Enrichment of Schwann cell cultures from neonatal rat sciatic nerve by differential adhesion

A novel method of Schwann cell purification from neonatal rat sciatic nerve has been developed using differential adhesion. After enzymatic and mechanical dissociation, the cell digest is allowed to settle on polylysine-coated glass coverslips for 30 min with intermittent shaking. After an 18-h incubation, bipolar cells comprise greater than 95% of the non-adherent population. Indirect immunofluorescence with the cell-specific markers rabbit anti-galactocerebroside and rabbit anti-bovine-P-2 basic protein antiserum confirmed light microscopic identification of these bipolar cells as Schwann cells. Rabbit anti-human fibronectin specifically labeled fibroblasts which comprised less than 5% of the cell population, but did not bind to Schwann cells. Schwann cells isolated by differential adhesion were injected into a rabbit. When absorbed with cultured rat skin fibroblasts, serum from this rabbit specifically surface labeled greater than 99% of the bipolar and round cells after 18 h and 5 days in vitro and also labeled Schwann cells in fetal rat dorsal root ganglia cultures, but not fibroblasts or neurons.

A homodimeric BODIPY rotor as a fluorescent viscosity sensor for membrane-mimicking and cellular environments

Fluorescence properties of a novel homodimeric BODIPY dye rotor for Fluorescence Lifetime Imaging Microscopy (FLIM) are reported. Steady state and time resolved fluorescence measurements established the viscosity dependent behaviour in vitro. Homodimeric BODIPY embedded in different membrane mimicking lipid vesicles (DPPC, POPC and POPC plus cholesterol) is demonstrated to be a viable sensor for fluorescence lifetime based viscosity measurements. Moreover, SKOV3 cells readily endocytosed the dye, which accumulated in membranous structures inside the cytoplasm thereby allowing viscosity mapping of internal cell components.

On the origin and correction for inner filter effects in fluorescence Part I: primary inner filter effect-the proper approach for sample absorbance correction

Fluorescence technologies have been the preferred method for detection, analytical sensing, medical diagnostics, biotechnology, imaging, and gene expression for many years. Fluorescence becomes essential for studying molecular processes with high specificity and sensitivity through a variety of biological processes. A significant problem for practical fluorescence applications is the apparent non-linearity of the fluorescence intensity resulting from inner-filter effects, sample scattering, and absorption of intrinsic components of biological samples. Sample absorption can lead to the primary inner filter effect (Type I inner filter effect) and is the first factor that should be considered. This is a relatively simple factor to be controlled in any fluorescence experiment. However, many previous approaches have given only approximate experimental methods for correcting the deviation from expected results. In this part we are discussing the origin of the primary inner filter effect and presenting a universal approach for correcting the fluorescence intensity signal in the full absorption range. Importantly, we present direct experimental results of how the correction works. One considers problems emerging from varying absorption across its absorption spectrum for all fluorophores. We use Rhodamine 800 and demonstrate how to properly correct the excitation spectra in a broad wavelength range. Second is the effect of an inert absorber that attenuates the intensity of the excitation beam as it travels through the cuvette, which leads to a significant deviation of observed results. As an example, we are presenting fluorescence quenching of a tryptophan analog, NATA, by acrylamide and we show how properly corrected results compare to the initial erroneous results. The procedure is generic and applies to many other applications like quantum yield determination, tissue/blood absorption, or acceptor absorption in FRET experiments.

Physical and functional antagonism between tumor suppressor protein p53 and fortilin, an anti-apoptotic protein

Tumor suppressor protein p53, our most critical defense against tumorigenesis, can be made powerless by mechanisms such as mutations and inhibitors. Fortilin, a 172-amino acid polypeptide with potent anti-apoptotic activity, is up-regulated in many human malignancies. However, the exact mechanism by which fortilin exerts its anti-apoptotic activity remains unknown. Here we present significant insight. Fortilin binds specifically to the sequence-specific DNA binding domain of p53. The interaction of fortilin with p53 blocks p53-induced transcriptional activation of Bax. In addition, fortilin, but not a double point mutant of fortilin lacking p53 binding, inhibits p53-dependent apoptosis. Furthermore, cells with wild-type p53 and fortilin, but not cells with wild-type p53 and the double point mutant of fortilin lacking p53 binding, fail to induce Bax gene and apoptosis, leading to the formation of large tumor in athymic mice. Our results suggest that fortilin is a novel p53-interacting molecule and p53 inhibitor and that it is a logical molecular target in cancer therapy.

