Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular characterization of elite cotton cultivars using ISSR markers.

Genetic variability and relationship between varieties are of great importance for cotton breeding. ISSR marker systems were used for identification and genetic diversity analysis of elite G. hirsutum, G. arboreum and introgressed lines. 12 cotton genotypes were subjected to ISSR analysis using 55 ISSR primers. PCR products were subjected to agarose gel electrophoresis and the banding patterns were compared among 12 elite cotton varieties of diploid, tetraploid and introgressed cotton. Out of 55 ISSR primers tested, 15 were scorable, producing 101 marker bands with 83 being polymorphic. The primer IS-08 generated the greatest number of polymorphic markers. The ISSR markers were found to be reproducible and polymorphic. A dendrogram constructed from ISSR data classified 12 cotton genotypes into two major clusters, one containing six genotypes belonging to G. hirsutum cultivars and the other contained 4 genotypes belonging to G. arboreum cultivars. Two introgressed cultivars PAIG-8/1 and PAIG-27 showed highest level of genetic similarity with G. arboretum varieties. ISSR technique was thus found to be efficient method for detecting DNA polymorphism useful for DNA fingerprinting and genetic diversity analysis in cotton. Asian Journal of Bio Science, Vol. 4 Issue 2 : 249-253 (October, 2009 to March, 2010)
Abstract 918: Evidence of Alterations of the Ubiquitin-Proteasome System in Mouse Models of Familial Hypertrophic Cardiomyopathy

Cardiac myosin-binding protein C (cMyBP-C) gene mutations are frequently involved in familial hypertrophic cardiomyopathy (FHC) and most of them are expected to produce truncated mutants. However, truncated mutants were not detected in myocardial tissue of FHC patients and were degraded by the ubiquitin-proteasome system (UPS) in rat cardiac myocytes. Moreover, the UPS was impaired by truncated cMyBP-C ex vivo . In the present study, we investigated whether UPS alterations contribute to the pathophysiology of FHC in vivo . We therefore developed two mouse models based on a cMyBP-C mutation associated with a severe phenotype and a poor prognosis in humans. It corresponds to a G->A transition on the last nucleotide of exon 6. The first model overexpressed a human myc-tagged cMyBP-C transgene deleted of exon 6 under the control of the alpha-MHC promoter (TG). These mice did not develop any cardiac phenotype up to the age of 13 months. No truncated protein was detected in the TG cardiac tissue despite the presence of mutant mRNA. The TG mice exhibited a slight increase in the steady-state level of ubiquitinated proteins but no change in the chymotrypsin-like activity of the 20S proteasome vs. wild-type (WT) mice. The second model was generated by targeted knock-in of the mutation at the homozygous state (KI). The KI mice exhibited eccentric left ventricular hypertrophy with cardiac dysfunction at 9 wks of age. The level of mutant mRNAs (containing both missense and frameshift cMyBP-C mutations) decreased by 80% in KI vs. WT mice. The level of full-length protein decreased by 90% in KI vs. WT mice and the truncated protein was not detected. The level of ubiquitinated proteins and the chymotrypsin-like activity significantly increased in the KI vs. WT. These data show that truncated mutants are unstable in both mouse models suggesting degradation by the UPS. In addition, the mutants are also regulated at the mRNA level in the KI mice, suggesting that nonsense-mediated mRNA decay is also involved. Finally, both models exhibited alterations of the UPS resulting in an increased level of ubiquitinated proteins. These data suggest that UPS alterations may contribute to the pathophysiology of FHC.
Effect of Heat Shock and Growth Atmosphere on the Heat Resistance of Escherichia coli 0157:H7.

