Journal articles on the topic 'DNA Replication Stre'
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Sutormin, Dmitry A., Alina Kh Galivondzhyan, Alexander V. Polkhovskiy, Sofia O. Kamalyan, Konstantin V. Severinov, and Svetlana A. Dubiley. "Diversity and Functions of Type II Topoisomerases." Acta Naturae 13, no. 1 (March 15, 2021): 59–75. http://dx.doi.org/10.32607/actanaturae.11058.
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The DNA double helix provides a simple and elegant way to store and copy genetic information. However, the processes requiring the DNA helix strands separation, such as transcription and replication, induce a topological side-effect supercoiling of the molecule. Topoisomerases comprise a specific group of enzymes that disentangle the topological challenges associated with DNA supercoiling. They relax DNA supercoils and resolve catenanes and knots. Here, we review the catalytic cycles, evolution, diversity, and functional roles of type II topoisomerases in organisms from all domains of life, as well as viruses and other mobile genetic elements.
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Mishra, Garima, Lavi S. Bigman, and Yaakov Levy. "ssDNA diffuses along replication protein A via a reptation mechanism." Nucleic Acids Research 48, no. 4 (January 10, 2020): 1701–14. http://dx.doi.org/10.1093/nar/gkz1202.
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Abstract Replication protein A (RPA) plays a critical role in all eukaryotic DNA processing involving single-stranded DNA (ssDNA). Contrary to the notion that RPA provides solely inert protection to transiently formed ssDNA, the RPA–ssDNA complex acts as a dynamic DNA processing unit. Here, we studied the diffusion of RPA along 60 nt ssDNA using a coarse-grained model in which the ssDNA–RPA interface was modeled by both aromatic and electrostatic interactions. Our study provides direct evidence of bulge formation during the diffusion of ssDNA along RPA. Bulges can form at a few sites along the interface and store 1–7 nt of ssDNA whose release, upon bulge dissolution, leads to propagation of ssDNA diffusion. These findings thus support the reptation mechanism, which involves bulge formation linked to the aromatic interactions, whose short range nature reduces cooperativity in ssDNA diffusion. Greater cooperativity and a larger diffusion coefficient for ssDNA diffusion along RPA are observed for RPA variants with weaker aromatic interactions and for interfaces homogenously stabilized by electrostatic interactions. ssDNA propagation in the latter instance is characterized by lower probabilities of bulge formation; thus, it may fit the sliding-without-bulge model better than the reptation model. Thus, the reptation mechanism allows ssDNA mobility despite the extensive and high affinity interface of RPA with ssDNA. The short-range aromatic interactions support bulge formation while the long-range electrostatic interactions support the release of the stored excess ssDNA in the bulge and thus the overall diffusion.
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Nurwanti, Ratri, Dian Putri Permatasari, Ika Fitria, Zakki Munawar Ahmad, and Yohana Dwivi Anggraini. "Efek Stres terhadap False Memory Recall dan Recognition." Suksma: Jurnal Psikologi Universitas Sanata Dharma 3, no. 2 (October 30, 2022): 60–73. http://dx.doi.org/10.24071/suksma.v3i2.5188.
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Memory is often thought of as a video recorder that can record and store events precisely as they occur. Whereas in addition to being constructive, memory is also reconstructive, which means that memory can change due to certain conditions, resulting in false memories. The effect of stress on false memory was tested in this between-subject design experiment. Participants in this study (N = 38) were divided into two conditions through a random assignment process, control conditions (N = 27) and stress or experiment conditions (N = 11). We used a modified Trier Social Stress Test-Group to induce stress and Deese-Roediger-McDermott Paradigm to measure false memory. The independent sample t-test showed that there was no significant difference on false memory recall and false memory recognition between participants in the experiment condition and participants in the control condition. This indicated that stress did not affect false memory. The implications of this finding are the importance of replicating similar studies investigating stress induction in various stages of memory processing and forms of stress induction to produce a more precise understanding of the stress and false memory mechanism.
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Taghfir, Dimas Bima, Syaiful Anwar, and Budi Adi Kristanto. "Kualitas benih dan pertumbuhan bibit cabai (Capsicum frutescens l.) pada perlakuan suhu dan wadah penyimpanan yang berbeda." Journal of Agro Complex 2, no. 2 (June 10, 2018): 137. http://dx.doi.org/10.14710/joac.2.2.137-147.
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Setting the temperature of the storage space of seeds and storage containers will greatly affect the quality of the seed. The aim of this research was to study the effect of temperature treatment, storage container and their interaction on seed quality and seedling growth of chilli. The study was conducted in Jetis Village and Laboratory of Plant Physiology and Breeding, Faculty of Animal and Agricultural Sciences, Diponegoro University from January to June 2017. The study was conducted using nesting experiments on the basis of Completely Randomized Design (RAL). The first factor was Storage Temperature (R1 = Room Temperature 24-29 oC, R2 = Refrigerator Temperature 5oC) and second factor was storage container nested at storage temperature that was (P1 = Alumunium foil, P2 = Paper and P3 = Plastic). Each treatment had 5 replications and each replication consisted of 100 seeds, so there were 30 experimental units. The data were analyzed by using analysis of variance (ANOVA) and continued with test of HSD (Honesty Significant Difference) 5% significance level. The results showed that the storage temperature (5oC) temperature increased the temperature and the seed vigor index was larger than the room temperature (28oC), the aluminum foil packaging produced the maximum growth potential and germination rate was higher than the plastic and paper packaging but there was no different growth rate and index vigor. Low storage space temperatures (5oC) can not maintain maximum seed quality where the 4 parameters were still below the standard quality of the seed. Seeds stored in low temperature (5oC) rooms producedfresh weight and dry weight of seedlings larger than high temperature (28oC), but the number of leaves, seed height and hypothetical vigor index were not significantly different. The aluminum foil packaging producedfresh weight and dry weight of seeds higher than plastic and paper packaging. However, the number of leaves, the height of seed and the hypothetical vigor index were notsignificantly different. Keywords : Temperature, container store, seeds quality, seedling growth, chilli.
