Miracle-dz/UniFAR-FTUs huggingface dataset:
Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development

Microglial cells play a key role in brain homeostasis from development to adulthood. Here we show the involvement of a site-specific phosphorylation of Presenilin 1 (PS1) in microglial development. Profiles of microglia-specific transcripts in different temporal stages of development, combined with multiple systematic transcriptomic analysis and quantitative determination of microglia progenitors, indicate that the phosphorylation of PS1 at serine 367 is involved in the temporal dynamics of microglial development, specifically in the developing brain rudiment during embryonic microgliogenesis. We constructed a developing brain-specific microglial network to identify transcription factors linked to PS1 during development. Our data showed that PS1 functional connections appear through interaction hubs at Pu.1, Irf8 and Rela-p65 transcription factors. Finally, we showed that the total number of microglia progenitors was markedly reduced in the developing brain rudiment of embryos lacking PS1 phosphorylation compared to WT. Our work identifies a novel role for PS1 in microglial development.
PRELIMINARY PHYTOCHEMICAL ANALYSIS OF SOME IMPORTANT INDIAN PLANT SPECIES

This present study reports 84 methanolic extracts prepared from the 54 Indian plants belonging to 33 different families collected from the forest located in Eastern Ghats of India. A qualitative preliminary phytochemical screening was performed on aforesaid extracts for the presence of alkaloids, flavonoids, steroids and terpenoids. Each analysis was carried out in triplicate, which resulted a total of 22, 19, 37 and 30 plant species were found to give positive results for alkaloids (41%), flavonoids (35%), steroids (69%) and terpenoids (56%), respectively.
Development of High-Density Genetic Linkage Maps and Identification of Loci for Chestnut Gall Wasp Resistance in Castanea spp.

Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar ‘Bouche de Bétizac’ (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between ‘Bouche de Bétizac’ and the susceptible cultivar ‘Madonna’ (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of ‘Bouche de Bétizac’ consisted of 1459 loci and spanned 809.6 cM; the map of ‘Madonna’ consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the ‘Bouche de Bétizac’ map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes.
Caring for Family Caregivers of Geriatric Patients: Results of a Participatory Health Research Project on Actual State and Needs of Hospital-Based Care Professionals

Because of societal changes, family caregivers are becoming vital in long-term care provision for geriatric patients after discharge from hospital. Hospital-based geriatric care teams need tools to prepare and support family caregivers for their future caregiving role in the home environment. To explore the actual state and needs for implementing a suitable family caregiver support concept in a large geriatric hospital in Germany, a Participatory Health Research methodology was chosen. An academic investigator, assisted by a critical friend, facilitated all research steps. Geriatric care professionals joined as co-researchers and performed qualitative data collection using semi-structured interviews and focus group discussions. The entire co-research team took part in the thematic analyses. The existing family caregiver support was perceived as uncoordinated and incomplete, and a lack of knowledge about support programmes in the community was apparent. The needs regarding a comprehensive family caregiver support concept that acts on both individual caregiver as well as on system level, but also connects the two levels, were formulated. High grades of participation of hospital-based co-researchers could be achieved. A critical reflection on the research strategy revealed that the participatory methodology, although time-consuming, was perceived as a useful strategy within the hierarchically organized hospital.
The Plasticity of Root Systems in Response to External Phosphate

Phosphate is an essential macro-element for plant growth accumulated in the topsoil. The improvement of phosphate uptake efficiency via manually manipulating root system architecture is of vital agronomic importance. This review discusses the molecular mechanisms of root patterning in response to external phosphate availability, which could be applied on the alleviation of phosphate-starvation stress. During the long time evolution, plants have formed sophisticated mechanisms to adapt to environmental phosphate conditions. In terms of root systems, plants would adjust their root system architecture via the regulation of the length of primary root, the length/density of lateral root and root hair and crown root growth angle to cope with different phosphate conditions. Finally, plants develop shallow or deep root system in low or high phosphate conditions, respectively. The plasticity of root system architecture responds to the local phosphate concentrations and this response was regulated by actin filaments, post-translational modification and phytohormones such as auxin, ethylene and cytokinin. This review summarizes the recent progress of adaptive response to external phosphate with focus on integrated physiological, cellular and molecular signaling transduction in rice and Arabidopsis.
NIR Absorbing AzaBODIPY Dyes for pH Sensing

