Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum protein pattern in interspecific and intergeneric hybrids of Heterobranchus longiflis, Clarias gariepinus and Clarias anguillaris in sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE)

Electrophoretic characterization of Heterobranchus longifilis, Clarias gariepinus, Clarias anguillaris and their intergeneric and interspecific hybrids were carried out using 12% sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). Twenty seven fish samples (three from each mating combination) were used and a total of 16 electrophoretic protein bands were scored. There were variations in the protein banding patterns especially among the hybrid mating combinations. The 14th, 2nd and 9th band resolved in H. longilis, C. gariepinus and C. anguillaris respectively are the only differentiating electrophoretic bands for their biochemical identification using SDS-PAGE. The interspecific and intergeneric hybrids also resolved the 6th and the 7th band respectively which were however absent in their putative parental species. Only the intergeneric hybrids resolved the 14th protein band also found in the parental H. longiflis in addition to the 2nd and 9th bands resolved in C. gariepinus and C. anguillaris, thus showing they are true fusion of two different species. Visual scoring of the protein bands shows that the hybrids resolved more of the maternal protein bands. The molecular phylogenetic tree constructed by Unweighted Pair-group Method with Arithmetic means (UPGMA) revealed that the various mating combinations generally have high genetic similarity. The similarity coefficients were 0.96 and 0.84 for the interspecific hybrids and the putative Clarias species, respectively. The parental H. longifilis was the most divergent with the least similarity coefficient of 0.75. This study recorded for the first time, the use of fish blood serum analysed using SDS-PAGE in the identification of H. longifilis, C . gariepinus, C. anguillarisand their various hybrid combinations. Key words: Electrophoresis, Heterobranchus longilis, Clarias gariepinus, Clarias anguillaris, sodium dodecyl sulphate polyacrylamide gel electrophoresis.
The human DNA damage sensor RAD9B affects CHK2-T68 phosphorylation, p21 stability and cell survival in G1

The RAD9 protein assembles with RAD1 and HUS1 in the 9-1-1 DNA damage sensor complex (RAD9-HUS1-RAD1) which plays a crucial role in the activation of the DNA damage checkpoints by recruiting repair enzymes to DNA lesions and by initiating a cell cycle arrest. Why human cells express two RAD9 proteins, RAD9A and RAD9B, which share significant similarity is still very enigmatic. Moreover, both genes encode several splice variants with unknown function. While RAD9A is intensively studied, very little information is available about RAD9B. To get a deeper insight into the biology of RAD9B, two stable HEK293 cell lines were constructed which either over-express full-length human RAD9B-002 (417aa) or its N-terminally truncated splice variant RAD9B-001 (345aa) from an inducible promotor. These studies were complemented by the expression analysis of all five RAD9B splice variants at mRNA level in human tissues. This study revealed for the first time specific activities of the two RAD9B variants. While both proteins target the CHK2-p21 signalling module, which regulates cell cycle progression from G1 into S phase and the response to DNA damage in G1/S, they do affect CHK2 kinase and the cell cycle regulator p21WAF1/CIP1 in distinct ways. Elevated protein levels of full-length RAD9B initiate cell death in G1, cause the moderate hyperposphorylation of CHK2 and delay the degradation of p21 in the presence of oxidative stress. On the contrary, high levels of the N-terminally truncated variant RAD9B-001 only transiently block G1-S transition, cause a strong hyper-phosphosphorylation of CHK2 and delay p21 degradation in the response to UV irradiation. While the shorter variant may block p21 degradation in a PCNA-dependent manner in S phase, the full-length protein may act through the anaphase promoting complex (APC) when cells exit mitosis. The work provides also evidence that the hyper-phosphorylation of CHK2 is not dependent on the normal upstream kinase ATM, but on the mitotic regulator MPS1/TTK kinase. Dissecting this novel regulatory network formed by the two splice variants of the human RAD9B gene may help to understand why RAD9B expression levels change in several human cancers including testicular cancer, myelogenous leukaemia, ovarian epithelial carcinoma and cervical carcinoma (HeLa) cells.
EWSR1 affects PRDM9-dependent histone 3 methylation and provides a link between recombination hotspots and the chromosome axis