Mechanothermally induced conformational switch of a porphyrin dimer in a polymer film

Stretching a polymer film induces a conformational change (from the twisted to planar state) in the embedded porphyrin dimer, as evidenced by steady-state and time-resolved emission spectra.

Solvatochromic dye LDS 798 as microviscosity and pH probe

Styryl dyes, specifically LDS group dyes, are known solvatochromic and electrochromic probes for monitoring mitochondrial potential in cellular environments. However, the ability of these dyes to respond to fluctuations in viscosity, pH and temperature has not been established. In this study, we demonstrated that LDS 798 (also known as Styryl-11) can sense environmental viscosity (via fluorescence lifetime changes) as well as pH changes (ratiometric intensity change) in the absence of polarity variations. Polarity changes can be probed by spectral changes using LDS 798. Therefore, all properties of the media should be considered, when these types of dyes are used as electrochromic/solvatochromic sensors in cellular environments.

Multiple-pulse pumping for enhanced fluorescence detection and molecular imaging in tissue

Applications of fluorescence based imaging techniques for detection in cellular and tissue environments are severely limited by autofluorescence of endogenous components of cells, tissue, and the fixatives used in sample processing. To achieve sufficient signal-to-background ratio, a high concentration of the probe needs to be used which is not always feasible. Since typically autofluorescence is in the nanosecond range, long-lived fluorescence probes in combination with time-gated detection can be used for suppression of unwanted autofluorescence. Unfortunately, this requires the sacrifice of the large portion the probe signal in order to sufficiently filter the background. We report a simple and practical approach to achieve a many-fold increase in the intensity of a long-lived probe without increasing the background fluorescence. Using controllable, well separated bursts of closely spaced laser excitation pulses, we are able to highly increase the fluorescence signal of a long-lived marker over the endogenous fluorescent background and scattering, thereby greatly increasing detection sensitivity. Using a commercially available confocal microscopy system equipped with a laser diode and time correlated single photon counting (TCSPC) detection, we are able to enhance the signal of a long-lived Ruthenium (Ru)-based probe by nearly an order of magnitude. We used 80 MHz bursts of pulses (12.5 ns pulse separation) repeated with a 320 kHz repetition rate as needed to adequately image a dye with a 380 ns lifetime. Just using 10 pulses in the burst increases the Ru signal almost 10-fold without any increase in the background signal.

Genomic Alterations and Tumor Mutation Burden in Merkel Cell Carcinoma

Importance

Merkel cell carcinoma (MCC) is a rare and highly aggressive cutaneous neuroendocrine carcinoma with increasing incidence. Cytotoxic chemotherapy and checkpoint inhibitors provide treatment options in the metastatic setting; however, there are no approved or standard of care targeted therapy treatment options.

Objective

To identify actionable alterations annotated by the OncoKB database therapeutic evidence level in association with tumor mutation burden (TMB).

Design, Setting, and Participants

This is a retrospective, cross-sectional study using data from the American Association for Cancer Research Genomics Evidence Neoplasia Information Exchange, a multicenter international cancer consortium database. Patients with MCC were enrolled in participating institutions between 2017 and 2022. Data from version 11.0 of the database were released in January 2022 and analyzed from April to June 2022.

Main Outcomes and Measures

The main outcome was the percentage of patients with high TMB and OncoKB level 3B and 4 alterations.

