Miracle-dz/UniFAR-FTUs huggingface dataset:
Enrichment of Brine Shrimp (Artemia franciscana) Nauplii with Potential Probiont Strains, Bacillus JAQ04 and Micrococcus JAQ07

The study of bacterial interaction with crustaceans used in aquaculture, such as brine shrimp Artemia is gaining importance. Thus, this study aims to evaluate the effect on survival, growth and development of Artemia nauplii enriched with potential probionts JAQ04 and JAQ07 in gnotobiotic condition. Brine shrimp lethality concentration assay (LC50) was carried out under monoxenic condition to identify the cytotoxity of these probionts. After decapsulation of the cyst, the Artemia nauplii were preincubated with high concentration of probiont Bacillus JAQ04 and Micrococcus JAQ07 at concentration of 10 CFU ml. These bacteria were previously isolated from juvenile of Tiger grouper (Epinephelus fuscoguttatus). Pathogenic and toxicity assay demonstrated that both probiont strains were not pathogenic to the host. Significant survival (p<0.05) was observed in Artemia nauplii enriched with Bacillus JAQ04 (73%) and Micrococcus JAQ07 (63%) as compared to the control (43%). This study also demonstrated that potential probionts significantly improve the growth of the Artemia nauplii as demonstrated by higher body length when compared to the control (p<0.05). Therefore, it is suggested that Bacillus JAQ04 and Micrococcus JAQ07 were not harmless, and had significant effect on the growth and development of Artemia.
Wintering ecology and nomadic movement patterns of Short-eared Owls Asio flammeus on a subtropical island

ABSTRACT Capsule: Short-eared Owls Asio flammeus showed a female-biased sex ratio in their southernmost wintering grounds in Oriental Asia. This is the first description of a nomadic movement pattern in this area. Aims: To investigate the sex ratio, movement patterns, home range size and habitat preference of non-breeding Short-eared Owls in subtropical Taiwan. Methods: Eleven Short-eared Owls were radio tracked following trapping and transportation away from an airport as part of the management of bird-strike risk for aeroplanes. Results: Our results indicated a female-skewed (75%) sex ratio for Short-eared Owls wintering in Taiwan. The owls demonstrated a nomadic behaviour by showing a repetitive pattern of high roosting site fidelity in the short term, followed by a long-distance movement to a different discrete area. Grasslands were commonly used as day-roosting sites but agricultural habitats were favoured at night. Conclusion: Compared to on the breeding ground, the wintering owls exhibited a much larger home range size and exploit more dispersed patches of suitable habitats. These results revealed a notable conservation issue for the wintering owls, especially in the degraded and partially developed landscapes in subtropical countries.
Chemical Composition and Bactericidal Activities of the Leaf Essential Oil of Eucalyptus maculata Hook

This study examined the phytochemicals and medicinal potentials of the leaf essential oil of E. maculata from Nigeria. The essential oil was extracted by hydro-distillation technique and was analysed for various chemical composition using GC-MS. The essential oil was also screened for its antimicrobial activities against multi-drug resistant gram-positive and gram-negative bacteria using the agar well diffusion method. The GC-MS analysis revealed that s-citronellol (18.5%), s-pinene (9.4%), 2,6-dimethyl-2,6-octadiene (8.3%), a-pinene (7.1%), 2,6-dimethyl-1,3,5,7- octatetraene (6.7%), and citronellyl acetate (6.0%) were the major compounds in the leaf essential oil. The essential oil exhibited strong antibacterial activities against most of the tested bacteria, with diameters of inhibition zones ranging from 15.0-30.0 mm. The leaf essential oil of E. maculata is a possible alternative antibiotic drug for treatment of disease caused by multi-drug resistant bacteria.
Biocontrol activity of the extract prepared from Zingiber zerumbet for the management of rhizome rot in Zingiber officinale caused by Pythium myriotylum

