Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-Molecule Studies of Replication Kinetics in Response to DNA Damage

In response to DNA damage during S phase, cells slow DNA replication. This slowing is orchestrated by the intra-S checkpoint and involves inhibition of origin firing and reduction of replication fork speed. Slowing of replication allows for tolerance of DNA damage and suppresses genomic instability. Although the mechanisms of origin inhibition by the intra-S checkpoint are understood, major questions remain about how the checkpoint regulates replication forks: Does the checkpoint regulate the rate of fork progression? Does the checkpoint affect all forks, or only those encountering damage? Does the checkpoint facilitate the replication of polymerase-blocking lesions? To address these questions, we have analyzed the checkpoint in the fission yeast Schizosaccharomyces pombe using a single-molecule DNA combing assay, which allows us to unambiguously separate the contribution of origin and fork regulation towards replication slowing, and allows us to investigate the behavior of individual forks. Moreover, we have interrogated the role of forks interacting with individual sites of damage by using three damaging agents—MMS, 4NQO and bleomycin—that cause similar levels of replication slowing with very different frequency of DNA lesions. We find that the checkpoint slows replication by inhibiting origin firing, but not by decreasing fork rates. However, the checkpoint appears to facilitate replication of damaged templates, allowing forks to more quickly pass lesions. Finally, using a novel analytic approach, we rigorously identify fork stalling events in our combing data
Mechanisms of Selective Autophagy of Peroxisomes

Author(s): Burnett, Sarah Frances | Abstract: The study of pexophagy (selective peroxisome degradation by autophagy) is relevant to other selective autophagy pathways that are implicated in human diseases. In this dissertation I explore the signaling of pexophagy by gamma;-aminobutyric acid (GABA), the protein-protein interactions of the pexophagy receptor and its regulation by phosphorylation and the putative role of a pexophagy receptor-associated protein in pexophagy. Yeast was used as a model organism to study the physiological effects of elevated levels of the inhibitory neurotransmitter, GABA, in mammalian disorders, such as succinic acid- semialdehydyde dehydrogenease (SSADH) deficiency. GABA blocked pexophagy and mitophagy specifically in yeast, but not general, or other selective autophagy pathways and increased intracellular levels of reactive oxygen species (ROS). Mechanistically, the GABA effect was mediated by elevation of Tor1 activity and the effects of GABA could be alleviated by rapamycin, a Tor1 inhibitor. These results were extended to studies in SSADH mice, suggesting the possibility of using rapamycin and its analogues to alleviate disorders caused by elevated GABA levels. In studies involving the Pichia pastoris pexophagy receptor, Atg30, we found that this protein is regulated by phosphorylation: determining the ability of Atg30 to interact with two key proteins of the core autophagy machinery, Atg8 and Atg11, thereby activating pexophagy. We also found that the phosphorylation state of the receptor is affected by its interaction with a component, Pex3 (of the peroxisome biogenesis machinery). We describe a new domain on, and a function for, Pex3 that regulates the phosphorylation, and therefore activation, of Atg30. Finally, by examining the protein-protein interactions of the Atg30 network to better understand the pexophagy signaling process, we identified using mass spectrometry, a potential interacting protein, Rvs167, that could also be involved in pexophagy. In summary, these studies shed light on the signaling and regulation of the important selective autophagy pathway of pexophagy
Environmental Flow for the Yamuna River in Delhi as an Example of Monsoon Rivers in India

With an eye on all the natural functions of a river, the present article considers the flow of the river Yamuna in Delhi as an example of monsoon rivers in India. About 80% of the total virgin flow of Indian rivers is during the monsoon period and the remaining 20% is during the non-monsoon period. In case of the river Yamuna in Delhi, we find that at least 50% of the vir-gin monsoon (July to September) flow is required for transport of the full spectrum of soil particles in the river sediment. A similar flow is needed for adequate recharge of the floodplain aquifers along the river. For the non-monsoon period (October to June), at least 60% of the virgin flow is necessary to avoid growth of still-water algae and to support river biodi-versity. We conclude that about 50-60% of the virgin flow is necessary throughout the year to maintain the health of the river system.
Heterosis for Grain Yield and Its Component Traits in Rice