Meiotic recombination in most mammals requires recombination hotspot activation through the action of the histone 3 lysine-4 and lysine-36 methyltransferase PRDM9 to ensure successful double-strand break initiation and repair. Here we show that EWSR1, a protein with a previously uncharacterized role in meiosis, binds to PRDM9 and increases the efficiency of trimethylation at hotspots in vivo. Additionally, EWSR1 provides a link between PRDM9-activated hotspots and the nascent chromosome axis through the phosphorylated meiosis-specific cohesin pREC8. Together, these two functions of EWSR1 affect the choice of which hotspots will be used for double-strand break formation and repair, assuring that a sufficient number of crossovers are properly positioned along the centromere-telomere axis. These results show that successful recombination and meiosis require proper association of activated hotspots with the chromosome axis, and that one of the pathways involved in this association is mediated by interactions between EWSR1, PRDM9, and pREC8.
Performance of Terrestrial Water Spinach (Ipomoea reptans) through Biofortification under Different Mode and Source of Iron Nutrition

Micronutrient malnutrition is a major health problem in India. Indian children and women suffer from anemia, deficiency of iron which creates an adverse effect on health. One of the main reasons for such situation is lack of availability of iron rich food. In such circumstances, it's essential to enhance the availability of iron rich food in India. Thus the field experiment was laid out in a split plot design with nine treatments and three replications during summer season of 2016 and 2017 at Instructional Farm, Faculty of Horticulture, Uttar Banga Krishi Viswavidyalaya, to find out the most viable mode and source of iron fertilizer for growth, yield and iron accumulation in Ipomoea reptans. For this purpose, three source of Fe solutions (Fe-EDTA, FeSO4. 7H2O and Fe2 (SO4)3 were applied in three different modes, i.e., 100% recommended dose through soil application, 100% Original Research Article Dukpa et al.; CJAST, 27(2): 1-8, 2018; Article no.CJAST. 41168 2 recommended dose through foliar spray at 4 weeks after sowing and 50% of recommended dose through soil application + 50% recommended dose through foliar at 4 weeks after sowing. It was noticed that growth and yield parameters increased with the treatment combination of FeSO4. 7H2O (containing 16% iron) as 100% of recommended dose through foliar spray (0.5 g/ L of water) at 4 weeks after sowing, secondly the iron content of plant (mg/100g) was found maximum with the treatment combination of FeSO4. 7H2O (containing 16% iron) as 50% of recommended dose through soil application + 50% recommended dose through foliar spray at 4 weeks after sowing. Treatment combination FeSO4. 7H2O (containing 16% iron) as 100% of recommended dose through foliar spray produced maximum yield. Application of FeSO4. 7H2O as 50% of recommended dose through soil application + 50% recommended dose through foliar at 4 weeks after sowing can also be suggested.
Type studies in Russula 1: on two species described by Kühner

Russula Pers. is a large and difficult genus. Relatively variable characters are used in species delimitation. This places special requirements for type specimens. Contradictory to that, numerous taxa are based on scanty, juvenile or mixed type specimens, even though they are not very old taxa. In this series of articles we will offer detailed observations of such specimens to help future studies. For instance, in 1975 Kühner described five new species and two new varieties of alpine/montane Russulas. Four of these were based partly or totally on Scandinavian material (Kühner 1975). The new taxa were described without any pictures or microscopic drawings. Combined with the fact that Kühner’s herbarium was practically not available before it was annexed to Geneve, it is not surprising that unanimous circumscription of these taxa was not reached. They have been included in some papers (Romagnesi 1985, Bon 1988, Sarnari 1998, 2005, Adamcík 2004, Adamcík & Knudsen 2004, Ronikier 2008, Knudsen et al. 2012) but the way they were described and the scarce original material have made interpretations difficult. Hence, fresh material collected in northern Fennoscandia has been difficult to name. The four species and their subsequent subsections were: R. pseudocampestris Kühner (Integrinae), R. heterochroa Kühner, R. purpureofusca Kühner (Tenellae), R. nuoljae Kühner (Viridantinae). In this paper we present detailed drawings of microscopical features of the two last-mentioned, as well as informative colour photos of recent specimens.
Fine scale diversification of endolithic microbial communities in the hyper-arid Atacama Desert