Abstract Zingiber zerumbet Smith or wild ginger is remarkable for its inherent resistance to Pythium spp. , which cause soft rot disease in Zingiber officinale Rosc. In the present study, various concentrations of extract prepared from Z. zerumbet were screened for its activity against Pythium myriotylum. Microscopic observation of P. myriotylum in presence of Z. zerumbet extract has confirmed the complete lysis of pathogen within 10 h. However, the same treatment with Z. officinale extract was found to have partial antifungal effect even after 24 h due to inability of its metabolites to prevent the growth of P. myriotylum. Due to the antifungal activity, extract from Z. zerumbet was subjected to GC–MS and LC-QTOF-MS which has identified Zerumbone with m/z 219 as the major compound. Further, in vivo study and the subsequent microscopic analysis have confirmed the applicability of extract from Z. zerumbet as a phytomedicine to control rhizome rot in ginger.
Morphological and Biochemical Profiles of the Gonadal Cycle in the Sea Urchin Paracentrotus lividus: Wild Type vs. Bred

Paracentrotus lividus gonads represent a valued gourmet delicacy, particularly appreci-ated in Europe and in Japan. Their commercial value is generally associated to their size, freshness, colour and texture. Diet, gametogenesis and environmental condi- tions have a marked influence, promoting the indispensable mechanisms of synthesis, selective storage and mobilization of the bioactive compounds, as lipids, proteins and carbohydrates of gonads in order to obtain nutrients. The objective of this work is to compare the morphological and biochemical profiles of reproductive life cycle of the gonads of adult P. lividus in its marine natural environment and adult captured sea urchins breeding into a fish aquaculture system. The reproductive cycle of male and female wild and breeding P. lividus was characterized during 1 year by analys ing variations of the gonadal content of lipids, proteins and carbohydrates of animals captured at four different locations of the south-western coast of Salento, Italy, with the animals grown in a fish farm and fed with four different types of diet. The gonadal and repletion indexes were determined before the specimen dissection for evaluation of sex, development stages and physiological aspects. Gonads were processed for his tological and biochemical analysis. The gonadal content of lipids, proteins and carbo hydrates was performed by the gas chromatography-mass spectrometry (GC-MS) and by spectrometry, respectively. in eggs for larval development and survival [ 50]. to wild
Changes in Fruit Quality and Carotenoid Profile in Tomato (Solanum lycopersicon L.) Genotypes under Elevated Temperature

Tomato (Solanum lycopersicon L.) is a rich source of carotenoids, especially lycopene, and is affected severely by high temperatures under tropical conditions. To study the effect of elevated temperature on lycopene content and other quality parameters, five tomato genotypes, viz., RF4A, Abhinava, Arka Saurabh, IIHR 2195 and Arka Vikas, were grown in a temperature gradient tunnel (TGT) facility under 33.4 and 35.4°C temperature conditions. Fruits were analyzed for total carotenoids, total phenols, total flavonoids, total sugars, TSS, acidity, Vitamin C besides carotenoids profile (β-carotene, lycopene, phytoene and luteoxanthin content). Results revealed that all the quality parameters studied were superior at 33.4°C, compared to 35.4°C in all the genotypes. 'IIHR 2195' recorded highest total phenols (479.28mg/100g dw), total flavonoids (70.27mg/100g dw), ferric reducing antioxidant potential (FRAP) (310.53mg/100g dw), diphenyl picryl hydrazyl (DPPH) radical (487.89mg/100g dw), Vitamin C content (292.25mg/ 100g dw) and total sugars (606.88mg/g dw) at 33.4°C and at 35.4°C. 'RF4A' and 'Arka Vikas' were found to have better total carotenoids content and lycopene at higher temperature than other genotypes. 'Arka Vikas' recorded highest total soluble solids (TSS) (8.9°Brix) and acidity (0.80%) at 35.4°C. Higher TSS and acidity were recorded at 35.4°C than at 33.4°C in all the five genotypes. Genotypic variation was observed in the above stated biochemical parameters in response to elevated temperatures.
Aminergic modulation of hippocampal synaptic plasticity in health and disease

Synaptische Plastizitat ist ein zellularer Prozess, der Lernen und Gedachtnisbildung ermoglicht. Abhangig von Alter und Gesundheitszustand konnen das Erwerben von Gedachtnis sowie die Stabilitat vom Erlernten variieren. Hier spielen Neuromodulatoren eine wichtige Rolle. In dieser Studie wurde der Einfluss spezifischer Rezeptor-Subformen auf synaptische Plastizitat im Gyrus Dentatus der Ratte untersucht. In jungen Ratten (2-4 Monate) beeinflusst der serotonerge 5-HT\(_4\) Rezeptor nur schwach die Exprimierung von Langzeit Potenzierung (LTP). Aktivierung der beta-adrenergen oder dopaminergen Rezeptoren der D1-Familie vereinfacht die Entstehung von LTP. Diese Eigenschaft geht in alteren Tieren (8-14 Monate) verloren. In beta-amyloid injizierten (Alzheimer Model) Tieren geht zudem LTP-Exprimierung verloren. Koaktivierung der beta-adrenergen und dopaminergen Rezeptoren, durch ein Verhaltensprotokoll oder pharmakologisch, ermoglicht erneut eine leichtere Entstehung von LTP in beiden Kohorten.
Human Scalp Hair Follicles Express Prostaglandin E2 Lipid Mediator and Receptors For Pge2