The challenge of increasing the annual rice production of the country calls for both short and long term planning encompassing genetic as well as crop management options. Among the innovative genetic options available, hybrid rice technology is practically feasible and readily adoptable (Viraktamath et al., 2010). Hybrid rice technology aims to increase the yield potential of rice beyond the level of popular high yielding varieties (HYVs) by exploiting hybrid vigour or heterosis. Hybrid rice technology particularly utilizing the Cytoplasm Genic Male Sterility (CGMS) has now been widely adopted across several countries in Asia and USA. This technology has been successfully developed and widely adopted by farmers in China during the past 25 years. During 2006, hybrids were cultivated in India in around 1 m.ha, and the National Food Security Mission (NFSM) has set a target of expanding the hybrid rice cultivation to 3 m.ha by 2011-12. Yield barrier in semi – dwarf inbred rice was broken by successful development of rice hybrids in China which yielded about 20 percent more than conventional inbred rice (Virmani et al., 1982).
A survey on family Andrenidae (Hymenoptera: Apoidea) in Gorgan County, Iran

We present the results of a survey of the andrenid bee fauna of Gorgan County, Golestan province, Iran between 2014 and 2015. The survey led to the identification of twenty-three species of the genus Andrena Fabricius and Melitturga Latreille belonging to subgenera Campylogaster (1 species), Chlorandrena (1 species), Holandrena (2 species), Hoplandrena (1 species), Melanapis (1 species), Melandrena (4 species), Micrandrena (4 species), Nobandrena (1 species), Notandrena (1 species), Plastandrena (2 species), Simandrena (1 species), Truncandrena (1 species), Zonandrena (2) and Melitturga (1 species). Of these, eight and six species are new to the fauna of Iran and Asia, respectively.
Characterization of the mitogenomes for two sympatric breeding species in Recurvirostridae (Charadriiformes) and their phylogenetic implications

Abstract Recurvirostridae is a family of Charadriiformes that displays an amazing amount of characterization at evolutionary level. The mitogenomes of Himantopus himantopus and Recurvirostra avosetta are 17,378 bp and 16,856 bp in size, respectively. Both two mitogenomes reveal the same gene order and genomic organization to that of typical avian mtDNA. The first conserved block with two interrupted poly-C and four long terminal repeats with 140 bp are present in H. himantopus control region. Phylogenetic analysis indicated that Recurvirostridae (H. himantopus and R. avosetta) has the closest relationship with Haematopodidae. We supported that Stercorariidea is a sister group to (Alcidae (Laridae, Sternidae)), and suggested that the status of Larus vegae should be further investigated.
Impact of Certain Heavy Metals on Histology and Physiology of Fishes: Interpretative Study

Heavy metals, as essential or non-essential ones, are present in aquatic systems at different levels. The over limited concentration of metals has a negative effects as physiological, histological and morphological patterns. The levels of contaminants in fish are of particular interest because of potential risk to human consuming them. Heavy metals bring about their effects as single or mixture on organs or tissues of fish. The influence starts at cellular or molecular level, then being at population level, particularly through early stages of development, and may result in species extinction, due to tendency towards accumulation and reduced biodegradation. The liver, gills and kidney seem to be the most interested organs included in current studies due to their sensitized feature towards metal impact. Fishes could be employed as biomarker indicator for environmental contamination, in particular with long term monitoring, and with trace levels of pollutants. Overlap between different factors, along with integrated responses must be considered in determination of heavy metals impact, in complementary of water quality parameters; and so, standardized methods being necessary for comparison among variable results obtained. This study is an interpretative effort of some aspects included in toxicity of five heavy metals for fish species.
study for intestinal parasites among children in AL-mahmoudyia area / Baghdad province

