Identifying Improved Sites for Heterologous Gene Integration Using ATAC-seq

Constructing efficient cellular factories often requires integration of heterologous pathways for synthesis of novel compounds and improved cellular productivity. Few genomic sites are routinely used, however, for efficient integration and expression of heterologous genes, especially in nonmodel hosts. Here, a data-guided framework for informing suitable integration sites for heterologous genes based on ATAC-seq was developed in the nonmodel yeast Komagataella phaffii. Single-copy GFP constructs were integrated using CRISPR/Cas9 into 38 intergenic regions (IGRs) to evaluate the effects of IGR size, intensity of ATAC-seq peaks, and orientation and expression of adjacent genes. Only the intensity of accessibility peaks was observed to have a significant effect, with higher expression observed from IGRs with low- to moderate-intensity peaks than from high-intensity peaks. This effect diminished for tandem, multicopy integrations, suggesting that the additional copies of exogenous sequence buffered the transcriptional unit of the transgene against effects from endogenous sequence context. The approach developed from these results should provide a basis for nominating suitable IGRs in other eukaryotic hosts from an annotated genome and ATAC-seq data

In vivo chemical and structural analysis of plant cuticular waxes using stimulated Raman scattering microscopy.

The cuticle is a ubiquitous, predominantly waxy layer on the aerial parts of higher plants that fulfils a number of essential physiological roles, including regulating evapotranspiration, light reflection, and heat tolerance, control of development, and providing an essential barrier between the organism and environmental agents such as chemicals or some pathogens. The structure and composition of the cuticle are closely associated but are typically investigated separately using a combination of structural imaging and biochemical analysis of extracted waxes. Recently, techniques that combine stain-free imaging and biochemical analysis, including Fourier transform infrared spectroscopy microscopy and coherent anti-Stokes Raman spectroscopy microscopy, have been used to investigate the cuticle, but the detection sensitivity is severely limited by the background signals from plant pigments. We present a new method for label-free, in vivo structural and biochemical analysis of plant cuticles based on stimulated Raman scattering (SRS) microscopy. As a proof of principle, we used SRS microscopy to analyze the cuticles from a variety of plants at different times in development. We demonstrate that the SRS virtually eliminates the background interference compared with coherent anti-Stokes Raman spectroscopy imaging and results in label-free, chemically specific confocal images of cuticle architecture with simultaneous characterization of cuticle composition. This innovative use of the SRS spectroscopy may find applications in agrochemical research and development or in studies of wax deposition during leaf development and, as such, represents an important step in the study of higher plant cuticles

Conversion of Biomass to Chemicals via Electrofermentation of Lactic Acid Bacteria

This is the final version. Available on open access from MDPI via the DOI in this recordMicrobial electrosynthesis is the process of supplying electrons to microorganisms to reduce CO2 and yield industrially relevant products. Such systems are limited by their requirement for high currents, resulting in challenges to cell survival. Electrofermentation is an electron-efficient form of microbial electrosynthesis in which a small cathodic or anodic current is provided to a culture to alter the oxidation–reduction potential of the medium and, in turn, alter microbial metabolism. This approach has been successfully utilised to increase yields of diverse products including biogas, butanediol and lactate. Biomass conversion to lactate is frequently facilitated by ensiling plant biomass with homofermentative lactic acid bacteria. Although most commonly used as a preservative in ensiled animal feed, lactate has diverse industrial applications as a precursor for the production of probiotics, biofuels, bioplastics and platform chemicals. Lactate yields by lactic acid bacteria (LAB) are constrained by a number of redox limitations which must be overcome while maintaining profitability and sustainability. To date, electrofermentation has not been scaled past laboratory- or pilot-stage reactions. The increasing ease of genetic modification in a wide range of LAB species may prove key to overcoming some of the pitfalls of electrofermentation at commercial scale. This review explores the history of electrofermentation as a tool for controlling redox balance within bacterial biocatalysts, and the potential for electrofermentation to increase lactate production from low-value plant biomass.Shell Research Ltd

Estimating Residual Strength in Filament Wound Casings from Nondestructive Evaluation of Impact Damage

The purpose of this study is to improve the ability to detect hidden impact damage in thick composites caused by low velocity impact and to predict the remaining strength of those materials. An impact study has been undertaken on filament wound graphite/epoxy casings, such as those proposed for NASA’s space shuttle solid fuel rocket boosters. In thick composite materials, low-velocity impact damage may not be visually evident, depending on the impacter shape; yet the damage may compromise the composite’s ultimate strength. A model of a filament wound casing was fabricated with one fifth of the diameter (30 inches) but with the full thickness (1.4inches) of the full rocket motor (12 feet and 1.4 inches, respectively). It was impacted with various masses and energy levels using a one inch diameter ball as the indenter. This casing was subsequently cut into coupons of 2 in. width by 12 in. length. These samples were nondestructively examined for the degree of damage. Next, these samples were loaded in tension until failure. Efforts to accurately detect the damage with dye penetrants and x-ray methods have proven unsatisfactory in the samples that displayed no visible damage. In spite of the high attenuation of this material, ultrasonic phase velocity and attenuation images show promise in predicting the residual strength of the coupons. Predictions of the damage profile, and therefore the cross-section of the damage in the direction of loading, were obtained by assuming an “effective” value for the attenuation of the damaged part of the filament wound casing material (15 dB/MHz-cm) and an “effective” value for the velocity of the damaged part of the filament wound casing material (2250 m/s). These estimates were based partially on measurements made on impact damaged thin composite material. The remaining strength predictions from these ultrasonic data showed a significant improvement over the x-ray predictions of remaining strength and the method may be usable for predictions of remaining strength of full scale rocket motors that may have suffered impact damage.</p