Log phase cells of Escherichia coli 0157:H7 were grown aerobically at 30°C and heat shocked at various time/temperature combinations to determine the optimum conditions that would result in the highest number of survivors to a subsequent 55°C heat treatment. Heat shocking at 42°C for 5 min resulted in the largest increase in D55 value over nonheat-shocked controls of all heat-shock time/temperature combinations tested. Growth atmosphere significantly contributed to the heat resistance of both heat-shocked and nonheat-shocked cells, with anaerobically grown cells having D55 values higher than those of cells grown aerobically. Therefore, both heat shocking and anaerobic growth contributed to an increase in the number of survivors of E. coli 0157:H7 cells when compared with nonheat-shocked cells grown aerobically. Aerobically grown, heat-shocked cells, and anaerobically grown cells, both heat-shocked and nonheat-shocked, contained a 71,000 dalton protein not present in aerobically grown, nonheat-shocked controls. This protein was found to be immunologically similar to a sigma32 subunit of RNA polymerase, as evidenced by Western Blot using monoclonal antibodies specific for the sigma subunit. In addition to heat, anaerobic growth appeared to be a form of stress, since it resulted in the synthesis of heat-shock proteins and in an increased survival of cells to a heat treatment.
Cerebellar degeneration in harlequin mice is associated with inflammation unaltered by low-dose phenobarbital treatment

III CO-AUTHORSHIP . V ACKNOWLEDGEMENTS . VI TABLE OF CONTENTS . VIII LIST OF FIGURES . XIII LIST OF TABLES . XV LIST OF APPENDICES . XVI LIST OF ABBREVIATIONS . XVII CHAPTER ONE INTRODUCTION . 1 1.1 Aging-associated neurodegenerative diseases . 1 1.2 Genetic basis behind early-onset neurodegenerative diseases . 2 1.3 Late-onset neurodegenerative disorders . 2 1.4 Early mechanisms underlying aging-associated neurodegeneration . 3 1.4. 1 Oxidative stress as a common denominator in aging-associated neurodegeneration . 3 1.4. 2 Mitochondrial dysfunction in aging-associated neurodegeneration. 5 1.4. 3 Inflammation in aging-associated neurodegeneration. 5 1.4. 4 Gene expression in aging-associated neurodegeneration . 7 1.5 The use of mice in studying neurodegeneration . 9 1.6 Mice having aging-associated neurodegeneration . 10 1.7 Altered mouse behaviour with neurodegeneration . 11 1.8 Human cerebellar ataxias are a model of neurodegeneration . 12 1.9 The cerebellum as a model for studying neurodegenerative diseases . 13 1.10 The function and organization of the cerebellum . 14 1.11 Age-associated changes in the cerebellum . 22 1.12 Similarities and differences in the human and mouse cerebellum . 25 1.13 Mouse models of cerebellar degeneration . 26 1.14 The harlequin mouse as a model of oxidative stress and cerebellar neurodegeneration . 27 1.15 Disease progression timeline in hq mice. 31
Von der Sequenz zur Funktion : systematische Modellierung verschiedener Proteinfamilien auf Sequenz- und Strukturebene

Das Verstandnis der Sequenz-Struktur-Funktionsbeziehung ist Voraussetzung, um experimentell beobachtete Unterschiede bei Enzymen hinsichtlich Selektivitat und Substratspezifitat erklaren und verstehen zu konnen. Eine systematische Analyse der Enzyme innerhalb einer umfassenden Proteinfamilie verwandter Proteine ist zum Verstandnis dieser Beziehung von Vorteil. Dadurch konnen in Sequenz und Struktur konservierte Bereiche aufgedeckt und familienspezifische Parameter abgeleitet werden. Im Rahmen dieser Arbeit wurde am Beispiel von drei verschiedenen Proteinfamilien eine systematische Untersuchung der Proteinfamilie oder einzelner Vertreter durchgefuhrt, um familienspezifische Regeln aufzustellen und diese fur das Proteindesign zu nutzen. Unterschiedliche Substratspezifitaten und Selektivitaten konnten mit einfachen Modellen beschrieben werden. Fur zwei der Proteinfamilien wurden Proteinfamiliendatenbanken etabliert, die eine erweiterte und umfassendere systematische Analyse dieser Proteinfamilien ermoglichen. Fur die Familie der Thiamindiphosphat-abhangigen Enzyme wurden systematische Strukturvergleiche verwandter Proteine durchgefuhrt, um Unterschiede bezuglich Selektivitat und Substratspezifitat zu erklaren. Fur die Familien der mittelkettigen Alkoholdehydrogenasen und der Cytochrom P450 Monooxygenasen wurden umfassende Proteinfamiliendatenbanken etabliert, die eine systematische Analyse dieser Familien ermoglichen. The knowledge of sequence, structure, and function relationship of enzymes is prerequisite to understand and explain experimentally observed differences in substrate specificity and selectivity. This is best achieved by investigating an enzyme in the framework of its complete enzyme family in order to derive family-specific parameters. Derived rules from a systematic analysis of protein families can then subsequently be applied for biocatalyst design. In this study, systematic family analysis was performed for three different protein families, and family-specific parameters were derived and applied to predict enzymes with improved properties. Simple models were established, explaining differences in substrate specificity and selectivity. For two of the investigated families protein family databases were established to enable a systematic family-specific analysis of these huge families. For the family of thiamin diphosphate (ThDP)-dependent enzymes systematic structure comparisons were performed, whereas protein family databases were established for the family of medium-chain dehydrogenases/reductases (MDRs) and for the family of cytochrome P450 monooxygenases.
Nutritional Contributions of Pork to the Diets of the US Population

