On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei

Background: Although technical advances in genomics and proteomics research have yielded a better understanding of the coding capacity of a genome, one major challenge remaining is the identification of all expressed proteins, especially those less than 100 amino acids in length. Such information can be particularly relevant to human pathogens, such as Trypanosoma brucei, the causative agent of African trypanosomiasis, since it will provide further insight into the parasite biology and life cycle. Results: Starting with 993 T. brucei transcripts, previously shown by RNA-Sequencing not to coincide with annotated coding sequences (CDS), homology searches revealed that 173 predicted short open reading frames in these transcripts are conserved across kinetoplastids with 13 also conserved in representative eukaryotes. Mining mass spectrometry data sets revealed 42 transcripts encoding at least one matching peptide. RNAi-induced down-regulation of these 42 transcripts revealed seven to be essential in insect-form trypanosomes with two also required for the bloodstream life cycle stage. To validate the specificity of the RNAi results, each lethal phenotype was rescued by co-expressing an RNAi-resistant construct of each corresponding CDS. These previously non-annotated essential small proteins localized to a variety of cell compartments, including the cell surface, mitochondria, nucleus and cytoplasm, inferring the diverse biological roles they are likely to play in T. brucei. We also provide evidence that one of these small proteins is required for replicating the kinetoplast (mitochondrial) DNA. Conclusions: Our studies highlight the presence and significance of small proteins in a protist and expose potential new targets to block the survival of trypanosomes in the insect vector and/or the mammalian host

Tunneling splitting of magnetic levels in Fe8 detected by 1H NMR cross relaxation

Measurements of proton NMR and the spin lattice relaxation rate 1/T1 in the octanuclear iron (III) cluster [Fe8(N3C6H15)6O2(OH)12][Br8 9H2O], in short Fe8, have been performed at 1.5 K in a powder sample aligned along the main anisotropy z axis, as a function of a transverse magnetic field (i.e., perpendicular to the main easy axis z). A big enhancement of 1/T1 is observed over a wide range of fields (2.5-5 T), which can be attributed to the tunneling dynamics; in fact, when the tunneling splitting of the pairwise degenerate m=+-10 states of the Fe8 molecule becomes equal to the proton Larmor frequency a very effective spin lattice relaxation channel for the nuclei is opened. The experimental results are explained satisfactorily by considering the distribution of tunneling splitting resulting from the distribution of the angles in the hard xy plane for the aligned powder, and the results of the direct diagonalization of the model Hamiltonian.Comment: J. Appl. Phys., in pres

Small interfering RNA-producing loci in the ancient parasitic eukaryote Trypanosoma brucei

BACKGROUND: At the core of the RNA interference (RNAi) pathway in Trypanosoma brucei is a single Argonaute protein, TbAGO1, with an established role in controlling retroposon and repeat transcripts. Recent evidence from higher eukaryotes suggests that a variety of genomic sequences with the potential to produce double-stranded RNA are sources for small interfering RNAs (siRNAs). RESULTS: To test whether such endogenous siRNAs are present in T. brucei and to probe the individual role of the two Dicer-like enzymes, we affinity purified TbAGO1 from wild-type procyclic trypanosomes, as well as from cells deficient in the cytoplasmic (TbDCL1) or nuclear (TbDCL2) Dicer, and subjected the bound RNAs to Illumina high-throughput sequencing. In wild-type cells the majority of reads originated from two classes of retroposons. We also considerably expanded the repertoire of trypanosome siRNAs to encompass a family of 147-bp satellite-like repeats, many of the regions where RNA polymerase II transcription converges, large inverted repeats and two pseudogenes. Production of these newly described siRNAs is strictly dependent on the nuclear DCL2. Notably, our data indicate that putative centromeric regions, excluding the CIR147 repeats, are not a significant source for endogenous siRNAs. CONCLUSIONS: Our data suggest that endogenous RNAi targets may be as evolutionarily old as the mechanism itself