Two near-infrared (NIR) absorbing di(thien-2-nyl)-di(dimethylanilino)azaBODIPY dyes 2a and 2b were synthesized and characterized that differ depending on whether the dimethylaniline substituents are introduced at the 3,5- or 1,7-positions of the azaBODIPY core. The main spectral bands lie at 824 and 790 nm, respectively, in CH2Cl2. The effect of substituent position on the photophysical and pH sensing properties was analyzed through a comparison of the optical properties with the results of time-dependent density functional theory (TD-DFT) calculations. Protonation of the dimethylamino nitrogen atoms eliminates the intramolecular charge transfer properties of these compounds, and this results in a marked blue-shift of the main absorption bands to 696 and 730 nm, respectively, in CH2Cl2, and a fluorescence “turn-on” effect in the NIR region. The pH dependence studies reveal that the pKa values of the non-protonated 2a and 2b molecules are ca. 6.9 (±0.05) and 7.3 (±0.05), respectively, while that of the monoprotonated species for both dyes is ca. 1.4 (±0.05) making them potentially suitable for use as colorimetric pH indicators under highly acidic conditions.
Phylogenetic Analyses of Glycosyl Hydrolase Family 6 Genes in Tunicates: Possible Horizontal Transfer

Horizontal gene transfer (HGT) is the movement of genetic material between different species. Although HGT is less frequent in eukaryotes than in bacteria, several instances of HGT have apparently shaped animal evolution. One well-known example is the tunicate cellulose synthase gene, CesA, in which a gene, probably transferred from bacteria, greatly impacted tunicate evolution. A Glycosyl Hydrolase Family 6 (GH6) hydrolase-like domain exists at the C-terminus of tunicate CesA, but not in cellulose synthases of other organisms. The recent discovery of another GH6 hydrolase-like gene (GH6-1) in tunicate genomes further raises the question of how tunicates acquired GH6. To examine the probable origin of these genes, we analyzed the phylogenetic relationship of GH6 proteins in tunicates and other organisms. Our analyses show that tunicate GH6s, the GH6-1 gene, and the GH6 part of the CesA gene, form two independent, monophyletic gene groups. We also compared their sequence signatures and exon splice sites. All tunicate species examined have shared splice sites in GH6-containing genes, implying ancient intron acquisitions. It is likely that the tunicate CesA and GH6-1 genes existed in the common ancestor of all extant tunicates.
Tunnel/Pouch versus Coronally Advanced Flap Combined with a Connective Tissue Graft for the Treatment of Maxillary Gingival Recessions: Four-Year Follow-Up of a Randomized Controlled Trial

Background: The long-term stability after soft tissue graft for covering gingival recession remains a pivotal goal for both patient and periodontist. Therefore, the aim of this study was to compare the four-year outcomes of the coronally advanced flap (CAF) versus the pouch/tunnel (POT) technique, both combined with connective tissue graft (CTG), for gingival recession treatment. Methods: Forty patients were initially randomly assigned to the control group (CAF + CTG; N = 20) and the test group (POT + CTG; N = 20). Clinical outcomes included mean root coverage (MRC) and complete root coverage (CRC), gingival thickness (GT), and keratinized tissue (KT) gain. Esthetic outcomes were also analyzed using the pink esthetic score (PES) and patient-reported outcome measures (PROMs). All outcomes initially assessed at six months were extended to four years post-surgery. Results: No significant differences were observed between the two patient groups in terms of MRC and CRC. At four years, significantly greater GT and KT gain were noted in the POT + CTG group, and tissue texture enhancement was also more prominent in the test group. Conclusions: The POT + CTG technique allows for long-term clinical coverage of gingival recessions comparable to that of the CAF + CTG technique, but it potentially improves gingival thickness, keratinized tissue and esthetic results.
Double‐blind, placebo‐controlled study of lurasidone monotherapy for the treatment of bipolar I depression

