Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryopreservation of Mycobacterium bovis isolates

Research, development of new biotechnological methods, diagnostic tests, confirmation of results, and reinvestigations are possible because of the availability of well-preserved living organisms maintained without any changes. Cryopreservation is a simpler, more reliable and long-term stable method for culture maintenance. Storage temperature and composition of the suspending vehicle are factors that affect the viability of mycobacterial strains. Three vehicles and three storage temperatures were evaluated to define a suitable cryoprotective medium for the preservation of Mycobacterium bovis strains. Colonies of sixteen M. bovis isolates were used to prepare the suspensions, which were then added to three vehicles: sterile 0.85% saline solution (SS), Middlebrook 7H9 broth (7H9), and Middlebrook 7H9 broth with sodium pyruvate (7H9p) replacing glycerol. Aliquots of these suspensions were frozen by three different methods, directly in the -20°C freezer, directly in the -80°C freezer, and at -196°C by immersion in liquid nitrogen (LN). The frozen aliquots were thawed at room temperature after 45, 90 and 120 days. Mycobacterial viability was assessed by counting the living cells on plates of Stonebrink medium before and after the freezing procedure. Storage at -20°C exhibited a lower recovery of M. bovis compared to storage at -80°C (Dunn’s test, p=0.0018) and LN (Dunn’s test, p=0.0352). There was no statistically significant difference between storage at -80°C and in LN (Dunn’s test, p=0.1403), yet -80°C showed better results than LN. All three suspending vehicles showed no statistically significant difference in terms of viability (Friedman’s test, p=0.7765). Given the low loss proportion of 5% during storage at -20°C and the high cost equipment required for storage at -80°C and LN, we recommend storage at -20°C or -80°C, when this is available, for preservation of M. bovis field strains.
New records and observations of macroalgae and associated pathogens from the Falkland Islands, Patagonia and Tierra del Fuego

Abstract Subantarctic and Antarctic regions remain little explored with regards to their seaweed diversity. This study is based upon collections in the early 1970s and 2007–2013. It is supported by sequencing COI (mitochondrial cytochrome oxidase I) and reports new records for four species of brown algae (Hincksia granulosa, Hincksia sandriana, Myriotrichia clavaeformis, Syringoderma australe), four red algae (Erythrotrichia carnea, Paraglossum salicifolium, Phycodrys antarctica, Plumariopsis eatonii), one green alga (Chaetomorpha aerea) and of the oomycete Anisolpidium ectocarpii. A further four brown algae are reported at genus level and discussed (Cladostephus sp., Colpomenia sp., Dictyota sp., Punctaria sp.). Observations of the biology of three brown algal taxa (Cladothele decaisnei, Geminocarpus geminatus, Halopteris obovata) from the region are also reported here.
SERUM TRACE ELEMENTS IN CORRELATION TO SERUM PROTEIN ELECCTROPHORESIS PATTERN IN BAGHDAD HOSPITAL PATIENTS WITH MULTIPLE MYELOMA

Multiple myeloma (MM) is characterized by the neoplastic proliferation of a plasma cell clone that produces a monoclonal immunoglobulin. [1] The results of present study showed that an elevation of all serum trace elements in multiple myeloma patients with highly significant (P < 0.01) except serum zinc levels (μg/dl), (61.81 ± 8.82) which documented as decrease with highly significant (P < 0.01) compared to the control groups (128.44 ± 13.73). While gamma region (g/l) consist of more than two folds increase in sera of multiple myeloma (27.09 ± 17.26) than control groups (13.31 ± 2.64) with highly significant difference (P < 0.01). Gamma globulin. Levels (g/l) was correlated significantly (P < 0.05) with zinc levels (μg/dl), r = - 0.26 (negative correlations). In conclusion: A relation between trace elements and multiple myeloma were recorded as the serum levels (μg/dl) of iron, copper and manganese were significantly (P < 0.01) elevated, while serum levels (μg/dl) of zinc were significantly (P < 0.01) declined. Serum levels (g/l) of gamma globulin were negatively correlated to serum zinc levels (μg/dl) with significant difference (P < 0.05).
The complete mitochondrial genome of Tylototriton kweichowensis and implications for Tylototriton taxonomy