The expansion of desertification across our planet is accelerating as the result of human activity and global climate change. In hyper-arid deserts, endolithic microbial communities colonize the rocks’ interior as a survival strategy. Yet, the composition of these communities and the drivers promoting their assembly are still poorly understood. Using a sampling strategy that minimized climate regime and biogeography effects, we analyzed the diversity and community composition of endoliths from four different lithic substrates – calcite, gypsum, ignimbrite and granite – collected in the hyper-arid zone of the Atacama Desert, Chile. By combining microscopy, mineralogy, and high throughput sequencing, we found these communities to be highly specific to their lithic substrate, although they were all dominated by the same four main phyla, Cyanobacteria, Actinobacteria, Chloroflexi and Proteobacteria. This finding indicates a fine scale diversification of the microbial reservoir driven by substrate properties. Our data suggest that the overall rock chemistry is not an essential driver of community structure and we propose that the architecture of the rock, i.e. the space available for colonization and its physical structure, linked to water retention capabilities, is ultimately the driver of community diversity and composition at the dry limit of life. Originality-Significance Statement In this study, we demonstrated that endolithic microbial communities are highly specific to their substrates, suggesting a fine scale diversification of the available microbial reservoir. By using an array of rock substrates from the same climatic region, we established, for the first time, that the architecture of the rock is linked to water retention and is ultimately the driver of community diversity and composition at the dry limit for life.
A DNA Barcoding Survey of Ulva (Chlorophyta) in Tunisia and Italy Reveals the Presence of the Overlooked Alien U. ohnoi

Abstract The cosmopolitan genus Ulva Linnaeus includes species of green macroalgae found in marine, brackish and some freshwater environments. Although there is a wide literature for the determination of Ulva taxa in Europe, they are among the most problematic algae to accurately identify, because they have few distinctive features, as well as a high intraspecific variation. At present, the knowledge of both diversity and distribution of the genus Ulva in the Mediterranean Sea is almost entirely based on morphological studies and there is only a few published papers dealing with molecular data. Tunisia has a key position in the Mediterranean and constitutes a transition area with a rich habitat diversity between eastern and western basins. The latest inventory of marine macrophytes dates back to 1987, updated in 1995. The aim of the present paper is to provide a molecular-assisted alpha taxonomy survey of Ulva spp. along Tunisian coasts, in comparison with a few Italian sites, using the tufA marker. Nine genetic species groups were resolved, including the non indigenous species Ulva ohnoi, newly reported for Tunisia. The actual picture of the taxonomy of Ulva spp. in the Mediterranean as a whole is far to be clarified and the present data on Tunisian collections aim to be a step towards its clarification. This paper is the first DNA barcoding study on green macroalgae in Tunisia and it contributes to add records to the Barcode Of Life Data Systems which are publically available.
Characterization of Chinese Hamster Ovary Cells Producing Coagulation Factor VIII Using Multi-omics Tools