Previous studies conducted primarily in the USA and Europe have demonstrated the efficacy and safety of lurasidone 20–120 mg/day for the treatment of bipolar I depression. The aim of the current study was to evaluate the efficacy and safety of lurasidone monotherapy for the treatment of bipolar I depression among patients from diverse ethnic backgrounds, including those from Japan.
Extending Cellulose-Based Polymers Application in Additive Manufacturing Technology: A Review of Recent Approaches

The materials for additive manufacturing (AM) technology have grown substantially over the last few years to fulfill industrial needs. Despite that, the use of bio-based composites for improved mechanical properties and biodegradation is still not fully explored. This limits the universal expansion of AM-fabricated products due to the incompatibility of the products made from petroleum-derived resources. The development of naturally-derived polymers for AM materials is promising with the increasing number of studies in recent years owing to their biodegradation and biocompatibility. Cellulose is the most abundant biopolymer that possesses many favorable properties to be incorporated into AM materials, which have been continuously focused on in recent years. This critical review discusses the development of AM technologies and materials, cellulose-based polymers, cellulose-based three-dimensional (3D) printing filaments, liquid deposition modeling of cellulose, and four-dimensional (4D) printing of cellulose-based materials. Cellulose-based AM material applications and the limitations with future developments are also reviewed.
Jasmonate Signalling Contributes to Primary Root Inhibition Upon Oxygen Deficiency in Arabidopsis thaliana

Plants, including most crops, are intolerant to waterlogging, a stressful condition that limits the oxygen available for roots, thereby inhibiting their growth and functionality. Whether root growth inhibition represents a preventive measure to save energy or is rather a consequence of reduced metabolic rates has yet to be elucidated. In the present study, we gathered evidence for hypoxic repression of root meristem regulators that leads to root growth inhibition. We also explored the contribution of the hormone jasmonic acid (JA) to this process in Arabidopsis thaliana. Analysis of transcriptomic profiles, visualisation of fluorescent reporters and direct hormone quantification confirmed the activation of JA signalling under hypoxia in the roots. Further, root growth assessment in JA-related mutants in aerobic and anaerobic conditions indicated that JA signalling components contribute to active root inhibition under hypoxia. Finally, we show that the oxygen-sensing transcription factor (TF) RAP2.12 can directly induce Jasmonate Zinc-finger proteins (JAZs), repressors of JA signalling, to establish feedback inhibition. In summary, our study sheds new light on active root growth restriction under hypoxic conditions and on the involvement of the JA hormone in this process and its cross talk with the oxygen sensing machinery of higher plants.
Genome-Wide Analysis of the PIN Auxin Efflux Carrier Gene Family in Coffee

Coffee is one of the most popular beverages around the world, which is mainly produced from the allopolyploid Coffea arabica. The genomes of C. arabica and its two ancestors C. canephora and C. eugenioides have been released due to the development of next generation sequencing. However, few studies on C. arabica are related to the PIN-FORMED (PIN) auxin efflux transporter despite its importance in auxin-mediated plant growth and development. In the present study, we conducted a genome-wide analysis of the PIN gene family in the three coffee species. Totals of 17, 9 and 10 of the PIN members were characterized in C. Arabica, C. canephora and C. eugenioides, respectively. Phylogenetic analysis revealed gene loss of PIN1 and PIN2 homologs in C. arabica, as well as gene duplication of PIN5 homologs during the fractionation process after tetraploidy. Furthermore, we conducted expression analysis of PIN genes in C. arabica by in silico and qRT-PCR. The results revealed the existence of gene expression dominance in allopolyploid coffee and illustrated several PIN candidates in regulating auxin transport and homeostasis under leaf rust fungus inoculation and the tissue-specific expression pattern of C. arabica. Together, this study provides the basis and guideline for future functional characterization of the PIN gene family.
Engineering Solutions for Mitigation of Chimeric Antigen Receptor T-Cell Dysfunction

