactin secretion or translocation from the bacterial cell, remain unclear. Here, we report high-resolution electron microscopy images ofE. coliIHE3034 strain, a known colibactin producer, and a deletion mutant that is known to accumulate colibactin intermediates. The images reveal a predominantly spherical morphology that is unaffected by the accumulation of colibactin precursors and intermediates.
SMARCA4 supports the oncogenic landscape ofKRAS-driven lung tumors
Authors: Malik Shivani , Oshima Masaya , Roy Nilotpal , Kaushik Swati , Kuvshinova Ora , Wu Wei , Greer John E. , Green Shon , McMahon Martin , Jen Kuang-Yu , Hebrok Matthias , Bandyopadhyay Sourav , Hargreaves Diana C. , Collisson Eric A.
Published: April 2020

Cancer resequencing studies identify recurrent mutations in the switch/sucrose non-fermentable (SWI/SNF) complex at an unexpectedly high frequency across many cancer types. Some SWI/SNF mutations appear to be loss-of-function events, implying that the intact SWI/SNF complex is tumor suppressive. We examined the distribution and function ofSMARCA4mutations, the most frequently mutated SWI/SNF complex gene in lung adenocarcinoma, using human cancers, cell lines and mouse model systems. We found that lung adenocarcinomas harboring activated oncogenes have fewer deleterious mutations inSMARCA4and express higher levels of the mRNA than cancers without activated oncogenes, indicating distinct dependencies onSMARCA4in these two settings. Surprisingly, intactSmarca4promoted the growth and tumorgenicity ofKrasG12D-driven mouse lung tumors and human cells. Mechanistically, we found thatSmarca4supports the oncogenic transcriptional/signaling landscape ofKrasG12D-driven mouse lung cancer. This dependency on the chromatin maintenance machinery in established cancer cells support treatments directed towards pathogenic SWI/SNF complexes in lung adenocarcinoma and other malignancies.
Reflections of Idiographic Long-Term Memory Characteristics In Resting-State Neuroimaging Data
Authors: Zhou Peiyun , Sense Florian , van Rijn Hedderik , Stocco Andrea
Published: April 2020

Translational applications of cognitive science depend on having predictive models at the individual, oridiographic, level. However, idiographic model parameters, such as working memory capacity, often need to be estimated from specific tasks, making them dependent on task-specific assumptions. Here, we explore the possibility that idiographic parameters reflect an individual’s biology and can be identified from task-free neuroimaging measures. To test this hypothesis, we correlated a reliable behavioral trait, the individual rate of forgetting in long-term memory, with a readily available task-free neuroimaging measure, the resting-state EEG spectrum. Using an established, adaptive fact-learning procedure, the rate of forgetting for verbal and visual materials was measured in a sample of 50 undergraduates from whom we also collected eyes-closed resting-state EEG data. Statistical analyses revealed that the individual rates of forgetting were significantly correlated across verbal and visual materials. Importantly, both rates correlated with resting-state power levels in the low (13-15 Hz) and upper (15-17 Hz) portion of the beta frequency bands. These correlations were particularly strong for visuospatial materials, were distributed over multiple fronto-parietal locations, and remained significant even after a correction for multiple comparisons (False Discovery Rate) and after robust correlation methods were applied. These results suggest that computational models could be individually tailored for prediction using idiographic parameter values derived from inexpensive, task-free imaging recordings.
Analysis of Pan-Omics Data in Human Interactome Network (APODHIN)
Authors: Biswas Nupur , Kumar Krishna , Bose Sarpita , Bera Raisa , Chakrabarti Saikat
Published: April 2020

Analysis of Pan-Omics Data in Human Interactome Network (APODHIN) is a platform for integrative analysis of transcriptomics, proteomics, genomics, and metabolomics data for identification of key molecular players and their interconnections exemplified in cancer scenario. APODHIN works on a meta-interactome networks consisting of human protein-protein interactions, miRNA-target gene regulatory interactions, and transcription factor-target gene regulatory relationships, respectively. In its first module, APODHIN maps proteins/genes/miRNAs from different omics data in its meta-interactome network and extracts the network of biomolecules that are differentially altered in the given scenario. Using this context specific, filtered interaction network, APODHIN identifies topologically important nodes (TINs) implementing graph theory based network topology analysis and further justifies their role via pathway and disease marker mapping. These TINs could be used as prospective diagnostic and/or prognostic biomarkers and/or potential therapeutic targets. In its second module, APODHIN attempts to identify cross pathway regulatory and protein-protein interaction (PPI) links connecting signaling proteins, transcription factors, and miRNAs to metabolic enzymes via utilization of single-omics and/or pan-omics data and implementation of mathematical modeling. Interconnections between regulatory components such as signaling proteins/TFs/miRNAs and metabolic pathways need to be elucidated more elaborately in order to understand the role of oncogene and tumor suppressors in regulation of metabolic reprogramming during cancer.