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Harami, Gábor M., Zoltán J. Kovács, Rita Pancsa, János Pálinkás, Veronika Baráth, Krisztián Tárnok, András Málnási-Csizmadia, and Mihály Kovács. "Phase separation by ssDNA binding protein controlled via protein−protein and protein−DNA interactions." Proceedings of the National Academy of Sciences 117, no. 42 (October 5, 2020): 26206–17. http://dx.doi.org/10.1073/pnas.2000761117.
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Bacterial single-stranded (ss)DNA-binding proteins (SSB) are essential for the replication and maintenance of the genome. SSBs share a conserved ssDNA-binding domain, a less conserved intrinsically disordered linker (IDL), and a highly conserved C-terminal peptide (CTP) motif that mediates a wide array of protein−protein interactions with DNA-metabolizing proteins. Here we show that theEscherichia coliSSB protein forms liquid−liquid phase-separated condensates in cellular-like conditions through multifaceted interactions involving all structural regions of the protein. SSB, ssDNA, and SSB-interacting molecules are highly concentrated within the condensates, whereas phase separation is overall regulated by the stoichiometry of SSB and ssDNA. Together with recent results on subcellular SSB localization patterns, our results point to a conserved mechanism by which bacterial cells store a pool of SSB and SSB-interacting proteins. Dynamic phase separation enables rapid mobilization of this protein pool to protect exposed ssDNA and repair genomic loci affected by DNA damage.
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Brazda, Vaclav, Miroslav Fojta, and Richard P. Bowater. "Structures and stability of simple DNA repeats from bacteria." Biochemical Journal 477, no. 2 (January 22, 2020): 325–39. http://dx.doi.org/10.1042/bcj20190703.
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DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.
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Kobayashi, Masaki, Yusuke Deguchi, Yuka Nozaki, and Yoshikazu Higami. "Contribution of PGC-1α to Obesity- and Caloric Restriction-Related Physiological Changes in White Adipose Tissue." International Journal of Molecular Sciences 22, no. 11 (June 2, 2021): 6025. http://dx.doi.org/10.3390/ijms22116025.
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Peroxisome proliferator-activated receptor γ coactivator-1 α (PGC-1α) regulates mitochondrial DNA replication and mitochondrial gene expression by interacting with several transcription factors. White adipose tissue (WAT) mainly comprises adipocytes that store triglycerides as an energy resource and secrete adipokines. The characteristics of WAT vary in response to systemic and chronic metabolic alterations, including obesity or caloric restriction. Despite a small amount of mitochondria in white adipocytes, accumulated evidence suggests that mitochondria are strongly related to adipocyte-specific functions, such as adipogenesis and lipogenesis, as well as oxidative metabolism for energy supply. Therefore, PGC-1α is expected to play an important role in WAT. In this review, we provide an overview of the involvement of mitochondria and PGC-1α with obesity- and caloric restriction-related physiological changes in adipocytes and WAT.
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Yurliasni, Yurliasni, and Herawati Latif. "Pengaruh Warna Kerabang Dan Lama Penyimpanan Pada Suhu Beebeda Terhadap Kualitas Suhu Konsumsi." Jurnal Agripet 7, no. 1 (March 29, 2016): 35–38. http://dx.doi.org/10.17969/agripet.v7i1.3310.
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ABSTRACT. The objective of this research is to learn the effect of shell color and storage length on egg quality. The research was held at the Animal Nutrion Laboratory Departement of Agriculture, Syiah Kuala University. The treatments were shell color 30 SC (dark brown): 30-40 SC (white) with 10 replication and store in 27 0C and 10 0C for 35 days. The observation was taken every 7 days. Parameters measured were foam ability and Haugh Unit by group random sampling design with factorial pattern. The result shows that temperature and storage length significantly effect foam ability but not in haugh unit. Storage temperature and storage temperature at 10 0C show that foam ability is better with the average of 422.31 cm3. Compared to 27 0C with the average of 394.04 cm3. On the other hand shell color has no effect both on foam ability and Haugh Unit. In general, shell color, storage length and storage temperature have no effect on egg quality.
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Andriyani Lestariningsih, Wiwid, Muhamad Gilang Arindra Putra, Aulia Rahmania Putri, Budi Prabowo, Fadel Muhammad, Prakas Santoso, Cakra Adiwijaya, et al. "Struktur Komposisi dan Estimasi Cadangan Karbon Tegakan Ekosistem Mangrove di Pulau Sangiang, Banten." Jurnal Ilmu Kelautan Lesser Sunda 2, no. 2 (July 29, 2022): 13–20. http://dx.doi.org/10.29303/jikls.v2i2.59.
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The mangrove ecosystem is a coastal ecosystem that is important for humans. Mangroves absorb carbon in the atmosphere and store it in biomass or sediment. So, in other words, mangroves play a significant role in mitigating global climate change. This study aimed to examine the structure of the mangrove ecosystem composition and estimate standing carbon stocks on Sangiang Island, Banten. The data taken was for the categories of trees, saplings, and seedlings (consisting of mangrove species, DBH, and height). The study was conducted at three stations with three replications for each station. The allometric formula obtained the estimated carbon stock from the stand biomass value. The results showed that 11 species of mangrove species were found with an average density of 1266 ind/ha (trees), 3733 ind/ha (saplings), and <70% (seedlings). Then the estimated average carbon stock in Sangiang Island, Banten is 271.29 tons/ha.
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Sinansari, Shofihar, Vitas Atmadi Prakoso, Erma Primanita Hayuningtyas, Bambang Priadi, Sri Sundari, and Eni Kusrini. "Pengaruh Padat Tebar terhadap Konsumsi Oksigen dan Respons Stres Ikan Cupang Alam (Betta imbellis)." OLDI (Oseanologi dan Limnologi di Indonesia) 6, no. 1 (April 28, 2021): 11. http://dx.doi.org/10.14203/oldi.2021.v6i1.314.