A typical 3‐oz serving of pork is an excellent source of protein, and a good or excellent source of several vitamins and minerals. Many cuts of pork, including several cuts of chops and ham, meet the USDA criteria for lean meat. Data from the 2003–06 NHANES were used to estimate pork consumption by the US population age 2 years and older and the nutritional contributions of pork to the diet. More than 50% of the US population reported eating pork, either alone or in a mixed dish. Processed pork was most commonly consumed, with 58% of the population consuming it, while 16% of the population reported eating fresh pork. Lean (fresh or processed) pork was consumed by 28% of the population. Two‐day mean intakes by consumers were 38 g for lean (fresh or processed) pork, 38 g for all fresh pork and 45 g for all processed pork. Analyses of usual intake (using C‐Side) of nutrients from pork indicate that pork provides on average 11 to 18% of the total daily intake of protein, thiamin, selenium, vit B6, vit B12, niacin, zinc and phosphorus on the days people consume pork. Analyses of 2‐day intake data show that lean pork cuts account for 10% of total protein and 3% of total energy, fat and saturated fat in the diets of lean pork consumers, along with 7 to 14% of consumers’ daily intake of phosphorus, zinc, selenium, thiamin, niacin and vit B6. These results indicate that pork is an important source of several key nutrients. Supported by the National Pork Board.
ADVECTION AND ZOOPLANKTON FITNESS

Abstract Successful adaptation to the environment by zooplankton is constrained by the agents of mortality (starvation, predation) and losses due to advection. A fitness measure which explicitly includes risk of advective loss is presented. The authors show that as horizontal current speeds and vertical shear increase, the behavioral strategies that maximize fitness of zooplankton possessing different life history strategies are affected. For a Calanus finmarchicus-type life history, fitness is maximized by diel vertical migrations when advection risk in surface waters is low and by spending less time in the surface layers as flow rate increases. For a Paracalanus parvus-type life history, vertical migration is postulated to occur as advective loss increases. The geographic length scale of the habitat of residence also affects the optimal mode of habitat selection. In the Calanus case an abrupt change in the optimal vertical migration pattern is postulated as a function of length scale of habitat and rate.
Studies on Cycasin, a New Toxic Glycoside, of Cycas revoluta Thunb. : Part IX. Cleavage into Cycasin from Macrozamin.

The enzymatic hydrolysis of cycasin with cycad-emulsin, prepared from the seeds of Cycas revoluta, is described. As the complete degradation products we obtained about one mole each of formaldehyde, nitrogen gas, and methanol per mole of cycasin, in addition to glucose, the sugar component. These products are the same as those found in the acid hydrolysis of cycasin which has been reported previously. Therefore, it is concluded that the aglycone of cycasin can not be liberated intact as a single component, but decomposes into those smaller molecules as above even by means of the enzymatic hydrolysis.
High Voltage Electron Microscopy of Structural Patterns of Plastid Crystalline Bodies in Sedum rotundifolium

