| 1. |
- Beal, Jacob, et al.
(author)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Journal article (peer-reviewed)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.
|
|
| 2. |
- Zhu, Yuhui, et al.
(author)
-
Devils in the Clouds : An Evolutionary Study of Telnet Bot Loaders
- 2023
-
In: ICC 2023 - IEEE International Conference on Communications. - : IEEE. - 9781538674628 - 9781538674635 ; , s. 2338-2344
-
Conference paper (peer-reviewed)abstract
- One of the innovations brought by Mirai and its derived malware is the adoption of self-contained loaders for infecting IoT devices and recruiting them in botnets. Functionally decoupled from other botnet components and not embedded in the payload, loaders cannot be analysed using conventional approaches that rely on honeypots for capturing samples. Different approaches are necessary for studying the loaders evolution and defining a genealogy. To address the insufficient knowledge about loaders' lineage in existing studies, in this paper, we propose a semantic-aware method to measure, categorize, and compare different loader servers, with the goal of highlighting their evolution, independent from the payload evolution. Leveraging behavior-based metrics, we cluster the discovered loaders and define eight families to determine the genealogy and draw a homology map. Our study shows that the source code of Mirai is evolving and spawning new botnets with new capabilities, both on the client side and the server side. In turn, shedding light on the infection loaders can help the cybersecurity community to improve detection and prevention tools.
|
|
| 3. |
- Wang, Yongbo, et al.
(author)
-
Integrative analysis revealed the molecular mechanism underlying RBM10-mediated splicing regulation
- 2013
-
In: EMBO Molecular Medicine. - : EMBO. - 1757-4676 .- 1757-4684. ; 5:9
-
Journal article (peer-reviewed)abstract
- RBM10 encodes an RNA binding protein. Mutations in RBM10 are known to cause multiple congenital anomaly syndrome in male humans, the TARP syndrome. However, the molecular function of RBM10 is unknown. Here we used PAR-CLIP to identify thousands of binding sites of RBM10 and observed significant RBM10-RNA interactions in the vicinity of splice sites. Computational analyses of binding sites as well as loss-of-function and gain-of-function experiments provided evidence for the function of RBM10 in regulating exon skipping and suggested an underlying mechanistic model, which could be subsequently validated by minigene experiments. Furthermore, we demonstrated the splicing defects in a patient carrying an RBM10 mutation, which could be explained by disrupted function of RBM10 in splicing regulation. Overall, our study established RBM10 as an important regulator of alternative splicing, presented a mechanistic model for RBM10-mediated splicing regulation and provided a molecular link to understanding a human congenital disorder.
|
|
