Tawuran antar pelajar: penelitian di SMK Diponegoro Kecamatan Ploso dan SMK Dwijaya Bhakti Jombang

Ada dua persoalan yang dikaji dalam penelitian ini, yaitu: (1) Faktor apa saja yang menyebabkan terjadinya aksi tawuran antar pelajar di SMK Diponegoro Kecamatan Ploso dan SMK Dwijaya Bhakti Jombang; (2) Faktor apa yang paling dominan yang meyebabkan terjadinya tawuran antar pelajar. Adapun tujuan dari penelitian ini adalah untuk mengetahui apa saja faktor-faktor penyebab terjadinya tawuran antar pelajar dan faktor yang paing dominan penyebab terjadinya tawuran antar pelajar. Untuk mengungkap persoalan tersebut secara menyeluruh dan mendalam maka dalam penelitian ini menggunakan metode analisis deskriptif yang bersifat kualitatif dalam menganalisis data-data yang diperoleh dilapangan melalui observasi, interview dan dokumentasi. Kemudian data tersebut dianalisis dengan dasar teori Konflik Lewis A. Coser tentang adanya konflik yang dapat menimbulkan dampak positif terhadap kelompok dalam. Hal ini dimaksudkan adanya konflik yang dapat meningkatkan rasa solidaritas clan kebersamaan antara satu dengan yang lain karena faktor lingkungan keseharian mereka yang mengharuskan untuk ikut terlibat kedalam aksi tawuran antar pelajar, mereka bersatu untuk melindungi kelompok mereka dari siapapun yang mengganggu dan menyakiti anggota dalam kelompok yang sudah mereka bentuk. Dari hasil penelitian ini ditemukan bahwa (I) Faktor penyebab terjadinya tawuran antar pelajar adalah faktor lingkungan dan pergaulan, faktor membela teman, faktor balas dendam, faktor keluarga serta pengaruh perubahan zaman (2) Dari beberapa faktor yang telah dikemukakan faktor lingkungan merupakan faktor yang paling dominan dan paling berpangaruh terhadap terjadinya tawuran antar pelajar, karena baik dan buruknya tingkah laku remaja semua itu tidak akan lepas dari lingkungan tempat mereka beradaptasi dan menghabiskan waktu kesehariannya dengan teman-teman mereka

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Designing transmissible viral vaccines for evolutionary robustness and maximum efficiency

The danger posed by emerging infectious diseases necessitates the development of new tools that can mitigate the risk of animal pathogens spilling over into the human population. One promising approach is the development of recombinant viral vaccines that are transmissible, and thus capable of self-dissemination through hard to reach populations of wild animals. Indeed, mathematical models demonstrate that transmissible vaccines can greatly reduce the effort required to control the spread of zoonotic pathogens in their animal reservoirs, thereby limiting the chances of human infection. A key challenge facing these new vaccines, however, is the inevitability of evolutionary change resulting from their ability to self-replicate and generate extended chains of transmission. Further, carrying immunogenic transgenes is often costly, in terms of metabolic burden, increased competition with the pathogen, or due to unintended interactions with the viral host regulatory network. As a result, natural selection is expected to favor vaccine strains that down-regulate or delete these transgenes resulting in increased rates of transmission and reduced efficacy against the target pathogen. In addition, efficacy and evolutionary stability will often be at odds; as when longer, more efficacious antigens experience faster rates of evolutionary decay. Here, we ask how such trade-offs influence the overall performance of transmissible vaccines. We find that evolutionary instability can substantially reduce performance, even for vaccine candidates with the ideal combination of efficacy and transmission. However, we find that, at least in some cases, vaccine stability and overall performance can be improved by the inclusion of a second, redundant antigen. Overall, our results suggest that the successful application of recombinant transmissible vaccines will require consideration of evolutionary dynamics and epistatic effects, as well as basic measurements of epidemiological features

Model source code

Contains C++ files used to model inbreeding depression in autotetraploid

Data from: Bottlenecks and inbreeding depression in autotetraploids

Inbreeding depression is dependent on the ploidy of populations and can inhibit the evolution of selfing. While polyploids should generally harbor less inbreeding depression than diploids at equilibrium, it has been unclear whether this pattern holds in non-equilibrium conditions following bottlenecks. We use stochastic individual based simulations to determine the effects of population bottlenecks on inbreeding depression in diploids and autotetraploids, in addition to cases where neo-autotetraploids form from the union of unreduced gametes. With a ploidy-independent dominance function based on enzyme kinetics, inbreeding depression is generally lower in autotetraploids for fully and partially recessive mutations. Due to the sampling of more chromosomes during reproduction, bottlenecks generally reduce inbreeding depression to a lesser extent in autotetraploids. All else being equal, population bottlenecks may have ploidy dependent effects for another reason – in some cases mating between close relatives temporarily increases inbreeding depression in autotetraploids by increasing the frequency of the heterozygous genotype harboring the most harmful mutations. When neo-autotetraploids are formed by few individuals, inbreeding depression is dramatically reduced, given extensive masking of harmful mutations following whole genome duplication. This effect persists as nascent tetraploids reach mutation-selection-drift balance, providing a transient period of permissive conditions favoring the evolution of selfing

