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  1. Free, publicly-accessible full text available January 1, 2024
  2. Abstract

    Phytopathogenic bacteria play important roles in plant productivity, and developments in gene editing have potential for enhancing the genetic tools for the identification of critical genes in the pathogenesis process. CRISPR-based genome editing variants have been developed for a wide range of applications in eukaryotes and prokaryotes. However, the unique mechanisms of different hosts restrict the wide adaptation for specific applications. Here, CRISPR-dCas9 (dead Cas9) and nCas9 (Cas9 nickase) deaminase vectors were developed for a broad range of phytopathogenic bacteria. A gene for a dCas9 or nCas9, cytosine deaminase CDA1, and glycosylase inhibitor fusion protein (cytosine base editor, or CBE) was applied to base editing under the control of different promoters. Results showed that the RecA promoter led to nearly 100% modification of the target region. When residing on the broad host range plasmid pHM1, CBERecApis efficient in creating base edits in strains ofXanthomonas,Pseudomonas,ErwiniaandAgrobacterium. CBE based on nCas9 extended the editing window and produced a significantly higher editing rate inPseudomonas. Strains with nonsynonymous mutations in test genes displayed expected phenotypes. By multiplexing guide RNA genes, the vectors can modify up to four genes in a single round of editing. Whole-genome sequencing of base-edited isolates ofXanthomonas oryzaepv.oryzaerevealed guide RNA-independent off-targetmore »mutations. Further modifications of the CBE, using a CDA1 variant (CBERecAp-A) reduced off-target effects, providing an improved editing tool for a broad group of phytopathogenic bacteria.

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  3. A great part of software development involves conceptualizing or communicating the underlying procedures and logic that needs to be expressed in programs. One major difficulty of programming is turning concept into code , especially when dealing with the APIs of unfamiliar libraries. Recently, there has been a proliferation of machine learning methods for code generation and retrieval from natural language queries , but these have primarily been evaluated purely based on retrieval accuracy or overlap of generated code with developer-written code, and the actual effect of these methods on the developer workflow is surprisingly unattested. In this article, we perform the first comprehensive investigation of the promise and challenges of using such technology inside the PyCharm IDE, asking, “At the current state of technology does it improve developer productivity or accuracy, how does it affect the developer experience, and what are the remaining gaps and challenges?” To facilitate the study, we first develop a plugin for the PyCharm IDE that implements a hybrid of code generation and code retrieval functionality, and we orchestrate virtual environments to enable collection of many user events (e.g., web browsing, keystrokes, fine-grained code edits). We ask developers with various backgrounds to complete 7 varieties ofmore »14 Python programming tasks ranging from basic file manipulation to machine learning or data visualization, with or without the help of the plugin. While qualitative surveys of developer experience are largely positive, quantitative results with regards to increased productivity, code quality, or program correctness are inconclusive. Further analysis identifies several pain points that could improve the effectiveness of future machine learning-based code generation/retrieval developer assistants and demonstrates when developers prefer code generation over code retrieval and vice versa. We release all data and software to pave the road for future empirical studies on this topic, as well as development of better code generation models.« less
  4. This research note illustrates the importance of a holistic approach to family demography and children’s well-being. Using the family configurations published in a previous study, we show that a configurational measure of family patterns predicts better the country-level proportion of stunted and wasted children across 75 low- and middle-income countries than 20 single family-related variables, world regions, and the Human Development Index. We contend that demographers need to do a better job of measuring social systems because individuals’ choices are influenced by contexts that are better represented with measures that capture multiple related factors (holistic approach) than with a single variable (analytical approach).
  5. Drought stress is a major constraint in global maize production, causing almost 30–90% of the yield loss depending upon growth stage and the degree and duration of the stress. Here, we report that ectopic expression of Arabidopsis glutaredoxin S17 (AtGRXS17) in field grown maize conferred tolerance to drought stress during the reproductive stage, which is the most drought sensitive stage for seed set and, consequently, grain yield. AtGRXS17-expressing maize lines displayed higher seed set in the field, resulting in 2-fold and 1.5-fold increase in yield in comparison to the non-transgenic plants when challenged with drought stress at the tasseling and silking/pollination stages, respectively. AtGRXS17-expressing lines showed higher relative water content, higher chlorophyll content, and less hydrogen peroxide accumulation than wild-type (WT) control plants under drought conditions. AtGRXS17-expressing lines also exhibited at least 2-fold more pollen germination than WT plants under drought stress. Compared to the transgenic maize, WT controls accumulated higher amount of proline, indicating that WT plants were more stressed over the same period. The results present a robust and simple strategy for meeting rising yield demands in maize under water limiting conditions.