Miracle-dz/UniFAR-FTUs huggingface dataset:
Intracellular Ca2+ Signaling in Protozoan Parasites: An Overview with a Focus on Mitochondria

Ca2+ signaling has been involved in controling critical cellular functions such as activation of proteases, cell death, and cell cycle control. The endoplasmatic reticulum plays a significant role in Ca2+ storage inside the cell, but mitochondria have long been recognized as a fundamental Ca2+ pool. Protozoan parasites such as Plasmodium falciparum, Toxoplasma gondii, and Trypanosoma cruzi display a Ca2+ signaling toolkit with similarities to higher eukaryotes, including the participation of mitochondria in Ca2+-dependent signaling events. This review summarizes the most recent knowledge in mitochondrial Ca2+ signaling in protozoan parasites, focusing on the mechanism involved in mitochondrial Ca2+ uptake by pathogenic protists.
Expression and characterization of chimeric spidroins from flagelliform‐aciniform repetitive modules

Spiders can produce up to seven different types of silks or glues with different mechanical properties. Of these, flagelliform (Flag) silk is the most elastic, and aciniform (AcSp1) silk is the toughest. To produce a chimeric spider silk (spidroin) FlagR‐AcSp1R, we fused one repetitive module of flagelliform silk from Araneus ventricosus and one repetitive module of aciniform silk from Argiope trifasciata. The recombinant protein expressed in E. coli formed silk‐like fibers by manual‐drawing. CD analysis showed that the secondary structure of FlagR‐AcSp1R spidroin remained stable during the gradual reduction of pH from 7.0 to 5.5. The spectrum of FTIR indicated that the secondary structure of FlagR‐AcSp1R changed from α‐helix to β‐sheet. The conformation change of FlagR‐AcSp1R was similar to other spidroins in the fiber formation process. SEM analysis revealed that the mean diameter of the fibers was around 1 ~ 2 μm, and the surface was smooth and uniform. The chimeric fibers exhibited superior toughness (~33.1 MJ/m3) and tensile strength (~261.4 MPa). This study provides new insight into design of chimeric spider silks with high mechanical properties.
Manipulation of Developmental Gamma-Globin Gene Expression: an Approach for Healing Hemoglobinopathies

β-Hemoglobinopathies are the most common monogenic disorders, and a century of research has provided us with a better understanding of the attributes of these diseases. Allogenic stem cell transplantation was the only potentially curative option available for these diseases until the discovery of gene therapy. The findings on the protective nature of fetal hemoglobin in sickle cell disease (SCD) and thalassemia patients carrying hereditary persistence of fetal hemoglobin (HPFH) mutations has given us the best evidence that the cure for β-hemoglobinopathies remains hidden in the hemoglobin locus. ABSTRACT β-Hemoglobinopathies are the most common monogenic disorders, and a century of research has provided us with a better understanding of the attributes of these diseases. Allogenic stem cell transplantation was the only potentially curative option available for these diseases until the discovery of gene therapy. The findings on the protective nature of fetal hemoglobin in sickle cell disease (SCD) and thalassemia patients carrying hereditary persistence of fetal hemoglobin (HPFH) mutations has given us the best evidence that the cure for β-hemoglobinopathies remains hidden in the hemoglobin locus. The detailed understanding of the developmental gene regulation of gamma-globin (γ-globin) and the emergence of gene manipulation strategies offer us the opportunity for developing a γ-globin gene-modified autologous stem cell transplantation therapy. In this review, we summarize different therapeutic strategies that reactivate fetal hemoglobin for the gene therapy of β-hemoglobinopathies.
Dissecting Total Plasma and Protein-Specific Glycosylation Profiles in Congenital Disorders of Glycosylation

