| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Chen, Chao, et al.
(författare)
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Epigenome-wide gene-age interaction analysis reveals reversed effects of PRODH DNA methylation on survival between young and elderly early-stage NSCLC patients
- 2020
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Ingår i: Aging. - : Impact Journals, LLC. - 1945-4589. ; 12:11, s. 10642-10662
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Tidskriftsartikel (refereegranskat)abstract
- DNA methylation changes during aging, but it remains unclear whether the effect of DNA methylation on lung cancer survival varies with age. Such an effect could decrease prediction accuracy and treatment efficacy. We performed a methylation-age interaction analysis using 1,230 early-stage lung adenocarcinoma patients from five cohorts. A Cox proportional hazards model was used to investigate lung adenocarcinoma and squamous cell carcinoma patients for methylation-age interactions, which were further confirmed in a validation phase. We identified one adenocarcinoma-specific CpG probe, cg14326354PRODH, with effects significantly modified by age (HRinteraction = 0.989; 95% CI: 0.986-0.994; P = 9.18×10-7). The effect of low methylation was reversed for young and elderly patients categorized by the boundary of 95% CI standard (HRyoung = 2.44; 95% CI: 1.26-4.72; P = 8.34×10-3; HRelderly = 0.58; 95% CI: 0.42-0.82; P = 1.67×10-3). Moreover, there was an antagonistic interaction between low cg14326354PRODH methylation and elderly age (HRinteraction = 0.21; 95% CI: 0.11-0.40; P = 2.20×10-6). In summary, low methylation of cg14326354PRODH might benefit survival of elderly lung adenocarcinoma patients, providing new insight to age-specific prediction and potential drug targeting.
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| 4. |
- Lai, Xin-He, et al.
(författare)
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Delineation of the molecular mechanisms of Francisella tularensis-induced apoptosis in murine macrophages
- 2003
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Ingår i: Infection and Immunity. - 0019-9567 .- 1098-5522. ; 71:8, s. 4642-4646
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Tidskriftsartikel (refereegranskat)abstract
- Francisella tularensis is a facultative intracellular bacterium capable of inducing apoptosis in murine macrophages. Here we analyzed the pathway leading to apoptosis in the murine macrophage-like cell line J774A.1 after infection with F. tularensis strain LVS (named LVS for live vaccine strain). We obtained evidence that the infection affected the mitochondria of the macrophages, since it induced release of the mitochondrial molecule cytochrome c into the cytosol and changed the potential over the mitochondrial membrane. Moreover, activation of caspase 9 and the executioner caspase 3 was also observed in the LVS-infected J774A.1 macrophages. The activated caspase 3 degraded poly(ADP-ribose) polymerase (PARP). All of these events were observed within 9 to 12 h after the initiation of infection, and maximum degradation of a synthetic caspase 3 substrate occurred at 18 h. The internucleosomal fragmentation and PARP degradation resulting from activation of this apoptotic pathway was prevented by the caspase 3 inhibitor Z-DEVD-fmk. No involvement of caspase 1, caspase 8, Bcl-2, or Bid was observed. Thus, the F. tularensis infection induces macrophage apoptosis through a pathway partly resembling the intrinsic apoptotic pathway.
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| 5. |
- Lai, Xin-He, et al.
(författare)
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Expression of iglC is mecessary for intracellular growth and induction of apoptosis in murine macrophages by Francisella tularensis
- 2004
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Ingår i: Microbial Pathogenesis. - London : Academic P.. - 0882-4010 .- 1096-1208. ; 37:5, s. 225-230
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Tidskriftsartikel (refereegranskat)abstract
- Francisella tularensis is a facultative intracellular bacterium capable of inducing apoptosis in murine macrophages. In a previous study, an iglC null mutant of F. tularensis live vaccine strain LVS was generated by allelic replacement and in the current study this iglC mutant was successfully complemented in trans. We characterized the capacity of this iglC mutant and the complemented strain to induce macrophage apoptosis. The iglC mutant did not induce apoptosis in the infected cells. In contrast, the complemented iglC strain was able to multiply in the murine macrophage-like cell line J774A.1 and induced apoptosis similar to that of the wild-type strain. It is the first successful example of complementation in trans of a F. tularensis mutant strain and more importantly this work provides direct evidence that the intracellular growth ability is essential for F. tularensis to induce macrophage apoptosis.
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| 6. |
- Lai, Xin-He, et al.
(författare)
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Fancisella tularensis induces cytopathogenicity and apaptosis in murine macrophages via a mechanism that requires intracellular bacterial multiplication
- 2001
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Ingår i: Infection and Immunity. - 0019-9567 .- 1098-5522. ; 69:7, s. 4691-4694
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Tidskriftsartikel (refereegranskat)abstract
- The murine macrophage-like cell line J774.A1 ingests and allows intracellular growth of Francisella tularensis. We demonstrate that, after 24 h of infection, a pronounced cytopathogenicity resulted and the J774 cells were undergoing apoptosis. Despite this host cell apoptosis, no decrease in bacterial numbers was observed. When internalization of bacteria was prevented or intracellularly located F. tularensis bacteria were eradicated within 12 h, the progression of host cell cytopathogenicity and apoptosis was prevented.
