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ABSTRACT Histone proteins are found across diverse lineages of Archaea, many of which package DNA and form chromatin. However, previous research has led to the hypothesis that the histone-like proteins of high-salt-adapted archaea, or halophiles, function differently. The sole histone protein encoded by the model halophilic species Halobacterium salinarum, HpyA, is nonessential and expressed at levels too low to enable genome-wide DNA packaging. Instead, HpyA mediates the transcriptional response to salt stress. Here we compare the features of genome-wide binding of HpyA to those of HstA, the sole histone of another model halophile, Haloferax volcanii. hstA, like hpyA, is a nonessential gene. To better understand HpyA and HstA functions, protein-DNA binding data (chromatin immunoprecipitation sequencing [ChIP-seq]) of these halophilic histones are compared to publicly available ChIP-seq data from DNA binding proteins across all domains of life, including transcription factors (TFs), nucleoid-associated proteins (NAPs), and histones. These analyses demonstrate that HpyA and HstA bind the genome infrequently in discrete regions, which is similar to TFs but unlike NAPs, which bind a much larger genomic fraction. However, unlike TFs that typically bind in intergenic regions, HpyA and HstA binding sites are located in both coding and intergenic regions. The genome-wide dinucleotide periodicity known to facilitate histone binding was undetectable in the genomes of both species. Instead, TF-like and histone-like binding sequence preferences were detected for HstA and HpyA, respectively. Taken together, these data suggest that halophilic archaeal histones are unlikely to facilitate genome-wide chromatin formation and that their function defies categorization as a TF, NAP, or histone. IMPORTANCE Most cells in eukaryotic species—from yeast to humans—possess histone proteins that pack and unpack DNA in response to environmental cues. These essential proteins regulate genes necessary for important cellular processes, including development and stress protection. Although the histone fold domain originated in the domain of life Archaea, the function of archaeal histone-like proteins is not well understood relative to those of eukaryotes. We recently discovered that, unlike histones of eukaryotes, histones in hypersaline-adapted archaeal species do not package DNA and can act as transcription factors (TFs) to regulate stress response gene expression. However, the function of histones across species of hypersaline-adapted archaea still remains unclear. Here, we compare hypersaline histone function to a variety of DNA binding proteins across the tree of life, revealing histone-like behavior in some respects and specific transcriptional regulatory function in others.

Microneedle design for biomedical applications, such as transdermal drug delivery, vaccination and transdermal biosensing, has lately become a rapidly growing research field. In this sense, finite element analysis has been extendedly used by microneedle designers to determine the most suitable structural parameters for their prototypes, and also to predict their mechanical response and efficiency during the insertion process. Although many proposals include computer-aided tools to build geometrical models for mechanical analysis, there is a lack of software utilities intended to automate the design process encompassing geometrical modeling, simulation setup and postprocessing of results. This work proposes a novel MATLAB-based design tool for microneedle arrays that permits personalized selection of the basic characteristics of a mechanical model. The tool automatically exports the selected options to an ANSYS batch file, including instructions to run a static and a linear buckling analysis. Later, the subsequent simulation results can be retrieved for on-screen display and potential postprocessing. In addition, this work reviews recent proposals (2018–2022) about finite element model characterization of microneedles to establish the minimum set of features that any tool intended for automating a design process should provide.

Despite intense recent research interest in archaea, the scientific community has experienced a bottleneck in the study of genome-scale gene expression experiments by RNA-seq due to the lack of commercial and specifically designed rRNA depletion kits. The high rRNA:mRNA ratio (80–90%: ~10%) in prokaryotes hampers global transcriptomic analysis. Insufficient ribodepletion results in low sequence coverage of mRNA, and therefore, requires a substantially higher number of replicate samples and/or sequencing reads to achieve statistically reliable conclusions regarding the significance of differential gene expression between case and control samples. Here, we show that after the discontinuation of the previous version of RiboZero (Illumina, San Diego, CA, USA) that was useful in partially or completely depleting rRNA from archaea, archaeal transcriptomics studies have experienced a slowdown. To overcome this limitation, here, we analyze the efficiency for four different hybridization-based kits from three different commercial suppliers, each with two sets of sequence-specific probes to remove rRNA from four different species of halophilic archaea. We conclude that the key for transcriptomic success with the currently available tools is the probe-specificity for the rRNA sequence hybridization. With this paper, we provide insights into the archaeal community for selecting certain reagents and strategies over others depending on the archaeal species of interest. These methods yield improved RNA-seq sensitivity and enhanced detection of low abundance transcripts.