The hair follicle, which is a unique characteristic of the mammals, plays a vital role in a personal appearance and self-image confidence throughout the life and hair growth disorders cause serious psychological distress. The common pathological abnormalities are abnormal hair loss (alopecia) and excessive hair growth (hirsutism), but they are poorly controlled. Therefore an improved treatment for these disorders requires a better understanding of the mechanisms regulating hair growth. Prostaglandin analogues such as latanoprost, which are used for glaucoma treatment, also makes eyelashes grow longer. The mechanism of action by which these drugs stimulate eyelash hair growth is poorly understood. To determine whether PGE2 lipid mediator and receptors for PGE2 (EP2) are expressed in scalp hair follicle, electrospray tandem mass spectrometry coupled to liquid chromatography (LC/ESI-MS/MS), RT-PCR and Immunohistochemistry were carried out. Human scalp skin from non-balding areas (occipital and parietal) was obtained from healthy donors undergoing elective cosmetic surgery; with appropriate ethical approval. Isolated scalp hair follicle expresses PGE2 lipid mediator genes and protein for EP2. So isolated human scalp follicles contain PGE2 lipid mediator and express genes and protein for EP2 indicating that PGE2 may play a vital role in regulating hair growth, which may lead to a new method for hair loss treatment.
Microbial Evolution and the Rise of Oxygen: The Roles of Contingency and Context in Shaping the Biosphere through Time

We are shaped by our environment, but we then shape it in turn. This interplay between life and the Earth, and how these interactions have shaped both parties through time, is the heart of the discipline of geobiology. My research is fundamentally motivated by a desire to understand how life and the Earth have changed together through time to reach the state that they’re at today, and to understand from this history how the coevolution of planet and life may be different on other worlds. The focus of my work has been on how the structure and productivity of the biosphere across time and space has been shaped by the metabolic opportunities provided by the environment—as a result of both biotic and abiotic factors—and the metabolic pathways that are available to life, as a result of evolutionary contingency in the evolution of pathways and their inheritance and horizontal transfer. The biosphere on Earth today is incredibly productive due to the coupled dominant metabolisms of oxygenic photosynthesis and aerobic respiration, yet these can’t always be assumed to have been present—considering life more broadly, for instance in the context of the early Earth and other planets, we have to grapple with how evolutionary contingency and planetary environments interact to constrain the metabolic opportunities and rates of productivity available to the biosphere. In this dissertation, I broadly consider how the size and structure of Earth’s biosphere has changed through time as surface environments evolve and metabolic innovations accumulate. These investigations make use of information gleaned from the rock record of the early Earth, as well as the biological record of the history of life as preserved in the genomes, biochemistry, and ecology of extant organisms. These coupled records provide opportunities for constraining estimates of the opportunities for life throughout Earth history and elsewhere in the universe.
Peptide Fingerprinting Using Single-Molecule Fluorescence

