Miracle-dz/UniFAR-FTUs huggingface dataset:
Different responses to environmental factors in terpene composition of Pinus heldreichii and P. peuce: Ecological and chemotaxonomic considerations

Many studies show the influence of the environment on terpene composition, but not many of them deal with the terpene composition variability in correlation with environmental factors in Pinus. We chose two endemic species ? P. heldreichii Christ. (Bosnian pine) and P. peuce Griseb. (Macedonian pine) ? two relict and (sub)endemic species of the Balkan peninsula. They mainly form pure stands but can appear in mixed populations, most commonly with each other. These species belong to different subgenera and thus differ greatly, especially in needle anatomy. -pinene, limonene and germacrene D predominated in Bosnian pine leaf oleoresins, while Macedonian pine oleoresin contained high amounts of ? -pinene. Furthermore, there were three chemotypes present in Bosnian, and only one in Macedonian pine. Oleoresins of Bosnian pine did not show correlation with climate, however, its composition changed in response to geological substrate type. Macedonian pine oleoresin showed a high correlation with the climate but changed only a little in response to geological substrate type. The oleoresin profiles showed strong species-dependent composition and variability. However, since each species expressed different responses to tested environmental conditions, it is important to take into consideration these variables when analyzing natural populations of the species.
Polygenic risk scores of several subtypes of epilepsies in a founder population

Objective Polygenic risk scores (PRSs) are used to quantify the cumulative effects of a number of genetic variants, which may individually have a very small effect on susceptibility to a disease; we used PRSs to better understand the genetic contribution to common epilepsy and its subtypes. Methods We first replicated previous single associations using 373 unrelated patients. We then calculated PRSs in the same French Canadian patients with epilepsy divided into 7 epilepsy subtypes and population-based controls. We fitted a logistic mixed model to calculate the variance explained by the PRS using pseudo-R2 statistics. Results We show that the PRS explains more of the variance in idiopathic generalized epilepsy than in patients with nonacquired focal epilepsy. We also demonstrate that the variance explained is different within each epilepsy subtype. Conclusions Globally, we support the notion that PRSs provide a reliable measure to rightfully estimate the contribution of genetic factors to the pathophysiologic mechanism of epilepsies, but further studies are needed on PRSs before they can be used clinically.
Endophytic fungi associated with cabbage in New Zealand and their potential for biological control

Agricultural crops such as cabbage (Brassica oleracea var. capitata) are vulnerable to a plethora of pests and diseases. Endophytic fungi are increasingly used in biological control against these pests and diseases as agricultural producers attempt to reduce their environmental footprint. In this study, putative endophytic fungi were isolated from cabbage grown in three regions in New Zealand in order to identify isolates with potential to assist crop production. Isolation method was optimised in an exploratory study, and subsequently large scale sampling took place, where a culture-independent method was also used to detect fungi associated with cabbage. Spatial patterns in fungal communities in various plant tissues and geographical regions were investigated based on data obtained by culture-dependent and culture-independent methods. Selected fungal isolates were tested in bioassays to determine their potential for biological control of a fungal disease caused by Sclerotinia sclerotiorum and an insect pest of cabbage Diamondback moth (Plutella xylostella). Over 100 species were cultured, but high-throughput sequencing suggested the number of fungal species associated with cabbage tissues could be over 300. Distinct fungal communities were found in two scales of spatial distribution various host plant tissues and geographical regions. Increased mortality of Diamondback moth larvae feeding on cabbage leaves treated with spore suspensions of several isolates of Lecanicillium sp. was observed. None of the tested isolates used as seed inoculants significantly reduced disease symptoms caused by Sclerotinia sclerotiorum in a bioassay on cabbage seedlings. In this study several fungal isolates were identified as promising biological control agents of an insect pest of cabbage. However, these isolates are members of a large consortium of fungi. The patterns uncovered in the fungal communities underline the importance of understanding the microbial communities associated with agricultural crops.
Multimerization of Zika Virus-NS5 causes a ciliopathy and forces premature neurogenesis

