Miracle-dz/UniFAR-FTUs huggingface dataset:
Architecture of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci

By incorporating the information of human chromosome inferred from Hi-C experiments into a heteropolymer model of chromatin chain, we generate a conformational ensemble to investigate its spatiotemporal dynamics. The heterogeneous loci interactions result in hierarchical organization of chromatin chain, which obeys compact space-filling (SF) statistics at intermediate length scale. Remarkably, the higher order architecture of the chromatin, characterized by the single universal Flory exponent (ν = 1/3) for condensed homopolymers, provides quantitative account of the dynamical properties of the chromosome. The local chromosome structures, exemplified by topologically associated domains (~ 0.1 − 1 Mb), display dynamics with fast relaxation time (≲ 50 sec), whereas the long-range spatial reorganization of the entire chromatin occurs on a much longer time scale (≳ hour), suggestive of glass-like behavior. This key finding provides the dynamic basis of cell-to-cell variability. Active forces, modeled using stronger isotropic white noises, accelerate the relaxation dynamics of chromatin domain described by the low frequency modes. Surprisingly, they do not significantly change the local scale dynamics from those under passive condition. By linking the spatiotemporal dynamics of chromosome with its organization, our study highlights the importance of physical constraints in chromosome architecture on the sluggish dynamics. Significance Statement Chromosomes are giant chain molecules made of hundreds of megabase-long DNA intercalated with proteins. Structure and dynamics of interphase chromatin in space and time hold the key to understanding the cell type-dependent gene regulation. In this study, we establish that the crumpled and space-filling organization of chromatin fiber in the chromosome territory, characterized by a single universal exponent used to describe polymer sizes, is sufficient to explain the complex spatiotemporal hierarchy in chromatin dynamics as well as the subdiffusive motion of the chromatin loci. While seemingly a daunting problem at a first glance, our study shows that relatively simple principles, rooted in polymer physics, can be used to grasp the essence of dynamical properties of the interphase chromatin.
Variation in Juniperus communis trees and shrubs from Bulgaria: Analyses of nrDNA and cpDNA regions plus leaf essential oil

DNA sequence data from nrDNA plus four cp DNA regions (4315 bp) was congruent with leaf essential oils data. Based on leaf essential oils, DNA sequences and morphology, J. sibirica, Bulgaria, should be treated as J. communis var. saxatilis. Combined data on leaf essential oils, DNA sequences and morphology indicates that J. pygmaea, Bulgaria, should be treated as a shrubby form of J. communis: Juniperus communis forma pygmaea (K. Koch) R. P. Adams & A. N. Tashev, comb. nov. Published on-line www.phytologia. org Phytologia 96(2): 124-129 (April 1, 2014). ISSN 030319430.
Sub-Cloning of ads Gene Into pETDUET1_cyp For Co-Expression in Escherichia coli

CYP71AV1 and ADS are two enzymes involved in artemisinin biosynthesis. In this research, sub-cloning of cyp71av1 and ads in pETDUET1 (pETDUET1_cyp/ads) has been done. The result of transformation has been confirmed by migration, restriction and sequencing analysis. Overproduction of CYP71AV1 and ADS was done at temperature 37 °C using 0,5 mM IPTG induction. The protein produced mostly formed as inclusion bodies, therefore the optimization of overproduction condition is still needed. Keywords— CYP71AV; ADS; pETDUET1; Sub-cloning
The Effect of Methanolic Extract of Quercus infectoria Against Some Causative Agents of Diarrhea and Eliminate their Antimicrobial Resistance

We obtained 124 bacterial isolates including: Escherechia. coli. I (35 isolates 7%) isolates, E. coli II (8 isolates 1.6%), E. coli III (17 isolates 3.4%), E. coli IV (22 isolates 4.4%), Shigella dysenteriae (8 isolates 1.6%), Salmonella arizonae (16 isolates 3.2%), Salmonella typhi (12 isolates 2.4%) and Vibrio cholera (6 isolates 1.2%) Sensitivity test showed high resistance to amoxicillin/clavulanic acid, amoxicillin, ampicillin, erythromycin, streptomycin, nitrofurantoin, cefixime, rifampicin, tetracycline, trimethoprim sulfamethoxazole and tobramycin. Most of the isolates appeared sensitive to nalidixic acid, gentamycin, amikacin, doxycyclin, cefotaxime, cephalexine and chloramphenicol. All isolates were sensitive to ciprofloxacin. The MIC of the methanol extracts of Quercus infectoria against different pathogenic bacteria was ranging between 2.5 mg/ml 20.0 mg / ml and the MBC was 1.25 mg/ml 20.0mg/ ml. The isolates revealed high resistance to most widely used antibiotic, the methanol extracts of Quercus infectoria showed high potential as antibacterial agent.
Chemical composition and antioxidant activity of essential oils in Origanum vulgare subsp. gracile at different phenological stages and plant parts

