bluuebunny/crossref_metadata_2025_split huggingface dataset:
High rates of plasmid cotransformation in E. coli overturn the clonality myth and reveal colony development
Authors: Tomoiaga Delia , Bubnell Jaclyn , Herndon Liam , Feinstein Paul 
Published: July 2022

AbstractThe concept of DNA transfer between bacteria was put forth by Griffith in 1928. During the dawn of molecular cloning of DNA in the 1980s, Hanahan described how the transformation of DNA plasmids into bacteria would allow for cloning of DNA fragments. Through this foundational work, it is widely taught that a typical transformation produces clonal bacterial colonies. Using low concentrations of several plasmids that encode different fluorescent proteins, under the same selective antibiotic, we show that E. coli bacteria readily accept multiple plasmids, resulting in widespread aclonality and reveal a complex pattern of colony development. Cotransformation of plasmids occurs by either CaCl2 or by electroporation methods. A bacterium rod transformed with three plasmids—each expressing a high level of a unique fluorescent protein—and replated on agar, appears to reassign a random number of the three fluorescent plasmids to its daughter cell during cell division. The potential to simultaneously follow multiple lineages of clonally related bacteria in a bacteria colony would allow for mosaic analysis of gene function. We show that clonally related bacterium rods self-organize in a fractal growth pattern and can remain linked during colony development revealing a potential target against microbiota growth.
Nonreproductive effects are more important than reproductive effects in a host feeding parasitoid
Authors: Zhang Yibo , Tian Xiaocao , Wang Hao , Castañé Cristina , Arnó Judit , Wu Suran , Xian Xiaoqing , Liu Wanxue , Desneux Nicolas , Wan Fanghao , Zhang Guifen 
Published: July 2022

AbstractWhen female host feeding parasitoids encounter a potential host, they face a complicated trade-off between either laying an egg for investing in current reproduction or feeding on or killing the host for future reproduction. Few studies have measured these behavioral shift patterns in a given host-parasitoid association thus far. We systematically assessed the behavioral shifts and life history traits of a host feeding parasitoid, Necremnus tutae, on different instars of its host Tuta absoluta. N. tutae females, as idiobiont host feeding parasitoids, can act on the 1st–4th instar larvae of T. absoluta by either host feeding, parasitizing or host killing. Moreover, a significant behavioral shift was observed on different instar hosts. N. tutae preferred to feed on the young hosts (1st and 2nd instars), lay eggs on middle-aged hosts (3rd instars) and kill old hosts (4th instars) by ovipositor-mediated stinging. The offspring of N. tutae showed a significant female-biased sex ratio, with the number of instars of T. absoluta larvae that were parasitized increasing. Specifically, nonreproductive host mortality induced by host feeding and host killing accounted for high percentages of the total mortality (ranging from 70% on 3rd instar hosts to 88% on 1st instar and 4th instar hosts). We hypothesize that N. tutae could be not merely a parasitoid but also a predator. Our results shed light on the nonreproductive abilities of a host feeding parasitoid that should be given further attention, especially when evaluating the efficacy of parasitoids.
Phyllanthus amarus shoot cultures as a source of biologically active lignans: the influence of selected plant growth regulators
Authors: Sparzak-Stefanowska Barbara , Krauze-Baranowska Mirosława 
Published: July 2022

AbstractThis is the first comprehensive study of the influence of plant growth regulators (PGRs) on the development of shoots and accumulation of biologically active lignans—phyllanthin and hypophyllanthin, in the shoot culture ofP. amarusSchum. & Thonn. (Euphorbiaceae) obtained by direct organogenesis. The following PGRs were included in the experiments—cytokinins: kinetin (Kin), 6-benzylaminopurine (BAP), 2-isopentenyladenine (2iP), 1-phenyl-3-(1,2,3-thiadiazol-5-yl)urea, thidiazuron (TDZ) and auxin, indole-3-butyric acid (IBA) and used at various concentrations. Depending on PGRs and their concentrations, differences in the culture response and lignan accumulation were observed. The highest content of the investigated compounds was found in the shoot culture grown on Murashige and Skoog’s (MS) medium supplemented with Kin 0.25 mg/L. The sum of phyllanthin and hypophyllanthin was  ~ 10 mg/g of dry weight (DW), which was similar or even higher than that in the plant material obtained from natural conditions. The results of the research provide new data on the selection of the optimal growth medium for the production of plant material with a significant level of phyllanthin and hypophyllanthin biosynthesis. The obtained data may also be valuable in designing systems for large-scale cultivation ofP. amarusshoots with high productivity of hepatoprotective lignans.
Adipocyte differentiation between obese and lean conditions depends on changes in miRNA expression
Authors: Heo Yerim , Kim Hyunjung , Lim Jiwon , Choi Sun Shim 
Published: July 2022