APODHIN platform contains a web server component where users can upload single/multi omics data to identify TINs and cross-pathway links. Tabular, graphical and 3D network representations of the identified TINs and cross-pathway links are provided for better appreciation. Additionally, this platform also provides a database part where cancer specific, single and/or multi omics dataset centric meta-interactome networks, TINs, and cross-pathway links are provided for cervical, ovarian, and breast cancers, respectively. APODHIN platform is freely available athttp://www.hpppi.iicb.res.in/APODHIN/home.html.
Anthropogenic food enhancement alters the timing of maturational landmarks among wild savanna monkeys (Chlorocebus pygerythrus)
Authors: Schmitt Christopher A. , Rich Alicia M. , Parke Stacy-Anne R. , Blaszczyk Maryjka B. , Cramer Jennifer Danzy , Freimer Nelson B. , Grobler J. Paul , Turner Trudy R.
Published: April 2020

Anthropogenic landscapes are rapidly replacing natural nonhuman primate habitats. Yet, the access to anthropogenic resources on primate biology, health, and fitness remain poorly studied. Given their ubiquity across a range of human impacted landscapes, from cities to national parks, savanna monkeys (Chlorocebusspp.) provide an excellent study system in which to test these effects. We compared body condition and reproductive maturation in vervets (Chlorocebus pygerythrus) inhabiting a private farm in !Gariep Dam, with ample access to anthropogenic foods, and wild-foraging vervets in Soetdoring Nature Reserve, South Africa. Overall, vervets in !Gariep show significantly thicker skin folds, and higher BMI and body mass, than those in Soetdoring, suggesting increased fat deposition. Males in !Gariep have larger relative testis volumes at peri-pubescent ages compared to those in Soetdoring, suggesting early reproductive maturation associated with age-specific increases in body mass. Females from !Gariep showed evidence of an earlier onset of reproduction than those in Soetdoring, based on parity status as assessed by nipple length and evidence of lactation. Parity status at sub-adult dental ages was also strongly associated with body mass. These results are consistent with a positive effect of anthropogenic food-enhancement on body fat deposition, potentially linked to an earlier onset of reproductive maturation. Further investigation into primate responses to cultivated resources will inform our understanding of the broader effects of food enhancement on developmental plasticity.
Mycobiome analysis in fungal Infected formalin-fixed and paraffin-embedded tissues for identification of pathogenic fungi: A pilot study
Authors: Lee Taebum , Na Hee Young , Kim Kyoung-Mee , Lee Hey Seung , Park Sung-Hye , Choe Ji-Young , Choi Kyoung Chan , Byeon Sun-ju
Published: April 2020

Background

Fungal organisms are frequently observed in surgical pathological diagnosis. In order to more accurately identify fungi in formalin-fixed and paraffin-embedded (FFPE) tissues, it is necessary to use genomic information. The purpose of our pilot study is to identify the factors to be considered for the identification of pathogenic fungi using mycobiome analysis in FFPE tissues.

Methods

We selected 49 cases in five hospitals. In each case, FFPE tissue was cut into 50 µm and DNA was extracted. Multiplex PCR with four primers (ITS1, ITS2, ITS3 and ITS4) was performed. Multiplex sequencing was performed using MinION device according to the manufacturer’s protocol. Sequences of each case were searched using BLASTN with an ITS database from NCBI RefSeq Targeted Loci Project with default parameter.

Results

A total of 2,526 DNA nucleotides were sequenced. We were able to identify 342 fungal nucleotides in 24 (49.0%, 24/49) cases. The median value of the detected fungal DNA per case was 3 (1Q: 1 and 3Q: 14.25). The 215 (62.87%) fungal DNA contained the entire region of ITS1 or ITS2. The remaining 127 fungal DNAs were identified as fungi using partial sequence of ITS1, ITS2, 5.8S, LSU or SSU.