An update: improvements in imaging perfluorocarbon-mounted plant leaves with implications for studies of plant pathology, physiology, development and cell biology.

Plant leaves are optically complex, which makes them difficult to image by light microscopy. Careful sample preparation is therefore required to enable researchers to maximize the information gained from advances in fluorescent protein labeling, cell dyes and innovations in microscope technologies and techniques. We have previously shown that mounting leaves in the non-toxic, non-fluorescent perfluorocarbon (PFC), perfluorodecalin (PFD) enhances the optical properties of the leaf with minimal impact on physiology. Here, we assess the use of the PFCs, PFD, and perfluoroperhydrophenanthrene (PP11) for in vivo plant leaf imaging using four advanced modes of microscopy: laser scanning confocal microscopy (LSCM), two-photon fluorescence microscopy, second harmonic generation microscopy, and stimulated Raman scattering (SRS) microscopy. For every mode of imaging tested, we observed an improved signal when leaves were mounted in PFD or in PP11, compared to mounting the samples in water. Using an image analysis technique based on autocorrelation to quantitatively assess LSCM image deterioration with depth, we show that PP11 outperformed PFD as a mounting medium by enabling the acquisition of clearer images deeper into the tissue. In addition, we show that SRS microscopy can be used to image PFCs directly in the mesophyll and thereby easily delimit the "negative space" within a leaf, which may have important implications for studies of leaf development. Direct comparison of on and off resonance SRS micrographs show that PFCs do not to form intracellular aggregates in live plants. We conclude that the application of PFCs as mounting media substantially increases advanced microscopy image quality of living mesophyll and leaf vascular bundle cells

Borrelia Burgdorferi Induces a Type I Interferon Response During Early Stages of Disseminated Infection in Mice

BACKGROUND: Lyme borrelia genotypes differ in their capacity to cause disseminated disease. Gene array analysis was employed to profile the host transcriptome induced by Borrelia burgdorferi strains with different capacities for causing disseminated disease in the blood of C3H/HeJ mice during early infection. RESULTS: B. burgdorferi B515, a clinical isolate that causes disseminated infection in mice, differentially regulated 236 transcripts (P \u3c 0.05 by ANOVA, with fold change of at least 2). The 216 significantly induced transcripts included interferon (IFN)-responsive genes and genes involved in immunity and inflammation. In contrast, B. burgdorferi B331, a clinical isolate that causes transient skin infection but does not disseminate in C3H/HeJ mice, stimulated changes in only a few genes (1 induced, 4 repressed). Transcriptional regulation of type I IFN and IFN-related genes was measured by quantitative RT-PCR in mouse skin biopsies collected from the site of infection 24 h after inoculation with B. burgdorferi. The mean values for transcripts of Ifnb, Cxcl10, Gbp1, Ifit1, Ifit3, Irf7, Mx1, and Stat2 were found to be significantly increased in B. burgdorferi strain B515-infected mice relative to the control group. In contrast, transcription of these genes was not significantly changed in response to B. burgdorferi strain B331 or B31-4, a mutant that is unable to disseminate. CONCLUSIONS: These results establish a positive association between the disseminating capacity of B. burgdorferi and early type I IFN induction in a murine model of Lyme disease

Ruptured renal artery aneurysm during pregnancy, a clinical dilemma

BACKGROUND: Rupture of a renal artery aneurysm (RAA) during pregnancy is a rare event, with a high mortality rate for both mother and fetus. Increased blood flow and intra-abdominal pressure, and vascular changes secondary to increased steroid production are postulated as contributory to the increased risk of rupture during pregnancy. CASE PRESENTATION: We present here a case report of total avulsion of solitary kidney secondary to rupture of RAA in a pregnant patient with congenital absence of the contralateral kidney. The main indication for nephrectomy was severely damaged kidney. Diagnosis was made during operation and both mother and fetus were saved. There are no previous reports of an intact renal artery aneurysm diagnosed either antepartum or postpartum. CONCLUSION: The possibility of a ruptured RAA should be considered in pregnant women with evidence of retroperitoneal hemorrhage. This case was unusual because it occurred in a solitary kidney, during the third trimester of pregnancy