Origanum vulgare, a popular flavoring herb, is valued for several biological properties. The present study focused on the chemical composition and antioxidant activity of the essential oils of Origanum vulgare subsp. gracile in different plant parts and at different phenological stages. Qualitative and quantitative analyses of the essential oil identified 41 constituents that varied with plant age and organ. The phenolic monoterpenoid carvacrol (18.1–79.2%) was predominant in all the essential oil samples. Other major constituents were p-cymene (3.9–18.0%), γ-terpinene (0.9–15.8%), carvacrol methyl ether (0.8–9.9%), and (Z)-α-bisabolene (0.5–8.7%). Among the different plant parts and phenological growth stages, the highest levels of carvacrol were identified in the essential oils from flowers (79.2%), roots (70%), and the early vegetative growth (67.34%). All the essential oils exhibited high radical-scavenging properties as shown in the DPPH* assay. The essential oils from flowers, however, exhibited the highest antioxidant activity and could be used as a preservative agent on an industrial scale. Practical applications Results suggest that yield and quality of oregano essential oil can be scaled-up by optimizing plant development and harvesting time. Also, the essential oils from flowers exhibited the highest antioxidant activity and could be used on an industrial level to reduce oxidation in food products.
Analysis of Molecular Events Involved in Chondrogenesis and Somitogenesis by Global Gene Expression Profiling

In order to better understand the molecular mechanisms that control chondrogenesis and somitogenesis, a global quantitative expression profiling using SAGE (Serial Analysis of Gene Expression) was performed on a chondrogenic cell line, ATDC5, and on somitic tissues dissected from mouse E10.5 embryos. Among a total of 43,656 SAGE tags derived from mouse chondrogenic ATDC5 cells (21,875 from uninduced cells and 21,781 from cells induced with BMP4 for 6 h), 139 transcripts were differentially represented in the two libraries (P >= 0.05). Ninety-five of them matched to single UniGene entries (77 known genes and 18 ESTs), but surprisingly, many of them have never been implicated in chondrogenic differentiation. Interestingly, a significant fraction of these genes formed physical linkage groups. For the study of somitogenesis, the expression profiles in four different subsets of the caudal part of E10.5 embryos was compared: The tail bud (A), the caudal 2/3 (B) and the rostral 1/3 (C) of the presomitic mesoderm, and two pairs of nascent somites (D). A total of 171,639 LongSAGE tags (A: 21,595; B: 50,699; C: 49,732; D: 49,613) were generated leading to the identification of 1007 transcripts differentially represented between at least two of the libraries (P >= 0.05). The LongSAGE tags with a count of two or more were compared against the current genome annotation of EnsEMBL. The analysis of LongSAGE tags with no corresponding EnsEMBL gene lead to the identification of 1872 genes, that were not yet annotated to the genome, but represented by a UniGene cluster. Furthermore, 2348 GeneScan predictions could be verified with LongSAGE tags and 547 antisense genes were identified. A analysis of publically available SAGE libraries showed that target genes of signaling pathways other than BMP also cluster to the genome. Furthermore, the observed changes in the expression of ribosomal protein genes in various tissues under different conditions were examined. Surprisingly, cluster analysis showed that different tissue types had distinct profiles of ribosomal protein gene expression. In conclusion, the transcriptome analyses of both BMP-induced chondrogenesis and somitogenesis provided an insight on the molecular events during both developmental processes. In general, multiple signaling pathways and a variety of cellular processes are involved. Further study will clarify how these changes in gene expression are brought about and are organized into the concerted cellular events of chondrogenic and somitogenic differentiation.
Feed resource selection by Criollo goats browsing a tropical deciduous forest

