Miracle-dz/UniFAR-FTUs huggingface dataset:
Anther Culture in Red Cabbage (Brassica oleraceae L. var. capitata subvar. rubra): Embryogenesis and Plantlet Initiation

Cabbages, cauliflower and broccoli breeding activities are very low level compared with the other vegetable species. This study was conducted to determine the efficacy of the anther culture technique on the in vitro embryogenesis and according plantlet initiation and to the author’s knowledge, this is the first reports in red cabbage species. The anthers at uninucleate microspore stage (about 3-5 mm long) were collected at florescence times and then cultured on a solid MS and B5 medium with the addition of 2,4-D, NAA, Glutamine, Serine, Silver nitrate, IAA, BAP and different sucrose concentration to induce callogenesis, embryogenesis, and plantlet initiation. The culture medium, sucrose concentration, and genotype were found to be highly effective on androgenesis. Among the genotype, Zencibas cv. produced the best result with a combination of M medium+30 g/l sucrose for embryogenesis and plantlet initiation, while, Integro F1 and Cabellero F1 did not generate an androgenic response. This results can assist cabbage breeders to develop new hybrid cultivars in breeding programs
The Object Constraint Language Second Edition, Getting Your Models Ready for MDA, by Jos Warmer and Anneke Kleppe.

As a mathematician, I have always been drawn to the more formal programming methods of the Object Constraint Language (OCL). With it, you can place precise mathematical descriptions of what must be true before the code executes and what is guaranteed to be true after the code has run. Given the concise nature of mathematical notation, the OCL expressions also can replace many times their text in comments. The combination of Unified Modeling Language (UML) and OCL is a powerful one, allowing you to precisely describe the actions that code is expected to perform. However, the OCL is unlike other formal mathematical languages in that it must change in response to new ways of creating code.
Insecticide susceptibility status of Culex quinquefasciatus [Diptera: Culicidae] in Umudike, Ikwuano LGA Abia State, Nigeria

Larval and pupal stages of Culex quinquefasciatus mosquito were collected from different points within Umudike, Abia State, Nigeria, and reared to adulthood in the laboratory. The adults that emerged were tested on 4% DDT (Organochlorines); 0.1% bendiocarb (Carbamates); 0.25% Primiphos-methyl (Organophosphates); and 0.05% Deltamethrin (Pyrethroids) procured from National Arbovirus and Vector Research Institute Enugu. Twenty sugar fed female Culex quinquefasciatus mosquitoes aged 35days were used for the bioassay which was replicated four times with two control. Knockdown was recorded at five minutes, and then 10 minutes interval for 1 hour and then maintained for 24hrs postexposure on 7% sugar solution, after which a final mortality was recorded. The Knockdown times (KDT50 and KDT90) were determined by Probit analysis. Culex quinquefasciatus was resistant to all the insecticides, with 24hours post exposure percentage mortalities of 10.48, 39.20, 0.00, and 10.15 in DDT, bendiocarb, primiphos-methyl and deltamethrin respectively.
Seed Mucilage Contents in Some Taxa of Aubrieta Adans. Genus (Brassicaceae) and Their Systematic Importance

Bu calismada, 3 Aubrieta taksonunun (A. deltoidea, A. canescens subsp. canescens ve A. canescens subsp. cilicica) tohumlarindaki musilaj karakterizasyonu ve onlarin sistematik onemi tartisilmistir. Ġncelenilen taksonlarda tohumlarin yuzeyinde su ile temas halinde kaygan bir sivi ureten musilaj hucreleri bulunmustur. Calisilan taksonlardaki musilaj pektin veya seluloz yapidadir. Dahasi, incelenilen taksonlardaki kolumela sekillerinde belirgin, indirgenmis ve yassilasmis sekillerde varyasyonlar vardir. Ayrica, calisilan taksonlarin topraga yapisma kapasiteleri 83 mg ve 175 mg arasinda degismistir. Musilaj olusumu Aubrieta taksonlarinda yeni habitasyon acisindan tohum dagilimi ve kolonizasyonda onemli bir rol saglayabilir.
Association of polymorphisms in the GH and GHR genes with growth and carcass traits in rabbits (Oryctolagus cuniculus)

