Inferring the Phylogeny of Bovidae Using Mitochondrial DNA Sequences: Resolving Power of Individual Genes Relative to Complete Genomes

Molecular techniques that assess biodiversity through the analysis of a small segment of mitochondrial genome have been getting wide attention for inferring the mammalian diversity. Due to their highly conserved nature, specific mitochondrial genes offer a promising tool for phylogenetic analysis. However, there is no established criteria for selecting the typical mitochondrial DNA (mtDNA) segments to achieve a greater resolving power. We therefore chose the family Bovidae as a model and compared the tree-topologies resulting from the commonly used and phylogenetically-informative genes including 16S rRNA, 12S rRNA, COI, Cyt b and D-loop with respect to complete mitochondrial genome. The tree topologies from the whole mitochondrial genome of 12 species were not identical albeit similar with those resulting from the five individual genes mentioned above. High bootstrap values were observed for mtDNA compared with that of any single gene. The average pair-wise sequence divergence using different genetic modes was found to be: D-loop (0.229) > Cyt b (0.159) > COI or complete mtDNA (0.143) > 12S rRNA (0.094) > 16S rRNA (0.091). The tree resulting from complete mtDNA clearly separated the 12 taxa of Bovidae into 3 major clusters, one cluster each for subfamily Cervinae and Bovinae and the third cluster comprised the distinctive clades of Caprinae and Antilopinae. However, jumping clades of Antilopinae were observed while using the individual genes. This study showed that Bison bison and Bos Taurus have very close phylogenetic relationship compared to Bubalus bubalis (Bovinae), irrespective of the method used. Our findings suggest that complete mtDNA genome provides most reliable understanding of complex phylogenetic relationships while the reliability of individual gene trees should be verified with high bootstrap support

Modes of Action of Different Classes of Herbicides

The mode of action of herbicides is important for understanding the management, classification, organization, and hierarchy of the herbicides. It also provides an insight into herbicide resistance, which continues to be a problem in sustainable agricultural management. The overuse of herbicides, just like other pesticides such as insecticides, has led to increased development of resistance among weeds, causing injury and destruction of useful plants in agriculture, land management, and other related industries. This chapter focuses on the main theme while providing in-depth analysis of the different modes of action of various classes of herbicides. The modes of action of herbicides are as variable as their chemical compositions as they focus on controlling susceptible plants through various biochemical means. Depending upon the specific mode of action at work, it may involve a plant enzyme or a biological system that the herbicide may interrupt, thus injuring or disrupting the regular plant growth and development and causing eventual plant death. Having an in-depth knowledge of the mode of action of herbicides is important in choosing a specific herbicide for a specific crop, understanding the injury symptoms, and devising an appropriate crop-management strategy

Economic Load Dispatch Unit Pembangkit Termal Mempertimbangkan Penambahan Pembangkit Tenaga Angin dengan Menggunakan Firefly Algorithm

Maraknya isu global warming serta keterbatasan sumber daya alam membuat mulai banyaknya dibangun pembangkit-pembangkit listrik dengan renewable energy, salah satunya adalah pembangkit tenaga angin. Pada jurnal ini, firefly algorithm diterapkan untuk mengoptimasi total biaya pembangkitan 2 buah sistem uji, tanpa dan dengan mempertimbangkan penambahan tenaga angin. Hasil simulasi menunjukkan bahwa dengan penambahan pembangkit tenaga angin ke dalam sistem tenaga listrik, total biaya pembangkitan tidak selalu lebih murah. Selain itu, hasil simulasi juga menunjukkan bahwa firefly algorithm sebagai metode optimasi dapat menyelesaikan permasalahan economic load dispatch (ELD) lebih baik dibandingkan metode lain yang sudah dilakukan, yaitu particle swarm optimization (PSO), bat algorithm (BA), biogeography-based optimization (BBO) dan plant growth simulation algorithm (PGSA) dengan persentase selisih nilai penghematan total biaya berkisar antara 0.32% ($50) hingga 9.27$11884)

Larvicidal, nematicidal, antifeedant and antifungal, antioxidant activities of Mentha spicata (Lamiaceae) root extracts