Protein N-glycosylation is a multifactorial process involved in many biological processes. A broad range of congenital disorders of glycosylation (CDGs) have been described that feature defects in protein N-glycan biosynthesis. Here, we present insights into the disrupted N-glycosylation of various CDG patients exhibiting defects in the transport of nucleotide sugars, Golgi glycosylation or Golgi trafficking. We studied enzymatically released N-glycans of total plasma proteins and affinity purified immunoglobulin G (IgG) from patients and healthy controls using mass spectrometry (MS). The applied method allowed the differentiation of sialic acid linkage isomers via their derivatization. Furthermore, protein-specific glycan profiles were quantified for transferrin and IgG Fc using electrospray ionization MS of intact proteins and glycopeptides, respectively. Next to the previously described glycomic effects, we report unprecedented sialic linkage-specific effects. Defects in proteins involved in Golgi trafficking (COG5-CDG) and CMP-sialic acid transport (SLC35A1-CDG) resulted in lower levels of sialylated structures on plasma proteins as compared to healthy controls. Findings for these specific CDGs include a more pronounced effect for α2,3-sialylation than for α2,6-sialylation. The diverse abnormalities in glycomic features described in this study reflect the broad range of biological mechanisms that influence protein glycosylation.
The emerging weed challenge of managing native plant species: What are we doing in New South Wales?

Plant species that are native to Australia can be significant weeds of primary production and the environment, both within and outside their endemic ranges. Of the 6049 taxa native to New South Wales, over 165 (2.7%) are considered to be weedy within their indigenous range. With only one exception, none are managed as noxious under the New South Wales Noxious Weeds Act 1993. Two groups of native species are managed as noxious weeds. With one exception, the first group includes a range of 14 tree, shrub, vine and epiphytic species found in northern and eastern rainforests and high rainfall areas. These species are generally of concern outside their endemic range, for example sweet pittosporum (Pittosporum undulatum Vent.), some lilly-pilly species (both Acmena and Syzygium species), bower vine (Pandorea jasminoides (Lindl.) Schum. ) and staghorn fern (Platycerium superbum de Jonch. & Hennipman). The exception is coastal teatree (Leptospermum laevigatum (Gaertn.) F.Muell. ), a species that is invasive in coastal dune areas in New South Wales. The second group are those found (and declared) within their endemic range. Galvanised burr (Sclerolaena birchii (F.Muell.) Domin), an early colonising shrub of rangeland throughout western New South Wales, is the only current example. This paper discusses the use of legislation to enable the management of native plant species, particularly with the Noxious Weeds Act 1993 and the Native Vegetation Act 2003 (and associated legislation). The problems encountered are also examined. Importantly, options for the management of native species in New South Wales are suggested so as to address some of the conflicting issues identified. The principles, practices and examples examined in this paper provide essential guidance to the emerging challenges of the management of native plant species across many jurisdictions in Australia.
Plasmacytoid dendritic cells regulate host immune response to Citrobacter rodentium induced colitis in colon‐draining lymph nodes

Dendritic cells (DCs) are first in line to sense invading microbes and to deliver signals to other immune cells. Plasmacytoid DCs (pDC) produce high amounts of type I interferons (IFNs) but also regulate immune responses. Using the Clec4C (BDCA2)‐diphtheria toxin receptor mouse model allowing conditional pDC depletion, we identified an essential role for pDCs in regulating intestinal inflammation locally in the gut. In pDC‐depleted mice, Citrobacter rodentium infection led to enhanced activation of conventional DCs and induction of IFN‐γ‐producing Th1‐cells in colon‐draining lymph nodes, while induction of Foxp3+/CD25+ Treg and IL‐17‐producing Th17 cells was impaired. Concomitantly, F4/80+ macrophages accumulated into the colon lamina propria in excess, and levels of Il‐1β and Tnf transcripts increased and Foxp3+ Treg were fewer. Our results indicate that pDCs control inflammation in the gut during C. rodentium infection and that they have an important immune regulatory role in colon‐draining lymph nodes.
Cytokinesis-Block Micronucleus Cytome Assay Evolution into a More Comprehensive Method to Measure Chromosomal Instability

