Golden Horn Estuary: Description of the ecosystem and an attempt to assess its ecological quality status using various classification metrics

In this paper, we describe the pelagic and benthic ecosystem of the Golden Horn  estuary opening into the Marmara Sea. To improve the water quality of the estuary, which had long been subject to severe anthropogenic pollution (industrial, chemical, shipping),  industrial facilities were moved from the estuary in the 1980s, followed by a rehabilitation plan in the 1990s. Our results, based on chemical parameters and phytoplankton showed some signs of improvement of water conditions in the upper layer. However, macrozoobenthic findings of this study did not reflect such a recovery in bottom life.An approach to the Ecological Quality Status (EQS) assessment was performed by applying the biotic indices BENTIX, AMBI, BOPA, BO2A. Our final assessment was based on 'expert-judgements' and revealed a very disturbed overall ecosystem with 'bad' EQS for the station at the head of the estuary,  'poor' in the rest of the estuary and 'moderate' EQS only in the middle station

Penerapan Model Pembelajaran Problem Based Introduction untuk Meningkatkan Hasil Belajar Geografi Siswa Kelas XI Sman 2 Banda Aceh

Model pembelajaran problem based introduction merupakan sebuah model pembelajaran yang menyajikan masalah kontekstual sehingga merangsang peserta didik untuk belajar. Tujuan penelitian ini yaitu untuk mengetahui: (1) Peningkatan hasil belajar geografi siswa kelas XI SMAN 2 Banda Aceh dengan menerapkan model problem based introduction; (2) Aktivitas guru dan siswa dalam pembelajaran geografi dengan model problem based introduction; (3) Keterampilan guru mengelola pembelajaran dengan model problem based introduction; dan (4) Respon siswa setelah pembelajaran dengan menggunakan model problem based introduction. Subjek penelitian ini adalah siswa kelas XI IIS 2 SMAN 2 Banda Aceh yang berjumlah 32 siswa. Pengumpulan data dilakukan dengan menggunakan tes hasil belajar, lembar pengamatan aktivitas guru dan siswa, lembar pengamatan keterampilan guru mengelola pembelajaran, dan angket respon siswa menggunakan model problem based introduction. Analisis data menggunakan statistik deskriptif persentase. Hasil penelitian menunjukkan bahwa: (1) Persentase ketuntasan individual pada siklus I sebesar 93% dengan 2 siswa dinyatakan tidak tuntas. Pada siklus II persentase ketuntasan individual mengalami peningkatan menjadi 96%. Hanya terdapat 1 siswa yang tidak tuntas secara individual pada siklus ini. Pada siklus III keseluruhan siswa dinyatakan tuntas belajar secara individual. Persentase ketuntasan klasikal pada siklus I sebesar 50%, siklus II meningkat menjadi 70% dan siklus III menjadi 90%; (2) Aktivitas guru dan siswa dari siklus I hingga siklus III sudah mencerminkan keterlaksanaan model problem based introduction; (3) Keterampilan guru mengelola pembelajaran dengan menggunakan model problem based introduction mengalami peningkatan. Pada siklus I diperoleh skor rata-rata sebesar 3,65, kemudian meningkat pada siklus II menjadi 3,7 dan siklus III dengan skor 3,8 yang dikategorikan baik sekali; (4) Respon siswa terhadap model problem based introduction dapat dikatakan baik sekali dengan 94% dari 32 siswa berpendapat bahwa pembelajaran menggunakan model problem based introduction dapat meningkatkan pemahaman mereka terhadap materi pelestarian lingkungan hidup dan pembangunan berkelanjutan yang telah dipelajari

Bisbibenzyls, a New Type of Antifungal Agent, Inhibit Morphogenesis Switch and Biofilm Formation through Upregulation of DPP3 in Candida albicans

