Functional MRI of murine olfactory bulbs at 15.2T reveals characteristic activation patters when stimulated by different odors

Thanks to its increased sensitivity, single-shot ultrahigh field functional MRI (UHF fMRI) could lead to valuable insight about subtle brain functions such as olfaction. However, UHF fMRI experiments targeting small organs next to air voids, such as the olfactory bulb, are severely affected by field inhomogeneity problems. Spatiotemporal Encoding (SPEN) is an emerging single-shot MRI technique that could provide a route for bypassing these complications. This is here explored with single-shot fMRI studies on the olfactory bulbs of male and female mice performed at 15.2T. SPEN images collected on these organs at a 108 µm in-plane resolution yielded remarkably large and well-defined responses to olfactory cues. Under suitable T2* weightings these activation-driven changes exceeded 5% of the overall signal intensity, becoming clearly visible in the images without statistical treatment. The nature of the SPEN signal intensity changes in such experiments was unambiguously linked to olfaction, via single-nostril experiments. These experiments highlighted specific activation regions in the external plexiform region and in glomeruli in the lateral part of the bulb, when stimulated by aversive or appetitive odors, respectively. These strong signal activations were non-linear with concentration, and shed light on how chemosensory signals reaching the olfactory epithelium react in response to different cues. Second-level analyses highlighted clear differences among the appetitive, aversive and neutral odor maps; no such differences were evident upon comparing male against female olfactory activation regions.

Structural Insights into Cellulose-Coated Oil in Water Emulsions

Cellulose is a renewable biopolymer, abundant on Earth, with a multi-level supramolecular structure. There has been significant interest and advancement in utilizing natural cellulose to stabilize emulsions. In our research, we develop and examine oil in water emulsions surrounded by unmodified cellulose as microreactors for the process of transformation of cellulose into valuable chemicals such as biodiesel. This study presents morphological characterization of cellulose-coated emulsions that can be used for such purposes. Cryogenic-scanning electron microscopy imaging along with light microscopy and light scattering reveals a multi-layer inner structure: an oil core surrounded by a porous cellulose hydrogel shell, coated by an outer shell of regenerated cellulose. Measurements of small-angle X-ray scattering provide quantification of the nano-scale structure within the porous cellulose hydrogel inner shell of the emulsion particle. These characteristics are relevant to utilization of cellulose-coated emulsions in various applications such as controlled release and as hosts for enzymatic biotechnological reactions.

SCAPP: an algorithm for improved plasmid assembly in metagenomes

BACKGROUND

Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples.

RESULTS

We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)-an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets.

CONCLUSIONS

SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP . Video abstract.

Naturally-occurring myopia and loss of cone function in a sheep model of achromatopsia

Achromatopsia is an inherited retinal disease characterized by loss of cone photoreceptor function. Day blind CNGA3 mutant Improved Awassi sheep provide a large animal model for achromatopsia. This study measured refractive error and axial length parameters of the eye in this model and evaluated chromatic pupillary light reflex (cPLR) testing as a potential screening test for loss of cone function. Twenty-one CNGA3 mutant, Improved Awassi, 12 control Afec-Assaf and 12 control breed-matched wild-type (WT) Awassi sheep were examined using streak retinoscopy and B-mode ocular ultrasonography. Four CNGA3 mutant and four Afec-Assaf control sheep underwent cPLR testing. Statistical tests showed that day-blind sheep are significantly more myopic than both Afec-Assaf and WT Awassi controls. Day-blind sheep had significantly longer vitreous axial length compared to WT Awassi (1.43 ± 0.13 and 1.23 ± 0.06 cm, respectively, p < 0.0002) and no response to bright red light compared to both controls. Lack of response to bright red light is consistent with cone dysfunction, demonstrating that cPLR can be used to diagnose day blindness in sheep. Day-blind sheep were found to exhibit myopia and increased vitreous chamber depth, providing a naturally occurring large animal model of myopia.

The Role of Interleukin-1 in the Pathogenesis of Cancer and its Potential as a Therapeutic Target in Clinical Practice

Interleukin-1 (IL-1) has long been known to be a key mediator of immunity and inflammation. Its dysregulation has been implicated in recent years in tumorigenesis and tumor progression, and its upregulation is thought to be associated with many tumors. Overexpression of the IL-1 agonists IL-1α and IL-1β has been shown to promote tumor invasiveness and metastasis by inducing the expression of angiogenic genes and growth factors. IL-1 blockers such as anakinra and canakinumab are already approved and widely used for the treatment of some autoimmune and autoinflammatory diseases and are currently being tested in preclinical and human clinical trials for cancer therapy. In this paper we review the most recent discoveries regarding the association between IL-1 dysregulation and cancer and present the novel IL-1 blockers currently being tested in cancer therapy and their corresponding clinical trials.

Expression of a recombinant, 4'-Phosphopantetheinylated, active M. tuberculosis fatty acid synthase I in E. coli

Background

Fatty acid synthase 1 (FAS I) from Mycobacterium tuberculosis (Mtb) is an essential protein and a promising drug target. FAS I is a multi-functional, multi-domain protein that is organized as a large (1.9 MDa) homohexameric complex. Acyl intermediates produced during fatty acid elongation are attached covalently to an acyl carrier protein (ACP) domain. This domain is activated by the transfer of a 4'-Phosphopantetheine (4'-PP, also termed P-pant) group from CoA to ACP catalyzed by a 4'-PP transferase, termed acyl carrier protein synthase (AcpS).

Methods

In order to obtain an activated FAS I in E. coli, we transformed E. coli with tagged Mtb fas1 and acpS genes encoded by a separate plasmid. We induced the expression of Mtb FAS I following induction of AcpS expression. FAS I was purified by Strep-Tactin affinity chromatography.

Results

Activation of Mtb FAS I was confirmed by the identification of a bound P-pant group on serine at position 1808 by mass spectrometry. The purified FAS I displayed biochemical activity shown by spectrophotometric analysis of NADPH oxidation and by CoA production, using the Ellman reaction. The purified Mtb FAS I forms a hexameric complex shown by negative staining and cryo-EM.

Conclusion

Purified hexameric and active Mtb FAS I is required for binding and drug inhibition studies and for structure-function analysis of this enzyme. This relatively simple and short procedure for Mtb FAS I production should facilitate studies of this enzyme.