Miracle-dz/UniFAR-FTUs huggingface dataset:
Repair of base-base mismatches and four-base loops formed during meiotic recombination in S. cerevisiae

Jana E. Stone Repair of Base-Base Mismatches and Four-Base Loops Formed During Meiotic Recombination in S. cerevisiae (under the direction of Thomas D. Petes) DNA mismatches are generated when heteroduplexes formed during recombination involve DNA strands that are not completely complementary. I used tetrad analysis in Saccharomyces cerevisiae to examine the meiotic repair of a base-base mismatch and a four-base loop in a wild-type strain and in strains with mutations in genes implicated in DNA mismatch repair. Efficient repair of the base-base mismatch required Msh2p, Msh6p, Mlh1p, and Pms1p, but not Msh3p, Msh4p, Msh5p, Mlh2p, Mlh3p, Exo1p, Rad1p, Rad27p, or the proofreading exonuclease of DNA polymerase δ. Efficient repair of the four-base loop required Msh2p, Msh3p, Mlh1p, and Pms1p, but not Msh4p, Msh5p, Msh6p, Mlh2p, Mlh3p, Exo1p, Rad1p, Rad27p, or the proofreading exonuclease of DNA polymerase δ. I find evidence that a novel Mlh1p-independent complex competes with an Mlh1p-dependent complex for the repair of a four-base loop. I also found that the frequency and position of local double-strand DNA breaks affect the ratio of mismatch repair events that lead to gene conversion versus restoration of Mendelian segregation. Mutations in POL30, which encodes PCNA (proliferating cell nuclear antigen) in S. cerevisiae, increase the rate of mutations in vegetative cells.
Investigations sur les mammites subcliniques dans les élevages caprins laitiers au Maroc

Pour déterminer la fréauence et la cause des mammites subcliniaues caprines, une investigation basée sur le diagnostic bactériologiqûe a été réalisée sur 3 groupes de troupeaux laitiers (A, B et C) constitués resnectivement de la race Saanen. la race Amine et une race locale. Draa. Parmi les 287 prélèvements analysés, 98 trayons (soit 34 p. 100) se sont révélés infectés. Les staphylocoques à coagulase négative sont les alus fréauemment isolés (43 D. 100 de l’ensemble des germes) suivis de Bac~llus spp. (27 p. 100) *et de Staphylococcus aureus (13 p. 100). Les autres bactéries isolées étaient Pseudomonas spp. (6 p. lOO), Streptococcus spp. et coliformes (5 p. 100) et MicroCO~CUS spp. (2 p. 100). Aucun mycoplasme n’a été isolé. L’étude épidémiologique a mis eu évidence l’effet significatif du mode de conduite de l’élevage, de la race, du numéro et du mois de lactation.
THE EXPRESSION AND PURIFICATION OF OCTA-ARGININE APOPTIN AND ITS ABILITY TO KILL CANCER CELLS

Objective: In this research, chicken anemia virus apoptin optimized genetically for expression in Escherichia coli and also modified using (His) 6 tag, (Arg) 8 tag, and HlyA tag intended for purification needs, penetration enhancement, and secretion from bacterial host to the growth media. Methods : The modified apoptin gene was optimized using an Integrated DNA Technology (IDT). The gene (606 bp) then ordered and synthesized by Eurofins. The apoptin gene was expressed using E. coli BL21 CodonPlus as host, in cultivation temperature of 37 °C, and 25 °C and purified using Ni-NTA agarose beads. The addition of (His) 6 tag enabled the apoptin to be purified in only one step by using nickel column. The expression and purification data analyzed qualitatively as well as quantitatively using SDS-PAGE. MTT assay was used to identify the antitumor effect of octa arginine-apoptin to two kinds of cancer cells, cervix HeLa cancer cell and colon Widr cancer cell. The viability of cell was analyzed when the cell incubated in the variation concentration protein for 72 h. Results: The constructed apoptin gene were expressed in E. coli successfully. The MTT assay indicated that Octaarginin-Apoptin was able to induce apoptosis of HeLa and Widr cells lines in a dose-dependent manner. The recombinant apoptin without tagging with octa-arginine, have no ability to induce apoptosis of HeLa and Widr cells lines. Conclusion: This octa arginine-apoptin may in the future allow the development of a therapeutic protein that is able to kill cancer cells specifically.
Changes in prey preferences of dragonfly naiads of Rhionaeschna multicolour (Hagen, 1861) (Odonata: Aeshnidae) in the presence and the absence of macrophytes

