Miracle-dz/UniFAR-FTUs huggingface dataset:
More limbs on the tree: mitogenome characterisation and systematic position of ‘living fossil’ species Neoglyphea inopinata and Laurentaeglyphea neocaledonica (Decapoda : Glypheidea : Glypheidae)

Abstract. Glypheids first appeared in the Lower Triassic period and were believed to be extinct until specimens of Neoglyphea inopinata Forest & Saint Laurent and Laurentaeglyphea neocaledonica Richer de Forges were described in 1975 and 2006, respectively. The finding of extant species has meant that molecular data can now be used to complement morphological and fossil-based studies to investigate the relationships of Glypheidea within the Decapoda. However, despite several molecular studies, the placement of this infraorder within the decapod phylogenetic tree is not resolved. One limitation is that molecular resources available for glypheids have been limited to a few nuclear and mitochondrial gene fragments. Many of the more recent large-scale studies of decapod phylogeny have used information from complete mitogenomes, but have excluded the infraorder Glypheidea due to the unavailability of complete mitogenome sequences. Using next-generation sequencing, we successfully sequenced and assembled complete mitogenome sequences from museum specimens of N. inopinata and L. neocaledonica, the only two extant species of glypheids. With these sequences, we constructed the first decapod phylogenetic tree based on whole mitogenome sequences that includes Glypheidea as one of 10 decapod infraorders positioned within the suborder Pleocyemata. From this, the Glypheidea appears to be a relatively derived lineage related to the Polychelida and Astacidea. Also in our study, we conducted a survey on currently available decapod mitogenome resources available on National Center for Biotechnology Information (NCBI) and identified infraorders that would benefit from more strategic and expanded taxonomic sampling.
Assessment of the effects of genetically modified potatoes on structure and functioning of soil fungal communities

This thesis investigates the effects of genetic modification of the starch quality in potato on the structure and function of the soil fungal community via changes in root-exudates and litter composition, and compares the observed differences between the GM- and its parental variety in the context of the ‘normal’ variation effected by conventionally produced cultivars. In order to study the fungal community composition and functionality, an integrated approach of molecular fingerprinting methods and measurements of fungal enzymes involved in degradation of organic matter in the soil was employed. In field experiments the effect of soil type, season and plant growth stage on rhizosphere fungi were evaluated and in the greenhouse experiments stable isotopes were employed to monitor carbon flow from the plant to rhizosphere microbes and a decomposer experiment was designed to investigate the faith of the potatoes and leaves possibly left into the soil. The detailed greenhouse studies revealed differences between GM- and its parental variety. The field studies, however, confirmed that these differences are transient in field conditions and that fungi in the potato rhizosphere are affected more by soil type, sampling year, plant growth stage and cultivar type than the genetic modification.
Confirmation of First Report of Orchid fleck virus in Phalaenopsis Hybrid Orchids in the U.S.A.

The results also suggest one-step RT-PCR from Phalaenopsis plants and Orchid fleck virus (OFV) isolates can give false negatives for asymptomatic plants. Further work on detection methods for OFV is under way. This is the first confirmation of OFV infecting orchids in the United States.
Inhibitory Effect of 6,7-dimethoxy-5-hydroxyflavone on Human Cervix Carcinoma in Vitro

Natural products derived from plants play a significant role in drug discovery due to the revealing a large variety of pharmaceutical effects. Kickxia spuria was collected from Bingol, Turkey. Aerial parts of the plant were boiled in water for 2 h then extracted with ethyl acetate. After evaporation of the solvent by rotary evaporator, the extract was subjected to column chromatography to yield the compound identified as 6,7-dimethoxy-5-hydroxyflavone by spectroscopic method including 1D-, 2D-NMR, LC-TOF/MS. Antiproliferative activity of isolated compound was tested against HeLa (human cervix carcinoma) cell lines by xCELLigence assay, and found out that the compound exhibited excellent activity.
Comparison of photosynthesis activities among ten species of Salvia L.