The yeast-to-hypha transition plays a crucial role in the pathogenesis of C. albicans. Farnesol, a quorum sensing molecule (QSM) secreted by the fungal itself, could prevent the formation of hyphae and subsequently lead to the defect of biofilm formation. The DPP3, encoding phosphatase, is a key gene in regulating farnesol synthesis. In this study, we screened 24 bisbibenzyls and 2 bibenzyls that were isolated from bryophytes or chemically synthesized by using CLSI method for antifungal effect. Seven bisbibenzyls were found to have antifungal effects with IC80 less than 32 µg/ml, and among them, plagiochin F, isoriccardin C and BS-34 were found to inhibit the hyphae and biofilm formation of C. albicans in a dose-dependent manner. To uncover the underlying relationship between morphogenesis switch and QSM formation, we measured the farnesol production by HPLC-MS and quantified Dpp3 expression by detecting the fluorescent intensity of green fluorescent protein tagged strain using Confocal Laser Scanning microscopy and Multifunction Microplate Reader. The DPP3 transcripts were determined by real-time PCR. The data indicated that the bisbibenzyls exerted antifungal effects through stimulating the synthesis of farnesol via upregulation of Dpp3, suggesting a potential antifungal application of bisbibenzyls. In addition, our assay provides a novel, visual and convenient method to measure active compounds against morphogenesis switch

A rapid and sensitive system for recovery of nucleic acids from Mycobacteria sp. on archived glass slides

The field of diagnostics continues to advance rapidly with a variety of novel approaches, mainly dependent upon high technology platforms. Nonetheless much diagnosis, particularly in developing countries, still relies upon traditional methods such as microscopy. Biological material, particularly nucleic acids, on archived glass slides is a potential source of useful information both for diagnostic and epidemiological purposes. There are significant challenges faced when examining archived samples in order that an adequate amount of amplifiable DNA can be obtained. Herein, we describe a model system to detect low numbers of bacterial cells isolated from glass slides using (laser capture microscopy) LCM coupled with PCR amplification of a suitable target. Mycobacterium smegmatis was used as a model organism to provide a proof of principle for a method to recover bacteria from a stained sample on a glass slide using a laser capture system. Ziehl-Neelsen (ZN) stained cells were excised and catapulted into tubes. Recovered cells were subjected to DNA extraction and pre-amplified with multiple displacement amplification (MDA). This system allowed a minimum of 30 catapulted cells to be detected following a nested real-time PCR assay, using rpoB specific primers. The combination of MDA and nested real-time PCR resulted in a 30-fold increase in sensitivity for the detection of low numbers of cells isolated using LCM. This study highlights the potential of LCM coupled with MDA as a tool to improve the recovery of amplifiable nucleic acids from archived glass slides. The inclusion of the MDA step was essential to enable downstream amplification. This platform should be broadly applicable to a variety of diagnostic applications and we have used it as a proof of principle with a Mycobacterium sp. model system

Pollution Monitoring Using Mytilus galloprovincialis and Fishes: A Case Study on the Southern Black Sea Shelf

In this study, the heavy metal bioaccumulations in mussels (Mytilus galloprovincialis) and fishes (Merlangius merlangus euxinus) have been studied along the Southern Black Sea Shelf. Generally, Pb and Cd contents were higher than the critical limits set by the Turkish Ministry of Environment for Aquatic Products (1 mu g g(-1) wet wt. and 0.1 mu g g(-1) wet wt., respectively) and European countries (2.0 mu g g(-1) UNEP, 1985). They showed increases towards the eastern end of the shelf. As contents were observed higher than the critical limits set by the Turkish Ministry of Environment for Aquatic Products (1.0 mu g g(-1) wet wt.) at stations Terkos, Samsun and Ordu in 2009. In contrast, Hg levels were also higher than the critical limits set by the Turkish Ministry of Environment for Aquatic Products (0.5 mu g g(-1) wet wt.) in 2005 and the highest Hg concentrations were found in the west and middle of the shelf

Pollution Monitoring Using Mytilus galloprovincialis and Fishes: A Case Study on the Southern Black Sea Shelf

In this study, the heavy metal bioaccumulations in mussels (Mytilus galloprovincialis) and fishes (Merlangius merlangus euxinus) have been studied along the Southern Black Sea Shelf. Generally, Pb and Cd contents were higher than the critical limits set by the Turkish Ministry of Environment for Aquatic Products (1 mu g g(-1) wet wt. and 0.1 mu g g(-1) wet wt., respectively) and European countries (2.0 mu g g(-1) UNEP, 1985). They showed increases towards the eastern end of the shelf. As contents were observed higher than the critical limits set by the Turkish Ministry of Environment for Aquatic Products (1.0 mu g g(-1) wet wt.) at stations Terkos, Samsun and Ordu in 2009. In contrast, Hg levels were also higher than the critical limits set by the Turkish Ministry of Environment for Aquatic Products (0.5 mu g g(-1) wet wt.) in 2005 and the highest Hg concentrations were found in the west and middle of the shelf