PENGUATAN CIVIC ENGAGEMENT PADA PEMUDA DESA LELEA MELALUI TRADISI NGAROT (Studi Kualitatif Masyarakat Desa Lelea, Kab. Indramayu)

Tujuan penelitian ini adalah untuk menggali secara mendalam bagaimana nilai – nilai yang terkandung dalam tradisi Ngarot dapat diimplementasikan pada konsep penguatan keterlibatan warga negara khususnya bagi pemuda. Metode yang digunakan dalam penelitian ini adalah studi kasus dengan pendekatan kualitatif. Adapun yang menjadi objek penelitian adalah masyarakat desa Lelea, kecamatan Lelea, kabupaten Indramayu. Objek tersebut dipilih karena masyarakat Lelea merupakan kelompok yang paling kental dengan tradisi Ngarot. Penelitian ini dilaksanakan pada rentang bulan Februari hingga Juni 2021. Data – data penelitian dikumpulkan menggunakan teknik studi pustaka, observasi dan wawancara. Kemudian, data yang telah didapatkan dianalisis menggunakan teknik reduksi data, sajian data, dan verifikasi. Hasil dari penelitian ini menunjukan bahwa tradisi Ngarot memiliki beberapa nilai di dalamnya, seperti nilai demokrasi, nilai edukasi, nilai pemberdayaan masyarakat, dan nilai tanggung jawab sosial yang tergambarkan dari setiap tahapan tradisi Ngarot yang diikuti oleh pemuda desa Lelea. Nilai – nilai yang ada pada tradisi Ngarot menjadi dasar yang baik untuk pemuda dalam memberikan kontribusinya untuk kehidupan masyarakat Lelea. Berbagai kegiatan yang dilakukan pemuda desa Lelea dapat mengarah kepada indikator dari dimensi keterlibatan warga negara, baik melalui tindakan individu maupun aktifitas kelompok dalam rangka melakukan perubahan pada masyarakat. Hal tersebut merupakan esensi dari konsep keterlibatan warga negara. Kesimpulan penelitian ini adalah nilai – nilai dalam tradisi Ngarot dapat memperkuat konsep keterlibatan pada pemuda desa Lelea. Penelitian ini membawa implikasi terhadap kebudayaan yang dapat menjadi suatu media baru untuk mengembangkan konsep keterlibatan warga negara, khususnya dalam lingkup sosial kemasyarakatan. ************ The purpose of this study is to explore in depth how the values contained in the Ngarot tradition can be implemented in the concept of strengthening civic engagement, especially for youth. The method used in this research is a case study with a qualitative approach. The object of research is the community of Lelea village, Lelea sub-district, Indramayu district. The object was chosen because the Lelea community is the group most strongly associated with the Ngarot tradition. This research was conducted in the range of February to June 2021. Research data were collected using literature study, observation and interview techniques. Then, the data that has been obtained is analyzed using data reduction techniques, data display, and verification. The results of this study indicate that the Ngarot tradition has several values in it, such as the value of democracy, the value of education, the value of community empowerment, and the value of social responsibility which is depicted from each stage of the Ngarot tradition which is followed by the youth of Lelea village. The values that exist in the Ngarot tradition are a good basis for youth to contribute to the life of the Lelea community. Various activities carried out by youth of Lelea village can lead to indicators of the dimensions of civic engagement, both through individual actions and group activities in order to make changes to society. This is the essence of the concept of civic engagement. The conclusion of this study is that values in the Ngarot tradition can strengthen the concept of engagement in youth of Lelea village. This research has implications for culture which can become a new medium to develop the concept of civic engagement, especially in the social sphere

Perancangan Sistem Data Wirehouse untuk Meningkatkan Kinerja Pelayanan Bantuan Bagi Masyarakat pada Kantor Lurah Oebobo dengan Menggunakan Borland Delphi 7.0

