Miracle-dz/UniFAR-FTUs huggingface dataset:
Ancient coding sequences underpin the spatial patterning of gene expression in C4 leaves

Photosynthesis is compromised in most plants because an enzymatic side-reaction fixes O2 instead of CO2. The energetic cost of oxygenation led to the evolution of C4 photosynthesis. In almost all C4 leaves compartmentation of photosynthesis between cells reduces oxygenation and so increases photosynthetic efficiency. Here we report that spatial expression of most C4 genes is controlled by intragenic cis-elements rather than promoter sequence. Two DNA motifs that co-operatively specify the patterning of genes required for C4 photosynthesis are identified. They are conserved in plants and algae that use the ancestral C3 pathway. As these motifs are located in exons they represent duons determining both gene expression and amino acid sequence. Our findings provide functional evidence for the importance of transcription factors recognising coding sequence as previously defined by genome-wide binding studies. Furthermore, they indicate that C4 evolution is based on ancient DNA motifs found in exonic sequence.
Hepatoprotective Effect of Stamen Extracts of Mesua ferrea L. against Oxidative Stress induced by $CCl_4$ in Liver Slice Culture Model

Stamens of Mesua ferrea L. are a well-known herbal drug used in Indian System of Traditional Medicine to treat various diseases. The claimed activity of this plant part is necessitated to investigate antioxidant and hepatoprotective activity. Authenticated plant sample was extracted with hexane, ethanol (EtOH) and water (aq.) using ASE 100 accelerated solvent extractor. Antioxidant activity was evaluated by means of different in vitro assays. Hepatoprotective effect was investigated on carbon tetrachloride induced oxidative stress in liver slice culture model. Cytotoxic marker lactate dehydrogenase (LDH) released in culture medium and the activity of lipid peroxidation along with antioxidant enzymes (AOEs) namely superoxide dismutase (SOD), catalase (CAT) and glutathione reductase (GR) were estimated. Hexane and EtOH extracts were significantly inhibited DPPH, NO, SOD and radical in dose dependent manner. The trade of phenol content was: aq. extract
Sustainability reports: Differences between developing and developed countries

Achieving sustainability is a major challenge faced by many societies. The increasing moral consciousness of stakeholders has put pressure on companies, forcing these companies to include long-term policies that reflect the regionally specific needs of stakeholders. Using a structural topic model, this study identified differences between developing and developed countries with respect to sustainability disclosures. Data were obtained from 2100 sustainability reports published in the United Nations Global Compact database for the year 2020. In global terms, these sustainability reports addressed three main topics: 1) human rights, 2) diversity, equity, and inclusion, and 3) sustainable production. Moreover, the sustainability reports from developing and developed countries incorporated different communication strategies. Based on the prevalence (rate of occurrence) of content, sustainability reports from developed countries predominantly communicated issues related to “sustainable production” and “supply chain emissions”, whereas sustainability reports from developing countries more frequently communicated issues related to “education” and “human rights".
Alfalfa nutritive quality as influenced by drought in South-Eastern Oasis of Tunisia

Abstract Medicago sativa is the main perennial legume in many places in the world such as South-East Tunisian Oases. The widespread use of this species is due to its high adaptability, forage yield potential and to its good quality. Furthermore, the succession of drought years in South-East Tunisian Oases especially in Gabes influenced fodder distribution and digestibility. To a better understanding of the variation of the nutritive value of (Medicago sativa L.) plants, the effect of four drought levels (25%; 50%; 75% and 100% of field capacity) on nutritive quality was investigated for three populations [P1 (Gannouch); P2 (Chenini) and P3 (Tebelbou)] cultivated in these oases. Results showed that drought reduced leaves, shoots and roots dry matter, while this effect was more pronounced for above organs (values reached 1.2 mg) than below organs (values reached 1.8 mg). However, drought decreased phosphor, calcium, magnesium and nitrogen contents, neutral detergent fibre, acid detergent fibre and in acid detergent lignin content for P1 and P2, this stress enhanced potassium uptake, leaves shoots and roots shoots ratios especially for P3, values passed from 1.56 for control treatment to 2.06 for 25% of field capacity. This population seems to be the most resistant to drought by maintaining reduced leaf area and elevated ratios. This result indicates that Medicago sativa succeed to maintain a good nutritive value under stress conditions. To the best of our knowledge, it is important to study the effect of this stress on others varieties to more understand its effect on nutritive value.
Effect of nutritional status on phenotypic characteristics of Arabidopsis and alfalfa in relation to the expression of AtSnRK2.9