This study was carried out to find the infection with intestinal protozoa such as ( Entamoeba histolytioca , Giardia lamblia ) and Enterobius vermicularis in children as diarrhea causative in AL-mahmmodia public hospital for a period from the beginning of June 2010 to the end of August 2010 . out of (332) stool samples there were (296) positive sample which represented (57.8%) these sample were examined by using direct normal saline method , Iodin solution and sedimentation method . the percentage of infection with intestinal parasite as followed Entamoeba histoloytica (41%) , Giardia lamblia (34%) ,and Enterobius vermicularis (25%) . These results considered high in compression with other studies carried out in Iraq . The infection percentage in male was (57%) which in female was (43%) . July was the highest month in compression with may , June –respectively .
Estimação de valores genéticos para codornas europeias em função dos níveis da relação treonina: lisina da dieta: do nascimento aos 21 dias de idade

This research was carried out to evaluate the sensitivity of breeding values of body weight and carcass traits in two lines of European quails (LF1 and LF2) to changes in the environment gradient (levels of threonine: lysine ratio of diets) from hatch to 21 days of age in two lines LF1 and LF2 using Random Regression Models with different classes of residual variance. Records are from 915 quails of line LF1 and 839 of line LF2 belonging to the Breeding Improvement Program of Universidade Federal dos Vales do Jequitinhonha e Mucuri. Live body weight and weights and yields of carcass, breast, and thigh and drumstick were measured. The sensitivities of breeding values to changes in threonine: lysine ratios (genotype x environment interaction) of diets were obtained by random regression models (reaction model) using the WOMBAT program using the Restricted Maximum Likelihood principle. Model considering two classes of residual variance showed the best goodness of fit. The Reaction Norms analyses indicated changes in the ranking of breeding values for both lines suggesting quails selected in one level of threonine: lysine ratio will not express all their genetic potential if fed different threonine: lysine ratio diets. This behavior indicates sensitivity of breeding values to changes in the nutrition characterizing the genotype by environment interaction. The prediction of breeding values must be performed using the same level of threonine: lysine ratio in diet the quails will be fed in the production system.
The true cost of partial fencing: Evaluating strategies to reduce reptile road mortality

One of the deadliest roads in North America for species at risk fragments a marsh-lake ecosystem. To reduce road mortality, stakeholders installed >5 km of exclusion fencing along a southwestern Ontario, Canada, causeway in 2008–2009. Between 2012 and 2014, 7 culverts were installed to provide safe crossings. We evaluated the success of these mitigation strategies by 1) comparing results of road surveys conducted 5 years before and 5 years after fencing installation; and 2) monitoring use of culverts by turtles using motion-activated cameras at culvert openings and stationary antennas placed to detect movements of passive integrated transponder (PIT)-tagged turtles (68 Blanding's turtles [Emydoidea blandingii] and 30 spotted turtles [Clemmys guttata]). We also radio-tracked 30 Blanding's turtles to measure culvert use in relation to home ranges. Turtle and snake abundance was 89% and 53% lower, respectively, in completely fenced road sections than in unfenced sections; abundance was 6% and 10% higher, respectively, between partially fenced and unfenced sections. After mitigation, locations where we found reptiles on the road were associated with fence ends, underscoring the importance of fence integrity and ineffectiveness of partial fencing as a mitigation strategy. We confirmed use of culverts by Blanding's turtles, northern map turtles (Graptemys geographica), snapping turtles (Chelydra serpentina), and midland painted turtles (Chrysemys picta). Through radio-tracking, we determined that male and female Blanding's turtles home ranges overlapped with different segments of the causeway. We recommend that stakeholders emphasize ensuring fence integrity and continuity, limiting impact of edge effects, and conducting a comprehensive monitoring program. © 2017 The Wildlife Society.
Serological Survey of Rabies Virus Infection among Bats in Brazil