Zika virus (ZikV) is a flavivirus that infects neural tissues, causing congenital microcephaly. ZikV has evolved multiple mechanisms to restrict proliferation and enhance cell death, although the underlying cellular events involved remain unclear. Here we show that the ZikV-NS5 protein interacts with host proteins at the base of the primary cilia in neural progenitor cells, causing an atypical non-genetic ciliopathy and premature neuron delamination. Furthermore, in human microcephalic fetal brain tissue, ZikV-NS5 persists at the base of the motile cilia in ependymal cells, which also exhibit a severe ciliopathy. While the enzymatic activity of ZikV-NS5 appears to be dispensable, the Y25, K28 and K29 residues in the protein, that are involved in NS5-oligomerization, are essential for the localization and interaction with components of the cilium base, promoting ciliopathy and premature neurogenesis. These findings lay the foundation to develop therapies that target ZikV-NS5-multimerization, preventing the developmental malformations associated with congenital Zika syndrome
Signaling Pathways, Chemical and Biological Modulators of Nucleotide Excision Repair: The Faithful Shield against UV Genotoxicity

The continuous exposure of the human body's cells to radiation and genotoxic stresses leads to the accumulation of DNA lesions. Fortunately, our body has several effective repair mechanisms, among which is nucleotide excision repair (NER), to counteract these lesions. NER includes both global genome repair (GG-NER) and transcription-coupled repair (TC-NER). Deficiencies in the NER pathway underlie the development of several DNA repair diseases, such as xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). Deficiencies in GG-NER and TC-NER render individuals to become prone to cancer and neurological disorders, respectively. Therefore, NER regulation is of interest in fine-tuning these risks. Distinct signaling cascades including the NFE2L2 (NRF2), AHR, PI3K/AKT1, MAPK, and CSNK2A1 pathways can modulate NER function. In addition, several chemical and biological compounds have proven success in regulating NER's activity. These modulators, particularly the positive ones, could therefore provide potential treatments for genetic DNA repair-based diseases. Negative modulators, nonetheless, can help sensitize cells to killing by genotoxic chemicals. In this review, we will summarize and discuss the major upstream signaling pathways and molecules that could modulate the NER's activity.
Distributional dynamics of a specialized subterranean community oppose the classical understanding of the preferred subterranean habitats

The most specialized organisms to living in the subterranean environment, i.e., troglobionts, reside prevalently in the deepest cave zone and shallow subterranean habitats and complete their whole life cycles therein. Since troglobionts in most caves depend on surface organic matter resources, we hypothesized that they could also select the surface-most cave sections, so far the other environmental conditions there are
Mutations of R882 in DNMT3A change flanking sequence preferences and cellular methylation patterns in AML

DNMT3A R882 mutations are frequently observed in AML including the abundant R882H and the rare R882C, R882P and R882S. Using deep enzymology we show here that the DNMT3A-R882H has more than 70-fold altered flanking sequence preferences when compared with wildtype DNMT3A. The R882H flanking sequence preferences mainly differ on the 3’ side of the CpG site, where they resemble DNMT3B, while 5’ flanking sequence preferences of R882H resemble wildtype DNMT3A, indicating that R882H behaves like a DNMT3A/DNMT3B chimera. Activities and flanking sequence preferences of R882C, R882P and R882S were determined as well. Genomic methylation patterns after expression of wildtype DNMT3A and R882H in human cells reflect the flanking sequence preferences. R882H specific hypermethylation in AML patients are correlated with R882H flanking sequence preferences. The hypermethylation events are accompanied by R882H specific misregulation of several genes with strong cancer connection in AML patients, which are potential downstream targets of R882H.
Estimation of genetic parameters for some performance traits in a selected Barred Rock line