In rabbits, growth and carcass traits are important for the breeding programme. An increasing number of annotated polymorphisms demands validation of their influence on those traits before they can be implemented in breeding practice. Therefore, the aim of this study was to investigate GH c. -78C>T, GHR c.106G>C polymorphisms in the population of Belgian Giant Grey, Termond White, and a crossbreed between New Zealand White and Belgian Giant Grey (NZW × BGG) rabbits. In total 379 animals were genotyped and association analyses with growth traits and carcass traits were conducted. Our results demonstrated that GH c. -78C>T showed an association with growth weight in Belgian Grey and NZW × BGG rabbits. Meat weight in intermediate and hind parts for GH c. -78C>T statistically differed between Belgian Giant Grey and crossbred rabbits. GHR c.106G>C showed an association with meat weight in the intermediate part and dressing percentage in Termond White. TT/CC haplotype in Belgian Giant Grey had significantly higher meat weight in hind part, while in crossbred rabbits CC/CC haplotype was characterised by the lowest meat weight in intermediate and hind parts. Results from our study confirm that GH c. -78C>T, GHR c.106G>C polymorphisms constitute good molecular markers for growth and carcass traits.
Cas13b is a Type VI-B CRISPR-associated RNA-Guided RNase differentially regulated by accessory proteins Csx27 and Csx28

CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two Class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 or Csx28. We establish that these CRISPR-Cas systems can achieve RNA interference when heterologously expressed. Through a combination of biochemical and genetic experiments, we show that Cas13b processes its own CRISPR array with short and long direct repeats, cleaves target RNA, and exhibits collateral RNase activity. Using an E. coli essential gene screen, we demonstrate that Cas13b has a double-sided protospacer-flanking sequence and elucidate RNA secondary structure requirements for targeting. We also find that Csx27 represses, whereas Csx28 enhances, Cas13b-mediated RNA interference. Characterization of these CRISPR systems creates opportunities to develop tools to manipulate and monitor cellular transcripts.
Synthesis and role of melanin for tolerating in vitro rumen digestion in Duddingtonia flagrans, a nematode-trapping fungus

ABSTRACT We describe the synthesis and a function of melanin in Duddingtonia flagrans, a nematode-trapping fungus. We tested various culture media treated with L-DOPA, glucose and tricyclazole on fungal growth and melanin distribution using infrared spectroscopy (IS), electron paramagnetic resonance (EPR) and transmission electron microscopy (TEM). In vitro rumen digestion was used to test the environmental stress and then to evaluate the capacity of this fungus to trap nematode larvae. The growth and melanization of the fungus after 21 days of incubation at 30°C were best in Sabouraud dextrose medium. IS indicated the presence of melanin in D. flagrans, with similar bands for commercial melanin used as a control, and assigned the values obtained by EPR (g of 2.0051 ± 0.0001) to the production of melanin by the fungus. TEM indicated that melanin was produced in melanosomes but was not totally inhibited by tricyclazole. Within the limits of experimental error, the predatory activity of fungus treated with tricyclazole was drastically affected after 27 h of in vitro anaerobic stress with rumen inoculum. The deposition of melanin particles on the fungal cell wall contributed to the maintenance of D. flagrans predatory abilities after in vitro anaerobic ruminal stress.
Foliar application of nitrogenous compounds and elicitors to Tempranillo grapevines: Microbiological implications

This study was aimed to analyze the effects of the nitrogen foliar application, and elicitation used on microbial populations of musts. The nitrogenous compounds were raw and treated wastewater from mushroom industry and a commercial yeast derivate; the elicitors were methyl jasmonate, chitosan and one commercial elicitor from a yeast source. Those six products were sprayed as pre-harvest treatment over the leaves of Tempranillo grapevines for improving quality and maturity of grapes. The applications of raw and treated wastewaters from mushroom industry, chitosan and methyl jasmonate elicitation did not cause changes in microbial diversity of must samples. In contrast, spraying commercial yeast derivate products made the must microbiota reach a high richness of species that would be positive in ecological terms. This research succeeded in establishing the impacts of foliar applications in the grapevines on the microbial community, and in any case, negative impacts were observed so that, presumably, these foliar applications can be perfectly implemented as agronomic practice.
Lipid Profile and Haematological Indices of Wistar Albino Rats fed Riped, Unripe and Artificially Riped Mangifera indica (Mango) Pulp Formulated Diets