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<strong>Effect of Stocking Density on Oxygen Consumption and Stress Response in Crescent Betta (<em>Betta imbellis</em>)</strong>. Stocking density is one of the determinant parameters for fish growth optimization in aquaculture systems due to its relationship with fish metabolism. Information about the impact of different stocking densities on crescent betta (<em>Betta imbellis</em>) metabolism was not available yet. This study was aimed to analyze the effect of stocking density on oxygen consumption, critical oxygen level, and stress responses in crescent betta.The study was carried out under three different stocking density treatments: 5, 10, and 15 fish/L with three replications using 2.74 ± 0.23 cm total length and 0.22 ± 0.05 g body weight tested fishes.The parameters observed were oxygen consumption, ventilation rate, blood glucose level, cortisol, and critical oxygen level. The result showed that the highest oxygen consumption was found at 5 fish/L stocking density treatment (3.01 ± 0.28 mg O<sub>2</sub>/g/h), which was significantly different from 10 fish/L (1.01 ± 0.21 mg O<sub>2</sub>/g/h) and 15 fish/L (0.92 ± 0.08 mg O<sub>2</sub>/g/h) stocking density treatments. Oxygen consumptions under hypoxic condition was not significantly different compared to normoxic condition.The ventilation rate tends to increase significantly along with the increasing of stocking densities. Critical oxygen levels were not significantly different among the treatments,with the value of 3.31 ± 0.65 mg/L, 3.14 ± 0.29 mg/L, and 2.83 ± 0.19 mg/L for stocking density of 5, 10, and 15 fish/L, respectively. The blood glucose level at 15 fish/L stocking density was significantly higher than others, whereas the cortisol levels was not significantly different among the treatments. The results of this study provided information that the increasing stocking density of cressent betta will decrease their metabolism activity and increase ventilation rate. However, the increase of ventilation rate was negatively correlated with oxygen consumption per breath at higher stocking densities due to decrease in fish activity; and higher stocking densities will decrease oxygen consumption. Based on the results, it can be concluded that the ideal stocking density for crescent betta is 5 fish/L. The increasing of stocking density will decrease oxygen consumption rates and increase the stress level of crescent betta.
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Ulus, Egidius, Enike Dwi Kusumawati, and Aju Tjatur Nugroho Krisnaningsih. "Pengaruh pengencer dan lama simpan semen Ayam kampung pada suhu ruang terhadap Motilitas dan viabilitas spermatozoa." Jurnal Sains Peternakan 7, no. 1 (June 30, 2019): 29–40. http://dx.doi.org/10.21067/jsp.v7i1.3609.
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The study was conducted from February to April 2018 in the field laboratory and integrated laboratory of University Kanjuruhan Malang. The purpose of this research is to know the effect of diluent and timetorage of kampung chicken sperm at room temperature to motility and viability of spermatozoa. The diluent used was NaCl, egg yolk tris aminomethane and no diluent with sperm duration of 0, 3, 6, 9, 12, 15, 18, 21, 24, 27, 30 hours and 10 replications. This research method is experimental laboratory by using completely randomize design of factorial. The data obtained in the study will be analyzed using the method of analysis of variance. The results showed that there was no significant effect (P> 0,05) of diluent, time storage as well as interaction between diluent and time storage to sperm motility and viability. Diluent and time storage which still maintain motility up to the minimum limit for AI was NaCl in 18 hours (41,5%), egg yolk tris aminomethan and without diluent at 12 hours of time storage that was equal to 49% and 42%. While the diluent and the time store that still can maintain viability up to the minimum limit for AI was NaCl and egg yolk tris aminomethan on the 18-hour (82.5%), without diluent on the time storage 12 hours (81.5%). It can be concluded that the optimum spermatozoa motility on NaCl diluent with 6 hours of time storage. While the optimum viability of the NaCl and egg yolk tris aminomethan on the time storage 18 hours.
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Sunarno, Sunarno, and Sri Isdadiyanto. "Profil Kadar Kolagen Kulit dan Tulang Tikus Wistar pada Berbagai Umur yang Mendapat Perlakuan Stres Oksidatif Hiperkolesterolemia dan Oleoresin Kulit Batang Kayu Manis (Cinnamomum sp)." Bioma : Berkala Ilmiah Biologi 12, no. 2 (April 27, 2012): 56. http://dx.doi.org/10.14710/bioma.12.2.56-62.
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Oleoresin cinnamon bark belonging to the phenolic compounds that are known to have potential as antioxidants. On the basis of the potential of these compounds may be used to prevent or repair tissue damage, whether caused by the factors of age and condition of oxidative stress hypercholesterolemia. This study aimed to obtain skin and bone collagen profile of Wistar rats at various ages after oxidative stress treated hypercholesterolemia and oleoresin from the bark of cinnamon (Cinnamomum sp). This study used 54 male Wistar rats with body weight (200 ± 5 g), which are grouped into six treatment groups combined with the three age groups of mice that is three, six or nine months with three replications. Each group received treatment oleoresin and hypercholesterolemia. Giving oral oleoresin conducted on rats given oral way during the 7 days with a dose of 12 rats mg/200-gr bw / day. Hypercholesterolemic rats was conducted by feeding cholesterol content within 1% during the two months. The results showed that the profile of skin and bone collagen content of the highest found on threemonth old rats treated with oleoresin, oleoresin hypercholesterolemia and given again (P6, 2), namely 57.44 tg / mg and 33.47 tg / mg, while the profile of skin and bone collagen content of the lowest found in rats aged 9 months to get treatment without treatment of hypercholesterolemia oleoresin (P2, 9), namely 28.26 tg / mg and 10.65 tg / mg. From this research can be concluded that the condition of hypercholesterolemia and duration of the aging effect on skin collagen levels decrease and bone, and vice versa oleoresin at the age of young rats that received the treatment of oxidative stress could repair or prevent hypercholesterolemia decreased content of skin collagen and bone. In general, the rats are treated oleoresin and young age profile of the collagen content of skin and bones better compared with rats that do not get treatment in conditions of oxidative stress oleoresin hypercholesterolemia.