This study was conducted to determine the genetic correlation and heritability for age at sexual maturity, body weight at sexual maturity, egg yield, egg weight, egg shape index and L*, a*, b* values of egg shell in a Barred Rock line was applied selection. For this aim, a total of 1622 pedigreed Barred Rocks were selected. The present estimated heritability values for investigated traits were found between moderate-to-high. However, the heritability of egg yield, eggshell color and body weight at sexual maturity were found lower than those of other traits. It was calculated positive correlations among monthly egg yields, especially between egg yield at the second month with total egg yield. As a conclusion, selection studies did not cause much decrease in genetic variation of studied traits, except for egg yield and body weight at sexual maturity. Monthly egg yield data can be used selection studies.
GV1001 prevents ovarian follicle loss triggered by an anti-VEGF monoclonal antibody targeting non-small cell lung carcinoma xenografts in mice

Premature ovarian failure (POF) that could result from chemotherapy applied to young female cancer patients is a significant challenge in reproductive biology. It is widely believed that the hyperactivation of dormant primordial follicles following chemotherapy is a leading cause of POF, but it remains unclear how therapeutic cues are generated and transduced into follicular activation. Here, we provide evidence that supports that GV1001, an immunotherapeutic peptide targeting telomerase, plays a role in the deterrence of POF in mice. In vivo non-small cell lung carcinoma (NSCLC) tumor xenografts were produced by inoculating NSCLC cells into the flank of BALB/c female athymic mice and then subjected to cancer chemotherapy with GV1001 and bevacizumab, an anti-cancer antibody drug, humanized anti-VEGF monoclonal antibody. Bevacizumab when administered at the dosage of 5 mg/kg for three weeks was effective in inhibiting growth of NSCLC tumor xenografts, and its anti-cancer efficacy was not interfered by the presence of GV1001. As expected, bevacizumab induced follicular loss by accelerating primordial follicle growth into primary or secondary follicles concomitant with a decline of serum antimullerian hormone (AMH) level and deactivation of Foxo3 signaling as evidenced by immunohistochemical and immunofluorescent assessment. However, bevacizumab-induced follicle stimulating effects were mitigated by GV1001 co-administration as evidenced by the analysis of follicular count, serum AMH level, and Foxo3a expression. From this study, we propose that a combinatorial administration of GV1001 and bevacizumab could deter POF of young female cancer patients without hampering the anti-cancer effectiveness of bevacizumab.
Structural control energy of resting-state functional brain states reveals inefficient brain dynamics in psychosis vulnerability

How the brain’s white-matter anatomy constrains brain activity is an open question that might give insights into the mechanisms that underlie mental disorders such as schizophrenia. Chromosome 22q11.2 deletion syndrome (22q11DS) is a neurodevelopmental disorder with an extremely high risk for psychosis providing a test case to study developmental aspects of schizophrenia. In this study, we used principles from network control theory to probe the implications of aberrant structural connectivity for the brain’s functional dynamics in 22q11DS. We retrieved brain states from resting-state functional magnetic resonance images of 78 patients with 22q11DS and 85 healthy controls. Then, we compared them in terms of persistence control energy; i.e., the control energy that would be required to persist in each of these states based on individual structural connectivity and a dynamic model. Persistence control energy was altered in a broad pattern of brain states including both energetically more demanding and less demanding brain states in 22q11DS. Further, we found a negative relationship between persistence control energy and resting-state activation time, which suggests that the brain reduces energy by spending less time in energetically demanding brain states. In patients with 22q11DS, this behavior was less pronounced, suggesting a dynamic inefficiency of brain function in the disease. In summary, our results provide initial insights into the dynamic implications of altered structural connectivity in 22q11DS, which might improve our understanding of the mechanisms underlying the disease.
Preliminary phylogenetic and morphological studies in the Gyromitra gigas lineage (Pezizales): Epitypification of Gyromitra gigas and G. ticiniana