AbstractAdipogenesis is the process by which precursor cells, preadipocytes (preACs), differentiate into adipocytes (ACs). Here, we investigated differentially expressed miRNAs (DEMs) between the two conditions to understand the regulatory role of miRNAs in altering adipogenesis-related mRNAs. A total of 812 and 748 DEMs were obtained in lean and obese conditions, respectively. The up- and downregulated DEMs were highly concordant with each other in both lean and obese conditions; however, DEMs related to adipogenesis in obese conditions were more strongly downregulated than DEMs related to adipogenesis in lean conditions. There were more obese-specific downregulated DEMs than lean-specific downregulated DEMs; in contrast, there were more lean-specific upregulated DEMs than obese-specific upregulated DEMs. Approximately 45% of DEMs were mapped to the list of miRNA-target mRNA pairs when DEMs were matched to the experimentally validated list of miRNA-target mRNA information of miRTarBase. Many of the target mRNAs were differentially expressed genes (DEGs) with functions in processes such as inflammatory responses and fat metabolism. In particular, a total of 25 miRNAs that target three upregulated adipogenesis-associated inflammatory genes (IL-6, TNF-α, and IL-1β) were commonly altered during adipogenesis. Taken together, our study reveals the types of adipogenesis-related miRNAs that are altered and the degree to which they influence healthy or pathogenic adipogenesis.
Mesenchymal stem cells promote spermatogonial stem/progenitor cell pool and spermatogenesis in neonatal mice in vitro
Authors: Önen Selin , Köse Sevil , Yersal Nilgün , Korkusuz Petek 
Published: July 2022

AbstractPrepubertal cancer treatment leads to irreversible infertility in half of the male patients. Current in vitro spermatogenesis protocols and cryopreservation techniques are inadequate to expand spermatogonial stem/progenitor cells (SSPC) from testicles. Bone marrow derived mesenchymal stem cells (BM-MSC) bearing a close resemblance to Sertoli cells, improved spermatogenesis in animal models. We asked if a co-culture setup supported by syngeneic BM-MSC that contributes to the air–liquid interphase (ALI) could lead to survival, expansion and differentiation of SSPCs in vitro. We generated an ALI platform able to provide a real-time cellular paracrine contribution consisting of syngeneic BM-MSCs to neonatal C57BL/6 mice testes. We aimed to evaluate the efficacy of this culture system on SSPC pool expansion and spermatogenesis throughout a complete spermatogenic cycle by measuring the number of total germ cells (GC), the undifferentiated and differentiating spermatogonia, the spermatocytes and the spermatids. Furthermore, we evaluated the testicular cell cycle phases, the tubular and luminal areas using histochemical, immunohistochemical and flow cytometric techniques. Cultures in present of BM-MSCs displayed survival of ID4(+) spermatogonial stem cells (SSC), expansion of SALL4(+) and OCT4(+) SSPCs, VASA(+) total GCs and Ki67(+) proliferative cells at 42 days and an increased number of SCP3(+) spermatocytes and Acrosin(+) spermatids at 28 days. BM-MSCs increased the percentage of mitotic cells within the G2-M phase of the total testicular cell cycle increased for 7 days, preserved the cell viability for 42 days and induced testicular maturation by enlargement of the tubular and luminal area for 42 days in comparison to the control. The percentage of PLZF(+) SSPCs increased within the first 28 days of culture, after which the pool started to get smaller while the number of spermatocytes and spermatids increased simultaneously. Our findings established the efficacy of syngeneic BM-MSCs on the survival and expansion of the SSPC pool and differentiation of spermatogonia to round spermatids during in vitro culture of prepubertal mice testes for 42 days. This method may be helpful in providing alternative cures for male fertility by supporting in vitro differentiated spermatids that can be used for round spermatid injection (ROSI) to female oocyte in animal models. These findings can be further exploited for personalized cellular therapy strategies to cure male infertility of prepubertal cancer survivors in clinics.
Detecting lineage-defining mutations in SARS-CoV-2 using colorimetric RT-LAMP without probes or additional primers
Authors: dos Santos Carlos Abelardo , Silva Lívia do Carmo , Souza Júnior Marcio Neres de , Mendes Geovana de Melo , Estrela Paulo Felipe Neves , de Oliveira Kézia Gomes , de Curcio Juliana Santana , Resende Paola Cristina , Siqueira Marilda Mendonça , Pauvolid-Corrêa Alex , Duarte Gabriela Rodrigues Mendes , Silveira-Lacerda Elisângela de Paula 
Published: July 2022