The mechanisms of plant response to nutrient limitation and utilisation are of great interest for agricultural purposes. Phosphate is a non-renewable resource and is one of the most important nutrients required for plant growth. Recently a new family of plant protein kinases, composed of 10 members, were discovered because of their involvement in stresses and their responses to the hormone abscisic acid (ABA). In Arabidopsis, all of these SnRK2 protein kinases have been shown to be activated by drought or hyperosmostic stress, with the exception of SnRK2.9. Five members are also activated by ABA treatment. Recently SnRK2.8 was linked to metabolic processes by being down regulated in low nutrient level conditions. In the present study, SnRK2.9 was investigated and shown to play a role in metabolic pathways, but in an opposite manner. Contrarily to SnRK2.8, transcripts level of SnRK2.9 is induced in response to phosphate, nitrogen, and sulphur deprivation. Interestingly, opposite to most phosphate-starvation inducible genes, sucrose decreases SnRK2.9's transcripts level. Transgenic plants that overexpress SnRK2.9 do not appear to be affected in terms of growth. On the other hand, overexpressing antisense SnRK2.9 or mutated snrk2.9 at residue Asp-123 by conversion to Glu (D123E), showed reduced plant growth. This phenotype was more pronounced in the absence of phosphate. A T-DNA knockout line for SnRK2.9 showed a 45% decrease in root and shoot biomass compared to wild-type Arabidopsis when grown under phosphate deprivation. Similar trends were observed when the Arabidopsis gene was introduced in Medicago sativa (alfalfa) under the control of the CaMV 35S promoter. Overexpressing D123E Atsnrk2.9 had a serious inhibitory effect on growth and the plants
Natural allelic variation in blueberry TERMINAL FLOWER 1

Abstract A blueberry (Vaccinium sp.) germplasm collection was screened for allelic variation in TERMINAL FLOWER 1 (TFL1) that could be used in breeding flowering or architecture traits. TFL1 has been found to repress the transition from vegetative to reproductive growth in diverse plant species, with mutations leading to altered flowering and form. The VcTFL1 gene sequence was determined from the draft genome sequence of diploid V. corymbosum line W8520. VcTFL1 is a member of a PEBP gene family and it could be distinguished from its family members by sequence comparison with PEBP family genes from other plants. High-resolution DNA melting analysis of 160 Vaccinium accessions detected VcTFL1 exons that differed in sequence from the W8520 control. DNA sequence analysis confirmed the presence of single nucleotide polymorphisms (SNPs) and identified haplotypes of tetraploid accessions. A total of 18 SNP sites were detected in VcTFL1 coding sequences of the Vaccinium germplasm screened. A SNP causing an alanine-to-valine change in exon 4 (A159V) was determined by multiple bioinformatic tools to be deleterious to VcTFL1 function. A diploid V. corymbosum accession heterozygous for the VcTFL1 mutation was identified as a candidate for breeding novel traits for blueberry.
Exposure to proton pump inhibitors is associated with the development of pediatric autoimmune diseases

Proton pump inhibitors (PPIs) have been associated with decreased gut microbiota diversity. Disrupted gut microbiota composition has been reported in several autoimmune diseases (ADs), such as type 1 diabetes mellitus (DM), autoimmune thyroiditis (AIT), juvenile idiopathic arthritis (JIA), and inflammatory bowel diseases (IBD). We investigated whether PPIs are associated with the development of ADs in children and concluded that PPI exposures could be related to the onset of ADs, especially IBD and potentially AIT as well.
Multiple Allelic Frequencies in Populations at Equilibrium: Algorithms and Applications

