Peran Daya Dukung Wilayah Terhadap Pengembangan USAha Peternakan Sapi Madura

Research conducted on the island of Madura. The aim of the research was analyzed the area-based development of beef cattle in Madura island. Primary research data was sourced from statistics in the Madura district in figures. Data was analyzed using Location Quotient (LQ) method. Data procesing conducted whith spreadsheet from Excel on Microsoft Windows 7. The results showed that the basis for the development of Madura cattle each regency were Pamekasan (sub-district Larangan, Pasean, Batumamar, Palengan, Proppo, Tlanakan, and Pegantenan), Sumenep (sub-district Gayam, Nonggunong and Batuputih), Bangkalan (subdistrict Kokop, Geger, Galis, Tanah Merah, and Blega) and Bangkalan (sub-district Ketapang, Sokobanah, Kedungdung, Sampang, Banyuates, Robatal, and Omben. Conclusion of the research was the development of Madura cattle concentrated in the base region of Madura cattle

Novel Modes of Regulation of Cyclin Dependent Kinase Cdk1

Les quinases dependents de ciclina (CDKs) dirigeixen la progressió del cicle cel·lular a les cèl·lules eucariotes. A l’organisme eucariota model Saccharomyces cerevisiae (llevat de gemmació) una sola quinasa dependent de ciclina, Cdk1, és essencial i suficient per dirigir el cicle cel·lular. Unida alternativament a ciclines de fase G1, S i G2/M, Cdk1 regula els programes transcripcionals del cicle cel·lular, la replicació i segregació dels cromosomes, la dinàmica del fus mitòtic, el creixement cel·lular polar, la morfogènesi, etc. La desregulació de l’activitat CDK promou la proliferació descontrolada i la inestabilitat genòmica. Donada la seva funció essencial en la progressió del cicle cel·lular, Cdk1 és estretament regulada per proteïnes associades (les ciclines, Cks1, i inhibidors de les CDKs –CKIs) i per modificacions post-traduccionals. Tanmateix, molts detalls de la regulació de Cdk1 romanen desconeguts, com és el cas de com les activitats CDK de fase G1 o de fase M són inhibides en resposta a determinats estressos cel·lulars. Quan la progressió del cicle cel·lular és amenaçada per la presència d’estressos genotòxics tals com l’estrès replicatiu o la presència de dany al DNA, un mecanisme de vigilància, l’anomenat checkpoint de la fase S, s’activa per tal de protegir la integritat del genoma. Al llevat de gemmació, el checkpoint de la fase S és mediat per la quinasa Mec1 (ATR/ATM a humans) i la seva quinasa efectora Rad53 (Chk2 a humans). Per explorar si la quinasa efectora Rad53 regula Cdk1 en resposta a estrès genotòxic, hem explorat dues qüestions principals: (1) la fosforilació de Cdk1 per Rad53 i (2) la regulació per Rad53 de proteïnes associades a Cdk1. Pel que fa a la primera qüestió, aprofitant un assaig quinasa in vitro amb Rad53, mostrem que Cdk1 és fosforilat directament per Rad53. Hem identificat proteòmicament dos llocs de Cdk1 (Ser46, Ser258) fosforilats per Rad53 in vitro. Les cèl·lules dirigides per l’al·lel no-fosforilable (Cdk1-2A) mostren un fenotip wee, compatible amb una activitat CDK incrementada/desregulada. Les cèl·lules dirigides per l’al·lel fosfomimètic (Cdk1-2E) són allargades i més grans que les cèl·lules silvestres, compatible amb una activitat CDK reduïda. A més, assignem i quantifiquem les diferents formes fosforilades de Cdk1 in vivo mitjançant electroforesi Phos-tag. Respecte la segona qüestió, hem identificat proteòmicament proteïnes associades a Cdk1 en presència d’estrès replicatiu en forma dependent de Rad53. Hem estudiat en detall el producte del gen de funció desconeguda YPL014W, que bategem Cip1 (per Cdk1 Interacting Protein 1), que