4 DANSK SAMMENFATNING.5 PREFACE . 6 ACKNOWLEDGEMENTS . 7 ABBREVIATIONS . 9 TABLE OF CONTENT . 10 STRUCTURE OF THE THESIS . 12 CHAPTER 1 INTRODUCTION AND BACKGROUND . 13 1.1 HEMOPHILIA A . 13 1.2 EXPRESSION OF THE FVIII PROTEIN . 14 1.3 ENGINEERING FVIII FOR RECOMBINANT PROTEIN PRODUCTION . 16 1.4 THE CHINESE HAMSTER OVARY CELLS . 18 1.5 CHO SYSTEMS BIOLOGY BY OMICS TECHNOLOGIES . 20 1.5. 1 The current state of CHO genomics . 21 1.5. 2 State of CHO transcriptomics . 22 1.6 NEXT-GENERATION SEQUENCING . 23 1.6. 1 Analysis of NGS data . 26 1.7 REFERENCES . 27 CHAPTER 2 – CHO GENOMICS . 33 2.1 PUBLICATION 1: SEQUENCING THE CHO DXB11 GENOME REVEALS REGIONAL VARIATIONS IN GENOMIC STABILITY AND HAPLOIDY . 34 2.1.1 Abstract . 34 2.1.2 Background . 34 2.1.3 Results . 35 2.1.4 Discussion . 38 2.1.5 Conclusions . 40 2.1.6 Methods . 40 2.1.7 Acknowledgements . 42 2.1. 8 References . 42 2.2 OUTLOOK AND FUTURE PERSPECTIVES . 43 2.2.1 References . 44 CHAPTER 3 – TRANSGENE EXPRESSION IN CHO . 45 3.1 PUBLICATION 2: DEEP SEQUENCING REVEALS DIFFERENT COMPOSITIONS OF MRNA TRANSCRIBED FROM THE F8 GENE IN A PANEL OF FVIII-PRODUCING CHO CELL LINES . 46 3.1.1 Abstract . 46 3.1.2 Introduction . 46 3.1.3 Materials and methods . 47 3.1.4 Results . 49 3.1.5 Discussion . 51 3.1.6 References . 53 3.2 COMPOSITION OF THE TRANSGENE COMPOSITION IN THE GENOME OF CLONE 1 . 54 3.2.
Characterisation of populations of Heterodera trifolii Goffart, 1932 (Nematoda: Heteroderidae) in Japan and their phylogenetic relationships with closely related species

The Japanese populations of the clover cyst nematode, Heterodera trifolii , were characterised morphologically, morphometrically and molecularly. The morphology and morphometrics of six Japanese populations of H. trifolii were in congruence with those of previous descriptions of this species from Germany, Italy, Japan, New Zealand, Russia, The Netherlands, UK and USA. The results of the phylogenetic analyses of the D2-D3 expansion segments of 28S rRNA gene and the COI mtDNA gene sequences discriminated H. trifolii from most of the other closely related species of the Schachtii group. The intraspecific sequence differences in the Schachtii group were much higher in COI than in D2-D3. The H. trifolii populations displayed very low levels of intraspecific variations (up to 0.3%) in the COI mtDNA gene sequences. The phylogenetic relationships of H. trifolii with other Heterodera species, as inferred from the analyses of the ITS rRNA gene, D2-D3 of 28S rRNA gene and COI mtDNA gene sequences, were determined.
Monstrilloids (Crustacea: Copepoda) from the Mediterranean Sea (Northern Adriatic Sea), with a description of six new species

ABSTRACT Monstrilloid copepods collected during zooplankton surveys carried out over several years (2009–2016) in the Gulf of Trieste, northern Adriatic Sea, were examined. A total of seven species were found, of which six are undescribed, five of Cymbasoma and one of Monstrilla. These new species are described, illustrated and compared herein with its known congeners. Two of them are related to the C. rigidum species complex. One of these species is described based on both the male and the female; sexes were linked by identical details of the cephalic structure and the antennulary armature. Two previous reports of females attributed to C. tumorifrons from the Mediterranean relate to specimens that in fact belong to a new species, C. mediterranea. The most abundant species was M. grandis, which had a remarkable aggregation around the Trieste harbour in 2015. Male and female specimens of this assumedly widespread species were examined and the observed intra-specific morphological variability is reported and compared with previous illustrated reports; this nominal species probably this nominal species, probably represents a species complex. The addition of the new species here described brings the number of nominal species in the Mediterranean-Black Sea region to 26. www.zoobank.org/urn:lsid:zoobank.org:pub:3D4B38E4-CCCD-4BD6-AC57-B59343A865F7
Plant diversity increases predation by ground-dwelling invertebrate predators