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Haines, Anthony S., Karen Jones, Martin Cheung, and Christopher M. Thomas. "The IncP-6 Plasmid Rms149 Consists of a Small Mobilizable Backbone with Multiple Large Insertions." Journal of Bacteriology 187, no. 14 (July 2005): 4728–38. http://dx.doi.org/10.1128/jb.187.14.4728-4738.2005.
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ABSTRACT Plasmid Rms149, the archetype of Pseudomonas plasmid incompatibility group IncP-6, was identified in Pseudomonas aeruginosa as an agent conferring resistance to streptomycin, sulfanilamide, gentamicin, and carbenicillin in 1975. It has been classed as a broad-host-range plasmid due to its ability to replicate in both Escherichia coli (where it is designated IncG) and Pseudomonas species, although both species are γ-proteobacteria. To provide reference information on this Inc group, we have determined the complete sequence of Rms149 and found that, although the genome comprises 57,121 bp, it is essentially a small mobilizable plasmid carrying multiple mobile elements, which make up 79% (>45 kb) of its genome. A replicon has been identified which encodes a single polypeptide with moderate identity to other replication proteins. The region encoding this protein can replicate in Pseudomonas putida and E. coli. This sequence is directly downstream of a putative partitioning region highly similar to that of pRA2. A functional IncQ-type mobilization region is also present. Thus, the backbone appears to be a novel combination of modules already identified in other plasmid systems. Analysis of the segments that fall outside this core of stable inheritance and transfer functions show that this plasmid has been subject to multiple insertion events and that the plasmid appears to carry a considerable load of DNA that no longer should be phenotypically advantageous. The plasmid therefore functions not just as a vehicle for spread of selective traits but also as a store for DNA that is not currently under selection.
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Utami, Yunita Tri, Susanti Pudji Hastuti, and Bowo Nurcahyo. "Identifikasi Golongan Darah O dengan Metode Absorpsi Elusi pada Sampel Darah Kering yang Terdapat pada substrat Kain Jeans dalam Waktu dan Lingkungan Berbeda." Jurnal Biologi Indonesia 17, no. 2 (September 2021): 165–73. http://dx.doi.org/10.47349/jbi/17022021/165.
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This research aims to determine the time limit needed and the environmental conditions that provide the highest success rate in identifying dried blood samples on the fabric of stretch denim, ramie denim, black coated denim, and dry denim jeans using the elution absorption method. Also, to evaluate the effect of the fabric fabric, environmental condition, time, and interactions regarding the success rate of blood group identification. The study was conducted using 3 replications for each type of jeans fabric, which was carried out by exposing blood to a jeans fabric, leaving it in an indoor and outdoor environment for up to 336 hours (14 days), then continued by making a red blood cell suspension for comparison, and examining blood groups using the absorption-elution method. From the results obtained, it is known that the blood exposed in the jeans fabric that being placed indoor for up to 336 hours (14 days) can still be identified and has a success percentage rate of up to 100%. Meanwhile, the blood exposed on the jeans fabric that was placed outdoor could no longer be identified after 264 hours (11 days). Based on the result of this study, it can be concluded that the exposure time of 366 hours (14 days) for the indoor environment can still be identified properly, while the exposure time of 264 hours (11 days) for dry blood samples in the outdoor environment can no longer be identified. The indoor environment gives a better percentage of success than the outdoor environment in identifying blood types from dry blood samples. The best types of substrates that can store blood at an exposure time of up to 336 hours (14 days) are dry denim, black coated denim, and stretch denim.
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Suryadi, Suryadi, Suhessy Syarif, Darlis Darlis, and Muhammad Afdal. "Fermentasi Pucuk Tebu (Saccharum officinarum L) Menggunakan Trichoderma Harzianum : Degradasi in Sacco Komponen Serat." Jurnal Agripet 18, no. 1 (April 1, 2018): 30–35. http://dx.doi.org/10.17969/agripet.v18i1.10975.
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ABSTRAK. Pucuk tebu (Saccharum officinarum L) (PT) merupakan salah satu pakan alternatif yang dapat dimanfaatkan sebagai sumber pakan bagi ternak ruminansia. Penelitian bertujuan untuk mengetahui degradasi in sacco komponen serat PT yang difermentasikan dengan beberapa level Trichoderma harzianum. Penelitian ini menggunakan Rancangan Acak Lengkap dengan 4 perlakuan dan 5 ulangan, pengaruh perlakuan terhadap parameter yang diuji menggunakan analisis sidik ragam dan dilanjutkan dengan uji lanjut Duncan kalau ada perbedaan antar perlakuan. Pucuk tebu difermentasi dengan perlakuan Trichoderma harzianum dengan beberapa level yaitunya 0, 2, 4 dan 6% selama 1 minggu. Pucuk tebu hasil fermentasi digiling untuk dijadikan bubuk dengan ukuran saringan 2 mm kemudian dengan teknik in sacco diinkubasi ke dalam rumen sapi berfistula selama 72 jam. Peubah yang diukur adalah degradasi NDF, ADF dan hemiselulosa dari PT yang telah difermentasi sesuai dengan perlakuan. Hasil penelitian ini menunjukkan bahwa level T. Harzianum berpengaruh tidak nyata (P 0.05) terhadap degradasi NDF dan ADF dari PT fermentasi tetapi berpengaruh sangat nyata (P 0.01) terhadap degradasi hemiselulosa. Kesimpulan penelitian adalah degradasi NDF, ADF dan hemiselulosa dari PT fermentasi terbaik dicapai pada perlakuan dengan menggunakan 4% T. harzianum dibandingkan dengan perlakuan lainnya.(The fermentation of Saccharum officinarum L. shoot using Trichoderma harzianum: in sacco degradation of fiber component)ABSTRACT. Sugar can (Saccharum officinarum L) shoot (SCS) is one of an alternative feed that could be use as a source of feed for ruminant. The aim of this study was to reveal the in sacco degradation of SCS fermented with some level of Trichoderma harzianum. The design of this experiment was Completely Randomized Design with 4 treatments and 5 replications. The statistical analysis used in this experiment was Analysis of Variance and followed by Duncan Tets. Sugar can shoot was fermented with T. harzianum in some levels of 0, 2, 4 dan 6% for one week. The fermented SCS was dried, grounded in 2 mm mash and kept store until incubated. To evaluate the in sacco degradation, fermented SCS was incubated for 72 h. Parameters measured were the degradation of NDF, ADF dan hemiselulosa of treated SCS. Results showed that the level of T. harzianum did not significantly (P 0.05) affect on the degradation of NDF and ADF but it siginficantly (P 0.01) affected on the degradation of hemiselulosa. It could be concluded that the level of 4 % of T. harzianum in fermenting SCS showed the best in sacco degradation of NDF, ADF dan hemiselulosa among all treatments.