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| 7. |
- Lai, Xin-He, et al.
(författare)
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Francisella strains express hemolysins of distinct characteristics
- 2003
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Ingår i: FEMS Microbiology Letters. - : Elsevier. - 0378-1097 .- 1574-6968. ; 224:1, s. 91-95
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Tidskriftsartikel (refereegranskat)abstract
- Historically, Francisella strains have been described as nonhemolytic. In this study, we show by use of solid and liquid hemolysis assays that some Francisella strains have hemolytic properties. The Francisella novicida type strain U112 is hemolytic to horse erythrocytes and Francisella philomiragia type strain FSC144 is hemolytic towards both human and horse erythrocytes. The F. novicida strain U112 released a protein (novilysin A) into the culture supernatant which cross-reacted with antiserum against Escherichia coli HlyA whereas there was no similar protein detectable with this cross-reactive property from the supernatant of the F. philomiragia strain.
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| 8. |
- Lai, Xin-He, 1963-
(författare)
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Francisella tularensis infection induces macrophage cell death
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Francisella tularensis, the causative agent of tularemia, is a potent human and animal pathogen. Its principal survival mechanism is rapid intracellular multiplication. The mechanisms that enables it to multiply intracellularly have been ill-defined and the thesis focused on characterizing the outcome of the macrophage-Francisella interaction and also if the interactions differ between the various subspecies of F tularensis. The nature of host cell death was examined and the correlation of macrophage killing with intramacrophage Francisella growth was investigated by in vitro infection of J774A.1 macrophages with either the live vaccine (LVS) strain of F. tularensis, belonging to subspecies holarctica, or the subspecies novicida strain U112 Macrophage entry was in both cases cytochalasin D-sensitive but the intramacrophage growth of the two Francisella strains led to distinct types of host cell death, i.e., apoptosis vs. necrosis. The macrophage apoptosis induced by infection with the LVS strain was mediated via the intrinsic pathway with critical involvement of caspase-3 and the mitochondria. The infected and apoptotic macrophages were shrunken, their chromatin was specifically degraded and revealed a typical DNA ladder pattern upon electrophoresis. Moreover, they were TUNEL positive, indicating the occurrence of apoptosis-dependent DNA fragmentation. The necessity of intracellular growth for the apoptosis was shown by the use of an isogenic mutant, denoted iglC, which lacked the ability to multiply intracellularly and this infection did not result in apoptosis. The F. novicida strain U112, on the other hand, inhibited NF- B activity and ultimately induced macrophage necrosis. The infected and necrotic macrophages were enlarged, their chromatin was randomly degraded which gave a diffuse DNA pattern typical of necrosis. There was no apoptosis-specific caspase activation. By the use of an isogenic mutant, denoted mglA, it was shown that intracellular replication was necessary for the induction of necrosis. A hemolytic protein, novilysin A, was found in the F. novicida strain U112 but lacking in other subspecies of F. tularensis. The protein is a putative virulence factor but most likely not involved in the induction of necrosis. Its significance for the pathogenesis of F. novicida remains to be determined. The findings of the thesis provide a detailed picture of the interaction between the host cells and various subspecies of F. tularensis. It also shows that the outcome of the interaction is critically dependent on the type of F. tularensis subspecies. The findings also question the use of F. novicida as a model organism for understanding pathogenicity mechanisms of the species in general. The induction of the host cell death is presumably an important mechanism for the survival of F. tularensis since it allows the bacterium to escape from cells deplete of nutrients and subsequently to invade cells with an intact supply of nutrients necessary for its continuous multiplication.
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| 9. |
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| 10. |
- Vromman, Marieke, et al.
(författare)
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Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision
- 2023
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Ingår i: Nature Methods. - 1548-7091 .- 1548-7105. ; 20:8, s. 1159-1169
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Tidskriftsartikel (refereegranskat)abstract
- The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed using computational tools. Numerous such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools detected more than 315,000 unique circRNAs in three deeply sequenced human cell types. Next, 1,516 predicted circRNAs were validated using three orthogonal methods. Generally, tool-specific precision is high and similar (median of 98.8%, 96.3% and 95.5% for qPCR, RNase R and amplicon sequencing, respectively) whereas the sensitivity and number of predicted circRNAs (ranging from 1,372 to 58,032) are the most significant differentiators. Of note, precision values are lower when evaluating low-abundance circRNAs. We also show that the tools can be used complementarily to increase detection sensitivity. Finally, we offer recommendations for future circRNA detection and validation. This study describes benchmarking and validation of computational tools for detecting circRNAs, finding most to be highly precise with variations in sensitivity and total detection. The study also finds over 315,000 putative human circRNAs.
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