Current CMOS-micro-electro-mechanical systems (MEMS) fabrication technologies permit cardiological implantable devices with sensing capabilities, such as the iStents, to be developed in such a way that MEMS sensors can be monolithically integrated together with a powering/transmitting CMOS circuitry. This system on chip fabrication allows the devices to meet the crucial requirements of accuracy, reliability, low-power, and reduced size that any life-sustaining medical application imposes. In this regard, the characterization of stand-alone prototype sensors in an efficient but affordable way to verify sensor performance and to better recognize further areas of improvement is highly advisable. This work proposes a novel characterization method based on an atomic force microscope (AFM) in contact mode that permits to calculate the maximum deflection of the flexible top plate of a capacitive MEMS pressure sensor without coating, under a concentrated load applied to its center. The experimental measurements obtained with this method have allowed to verify the bending behavior of the sensor as predicted by simulation of analytical and finite element (FE) models. This validation process has been carried out on two sensor prototypes with circular and square geometries that were designed using a computer-aided design tool specially-developed for capacitive MEMS pressure sensors.

Background: Comprehensive, patient‐specific models are essential to study calcium deposition and mobilization during dialysis. We aim to develop tools to support clinical prescriptions with a more accurate approach for the prediction of calcium mobilization while also considering major electrolytes and catabolites. Methods: We modified a multi‐solute model predicting patient‐specific dialysis response by incorporating a calcium buffer to represent bone exchanges. Data from four centers, involving 127 patients with six sessions each, were utilized. For each patient, three sessions were allocated for model training (ID123), while the remaining sessions were for validation (PRED456). The normalized root mean square error (nRMSE%) was used to evaluate both descriptive and predictive accuracy. Correlations between initial data and calcium exchanges were also assessed. Results: The overall nRMSE% for ID123 was 3.92%. For PRED456, it was 3.46% (ranging from a minimum of 1.17% for [Na+] to a maximum of 6.62% for [urea]). The median nRMSE% for plasma calcium varied between 1.13 and 8.32 for SHD sessions, depending on whether Ca_dialysis fluid (Cad) was ≥ or <1.50 mmol/L, respectively. For HDF sessions, the range was between 2.90 and 5.89. A significant and moderate correlation was found between overall calcium removal and the buffer balance. The most robust correlation observed was between the amount of calcium administered via post‐dilution fluid and the overall calcium removal in the dialysis filter. Conclusions: Identical therapy settings do not uniformly affect calcium mobilization, and our approach offers insight into calcium distribution across body compartments. This understanding will enhance clinical prescription practices. [ABSTRACT FROM AUTHOR]

Bactofilins are rigid, nonpolar bacterial cytoskeletal filaments that link cellular processes to specific curvatures of the cytoplasmic membrane. Although homologs of bactofilins have been identified in archaea and eukaryotes, functional studies have remained confined to bacterial systems. Here, we characterize representatives of two families of archaeal bactofilins from the pleomorphic archaeon Haloferax volcanii, halofilin A (HalA) and halofilin B (HalB). HalA and HalB polymerize in vitro, assembling into straight bundles. HalA polymers are highly dynamic and accumulate at positive membrane curvatures in vivo, whereas HalB forms more static foci that localize in areas of local negative curvatures on the outer cell surface. Gene deletions and live-cell imaging show that halofilins are critical in maintaining morphological integrity during shape transition from disk (sessile) to rod (motile). Morphological defects in ΔhalA result in accumulation of highly positive curvatures in rods but not in disks. Conversely, disk-shaped cells are exclusively affected by halB deletion, resulting in flatter cells. Furthermore, while ΔhalA and ΔhalB cells imprecisely determine the future division plane, defects arise predominantly during the disk-to-rod shape remodeling. The deletion of halA in the haloarchaeon Halobacterium salinarum, whose cells are consistently rod-shaped, impacted morphogenesis but not cell division. Increased levels of halofilins enforced drastic deformations in cells devoid of the S-layer, suggesting that HalB polymers are more stable at defective S-layer lattice regions. Our results suggest that halofilins might play a significant mechanical scaffolding role in addition to possibly directing envelope synthesis. [ABSTRACT FROM AUTHOR]