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Zalewska-Piątek, Beata, and Rafał Piątek. "Bacteriophages as Potential Tools for Use in Antimicrobial Therapy and Vaccine Development." Pharmaceuticals 14, no. 4 (April 5, 2021): 331. http://dx.doi.org/10.3390/ph14040331.
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The constantly growing number of people suffering from bacterial, viral, or fungal infections, parasitic diseases, and cancers prompts the search for innovative methods of disease prevention and treatment, especially based on vaccines and targeted therapy. An additional problem is the global threat to humanity resulting from the increasing resistance of bacteria to commonly used antibiotics. Conventional vaccines based on bacteria or viruses are common and are generally effective in preventing and controlling various infectious diseases in humans. However, there are problems with the stability of these vaccines, their transport, targeted delivery, safe use, and side effects. In this context, experimental phage therapy based on viruses replicating in bacterial cells currently offers a chance for a breakthrough in the treatment of bacterial infections. Phages are not infectious and pathogenic to eukaryotic cells and do not cause diseases in human body. Furthermore, bacterial viruses are sufficient immuno-stimulators with potential adjuvant abilities, easy to transport, and store. They can also be produced on a large scale with cost reduction. In recent years, they have also provided an ideal platform for the design and production of phage-based vaccines to induce protective host immune responses. The most promising in this group are phage-displayed vaccines, allowing for the display of immunogenic peptides or proteins on the phage surfaces, or phage DNA vaccines responsible for expression of target genes (encoding protective antigens) incorporated into the phage genome. Phage vaccines inducing the production of specific antibodies may in the future protect us against infectious diseases and constitute an effective immune tool to fight cancer. Moreover, personalized phage therapy can represent the greatest medical achievement that saves lives. This review demonstrates the latest advances and developments in the use of phage vaccines to prevent human infectious diseases; phage-based therapy, including clinical trials; and personalized treatment adapted to the patient’s needs and the type of bacterial infection. It highlights the advantages and disadvantages of experimental phage therapy and, at the same time, indicates its great potential in the treatment of various diseases, especially those resistant to commonly used antibiotics. All the analyses performed look at the rich history and development of phage therapy over the past 100 years.
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""Pin"ning Down DNA Replication Checkpoints." Science Signaling 2000, no. 22 (March 7, 2000): tw5. http://dx.doi.org/10.1126/stke.2000.22.tw5.
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Nurisma, Immas, Agustiansyah Agustiansyah, and Muhammad Kamal. "Pengaruh Jenis Kemasan dan Suhu Ruang Simpan terhadap Viabilitas Benih Sorgum (Sorghum bicolor [L.] Moench)." Jurnal Penelitian Pertanian Terapan 15, no. 3 (July 5, 2017). http://dx.doi.org/10.25181/jppt.v15i3.128.
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This study aims to determine: (1) in response to the type of packaging savings and sorghum seed viability; (2) in response to the storage room temperature sorghum seed viability; (3) a combination of types of packaging store and storage room temperature for sorghum seed viability. The research was conducted in October 2013 to January 2014 at the Laboratory of Seed and Plant Breeding, Faculty of Agriculture, University of Lampung. This research is compiled using a completely randomized design with four replications. The design of the treatment applied is factorial (4x3) by the first factor is the type of packaging and the second factor is the temperature store room. Homogeneity of variance between treatments was tested by Bartlett test. Separation of median is done by using the test Least Significant Difference (LSD) at level α of 5%. The results showed that the seeds of sorghum were packed with cans stored at refrigerator temperature (4 ° C) have the ability better than a plastic jar packaging, cloth flour, and plastic at room temperature (32 ° C) and air conditioning (22 ° C), in maintaining sorghum seed viability after being stored for 4 months. Keywords : Type Packaging, Temperature Storage Room, Sorghum Seed Viability
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Falcone, Guido J., Chia-Ling Phuah, Farid Radmanesh, Gina M. Peloso, James F. Meschia, Magdy Selim, Devin L. Brown, et al. "Abstract 154: Genetic Variants in CETP That Increase HDL Levels also Increase Risk of Intracerebral Hemorrhage." Stroke 48, suppl_1 (February 2017). http://dx.doi.org/10.1161/str.48.suppl_1.154.