Abstract - Computer technology represent important medium which used in various actifity management of governance. But that way the applications in computer technology still have common traits, and there is no application which in making special for the making of bank statement able to water down service of aid to society in braiding cooperation between governmental institution and society. Result of which obtaining from this research is a System Data of Warehouse able to in utilizing to assist increase service of aid to society which in the form of giving certificate. &nbsp

Segmentasi Daun Cendana Berbasis Citra Menggunakan Otsu Thresholding

The segmentation process is the separation of parts of the object area from the background in an image, so that segmented objects can be processed for other purposes such as pattern recognition. The results of segmentation must be accurate, if it is not accurate in separating objects in the image it will affect the results of further processing. The segmentation process is carried out using the Otsu Thresholding method on sandalwood leaf images by first applying the Median filter to reduce noise. After obtaining the segmented image, then performing performance measurements. The segmentation results from each test are evaluated using the RAE (relative foreground area error) and ME (misclassification error). The segmentation results of 8 sandalwood leaf images from 2 existing conditions show that, sandalwood leaf image segmentation with good leaf conditions obtains the best segmentation results with smaller errors of 5 image data. While the images of sandalwood leaves affected by the disease as many as 3 image data have more diverse areas so that the segmentation results are not good without any morphological proces

tRNASec is transcribed by RNA polymerase II in Trypanosoma brucei but not in humans

Nuclear-encoded tRNAs are universally transcribed by RNA polymerase III (Pol-III) and contain intragenic promoters. Transcription of vertebrate tRNASec however requires extragenic promoters similar to Pol-III transcribed U6 snRNA. Here, we present a comparative analysis of tRNASec transcription in humans and the parasitic protozoa Trypanosoma brucei, two evolutionary highly diverged eukaryotes. RNAi-mediated ablation of Pol-II and Pol-III as well as oligo-dT induced transcription termination show that the human tRNASec is a Pol-III transcript. In T. brucei protein-coding genes are polycistronically transcribed by Pol-II and processed by trans-splicing and polyadenylation. tRNA genes are generally clustered in between polycistrons. However, the trypanosomal tRNASec genes are embedded within a polycistron. Their transcription is sensitive to α-amanitin and RNAi-mediated ablation of Pol-II, but not of Pol-III. Ectopic expression of the tRNASec outside but not inside a polycistron requires an added external promoter. These experiments demonstrate that trypanosomal tRNASec, in contrast to its human counterpart, is transcribed by Pol-II. Synteny analysis shows that in trypanosomatids the tRNASec gene can be found in two different polycistrons, suggesting that it has evolved twice independently. Moreover, intron-encoded tRNAs are present in a number of eukaryotic genomes indicating that Pol-II transcription of tRNAs may not be restricted to trypanosomatid

HUBUNGAN STATUS NUTRISI DENGAN KUALITAS HIDUP PASIEN GAGAL GINJAL KRONIK YANG MENJALANI HEMODIALISIS DI RSUD PROF. DR. W. Z. JOHANNES