Population genetics often serves as a bridge between units on Mendelian genetics and neo-Darwinian evolution in the teaching of introductory college biology and advanced high school biology. The value of teaching the Hardy-Weinberg principle to determine allelic frequencies in populations at equilibrium was presented several years ago to readers of The American Biology Teacher. Because there continues to be great interest in population biology and evolution, the principle is presently included in most introductory college textbooks (Schefler 1968). When students have mastered the Hardy-Weinberg concept and gained competence in calculating alternate allele frequencies, they begin asking for methods to determine allelic frequencies when series of multiple alleles for a gene locus exist. This paper presents a novel shortcut algorithm for solving problems related to multiple allelic frequencies in populations at equilibrium. Ceppellini et al. (1955) seem to be among the first to have presented an algebraic approach to the solution of multiple allelic frequency problems. Falconer (1960) simplified the method for applications dealing with the major alleles of the human ABO blood groups. Some standard introductory genetics textbooks (Burns 1983; Gardner et al. 1985) include Falconer's method for solving problems where three alleles of a gene locus exist. This paper, however, demonstrates how Falconer's method may be applied to determine multiple allelic frequencies in populations at equilibrium when more than three alleles of a gene locus exist. Coat Color in Rabbits
Identification and cDNA sequencing of vitellogenin in Bombyx mandarina Moore

The large subunit and small subunit of vitellogenin in Bombyx mandarina were identified through SDS-PAGE and Western blot, with molecular weight about 175 kD and 42 kD respectively based on high molecular weight marker. Several primers were designed according to cDNA sequence of vitellogenin in Bombyx mori and conservatism of insect vitellogenin. The cDNA sequence of vitellogenin in Bombyx mandarina (GenBank accession number:AY309967) was obtained through RT-PCR of the total RNA and RACE amplification of 3′-end and 5′-end. This sequence contains 5 754 bases, an open reading frame which encodes 1 780 amino acids, and the putative cleavage sites RSRR for the proteases of the subtilisin family at position 364-367 where provitellogenin is cleaved into two subunits. The molecular weights of the two subunits are 161.571 kD and 40.794 kD respectively based on amino acids, which are in accordance with the SDS-PAGE results if modification after translation is considered. The results of homology analysis suggested that amino acid sequence of insect vitellogenin be highly conserved within the same order for insects.
Detection of proviral DNA and viral RNA in various tissues early after avian leukosis virus infection.

Using molecular biological techniques, a study was made of the tissue tropism of avian leukosis virus (ALV) early after infection. Two strains of chickens, one with and the other without endogenous viral genes, were infected with ALV of subgroup A immediately after hatching; specimens of nine tissues and blood rumples were analyzed at various times thereafter. A polymerase chain reaction (PCR), specific to ALV subgroup A, was used to detect proviral DNA and viral RNA. In situ hybridization was used to confirm the presence of proviral DNA in tissue samples and to calibrate the PCR
Rapid emergence of HCMV drug resistance in immunocompromised paediatric patients detected using target enrichment and deep sequencing

Background Cytomegalovirus can cause fatal disease in immunocompromised patients. With the advent of new anti-HCMV drugs there is interest in using virus sequence data to monitor resistance and identify new mutations. Methods We used target-enrichment to deep sequence HCMV DNA from 11 immunosuppressed paediatric patients receiving single or combination anti-HCMV treatment, serially sampled over 1-27 weeks. Changes in consensus sequence and resistance mutations were analysed for three ORFs targeted by anti-HCMV drugs and the frequencies of drug resistance mutations monitored. Results Targeted-enriched sequencing of clinical material detected mutations occurring at frequencies of 2%. Seven patients showed no evidence of drug resistance mutations. Four patients developed drug resistance mutations a mean of 16 weeks after starting treatment. In two patients, multiple resistance mutations accumulated at frequencies of 20% or less, including putative resistance mutations P522Q (UL54) and C480F (UL97). In one patient, resistance was detected 14 days earlier than by PCR. Phylogenetic analysis suggested recombination or superinfection in one patient. Conclusions Deep sequencing of HCMV enriched from clinical samples excluded resistance in 7 of eleven subjects and identified resistance mutations earlier than conventional PCR-based resistance testing in 2 patients. Detection of multiple low level resistance mutations was associated with poor outcome.
LACK OF ANNUAL PERIODICITY IN CAMBIAL PRODUCTION OF PHLOEM IN TREES FROM MEDITERRANEAN AREAS