Lipid profile and haematological indices of Wistar albino rats fed naturally riped, unripe and artificially riped mango pulp formulated diets were investigated. Artificially riped mangoes were obtained by wrapping with dark polyethylene bag and others by treatment with calcium carbide and hot water. After inducing ripening, the mango samples were air-dried, ground and used to formulate the 10%, 20%, 30% diets fed to rats for 28 days. Results obtained indicated that at 10% level of incorporation, there was no significant difference in high density lipoprotein concentration in all the groups which ranged from 69.5±3.29mg/dl in calcium carbide group to 72.4±0.87mg/dl in the control group. At 20% and 30% levels of incorporation no significant difference in high density lipoprotein was obtained between the controls, unripe the polybag and hot water riped groups but each was significantly higher than values obtained for calcium carbide group. At 10% level of incorporation low density lipoprotein was highest in polybag group (88.60±5.95mg/dl) followed by calcium carbide group (88.67±5.95mg/dl) but was lowest in the control group (78.37±3.75mg/dl), whereas at 20% and 30% levels of incorporation, no consistent pattern was observed. At 10, 20 and 30% levels of incorporation ofsamples into the formulated diets, White blood cell count increased while Red blood cell count and haemoglobin concentration decreased in the artificially riped groups compared to the control. Generally, the values of lipid parameters and haematological indices suggest that artificial ripening especially by the use of carbide may not be a good candidate in the ripening of mango fruits.
Assessment of different fungicides against rust (Uromyces fabae de Bary) disease of field pea (Pisum sativum L.)

The present study was conducted during Rabi season of year 2017-18 at the experimental field of JNKVV, Jabalpur (M.P.) for assessment of different fungicides in controlling rust disease of field pea. Seven treatments including control with three replications were taken up by using RBD. Treatments of foliar spray of propiconazole (Tilt 25% EC) @ 0.1% (T1), tebuconazole (Folicure 25.9% EC) @ 0.17% (T2), difenoconazole (Score 25% EC) @ 0.06% (T3), hexaconazole (Contaf plus 5% SC) @ 0.2% (T4), azoxystrobin (Amistar 23% SC) @ 0.1% (T5), carbendazim + mancozeb (Saaf 75% WP) @ 0.2% (T6) and control (Spray of plain water)T7, were applied at the first initiation of disease symptoms and second at 15 days after the first spray. The data were recorded at 15 and 30 days after the spray. Results showed that the per cent disease intensity (PDI) was significantly low (11.40 and 14.96%) in Propiconazole 25% (EC), followed by Difenoconazole 25% (EC) with 14.66 and 16.09 per cent, respectively. The highest seed yield was recorded in Propiconazole 25% (EC) sprayed plot 19.61 q/ha, followed by Difenoconazole 25% (EC) with 19.40 q/ha, respectively as compared to control which recorded maximum per cent disease intensity (28.74 and 39.85%) and lowest yield 13.75 q/ha.
Cdc48/VCP and Endocytosis Regulate TDP-43 and FUS Toxicity and Turnover

Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron degenerative disease. TDP-43 (TAR DNA-binding protein 43) and FUS (fused in sarcoma) are aggregation-prone RNA-binding proteins that in ALS can mislocalize to the cytoplasm of affected motor neuron cells, often forming cytoplasmic aggregates in the process. Such mislocalization and aggregation are implicated in ALS pathology, though the mechanism(s) of TDP-43 and FUS cytoplasmic toxicity remains unclear. ABSTRACT Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron degenerative disease. TDP-43 (TAR DNA-binding protein 43) and FUS (fused in sarcoma) are aggregation-prone RNA-binding proteins that in ALS can mislocalize to the cytoplasm of affected motor neuron cells, often forming cytoplasmic aggregates in the process. Such mislocalization and aggregation are implicated in ALS pathology, though the mechanism(s) of TDP-43 and FUS cytoplasmic toxicity remains unclear. Recently, we determined that the endocytic function aids the turnover (i.e., protein degradation) of TDP-43 and reduces TDP-43 toxicity. Here, we identified that Cdc48 and Ubx3, a Cdc48 cofactor implicated in endocytic function, regulates the turnover and toxicity of TDP-43 and FUS expressed in Saccharomyces cerevisiae. Cdc48 physically interacts and colocalizes with TDP-43, as does VCP, in ALS patient tissue. In yeast, FUS toxicity also depends strongly on endocytic function but not on autophagy under normal conditions. FUS expression also impairs endocytic function, as previously observed with TDP-43. Taken together, our data identify a role for Cdc48/VCP and endocytic function in regulating TDP-43 and FUS toxicity and turnover. Furthermore, endocytic dysfunction may be a common defect affecting the cytoplasmic clearance of ALS aggregation-prone proteins and may represent a novel therapeutic target of promise.
Effect of Graded Levels of Spirulina (Arthropsira platensis) on Feed Intake and in vivo Digestibility of Trypsacum laxum in Guinea Pig (Cavia Porcellus L)