The study included survey to record ten species of Salvia L. (Lamiaceae)at spring session in three physical district of Iraqi vegetation within Kurdistanregion . After identified species of studied genus the study included fieldinvestigation of some photosynthetic parameters by PP system TPS-2.the resultshowed different pattern of these species in compared with the elasticity ofgeographic distribution especially in Compensation point of CO2 and the leafcontents of photosynthetic pigments.
Red Stripe/ Top Rot Disease of Sugarcane: A Review

Sugarcane (Saccharum officinarum L.) is one of the world’s most important crop plants and is cultivated in tropical and subtropical areas in more than 80 countries around the globe. The important sugarcane producing countries in the world are India, Cuba, Brazil, Mexico, Pakistan, China, Philippines, Columbia, Argentina, Australia, USA, Thailand, and South Africa. In India it is grown on 5.0 million hectare with total production of 338.963 million tonnes that contributes nearly 75 per cent to the total sugar (Anonymous 2015). It is one of the most important cash crops, contributing about 7.5 per cent of the gross value of agricultural production in the country. Cultivated sugarcane might have originated in Oceania, most probably in NewGuinea, where some closely related forms of thick, tall canes and wild species of Saccharum spontaneum are still found. The sugarcane is an important source of sugar and related products. Sugarcane in India is being cultivated throughout the country except in certain hilly tracts in Kashmir and Himachal Pradesh. The main cane growing states are Uttar Pradesh, Uttaranchal, Bihar, Punjab and International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 01 (2018) Journal homepage: http://www.ijcmas. com
A comparison of growth patterns between non‐indigenous Halophila nipponica and the native sympatric Zostera marina on the southern coast of the Korean peninsula

The growth dynamics of two co-occurring seagrass species, Zostera marina and Halophila nipponica, were examined on the southern coast of the Korean peninsula. Zostera marina is a native dominant seagrass species in Korean coastal waters, whereas H. nipponica is a non-native tropical and subtropical species that has extended its distributional range to the temperate coastal areas of Korea. To examine the differences in the growth dynamics of H. nipponica and Z. marina, their morphology, density, productivity and biomass, as well as local environmental conditions, were monitored monthly from January 2008 to July 2009. Underwater irradiance at the study site was the highest in April 2009 and the lowest in January 2008. Water temperature ranged from 10.4°C in January 2009 to 24.8°C in September 2008. Significant differences in growth dynamics were observed between the species, due to the effect of water temperature at the study site. Density and areal productivity were the highest in April 2008 and June 2008, respectively, for Z. marina but the highest in July 2008 for H. nipponica. Leaf size, shoot height and shoot weight were the highest in July 2008 for Z. marina but the highest in August 2008 or September 2008 for H. nipponica. The productivity of both species was strongly correlated with water temperature at the study site. However, the productivity of these species was not strongly correlated with underwater irradiance or the nutrient availability of either the water column or sediment pore water. Zostera marina exhibited the ecological characteristics of a temperate seagrass, whereas H. nipponica retained the features of a subtropical/tropical seagrass, even after adapting to the temperate coastal waters of Korea.
Varietal Distributions of Stilbenes in Grape Cane of Vitis vinifera L.

Abstract Grape cane is a waste product from viticulture, which can be used as a source of stilbenes, such as resveratrol and viniferins with high antioxidant values. These stilbenes have also important healthy effects for humans. Resveratrol and viniferins are known as phytoalexins since 1977. Biomass of grape canes in annual pruning is a very valuable source of stilbenes, e.g. trans-resveratrol, and trans-ε-viniferin in dry grape canes. The main goal of this article was to compare the distribution of resveratrol and viniferins in the grape cane varieties of Laurot, Hibernal, Malverina and Chardonnay. The highest content of trans-resveratrol was found in Hibernal (6,111 mg kg−1); for trans-ε-viniferin and r2-vinifein, the highest levels were found in Malverina (2,211 and 654 mg kg−1). These compounds can be obtained from this waste product (grape cane), by easy extraction process in winemaking or food-processing industry.
Interplay between Inflammation, Coagulation And Redox Status in Early Onset Neonatal Sepsis: Insight into Prediction, Diagnosis and Management

Neonatal sepsis is a serious problem associated with high degree of morbidity and mortality in both term and preterm infants (Camacho-Gonzalez et al., 2013). Beyond being a life-threatening condition, sepsis can significantly impair neuron-developmental outcome and can progress rapidly to septic shock and multiple organ dysfunction syndrome, early diagnosis is crucial to improve survival (Klinger et al., 2010). Unfortunately, the diagnosis of sepsis may be difficult in the neonate. The earliest signs of the disease are often subtle and nonspecific, and can be easily confused with International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 03 (2018) Journal homepage: http://www.ijcmas. com
Behavioral diversity assisting obstacle navigation during group transportation in ant