Goats browsing in a tropical deciduous forest (TDF) obtain a large proportion of their diet from a large number of plant species. Nevertheless, the goat’s feed resource selection has not been studied in such an ecosystem. This study aimed to determine whether goats browsing in a TDF display active feed resource selection. Two browsing sites were used (A = 2.2 ha and B = 2.6 ha). The effective availability (g) of all plant species available was measured for each site using 10 m × 20 m exclusion quadrants. Three non-pregnant adult goats (34.9 ± 2.4 kg liveweight) with browsing experience were observed using the continuous bite monitoring method to determine their respective dry matter intake. The selection of different plants was determined using the Jacobs’ selection index (JSI). The goats’ dry matter intake per day was 723 and 310.8 g for Sites A and B, respectively. At both browsing sites, the plant with the highest biomass availability was Gymnopodium floribundum (75.5% and 49.3% for Sites A and B, respectively). Nevertheless, the plant species most actively selected by goats were Eragrostis ciliaris at Site A (JSI = 0.99, P < 0.05) and Mimosa bahamensis at Site B (JSI = 0.96, P < 0.05). Some plant species were not consumed at Sites A and B (three and five species, respectively). In conclusion, feed resource selection was not associated with the biomass availability of the plants selected or refused. Goats were able to show active feed resource selection in the TDF, and this could change according to the characteristics of the browsing site.
EFFECT OF ETHANOL EXTRACT OF ARECA CATECHU AND SYZYGIUM AROMATICUM ON GLUTATHIONE-S-TRANSFERASE OF COTYLOPHORON COTYLOPHORUM

Paramphistomosis is an important parasitic disease in sheep and goats and causes considerable economic loss to the livestock industry. Anthelmintics are commonly used against rumen flukes. The problem of the development of resistance against the common chemical anthelmintics has been renewed the interest in the study of medicinal plants for the development of novel anthelmintics. Glutathione-Stransferase is a multifunctional enzyme that participates in the detoxification of endogenous and exogenous toxic metabolites which are fatal to the parasite. The anthelmintic activity of ethanol extracts of Areca catechu and Syzygium aromaticum on Glutathione-S-transferase activity of the digentic trematode Cotylophoron cotylophorum was studied. The parasites were exposed to five sub-lethal concentrations of ethanol extracts of Areca catechu and Syzygium aromaticum for 2, 4 and 8h. Glutathione-Stransferase was assayed in control and drug treated flukes. Maximum inhibition of Glutathione-S-transferase activity was observed @ 0.5 mg/ml of ethanol extracts of Areca catechu and Syzygium aromaticum after 8h of exposure. Inhibition of Glutathione-Stransferase activity was dose and time dependent. Decrease in Glutathione-S-transferase lead to accumulation of toxic metabolites which ultimately kill the parasites. The present investigation thus elucidated the anthelmintic potential of ethanol extracts of Areca catechu and Syzygium aromaticum which could be used to combat paramphistome infection in livestock.
Re‐evaluation of glutamic acid (E 620), sodium glutamate (E 621), potassium glutamate (E 622), calcium glutamate (E 623), ammonium glutamate (E 624) and magnesium glutamate (E 625) as food additives

Abstract The EFSA Panel on Food Additives and Nutrient Sources added to Food (ANS) provides a scientific opinion re‐evaluating the safety of glutamic acid–glutamates (E 620–625) when used as food additives. Glutamate is absorbed in the intestine and it is presystemically metabolised in the gut wall. No adverse effects were observed in the available short‐term, subchronic, chronic, reproductive and developmental studies. The only effect observed was increased kidney weight and increased spleen weight; however, the increase in organ weight was not accompanied by adverse histopathological findings and, therefore, the increase in organ weight was not considered as an adverse effect. The Panel considered that glutamic acid–glutamates (E 620–625) did not raise concern with regards to genotoxicity. From a neurodevelopmental toxicity study, a no observed adverse effect level (NOAEL) of 3,200 mg monosodium glutamate/kg body weight (bw) per day could be identified. The Panel assessed the suitability of human data to be used for the derivation of a health‐based guidance value. Although effects on humans were identified human data were not suitable due to the lack of dose–response data from which a dose without effect could be identified. Based on the NOAEL of 3,200 mg monosodium glutamate/kg bw per day from the neurodevelopmental toxicity study and applying the default uncertainty factor of 100, the Panel derived a group acceptable daily intake (ADI) of 30 mg/kg bw per day, expressed as glutamic acid, for glutamic acid and glutamates (E 620–625). The Panel noted that the exposure to glutamic acid and glutamates (E 620–625) exceeded not only the proposed ADI, but also doses associated with adverse effects in humans for some population groups.
The female of Oreiallagma oreas (Odonata: Coenagrionidae), with notes on the species natural history