AbstractDespite the advance of vaccination worldwide, epidemic waves caused by more transmissible and immune evasive genetic variants of SARS-CoV-2 have sustained the ongoing pandemic of COVID-19. Monitoring such variants is expensive, as it usually relies on whole-genome sequencing methods. Therefore, it is necessary to develop alternatives that could help identify samples from specific variants. Reverse transcription loop-mediated isothermal amplification is a method that has been increasingly used for nucleic acid amplification, as it is cheaper and easier to perform when compared to other molecular techniques. As a proof of concept that can help distinguish variants, we present an RT-LAMP assay capable of detecting samples carrying a group of mutations that can be related to specific SARS-CoV-2 lineages, here demonstrated for the Variant of Concern Gamma. We tested 60 SARS-CoV-2 RNA samples extracted from swab samples and the reaction showed a sensitivity of 93.33%, a specificity of 88.89% and a kappa value of 0.822 for samples with a Ct ≤ 22.93. The RT-LAMP assay demonstrated to be useful to distinguish VOC Gamma and may be of particular interest as a screening approach for variants in countries with poor sequencing coverage.
Research on remote sensing classification of fruit trees based on Sentinel-2 multi-temporal imageries
Authors: Zhou Xin-Xing , Li Yang-Yang , Luo Yuan-Kai , Sun Ya-Wei , Su Yi-Jun , Tan Chang-Wei , Liu Ya-Ju 
Published: July 2022

AbstractAccurately obtaining the spatial distribution information of fruit tree planting is of great significance to the development of fruit tree growth monitoring, disease and pest control, and yield estimation. In this study, the Sentenel-2 multispectral remote sensing imageries of different months during the growth period of the fruit trees were used as the data source, and single month vegetation indices, accumulated monthly vegetation indices (∑VIs), and difference vegetation indices between adjacent months (∆VIs) were constructed as input variables. Four conventional vegetation indices of NDVI, PSRI, GNDVI, and RVI and four improved vegetation indices of NDVIre1, NDVIre2, NDVIre3, and NDVIre4 based on the red-edge band were selected to construct a decision tree classification model combined with machine learning technology. Through the analysis of vegetation indices under different treatments and different months, combined with the attribute of Feature_importances_, the vegetation indices of different periods with high contribution were selected as input features, and the Max_depth values of the decision tree model were determined by the hyperparameter learning curve. The results have shown that when the Max_depth value of the decision tree model of the vegetation indices under the three treatments was 6, 8, and 8, the model classification was the best. The accuracy of the three vegetation index processing models on the training set were 0.8936, 0.9153, and 0.8887, and the accuracy on the test set were 0.8355, 0.7611, and 0.7940, respectively. This method could be applied to remote sensing classification of fruit trees in a large area, and could provide effective technical means for monitoring fruit tree planting areas with medium and high resolution remote sensing imageries.
EWAS of post-COVID-19 patients shows methylation differences in the immune-response associated gene, IFI44L, three months after COVID-19 infection
Authors: Lee Yunsung , Riskedal Espen , Kalleberg Karl Trygve , Istre Mette , Lind Andreas , Lund-Johansen Fridtjof , Reiakvam Olaug , Søraas Arne V. L. , Harris Jennifer R. , Dahl John Arne , Hadley Cathrine L. , Jugessur Astanand 
Published: July 2022