Rabies is a disease caused by a virus belonging to the family Rhabdoviridae, genus Lyssavirus (RABV), and is characterized as a progressive and acute encephalitis that presents high lethality. Between 2002 and 2012, 2149 wild animals were found positive for RABV in Brazil where 79% were associated with the aerial cycle of the disease. As part of the active surveillance of rabies in Brazil, the objective of this study was to investigate the presence of RABV infection in bats captured in two different regions of Brazil. Bat specimens were collected in (i) the metropolitan region of Rio de Janeiro city, (ii) Igrapiuna Municipality, Bahia State, and (iii) Serra do Tabuleiro State Park (PEST) in Santa Catarina State. Forty-four bats from the two first areas were tested for RABV at Institute Jorge Vaitsman (IJV), reference laboratory for rabies in Rio de Janeiro State. Of the individuals captured and sent for the diagnosis of rabies, a total of 15 were identified as being hematophagous, all of them belonging to the species Desmodus rotundus . Twenty-four individuals were considered as frugivorous, four as insectivores and one individual ( Lonchophylla peracchii ) identified as having a pollen/nectar feeding habit. All specimen sent to RABV diagnosis presented negative results. Considering the active surveillance for RABV in Brazil, studies of fauna survey with serological characterization are important in the strengthening of epidemiological surveillance and protection of human life.
Response surface modeling of natural alizarin production in hairy root cultures of Rubia tinctorum L. upon elicitation with fungal mycelia

The roots of Rubia tinctorum L. , the common madder contain natural red dye known as alizarin. In the current study, central composite design of response surface methodology was employed for modeling of fungal elicitor treatment on natural alizarin production in uniform hairy root cultures of common madder in liquid 1/2 B5 medium. Upon fungal elicitation assay, using two fungal mycelia elicitors ( Aspergillus niger and Bipolaris maydis ) at three different times (0, 12 and 24h), the production of alizarin was determined. According to the results, after 24h; modeling and optimization conditions, including combination of 2 % of both elicitors for alizarin production equal to 10.0 mg.g -1 DW was evaluated. Optimal process parameters have been determined by using a high desirability value of 1.00 in Design-Expert ® software. Our results, altogether, offer a promising method regarding to the improvement of the alizarin production, as a pivotal natural dye in industrial applications.
The Site of Damage in Amoebae Exposed to X-Rays

The technique of nuclear tranafer waa used to study the extent to which X-rays damage nuclei and cytoplasms of Amoeba proteus . Results showed that cytoplasm was directly damaged by the radiations. Cytoplasmic damage with doses below 280,000 r was reversible, though damaged cytoplasm could lethally damage normal nuclei. Damage with doses above 300,000 r caused lethal damage and death occurred without division in 0-3 days. Damage to nuclei was probably a combination of a direct action of the radiations and exposure to reversibly damaged cytoplasm. Nuclei were 2.4 times so sensitive as cytoplasms, the LD 50 doses being approximately 120,000 r for nuclei and 290,000 r for cytoplasm. Death due to nuclear damage generally occurred without division within 3 to 6 weeks. Nuclear damage cannot be interpreted in terms of the ‘target’ theory.
Characterization of paired Cas9 nickases induced mutations in maize mesophyll protoplasts

Targeted genome modifications are important for both fundamental and applied research. The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats / CRISPR-associated protein 9) technology has been successfully used in various plant species with high efficiency. Approaches with paired Cas9 nickase enhance the specificity of the CRISPR/Cas9 system by using guide RNA pairs to create two staggered single strand breaks on complementary DNA strands. Here we used maize mesophyll protoplasts as a transient test system and demon- strated the mutagenic potential of Cas9 nickases. Although we found activity for all the three different guide RNA pairs tested, their efficiency varied considerably. Characterization of the modification events revealed a high ratio of large deletions as well as insertions of donor DNA fragments. By the use of the maternally expressed in embryo 1 gene (mee1) as model target sequence, we could demonstrate that transcriptionally inactive and methylated genomic loci are practical targets of Cas9 nickase. The high specificity of Cas9 nickase approaches might provide advantage for genome modifications of certain loci in the complex and highly repetitive maize genome.
Grey matter volume in first-episode adult major depressive disorder with different age-onset