Results

A total of 324 tumor samples from 313 patients with MCC (107 women [34.2%]; 287 White patients [91.7%]; 7 Black patients [2.2%]) were cataloged in the database. The median (range) number of alterations was 4.0 (0.0-178.0), with a mean (SD) of 13.6 (21.2) alterations. Oncogenic alterations represented 20.2% of all alterations (862 of 4259 alterations). Tissue originated from primary tumor in 55.0% of patients (172 patients) vs metastasis in 39.6% (124 patients). TMB-high (≥10 mutations per megabase) was present in 26.2% of cases (82 patients). Next-generation sequencing identified 55 patients (17.6%) with a level 3B variation for a Food and Drug Administration-approved drug for use in a biomarker-approved indication or approved drug in another indication. An additional 8.6% of patients (27 patients) had a level 4 variation. Actionable alterations were more common among high TMB cases, with 37 of 82 patients (45.1%) harboring level 3 alterations compared with only 18 of 231 patients (7.8%) with low TMB. The most common level 3B gene variants included PIK3CA (12 patients [3.8%]), BRCA1/2 (13 patients [4.2%]), ATM (7 patients [2.2%]), HRAS (5 patients [1.6%]), and TSC1/2 (6 patients [1.9%]). The most common level 4 variants include PTEN (13 patients [4.1%]), ARID1A (9 patients [2.9%]), NF1 (7 patients [2.2%]), and CDKN2A (7 patients [2.2%]). Copy number alterations and fusions were infrequent. In 61.0% of cases (191 cases), a PanCancer pathway was altered, and 39.9% (125 cases) had alterations in multiple pathways. Commonly altered pathways were RTK-RAS (119 patients [38.0%]), TP53 (103 patients [32.9%]), cell cycle (104 patients [33.2%]), PI3K (99 patients [31.6%]), and NOTCH (93 patients [29.7%]). In addition, oncogenic DNA mismatch repair gene alterations were present in 8.0% of cases (25 patients).

Conclusions and Relevance

In this cross-sectional retrospective study of alterations and TMB in MCC, a minority of patients had potentially actionable alterations. These findings support the investigation of targeted therapies as single agent or in combination with immunotherapy or cytotoxic chemotherapy in selected MCC populations.

Genetics of adaptive radiation in Hawaiian species of Tetramolopium (Asteraceae). III. Evolutionary genetics of sex expression

Despite numerous studies of speciation on oceanic islands, few insights exist on the genetic changes involved in the origin and diversification of island taxa. Here we report a genetic analysis of the evolutionary change in sex expression in Hawaiian Tetramolopium. The most diverse clade in the genus is characterized by a monoecious breeding system. The breeding system resulted from a change in sex expression in disc florets from the ancestral hermaphroditic condition to the derived male state. Analysis of an F2 population from a cross between the two forms of sex expression indicates two regions of the Tetramolopium linkage map are associated with the loss of female function in disc florets. Quantitative trait locus mapping of the two linkage groups confirms that two loci control 56% of the phenotypic variation of the trait in the F2 population. Additive and dominance effects are apparent but no statistical evidence of epistasis was found. Several related reproductive traits also have few genetic associations on the linkage map, but are generally distinct from the control of sex expression. Although modifier loci are likely to be involved, the apparent simple genetic change underlying sex expression parallels a major evolutionary diversification in Hawaiian Tetramolopium and may have initiated the divergence of this novel clade.

Enhanced DNA detection using a multiple pulse pumping scheme with time-gating (MPPTG)

Fluorescence signal enhancement induced by the binding of intercalators to DNA has been broadly utilized in various DNA detection methods.

Response and recovery of acetylcholinesterase activity in freshwater shrimp, Paratya australiensis (Decapoda: Atyidae) exposed to selected anti-cholinesterase insecticides

The toxicity of carbaryl, chlorpyrifos, dimethoate and profenofos to the freshwater shrimp, Paratya australiensis was assessed by measuring acetylcholinesterase (AChE) inhibition after 96h exposures. Shrimp exposed to these pesticides exhibited significant AChE inhibition, with mortality in shrimp corresponding to 70-90% AChE inhibition. The sensitivity of P. australiensis to the four pesticides based on AChE inhibition can be given as chlorpyrifos > profenofos > carbaryl > dimethoate. Recovery of AChE activity was followed in shrimp after 96 h exposures to carbaryl, chlorpyrifos and dimethoate. Recovery after exposure to the carbamate pesticide carbaryl was more rapid than for the two organophosphorus pesticides, chlorpyrifos and dimethoate. The slow recovery of depressed AChE activity may mean that affected organisms in the natural system are unable to sustain physical activities such as searching for food or eluding predators. To investigate the ecological significance of AChE inhibition, chemotaxis behaviour was assessed in shrimp exposed to profenofos for 24h. Abnormal chemotaxis behaviour in the exposed shrimp was observed at concentrations representing 30-50% AChE inhibition. A clear relationship existed between the depression of AChE activity and observed chemotaxis responses, such as approaching and grasping the chemoattractant source. These results suggest that in vivo toxicity tests based on this specific biomarker are sensitive and present advantages over conventional acute tests based on mortality. Behavioural studies of test organisms conducted in conjunction with measurement of AChE inhibition will provide data to clarify the toxic effects caused by sublethal chemical concentrations of anti-cholinesterase compounds.