The clinical successes of chimeric antigen receptor (CAR)-T-cell therapy targeting cell surface antigens in B cell leukaemias and lymphomas has demonstrated the proof of concept that appropriately engineered T-cells have the capacity to destroy advanced cancer with long term remissions ensuing. Nevertheless, it has been significantly more problematic to effect long term clinical benefit in a solid tumour context. A major contributing factor to the clinical failure of CAR-T-cells in solid tumours has been named, almost interchangeably, as T-cell “dysfunction” or “exhaustion”. While unhelpful ambiguity surrounds the term “dysfunction”, “exhaustion” is canonically regarded as a pejorative term for T-cells. Recent understanding of T-cell developmental biology now identifies exhausted cells as vital for effective immune responses in the context of ongoing antigenic challenge. The purpose of this review is to explore the critical stages in the CAR-T-cell life-cycle and their various contributions to T-cell exhaustion. Through an appreciation of the predominant mechanisms of CAR-T-cell exhaustion and resultant dysfunction, we describe a range of engineering approaches to improve CAR-T-cell function.
Impact of Anticoagulation and Sample Processing on the Quantification of Human Blood-Derived microRNA Signatures

Blood-derived microRNA signatures have emerged as powerful biomarkers for predicting and diagnosing cardiovascular disease, cancer, and metabolic disorders. Platelets and platelet-derived microvesicles are a major source of microRNAs. We have previously shown that the inappropriate anticoagulation and storage of blood samples causes substantial platelet activation that is associated with the release of platelet-stored molecules into the plasma. However, it is currently unclear if circulating microRNA levels are affected by artificial platelet activation due to suboptimal plasma preparation. To address this issue, we used a standardized RT-qPCR test for 12 microRNAs (thrombomiR®, TAmiRNA GmbH, Vienna, Austria) that have been associated with cardiovascular and thrombotic diseases and were detected in platelets and/other hematopoietic cells. Blood was prevented from coagulating with citrate–theophylline–adenosine–dipyridamole (CTAD), sodium citrate, or ethylenediaminetetraacetic acid (EDTA) and stored for different time periods either at room temperature or at 4 °C prior to plasma preparation and the subsequent quantification of microRNAs. We found that five microRNAs (miR-191-5p, miR-320a, miR-21-5p, miR-23a-3p, and miR-451a) were significantly increased in the EDTA plasma. Moreover, we observed a time-dependent increase in plasma microRNAs that was most pronounced in the EDTA blood stored at room temperature for 24 h. Furthermore, significant correlations between microRNA levels and plasma concentrations of platelet-stored molecules pointed towards in vitro platelet activation. Therefore, we strongly recommend to (i) use CTAD as an anticoagulant, (ii) process blood samples as quickly as possible, and (iii) store blood samples at 4 °C whenever immediate plasma preparation is not feasible to generate reliable data on blood-derived microRNA signatures.
Large Lemurs: Ecological, Demographic and Environmental Risk Factors for Weight Gain in Captivity