This review describes the cytokinesis-block micronucleus (CBMN) cytome assay and its evolution into a molecular cytogenetic method of chromosomal instability (CIN). Micronuclei (MNi) originate from whole chromosomes or chromosome fragments that fail to segregate to the poles of the cell during mitosis. These lagging chromosomes are excluded from the daughter nuclei and are enveloped in their own membrane to form MNi. The CBMN assay was developed to allow MNi to be scored exclusively in once-divided binucleated cells, which enables accurate measurement of chromosome breakage or loss without confounding by non-dividing cells that cannot express MNi. The CBMN assay can be applied to cell lines in vitro and cells such as lymphocytes that can be stimulated to divide ex vivo. In the CBMN assay, other CIN biomarkers such as nucleoplasmic bridges (NPBs) and nuclear buds (NBUDs) are also measured. Use of centromere, telomere, and chromosome painting probes provides further insights into the mechanisms through which MNi, NPBs and NBUDs originate. Measurement of MNi is also important because entrapment within a micronucleus may cause chromosomes to shatter and, after nuclear reintegration, become rearranged. Additionally, leakage of DNA from MNi can stimulate inflammation via the cyclic GMP-AMP Synthase—Stimulator of Interferon Genes (cGAS-STING) DNA sensing mechanism of the innate immune system.
A Review of CFD Modelling and Performance Metrics for Osmotic Membrane Processes

Simulation via Computational Fluid Dynamics (CFD) offers a convenient way for visualising hydrodynamics and mass transport in spacer-filled membrane channels, facilitating further developments in spiral wound membrane (SWM) modules for desalination processes. This paper provides a review on the use of CFD modelling for the development of novel spacers used in the SWM modules for three types of osmotic membrane processes: reverse osmosis (RO), forward osmosis (FO) and pressure retarded osmosis (PRO). Currently, the modelling of mass transfer and fouling for complex spacer geometries is still limited. Compared with RO, CFD modelling for PRO is very rare owing to the relative infancy of this osmotically driven membrane process. Despite the rising popularity of multi-scale modelling of osmotic membrane processes, CFD can only be used for predicting process performance in the absence of fouling. This paper also reviews the most common metrics used for evaluating membrane module performance at the small and large scales.
Reduced expression of ppGalNAc‐T4 promotes proliferation of human breast cancer cells

Breast cancer, one of the most frequently diagnosed and aggressive malignancies, is the major cause of cancer‐related death greatly threatening women health. Polypeptide N‐acetylgalactosaminyltransferase 4 (ppGalNAc‐T4), responsible for the initial step of mucin‐type O‐glycosylation, has been reported to be implicated in diverse types of human tumors. However, the biological role of ppGalNAc‐T4 in breast cancer is still undetermined. In this study, we investigate the effects and mechanism of ppGalNAc‐T4 to breast cancer cell proliferation. From analysis of high throughput RNA sequencing datasets of Gene Expression Omnibus and ArrayExpress, a positive correlation between ppGalNAc‐T4 and the recurrence‐free survival was observed in multigroup of human breast cancer datasets. Moreover, transcriptomes analysis using RNA‐sequencing in MCF7 cells revealed that cell cycle‐related genes induced the effects of ppGalNAc‐T4 on breast cancer cell proliferation. Additionally, investigations showed that ppGalNAc‐T4 impaired cell proliferation in MCF‐7 and MDA‐MB‐231 breast cells. Furthermore, our results suggested that the ppGalNAc‐T4 knockout activated Notch signaling pathway and enhanced cell proliferation. Collectively, our data indicated that ppGalNAc‐T4 affected the proliferation of human breast cancer cells, which appears to be a novel target for understanding the underlying molecular mechanism of breast cancer.
Improving Antibody Production in Stably Transfected CHO Cells by CRISPR‐Cas9‐Mediated Inactivation of Genes Identified in a Large‐Scale Screen with Chinese Hamster‐Specific siRNAs

The Chinese hamster ovary (CHO) cell line is commonly used for the production of biotherapeutics. As cell productivity directly affects the cost of production, methods are developed to manipulate the expression of specific genes that are known to be involved in protein synthesis, folding, and secretion to increase productivity. However, there are no large‐scale CHO‐specific functional screens to identify novel gene targets that impact the production of secreted recombinant proteins. Here, a large‐scale, CHO cell‐specific small interfering RNA screen is performed to identify genes that consistently enhance antibody production when silenced in a panel of seven CHO cell lines. Four genes, namely, Cyp1a2, Atp5s, Dgki, and P3h2, are identified, and then selected for CRISPR‐Cas9 knockout validation in recombinant CHO cell lines. Single knockout of Cyp1a2, Atp5s, or Dgki, but not P3h2, results in a more than 90% increase in specific antibody productivity. Overall, the knockout of Cyp1a2 demonstrates the most significant improvement of antibody production, with a minimal impact on cell growth.
Ultrasonic Tenotomy and Debridement for Calcific Tendinopathy of the Shoulder: A Pilot Case Series