Purpose: To evaluate the larvicidal, nematicidal, antifeedant, and antifungal effects of 10 solvent extracts of Mentha spicata root.Methods: Ten solvent extracts were investigated for their total flavonoid and phenolic content and screened for larvicidal, nematicidal, antifeedant, and antifungal activities. The total phenolic content of the extracts was determined using the Folin–Ciocalteu method, while total flavonoid content was determined by aluminium chloride (AlCl3) colorimetric assay. Four solvents extracts were screened for antifungal activity against Aspergillus niger, Candida albicans, recultured Cryptococcus neoformans, and Microsporum audouinii using the agar diffusion method. The nematicidal activity of the compounds was evaluated against the juvenile Meloidogyne javanica organism, while larvicidal properties were evaluated against the urban mosquito Culex quinquefasciatus using a standard bioassay protocol. The antifeedant activity of marine acclimated Oreochromis mossambicus was used for evaluating ichthyotoxic potential.Results: The total flavonoid content in the extracts ranged from 18.5 to 83.4 mg/g, and the amount of free phenolic compounds ranged from 14.7 to 91.9 mg/g of extract powder. The water extract of these plants exhibited significant antioxidant activity and significant levels of phenolics and flavonoids. The water extract exhibited higher larvicidal (LD50 = 11.77 μg/mL), nematicidal (LD50 = 11.78 μg/mL), antifeedant (LD50 > 40 μg/mL), and antifungal activities (minimum inhibitory concentration: 16 μg/mL) against M. audouinii compared with the other extracts.Conclusion: These results show that the water extract of Mentha spicata may be used as a potential natural alternative source of nutritional and pharmaceutical ingredients.Keywords: Mentha spicata, Larvicidal, Nematicidal, Antifeedant and Antifungal activities, Nutritional supplement, Pharmaceutical ingredient

Bayesian, Maximum Parsimony and UPGMA Models for Inferring the Phylogenies of Antelopes Using Mitochondrial Markers

This investigation was aimed to compare the inference of antelope phylogenies resulting from the 16S rRNA, cytochrome-b (cyt-b) and d-loop segments of mitochondrial DNA using three different computational models including Bayesian (BA), maximum parsimony (MP) and unweighted pair group method with arithmetic mean (UPGMA). The respective nucleotide sequences of three Oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) and an out-group (Addax nasomaculatus) were aligned and subjected to BA, MP and UPGMA models for comparing the topologies of respective phylogenetic trees. The 16S rRNA region possessed the highest frequency of conserved sequences (97.65%) followed by cyt-b (94.22%) and d-loop (87.29%). There were few transitions (2.35%) and none transversions in 16S rRNA as compared to cyt-b (5.61% transitions and 0.17% transversions) and d-loop (11.57% transitions and 1.14% transversions) while comparing the four taxa. All the three mitochondrial segments clearly differentiated the genus Addax from Oryx using the BA or UPGMA models. The topologies of all the gamma-corrected Bayesian trees were identical irrespective of the marker type. The UPGMA trees resulting from 16S rRNA and d-loop sequences were also identical (Oryx dammah grouped with Oryx leucoryx) to Bayesian trees except that the UPGMA tree based on cyt-b showed a slightly different phylogeny (Oryx dammah grouped with Oryx gazella) with a low bootstrap support. However, the MP model failed to differentiate the genus Addax from Oryx. These findings demonstrate the efficiency and robustness of BA and UPGMA methods for phylogenetic analysis of antelopes using mitochondrial markers

PENINGKATAN HASIL BELAJAR KIMIA SISWA SMA N 1 INDRALAYA DI KELAS XI IPA 1 DENGAN MENERAPKAN MODEL PEMBELAJARAN KOOPERATIF TIPE JIGSAW II