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Introduction: In observational studies, higher plasma high-density lipoprotein cholesterol (HDL-C) has been associated with increased risk of spontaneous intracerebral hemorrhage (ICH). Common DNA sequence variants within the cholesteryl ester transfer protein ( CETP ) gene decrease CETP protein activity and increase plasma HDL-C; as such, medicines that inhibit CETP and raise HDL-C are in clinical development to combat coronary artery disease. Hypothesis: Common CETP DNA sequence variants associated with higher HDL-C also increase risk for ICH. Methods: We performed a two-stage case-control genetic association study in Caucasians. The discovery phase utilized data on 12 independent loci within CETP (+/- 50 kilobases) from 3 genome-wide association studies of ICH. Replication involved direct genotyping in 5 additional studies. We also constructed a genetic risk score with 7 independent CETP variants and tested it for association with HDL-C and ICH risk. We used principal component analysis to account for population structure and a Bonferroni-adjusted p<0.004 (12 tests) to declare statistical significance. Results: The discovery phase included 1149 ICH cases (43% lobar hemorrhages) and 1238 controls. Twelve variants were nominally associated (p<0.05) with ICH, with the strongest association at the rs173539 locus (Figure 1: OR 1.25, 95%CI 1.11-1.41; p=6.0x10 -4 ) and no heterogeneity across studies (I 2 =0%). This association was replicated in 1625 cases (43% lobar hemorrhages) and 1845 controls (OR 1.12, 95%CI 1.02-1.24; p=0.03). A genetic score of independent CETP variants known to increase HDL-C by ~2.85 mg/dL was strongly associated with ICH risk (OR 1.86, 95%CI 1.44-2.40; p=1.4x10 -6 ). Conclusion: Genetic variants in CETP associated with increased HDL-C raise the risk of ICH. Given ongoing therapeutic development in CETP inhibition and other HDL-raising strategies, further exploration of potential adverse cerebrovascular outcomes is warranted.
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Weinstein, Jonathan R., Richard V. Lee, Shahani Noor, Ryan Dodge, Jamie Colman, Anna Savos, Sean P. Murphy, and Thomas Möller. "Abstract 173: Effects of Ischemic Preconditioning on Microglial Phenotype and Transcriptome." Stroke 45, suppl_1 (February 2014). http://dx.doi.org/10.1161/str.45.suppl_1.173.
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Background: Ischemic preconditioning (IPC) is a robust neuroprotective phenomenon in which a brief period of cerebral ischemia confers transient tolerance to subsequent ischemic challenge. Microglia are critical in stroke pathophysiology however their role in IPC is unknown. Methods: We performed middle cerebral artery occlusion (MCAO) or sham surgery on 12 - 14 week old wild-type male mice following established paradigms for IPC ± stroke. We assessed infarct volume with 2,3,5-triphenyltetrazolium staining and used ex vivo flow cytometry (exFC) to quantify immune cell populations in cortex following IPC. We performed immunofluorescent microscopy (IFM) with stereology (optical dissector), Cavalieri point counting and Ki67 staining to characterize ionized calcium-binding adapter 1 molecule (IBA1)-positive immune cell number, morphology and proliferation, respectively. Finally, we performed mouse ST gene arrays (Affymetrix) on RNA isolated from sorted cortical microglia and carried out bioinformatic (Ingenuity Systems) and promoter analyses to characterize the effects of IPC on the microglial transcriptome. Results: IPC reduced infarct volume from 53±6 (mean±SEM) to 26±8 mm3 (p<0.01, n = ≥5 mice per group) and induced robust increases in the number of ipsilateral cortical microglia and macrophages relative to both sham and contralateral controls (n = ≥13 and ≥4 mice per group for exFC and IFM, respectively). IPC also induced marked increases in IBA1+ cell volume (processes and somata). Microarray analysis demonstrated marked changes in microglial transcriptome [2,230 gene probesets (6.5% of total) were significantly regulated]. The top three IPC-induced canonical gene expression pathways were: (i) DNA replication, recombination and repair, (ii) Cellular assembly and (iii) Cell cycle. Conclusions: Our novel in vivo microglia-specific, IPC-targeted, genomic dataset indicates profound activation of cell proliferation-related gene expression. This finding correlates well with the IPC-induced increases we found in microglia/macrophage cell number. These unexpected findings indicate that cell cycle regulation of CNS immune cells may be important in IPC-mediated neuroprotection.
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Chiota-McCollum, Nicole A., Matthew Ehrlich, Michelle Johansen, Shareena Rahman, Sherita Chapman Smith, and Bradford B. Worrall. "Abstract WP216: "BEAST" at the University of Virginia: Demographic and Phenotypic Data of Patients Contributing to a Biorepository to Establish the Etiology of Sinovenous Thrombosis." Stroke 48, suppl_1 (February 2017). http://dx.doi.org/10.1161/str.48.suppl_1.wp216.
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Introduction: Cerebral venous sinus thrombosis (CVST) occurs in 3-4 per 1 million individuals per year, accounting for approximately 1% of all strokes. Multiple etiologic risk factors for CVST have been identified, with known inherited thrombophilias accounting for 22% of cases. In 15% of cases, no known risk factor is identified. Studying the genetics of CVST holds the potential to identify at-risk groups, determine disease severity and prognosis, and consider novel therapies. BEAST is an international effort to identify genetic determinants of CVST, from which a recent discovery genome-wide association study (GWAS) identified 2 new associated loci. Methods: We are enrolling patients at least 18 years of age with a diagnosis of CVST who are willing to provide informed consent and a biospecimen to a central DNA repository. Patients are identified prospectively in clinical practice, and retrospectively using the Univ of Virginia clinical data repository. Results: Since 2012, twenty-eight patients have been enrolled. Demographic and phenotypic data are presented in the Table. Patients range in age from 19 to 65 years, with a mean of 40.5 (SD 14). Headache was the most common presenting symptom, occurring in 60%, followed by seizure (25%), mental status disturbance (21%), aphasia (11%) and mono- or hemiparesis (7%). Imaging revealed focal cerebral edema and/or venous infarction in 7 patients (25%) and hemorrhage in 5 patients (18%); no arteriovenous fistulae were identified. Acute treatments included intravenous or low molecular weight heparin (25/28, 89%) and anti-epileptic medications (7/28, 25%); three patients underwent local thrombolysis or endovascular intervention (11%). Conclusion: Understanding the association between phenotype and genetic determinants of CVST has the potential to advance the diagnosis and management of this challenging entity. Enrollment in BEAST continues and a replication cohort GWAS is anticipated in the near future.