Penyakit ginjal kronik menggambarkan kerusakan ginjal dan/atau penurunan fungsi ginjal selama 3 bulan atau lebih dengan laju filtrasi glomerulus kurang dari 60 ml/menit/1,73 m2. Pilihan pengobatan gagal ginjal kronik yang sering dilakukan adalah hemodialisis (HD). Terapi hemodialisis merupakan teknologi tinggi sebagai terapi pengganti untuk mengeluarkan sisa-sisa metabolisme atau racun tertentu dari peredaran darah manusia seperti air, natrium, kalium, hidrogen, urea, kreatinin, asam urat, dan zat-zat lain melalui membran semi permiabel sebagai pemisah darah dan cairan dialisat pada ginjal buatan dimana terjadi proses difusi, osmosis dan ultrafiltrasi. HD dapat dilakukan apabila ada penurunan kualitas hidup tanpa penyebab jelas dan HD dapat memberikan kualitas hidup baik. Berbagai faktor dapat mempengaruhi kualitas hidup, salah satunya status nutrisi dan masalah nutrisi tersering adalah malnutrisi energi protein. Tujuan penelitian mengetahui hubungan status nutrisi dengan kualitas hidup pasien gagal ginjal kronik yang menjalani hemodialisis di RSUD Prof. Dr. W. Z. Johannes. Metodologi penelitian ini merupakan penelitian analitik observasional dengan desain penelitian cross sectional. Sampel penelitian ini adalah pasien gagal ginjal kronik di RSUD Prof. DR. W. Z. Johannes yang berjumlah 48 responden. Pada penelitian ini 6 orang pasien di drop out karena meninggal dunia. Kemudian peneliti mencari 2 sampel baru karena sampel minimal adalah 44 orang. Pengukuran status nutrisi menggunakan Malnutrition Inflammation Score dan pengukuran  kualitas hidup menggunakan Quality Of Life Index Dialysis Version III. Analisis bivariat digunakan untuk mengetahui hubungan antara variabel independen dengan variabel dependen dengan menggunakan uji Pearson Chi-square. Hasil untuk uji kemaknaan hubungan antara variabel tersebut menggunakan uji Pearson Chi-square dengan angka kemaknaan = 0,05, diperoleh nilai p=0,340 yang berarti p > 0,05. Kesimpulan dari penelitian ini tidak ada hubungan antara status nutrisi dengan kualitas hidup pasien gagal ginjal kronik yang menjalani hemodialisis di RSUD Prof. Dr. W.Z. Johanne

Retention and loss of RNA interference pathways in trypanosomatid protozoans

RNA interference (RNAi) pathways are widespread in metaozoans but the genes required show variable occurrence or activity in eukaryotic microbes, including many pathogens. While some Leishmania lack RNAi activity and Argonaute or Dicer genes, we show that Leishmania braziliensis and other species within the Leishmania subgenus Viannia elaborate active RNAi machinery. Strong attenuation of expression from a variety of reporter and endogenous genes was seen. As expected, RNAi knockdowns of the sole Argonaute gene implicated this protein in RNAi. The potential for functional genetics was established by testing RNAi knockdown lines lacking the paraflagellar rod, a key component of the parasite flagellum. This sets the stage for the systematic manipulation of gene expression through RNAi in these predominantly diploid asexual organisms, and may also allow selective RNAi-based chemotherapy. Functional evolutionary surveys of RNAi genes established that RNAi activity was lost after the separation of the Leishmania subgenus Viannia from the remaining Leishmania species, a divergence associated with profound changes in the parasite infectious cycle and virulence. The genus Leishmania therefore offers an accessible system for testing hypothesis about forces that may select for the loss of RNAi during evolution, such as invasion by viruses, changes in genome plasticity mediated by transposable elements and gene amplification (including those mediating drug resistance), and/or alterations in parasite virulence

Cytochrome oxidase subunit VI of Trypanosoma brucei is imported without a cleaved presequence and is developmentally regulated at both RNA and protein levels

Mitochondrial respiration in the African trypanosome undergoes dramatic developmental stage regulation. This requires co-ordinated control of components encoded by both the nuclear genome and the kinetoplast, the unusual mitochondrial genome of these parasites. As a model for understanding the co-ordination of these genomes, we have examined the regulation and mitochondrial import of a nuclear-encoded component of the cytochrome oxidase complex, cytochrome oxidase subunit VI (COXVI). By generating transgenic trypanosomes expressing intact or mutant forms of this protein, we demonstrate that COXVI is not imported using a conventional cleaved presequence and show that sequences at the N-terminus of the protein are necessary for correct mitochondrial sorting. Analyses of endogenous and transgenic COXVI mRNA and protein expression in parasites undergoing developmental stage differentiation demonstrates a temporal order of control involving regulation in the abundance of, first, mRNA and then protein. This represents the first dissection of the regulation and import of a nuclear-encoded protein into the cytochrome oxidase complex in these organisms, which were among the earliest eukaryotes to possess a mitochondrion