ABSTRACT We offered prey consisting of the rotifers, cladocerans, copepods, amphipods, dipterans and ephemeropterans to the pre-starved and sorted in three size groups of naiads of Rhionaeschna multicolour (Hagen, 1861) in the presence of the macrophyte Egeria densa Planchon and without it. The naiads consumed up to 25 prey items or in terms of biomass (wet weight) up to 7 mg within 2 h. Biomass intake increased with increasing predator's size. Prey consumption was significantly lower in presence of plants. The cladocerans Ceriodaphnia dubia Rihcard, 1894, Daphnia mendotae (Taylor and Hebert, 1993) and Ilyocryptus sp. were consistently preferred by the dragonfly naiads while Simocephalus vetulus (Müller, 1776), Alona guttata Sars, 1862 and Scapholeberis kingi Sars, 1888 were avoided with and without macrophytes. This study suggests that dragonfly naiads structure the zooplankton community by selective feeding.
The mitotic genome: Accessibility and transcriptional control

THE MITOTIC GENOME: ACCESSIBILITY AND TRANSCRIPTIONAL CONTROL Chris Chuan Shu Hsiung Supervisors: Gerd Blobel, M.D., Ph.D., and Arjun Raj, Ph.D. Mitosis entails dramatic global alterations to genome structure and regulation, including chromosome condensation, dissociation of the transcriptional machinery from chromosomes, and transcriptional silencing. Here I report studies that address the macromolecular accessibility of the mitotic genome and the control of transcriptional reactivation upon mitotic exit in a mammalian cell line. The results obtained from measuring the sensitivity of chromatin to DNase I cleavage by sequencing (DNase-seq) in pure mitotic cell populations demonstrate that macromolecular accessibility of the mitotic genome is widely preserved. Thus, steric hindrance from chromatin condensation is insu cient for explaining the eviction of transcription factors from mitotic chromatin. Several lines of evidence point to local modulation of chromatin accessibility; for example, promoters overall exceed predicted distal enhancers in their maintenance of accessibility during mitosis, suggesting the molecular control of these two classes of cis-regulatory elements are di↵erentially susceptible to mitotic perturbation. Other characteristics associated with maintenance of chromatin accessibility during mitosis include the ubiquity of tissue distribution of interphase chromatin accessibility and large domains of DNA hypomethylation, whereas mitotic occupancy of hematopoietic transcription factor GATA1 is not predictive of the degree of mitotic accessibility. To map the transcriptional reactivation of the genome upon mitotic exit, anti-RNA polymerase II (Pol II) chromatin immunoprecipitation-sequencing (ChIP-seq) was performed in a time course spanning anaphase through late G1. This data enabled unambiguous observation of the pioneering round of transcription upon mitotic exit, and classification of quantitative postmitotic transcriptional patterns across genes and distal enhancers aided by unsupervised pattern discovery. Surprisingly, the earliest rounds of transcription upon mitotic exit are vi hyperactive, compared to late G1. This post-mitotic spike in Pol II binding encompasses approximately 50% of active genes and intergenic enhancers, but the post-mitotic spike in gene transcription can be uncoupled from regulation by enhancers. Single-cell imaging by single-molecule RNA fluorescence in situ hybridization (FISH) of nascent and mature mRNAs demonstrates that this post-mitotic transcriptional spike can propagate to cell-to-cell heterogeneity in the mature mRNA levels of key developmental regulators. Together, these findings raise important considerations for the commonly proposed “mitotic bookmark” hypothesis of transcriptional memory, and have broad implications for the stability of gene expression states through cell divisions.
EFFECT OF DIVALENT CATIONS ON THE ACTIVITY AND CONFORMATION OF YEAST ALCOHOL DEHYDROGENASE

The divalent metal chlorides affect the activity of yeast alcohol dehydrogenase (YADH). The activity of the enzyme in the presence of 20 µM of these metal chlorides decreased in the following order: CaCl 2 > MgCl 2 > no salt > MnCl 2 > CoCl 2 > CuCl 2 > CdCl 2 . The EC50 values for the incubation of YADH in the presence of CaCl 2 , MgCl 2 , MnCl 2 , CoCl 2 , CuCl 2 and CdCl 2 were 14.5, 37.8, 0.25, 0.21, 0.18 and 0.005 mM, respectively. The most potent inhibitor was CdCl 2 . Fluorescence studies revealed that the conformation of YADH undergoes huge changes in the presence of these metal chlorides. By far UV-CD spectra, some secondary structural changes were observed in YADH in the presence of CaCl 2 , MgCl 2 , MnCl 2 and CoCl 2 , however the changes were very significant in case of CdCl 2 and CuCl 2 . The removal of zinc from YADH resulted in complete loss of enzymatic activity which is regained back by addition of Zn. Mg, Ca and Mn can substitute Zn in YADH, and the enzyme exhibits comparable activity as in presence of Zn. However, Co, Cu, and Cd cannot substitute Zn in YADH. The results obtained here might be useful in the biotechnological applications of alcohol dehydrogenase.
Virus-Induced Diabetes: Koch's Postulate Fulfillable?