Oreiallagma oreas (Ris, 1918) is a recently rediscovered Colombian Andean endemic species, for which the information available is very scarce. It was originally described from a single male. Since 2008, O. oreas has been recorded in new localities but its life history remained unknown. Here we describe and diagnose the species female for the first time and show evidence of female dichromatism in the genus. Also, we present photographs and illustrations of males and females, a distribution map, and information on this species biology, reporting that it breeds on bromeliads as other species in the genus.
Identification, variabilité, et connaissance in planta des effecteurs de pathogénicité de l'oomycète plasmopara halstedii, l'agent du mildiou du tournesol

Plasmopara halstedii, l'oomycete phytopathogene a l'origine du mildiou chez le tournesol, est responsable de pertes agronomiques importantes. Pour lutter contre cet agent pathogene, des moyens de luttes genetiques existent sous forme de genes de resistance (genes Pl). Cependant, on observe ces 20 dernieres annees une recrudescence des isolats de P. halstedii contournant les genes de resistance du tournesol utilises en culture. Au sein des pathosystemes, l'issue d'une interaction plante-agent pathogene depend en grande partie de la co-evolution entre, (i) les proteines de resistance de la plante, et (ii) des proteines secretees de l'agent pathogene appelees effecteurs et dont le role est de modifier la physiologie de l'hote pour favoriser l'infection. Au cours de cette these nous avons mis en place differentes approches de microscopie, de genomique et de biologie moleculaire pour etudier l'impact des effecteurs de P. halstedii dans sa virulence.
Preussia sp. BSL-10 producing nitric oxide, gibberellins, and indole acetic acid and improving rice plant growth

ABSTRACT Preussia sp. have been least known to improve plant growth and produce phytohormones. The current study investigated the production of nitric oxide (NO), indole-3-acetic acid (IAA), and gibberellins (GA4, GA7, GA15, and GA53) by a novel endophytic-fungal strain Preussia sp. BSL-10 using advanced chromatographic and spectroscopic techniques. Production of these phytohormones were validated by RT–PCR analysis, which indicated the expression of genes encoding tryptophan synthase (TRP), indole-3-acetamide hydrolase (IAAH), tryptophan-2-monooxygenase (IAAM), aldehyde dehydrogenase (ALD), GA4 desaturase (DES), geranylgeranyl-diphosphate synthase (GGS2), ent-desaturase oxidase (P450-4), GA14 synthase (P450-1) and nitrite reductase (NIRK/NIRS), cytochrome P450 (P450nor), nitrate reductase (NR), NOS-like (NOL), and nitric oxide reductase (QNOR/CNOR). In plant growth-promoting effects, the inoculation of Preussia sp. BSL-10 significantly increased the growth of dwarf mutant Waito-C and wild-type rice cultivars. In conclusion, utilizing new endophytic with the ability to produce NO, IAA, and gibberellins can be used to promote growth and yield of marginalized crops.
The ecological significance of intraspecific variation among freshwater ciliates

The biodiversiry of ciliates is currently a controversial issue (e.g. fiNLAY & fENCHEL 1999, fOISSNER 1999). The issue focuses on the rota! number of extant ciliate species. Species are pragmatically defined according ro the morphospecies concept (FINLAY et al. 1996, FoiSSNER et al. 1999), which is, according ro the former authors, as valid as any other species concept. Those authors who assume that the total number of free-living ciliate species is rather smaJJ, i.e. dose to 3000 (fiNLAY & fENCHEL 1999 and references therein), argue that this is mainly because ciliate species and genera have cosmopolitan distributions (FINLAY et al. 1996, 1998), and that the total number of niches available for ciliates is restricted. This assumption seems ro hold true, in particular, for plankronic freshwater species (FmssNER et al. 1999). While the rota! number of ciliate species found in the freshwater plankron is dose ro 700, only ca. 180 are euplankronic (FOISSNER et al. 1999). It is, however, obvious that cosmopolitan freshwater ciliate species will experience a range of environmental conditions. Morphologically indistinguishable populations can be sufficiently isolated ro allow genetic divergence (DINI & NYBERG 1993). Thus, differing environmenral regimes should create niches for ciliate species and dones; such dona! diversiry is common in other freshwater taxa that primarily reproduce asexually (reviewed by CARVALHO 1994, DE MEESTER 1996). Considerable growth rate variabiliry has already been reported for planktonic ciliates isolated from different marine (PEREz-Uz 1995) and freshwater (WEISSE & MoNTAGNES 1998) localities. Thus, although the total number of planktonic ciliate species may be relatively small, various ecorypes (TURESSON 1922) may exist within each species, and the functional biodiversiry may be considerably larger than is presently assumed, mainly based on species numbers (MONTAGNES & WEISSE 2000).
Prey Species Influences Foraging Behaviors: Rattlesnake (Sistrurus miliarius) Predation on Little Brown Skinks (Scincella lateralis) and Giant Centipedes (Scolopendra viridis)