Cooperative transportation behavior in ants has attracted attention from a wide range of researchers, from behavioral biologists to roboticists. Ants can accomplish complex tasks as a group whereas individual ants are not intelligent (in the context of thisstudy’s tasks). In this study, group transportation and obstacle navigation in Formica japonica, an ant species exhibiting ‘uncoordinated transportation’ (primitive group transportation), are observed using two differently conditioned colonies. Analysesfocus on the effect of group size on two key quantities: transportation speed and obstacle navigation period. Additionally, this study examines how these relationships differ between colonies. The tendencies in transportation speed differ between colonies whereas the obstacle navigation period is consistently reduced irrespective of the colony. To explain this seemingly inconsistent result in transportation speed, we focus on behavioral diversity in ‘directivity’, defined as the tendency of individual ants totransport a food item toward their own preferential direction. Directivity is not always toward the nest, but rather is distributed around it. The diversity of the first colony is less than that of the second colony. Based on the above results, a mechanical model is constructed. Using the translational and rotational motion equations of a rigid rod, the model mimics a food item being pulled by single or multiple ants. The directions of pulling forces exerted by individual ants are assumed to be distributed around the direction pointing toward the nest. The simulation results suggest that, as diversity in directivity increases, so does the success rate in more complicated obstacle navigation. In contrast, depending on group size, the speed of group transportation increases in the case of lower diversity while it is almost constant in the case of higher diversity. Transportation speed and obstacle navigation success rate are in a trade-off relationship.
Arbuscular mycorrhizal symbiosis alters plant gene expression and aphid weight in a tripartite interaction

ABSTRACT Mutualistic root associations with arbuscular mycorrhizal (AM) fungi are known to alter interactions with insects aboveground. In this study, we investigated whether root symbiosis with Rhizophagus irregularis modulates alterations in Medicago truncatula that affect pea aphid’s (Acyrthosiphon pisum) fitness. The results indicate that aphid colony weight increased after feeding on shoots of high R. irregularis-colonized plants relative to non-mycorrhizal controls. Moreover, when given a choice, aphid adults preferred high R. irregularis-colonized plants compared to non-mycorrhizal plants. Interestingly, we identified genes strongly regulated by aphid feeding in shoots (β-1,3 glucanase, thaumatin-like protein, ethylene response factor (ERF) 1, gibberellin (GA) 20-oxidase, and GA 2-oxidase), by AM symbiosis in roots (oxo-phytodienoic acid reductase, ERF1, and GA 20-oxidase), and a gene (GA 2-oxidase) exclusively induced in roots during this tripartite interaction. Our data provide novel information about changes in plant gene expression during aphid-plant-AM fungus interactions, and serve as foundation for future transcriptome studies.
Transcriptional dysregulation study reveals a core network involving the genesis for Alzheimer’s disease

Background The pathogenesis of Alzheimer’s disease is associated with dysregulation at different levels from transcriptome to cellular functioning. Such complexity necessitates investigations of disease etiology to be carried out considering multiple aspects of the disease and the use of independent strategies. The established works more emphasized on the structural organization of gene regulatory network while neglecting the internal regulation changes. Methods Applying a strategy different from popularly used co-expression network analysis, this study investigated the transcriptional dysregulations during the transition from normal to disease states. Results 97 genes were predicted as dysregulated genes, which were also associated with clinical outcomes of Alzheimer’s disease. Both the co-expression and differential co-expression analysis suggested these genes to be interconnected as a core network and that their regulations were strengthened during the transition to disease states. Functional studies suggested the dysregulated genes to be associated with aging and synaptic function. Further, we checked the evolutionary conservation of the gene co-expression and found that human and mouse brain might have divergent transcriptional co-regulation even when they had conserved gene expression profiles. Conclusion Overall, our study reveals a profile of transcriptional dysregulation in the genesis of Alzheimer’s disease by forming a core network with altered regulation; the core network is associated with Alzheimer’s diseases by affecting the aging and synaptic functions related genes; the gene regulation in brain may not be conservative between human and mouse.
Robust Estimation Of Hi-C Contact Matrices Using Fused Lasso Reveals Preferential Insulation Of Super-Enhancers By Strong TAD Boundaries