The International Diabetes Federation (IDF) announced an increase in the number of diabetic patients in the world, reaching 415 million, and predicted to be 642 million in 2040 if effective measures are not taken [1]. In addition, 85,000 children worldwide develop type 1 diabetes in a year, and the incidence is increasing 3% year by year [1]. This explosive increase of diabetes is commonly supposed to be due to improved socioeconomic conditions followed by elevated calorie intake, obesity and reduced amount of exercise. However, accumulating evidence has suggested that environmental factors most importantly viruses play an important role to induce type 1 diabetes associated with viral infection, and may also serve as a risk for type 2 diabetes [2,3]. There is an attractive hypothesis that viruses, especially enter viruses, may acquire diabetogenicity over time.
Some new and less known Acrididae from Turkey (Orthoptera)

After studying the material collected by Oeme Kaya Gülen, Dr. P. H. Davis and myself, in different parts of Turkey, one new species and two new subspecies are described and four insufficiently known species are re-described below. I am grateful to Dr. B. P. Uvarov for kind help during my second visit to the British Museum (Natural History), where the types of the new species have been deposited.
Mechanisms of Neurotrophic Activities via Low-molecular-weight Compounds: Post-transcriptional Regulation in PC12 Cells and Neurons

Recently, it was reported that some low-molecular-weight compounds mimic neurotrophic activities including neurite outgrowth and neuroprotection. Carnosic acid (CA) promotes neurite outgrowth through the activation of Nrf2 in a model of neuron PC12 cells. CA also protects neurons from oxidative stress via the keap/Nrf2 transcriptional pathway. Luteolin induces neurite outgrowth via MAPK, PKC, and cAMP/PKA signaling pathways. In addition, luteolin protects PC12 cells from serum withdrawal-induced oxidative stress. Forskolin-induced neurite outgrowth is mediated by the activation of the PKA signaling pathway, and this PKAmediated neurite outgrowth is achieved by the expression of Nur77 in PC12 cells. In addition, a low concentration of forskolin is closely related to the cAMP-induced protective function against L-DOPA-induced cytotoxicity. The post-transcriptional regulation of gene expression including microRNAs and the acetylation of non-histone protein plays critical roles in neurotrophic activities. Recently, it was revealed that miR-132 modulates luteolin-induced neurite outgrowth via cAMP/PKA- and MAPK-dependent CREB signaling pathways in PC12 cells. Moreover, it has been reported that acetylated Nrf2 binds to the transcriptional activator, CBP/p300 directly, and that Nur77 is acetylated in vivo and in vitro by CBP/p300. The modulation of miR-132 and acetylation of Nrf2 and Nur77 by CBP/p300 may constitute a similar novel regulatory mechanism for low-molecular-weight compounds with neurotrophic activities.
Crecimiento de Nocardia brasiliensis como biopelículas en superficies inertes

BACKGROUND: Biofilms are microbial communities that are the most successful colonization of microorganisms, are ubiquitous in nature and responsible for many diseases. These communities embedded in an extracellular matrix growing inside self-produced exopolysaccharide and attached irreversibly to an inert surface or a living tissue. Biofilm formation occurs as a continuous process with various stages of development. Biofilms are present in various tissues including skin, interfering with the wound healing and associated with various diseases such as atopic dermatitis, acne, candidiasis, bullous impetigo and pemphigus foliaceus, among others. Actinomycetoma is an infectious process of the skin caused by Nocardia brasiliensis, the grains are formed in vivo consisting of a polysaccharide bonding cement which amalgamates these bacteria, this component may represent the association as microbial biofilm in this condition. OBJECTIVE: To obtain Nocardia brasiliensis biofilms growing in different inert surfaces such as acetates and catheters. MATERIAL AND METHOD: An experimental, descriptive and observational study was made to develop the growth curve of the reference strain CECT3032 of N. brasiliensis in Sabouraud medium. As inert surfaces 24 culture plates and 1x1 cm acetates trademarks Apollo, PCM and Kronaline catheters and 0.2, 0.5 and 1 cm diameter were used. These materials were inoculated with 200x106 CFU/mL for 50 days and readings were taken every other day for the first week and once weekly to complete 50 days of growth. CFUs/mL were measured and the biofilm was observed by microscopic analysis readings of acetic acid extract obtained after crystal violet staining. RESULTS: It is possible to obtain the growth of biofilms on N. brasiliensis as acetates proposing as a possible model for study in the laboratory. Nocardia brasiliensis growth in catheters form BP was able to obtain differences between the materials used being the catheter 0.6 cm thick 1 cm in length (balloon for percutaneous transluminal coronary angioplasty) which favored further growth. Moreover the increase in the diameter reflected in the number of CFU/mL recovered. CONCLUSION: Nocardia brasiliensis has the ability to form biofilms in vitro acetates and catheters and can be considered a risk factor for clinical handling.
STRUCTURAL AND FUNCTIONAL CHANGES IN A GENERATION IN TETRAHYMENA