Abstract In this paper, the complete 16,725 bp nucleotide sequence of the mitochondrial genome was determined for the Tylototriton kweichowensis (Caudata:Salamandridae). It contains 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). Overall base composition of the complete mitochondrial DNA is A (33.8%), G (14.4%), C (26.2%), and T (25.6%), so the percentage of A and T (59.4%) is higher than G and C (40.6%). All the genes in T. kweichowensis are distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which are encoded on the L-strand.
Field efficacy of flonicamid 50 WG against sucking insect pests and predatory complex on Bt cotton

Flonicamid 50WG was evaluated @ 50, 75 and 100 g a.i. ha−1 against sucking insect pests and predatory complex on Bt cotton during 2007, 2008 and 2009. Based on pooled analysis of three years, per cent reduction of leafhopper over control in flonicamid @ 75 g a.i. ha−1 was found to be higher or at par with standard checks after 3 and 7 days of spray. Flonicamid @ 75 g a.i. ha−1 provided up to 73.4 per cent reduction in whitefly population but was less effective than ethion @ 1000 g a.i. ha−1 with 80.1 per cent reduction. Per cent reduction of aphid was higher in flonicamid @ 75 g a.i. ha−1 after 3, 7 and 10 days of spray as compared to all other treatments. Seed cotton yield was significantly higher in treated plots than control. Among the treatments, flonicamid @ 75 and 100 g a.i. ha−1 recorded significantly higher seed cotton yield being at par with each other. Moreover, flonicamid was comparatively safer to predatory complex.
Quantification of Ralstonia solanacearum Colonization of Potato Germplasm Using Luminescence

[Abstract] We have developed an unsophisticated, non-disruptive and accurate method for evaluation of pathogen colonization in planta. In this protocol we use a Ralstonia solanacearum (R. solanacearum) UY031 strain genetically modified to constitutively generate light from a synthetic luxCDABE operon stably inserted in its chromosome. This system allows bacterial quantification in a high-throughput manner, avoiding time-consuming and tedious bacterial dilution plating and colony counting. In addition, this system could be especially useful in plant breeding programs to detect bacterial latent growth in symptomless parental lines before their inclusion in long-term disease resistance breeding programs.
Analysis of Powdery Mildew Resistant Characteristic and Genetic Relationship of Cultivated Soybean, Glycine max, in Vietnam for Parental Selection

Soybean, Glycine max, is an important crop in Vietnam. The yield of this crop can be reduced up to 35% due to powdery mildew (PMD), a common disease in soybean. In the present study, we analyzed the PMD resistance of soybean accessions for two seasons and subsequently used SSR markers to determine the genetic diversity of these accessions. Twenty three SSR markers were used to amplify polymorphic SSRs from all of these genotypes in eighteen linkage groups. By analyzing 69 alleles for all accessions, the number of alleles ranged from 2 to 7 with an average of 4.3 at each locus. The polymorphic information content of each marker ranged from 0.104 (Sct_187) to 0.818 (Satt009) with a mean of 0.578. The pairwise coefficients of genetic similarity (Jaccard’s coefficients) among all genotypes ranged from 0.28 to 0.98 with an average of 0.61. Unweighted pair-group method arithmetic average and principal coordinate analysis separated the accessions into two major groups containing 28 and 6 accessions. The results of this study suggested some appropriate parent pairs based on genetic relationship as well as the yield and resistant characteristics of soybean accessions for breeding soybean accessions with PMD resistance and high yield characteristic.
Physiological Changes in Yellow Summer Squash at Chilling and Nonchilling Temperatures

Summer squash (Cucurbita pepo L.) fruit were harvested 8 ± 1 day after anthesis and held at 2 or 15C. Samples were transferred from 2 to 15C after 3, 6, 9, or 12 days of storage. Respiration and ethylene production were measured 24 and 48 hr after fruit had been transferred to 15C. Electrolyte leakage from pericarp disks was determined 48 hr after transfer to 15C. Weight loss during storage was greater at 15 than at 2C; however, chilled fruit had a greater rate of weight loss after transfer to 15C than did nonchilled fruit. Surface pitting became obvious after 6 days at 2C and was progressively more severe with increased duration of chilling. Respiration rates of nonchilled fruit decreased with increased storage duration, whereas respiration rates of chilled fruit increased with increased storage duration. Ethylene production was <0.1 nl g-1hr-1 in nonchilled fruit. Ethylene production was enhanced in chilled fruit and increased with increased duration of chilling to a peak of 1.5 nl-g-1-hr-1 after 9 days at 2C, then decreased. Electrolyte leakage was not influenced by chilling.
The utility of optical detection system (qPCR) and bioinformatics methods in reference gene expression analysis