Conclusion

In conclusion, we have identified the possibility of finding pathogenic fungi through mycobiome analysis in fungal infected FFPE tissues using nanopore sequencing method. However, we have also found several limitations to be solved for further studies. If we develop a method to characterize pathogenic fungi in FFPE tissues in a follow-up study, we think it will help patients to use appropriate antifungal agents.
Efficient assessment of nocturnal flying insect communities by combining automatic light traps and DNA metabarcoding
Authors: Mata Vanessa A. , Ferreira Sónia , Campos Rebecca , da Silva Luís P. , Veríssimo Joana , Corley Martin F. V. , Beja Pedro
Published: April 2020

Increasing evidence for global insect declines is prompting a renewed interest in the survey of whole insect communities. DNA metabarcoding can contribute to assessing diverse insect communities over a range of spatial and temporal scales, but efforts are still needed to optimise and standardise procedures, from field sampling, through laboratory analysis, to bioinformatic processing.

Here we describe and test a methodological pipeline for surveying nocturnal flying insects, combining a customised automatic light trap and DNA metabarcoding. We optimised laboratory procedures and then tested the methodological pipeline using 12 field samples collected in northern Portugal in 2017. We focused on Lepidoptera to compare metabarcoding results with those from morphological identification, using three types of bulks produced from each sample (individuals, legs and the unsorted mixture).

The customised trap was highly efficient at collecting nocturnal flying insects, allowing a small team to operate several traps per night, and a fast field processing of samples for subsequent metabarcoding with low contamination risks. Morphological processing yielded 871 identifiable individuals of 102 Lepidoptera species. Metabarcoding detected a total of 528 taxa, most of which were Lepidoptera (31.1%), Diptera (26.1%) and Coleoptera (14.7%). There was a reasonably high matching in community composition between morphology and metabarcoding when considering the ‘individuals’ and ‘legs’ bulk samples, with few errors mostly associated with morphological misidentification of small microlepidoptera. Regarding the ‘mixture’ bulk sample, metabarcoding identified nearly four times more Lepidoptera species than morphological examination.

Our study provides a methodological metabarcoding pipeline that can be used in standardised surveys of nocturnal flying insects, showing that it can overcome limitations and potential shortcomings of traditional methods based on morphological identification. Our approach efficiently collects highly diverse taxonomic groups such as nocturnal Lepidoptera that are poorly represented when using Malaise traps and other widely used field methods. To enhance the potential of this pipeline in ecological studies, efforts are needed to test its effectiveness and potential biases across habitat types and to extend the DNA barcode databases for important groups such as Diptera.
A 29-year retrospective analysis of koala rescues in New South Wales, Australia
Authors: Charalambous Renae , Narayan Edward J.
Published: April 2020

The koala (Phascolactos cinereus) is currently listed by both the IUCN and the Australian Governments’ Threatened Species Scientific Committee as vulnerable to extinction with a decreasing population trend. This listing can be attributed to climate change and its impact on ecosystems, and anthropomorphic environmental change due to extensive land clearing and habitat fragmentation. These have both been proven to induce stress, which influences the onset of disease. This novel study performed a retrospective analysis whereby records for 12,543 wild, rescued koalas in New South Wales (NSW), Australia were studied in order to determine trends in koala sightings, clinical admissions and injury diagnoses over a period of 29 years (1989-2018). Results indicated that between all three study locations (Port Stephens, Port Macquarie and Lismore), the most common reason koalas were admitted into care was because of disease, the most common disease diagnosed was signs of chlamydia, and the most common outcome for koalas admitted into care was released. At Port Stephens, mature and female koalas were diagnosed with a disease more than any other age or sex, while juvenile and male koalas were released (back into the wild) more than any other age or sex. Additionally, there were fewer koalas with a disease and fewer koalas released in Port Stephens as each year progressed. At Port Macquarie, mature and male koalas were diagnosed with a disease more than any other age or sex, while juvenile and female koalas were released more than any other age or sex. Additionally, there were more koalas with a disease and fewer koalas released in Port Macquarie as each year progressed. At Lismore, adult and female koalas were diagnosed with a disease more than any other age or sex, while joey and male koalas were released more than any other age or sex. Additionally, there were more koalas with a disease and fewer koalas released in Lismore as each year progressed. Determining trends in clinical admissions and diagnosis over such a substantial period of time is an important factor in preventing the continuing decline of koalas throughout Australia, and in particular NSW. It is important to note that there are cultural differences between koala rescue groups in the three study locations (Port Stephens, Port Macquarie and Lismore). These differences may be reflected in the outcomes of koala patients as each group are driven by their own management team. It is essential that any further decline of koala populations is prevented, however this can only be achieved through informed recommendations through research studies such as these. These recommendations should lead to government legislation which can provide stronger protection to koala habitat.
Regulations of expressions of rat/human sulfotransferases (SULTs) by anti-cancer drug, nolatrexed and micronutrients
Authors: Maiti Smarajit , MaitiDutta Sangita , Chen Guangping
Published: April 2020