The time courses of structural events occurring in a synchronous generation of T. pyriformis, mating type I, variety 1, were compared with one another and with the time courses of functional events in a synchronous generation, and/or in a generation of single, normal ciliates, of other strains of the species.
Reproductive success of songbirds and waterfowl in native mixed-grass pasture and planted grasslands used for pasture and hay

ABSTRACT Conservation of grassland birds in agricultural landscapes requires an understanding of the demographic consequences of nesting in native and planted grasslands. Much of the native grassland in agricultural regions has been converted to cropland. Subsequently, seeding cropland to perennial grasslands has become a common strategy to restore habitat for grassland birds, but these grasslands also may be used as hay and pasture forage for livestock. Our objectives were to determine (1) if the abundance of grassland songbirds and the reproductive success of songbirds and waterfowl varied between native pasture and planted grassland, and (2) if the amount of grassland in the surrounding landscape influenced the abundance and reproductive success of songbirds or the nest survival of waterfowl in native and planted grasslands. Our results suggest that planted grasslands used for pasture and hay in our region are likely ecological sinks for grassland specialist songbirds. Sprague's Pipit (Anthus spragueii) nested only in native pasture, and Chestnut-collared Longspur (Calcarius ornatus), Lark Bunting (Calamospiza melanocorys), and Baird's Sparrow (Ammodramus bairdii) were sometimes more abundant in planted pasture or hayfields, but fledged 1.4–4.5 times as many young per nest in native pasture. The reproductive success of waterfowl and grassland songbird generalists was similar in planted grasslands and native pasture. The abundance of all songbirds varied with the amount of grassland or cropland in the surrounding landscape, but landscape composition only weakly influenced the nest survival rates of 1 of 8 songbirds and 4 of 6 waterfowl species. Our results demonstrate that the preservation of native pasture is critical for the conservation of grassland specialists. Other grassland songbirds and waterfowl likely will benefit from the conservation of native and planted grassland and conversion of cropland to perennial grassland used for pasture and hay.
A Comparative Analysis of the Effectiveness of Four Supply Chain Initiatives to Reduce Deforestation

Deforestation and forest degradation account for around 12–15% of global greenhouse gas emissions and are largely driven by agricultural expansion. In the absence of formal regulation, voluntary initiatives have been established to meet demands from consumers and environmental NGOs. This paper examines what explains the effectiveness of supply chain initiatives to reduce deforestation, comparing four supply chain initiatives in two countries: the Roundtable on Sustainable Palm Oil in Indonesia and the Roundtable on Responsible Soy, the Soy Moratorium and the Cattle Agreement in Brazil. The first two are certification schemes, incentivizing more sustainable production, while the latter two are moratoria under which certain actors no longer purchased from companies that engaged in deforestation after a certain date. The moratoria benefitted from a concentration of power among actors risking loss of customers and able to demand changes in behavior from their suppliers. Certification schemes of multi-stakeholder initiatives are based on consensus and have lower requirements for reducing deforestation. For all initiatives a risk of leakage – deforestation by others, for other purposes, or elsewhere – remains. Little seems to be known regarding the possibilities farmers have to alter production practices, potentially hampering the development of public policies to complement the private initiatives.
Evidence of an unbalanced mating pattern in a seed orchard composed of two larch species