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Debette, Stephanie, Ganesh Chauhan, Audrey Chu, Myriam Fornage, Josh C. Bis, Anita de Stefano, Benjamin Verhaaren, et al. "Abstract 56: Genome-wide Association Studies of Incident Stroke: The Charge Consortium." Stroke 45, suppl_1 (February 2014). http://dx.doi.org/10.1161/str.45.suppl_1.56.
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Background: Despite a high heritability, only few stroke risk genes are known. Genetic association studies performed in a hospital-based setting may fail to detect genes modulating both stroke susceptibility and severity, given early deaths at the acute stage. This selection bias is avoided when studying incident stroke in a population-based setting. Methods: We conducted a meta-analysis of genome-wide association studies of incident stroke in 11 community-based longitudinal studies from the Cohorts of Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Genome-wide Cox regressions were performed adjusting for age, gender and population substructure, using 1000GpIv3 imputed genotypes. Results were combined using inverse variance weighted meta-analysis. Results: The study sample comprised 65,204 participants (71.5% women) of European ancestry, aged 66.2±8.0 years at DNA draw, followed up for 10.8±3.8 years. In 11 studies, 3,389 participants developed incident stroke, and in 8 studies, 2,223 developed incident ischemic stroke (IS): 531 cardioembolic [CE] and 1,576 atherothrombotic [AT]. The most significant association with incident stroke was for a novel variant on chr9p23 (MAF=0.35), HR=1.15 [95%CI:1.09[[Unable to Display Character: ‒]]1.21], p=8.5х10-8: p=2.54x10-5 for IS; 1.19x10-4, AT-IS; and 0.019, CE-IS. Associations were in the same direction for all participating studies, and 5 additional SNPs in this locus reached p<10-6. The most significant association with incident IS was for rs11833579 [NINJ2], HR=1.21[1.13[[Unable to Display Character: ‒]]1.30], p=2.1х10-7, but p-random-effects=9.54x10-3 (p-heterogeneity=0.02, I2=57.9%). We replicated published associations for CE-IS (rs6843082-G [PITX2], HR=1.30[1.13-1.49], p=1.95x10-4) and for large artery stroke with AT-IS (rs2107595-A [HDAC9], HR=1.13[1.03[[Unable to Display Character: ‒]]1.24], p=0.012) Conclusion: In the largest GWAS of incident stroke, we detected one novel association with all stroke, requiring confirmation in independent samples. Expansion of the discovery sample and replication of findings are planned in the coming months. Detecting genetic variants associated with incident stroke may provide important clues for understanding pathways involved in stroke susceptibility and tolerance to acute vascular brain injury.
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Worrall, Bradford B., Fang Chen, Wei-Min Chen, Fang-Chi Hsu, Andrew M. Southerland, James F. Meschia, Pankaj Sharma, et al. "Abstract 189: Analysis of Hypertension Associated Genetic Variants in Stroke Cases and Controls." Stroke 43, suppl_1 (February 2012). http://dx.doi.org/10.1161/str.43.suppl_1.a189.
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BACKGROUND: Recent genome-wide association studies (GWAS) have identified a number of novel SNPs associated with blood pressure and hypertension-related traits although studies were very large (approaching 80K participants) and effect sizes were modest with per allele effect sizes as small variants as a single millimeter of mercury difference in blood pressure. However, because hypertension is the most potent modifiable risk factor for ischemic stroke, lowering blood pressure by a few mm Hg can translate into measurable decrease in stroke risk. METHODS: We investigated 22 hypertension (HTN) associated SNPs in a case-control analysis of ischemic stroke in multiple stroke studies including the Siblings With Ischemic Stroke Study (SWISS), the Ischemic Stroke Genetics Study (ISGS), the Bio-Repository of DNA in Stroke (BRAINS), the Vitamin Intervention for Stroke Prevention (VISP) trial, and the Women's Health Initiative (WHI). SWISS/ISGS/BRAINS were analyzed together and included subtype information. Genotyping was funded through the individual studies, the Genomics and Randomized Trials Network (GARNET) consortium, and the SHARe (SNP Health Association Resource). All studies had both raw and imputed GWAS data. Analyses included the following phenotypes: all ischemic stroke, stroke subtypes, and age-at-stroke-onset and were stratified by race. Analyses were minimally adjusted for age, sex and principal components 1 & 2. Alpha was set at 0.05. RESULTS: Eleven of the SNPs from the HTN GWAS were associated with ischemic stroke in European ancestry from one or more of the study populations. Two SNPs on chromosome 12 and one on chromosome 21 were associated in multiple European ancestry cohorts. No SNP was associated in all studies. A SNP previously associated with HTN in African ancestry populations was associated with stroke in African-Americans. Analysis of subtypes found associations with small vessel disease and cardioembolic stroke but not large artery disease. The case-only age-at-stroke-onset analysis also found associations for the two SNPs on chromosome 12. CONCLUSION: These data suggest that candidate SNPs from a HTN GWAS may be associated with ischemic stroke and warrant further investigation. Racial differences were observed. Replication in populations from the other SiGN (Stroke Genetics Network), GENEVA (Gene Environment Association Studies) consortium, and the ISGC (International Stroke Genetics Consortium) studies are underway.
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Asnawi, Abd Chalim, Saimul Laili, and Tintrim Rahayu. "Metode Hidroponik secara DFT ( Deep Flow Technique ) dan NFT (Nutrient Film Technique) pada beberapa Media Tanam terhadap Pertumbuhan Tanaman Bayam merah (Alternanthera amoena Voss)." Jurnal SAINS ALAMI (Known Nature) 3, no. 2 (March 6, 2021). http://dx.doi.org/10.33474/j.sa.v3i2.8433.