Objective To compare the whole brain grey matter volume (GMV) in first-episode major depressive disorder (MDD) with different age-onset. Methods 101 first-episode, drug-naive depressive patients were divided into three groups on the basis of age of MDD onset: 32 patients with early adult onset depression (18-29 years, EOD), 39 patients with middle age onset depression (30-44 years, MOD), and 30 patients with late adult onset depression (45-60 years, LOD). A total of 91 healthy controls (HCs),well matched by age and gender, were also collected into three groups: the 32 young HCs (18-29 years), the 30 middle-aged HCs (30-44 years), and the 29 late onset HCs (45-60 years). Magnetic resonance imaging was conducted on all subjects. The voxel-based morphometry (VBM) approach was employed to analyze the images. Results Compared to young HCs, the EOD group showed decreased GMV in the left thalamus, right lingual gyrus, right cuneus and cerebellum Ⅵ (t=-4.26--3.58, all P<0.01) , and increased GMV in right angular gyrus (t=4.45, P<0.01) . Compared to middle-aged HCs, the MOD group showed decreased GMV in the right middle frontal gyrus (t=-3.62, P<0.01) . Compared to late onset HCs, the LOD group exhibited decreased GMV in the right middle temporal gyrus, right lingual gyrus, left fusiform gyrus and bilateral cerebellum Ⅸ (t=-4.87- -3.91, P<0.01) , but an increased right amygdala (t=3.36, P<0.01) . The full factorial analysis revealed that the right middle frontal gyrus (t=7.40) and right cerebellum Crus1 (t=7.20) were significantly different among the three patient subgroups (P<0.005,unadjusted) . The whole brain GMV of EOD and MOD subgroups positively correlated with the symptom severity (r=0.553-0.641, P<0.01) , while the whole brain GMV of LOD subgroup negatively correlated with their symptom severity (r=-0.626, P<0.01) . Conclusions Individuals with MDD may have the GMV reduced in the limbic-cortical-striatal-pallidal-thalamic (LCSPT) circuit. The whole GMV changes are different in MDD patients with various age-onsets. The findings may suggest different pathophysiological characteristics among first episode MDD patients with different age-onset. Key words: Depressive disorder; Magnetic resonance imaging; Age of onset; Grey matter volume
Exploring the murky world of the sevengill shark, Notorynchus cepedianus, in southern New Zealand

i Acknowledgements . iii List of Figures . vii List of Tables . viii Chapter One: General Introduction . 1 1.1 Elasmobranchii . 1 1.2 Threats to Shark Populations . 1 1.3 Role of Shark Populations in Coastal Ecosystems . 2 1.4 Biology and Distribution of the Sevengill Shark . 4 1.5 Sevengill Sharks in New Zealand . 7 1.6 Research Objectives . 8 1.7 Thesis Outline . 8 Chapter Two: Distribution . 10 2.
COMPARISON OF ANTIBIOTIC RESISTANCE PATTERNS BETWEEN LABORATORIES IN ACCRA EAST, GHANA

Antibiotic resistance is increasing rapidly and developing countries are the worse affected since they provide conditions and practices that support the development and spread of resistant microbes. For better health policy on antibiotic use a national surveillance program is needed to provide baseline data from different settings. This study determines the distribution of antibiotic resistant microbes in two different laboratories and compares the results using statistical methods to ascertain if there is a variation due to human factors. Patients attending two laboratories in east Accra were recruited and samples obtained from them were cultured for microbial growth. Microbes isolated were characterized and their sensitivity to different antibiotics tested. A total of 513 samples were collected from the patients who were mostly females; 68%. The cultures that were mostly infected were urine (331), wound (116), HVS (78) and ear (26). There were few cases of throat, blood, uterus cultures but were all infected. Microbial isolates common in the different laboratories included S. aureus (96), E. coli (90), Pseudomonas aeruginosa and Proteus spp. Microbes isolated in the different laboratories were Salmonella typhi, Shigella spp. and Streptococcus pneumonia. Microbial isolates were found resistant (over 65%) to the antibiotics ampicillin (71% and 95%), cotrimoxazole (68% and 75%) and tetracycline (70% and 80%) and moderately resistant to gentamycin (29% and 23%), erythromycin (39% and 36%) and streptomycin, and sensitive to ceftazidine and minomycin. Statistically the results from the different laboratories were found to be similar hence having the same trend. The importance of incooperating a statistical method in national surveillance program to compare results from different settings is discussed.