Gyromitra gigas and G. ticiniana are epitypified with modern collections with known genetic data. The taxonomy of both species is revisited on the basis of new morphological studies and phylogenetic reconstruction based on molecular data. Results suggest that Gyromitra korfii could be a prioritary name for G. ticiniana. The replacement of the name Gyromitra littiniana with G. ticiniana is also discussed. Color images of fresh material and microscopical features are provided
Patterns of Biomass, Carbon, and Soil Properties in Masson pine (Pinus massoniana Lamb) Plantations with Different Stand Ages and Management Practices

Masson pine (Pinus massoniana Lamb) has been planted extensively in different parts of China for timber production and habitat restoration. The effects of stand age and management of these plantations on biomass, carbon storage, and soil physicochemical properties are poorly understood. In this study, we investigated biomass, carbon storage, and soil physicochemical properties of Masson pine plantations. The plantations were divided into four age groups (9, 18, 28, and 48 years), and into managed (MS) and unmanaged stands (UMS) in Hubei province, Central China. Tree biomass increased with stand age. A growth model indicated that maximum tree growth occurred when the plantations were 17 years old, and the average growth rate occurred when plantations were 23 years old. Tree biomass in managed stands was 9.75% greater than that in unmanaged ones. Total biomass carbon was estimated at 27.4, 86.0, 112.7, and 142.2 Mg ha−1, whereas soil organic carbon was 116.4, 135.0, 147.4, and 138.1 Mg ha−1 in 9-, 18-, 28-, and 48-year-old plantations, respectively. Total carbon content was 122.6 and 106.5 Mg ha−1, whereas soil organic carbon content was 104.9 and 115.4 Mg ha−1 in MS and UMS, respectively. Total carbon storage in the plantations studied averaged 143.7, 220.4, 260.1, and 280.3 Mg ha−1 in 9-,18-, 28-, and 48-year-old stands, and 227.3 and 222.4 Mg ha−1 in MS and UMS, respectively. The results of our study provide a sound basis for estimating ecosystem carbon as it relates to forest management activity and stand age.
The effect of different intensities of physical activity and diet on cardiometabolic markers, cardiac and vascular function, and gut microbiota

iv TABLE OF CONTENTS . viii LIST OF TABLES AND FIGURES . xiv APPENDIX . xvii LIST OF ABBREVIATIONS . xviii ACKNOWLEDGMENTS . xxi LIST OF PUBLICATIONS . xxii CONFERENCE PRESENTATIONS . xxiv CHAPTER 1: LITERATURE REVIEW . 1 1.
The generation of plasma cells and CD27−IgD− B cells during Hantavirus infection are associated with distinct pathological findings

Human hantavirus infections can cause hemorrhagic fever with renal syndrome (HFRS), major signs of the disease being thrombocytopenia and transient kidney dysfunction. By a comprehensive and longitudinal study of circulating B cells, we demonstrate that these two pathologies associate with distinct effects on the humoral immune system during HFRS. Low thrombocyte counts strongly associated with an abnormal frequency of plasmablasts in circulation, whereas kidney dysfunction was indicative of an accumulation of CD27− B cells and plasmablasts. Finally, we provide evidence that high levels of extracellular ATP in circulation during HFRS correlates with shedding of surface CD27 on B cells via a metallomatrix proteinase-8-mediated mechanism. Since extracellular ATP is known to regulate kidney function, our study reveals a link between kidney dysfunction and the generation of CD27−IgD− B cells, and a potential molecular target for treatment of the symptomatic phase of HFRS.
Improvement in phosphorus nutrition of wheat plants grown in a calcareous sandy soil by incorporating chemical phosphorus fertilizer with some selected organic substances