Abstract Predators often evolve specialized behaviors to feed on dangerous prey. Centipedes are widely documented in the diet of viperid snakes, but the behaviors snakes use to consume these dangerous prey have been reported only anecdotally. To determine how prey type influenced snake foraging behaviors, we ran laboratory predation trials using 29 field-captured Pigmy Rattlesnakes (Sistrurus miliarius) with centipedes (Scolopendra viridis) and skinks (Scincella lateralis). In skink trials, Pigmy Rattlesnakes were significantly more likely to engage in sit-and-wait predation than in centipede trials where active pursuit of prey was frequent. Centipedes were struck by snakes in significantly more trials than skinks and the mean length of strikes directed at centipedes was significantly shorter than for the strikes directed at skinks. Strike latency was significantly lower for centipedes than for skinks. The location on the prey's body where the strike was directed did not differ in skink and centipede trials. The mean time from snake strike to last prey locomotion and to prey ingestion were both significantly longer for centipedes. Pigmy Rattlesnakes exhibited several behaviors in centipede trials, including head elevation when approaching prey, that were never observed in skink trials. Centipedes occasionally struck rattlesnakes, but the snakes did not have any apparent injuries. Pigmy Rattlesnakes displayed plasticity in foraging behaviors to effectively prey on centipedes. The implications of centipede consumption in vipers merits increased attention given its occurrence in dozens of species.
Drivers of landscape evolution: multiple regimes and their influence on carbon sequestration in a sub‐tropical peatland

Typically, restoration goals target a point in history, i.e., pre-human influence state, however, ecosystems are dynamic and restoration goals must consider the potential evolution of the system, along with primary causes of landscape degradation and the resultant resilience. Using the Everglades as a case study, known disturbances were linked to biogeochemical and vegetation patterns to compare the divergence of the anthropogenically impacted landscape from that expected during natural peatland evolution. Specifically, landscape soil biogeochemistry of ~ 1100 sites was examined in context of hydroperiod, spatial and temporal trends in water quality from the 1940′s through present, elevation, and vegetation communities. This provided a link between carbon (C) accumulation and the influence of anthropogenic alterations. The network of canals created to manage water resulted in a greater ratio of surface water to rainfall contribution to the water budget, restored connectivity of groundwater to surface water, and facilitated overdrainage and mineral and nutrient enrichment of the ecosystem, causing multiple regime shifts and evidence of C loss. This study suggests that restoration can promote the accumulation of minerotrophic peats, but it is difficult to recreate the trajectory towards the ombrotrophic peatland, one of the end members and most C rich portions of the ecosystem, given changes in source waters and connectivity. In addition, a comparison with the literature and paleoecological data confirmed that while phosphorus (P) and C accumulation are positively related, even relatively small increases in P content reduced the proportional C content of peat soils. Overall, this study highlights the need to consider the potential natural trajectories of landscape development, the multiple coexisting resultant regimes, and the importance of soil biogeochemical properties when establishing and prioritizing restoration goals. Given the resilience and feedback loops of the anthropogenically impacted areas, active management of these areas may be necessary if we are to restore the vegetation community composition and biogeochemical characteristics to those of natural regimes, however, some legacy effects will constrain future restoration efforts. This article is protected by copyright. All rights reserved.
Repertoire des espèces et des genres nouveaux

Cœlomomyces Indiana Iyengar. Chytridiciceæ. Cavité générale. Larves d’Anopheles (Anopheles) barbirostris, A. (M.) hyrcanus var. nigerrimus, A. (Myzomyia) subpictus, A. (M.) aconitus, A. (M.) varuna, A. (M.) ramsayi, A. (M.) annularis, A. (M.) jamesi. Inde anglaise. Parasitology, XXVII, 1935, p. 446. Cœlomomyces anophelesica Iyengar. Chytridiaceæ. Cavité générale. Larves d’Anopheles (Myzomyia) superpictus, A. (M.) aconilus, A (M.) annularis, A. (M.) varuna. Inde anglaise. Parasitology, XXVII, 1935, p. 447. M. L a n c e r o n .