Microbial cells must continually adapt their physiology in the face of changing environmental conditions. Archaea living in extreme conditions, such as saturated salinity, represent important examples of such resilience. The model salt‐loving organism Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. However, the mechanisms regulating these lifestyle transitions remain unclear. In prior research, we showed that the transcriptional regulator, TrmB, maintains the rod shape in the related species Halobacterium salinarum by activating the expression of enzyme‐coding genes in the gluconeogenesis metabolic pathway. In Hbt. salinarum, TrmB‐dependent production of glucose moieties is required for cell surface glycoprotein biogenesis. Here, we use a combination of genetics and quantitative phenotyping assays to demonstrate that TrmB is essential for growth under gluconeogenic conditions in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name trmB suppressor, or TbsP (a.k.a. "tablespoon"). TbsP is required for adhesion to abiotic surfaces (i.e., biofilm formation) and maintains wild‐type cell morphology and motility. We use functional genomics and promoter fusion assays to characterize the regulons controlled by each of TrmB and TbsP, including joint regulation of the glucose‐dependent transcription of gapII, which encodes an important gluconeogenic enzyme. We conclude that TrmB and TbsP coregulate gluconeogenesis, with downstream impacts on lifestyle transitions in response to nutrients in Hfx. volcanii. [ABSTRACT FROM AUTHOR]

BackgroundParkinson's disease (PD) affects more than 6 million people worldwide. Along with motor impairments, patients and animal models exhibiting PD symptoms also experience cognitive impairment, fatigue, anxiety, and depression. Currently, there are no drugs available for PD that alter the progression of the disease. A body of evidence suggests that increased GABA levels contribute to the reduced expression of tyrosine hydroxylase (TH) and accompanying behavioral deficits. TH expression may be restored by blocking GABAA receptors. We hypothesized that golexanolone (GR3027), a well-tolerated GABAA receptor-modulating steroid antagonist (GAMSA), may improve Parkinson's symptoms in a rat model of PD.ObjectivesThe aims of this study were to assess whether golexanolone can ameliorate motor and non-motor symptoms in a rat model of PD and to identify some underlying mechanisms.MethodsWe used the unilateral 6-OHDA rat model of PD. The golexanolone treatment started 4 weeks after surgery. Motor symptoms were assessed using Motorater and CatWalk tests. We also analyzed fatigue (using a treadmill test), anhedonia (via the sucrose preference test), anxiety (with an open field test), and short-term memory (using a Y maze). Glial activation and key proteins involved in PD pathogenesis were analyzed using immunohistochemistry and Western blot.ResultsRats with PD showed motor incoordination and impaired locomotor gait, increased fatigue, anxiety, depression, and impaired short-term memory. Golexanolone treatment led to improvements in motor incoordination, certain aspects of locomotor gait, fatigue, anxiety, depression, and short-term memory. Notably, golexanolone reduced the activation of microglia and astrocytes, mitigated TH loss at 5 weeks after surgery, and prevented the increase of α-synuclein levels at 10 weeks.ConclusionsGolexanolone may be useful in improving both motor and non-motor symptoms that adversely affect the quality of life in PD patients, such as anxiety, depression, fatigue, motor coordination, locomotor gait, and certain cognitive alterations.