Multistrain Models of Recombinant Transmissible Vaccines with Mutational Decay

In the absence of gene flow, populations undergo local adaptation to their environment. Swamping occurs when migrant genes prevent local adaptation with high levels of gene flow. Although swamping is often depicted as a problem, it could be implemented to arrest unwanted evolution in GMOs which depend on the integrity of transgenes. In GMO vaccines, the fitness cost of carrying an antigen results in reversion to virulence or antigenic decay through a series of mutational steps. Zoonotic diseases pose an increasing threat to people, causing an estimated 2.7 million worldwide human deaths each year. Recombinant transmissible vaccines (RTVs) provide a way to reduce the risk of infectious diseases, especially zoonotic diseases with wildlife reservoirs that cannot be directly vaccinated. A well-documented two-strain SIR model, including pathogen and RTV, represents the situation where an RTV can mutate to its vector in one step. We built an n-strain model expanding upon this model by imagining a similar situation where the RTV must undergo n-1 mutations, rather than one, to revert to the vector. Although the vector is benign, it competes with the RTV for susceptible individuals, thereby reducing the benefits of the RTV. We found that the level of direct vaccination necessary depends on mutation rate and the decline in efficacy from each mutational step. This model allows us to quantify the amount of swamping in order to protect populations against infectious disease and prevent local adaptation

Data from: Costs of selfing prevent the spread of a self-compatibility mutation that causes reproductive assurance

In flowering plants, shifts from outcrossing to partial or complete self-fertilization have occurred independently thousands of times, yet the underlying adaptive processes are difficult to discern. Selfing’s ability to provide reproductive assurance when pollination is uncertain is an oft-cited ecological explanation for its evolution, but this benefit may be outweighed by genetic costs diminishing its selective advantage over outcrossing. We directly studied the fitness effects of a self-compatibility (SC) mutation that was backcrossed into a self-incompatible (SI) population of Leavenworthia alabamica, illuminating the direction and magnitude of selection on the mating-system modifier. In array experiments conducted in two years, SC plants produced 17-26% more seed, but this advantage was counteracted by extensive seed discounting -- the replacement of high-quality outcrossed seeds by selfed seeds. Using a simple model and simulations, we demonstrate that SC mutations with these attributes rarely spread to high frequency in natural populations, unless inbreeding depression falls below a threshold value (0.57 ≤ threshold ≤ 0.70) in SI populations. A combination of heavy seed discounting and moderate inbreeding depression likely explains why outcrossing adaptations such as self-incompatibility are maintained generally, despite persistent input of selfing mutations and frequent limits on outcross seed production in nature

Data from: Selfing ability and drift load evolve with range expansion

Colonization at expanding range edges often involves few founders, reducing effective population size. This process can promote the evolution of self-fertilization, but implicating historical processes as drivers of trait evolution is often difficult and requires an explicit model of biogeographic history. In plants, contemporary limits to outcrossing are often invoked as evolutionary drivers of self-fertilization, but historical expansions may shape mating system diversity, with leading-edge populations evolving elevated selfing ability. In a widespread plant, Campanula americana, we identified a glacial refugium in the southern Appalachian Mountains from spatial patterns of genetic drift among 24 populations. Populations farther from this refugium have smaller effective sizes and fewer rare alleles. They also displayed elevated heterosis in among-population crosses, reflecting the accumulation of deleterious mutations during range expansion. While populations with elevated heterosis had reduced segregating mutation load, the magnitude of inbreeding depression lacked geographic pattern. The ability to self-fertilize was strongly positively correlated with the distance from the refugium and mutation accumulation—a pattern that contrasts sharply with contemporary mate and pollinator limitation. In this and other species, diversity in sexual systems may reflect the legacy of evolution in small, colonizing populations, with little or no relation to the ecology of modern populations.,Phenotypic data for f inbreeding depression and drift loadPopulation attributes and phenotypic data used to calculate stage-specific and cumulative inbreeding depression and drift load for 24 populations of Campanula americana. Column header descriptions are provided in the \u27column header descriptions\u27 tab.Koskietal_EvoLett_PhenotypicData_DriftLoad_InbreedingDepression.xlsxipyrad paramsParameter file associated with our processing of RADseq data in ipyradbellmergeAfter processing reads in ipyrad, the resulting data are stored in the variant call format (VCF) in bellmerge.vcf. These data can be analyzed with 3 R scripts to generate results presented in the paper.diversity R scriptExtracts estimates of the population mutation parameter and Tajima\u27s Ddiversity.Rinbreeding coefficient R scriptCalculates observed and expected heterozygosity from genotypic data and the inbreeding coefficient of populations.inbreeding coefficient.RTDoA R scriptCalculates directionality statistics and identifies the geographic location of a recent range expansion. To properly run this file, one must set a filepath containing the files in the TDoA dependencies folder.TDoA.RREADM

Locus

This file contains functions called by the C++ code, main.cpp

Fragment Analysis 2015

Progeny array data for plants in the 2015 experimental arrays, in MLTR format. Plants were genotyped at 6 hypervariable microsatellite markers. Maternal plants are denoted with (!). These data were also used for paternity inference, following conversion to the Cervus file format