The intake and in vivo digestibility of Trypsacumlaxum in guinea pigs according to the graded level of spirulina was evaluated in Cameroon. 20 animals aged of 6 months with an average weight of 450 ± 50 g were randomly divided into 4 equivalent groups. Each group received T. laxum and 40g of compound feed containing 0% (TS0), 2% (TS2), 4% (TS4), and 6% (TS6) of spirulina. Feed intake was the different between the left over and the quantity served. The sample of T. laxum and those of each diet as well as feces were collected and analyzed for the apparent digestibility of each nutrient. Animals were weighed at the beginning and at the end of each period of the test to determine the body weight gain. This study showed that the average daily intake of dry matter (DM) for TS0, TS2, TS4 and TS6 was 74.39 ± 2.98, 78.66 ± 3.14, 83.89 ± 4.28 and 77.76 ± 4.40 g/head/day. The highest apparent digestibility coefficients of different nutrients were obtained with animals fed TS6 group while the lowest were observed in TS0.The apparent digestibility coefficient of dry matter (DM), organic matter (OM) and crude protein (CP) of the supplemented group were statistically higher than those of the control diet. Animals’ weight performances were statistically comparable between treatments. Thus, the combination of T. laxum with concentrated feed containing spirulina can be recommended for guinea-pigs, but the level of incorporation may not exceed 4% of its daily ration.
Biocontrol of Pear Postharvest Decay by Kombucha

Kombucha is sweetened, slightly alcoholic, and lightly effervescent tea drink. Its acidity inhibits the growth of harmful bacteria. Here, we studied effect of kombucha on post-harvest preservation of pear. The Hosui pears were soaked with the kombucha for 15 minutes, and in distilled water as the control, respectively. Superoxide dismutase (SOD), peroxidase (POD), malondialdehyde (MDA), hydrogen peroxide (H2O2), proline content, electric conductivity, weight loss rate and good fruit rate in pear were measured during storage at room temperature. The results showed that the kombucha could effectively prolong the storage time of pear fruit. The fruit quality of the treated group was 1.5 times higher than that of the control pear fruit when stored at room temperature for 18 days. The weight loss rate, MDA content and electric conductivity of the treatment group were lower than those of the control group during the whole storage period, indicating that kombucha can inhibit the transformation of polysaccharides such as starch and pectin, and delay the degradation of nutrients in the fruit, resulting in a decrease in weight loss rate, inhibition of membrane lipid peroxidation, reducing MDA content, electric conductivity, maintaining cell membrane stability, delaying pear fruit senescence. Kombucha can inhibit the content of H2O2 and proline, increase the activity of POD and SOD increase the storage stability of fruits. The purpose of this study was to elucidate the physiological mechanism of post-harvest preservation of pear by kombucha. The use of kombucha can prolong the supply period of pear, increase economic benefits and expand the market of pear. ********* In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 3, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI link will become active after the article will be included in the complete issue. *********
The oldest Inocelliidae (Raphidioptera) from the Eocene of western North America