The metazoan genome is compartmentalized in megabase-scale areas of highly interacting chromatin known as topologically associating domains (TADs), typically identified by computational analyses of Hi-C sequencing data. TADs are demarcated by boundaries that have been shown to be largely conserved across cell types and even across species. Increasing evidence suggests that the seemingly invariant TADs may exhibit some plasticity in certain cases and their boundary strength can vary. However, a genome-wide characterization of TAD boundary strength in mammals is still lacking. In this study, we use fused two-dimensional lasso as a machine-learning method to first improve Hi-C contact matrix reproducibility and subsequently categorize TAD boundaries based on their strength. We demonstrate that increased boundary strength is associated with elevated levels of CTCF and that TAD boundary insulation scores may differ across cell types. Intriguingly, we also found that super-enhancer elements are preferentially insulated by strong boundaries. Presumably, genetic or epigenetic inactivation of strong boundaries may lead to loss of insulation around super-enhancers, disrupt the physiological transcriptional program and cause disease.
High-fibre high-lipid by-product pellets containing calcium oxide-treated oat hulls as a partial replacement for barley grain in finishing diets for beef cattle

Abstract: Two studies were conducted to evaluate the effects of treating oat hulls with calcium oxide (CaO) prior to inclusion in a high-lipid by-product pellet (HLP) on dry matter intake (DMI), ruminal fermentation, and total-tract digestibility (Study 1) and growth performance (Study 2). In Study 1, six ruminally cannulated heifers were used in a replicated 3 × 3 Latin square design. Study 2 used 210 steers in 21 pens in a 113 d finishing study. Dietary treatments for both studies included a barley-based control diet (CON), a diet where HLP partially replaced barley grain (NT-HLP), and a diet where HLP contained oat hulls treated with 7.5% CaO [dry matter (DM) basis; CaO-HLP]. For Study 1, DMI and ruminal pH were not affected. Apparent total-tract digestibility of DM and organic matter (OM) were greater (P < 0.05) for CON than NT-HLP and CaO-HLP. In Study 2, final body weight tended to be greater for NT-HLP and CaO-HLP than CON (P = 0.065). For CaO-HLP and NT-HLP, DMI was greater than CON (P < 0.01), but average daily gain (ADG) (2.0 kg d-1) and gain:feed (G:F) (0.16 kg kg-1) were not different. Thus, HLP can partially replace barley grain in finishing diets without negatively affecting ruminal fermentation or growth performance, but treatment with CaO has no effect.
Increased Bacterial Adherence and Decreased Bacterial Clearance in Urinary Tract Infections with Diabetes Mellitus

15 CHAPTER 1 . 17 INTRODUCTION . 17 Urinary Tract Infections: An Overview . 17 Burden of UTI: Why UTI is a Problem . 18 Risk Factors for UTI . 19 UTI and Its Clinical Presentations . 20 Urothelium and Dynamism within Its Unique Biology . 21 Diabetes Mellitus and UTI . 23 DM and Asymptomatic Bacteriuria . 24 Uropathogenic E. coli: The Most Common Causative Microorganism . 25 UPEC Virulence Factors Contributing to Development of UTI . 25 UPEC Adherence with Type 1 Fimbriae (Pili) and FimH . 29 Possible Outcomes of UTI: Intracellular Bacterial Colonies (IBCs), Quiescent Intracellular Reservoirs (QIR), Recurrent and Chronic Cystitis . 31 Repertoire of Host Defenses Against UPEC-induced UTI . 34 Primary Bladder Defenses:. 34  Tamm-Horsfall Protein (THP) in UTI: . 35 Secondary Host Response Related Defenses: . 35 -Urothelial Cell Exfoliation . 36 -Urothelial Regeneration in Response to UPEC Infection . 37 Innate Immune Response in UPEC-induced UTI . 38 UPEC Recognition and TLR Signaling . 41 Calcium-Dependent Signaling in UPEC-induced UTI . 42 Cytokines and Chemokines. 43  General Characteristics . 43  Neutrophil Recruitment Relies On Chemokines During UTI: Important Roles of MIP-2, KC, MCP-1 and IL-6 . 45 Neutrophils: The First Line Soldiers of the Host Against UTI . 49
The elementary units of heredity.