Annual periodicity of cambium production of xylem and phloem cells has rarely been compared in trees from different environments. We compared the structure of cambium and the youngest xylem and phloem increments in four tree species, Fagus sylvatica, Picea abies, Pinus sylvestris and Pinus halepensis, from nine temperate and Mediterranean sites in Slovenia and Spain. In Picea abies, Pinus sylvestris and Fagus sylvatica from temperate locations in Slovenia, xylem and phloem growth ring boundaries could be identified. In Fagus sylvatica growing at two elevations on Moncayo mountain, Spain, phloem increment consisted of only early phloem. In Pinus sylvestris from the same two sites, growth ring boundaries were not as clear as in temperate Slovenian sites. In some cases we could identify phloem growth ring boundaries but in others it was very doubtful, which could be explained by collapse of the outermost early phloem sieve cells. In Pinus halepensis from all sites, we could only distinguish between collapsed and non-collapsed phloem, while phloem rings could not be identified. Widths of the youngest phloem and xylem annual increments could only be compared when phloem increments could be clearly defined, as with Picea abies, Fagus sylvatica and Pinus sylvestris from temperate sites. The visibility of the growth ring boundary in phloem was not related to the width of annual radial growth. The correlation between xylem and phloem ring widths was high, but moderate between the number of dormant cambial cells and xylem ring and phloem ring widths. Based on the structure of the youngest phloem increments, we concluded that there is no typical annual periodicity in cambial production of phloem cells in trees from certain Mediterranean sites. This may be due to continuous yearlong cell production and the absence of true cambium dormancy, at least on the phloem side, under mild winter conditions.
CONTROL OF POSTHARVEST DISEASES IN LONGAN FRUIT BY OZONE

In order to study the effects of ozone gas treatment on postharvest diseases of longan fruits, cultures of the fungi Lasiodiplodia sp. and Cladosporium sp. cultured on potato dextrose agar (PDA) were exposed to 20 ppm of ozone. The ozone was applied directly on mycelia of Lasiodiplodia sp. or spore suspension of Cladosporium sp. for 15, 30, 60 and 120 minutes. In vitro studies showed that ozone exposure for 60 minutes significantly reduced mycelial growth of Lasiodiplodia sp. and completely inhibited Cladosporium sp. After fumigation with ozone, microscopic observation revealed the presence of abnormal mycelia of Lasiodiplodia sp. Exposing fruits to ozone for 60 minutes soon after inoculation with Lasiodiplodia sp. and Cladosporium sp. was the most effective way of controlling the incidence of postharvest diseases. Therefore, application of ozone could be considered as a possible alternative method to control postharvest decay and prolong storage life of longan fruits.
Molecular Docking of Biologically Active Substances to Double Helical Nucleic Acids: Problems and Solutions

Molecular docking of ligands to DNA-targets is of great importance for the design of new anticancer drugs. Unfortunately, most docking programs were developed for protein-ligand docking which raises a question about their applicability for the DNA-ligand docking. In this study, the popular docking programs AutoDock Vina, AutoDock4 and AutoDock3 were compared for a test set of 50 DNA-ligand complexes taken from the Nucleic Acid Database. It was shown that the version 3.05 of the AutoDock program was the most successful in reproducing the structures of intercalation and minor-groove complexes. The program AutoDock4 was able to re-dock to within 2 Å RMSD most of the intercalation complexes of the test set, but showed poor performance for minor groove binders. While Vina, on the contrary, failed to construct six intercalation complexes of the test set, but showed satisfactory results for DNA-ligand minor-groove complexes when small search space was used.
In vitro characterization of bioadhesive metoclopramide tablets for buccal application prepared with polyacrylic acid and hydroxypropyl methylcellulose