Simple Summary Excessive body mass, i.e., being overweight or obese, is a health concern. Some lemur species are prone to extreme weight gain in captivity, yet for others a healthy body condition is typical. The first aim of our study was to examine possible ecological explanations for these species’ differences in susceptibility to captive weight gain across 13 lemur species. Our second aim was to explore demographic and environmental risk factors across individuals from the four best-sampled species. We found a potential ecological explanation for susceptibility to captive weight gain: being adapted to unpredictable wild food resources. Additionally, we also revealed one environmental and four demographic risk factors, e.g., increasing age and, for males, being housed with only fixed climbing structures. Our results indicate targeted practical ways to help address weight issues in affected animals, e.g., by highlighting at-risk species for whom extra care should be taken when designing diets; and by providing a mixture of flexible and fixed climbing structures within enclosures. Abstract Excessive body mass, i.e., being overweight or obese, is a health concern associated with issues such as reduced fertility and lifespan. Some lemur species are prone to extreme weight gain in captivity, yet others are not. To better understand species- and individual-level effects on susceptibility to captive weight gain, we use two complementary methods: phylogenetic comparative methods to examine ecological explanations for susceptibility to weight gain across species, and epidemiological approaches to examine demographic and environment effects within species. Data on body masses and living conditions were collected using a survey, yielding useable data on 675 lemurs representing 13 species from 96 collections worldwide. Data on species-typical wild ecology for comparative analyses came from published literature and climate databases. We uncovered one potential ecological risk factor: species adapted to greater wild food resource unpredictability tended to be more prone to weight gain. Our epidemiological analyses on the four best-sampled species revealed four demographic and one environmental risk factors, e.g., for males, being housed with only fixed climbing structures. We make practical recommendations to help address weight concerns, and describe future research including ways to validate the proxy we used to infer body condition.
Effects of climate change on economic feasibility of future date palm production: An integrated assessment in Iran

ABSTRACT This study set out to build a model identifying areas where a positive Net Present Value (NPV) could be obtained from date palm (Phoenix dactylifera) using CLIMEX and six parameters including (a) suitable soil taxonomy and physicochemical soil properties, (b) slopes of less than 10°, (c) land uses suitable for date palm cultivation, (d) availability of roads, (e) availability of water, and (f) low risk of the lethal disease caused by Fusarium oxysporum f. spp. in the years 2030, 2050, 2070, and 2100 in Iran. Here, we utilized the A2 scenario and two global climate models (GCMs): CSIRO-Mk3.0 (CS) and MIROC-H (MR). Economic feasibility was estimated based on the assumption that the decision to plant date palms by landholders is motivated by a desire to maximize their return to land. Our results indicate that only 5450 km2 of southern Iran will be highly profitable for cultivation of date palm, with NPV > 10,000, while profitable (with NPV between 4200 and 10,000) and moderately profitable (with NPV between 0 and 4200) areas would cover only 500 and 50 km2, respectively, in future. A comparison of mean outputs from the two chosen GCMs and those of the economic and CLIMEX output combination indicates that only about 0.01% of areas from both GCMs will be highly economically viable for cultivation of date palm. In this study we ensure that the predictions become robust, rather than producing hypothetical findings, limited purely to publication.
Pretreatment of Grape Stalks by Fungi: Effect on Bioactive Compounds, Fiber Composition, Saccharification Kinetics and Monosaccharides Ratio

Grape stalks, an inedible lignocellulosic residue from winemaking and agro-industrial grape juice production, can be valorized as a source of bioactive compounds and as feedstock for the saccharification and bioconversion of soluble sugars. Solid-state fermentation (SSF) by six white-rot fungi was applied as pretreatment. Fiber composition, free radical scavenging activity, four ligninolytic, and three hydrolytic enzyme activities were determined. Saccharification kinetics, yield, and productivity were evaluated and complemented with scanning electron microscopy (SEM), high performance liquid chromatography (HPLC) quantification of monosaccharides, and principal component analysis (PCA). After SSF, the biomass exhibited a drastic free radical scavenging activity decrease and the main enzymes produced were manganese-dependent peroxidase and xylanase. Scanning electron microscopy revealed the erosion of cell walls, and PCA exhibited a negative correlation between saccharification, and neutral detergent fiber and acid detergent lignin. Phlebia rufa pretreated biomass gave the highest sugars yield and productivity, representing a nearly three-fold increase compared to untreated samples. Also, monosaccharides quantification revealed that the 1:1 ratio of glucose to the sum of xylose plus galactose changes to the value of 2:1 after pretreatment. In this work, and for the first time, P. rufa proved to be an effective pretreatment of grape stalks for the saccharification and further bioconversion into value-added chemicals. In addition, lignocellulolytic enzymes were also produced through SSF.