obté la puntuació més alta en l’anàlisi. Les nostres dades mostren que Cip1 és una proteïna regulada al llarg del cicle cel·lular. A més, l’abundància de Cip1 s’incrementa en forma dependent de Rad53 en presència d’estrès replicatiu. La sobre-expressió de Cip1 bloqueja les cèl·lules a fase G1 i estabilitza el CKI de fase S Sic1 in vivo. A més, Cip1 interacciona específicament amb el complex de fase G1 Cln2-Cdk1, però no amb el complex de fase S Clb5-Cdk1 or el de fase M Clb2-Cdk1. Cip1 inhibeix l’activitat Cln2-CDK tant in vivo com in vitro. Els nostres resultats suggereixen que Cip1 pot ser un nou CKI de l’activitat CDK de fase G1.Cyclin dependent kinases are drive cell division cycle progression in eukaryotic cells. In the model eukaryotic organism Saccharomyces cerevisiae (budding yeast) a single Cyclin Dependent Kinase, Cdk1, is essential and sufficient to drive the cell cycle. Alternately bound to G1, S and G2/M phase cyclins, Cdk1 regulates cell cycle transcriptional programs, chromosome replication and segregation, spindle dynamics, polarized cell growth, morphogenesis, etc. Misregulated CDK activity induces unscheduled proliferation as well as genomic instability. Given its essential function in cell cycle progression, Cdk1 is tightly regulated by binding partners (cyclins, Cks1 and Cyclin dependent Kinase Inhibitors -CKIs) and post-translational modifications. However, many details on Cdk1 regulation remain unknown, such as how G1 or mitotic CDK activities are inhibited in response to challenging conditions. When the cell cycle progression is challenged by genotoxic stress such as DNA replication stress or DNA damage, a surveillance mechanism, the S phase checkpoint is activated to protect the integrity of the genome. In the budding yeast the S phase checkpoint is mediated by the Mec1 kinase (ATR/ATM in humans) and its downstream effector kinase Rad53 (Chk2 in humans). To explore whether the effector kinase Rad53 regulates Cdk1 in response to genotoxic stress, we have been exploring two main avenues: (1) Cdk1 phosphorylation by the S phase checkpoint effector kinase Rad53 and (2) Rad53 dependent regulation of Cdk1 associated factors. With respect to the first question, taking advantage of a Rad53 in vitro kinase assay, we show that recombinant Cdk1 is directly phosphorylated by Rad53. We also proteomically identified two sites of Cdk1 (Ser46, Ser258) phosphorylated by Rad53 in vitro. Cells carrying the non-phosphorylatable Cdk1 allele (Cdk1-2A) display a wee phenotype, compatible with increased/unrestrained CDK activity. Cells carrying the phosphomimetic Cdk1 allele (Cdk1-2E) are elongated and larger in size than wild type cells. Moreover, we also assign and quantify the different phosphorylation forms of Cdk1 in vivo using Phos-tag electrophoresis technology. With respect to the second question, we have proteomically identified proteins associated with Cdk1 in the presence of replication stress in a Rad53 dependent manner. The product of the unknown function gene YPL014W, which we name Cip1 (for Cdk1 Interacting Protein 1), with the highest score, is further studied. Our data shows that Cip1 is a cell cycle regulated protein. In addition, the abundance of Cip1 increases in a Rad53 dependent manner upon DNA replication stress. Overexpression of Cip1 blocks cells in G1 and stabilizes the S-phase-Cdk1 inhibitor Sic1 in vivo. Moreover, Cip1 specifically interacts with G1 phase Cln2-Cdk1 but not with S phase Clb5-Cdk1 or M phase Clb2-Cdk1. Cip1 inhibits Cln2-CDK activity both in vivo and in vitro. Our finding suggests that Cip1 may be a novel CKI of G1 phase CDK activity