Real-time quantitative polymerase chain reaction is consider as the most reliable method for gene expression studies. However, the expression of target gene could be misinterpreted due to improper normalization. Therefore, the crucial step for analysing of qPCR data is selection of suitable reference genes, which should be validated experimentally. In order to choice the gene with stable expression in the designed experiment, we performed reference gene expression analysis. In this study genes described in the literature and novel genes predicted as control genes, based on the in silico analysis of transcriptome data were used. Analysis with geNorm and NormFinder algorithms allow to create the ranking of candidate genes and indicate the best reference for flower morphogenesis study. According to the results, genes CACS and CYCL were characterised the most stable expression, but the least suitable genes were TUA and EF.
Quantitative Morphological and Molecular Divergence in Replicated and Parallel Radiations in Carex (Cyperaceae) Using Symbolic Data Analysis

Abstract Two species-rich lineages of Carex, C. sect. Phacocystis and the Vesicariae alliance, show a replicated and parallel radiation in the Northern hemisphere. Each group possesses a clade consisting of mostly boreal to arctic species and a second clade comprising more southerly distributed species. In this study, we ask if molecular differentiation is paralleled in both radiations by the diversification of quantitative morphological characters. We use nucleotide diversity to assess the molecular differentiation and methods derived from symbolic data analysis (SDA) for addressing the morphological diversification. The SDA turned out to be valuable for biological meta-analysis, because it is able to deal with the whole information content of interval and range data, respectively. We observed for some characters a weak correlation between molecular and morphological differentiation that, however, disappeared after Bonferroni correction. Therefore, in these phylogenetically young and radiating groups, diversification of molecular markers and quantitative morphological characters seem to be decoupled or hidden by homoplasy and plasticity.
Sequence-Related Amplified Polymorphism-PCR Analysis for Genetic Diversity in Rhizoctonia solani Populations Infecting Pulse Crops in Different Agro-Ecological Regions of India

A B S T R A C T Rhizoctonia solani is a destructive fungal pathogen infecting wide range of crop plants including pulses causing wet root rot or web blight disease. The present study was aimed to determine the genetic diversity of R. solani populations using Sequence-Related Amplified Polymorphism (SRAP) markers. The SRAP markers were used for genetic diversity analysis of 89 isolates of R. solani belonging to 7 Anastomosis Groups (AGs) isolated from different pulse crops representing 21 states from 16 agro-ecological regions of India. Out of 30 SRAP primer combinations evaluated, 16 combinations provided amplification with 100% polymorphism and the primer combinations Me1/Em1and Me1/Em4 provided the highest number of bands (14). The isolates of R. solani showed high level of genetic variability and grouped into 7 major clusters at 35% genetic similarity by using unweighted pair group method with an arithmetic average analysis. Bootstrap analysis grouped the isolates into five major clusters at 28% genetic similarity and about 95% isolates shared common sub-grouping patterns in both the analysis. The majority of the isolates representing various AGs were grouped together into different sub-clusters. The molecular clusters did not correspond to agro-ecological regions and crops of the origin of the isolates because of the diversity in the hosts and adopt ability of the pathogen under different environmental conditions prevalent in various parts of the country. First time an attempt was made in the present study to determine the genetic variability of the R. solani populations isolated from different pulse crops representing various AGs using SRAP markers.
Genetic Regulation of Cell Death and Disease Resistance in Arabidopsis

Plants and animals deploy intracellular immune receptors that perceive specific pathogen effector proteins and microbial products delivered i nto the host cell. We demonstrate that the ADR1 (Activated Disease Resistance 1) family of Arabidopsis NB-LRR receptors regulates accumulation of the defense hormone Sa licylic Acid (SA) during three different types of immune response: (i) they are requi red as ‘helper NBLRRs’ to transduce signals downstream of specific NB-LRR r eceptor activation during effector-triggered immunity (ETI), (ii) they are required for basal defense against virulent pathogens, and (iii) they regulate microbial associated molecular p attern (MAMP)dependent SA accumulation induced by infection with a disarmed pathogen. Re markably, these functions do not require an intact P-loop motif for at least one ADR1 family member. Our results suggest that some NB-LRR proteins can serve additional functions
Stochastic Forcings Associated with MJO Initiation during DYNAMO