Proteins belong to the most important molecules in living organisms. They function as messengers, transporters and catalysts, and provide cells and tissues with structure. The expression profile of proteins is rich in information, which can be used, for example, in diagnosing diseases. Therefore proteomics, the large scale study of proteins, can give us valuable information on molecular pathways and state of health. As a result, proteomics has the potential to transform personalized medicine. Recent advances in mass spectrometry have led to a draft of the human proteome. With current mass spectrometry based techniques, these types of large scale studies remain an enormous effort. Therefore, there is a great need for breakthrough technologies to push proteomics from fundamental research into the clinic. Genomics has benefitted from fast and inexpensive emerging single-molecule techniques. We envision similar effects for single-molecule protein sequencing. In this thesis we present our technology that will allow us to analyze protein expression profiles of samples as small as a single cell with large dynamic range. Back in 2011, when this project was initiated, there was hardly any literature available on this topic. However, the past years more research groups openly shifted their focus to single-molecule protein sequencing. In Chapter 1, we give an overview of recent efforts to establish single-molecule protein sequencing. The foremost reason for the absence of highly sensitive and high-throughput protein sequencing techniques is the complexity of primary protein structures compared to DNA/RNA molecules. Where DNA and RNA consist of four unique building blocks, proteins are built from 20 distinctive amino acids. Independent of the read out method of choice, this requires the detection of 20 distinguishable signals. A non-trivial challenge. Fortunately, a limited number of proteins occur compared to the theoretical number that could be created using 20 unique building blocks. While the exact number of protein coding genes in the human genome is still under debate, the number is believed to be roughly 20,000, resulting in a number of protein products that is finite. This, together with protein databases such as UniProt, allows for an alternative way of identifying protein sequences. Rather than detecting every single element, as is essential for DNA sequencing, we choose to focus on detecting the sequence of a subset of elements.
Mechanistic studies of two phosphatase enzymes involved in inostiol metabolism

Inositol-containing molecules and inositol phosphatases have diverse roles in cells. One of the inositol phospholipids phosphatases, PTEN (Phosphatase and Tensin Homolog deleted on Chromosome Ten), is a tumor suppressor and antagonizes the PI3K signaling pathway by dephosphorylating PI(3,4,5)P3 at the 3 position of the inositol ring. In testing predictions of a molecular dynamics simulation, a hydrophobic site adjacent to the active site on PTEN was identified and verified by protein kinetic studies. This hydrophobic site plays an important role in substrate and substrate analogue binding with one of residues, Arg47, critical for PTEN phosphatase activity. Mutations of Arg47 reduced enzyme activities toward both the short-chain substrate as monomers and micelles and long-chain phospholipid presented in vesicles. PI(4,5)P2, the product of PI(3,4,5)P3 dephosphorylation, activates PTEN. Studies by others suggested this occurred when the product was bound to the N-terminal region of the protein (not visible in the crystal structure). However, no direct proof of this existed. The effect of PI(4,5)P2 on PTEN enzyme activities in different substrates systems was studied. P NMR was used to probe the spatial location and functional role of PI(4,5)P2 binding site. The fixed field P NMR and high resolution field cycling P NMR results indicated there are discrete sites for both substrate and activator lipids on PTEN, and both of sites are spatially separate from the hydrophobic site. The active site, adjacent hydrophobic site, and N-terminal activator binding site worked synergistically to regulate PTEN interacting with the membrane. Thermophilic and hyperthermophilic archaea and bacteria thrive at high temperatures. They often accumulate small organic molecules, called compatible solutes or osmolytes, to protect proteins from thermal denaturation. The thermoprotection mechanism of compatible solutes was explored using inositol monophosphatase (IMPase) from Archaeoglobus fulgidus as the model protein. The protective effect of unusual compatible solutes, di-inositol-1,1’-phosphate (DIP) and diglycerol phosphate (DGP), as well as common compatible solutes glutamate and other anions, on the IMPase thermostability was studied. Specific binding sites of glutamate ions on the IMPase were identified by crystallography and field cycling NMR. However, mutations at these discrete binding sites did not eliminate the thermoprotection, but reduced the thermal stability (Tm) of the protein. Our results indicate the specific binding of osmolytes to the protein exists, but they do not account for the thermoprotection.
World University Rankings and Subject Ranking in Engineering and Technology (2015-2016):A Case for Greater Transparency

There has been a great deal of interest in the ranking of academic and research universities across the world, especially in developing economies including India. Ranking lists are periodically released by many for-profit agencies, including Times Higher Education (THE) and Quacquarelli Symonds (QS). All universities vie for a ranking in them, and wish to be listed in the top 100. These ranking exercises are based partly on hard data and partly on the perception of the university. Ranking helps students choose universities and funding agencies supporting research, and add to the overall reputation of universities. Lack of transparency in providing access to the critical data used in the ranking exercise for public scrutiny/verification has drawn intense criticisms on the accuracy and credibility of the process. In this paper, fallacy of recent ranking exercise carried out by THE is illustrated with a study of two institutions in Asia.
Coccidiosis in Awassi, Romanov, Charollais and Suffolk sheep breeds during the winter and summer seasons in Jordan