Modifying optical properties of reduced/graphene oxide with controlled ozone and thermal treatment in aqueous suspensions

Graphene possesses a number of advantageous properties, however, does not exhibit optical emission, which limits its use in optoelectronics. Unlike graphene, its functional derivative, graphene oxide (GO) exhibits fluorescence emission throughout the visible. Here, we focus on controlled methods for tuning the optical properties of GO. We introduce ozone treatment of reduced graphene oxide (RGO) in order to controllably transform it from non-emissive graphene-like material into GO with a specific fluorescence emission response. Solution-based treatment of RGO for 5-45 min with ∼1.2 g l^-1 ozone/oxygen gas mixture yields a drastic color change, bleaching of the absorption in the visible and the stepwise increase in fluorescence intensity and lifetime. This is attributed to the introduction of oxygen-containing functional groups to RGO graphitic platform as detected by the infrared spectroscopy. A reverse process: controllable quenching of this fluorescence is achieved by the thermal treatment of GO in aqueous suspension up to 90 °C. This methodology allows for the wide range alteration of GO optical properties starting from the dark-colored non-emissive RGO material up to nearly transparent highly ozone-oxidized GO showing substantial fluorescence emission. The size of the GO flakes is concomitantly altered by oxidation-induced scission. Semi-empirical PM3 theoretical calculations on HyperChem models are utilized to explore the origins of optical response from GO. Two models are considered, attributing the induced emission either to the localized states produced by oxygen-containing addends or the islands of graphitic carbon enclosed by such addends. Band gap values calculated from the models are in the agreement with experimentally observed transition peak maxima. The controllable variation of GO optical properties in aqueous suspension by ozone and thermal treatments shown in this work provides a route to tune its optical response for particular optoelectronics or biomedical applications.

On the origin and correction for inner filter effects in fluorescence. Part II: secondary inner filter effect -the proper use of front-face configuration for highly absorbing and scattering samples

Fluorescence is an established technology for studying molecular processes and molecular interactions. More recently fluorescence became a leading method for detection, sensing, medical diagnostics, biotechnology, imaging, DNA analysis, and gene expression. Consequently, precise and accurate measurements in various conditions have become more critical for proper result interpretations. Previously, in Part 1, we discussed inner filter effect type I, which is a consequence of the instrumental geometrical sensitivity factor and absorption of the excitation. In this part, we analyze inner filter effect type II and discuss the practical consequences for fluorescence measurements in samples of high optical density (absorbance/scattering). We consider both the standard square and front-face experimental configurations, discuss experimental approaches to limit/mitigate the effect and discuss methods for correcting and interpreting experimental results.

Identification of fungal metabolites from inside Gallus gallus domesticus eggshells by non-invasively detecting volatile organic compounds (VOCs)

The natural porosity of eggshells allows hen eggs to become contaminated with microbes from the nesting material and environment. Those microorganisms can later proliferate due to the humid ambient conditions while stored in refrigerators, causing a potential health hazard to the consumer. The microbes' volatile organic compounds (mVOCs) are released by both fungi and bacteria. We studied mVOCs produced by aging eggs likely contaminated by fungi and fresh eggs using the non-invasive detection method of gas-phase sampling of volatiles followed by gas chromatography/mass spectrometry (GC/MS) analysis. Two different fungal species (Cladosporium macrocarpum and Botrytis cinerea) and two different bacteria species (Stenotrophomas rhizophila and Pseudomonas argentinensis) were identified inside the studied eggs. Two compounds believed to originate from the fungi themselves were identified. One fungus-specific compound was found in both egg and the fungi: trichloromethane. Graphical abstract Trichloromethane is a potential biomarker of fungal contamination of eggs.