The ability to forecast the Madden-Julian Oscillation (MJO) is of critical importance because of its direct and indirect influences on weather around the globe. However the medium-range weather forecasting models and the general circulation models (GCMs) on which climate simulations depend don’t simulate the MJO well. The MJO is often too weak, propagates at the wrong speed, and/or has the wrong planetary scale, seasonal cycle, or dynamical-thermodynamical coupling (e.g. Slingo et al. (1996), Sperber et al. (1997), Sperber (2004)). This may be due in part to model deficiencies such as inadequate subgrid parameterizations.
I Governance For Systems Support And Maintenance – Views From CIOS In Multinational Enterprises

This paper explores IS governance as it relates to systems support and maintenance (SS&M). We argue, that can be critically supportive of business operations, decision making, innovation and knowledge management strategies. Based on interviews with high level IS practitioners from large IT companies, we find that the value of SS&M as a potential link between the IT side and the business side of the organization, while recognized is still under-utilized. We enumerate and discuss a number of reasons for this situation from an IT governance perspective and call for a comprehensive research agenda to develop an integrated approach to link SS&M more closely.
COMPUTATION OF TURBULENT NATURAL CONVECTION IN A COMPOSITE CAVITY

Turbulent natural convection in a two-dimensional vertical composite square cavity, isothermally heated at the left side and cooled from the opposing side, is numerically analyzed using the finite volume method in a generalized coordinate system. Governing equations are written in terms of primitive variables and are recast into a general form. The composite square cavity is formed by three distinct regions, namely, clear, porous and solid region. Accordingly, the development of a numerical tool able to treat all these regions as one computational domain is of advantage for engineering design of thermal systems.
Genome-wide Identification, Phylogenetic and Expression Analysis of ABC1K Gene Family in Tomato (Solanum lycopersicum L.)

Activity of bc1 complex (ABC1K) is a protein kinase commonly found in eukaryotes and prokaryotes. It plays an important role in various developmental and physiological processes, especially critical for plant response to diverse biotic and abiotic stresses. In this study, a genome analysis was carried out and 18 genes of ABC1K family were identified in tomato. Phylogenetic results showed that these members could be classified into three groups - ancestral clade, mitochondrial clade and photosynthetic- specific clade, with several subgroups based on subcellular location prediction by WoLF PSORT and all the SlABC1K proteins contained an ABC1K conserved kinase motifs-VAIK (VAVK, VAMK) and DFG (DEG). Conserved motifs analyzed by MEME program indicated that all ABC1K protein contains motif 2, 5, 6 and 8. Predictably, the SlABC1K proteins were localized in chloroplasts or mitochondria; in our analysis of expression patterns, SlABC1K genes could be detected in all tomato organs, and eight genes were specifically expressed in tomato leaf, which implied that the SlABC1Ks might be involved in energy metabolism in tomato. The expression of several genes was significantly changed under abiotic stress, implying their probability of performing various roles in abiotic stresses (NaCl, high temperature, cold, abscisic acid and salicylic acid).
Detection of DNA Methylation Changes Surrounding Transposable Elements

[Abstract] Transposable elements (TEs) are a major component of all genomes, thus the epigenetic mechanisms controlling their activity is an important field of study. Cytosine methylation is one of the factors regulating the transcription and transposition of TEs, alongside Histone modifications and small RNAs. Adapter PCR-based methods [such as Amplified Fragment Length Polymorphism (AFLP)] have been successfully used as high-throughput methods to genotype un-sequenced genomes. Here we use methylation-sensitive restriction enzymes, in combination with PCR on adaptor-ligated restriction fragments, to evaluate epigenetic changes in TEs between genomic DNA samples.
EFEKTIVITAS EKTRAK PROPOLIS LEBAH KELULUT (Trigona spp) DALAM MENGHAMBAT PERTUMBUHAN Salmonella typhi, Staphylococcus aureus DAN Candida albicans