Major contributions has been made in cellular ultrastructure studies with the use of high voltage electron microscopy (HVEM) and tomography. Applications of HVEM, accompanied by appropriate image processing, have provided great improvements in the analysis of three-dimensional cellular structures. In the present study, structural patterns of the crystalline bodies that are distinguished in mesophyll plastids of CAM-performing Sedum rotundifolium L. , have been investigated using HVEM and tomography. Tilting, and diffraction pattern analysis were performed during the investigation. The titlting was performed at increments while examining serial sections ranging from 0.125 to in thickness. The young plastids exhibited crystalline inclusion bodies that revealed a peculiar structural pattern. They were irregular in shape and also variable in size. Their structural attributes affected the plastid morphology. The body consisted of a large number of tubular elements, often reaching up to several thousand in number. The tubular elements typically aggregated to form a fluster The elements demonstrated either a parallel or lattice arrangement depending on the sectioning angle. The distance between the elements was approximately 20nm as demonstrated by the diffraction analysis. HVEM examination of the serial sections revealed an occasional fusion or branching of elements within the inclusion bodies. Finally, a three-dimensional reconstruction of the plastid crystalline bodies has been attempted using two different image processing methods.
Produção e composição bromatológica do capim-tifton 85 ( Cynodon spp.) submetido a doses de nitrogênio - doi: 10.4025/actascianimsci.v33i2.9261

The experiment was carried out in Caceres, Mato Grosso State, Brazil, aiming to evaluate the effect of nitrogen (N) on forage production and chemical composition of Tifton 85 bermudagrass ( Cynodon spp.). A randomized complete block design was used, with five treatments (0, 60, 120, 180 and 240 kg ha -1 ) and four replications in 4.0 x 5.0 m plots. Four cuts were made at intervals of 30 days, at the height of 5 cm above ground level. N was applied after each cut, in the form of urea. For each kg ha -1 of N applied, we observed increases of 22.67 kg ha -1 in the production of total dry mass, 11.37 kg ha -1 in the production of green leaf blade, 0.052 cm in sward height, and 0.00955 dag kg -1 in crude protein content, and a reduction of 0.0142 dag kg -1 in NDF content. There was an increase in the extraction of N at a rate of 0.537 kg kg -1 of N, and sharp decline in the efficiency of N utilization from the estimated dose of 155 kg ha -1 of N.
Cutinase 1s Not Required for Funga1 Pathogenicity on Pea

Cutinase, a fungal extracellular esterase, has been proposed to be crucial in the early events of plant infection by many pathogenic fungi. To test the long-standing hypothesis that cutinase of Nectria haematococca (Fusarium solani f sp piso is essential to pathogenicity, we constructed cutinase-deficient mutants by transformation-mediated gene disruption of the single cutinase gene of a highly virulent N. haematococca strain. Four independent mutants were obtained lacking a functional cutinase gene, as confirmed by gel blot analyses and enzyme assays. Bioassays of the cutinasedeficient strains showed no difference in pathogenicity and virulence on pea compared to the wild type and a control transformant. We conclude that the cutinase of N. haematococca is not essential for the infection of pea.
Seed deterioration: Physiology, repair and assessment

Unpalatable food and unsatisfactory stand establishment are undesirable consequences of seed and grain deterioration. Considerable research has been generated in the last 15 years focusing on the physiology, repair, and assessment of seed deterioration, but this information has yet to be collated into a comprehensive review. The objective of this report is to systematically summarize these findings from a physiological perspective. A model of seed deterioration is forwarded arguing that free radical assault on mitochondrial membranes may be a primary event of seed deterioration. The purpose of the review is to stimulate debate about the mechanism(s) of seed deterioration thereby improving our understanding and directing future study of this important event that compromises seed and grain quality.
Studies of adeno-associated virus-induced DNA damage responses