Subclinical infection of coccidiosis in adult sheep cause loses in animal production especially for animals under stress including susceptible animals imported to a new environment. Local breeds usually are adapted to local environmental stress and more resistant to local parasite species/strains than exotic breeds. In this study, we investigate; coccidia infection rate, oocyct output and differential blood cell count in four groups of local Awassi sheep and three exotic breeds (Romanov, Charollais and Suffolk) in the Summer and Winter seasons. About 63.4% of animals were infected with Eimeria spp. The highest infection rates were in Romanov (81.5%), and in winter (P<0.05) than in summer for all breeds. The lowest infection rate and oocyct per gram (OPG) were recorded for Awassi breed during the summer season (11.1%). A negative correlation (P <0.05) between the OPG and lymphocyte (L) blood level was detected; while a positive (P <0.05) correlation with neutrophil (N) was only detected in the Awassi breed. Repeatability estimates for OPG were 0.32, 0.22, 0.30 and 0.42 for Awassi, Charollais, Romanov and Suffolk breeds, respectively. The N/L ratio estimates of repeatability were ranged between 0.04 in Charollais to 0.25 in Awassi breed. The current results demonstrated within and between breeds variations that can be utilized in genetic selection and breeding programs to increase genetic resistance to coccidiosis.
Review of Tarphiomimus species of New Zealand (Coleoptera: Zopheridae)

ABSTRACT The endemic New Zealand beetle genus Tarphiomimus Wollaston is revised with two new species described. A total of five species are included in the genus: Tarphiomimus indentatus Wollaston, 1873; T. wollastoni Sharp, 1882; T. triregius sp. nov.; T. miyakadoi sp. nov.; and Tarphiomimus undosus (Broun) comb. nov. which is transferred from the genus Pristoderus Hope. A single specimen from the Chatham Islands is very similar to T. triregius, but further study and material is needed to evaluate its species status. All Tarphiomimus are described and illustrated and a key to species is provided. http://zoobank.org/urn:lsid:zoobank.org:pub:842D49C4-C75E-458E-9897-C3045ABC9C80
Epigenetic Regulation of Mammalian Cardiac Myocyte Cell Cycle

Author(s): El-Nachef, Danny Omar | Advisor(s): MacLellan, William Robb; Vondriska, Thomas M | Abstract: Cardiac myocyte (CM) proliferation is required for the heart regeneration seen in lower vertebrates and neonatal mammalian injury models. However, mammalian CMs stop proliferating soon after birth and subsequent heart growth comes from hypertrophy, limiting the adult heart’s regenerative potential after injury. The molecular events blocking CM proliferation in the adult heart remain poorly understood. We hypothesized repressive epigenetic mechanisms are responsible for the stable silencing of cell cycle genes in adult CMs (ACMs). Studies from our lab and others have suggested trimethylation of Lysine 9 of Histone H3 (H3K9me3) and H3K27me3, histone modifications associated with heterochromatin, are associated with permanent cell cycle exit. To test if depleting these repressive methylations in ACMs could relieve the silencing of cell cycle genes, we developed an adenoviral-gene-transduction model for combined H3K9me3- and H3K27me3-depletion in vitro. We tested this hypothesis in vivo using a transgenic mouse model where H3K9me3 is specifically removed by histone demethylase KDM4D in CMs. Loss of H3K9me3 in CMs disrupts ACM cell cycle gene silencing preferentially and results in increased CM cycling. Normalized heart mass was increased by postnatal day 14 (P14) and continued to increase until 9-weeks of age. ACM number, but not size, was significantly increased in BiTg hearts, suggesting CM hyperplasia accounts for the increased heart mass. Challenging H3K9me3-depleted hearts with a hypertrophic growth signal stimulated ACM mitotic activity. Thus, we demonstrated that H3K9me3 is required for cell cycle gene silencing in ACMs and depletion of H3K9me3 allows hyperplastic growth in vivo. To gain mechanistic understanding of the observed proliferation-competence we examined global chromatin structure and loci-specific DNA accessibility in H3K9me3-depleted and control ACMs. Combined with DNA methylation bisulfite sequencing (DNAme-Seq) and chromatin-immunoprecipitation (ChIP) studies, these data suggest a model where cell cycle genes have a unique chromatin signature, where the gene bodies are heterochromatinized and the gene promoters are regulated by canonical cell cycle transcription factor pathways that are modulated by H3K9me3.