Mating patterns of a larch seed orchard composed of one clone of Larix sibirica and 6 clones of L. decidua, were investigated using allozymes as genetic markers. The studied orchard was designed to produce interspecific hybrid seeds. It was found that the orchard constitutes a population with a mating system that is far from panmixis. Studying outcrossing rates of individual clones by the mixed-mating model, some of the symptoms of non-random mating could be detected. They ranged between 0.096 for the Siberian larch clone, and 0.952 to 1.019 for the European larch clones. However, the most profound insight into the mating patterns was possible through the use of the mating model methods. Detailed mating model analyses revealed that the Siberian larch pollinated almost 93% of all sampled ovules, while the remaining European larches only 7%, with some clones contributing less than 0.2% of all pollen gametes. The effectiveness of Siberian larch as a pollinator could be explained by its high flowering abundance and earlier flowering phenology, as well as by the specific design of the orchard, where a half of the grafts were of Siberian larch. The neighborhood model (variant of the mating model) applied in this study indicated that fecundity of males and their distance to maternal trees significantly influenced male mating success. The mating model studies allowed also for an in depth analysis of the hybridization pattern between the 2 species. Its level for European larches functioning as females averaged on 93.9%, while only 10.5% Siberian larch seeds were hybrids, which has significant implications for forest tree improvement programs. The advantages of applying the mating model approach in the studies of mating systems of forest trees, mainly seed orchards, are briefly discussed.
Impact of Environmental Conditions on the Germination Time of Penicillium chrysogenum

In predictive mycology, most of the studies have been concerned with the influence of some environmental factors on fungal growth and production of mycotoxins at steady-state. However, germination should be the main step to be focused on, because a product is spoiled shortly after fungal conidia had germinated. In most of the studies dedicated to fungi, germination experiments were carried out immediately after spores were produced and harvested. Very few studies were concerned with the effect of storage conditions on the germination of fungal spores. The aim of this study is to show the impact of relative humidity, time of storage and temperature on germination time for the mould free shelf-life of food products determination. The effects of relative humidity, RH, time of storage, t and temperature, T on τ were assessed according to a Doehlert design in the range, 20-100%, 2-28 days and 5-25°C, respectively. The paramount influence of the relative humidity during storage on the germination time of the conidia of Penicillium chrysogenum was highlighted. An increase of the germination time was shown at reduced RH's, for increased periods of time and at lower temperatures. We can also observe a germination time, more important for conidia stored compared to fresh conidia obtained in the laboratory. The key factor was relative humidity, but time may be also of paramount importance for storage periods that exceed many weeks.
Effects of olive leaf extract and vitamin E supplementation in quail diet on some blood parameters and egg yolk fatty acids composition

Bu arastirma, bildircin karma yemlerine zeytin yapragi ozutu (ZYO) katilmasinin kimi kan parametreleri ile yumurta sarisi yag asitleri uzerine etkilerini belirlemek uzere planlandi. Bu amacla 60 gunluk yasta toplam 192 adet disi bildircin (Coturnix Coturnix Japanica), her grupta 4 alt grup ve her alt grupta 12 bildircin olacak sekilde 4 deneme grubuna ayrildi. Bildircinlar deneme suresince kafeste barindirildi, yem ve su serbest olarak verildi. Bildircinlara misir ve soya kuspesine dayali temel yem (%19.1 HP, 2940 kcal/kg ME, % 3.0 Ca ve % 0.39 kullanilabilir P) vitamin ve mineral karistirilarak hazirlandi. Bu yemi tuketen grup Kontrol, temel yeme 200 ppm α-tokoferol asetat katilan grup (Grup E), 80 ve 120 ppm Oleuropein (OLE) olacak sekilde ZYO katilan gruplar OLE-80 ve OLE-120 gruplarini olusturdu. Deneme sonunda alinan yumurta sarisi orneklerinde, OLE-80 ve OLE-120 diyetleri tuketen gruplarda kolesterol duzeyi kontrol grubuna gore daha yuksek bulunurken (p<0.01); E vitamini katilan diyetleri tuketen grupta A vitamini duzeyi, kontrol ve OLE-80 gruplarina gore onemli duzeyde dusuk (p<0.05), E vitamini duzeyi ise diger gruplara gore onemli duzeyde yuksek bulunmustur (p<0.001). Karma yemlere ZYO katilmasi yumurta sarisi yag asitlerini etkilemistir. OLE80 grubunun yumurta sarisi oleik ve linoleik asit duzeyleri diger gruplardan daha yuksek bulunmustur (p<0.05). OLE-80 grubunun yumurta sarisi PUFA, n-6 yag asitleri ve n-6/n-3 yag asidi orani diger gruplardan daha yuksek bulunmustur. Bu sonuclara gore, bildircin karma yemlerine 80 ppm OLE katilmasi, yumurta sarisi oleik, linoleik ve n-6 yag asitleri ile n-6/n-3 yag asidi oranini artirmistir