Established fertilizer recommendations for wheat is urgently required to enhance the application efficiency of commercial phosphorus (P) fertilizers. This study evaluated the effect of inorganic P combined with some organic supplements i.e., citric acid (CA) or pigeon manure juice (PMJ), on alkaline-calcareous soil as well as plant measurements and phosphorus efficiency parameters of wheat (Triticum durum ’Boussalem’). Different concentrations of P in solution i.e., 0.05, 0.10, 0.15, 0.20, and 0.40 mg l−1, were worked out theoretically using the Freundlich model. A greenhouse study was conducted on a permanent layout with three replicates. As a result, phosphorus in the control was 0.493 mg P pot−1. However, in amended pots with organic substances, the averages of P uptake were 0.701 and 0.785 mg P pot−1, respectively for PMJ and CA treatments. A lower P requirement of 0.195 and 0.245 mg P l−1 may be required in CA and PMJ treatments, compared to the control treatments (0.345 mg P l−1). In addition, the phosphorus absorption efficiency (PAE) was higher in the CA and PMJ treatments. So, it is recommended to apply P fertilizers with poultry manure juice as an alternative solution in order to improve the efficiency of inorganic P fertilizers and consequently reduce their application rates in alkaline calcareous soils.
Bacillus subtilis ameliorates water stress tolerance in maize and common bean

ABSTRACT Water stress is one important abiotic stress with negative impacts on plant productivity. In order to ameliorate abiotic stress, plant growth-promoting rhizobacteria (PGPR), such as Bacillus subtilis, can be used due to their positive effects on plant physiology. The present study aimed to evaluate the effects of B. subtilis on the performance of maize and common bean under water deficit conditions. The study was performed in a plant growth chamber and the growth, gas exchange parameters and antioxidant activity were evaluated. B. subtilis promoted the growth of common bean and maize, and also increased the water use efficiency. The inoculation with B. subtilis increased leaf water content and the regulation of stomata, without damaging photosynthetic rates. Overall, B. subtilis decreased antioxidant activities in both plants. The results suggest that B. subtilis could be used as inoculants for common bean and maize to protect against water stress.
Screening and optimization of some Egyptian soil-born fungi for lipids production as possible source for biofuel

Depletion of fossil fuel is the largest challenge facing human industrial and technological revolution in the current era. Exploration of widely distributed microorganisms for the production of renewable biofuel is the most priority for scientific research in the last decades. In this context, thirteen fungal isolates were collected from Tanta city, El-Gharbia Governorate, Egypt belonging to four genera (Aspergillus, Penicillium, Fusarium and Alternaria) were screened on minimal media for their ability to accumulate lipid in their biomass. The maximum lipid contents were 25.31% for Aspergillus versicolor and 20.15% for Aspergillus niveus. The optimization result showed that pH 4, incubation temperature 32°C, sucrose at concentration of 40g/L, glutamic acid at concentration of 0.5 g/L (C/N ratio at 40:0.5 w/w) after 5 days of incubation with agitation rate of 150 rpm on orbital shaker were the most appropriate conditions for the highest lipid accumulation in the case of Aspergillus versicolor. However, in case of Aspergillus niveus, pH 4, incubation temperature at 32°C, sucrose at concentration of 20 g/L, NaNO3 at concentration of 1.0 g/L (C/N ratio at 20:1.0 w/w) after 11 days of incubation with agitation rate of 150 rpm were the most appropriate for the highest lipid accumulation.
Precision of tissue patterning is controlled by dynamical properties of gene regulatory networks

ABSTRACT During development, gene regulatory networks allocate cell fates by partitioning tissues into spatially organised domains of gene expression. How the sharp boundaries that delineate these gene expression patterns arise, despite the stochasticity associated with gene regulation, is poorly understood. We show, in the vertebrate neural tube, using perturbations of coding and regulatory regions, that the structure of the regulatory network contributes to boundary precision. This is achieved, not by reducing noise in individual genes, but by the configuration of the network modulating the ability of stochastic fluctuations to initiate gene expression changes. We use a computational screen to identify network properties that influence boundary precision, revealing two dynamical mechanisms by which small gene circuits attenuate the effect of noise in order to increase patterning precision. These results highlight design principles of gene regulatory networks that produce precise patterns of gene expression. Summary: Experiments and modeling reveal sharp boundaries of gene expression in the vertebrate neural tube depend on the dynamics of the gene regulatory network that patterns the tissue.