Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters

The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Cas12a due to its improved affinity (K_m) for hairpin DNA structures, and provide mechanistic insights of our findings through Molecular Dynamics simulations. Using hairpin DNA probes we significantly enhance FRET-based signal transduction compared to the widely used linear single stranded DNA reporters. Our signal transduction enables faster detection of clinically relevant double stranded DNA targets with improved sensitivity and specificity either in the presence or in the absence of an upstream pre-amplification step.     

Marinobacter persicus sp. nov., a moderately halophilic bacterium from a saline lake in Iran

A Gram-negative, non-endospore-forming, rod shaped, strictly aerobic, moderately halophilic bacterium, designated strain M9B^T, was isolated from the hypersaline lake Aran-Bidgol in Iran. Cells of strain M9B^T were found to be motile and produce colonies with an orange-yellow pigment. Growth was determined to occur between 5 and 20 % (w/v) NaCl and the isolate grew optimally at 7.5–10 % (v/w) NaCl. The optimum pH and temperature for growth of the strain were determined to be pH 7.0 and 35 °C, respectively, while it was able to grow over pH and temperature ranges of 6–8 and 25–45 °C, respectively. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain M9B^T is a member of the genus Marinobacter. The closest relative to this strain was found to be Marinobacter hydrocarbonoclasticus MBIC 1303^T with a similarity level of 97.7 %. DNA–DNA hybridization between the novel isolate and this phylogenetically related species was 13 ± 2 %. The major cellular fatty acids of the isolate were identified as C_16:0, C_19:1 ω6c, C_18:1 ω9c and C_16:1 ω9c. The polar lipid pattern of strain M9B^T was determined to consist of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and three phospholipids. Ubiquinone 9 (Q-9) was the only lipoquinone detected. The G+C content of the genomic DNA of this strain was determined to be 58.6 mol%. Phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data suggest that this strain represents a novel species of the genus Marinobacter, for which the name Marinobacter persicus sp. nov. is proposed. The type strain of Marinobacter persicus is strain M9B^T (=IBRC-M 10445^T = CCM 7970^T = CECT 7991^T = KCTC 23561^T).     

Amyloid Beta1-40-Induced Astrogliosis and the Effect of Genistein Treatment in Rat: A Three-Dimensional Confocal Morphometric and Proteomic Study

Astrocytes are highly involved in regulation and homeostasis of the extracellular environment in the healthy brain. In pathological conditions, these cells play a major role in the inflammatory response seen in CNS tissues, which is called reactive astrogliosis and includes hypertrophy and proliferation of astrocytes. Here, we performed 3D confocal microscopy to evaluate the morphological response of reactive astrocytes positive for glial fibrillary acidic protein (GFAP) in rats, to the presence of Aβ_1–40 in the rat brain before and after treatment with genistein. In 50 astrocytes per animal, we measured the volume and surface area for the nucleus, cell body, the entire cell, the tissue covered by single astrocytes and quantified the number and length of branches, the density of the astrocytes and the intensity of GFAP immunoreactivity. Injecting Aβ_1–40 into the brain of rats caused astrogliosis indicated by increased values for all measured parameters. Mass spectrometric analysis of hippocampal tissue in Aβ_1–40-injected brain showed decreased amounts of tubulins, enolases and myelin basic protein, and increased amounts of dihydropyrimidinase-related protein 2. In Aβ_1–40-injected rats pretreated with genistein, GFAP intensity was decreased to the sham-operated group level, and Aβ_1–40-induced astrogliosis was significantly ameliorated.     

Energetic domains and conformational analysis of human serum albumin upon co-incubation with sodium benzoate and glucose

Sodium benzoate (SB), a powerful inhibitor of microbial growth, is one of the most commonly used food preservative. Here, we determined the effects of SB on human serum albumin (HSA) structure in the presence or absence of glucose after 35?days of incubation under physiological conditions. The biochemical, biophysical, and molecular approaches including free amine content assay (TNBSA assay), fluorescence, and circular dichroism spectroscopy (CD), differential scanning calorimetry (DSC), and molecular docking and LIGPLOT studies were utilized for structural studies. The TNBSA results indicated that SB has the ability to bind Lys residues in HSA through covalent bonds. The docking and LIGPLOT studies also determined another specific site via hydrophobic interactions. The CD results showed more structural helicity for HSA incubated with SB, while HSA incubated with glucose had the least, and HSA incubated with glucose?+?SB had medium helicity. Fluorescence spectrophotometry results demonstrated partial unfolding of HSA incubated with SB in the presence or absence of glucose, while maximum partial unfolding was observed in HSA incubated with glucose. These results were confirmed by DSC and its deconvoluted thermograms. The DSC results also showed significant changes in HSA energetic structural domains due to HSA incubation with SB in the presence or absence of glucose. Together, our studies showed the formation of three different intermediates and indicate that biomolecular investigation are effective in providing new insight into safety determinations especially in health-related conditions including diabetes.     