Calcific tendinopathy of the rotator cuff is a common cause of shoulder pain and debility. Minimally invasive treatment options have been employed for management; however, ultrasonic tenotomy has not been previously described for management of calcific tendinopathy of the shoulder. The purpose of the current case series was to provide preliminary evidence in support of a novel treatment modality for calcific tendinopathy of the rotator cuff. This descriptive pilot case series included a total of 8 patients with calcific tendinopathy of the supraspinatus that underwent ultrasound-guided ultrasonic debridement in the sports medicine clinic. All procedures were performed by the same physician (JLE). All patients had confirmation of the diagnosis with MRI and ultrasound imaging. Pain was measured pre-procedure and followed until 3-months post-procedure. Very large, statistically significant, reductions (P < .01) in pain scores were observed at 1 (ES = 1.93), 2 (ES = 1.84) and 3 (ES = 2.20) months post-procedure, respectively. All patients experienced a significant reduction in pain scores, regardless of hardness of the calcium deposit, at 1 month post-procedure with pain scores remaining lower than at baseline at 2 and 3 months post-procedure. No adverse events were noted in any patients. Ultrasonic tenotomy and debridement appears to be a safe and effective treatment option for patients with calcific tendinopathy of the supraspinatus.
A Health Economic Evaluation of the World Health Organization Surgical Safety Checklist

Objectives: To evaluate cost-effectiveness of the WHO Surgical Safety Checklist. Background: The clinical effectiveness of surgical checklists is largely understood. Few studies to-date have evaluated the cost-effectiveness of checklist use. Methods: An economic evaluation was carried out using data from the only available randomized controlled trial of the checklist. Analyses were based on 3702 procedures. Costs considered included checklist implementation costs and length and cost of hospital stay, costs of warming blanket use, blood transfusions and antibiotics used in the operating room, and the cost of clinical time in the operating room – all calculated for each procedure and its associated admission. Nonparametric bootstrapping was used to simulate an empirical distribution of the mean effect of the checklist on total admission costs and the probability of observing a complication-free admission and to quantify sampling uncertainty around mean cost estimates. Results: The overall cost of checklist implementation was calculated to be $900 per 100 admissions. Implementation of the WHO checklist resulted in an additional 5.9 complication-free admissions per 100 admissions and an average of 110 bed-days saved per 100 admissions. Accounting for all costs included in the analysis, for every 100 admissions, use of the WHO checklist was estimated to save $55,899. Conclusions: Implementation of the WHO checklist was a cost-effective strategy for improving surgical safety.
PARIS–DJ-1 Interaction Regulates Mitochondrial Functions in Cardiomyocytes, Which Is Critically Important in Cardiac Hypertrophy

Mitochondrial dysfunction is one of the major pathological attributes of cardiac hypertrophy and is associated with reduced expression of PGC1α in cardiomyocytes. However, the transcriptional regulation of PGC1α remains elusive. Here, we show that parkin interacting substrate (PARIS), a KRAB zinc finger protein, prevented PGC1α transcription despite the induction of cardiomyocytes with hypertrophic stimuli. Moreover, PARIS expression and its nuclear localization are enhanced in hypertrophy both in vitro and in vivo. ABSTRACT Mitochondrial dysfunction is one of the major pathological attributes of cardiac hypertrophy and is associated with reduced expression of PGC1α in cardiomyocytes. However, the transcriptional regulation of PGC1α remains elusive. Here, we show that parkin interacting substrate (PARIS), a KRAB zinc finger protein, prevented PGC1α transcription despite the induction of cardiomyocytes with hypertrophic stimuli. Moreover, PARIS expression and its nuclear localization are enhanced in hypertrophy both in vitro and in vivo. Knocking down PARIS resulted in mitochondrial biogenesis and improved respiration and other biochemical features that were compromised during hypertrophy. Furthermore, a PARIS-dependent proteome showed exclusive binding of a deSUMOylating protein called DJ-1 to PARIS in control cells, while this interaction is completely abrogated in hypertrophied cells. We further demonstrate that proteasomal degradation of DJ-1 under oxidative stress led to augmented PARIS SUMOylation and consequent repression of PGC1α promoter activity. SUMOylation-resistant mutants of PARIS failed to repress PGC1α, suggesting a critical role for PARIS SUMOylation in hypertrophy. The present study, therefore, proposes a novel regulatory pathway where DJ-1 acts as an oxidative stress sensor and contributes to the feedback loop governing PARIS-mediated mitochondrial function.
KPC-3–Producing Serratia marcescens Outbreak between Acute and Long-Term Care Facilities, Florida, USA