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Hydroponics is agricultural cultivation without using soil media, where the media can be replaced with husk charcoal or cocopeat media. However, hydroponics is actually the use of nutrients in a solution so that the nutritional needs of the plant are as desired. Accordingly, plant growth can be maximized. The use of media other than soil does not inhibit plant growth because both charcoal husk and cocopeat can store nutrients so that plant growth is not disturbed. This study aims to determine the response of red spinach (Alternanthera amoena Voss.) to Cocopeat and husk charcoal, and also to determine the use of DFT (Deep Flow Technique) and NFT (Nutrient Film Technique) hydroponic systems on the growth and development of red spinach. The method used was RBD where Rockwool media as a control, with 6 treatments and 4 replications. From the research results, the cocopeat media and husk charcoal media gave different results where the cocopeat growing medium was greater than the husk charcoal growing medium and the DFT and NFT systems gave significantly different results where the NFT yield was greater than DFT.Keywords: Hydroponics, Red Spinach, Cocopeat, Husk Charcoal, DFT, NFTABSTRAKHidroponik adalah lahan budidaya pertanian tanpa menggunakan media tanah, dimana media dapat digantikan dengan media arang sekam ataupun cocopeat. namun hidroponik sesungguhnya yakni penggunaan nutrisi dalam larutan sehingga kebutuhan nutrisi pada tanaman sesuai keinginan. Maka pertumbuhan tanaman bisa lebih maksimal. penggunaan media selain tanah tidak menghambat pertumbuhan tanaman karena baik media arang sekam maupun cocopeat dapat menyimpan unsur hara sehingga pertumbuhan tanaman tidak terganggu. Penelitian ini bertujuan untuk mengetahui respon pada tanaman bayam merah (Alternanthera amoena Voss.) terhadap media tanam Cocopeat, dan Arang sekam, dan juga untuk mengetahui penggunaan sistem hidroponik DFT (Deep Flow Technique) dan NFT (Nutrient Film Technique) terhadap pertumbuhan dan perkembangan bayam merah. Metode yang digunakan adalah RAK dimana media rockwool sebagai kontrol, dengan 6 perlakuan dan 4 ulangan. Dari hasil penelitian Media tanam cocopeat dan media arang sekam memberikan hasil yang berbeda dimana media tanam cocopeat lebih besar dari pada media tanam arang sekam dan pada sistem DFT dan NFT memberikan hasil yang berbeda nyata dimana hasil NFT lebih besar dari pada DFT.Kata kunci : Hidroponik, Bayam Merah, Cocopeat, Arang sekam, DFT, NFT
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Maniskas, Michael E., Yun-ju Lai, Sean P. Marrelli, Louise D. McCullough, and Jose F. Moruno-manchon. "Abstract MP17: Upregulating E2F1 Mitigates Senescence-Associated Phenotypes in Cultured Primary Endothelial Cells." Stroke 52, Suppl_1 (March 2021). http://dx.doi.org/10.1161/str.52.suppl_1.mp17.
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Vascular contributions to cognitive impairment and dementia (VCID) includes multiple disorders that are identified by cognitive deficits secondary to cerebrovascular pathology. The risk of VCID is higher in people after the age of 70, and, currently, there is no effective treatment. Vascular endothelial cells (VEC) are critical components of the brain vasculature and neurovascular unit and their health is vital to the capacity of the brain vasculature to respond to stressors. However, aged VEC may enter an irreversible replicative-arrest state (senescence), which has been associated with dementia. E2F transcription factor 1 (E2F1) regulates cell cycle progression and DNA damage repair. Importantly, E2F1 deficiency is associated with cell senescence. We hypothesized that E2F1 downregulation contributes to senescence in the cerebral endothelium during aging. We used cultured primary VEC from young (4-months old, mo) and aged (18-mo) male and female mice for RNA sequencing, plasmid-based gene delivery, high-resolution microscopy, and (4-, 12-, and 18-mo) mice of the bilateral carotid artery stenosis (BCAS) model, which produces chronic cerebral hypoperfusion and recapitulates some of the features seen in patients with VCID. We found that overexpression of E2F1 reduced the levels of senescence-associated phenotypes in cultured VEC from young mice that were exposed to oxygen and glucose deprivation (p<0.001), which induces endothelial senescence. Our RNA seq data showed that the expression of E2f1 was reduced (~40%) in cultured primary VEC from aged mouse brains compared with young cells (p<0.001). E2F1 levels were reduced in the brains of aged mice. Interestingly, we found sex differences in E2F1 levels, with less protein levels (~30%) in males vs females (p<0.05), independently of age. Also, aged BCAS mice (1 month after surgery) had more severe senescence phenotypes, reduced cerebral blood flow, and worse memory deficits compared with control mice (p<0.05). The effect of BCAS was more prominent in aged mice compared with younger (4- and 12-mo) mice. In conclusion , our study identifies E2F1 as a potential regulator of endothelial senescence in mice and highlights the contribution of aging as an important factor in losing endothelial resilience.
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Shmakov, Sergey A., Vassilii Sitnik, Kira S. Makarova, Yuri I. Wolf, Konstantin V. Severinov, and Eugene V. Koonin. "The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes." mBio 8, no. 5 (September 19, 2017). http://dx.doi.org/10.1128/mbio.01397-17.
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ABSTRACT Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR “dark matter.” We performed a comprehensive analysis of the spacers from all CRISPR- cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes. IMPORTANCE The principal function of CRISPR-Cas systems is thought to be protection of bacteria and archaea against viruses and other parasitic genetic elements. The CRISPR defense function is mediated by sequences from parasitic elements, known as spacers, that are inserted into CRISPR arrays and then transcribed and employed as guides to identify and inactivate the cognate parasitic genomes. However, only a small fraction of the CRISPR spacers match any sequences in the current databases, and of these, only a minority correspond to known parasitic elements. We show that nearly all spacers with matches originate from viral or plasmid genomes that are either free or have been integrated into the host genome. We further demonstrate that spacers with no matches have the same properties as those of identifiable origins, strongly suggesting that all spacers originate from mobile elements.