Seymour Benzer's work changed our notion of the concept of the gene, by demonstrating that the gene had a fine structure consisting of a linear array of subelements. At the time Benzer began his classic work, the concept of the gene was different from what it is today. Genes were thought to be indivisible and to be the smallest units of recombination, mutation, and function. Genes could have different allelic states, but these alleles represented the whole gene, not parts of it. In one sense, genes were thought of as beads on a necklace, the necklace being the chromosome. This picture of the gene proved to be at odds with the physical structure of DNA elucidated by Watson and Crick in 1953, which revealed the physical structure of the gene to consist of a sequence of nucleotides. Each nucleotide should be able to mutate and should also be the smallest unit of recombination. Benzer's work bridged the gap between the classic view of the gene as an indivisible unit and the physical structure of DNA. By exploiting the rII system of phage T4 and refining high-resolution genetic selection, Benzer was able to show that the subelements in the gene could mutate and recombine with one another. The smallest unit of mutation and recombination was now shown to be on the order of only a few nucleotides or less, based mainly on genetic analysis. Benzer also refined the cis-trans test for use with phage T4, and he defined the cistron as a unit of gene function, a term and concept that were used for many years. Benzer developed the use of deletions in genetic crosses, which opened up the entire field of fine structure analysis. It laid the groundwork for his subsequent studies, which defined the concept of mutational hot spots, and profoundly influenced work on mutagenesis for a generation. JEFFREY H. MILLER
Effect of Vitamin E Supplementation and High Stocking Density on the Performance and Stress Parameters of Broilers

The present study was carried out to investigate the effect of dietary supplementation with vitamin E and stocking density on the mortality, body weight gain, feed conversion ratio, European production efficiency factor, heterophil/lymphocyte (H/L) ratio and liver glutathione (GSH) and malondialdehyde (MDA) levels of broilers. In total, 570 one-dayold Vencobb 400 broiler chickens were randomly assigned to three treatments, with six replicates each. G1 served as normal control and birds were provided a normal floor space (0.0465 m2/bird from day 1 to 21 and 0.0929 m2/bird from day 22 to 42) and basal diet containing vitamin E at 70 g/ton feed (n=150). G2 and G3 birds were subjected to high stocking density (0.0279 m2/bird from day 1 to 21 and 0.0557 m2/ bird from day 22 to 42). G2 served as the high stocking density (HSD) control, birds were offered a basal diet with no vitamin E (n=210), whereas G3 birds were fed a basal diet containing vitamin E at 70 g/ ton feed (n=210). The birds were fed with feed and water ad libitum throughout the study period. The supplementation of vitamin E to the birds subjected to HSD had a positive effect on body weight gain, feed conversion ratio (FCR), European Production Efficiency Factor (EPEF), H/L ratio, and liver GSH and MDA levels with those subjected to HSD and not supplemented with vitamin E. The results of the present study indicate that the supplementation of vitamin E at 70g/ton of feed to broilers subjected to HSD could effectively reverse the negative effects of HSD, and improve broiler performance.
A probable anthropic origin of Nerium oleander L. (Apocynaceae) population in Montecristo island (Italy, Tuscany): evidence from loci polymorphism and ISSR analysis

Abstract Nerium oleander (hereafter oleander) is a Mediterranean evergreen shrub representing the only species in the genus Nerium (Apocynaceae). Oleander is widespread across the entire Mediterranean basin both as spontaneous native plant and as ornamental cultivated plant. Concerns regarding the native origin of oleander populations may arise particularly in case of ecosystem restoration interventions, when the introduction of alien species or populations should be avoided. Within this work we evaluate the origin of oleander population on the Island of Montecristo (Central Italy), aiming to provide useful information for the implementation of conservation actions on the Island. We used ISSR markers to assess its native or feralized origin by comparison with two reference populations. Our results indicate a probable anthropic origin for the population of Montecristo, which share several characters close to the anthropic reference population, such as a relatively high polymorphism detected and a close ISSR profile.