Abstract One new genus of Inocelliidae (Raphidioptera) with one new species and one undetermined specimen is described from the Eocene of North America: Paraksenocellia borealis new genus, new species from the early Eocene (Ypresian) Okanagan Highlands shale at Driftwood Canyon, British Columbia, Canada (a forewing), and Paraksenocellia species from the middle Eocene (Lutetian) of the Coal Creek Member of the Kishenehn Formation, northwestern Montana, United States of America (a hind wing). These are the oldest records of the family. The new genus possesses many character states that are rare in Inocelliidae, e.g., a very long pterostigma extending to ScP in both the forewings and hind wings; the forewing subcostal space has three crossveins; the forewing and hind wing AA1 are deeply forked; the crossvein between CuA and CuP is located far distad the crossvein 1r-m. Paraksenocellia is confidently a member of the Inocelliidae, as it possesses a proximal shift of the basal crossvein 1r-m (connecting R and M) in the forewing and the loss of the basal crossvein 1r-m in the hind wing, both apomorphies of the family. It shares some character states with the Mesozoic Mesoraphidiidae, which we consider to be mostly stem-group plesiomorphies.
Isolation and identification of caffeine-degrading bacteria from soil, coffee pulp waste and excreted coffee bean in Luwak feces

Abstract. Iswanto T, Shovitri M, Altway A, Widjaja T, Kusumawati DI, Lisdiyanti P. 2019. Isolation and identification of caffeine-degrading bacteria from soil, coffee pulp waste and excreted coffee bean in Luwak feces. Biodiversitas 20: 1580-1587. The present study deals with the isolation and identification of caffeine-degrading bacteria obtained from the caffeine contaminated environment or caffeinated wastes. These bacteria are useful for various biotechnological applications especially in increasing the potential utilization of caffeinated wastes and producing the high-value chemicals. The suspected caffeine-degrading bacteria have been isolated from the soil of coffee plantation area, coffee pulp waste, and the excreted coffee bean in fresh feces of Luwak (Paradoxurus hermaphroditus or Asian Palm Civet) by growing them on the caffeinated agar medium (CAM) containing basal salt medium (M9) and caffeine as a sole source of carbon and nitrogen. CAM-supplemented with 1.5 to 10 g L-1 of caffeine has been used for screening of the potential bacteria which able to grow in high caffeine concentration. Molecular identification based on 16S rRNA gene sequence was performed to identify the selected bacteria. The result revealed that there were 11 and 3 strains of 12 selected bacteria which could grow on the CAM-supplemented with caffeine up to 7 and 10 g L-1, respectively. Based on 16S rRNA gene sequence and phylogenetic analysis, those bacteria were from 5 Gram-negative species, namely Pseudomonas japonica (4/12), Methylobacterium populi (5/12), Raoultella ornithinolytica (1/12), Klebsiella quasipneumoniae (1/12), and Stenotrophomonas chelatiphaga (1/12). Further investigations to determine their metabolic pathway, enzyme, and growth kinetics in the caffeinated medium may provide insights into its possible utilization for scientific or other applications.
Deep targeted sequencing analysis of hot spot mutations in non-small cell lung cancer patients from the Middle Eastern population.

Background The overall 5-year survival of lung cancer remains dismal despite the current treatment regimens. Testing for driver mutations has become routine practice for oncologists due to the presence of targeted therapy readily available for patients. Deep targeted sequencing through next generation sequencing (NGS) is an adequate methodology to detect mutations at multi-genetic levels. The molecular pathology of non-small cell lung cancer (NSCLC) is poorly understood in the Middle East and, to date, no other reports have been published on deep targeted sequencing of lung adenocarcinoma (LUAD) tissues. Methods Deep targeted sequencing using TruSeq Amplicon Cancer panel of 48 genes was performed on 85 formalin-fixed paraffin-embedded tissues from patients with LUAD who were treatment-naive at the time of the collection. Variants with an allele frequency higher than 10% were retained. Results Variant calling identified a total of 2,455 variants of which missense mutations were the most frequent (75.6%). All of our samples showed at least one mutation in one of the 10 most commonly mutated genes with FLT3 being the gene with the highest mutation rate (67%). TP53, KRAS and STK11 were the second, third and fourth most commonly mutated genes, respectively while EGFR mutation rate reached 22.4%. Conclusions To the best of our knowledge, this is the first hot spot profiling study on patients from this area. The frequencies of mutated genes presented in our study showed similarity to other reported outcomes. At least one mutation was detected in our cohort of LUAD.