Diversity and Biocontrol Potential of Endophytic Fungi and Bacteria Associated with Healthy Welsh Onion Leaves in Taiwan

Foliar diseases caused by Stemphylium and Colletotrichum species are among the major biotic factors limiting Welsh onion production in Taiwan. Owing to concerns about the environment and the development of pathogen resistance to existing fungicides, biological control using endophytes is emerging as an eco-friendly alternative to chemical control. The aim of the present study was to isolate endophytes from healthy Welsh onion leaves and investigate their antagonistic potential against the major phytopathogenic fungi associated with Welsh onion plants in Taiwan. A total of 109 bacterial and 31 fungal strains were isolated from healthy Welsh onion leaves and assigned to 16 bacterial and nine fungal genera using morphological and molecular characterization based on DNA sequence data obtained from nuclear internal transcribed spacer (nrITS) (fungi) and 16S rRNA (bacteria). Evaluation of these endophytic isolates for biocontrol activity against leaf blight pathogens Colletotrichum spaethianum strain SX15-2 and Stemphylium vesicarium strain SX20-2 by dual culture assay and greenhouse experiments resulted in the identification of two bacterial isolates (GFB08 and LFB28) and two fungal isolates (GFF06 and GFF08) as promising antagonists to leaf blight pathogens. Among the four selected isolates, Bacillus strain GFB08 exhibited the highest disease control in the greenhouse study. Therefore, Bacillus strain GFB08 was further evaluated to understand the mechanism underlying its biocontrol efficacy. A phylogenetic analysis based on six genes identified Bacillus strain GFB08 as B. velezensis. The presence of antimicrobial peptide genes (baer, bamC, bmyB, dfnA, fenD, ituC, mlna, and srfAA) and the secretion of several cell wall degrading enzymes (CWDEs), including cellulase and protease, confirmed the antifungal nature of B. velezensis strain GFB08. Leaf blight disease suppression by preventive and curative assays indicated that B. velezensis strain GFB08 has preventive efficacy on C. spaethianum strain SX15-2 and both preventive and curative efficacy on S. vesicarium strain SX20-2. Overall, the current study revealed that healthy Welsh onion leaves harbour diverse bacterial and fungal endophytes, among which the endophytic bacterial strain, B. velezensis strain GFB08, could potentially be used as a biocontrol agent to manage the leaf blight diseases of Welsh onion in Taiwan.

First Report of a Pythiogeton sp. Causing Root and Basal Stalk Rot of Wild Rice in California

In the summer of 2012, an outbreak of a newly discovered root and basal stalk rot of wild rice (Zizania palustris L.) cv. Franklin was observed in a 16-ha field in Big Valley, Lassen County, California (GPS coordinates 41°08'41.93″ N 121°10'07.49″ W). Infected plants exhibiting rot and dieback of roots and stalks were in various stages of decline, including death. Symptomatic stem and root tissues from affected plants were surface disinfected in 1% NaOCl for 90 s and placed on PARP agar plates, which were then incubated at 25°C in the dark for 1 week. Hyphal tips were used to start and maintain the organism in pure cultures. Isolates were transferred into petri plates with water and sterilized blades of turfgrass for the production of hyphae and reproductive structures. Isolates had coenocytic hyphae and produced zoospores 20 to 30 μm in diameter outside of sporangia (75 to 160 × 46 to 110 μm) from a naked mass of protoplasm, unlike from a vesicle, which is characteristic of Pythium spp. (2). Based on these morphological features, the isolate was tentatively identified as a Pythiogeton sp. Total genomic DNA was extracted from mycelia using the DNeasy Plant Mini Kit (Qiagen Inc., Valencia, CA). The internal transcribed spacers (ITS) 1 and 2 flanking the 5.8S rRNA regions were amplified by PCR and sequenced using universal ITS5 and ITS4 primers. A BLAST search of the 855-bp sequences revealed 98% similarity with a sequence of P. ramosum isolate Pg-164 (GenBank Accession No. JQ610190.1). The 21 nucleotide differences suggest that the isolate from wild rice may be an unreported species. The sequences were submitted to GenBank (KF719169). To fulfill Koch's postulates and confirm pathogenicity, 100 wild rice seeds were surface disinfected in 1% NaOCl for 90 s and placed in a 500 ml sterile pot with 250 g of autoclaved sand. Three 5 mm-diameter disks from the margin of a 7-day-old culture growing on PARP were placed in each of five pots. As a control, three 5 mm-diameter disks from a non-inoculated PARP plate were placed in five different pots, and five pots with autoclaved sand were not inoculated. All pots were kept in a randomized complete block design at 25°C for 14 days under a 14-h photoperiod. The pathogenicity test was repeated three times. After 14 days, the inoculated plants in all tests developed root and basal stalk rot, consistent with the symptoms observed on diseased wild rice in the field. The Pythiogeton sp. was consistently re-isolated on PARP from symptomatic plants but not from control plants. The non-inoculated wild rice plants remained asymptomatic. DNA sequences of the ITS region of the re-isolated Pythiogeton sp. revealed 100% identity with the isolate from the field. There have been reports of P. zeae on corn in Korea and P. zizaniae on water bamboo in Taiwan (1,2,3). This is the first report of a Pythiogeton sp. on wild rice. References: (1) P. J. Ann et al. Mycologia 98:116, 2006. (2) J. Huang et al. Mycoscience 54:130, 2013. (3) H. J. Jee et al. Mycologia 92:522, 2000.