Penelitian ini menggunakan model pembelajaran kooperatif tipe jigsaw II di kelas XI IPA 1 SMA N 1 Indralaya. Metode yang digunakan dalam penelitian ini adalah Penelitian Tindakan Kelas. Penelitian Tindakan Kelas ini dilakukan dengan tiga siklus yang terdiri dari empat tahap, yaitu: 1. Persiapan, 2. Pelaksanaan Tindakan, 3. Pengamatan, 4. Refleksi. Kesimpulan yang didapat melalui penelitian ini bahwa dengan menerapkan model kooperatif tipe jigsaw II dapat meningkatkan keaktifan dan hasil belajar kimia siswa. Tingkat keaktifan siswa pada siklus 1 sebesar 55,64%, siklus II sebesar 70,52% dan siklus III sebesar 82,64%. Ketuntasan hasil belajar siswa dapat dilihat dari tes setiap siklus mengalami peningkatan. Ketuntasan hasil belajar kimia siswa pada siklus I mencapai 60,61%, siklus II mencapai 81,81% dan pada siklus III mencapai 87,87%. Adapun saran dari penelitian yaitu hendaknya para guru kimia menggunakan model pembelajaran kooperatif tipe jigsaw II dan mengembangkannya karena dapat meningkatkan hasil belajar kimia

PENGEMBANGAN LEMBAR KERJA MAHASISWA BERBASIS PROYEK DENGAN MATERIAL LOKAL PADA PRAKTIKUM BIOKIMIA

The student creativity in project-based Biochemistry practicum lectures with local materials can be obtained when teaching materials support the achievement of learning outcomes. The purpose of this study is to develop teaching materials for project-based biochemical practicum with local materials that can enhance student creativity. This research is classified into Development research with the ADDIE development model and Tessmer formative evaluation. The stages of this research consisted of self-evaluation, expert reviews, one to one and small group. The results of this study indicate that teaching materials in the form of Student Work Sheets (LKM) based on projects with local materials have passed the expert review stage by obtaining a material validity score of 0.75 including eligibility criteria, pedagogical validity of 0.77 including eligibility criteria, design of 0.75 including the eligible criteria. Based on one to one trial, it was obtained a value of 90.67% included in the excellent category and a small group obtained a value of 90.67% included in the excellent category. The implementation of LKM based on local material projects has an impact on increasing the creativity of students in the high category

The Role of Metagenomic Approaches in the Analysis of Microbial Community in Extreme Environment

Metagenomic is a promising technique that has many applications in different fields. In fact, metagenomics is the ideal culture-independent technique that unravels the microbial composition and biodiversity in the sample, which helps scientists to study and understand how this biodiversity is affected by continuously changing conditions in the environment and how this microbial community interacts with each other. In the past, the microbial composition in extreme environments was undiscovered due to the difficulty of isolation, culturing, and identification of microbes living there. However, nowadays after the development and combination of metagenomic and next-generation sequencing techniques, it became more easy to study the microbial composition in extreme environments without culturing. In this chapter, the use of metagenomic techniques to study the microbial biodiversity in different extreme environments are discussed. In addition, different NGS platforms are discussed in terms of principles, advantages, and limitations

DNA Barcodes of Asian Houbara Bustard (Chlamydotis undulata macqueenii)

Populations of Houbara Bustards have dramatically declined in recent years. Captive breeding and reintroduction programs have had limited success in reviving population numbers and thus new technological solutions involving molecular methods are essential for the long term survival of this species. In this study, we sequenced the 694 bp segment of COI gene of the four specimens of Asian Houbara Bustard (Chlamydotis undulata macqueenii). We also compared these sequences with earlier published barcodes of 11 individuals comprising different families of the orders Gruiformes, Ciconiiformes, Podicipediformes and Crocodylia (out group). The pair-wise sequence comparison showed a total of 254 variable sites across all the 15 sequences from different taxa. Three of the four specimens of Houbara Bustard had an identical sequence of COI gene and one individual showed a single nucleotide difference (G > A transition at position 83). Within the bustard family (Otididae), comparison among the three species (Asian Houbara Bustard, Great Bustard (Otis tarda) and the Little Bustard (Tetrax tetrax)), representing three different genera, showed 116 variable sites. For another family (Rallidae), the intra-family variable sites among the individuals of four different genera were found to be 146. The COI genetic distances among the 15 individuals varied from 0.000 to 0.431. Phylogenetic analysis using 619 bp nucleotide segment of COI clearly discriminated all the species representing different genera, families and orders. All the four specimens of Houbara Bustard formed a single clade and are clearly separated from other two individuals of the same family (Otis tarda and Tetrax tetrax). The nucleotide sequence of partial segment of COI gene effectively discriminated the closely related species. This is the first study reporting the barcodes of Houbara Bustard and would be helpful in future molecular studies, particularly for the conservation of this threatened bird in Saudi Arabia