Carbon Quantum Dots as Multi-Purpose Nanomaterial in Stem Cell Therapy

During stem cell therapy, some issues, such as obscure fate of stem cells or their low survival rate in the body, should be addressed to boost their therapeutic efficiency. Nanotechnology offers a suitable solution to combat such limitations. Carbon quantum dots (CQDs) are carbon-based nanomaterials and may be used as multi-purpose compounds in stem cell therapy. CQDs are excellent choices for stem cell labeling thanks to their special features such as optical properties and good biocompatibility. Besides, they can modulate the biological function of stem cells, such as their proliferation, homing ability, and differentiation properties. Considering the charismatic feature of CQDs and their broad unique effect on stem cells, the current review aims to summarize the most advancements in this field. Hence, we first focused on CQDs synthesis and their applications. In the next section, the stem cell categories will be discussed, and the final part is dedicated to the recent research evaluating the impact of CQDs on stem cell therapy.     

Biochemical responses as early and reliable biomarkers of organophosphate and carbamate pesticides intoxication: A systematic literature review

Inhibition of cholinesterase (ChE) activity has been long considered as the main diagnostic method of organophosphate (OP) and carbamate pesticides poisoning; however, it has been shown that ChE activity may also be altered due to exposure to other non-organophosphorus toxicants and variety of different medical conditions. Hence, to avoid misdiagnosis, we aimed to systematically review available documents to look for additional biomarkers of OP and carbamate poisoning. The electronic databases in addition to Google scholar were searched for eligible articles on March 2022 using “organophosphate,” “carbamate,” and “biomarker” including all their similar terms. After collecting the relevant documents, the data were extracted and described qualitatively. In total, data of 66 articles from 51 human and 15 animal studies were extracted. Findings demonstrated that enzymes such as β-glucuronidase, neuropathy target esterase, amylase, and lipase, in addition to hematological indicators such as CBC, CRP, lactate dehydrogenase, and CPK have high sensitivity and accuracy in the diagnosis of OP poisoning. Findings suggest that using various markers for diagnosis of OP intoxication is helpful for appropriate management, and early identifying the patients at risk of death. The suggested biomarkers also help to avoid misdiagnosis of OP poisoning with other similar conditions.     

Production of sodium-chloride-tolerant Brassica juncea plants by in vitro selection at the somatic embryo level

Summary Somatic embryos, developed from hypocotyl segments of light-grown seedlings of Brassica juncea cv RLM198, were subjected to selection at varying concentrations of sodium chloride (NaCl). Plants were developed from proliferated somatic embryos selected on NaCl-containing medium. The selections were characterized for salt tolerance, esterase isozyme pattern, and proline accumulation. It has been found that: (i) selected tolerant lines showed better root growth, shoot growth, and fresh weight accumulation on salt-containing medium when compared to the control; (ii) salt tolerance was transmitted to the next generation in seed progeny of tolerant plants grown in the absence of exposure to salt; (iii) both the starting material and the tolerant selections accumulated proline, even when grown in salt-free medium. On salt-containing medium, however, the differences in accumulated proline between the control and tolerant lines became more pronounced, and (iv) the patterns of esterase isozymes of two tolerant selections were similar but distinctly different from that of the parental control.     

Genetic variation in the response of pea (Pisum sativum L.) to high soil concentrations of boron

In a greenhouse experiment nine current Australian cultivars of pea were grown to flowering time under five levels of soil boron (0, 10, 20, 30 and 40 mg kg^–1) applied to the soil. This study was conducted to identify the genetic range in tolerance to boron within the group and to identify specific responses which may be utilised as selection criteria in a breeding program. Significant differences in response to increasing levels of boron were found between cultivars for dry-weight yield, and boron concentrations were lowest in shoots of the most tolerant cultivars. Of the other parameters measured, emergence was not affected but plant height and the number of nodes were reduced and the severity of symptom expression increased at the higher boron treatments. Symptom expression was the most efficient observation for predicting the response of cultivars, as determined by dry-weight yield and concentration of boron in shoots, and it was found that the correlation coefficients between symptoms and the latter two measurements were r=–0.78 (p<0.01) and r=0.81 (p<0.01), respectively. Early Dun, Dundale, Alma and Maitland were the more tolerant of the cultivars and these happen to be the most widely grown cultivars in southern Australia.     

Intracellular survival and replication of Vibrio cholerae O139 in aquatic free-living amoebae

Vibrio cholerae is a highly infectious bacterium responsible for large outbreaks of cholera among humans at regular intervals. A seasonal distribution of epidemics is known but the role of naturally occurring habitats are virtually unknown. Plankton has been suggested to play a role, because bacteria can attach to such organisms forming a biofilm. Acanthamoebea castellanii is an environmental amoeba that has been shown to be able to ingest and promote growth of several bacteria of different origin. The aim of the present study was to determine whether or not an intra-amoebic behaviour of V. cholerae O139 exists. Interaction between these microorganisms in co-culture was studied by culturable counts, gentamicin assay, electron microscopy, and polymerase chain reaction. The interaction resulted in intra-amoebic growth and survival of V. cholerae in the cytoplasm of trophozoites as well as in the cysts of A. castellanii. These data show symbiosis between these microorganisms, a facultative intracellular behaviour of V. cholerae contradicting the generally held view, and a role of free-living amoebae as hosts for V. cholerae O139. Taken together, this opens new doors to study the ecology, immunity, epidemiology, and treatment of cholera.