AbstractAlthough substantial progress has been made in managing COVID-19, it is still difficult to predict a patient’s prognosis. We explored the epigenetic signatures of COVID-19 in peripheral blood using data from an ongoing prospective observational study of COVID-19 called the Norwegian Corona Cohort Study. A series of EWASs were performed to compare the DNA methylation profiles between COVID-19 cases and controls three months post-infection. We also investigated differences associated with severity and long-COVID. Three CpGs—cg22399236, cg03607951, and cg09829636—were significantly hypomethylated (FDR < 0.05) in COVID-19 positive individuals. cg03607951 is located in IFI44L which is involved in innate response to viral infection and several systemic autoimmune diseases. cg09829636 is located in ANKRD9, a gene implicated in a wide variety of cellular processes, including the degradation of IMPDH2. The link between ANKRD9 and IMPDH2 is striking given that IMPDHs are considered therapeutic targets for COVID-19. Furthermore, gene ontology analyses revealed pathways involved in response to viruses. The lack of significant differences associated with severity and long-COVID may be real or reflect limitations in sample size. Our findings support the involvement of interferon responsive genes in the pathophysiology of COVID-19 and indicate a possible link to systemic autoimmune diseases.
Tripling the light extraction efficiency of a deep ultraviolet LED using a nanostructured p-contact
Authors: López-Fraguas Eduardo , Binkowski Felix , Burger Sven , Hagedorn Sylvia , García-Cámara Braulio , Vergaz Ricardo , Becker Christiane , Manley Phillip 
Published: July 2022

AbstractDespite a wide array of applications, deep ultra-violet light emitting diodes offer relatively poor efficiencies compared to their optical counterparts. A contributing factor is the lower light extraction efficiency due to both highly absorbing p-contacts and total internal reflection. Here, we propose a structure consisting of a hexagonal periodic array of cylindrical nanoholes in the multi-layered p-contact which are filled with platinum. This nanostructure reduces the absorption of the p-contact layer, leading to a higher emission into the n-contact compared to a planar reference. An optimum geometry of the nanostructure allows a light extraction efficiency of 15.0%, much higher than the typical 4.6% of a planar reference. While the nanostructure strongly decreases the light absorption in the p-contact, it is still not able to considerably reduce the total internal reflection. Consequently, the nanostructured p-contact should be combined with other optical strategies, such as nanopatterned sapphire substrates to increase the efficiency even further. Despite this, the nanostructure described in this work provides a readily realizable path to enhancing the light extraction efficiency of state-of-the-art deep ultra-violet light emitting diodes.
Anti-neoplastic action of Cimetidine/Vitamin C on histamine and the PI3K/AKT/mTOR pathway in Ehrlich breast cancer
Authors: Ibrahim Sherihan Salaheldin Abdelhamid , El-Aal Sarah A. Abd , Reda Ahmed M. , Achy Samar El , Shahine Yasmine 
Published: July 2022

AbstractThe main focus of our study is to assess the anti-cancer activity of cimetidine and vitamin C via combating the tumor supportive role of mast cell mediators (histamine, VEGF, and TNF-α) within the tumor microenvironment and their effect on the protein kinase A(PKA)/insulin receptor substrate-1(IRS-1)/phosphatidylinositol-3-kinase (PI3K)/serine/threonine kinase-1 (AKT)/mammalian target of rapamycin (mTOR) cue in Ehrlich induced breast cancer in mice. In vitro study was carried out to evaluate the anti-proliferative activity and combination index (CI) of the combined drugs. Moreover, the Ehrlich model was induced in mice via subcutaneous injection of Ehrlich ascites carcinoma cells (EAC) in the mammary fat pad, and then they were left for 9 days to develop obvious solid breast tumor. The combination therapy possessed the best anti-proliferative effect, and a CI < 1 in the MCF7 cell line indicates a synergistic type of drug interaction. Regarding the in vivo study, the combination abated the elevation in the tumor volume, and serum tumor marker carcinoembryonic antigen (CEA) level. The serum vascular endothelial growth factor (VEGF) level and immunohistochemical staining for CD34 as markers of angiogenesis were mitigated. Additionally, it reverted the state of oxidative stress and inflammation. Meanwhile, it caused an increment in apoptosis, which prevents tumor survival. Furthermore, it tackled the elevated histamine and cyclic adenosine monophosphate (cAMP) levels, preventing the activation of the (PKA/IRS-1/PI3K/AKT/mTOR) cue. Finally, we concluded that the synergistic combination provided a promising anti-neoplastic effect via reducing the angiogenesis, oxidative stress, increasing apoptosis,as well as inhibiting the activation of PI3K/AKT/mTOR cue, and suggesting its use as a treatment option for breast cancer.
Aptamer-antibody hybrid ELONA that uses hybridization chain reaction to detect a urinary biomarker EN2 for bladder and prostate cancer
Authors: Kim Eunseon , Kang Minji , Ban Changill 
Published: July 2022