Novel Modes of Regulation of Cyclin Dependent Kinase Cdk1

Les quinases dependents de ciclina (CDKs) dirigeixen la progressió del cicle cel·lular a les cèl·lules eucariotes. A l'organisme eucariota model Saccharomyces cerevisiae (llevat de gemmació) una sola quinasa dependent de ciclina, Cdk1, és essencial i suficient per dirigir el cicle cel·lular. Unida alternativament a ciclines de fase G1, S i G2/M, Cdk1 regula els programes transcripcionals del cicle cel·lular, la replicació i segregació dels cromosomes, la dinàmica del fus mitòtic, el creixement cel·lular polar, la morfogènesi, etc. La desregulació de l'activitat CDK promou la proliferació descontrolada i la inestabilitat genòmica. Donada la seva funció essencial en la progressió del cicle cel·lular, Cdk1 és estretament regulada per proteïnes associades (les ciclines, Cks1, i inhibidors de les CDKs -CKIs) i per modificacions post-traduccionals. Tanmateix, molts detalls de la regulació de Cdk1 romanen desconeguts, com és el cas de com les activitats CDK de fase G1 o de fase M són inhibides en resposta a determinats estressos cel·lulars. Quan la progressió del cicle cel·lular és amenaçada per la presència d'estressos genotòxics tals com l'estrès replicatiu o la presència de dany al DNA, un mecanisme de vigilància, l'anomenat checkpoint de la fase S, s'activa per tal de protegir la integritat del genoma. Al llevat de gemmació, el checkpoint de la fase S és mediat per la quinasa Mec1 (ATR/ATM a humans) i la seva quinasa efectora Rad53 (Chk2 a humans). Per explorar si la quinasa efectora Rad53 regula Cdk1 en resposta a estrès genotòxic, hem explorat dues qüestions principals: (1) la fosforilació de Cdk1 per Rad53 i (2) la regulació per Rad53 de proteïnes associades a Cdk1. Pel que fa a la primera qüestió, aprofitant un assaig quinasa in vitro amb Rad53, mostrem que Cdk1 és fosforilat directament per Rad53. Hem identificat proteòmicament dos llocs de Cdk1 (Ser46, Ser258) fosforilats per Rad53 in vitro. Les cèl·lules dirigides per l'al·lel no-fosforilable (Cdk1-2A) mostren un fenotip wee, compatible amb una activitat CDK incrementada/desregulada. Les cèl·lules dirigides per l'al·lel fosfomimètic (Cdk1-2E) són allargades i més grans que les cèl·lules silvestres, compatible amb una activitat CDK reduïda. A més, assignem i quantifiquem les diferents formes fosforilades de Cdk1 in vivo mitjançant electroforesi Phos-tag. Respecte la segona qüestió, hem identificat proteòmicament proteïnes associades a Cdk1 en presència d'estrès replicatiu en forma dependent de Rad53. Hem estudiat en detall el producte del gen de funció desconeguda YPL014W, que bategem Cip1 (per Cdk1 Interacting Protein 1), que obté la puntuació més alta en l'anàlisi. Les nostres dades mostren que Cip1 és una proteïna regulada al llarg del cicle cel·lular. A més, l'abundància de Cip1 s'incrementa en forma dependent de Rad53 en presència d'estrès replicatiu. La sobre-expressió de Cip1 bloqueja les cèl·lules a fase G1 i estabilitza el CKI de fase S Sic1 in vivo. A més, Cip1 interacciona específicament amb el complex de fase G1 Cln2-Cdk1, però no amb el complex de fase S Clb5-Cdk1 or el de fase M Clb2-Cdk1. Cip1 inhibeix l'activitat Cln2-CDK tant in vivo com in vitro. Els nostres resultats suggereixen que Cip1 pot ser un nou CKI de l'activitat CDK de fase G1.Cyclin dependent kinases are drive cell division cycle progression in eukaryotic cells. In the model eukaryotic organism Saccharomyces cerevisiae (budding yeast) a single Cyclin Dependent Kinase, Cdk1, is essential and sufficient to drive the cell cycle. Alternately bound to G1, S and G2/M phase cyclins, Cdk1 regulates cell cycle transcriptional programs, chromosome replication and segregation, spindle dynamics, polarized cell growth, morphogenesis, etc. Misregulated CDK activity induces unscheduled proliferation as well as genomic instability. Given its essential function in cell cycle progression, Cdk1 is tightly regulated by binding partners (cyclins, Cks1 and Cyclin dependent Kinase Inhibitors -CKIs) and post-translational modifications. However, many details on Cdk1 regulation remain unknown, such as how G1 or mitotic CDK activities are inhibited in response to challenging conditions. When the cell cycle progression is challenged by genotoxic stress such as DNA replication stress or DNA damage, a surveillance mechanism, the S phase checkpoint is activated to protect the integrity of the genome. In the budding yeast the S phase checkpoint is mediated by the Mec1 kinase (ATR/ATM in humans) and its downstream effector kinase Rad53 (Chk2 in humans). To explore whether the effector kinase Rad53 regulates Cdk1 in response to genotoxic stress, we have been exploring two main avenues: (1) Cdk1 phosphorylation by the S phase checkpoint effector kinase Rad53 and (2) Rad53 dependent regulation of Cdk1 associated factors. With respect to the first question, taking advantage of a Rad53 in vitro kinase assay, we show that recombinant Cdk1 is directly phosphorylated by Rad53. We also proteomically identified two sites of Cdk1 (Ser46, Ser258) phosphorylated by Rad53 in vitro. Cells carrying the non-phosphorylatable Cdk1 allele (Cdk1-2A) display a wee phenotype, compatible with increased/unrestrained CDK activity. Cells carrying the phosphomimetic Cdk1 allele (Cdk1-2E) are elongated and larger in size than wild type cells. Moreover, we also assign and quantify the different phosphorylation forms of Cdk1 in vivo using Phos-tag electrophoresis technology. With respect to the second question, we have proteomically identified proteins associated with Cdk1 in the presence of replication stress in a Rad53 dependent manner. The product of the unknown function gene YPL014W, which we name Cip1 (for Cdk1 Interacting Protein 1), with the highest score, is further studied. Our data shows that Cip1 is a cell cycle regulated protein. In addition, the abundance of Cip1 increases in a Rad53 dependent manner upon DNA replication stress. Overexpression of Cip1 blocks cells in G1 and stabilizes the S-phase-Cdk1 inhibitor Sic1 in vivo. Moreover, Cip1 specifically interacts with G1 phase Cln2-Cdk1 but not with S phase Clb5-Cdk1 or M phase Clb2-Cdk1. Cip1 inhibits Cln2-CDK activity both in vivo and in vitro. Our finding suggests that Cip1 may be a novel CKI of G1 phase CDK activity