Propolis mempunyai khasiat sebagai antikanker, antivirus, antifungi dan antibiotika (Haryanto et al., 2012). Penelitian Agustina (2007), dihasilkan ekstrak propolis lebah asal Malang dapat mempengaruhi dan menghambat pertumbuhan bakteri gram positif Staphylococcus epidermidis pada konsentrasi 60% dan bakteri gram negatif Pseudomonas aeruginosa pada konsentrasi 70%. Penelitian mengenai efektivitas antibakteri dan anti jamur propolis dan lebah Trigona spp asal provinsi Kalimantan Selatan sejauh pengetahuan penulis belum pernah dilakukan. Tujuan umum penelitian ini untuk mengetahui konsentrasi yang efektif dari ekstrak propolis lebah kelulut ( Trigona spp ) dalam menghambat pertumbuhan bakteri Salmonella typhi Staphylococcus aureus dan Candida albicans. Hipotesis penelitian adalah Ekstrak propolis lebah kelulut ( Trigona spp ) efektif dalam menghambat pertumbuhan bakteri Salmonella typhi, Staphylococcus aureus dan Candida albicans. Jenis penelitian yang digunakan dalam penelitian ini adalah metode true eksperiment berupa rancangan-rancangan eksperimen sungguhan dengan menggunakan rancangan Postest Only Control Group Design (Notoatmodjo, 2010) . Bahan penelitian adalah propolis dari sarang lebah kelulut ( Trigona spp ) yang ada di daerah Banjarbaru, dengan kriteria sarang yang bertekstur rapuh dan berwarna gelap. Data yang diperoleh ditabulasikan dan dilakukan analisis secara statistik dengan one way anova dan Kruskal Wallis α 0,05 pada tingkat kepercayaan 95%. Hasil penelitian konsentrasi yang efektif dari ekstrak propolis untuk Salmonella typhi dan Staphylococcus aureus adalah 100% dan tidak terdapat zone hambat untuk Candida albicans . Saran perlu dilakukan uji aktivitas antimikroba propolis lebah kelulut ( Trigona spp ) asal daerah Kalimantan Selatan terhadap candida albicans dengan metode dilusi. Kata Kunci : Ekstrak Propolis, Trigona spp , Salmonella typhi , Staphylococcus aureus , Candida albicans
Introgression and species demarcation in western European Leuctra fusca (Linnaeus, 1758) and L. digitata Kempny, 1899 (Plecoptera: Leuctridae)

ABSTRACT The compilation of a DNA barcoding library of Norwegian stonefly (Plecoptera) species revealed that Leuctra fusca (Linnaeus, 1758) and Leuctra digitata Kempny, 1899 (Leuctridae) share haplotypes in northernmost Scandinavia. Phylogenetic analyses of the mitochondrial (mt) DNA barcode marker COI and the nuclear marker 28S show that the shared haplotypes must result from the introgression of a L. fusca mitochondrion into a L. digitata population on at least two occasions. Although mt introgression is widespread in animals, this represents the first documented case in Plecoptera. This study also included specimens of L. cf. fusca from the Sierra Nevada massif in Spain, a population previously known as L. carpentieri Despax, 1945. Their mt haplotypes are ca. 13% different from other European L. fusca. However, their 28S alleles are compatible with their morphological identification as L. fusca. In view of the possibility of mt introgression, the taxonomic status of this population remains undecided.
Production of extracellular laccase from the newly isolated Bacillus sp. PK4

Laccase belongs to the family of multicopper oxidase and have wide range of biotechnological applications starting from the food industry to bioremediation. However, the use of laccase at commercial scale is hindered by factors like high enzyme cost, low activity and /or stability under given conditions. This study was carried out with aim of screening for extracellular thermostable laccase producing bacteria. Twenty-two (22) laccase positive strains were isolated from the selected environmental samples while extracellular laccase activity was detected only in six strains namely TM1, TMT1, PK4, PS1, TMS1 and ASP3. The laccase enzyme produced from PK4 was found to be more thermostable with a half-life of 60 min at 80°C. The strain PK4 was identified and designated as Bacillus sp. PK4. The laccase production was optimized using one- factor-at-a-time method and maximum enzyme production were observed at the temperature of 37°C, pH 7.5, 10% inoculum size with yeast extract and glucose as the nitrogen and carbon sources, respectively at an agitation rate of 150 rpm. Copper sulphate at 0.1 mM concentration was found to maximize the laccase production among the tested inducers. Among the trace elements, FeSO 4 and ZnSO 4 gave the maximum laccase production for the isolated strain in comparison with the control. The effect of copper-induced time showed that the addition of copper before inoculation effectively increased the laccase production compared to the addition of copper after 2, 4, 6 and 8 h of inoculation. The optimization of the media resulted in 11.8 fold increase in laccase production. Keywords: Laccase, thermostability, Bacillus sp. , optimization