The influence of derivatives of acrylic acid (PAA), Carbopol 907, 941, 934 and 940, and hydroxypropyl methylcellulose (HPMC) on metoclopramide release from bioadhesive tablets designed for buccal use has been studied. Both the PAA/HPMC ratio and the molecular weight of the Carbopol gave statistically significant differences in drug release. The swelling and wettability of the tablets were also investigated, since these two factors influence release. Turbidity and viscosity studies revealed the formation of a complex between PAA and HPMC. The greater the turbidity due to the formation of the complex, the lower the degree of swelling. The release obtained for Carbopol 934 is greater compared with Carbopol 941 and 940, possibly due to the lower viscosity of the Carbopol. Nevertheless, the behaviour in solution is more influenced by the hydrophilic nature of the HPMC than by the formation of the complex.
Contribution of the schizophrenia associated protein DISC1 to mitochondrial dynamics and dendritic development

Correct neuronal function is an energy costly process, highly dependent upon the ATP production and calcium buffering capabilities of mitochondria. Further, it is crucial that these organelles are correctly distributed throughout the neuron, matching local energy demand. To achieve this, mitochondrial fusion and transport dynamics must be precisely regulated. Trafficking is dependent upon microtubule based transport of these organelles, mediated by kinesin motors, TRAK adaptors and the mitochondrial anchor, Miro. Mitofusins orchestrate mitochondrial fusion at the outer membrane. Disrupted in schizophrenia 1 (DISC1) – a major candidate susceptibility factor for psychiatric disease – also plays a role in mitochondrial transport. However, the mechanisms of this regulation, and subsequent roles in neuronal development, are poorly understood. In this study, the interactions between DISC1 and mitochondrial trafficking proteins Miro and TRAKs are investigated. DISC1 is shown to couple to the mitochondrial transport and fusion machinery in brain. Live cell imaging demonstrates the importance of these interactions for normal mitochondrial transport. A schizophrenia associated mutation in DISC1 – the DISC1-Boymaw fusion protein – is shown to disrupt these transport dynamics and similarly impair mitochondrial fusion. Further, this mutation alters contact area between the endoplasmic reticulum and the mitochondria. Moreover, disruption of mitochondrial dynamics by targeting the DISC1-Miro/TRAK complex or upon expression of the DISC1-Boymaw fusion protein impairs the correct development of neuronal dendrites. Finally, mitochondrial dynamics in human neurons, differentiated from induced pluripotent stem cells, are explored. This innovative system is used to investigate impact of pathogenic mutations associated with schizophrenia and Alzheimer’s disease upon mitochondrial dynamics. This work highlights DISC1 as an important regulator of mitochondrial dynamics in neurons to mediate transport, fusion and cross-talk of these organelles. Moreover, pathological DISC1 isoforms disrupt this critical function, leading to abnormal neuronal development. These findings implicate regulation of mitochondrial dynamics in aetiology of psychiatric disease.
Evaluation of Onion Genotypes for Resistance to Stunting Caused by Rhizoctonia solani AG 8

Thirty-ﬁve onion genotypes were evaluated for resistance to stunting caused by Rhizoctonia solani anastomosis group 8 (AG 8) in a growth chamber set at 15 ± 1 8 C. The trial was repeated. Resistance to R. solani AG 8 was deﬁned as a lack of signiﬁcant difference in plant height, root length, and/or total dry biomass between inoculated and noninoculated plants of the same genotype. Plant height was not reduced signiﬁcantly by R. solani AG 8 for 14 and 7 of the 35 genotypes in Trials 1 and 2, respectively. In Trial 1, plant height reduction caused by R. solani ranged from 24% for the cv. Lasalle to 62% for the experimental line R14882, and in Trial 2 plant height reduction ranged from 22% for the experimental line PX07713218 to 53% for the cv. Montblanc. However, the extent of reduction in plant height caused by R. solani did not differ signiﬁcantly among genotypes in either trial. Onion root length was not reduced by R. solani AG 8 for 26 and 18 of the 35 genotypes in Trials 1 and 2, respectively. The degree of reduction in root length ranged from 9% (R14889) to 76% (Sterling and SN232) in Trial 1, and 14% (SN325) to 74% (Sterling) in Trial 2. Onion dry biomass was not reduced by R. solani AG 8 for 19 and 7 of the 35 genotypes in Trials 1 and 2, respectively, and ranged from 18%