Cancer is a disease related to cellular proliferative-state. Drastically increase in cell-cycle regulations augments cellular folate-pool and folate-metabolism. So, this pathway is targeted therapeutically. A number of drugs are involved in this metabolism i.e. folic-acid/folinic-acid/nolatrexed(NT)/ methotrexate(MTX) for the research and treatment of cancer. Our previous study showed that MTX significantly modulated rat/human SULTs. Present study was an attempt to study the effect of NT (widely used in different cancers) and these micronutrients on the expressions of rat/human SULTs. Male Sprague-Dawley rats were treated with NT (01,10 or 100 mg/Kg) or both sexes were treated to folic acid (100,200 or 400 mg/kg) for 2-weeks and their AST-IV (2-napthol sulfation) and STa (DHEA-sulfation) activities, protein-expression (Western-Blot) and mRNA-expression (RT-PCR) were tested. In cultured HepG2 cells NT (1nM-1.2mM) or folonic-acid (10nM-10μM) were applied for 10 days. Folic acid (0-10μM) was treated to human hepatocarcinoma (HepG2) cells. PPST (phenol-catalyzing), MPST (dopamine) DHEAST (dehydroepiandrosterone,DHEA) and EST (estradiol-sulfating) protein-expressions (Western-blot) were tested in all HepG2 study. Present results suggest NT significantly increased SULTs expressions in rat (protein/mRNA/activity) and HepG2 cells. Folic acid increased SULTs activity/protein in sex-dependant manner (ASTIV in female/ STa in male). Both folic and folinic acid increased several hSULTs isoforms with varied level of significance (least or no increase at highest-dose) in HepG2 cells pointing its dose-dependent multi-phasic responses. The clinical importance of this study may be furthered in the verification of sulfation-metabolism of several exogenous/endogenous molecules, drug-drug interaction and their influences on the patho-physiological processes. Further studies are necessary in this regard.
Syd/JIP3 Controls Tissue Size by Regulating Diap1 Protein Turnover Downstream of Yorkie/YAP
Authors: Ahmad Vakil , Vadla Gangadhar P. , Chabu Chiswili Y.
Published: April 2020

How organisms control organ size is not fully understood. We found that Syd/JIP3 is required for proper wing size inDrosophila.JIP3mutations are associated with organ size defects in mammals. The underlying mechanisms are not well understood. We discovered that Syd/JIP3 inhibition results in a downregulation of the inhibitor of apoptosis protein1 (Diap1) in theDrosophilawing. Correspondingly, Syd/JIP3 deficient tissues exhibit ectopic cell death and yield smaller wings. Syd/JIP3 inhibition generated similar effects in mammalian cells, indicating a conserved mechanism. We found that Yorkie/YAP stimulates Syd/JIP3 inDrosophilaand mammalian cells. Notably, Syd/JIP3 is required for the full effect of Yorkie-mediated tissue growth. Thus Syd/JIP3 regulation of Diap1 functions downstream of Yorkie/YAP to control growth.

This study provides mechanistic insights into the recent and perplexing link betweenJIP3mutations and organ size defects in mammals, including in humans where de novoJIP3variants are associated with microcephaly.

Highlights

Syd/JIP3 is required for properDrosophilawing size

Syd/JIP3 stabilizes Diap1 to inhibit cell death inDrosophilaand in mammalian cells

Activation of Yorkie/YAP stimulates Syd/JIP3

Yorkie-mediated tissue growth is highly sensitive to Syd/JIP3 dosage