Global declines in biodiversity have raised concerns over the implications of diversity loss for the functioning of ecosystems. Plant diversity loss has impacts throughout food webs affecting both consumer communities and ecosystem functions mediated by consumers. Effects of plant diversity loss on communities of invertebrate predators have been documented, yet little is known about how these translate into variations in predation rates. We measured predation rates along two plant diversity gradients in grassland experiments manipulating species richness and functional diversity. Measurements were conducted at two different heights (ground and vegetation) and in two different seasons (spring and summer), using three different types of baits. Our results show that overall predation rates increase with plant species richness, but effects are seasonally variable and are much more pronounced on the ground than in the vegetation. Plant functional diversity did not consistently affect predation rates in our experiments. Potential mechanistic explanations for an effect of plant diversity on predation include higher complementarity between predator species or reduced intraguild predation with increasing structural complexity at higher plant diversity. These results underline the importance of high local plant diversity for natural pest control.
The effects of discharge variability on the contractile responses generated by the human leg muscles

During voluntary contractions, human motoneurones discharge with a physiological variability of ~20%. However, studies that have measured the contractile responses to microstimulation of single motor axons have used regular trains of stimuli with no variability. We tested the hypothesis that irregular (physiological) trains of stimuli produce greater contractile responses than regular (non-physiological) trains of identical mean frequency but zero variability. High-impedance tungsten microelectrodes were inserted into the common peroneal nerve and guided into fascicles supplying a toe extensor muscle. Selective microstimulation was achieved for 14 single motor axons. Contractile responses were measured via an angular displacement transducer over the relevant toe. After recording the responses to regular trains of 10 stimuli extending from
Genetic Variability and Correlation Studies for Seed Morphology, Seedling Growth and Biochemical Traits in Neem ( Azadirachta indica A. Juss)

Genetic parameters in seed morphology, germination, seedling growth and biochemical contents of seed traits in Azadirachta indica collected from different parts of Haryana, India were assessed. The 'F' values for all the characters studied were significant (P<0.05), indicating the presence of ample genetic variation for all characters. The estimated coefficient of variance ranged from 1.93 to 8.73 per cent. The genetic advance, as percentage of means ranged from 21.29 per cent for seed breadth to 88.27 per cent for root length. The other characters viz. collar diameter (73.56 %) and shoot length also showed high values for genetic advance as percentage of mean High heritability (99.00%) and genetic gain were recorded for 100-seed weight, seed germination, shoot length, palmitic acid and stearic acid indicating the additive gene action. Seed size (length and breadth) and 100-seed weight was significantly and positively correlated with oil content, positively correlated with azadirachtin content, palmitic acid and oleic acid, however negatively correlated with steric acid and myrstic acid. Considering seed morphology, germination, azairachtin content and quantitative and qualitative characters of oil, the best performing plus trees were,T6 (Kurukshetra) of the Karnal , T6 (Pinjore II) from Panchkula, (T6) from Premnagar of Bhiwani and tree (T4) from Jhatipur of Sonipat provenance.
Freezing Effect on Post-Thawed Sperm Characteristics Especially Sperm DNA Integrity Comparing between Liquid Nitrogen Vapour and Computerized Program Freezer

The aim of the study was to evaluate the cryodamage effects on human sperm characteristics, especially on sperm DNA integrity, after 6 months of freezing comparing between using liquid nitrogen vapour (LNV) and using computerized program freezer (CPF). Forty normal semen samples were collected for semen analysis. Each sample was mixed with cryoprotective media and divided into 2 straws. The first straw was frozen with LNV and the second one with CPF. After 6 months of cryostorage, semen samples were thawed, and sperm chromatin integrity as well as sperm motility, morphology, vitality and cryosurvival rate were determined. Percentages of DNA damage were higher (p<0.01) following freezing with LNV than with CPF. Sperm vitality was greater (p<0.05) after CPF than after LNV, as well as cryosurvival rate (p<0.001). Post-thawed sperm motility was greater after CPF than after LNV, either in grade A (p<0.001) or in grade B (p<0.05). No significant difference was observed in the percentage of normal sperm morphology comparing the two freezing methods. The current study demonstrated a post-thawed decrease in sperm DNA integrity as well as other sperm characteristics after freezing in both methods. The CPF significantly provided superior results in post-thawed sperm DNA integrity, sperm motility and vitality than LNV did. In case of 6 months of cryostorage, therefore, we recommend the computerized program freezer as a preference for sperm cryopreservation.