AbstractWe report an EN2-specific (Kd = 8.26 nM) aptamer, and a sensitive and specific enzyme-linked oligonucleotide assay (ELONA) for rapid and sensitive colorimetric detection of bladder and prostate cancer biomarker EN2 in urine. The assay relies on an aptamer-mediated hybridization chain reaction (HCR) to generate DNA nanostructures that bind to EN2 and simultaneously amplify signals. The assay can be performed within 2.5 h, and has a limit of detection of 0.34 nM in buffer and 2.69 nM in artificial urine. Moreover, this assay showed high specificity as it did not detect other urinary proteins, including biomarkers of other cancers. The proposed ELONA is inexpensive, highly reproducible, and has great chemical stability, so it may enable development of a simple, sensitive and accurate diagnostic tool to detect bladder and prostate cancers early.
Hypo-osmotic stress induces the epithelial alarmin IL-33 in the colonic barrier of ulcerative colitis
Authors: Gundersen Mona Dixon , Larsen Kenneth Bowitz , Johnsen Kay Martin , Goll Rasmus , Florholmen Jon , Haraldsen Guttorm 
Published: July 2022

AbstractEpithelial alarmins are gaining interest as therapeutic targets for chronic inflammation. The nuclear alarmin interleukin-33 (IL-33) is upregulated in the colonic mucosa of acute ulcerative colitis (UC) and may represent an early instigator of the inflammatory cascade. However, it is not clear what signals drive the expression of IL-33 in the colonic mucosa, nor is the exact role of IL-33 elucidated. We established an ex vivo model using endoscopic colonic biopsies from healthy controls and UC patients. Colonic biopsies exposed to hypo-osmotic medium induced a strong nuclear IL-33 expression in colonic crypts in both healthy controls and UC biopsies. Mucosal IL33 mRNA was also significantly increased following hypo-osmotic stress in healthy controls compared to non-stimulated biopsies (fold change 3.9, p-value < 0.02). We observed a modest induction of IL-33 in response to TGF-beta-1 stimulation, whereas responsiveness to inflammatory cytokines TNF and IFN-gamma was negligible. In conclusion our findings indicate that epithelial IL-33 is induced by hypo-osmotic stress, rather than prototypic proinflammatory cytokines in colonic ex vivo biopsies. This is a novel finding, linking a potent cytokine and alarmin of the innate immune system with cellular stress mechanisms and mucosal inflammation.
Performance evaluation of a non-invasive one-step multiplex RT-qPCR assay for detection of SARS-CoV-2 direct from saliva
Authors: Jenkins Harry H. , Lopez Ana A. Tellechea , Tarantini Francesco Saverio , Tomlin Hannah , Scales Danielle , Lee I-Ning , Wu Siyu , Hyde Ralph , Lis-Slimak Katarzyna , Byaruhanga Timothy , Thompson Jamie L. , Pijuan-Galito Sara , Doolan Lara , Kaneko Kazuyo , Gwynne Penny , Reffin Caroline , Park Emily , Dey Jayasree , Hill Jack , Arendt-Tranholm Asta , Stroud Amy , Petrie Moira , Denning Chris , Benest Andrew V. , Seedhouse Claire 
Published: July 2022

AbstractPolymerase chain reaction (PCR) has proven to be the gold-standard for SARS-CoV-2 detection in clinical settings. The most common approaches rely on nasopharyngeal specimens obtained from swabs, followed by RNA extraction, reverse transcription and quantitative PCR. Although swab-based PCR is sensitive, swabbing is invasive and unpleasant to administer, reducing patient compliance for regular testing and resulting in an increased risk of improper sampling. To overcome these obstacles, we developed a non-invasive one-step RT-qPCR assay performed directly on saliva specimens. The University of Nottingham Asymptomatic Testing Service protocol simplifies sample collection and bypasses the need for RNA extraction, or additives, thus helping to encourage more regular testing and reducing processing time and costs. We have evaluated the assay against the performance criteria specified by the UK regulatory bodies and attained accreditation (BS EN ISO/IEC 17,025:2017) for SARS-CoV-2 diagnostic testing by the United Kingdom Accreditation Service. We observed a sensitivity of 1 viral copy per microlitre of saliva, and demonstrated a concordance of > 99.4% between our results and those of other accredited testing facilities. We concluded that saliva is a stable medium that allows for a highly precise, repeatable, and robust testing method.