Multiple-site fragment deletion, insertion and substitution mutagenesis by modified overlap extension PCR

<p>Introducing various mutations at multiple specific sites within a gene requires multiple steps of DNA manipulation, which is the initial, but limiting step of protein structure–function studies. In the present work, we standardized a simple and fast procedure to perform site-directed mutagenesis, multiple-site fragment deletion, insertion and substitution mutagenesis by a modified version of overlap extension polymerase chain reaction (PCR). In this procedure, target genes divided into several fragments based on the site of mutagenesis are amplified and annealed with their complementary overhanging, followed by extension and amplification to full-length gene with expected mutation(s) by PCR. Vectors inserted with the modified target gene are screened by colony PCR. By using the standardized procedure, we have easily generated single-site mutations, replaced/deleted DNA fragment into/from a target gene and engineered a cysteine-free protein. Practically, the standardized procedure provides an efficient choice for almost all kinds of mutagenesis, especially for multiple-site and large DNA fragment modification mutagenesis. Therefore, this method can be utilized to analyze protein structure and function, to optimize codons of genes for protein expression and to assemble genes of interest.</p

Building an improved transcription factor-centered yeast one hybrid system to identify DNA motifs bound by protein comprehensively

Abstract Background Identification of the motifs bound by a transcription factor (TF) is important to reveal the function of TF. Previously, we built a transcription factor centered yeast one hybrid (TF-Centered Y1H) that could identify the motifs bound by a target TF. However, that method was difficult to comprehensively identify all the motifs bound by a TF. Results Here, we build an improved TF-Centered Y1H to comprehensively determine the motifs bound by a target TF. Recombination-mediated cloning in yeast was performed to construct a saturated prey library that contains 7 random base insertions. After TF-Centered Y1H screening, all the positive clones were pooled together to isolate pHIS2 vector. The insertion regions of pHIS2 were PCR amplified and the PCR product was subjected to high-throughput sequencing. The insertion sequences were then retrieved and analyzed using MEME program to identify the potential motifs bound by the TF. Using this technology, we studied the motifs bound by an ethylene-responsive factor (BpERF2) from birch. In total, 22 conserved motifs were identified, and most of them are novel cis-acting elements. Both the yeast one hybrid and electrophoretic mobility shift assay verified that the obtained motifs could be bound by BpERF2. In addition, chromatin immunoprecipitation (ChIP) study further suggested that the identified motifs can be bound by BpERF2 in cells of birch. These results together suggested that this technology is reliable and has biological significance. Conclusion This method will have wide application in DNA-protein interaction studies

Comparative Study of Gut Microbiota in Wild and Captive Giant Pandas (Ailuropoda melanoleuca)

Captive breeding has been used as an effective approach to protecting endangered animals but its effect on the gut microbiome and the conservation status of these species is largely unknown. The giant panda is a flagship species for the conservation of wildlife. With integrated efforts including captive breeding, this species has been recently upgraded from &ldquo;endangered&rdquo; to &ldquo;vulnerable&rdquo; (IUCN 2016). Since a large proportion (21.8%) of their global population is still captive, it is critical to understand how captivity changes the gut microbiome of these pandas and how such alterations to the microbiome might affect their future fitness and potential impact on the ecosystem after release into the wild. Here, we use 16S rRNA (ribosomal RNA) marker gene sequencing and shotgun metagenomics sequencing to demonstrate that the fecal microbiomes differ substantially between wild and captive giant pandas. Fecal microbiome diversity was significantly lower in captive pandas, as was the diversity of functional genes. Additionally, captive pandas have reduced functional potential for cellulose degradation but enriched metabolic pathways for starch metabolism, indicating that they may not adapt to a wild diet after being released into the wild since a major component of their diet in the wild will be bamboo. Most significantly, we observed a significantly higher level of amylase activity but a lower level of cellulase activity in captive giant panda feces than those of wild giant pandas, shown by an in vitro experimental assay. Furthermore, antibiotic resistance genes and virulence factors, as well as heavy metal tolerance genes were enriched in the microbiomes of captive pandas, which raises a great concern of spreading these genes to other wild animals and ecosystems when they are released into a wild environment. Our results clearly show that captivity has altered the giant panda microbiome, which could have unintended negative consequences on their adaptability and the ecosystem during the reintroduction of giant pandas into the wild

Additional file 6: of AFEAP cloning: a precise and efficient method for large DNA sequence assembly

Supporting Information. (DOCX 32 kb