Adeno-associated virus (AAV) infection triggers a DNA damage response in the cell. This response is not induced by viral proteins but by the structure of AAV ssDNA being recognized by the cell as damaged DNA. The consequence of this is the killing of cells lacking p53 activity. We have observed that cells that lack p21 or pRb activity are also sensitive to AAV-induced cell death. We report that cells respond to AAV infection by activating two DNA damage-signaling cascades. The first activates the p84N5 protein, which in turn activates caspase-6, leading to cell death. The second cascade activates the p53-21-pRb pathway, which inhibits activation of the p84N5 protein and thus prevents cell death. The result of the antagonistic interaction between these two pathways is that cells that do not exhibit functional p53-p21-pRb signaling undergo apoptosis as a consequence of AAV infection. Cells with a functional p53- 21-pRb pathway are refractory to AAV-induced cell death. These results show that p53, although a pro-apoptotic protein, together with pRb and p21 proteins, is a member of an anti-apoptotic cellular mechanism. As such, these experiments reveal features that may be exploited to specifically kill cells that lack the p53-p21-pRb pathway, such as cancer cells. We also consider the role of DNA damage signaling in the restriction of AAV replication. We report that helper viruses may inhibit ATM, ATR and DNA-PK signaling and that this may be advantageous for AAV replication. Inhibition of ATM and DNA-PK in tissue culture cell lines led to an increase in AAV replication. We show that ATM, ATR and DNA-PK may be responsible for the hyperphosphorylation of replication protein A (RPA) in response to AAV infection. We speculate that hyperphosphorylated RPA may be a fundamental restriction factor for viral replication and delineate novel experimental tools to test such a hypothesis. The implications of these observations for oncolytic therapy are discussed.
Speaking in Alzheimer’s Disease, is That an Early Sign? Importance of Changes in Language Abilities in Alzheimer’s Disease

It is known that Alzheimer’s disease (AD) influences the temporal characteristics of spontaneous speech. These phonetical changes are present even in mild AD. Based on this, the question arises whether an examination based on language analysis could help the early diagnosis of AD and if so, which language and speech characteristics can identify AD in its early stage. The purpose of this article is to summarize the relation between prodromal and manifest AD and language functions and language domains. Based on our research, we are inclined to claim that AD can be more sensitively detected with the help of a linguistic analysis than with other cognitive examinations. The temporal characteristics of spontaneous speech, such as speech tempo, number of pauses in speech, and their length are sensitive detectors of the early stage of the disease, which enables an early simple linguistic screening for AD. However, knowledge about the unique features of the language problems associated with different dementia variants still has to be improved and refined.
Atrial fibrillation influences automatic oscillometric ankle-brachial index measurement

Objective: The ABI (ankle - brachial index) repeated measurements using Doppler method were shown to be accurate despite atrial fibrillation (AF). However, they require expertise and are time consuming. Automatic oscillometric devices can be effective in ABI, but their accuracy during AF is unknown. The purpose of the study was to investigate whether AF influences ABI obtained with automatic oscillometric method. Design and method: Ninety-nine patients (age 66.6 ± 11 years, M/F - 63/36) who underwent AF electrical cardioversion (EC) were investigated. ABI measurements using oscillometric and Doppler methods were performed on both lower extremities (198 cases) before and after EC. Results: The ABI measured using oscillometric method on both lower limbs didn’t change after EC (1.21 [1.13–1.27] vs. 1.22 [1.14–1.26], p = 0.664, respectively). Correlation was found between measurements performed with oscillometric method before and after EC (r = 0.49, p < 0.001). ABI measured before and after EC using Doppler and oscillometric method showed significant difference (1.14 [1.07–1.22] vs. 1.21 [1.13–1.27], p < 0.001; and 1.18 [1.09–1.13] vs 1.22 [1.14–1.26], p < 0.001 respectively). Upper 95% CI margins for the median of difference in ABI between methods were 0.08 and 0.06 before and after EC and the difference was higher during AF than during sinus rhythm (0.07 vs 0.04, p = 0.002). That may be significant from clinical perspective suggesting clinical significance. Both methods showed week correlation before EC (r = 0.35, p < 0.001) and lack of correlation after EC (r = 0.12, p = 0.07). The Bland-Altman plot showed poor agreement between measurements performed with the Doppler and oscillometric method in sinus rhythm and during AF. ROC analysis revealed AUC of 0.57 (95% CI: 0.10–1) with 1.39 oscillometric cut-off for sensitivity (0.5) and specificity (0.96). Conclusions: The study results show, that atrial fibrillation can has an impact on ABI measurements performed with the oscillometric method. Therefore, we postulate, that the automated oscillometric method should not replace the reference Doppler method in patients with atrial fibrillation.