We describe an outbreak caused by Serratia marcescens carrying blaKPC-3 that was sourced to a long-term care facility in Florida, USA. Whole-genome sequencing and plasmid profiling showed involvement of 3 clonal lineages of S. marcescens and 2 blaKPC-3-carrying plasmids. Determining the resistance mechanism is critical for timely implementation of infection control measures.
Hydration/Dehydration Behavior of Hydroxyethyl Cellulose Ether in Aqueous Solution

Hydroxyethyl cellulose (HeC) maintains high water solubility over a wide temperature range even in a high temperature region where other nonionic chemically modified cellulose ethers, such as methyl cellulose (MC) and hydroxypropylmethyl cellulose (HpMC), demonstrate cloud points. In order to clarify the reason for the high solubility of HeC, the temperature dependence of the hydration number per glucopyranose unit, nH, for the HeC samples was examined by using extremely high frequency dielectric spectrum measuring techniques up to 50 GHz over a temperature range from 10 to 70 °C. HeC samples with a molar substitution number (MS) per glucopyranose unit by hydroxyethyl groups ranging from 1.3 to 3.6 were examined in this study. All HeC samples dissolve into water over the examined temperature range and did not show their cloud points. The value of nH for the HeC sample possessing the MS of 1.3 was 14 at 20 °C and decreased gently with increasing temperature and declined to 10 at 70 °C. The nH values of the HeC samples are substantially larger than the minimum critical nH value of ca. 5 necessary to be dissolved into water for cellulose ethers such as MC and HpMC, even in a high temperature range. Then, the HeC molecules possess water solubility over the wide temperature range. The temperature dependence of nH for the HeC samples and triethyleneglycol, which is a model compound for substitution groups of HeC, is gentle and they are similar to each other. This observation strongly suggests that the hydration/dehydration behavior of the HeC samples was essentially controlled by that of their substitution groups.
The Androgen Receptor in Prostate Cancer: Effect of Structure, Ligands and Spliced Variants on Therapy

The androgen receptor (AR) plays a predominant role in prostate cancer (PCa) pathology. It consists of an N-terminal domain (NTD), a DNA-binding domain (DBD), a hinge region (HR), and a ligand-binding domain (LBD) that binds androgens, including testosterone (T) and dihydrotestosterone (DHT). Ligand binding at the LBD promotes AR dimerization and translocation to the nucleus where the DBD binds target DNA. In PCa, AR signaling is perturbed by excessive androgen synthesis, AR amplification, mutation, or the formation of AR alternatively spliced variants (AR-V) that lack the LBD. Current therapies for advanced PCa include androgen synthesis inhibitors that suppress T and/or DHT synthesis, and AR inhibitors that prevent ligand binding at the LBD. However, AR mutations and AR-Vs render LBD-specific therapeutics ineffective. The DBD and NTD are novel targets for inhibition as both perform necessary roles in AR transcriptional activity and are less susceptible to AR alternative splicing compared to the LBD. DBD and NTD inhibition can potentially extend patient survival, improve quality of life, and overcome predominant mechanisms of resistance to current therapies. This review discusses various small molecule and other inhibitors developed against the DBD and NTD—and the current state of the available compounds in clinical development.