Linear dichroism and optical anisotropy of silver nanoprisms in polymer films

We present optical studies of two different size distributions of silver triangular nanoprisms, one with a dipole resonance at 520 nm and the other with a dipole resonance at 650 nm, placed in different media. Significant wavelength-dependent depolarization of scattered light from the silver nanoprisms suspended in water indicates strong interference of multiple surface plasmon resonant modes in the same particle. We use this depolarization as a probe of light scattering by the nanoprisms in a lipid solution due to the rejection of a polarized background scattering. Also, the silver nanoprisms were embedded in a polyvinyl alcohol polymer matrix and oriented by stretching the polymer/nanoprism nanocomposite films. We observe significantly increased linear dichroism in the region associated with the plasmonic in-plane dipole mode upon stretching. Additionally, there is a weaker linear dichroism in the region associated with out-of-plane modes, which vanish in the extinction spectrum of the stretched nanocomposite film.

Intertrial intervals and visual habituation in neonates

Eighteen 3-day-old human neonates were shown a 12 by 12 black-white checkerboard target for 45-sec. trials with either a 10-, 20-, or 30-sec. intertrial interval until their visual fixation time decreased to a set criterion for habituation. On subsequent recovery trials, a 2 by 2 black-white checkerboard target received significantly longer fixations from boys in the 10-sec. and girls in the 20-sec. conditions. 30-sec. intervals, however, produced little habituation and recovery. The implications of these findings are discussed.

Recent Enhancements to Interline and Electron Multiplying CCD Image Sensors

This paper describes recent process modifications made to enhance the performance of interline and electron-multiplying charge-coupled-device (EMCCD) image sensors. By use of MeV ion implantation, quantum efficiency in the NIR region of the spectrum was increased by 2×, and image smear was reduced by 6 dB. By reducing the depth of the shallow photodiode (PD) implants, the photodiode-to-vertical-charge-coupled-device (VCCD) transfer gate voltage required for no-lag operation was reduced by 3 V, and the electronic shutter voltage was reduced by 9 V. The thinner, surface pinning layer also resulted in a reduction of smear by 4 dB in the blue portion of the visible spectrum. For EMCCDs, gain aging was eliminated by providing an oxide-only dielectric under its multiplication phase, while retaining the oxide-nitride-oxide (ONO) gate dielectrics elsewhere in the device.

Assessing Participant Diversity in Acne Clinical Trials

A lack of clinical trials devoted specifically to treatment protocols in minority groups and diverse individuals with skin of color (SOC) exists. Treatment decisions often vary based on patient cultural preferences and have differing efficacies based on skin type. As such, it is important to evaluate the diversity of participants being included in dermatology clinical trials.