No abstract

For bacteria and bacteriophages, cell wall digestion by hydrolases is a very important event. We investigated one of the proteins involved in cell wall digestion, the yomI gene product (renamed CwlP). The gene is located in the SP-␤ prophage region of the Bacillus subtilis chromosome. Inspection of the Pfam database indicates that CwlP contains soluble lytic transglycosylase (SLT) and peptidase M23 domains, which are similar to Escherichia coli lytic transglycosylase Slt70, and the Staphylococcus aureus Gly-Gly endopeptidase LytM, respectively. The SLT domain of CwlP exhibits hydrolytic activity toward the B. subtilis cell wall; however, reverse phase (RP)-HPLC and mass spectrometry revealed that the CwlP-SLT domain has only muramidase activity. In addition, the peptidase M23 domain of CwlP exhibited hydrolytic activity and could cleave D-Ala-diaminopimelic acid cross-linkage, a property associated with DD-endopeptidases. Remarkably, the M23 domain of CwlP possessed a unique Zn 2؉ -independent endopeptidase activity; this contrasts with all other characterized M23 peptidases (and enzymes similar to CwlP), which are Zn 2؉ dependent. Both domains of CwlP could hydrolyze the peptidoglycan and cell wall of B. subtilis. However, the M23 domain digested neither the peptidoglycans nor the cell walls of S. aureus or Streptococcus thermophilus. The effect of defined point mutations in conserved amino acid residues of CwlP is also determined.The cycle of bacteriophage infection of microorganisms comprises adsorption, insertion of nucleic acids, production of bacteriophage nucleic acids and proteins, and finally, host cell lysis. The infection cycle follows a highly ordered sequence of events where cell wall hydrolases, encoded in bacteriophage genomes, are involved in adsorption to cell walls (first infection cycle) and host cell lysis (final infection cycle) (1).One of the best studied Gram-positive bacteria, Bacillus subtilis, has prophage-like elements including PBSX, skin, and SP-␤ (2). The SP-␤ prophage is the largest prophage-like element in B. subtilis (2). Inspection of the BSORF database indicates that the SP-␤ prophage chromosomal region contains 184 genes and one cell wall hydrolase called BlyA, which has been identified as an L-alanine amidase (3). Interestingly, the Pfam database predicts that another gene product, YomI (renamed CwlP (cell wall lytic enzyme related to phage)), has two cell wall hydrolase domains, a soluble lytic transglycosylase (SLT) 3 and peptidase M23 (Fig. 1). However, the function of the two domains (SLT and peptidase M23) remains unclear. BLAST searches of the BSORF and Pfam databases indicate that the SLT domain contains a soluble lytic transglycosylase and a muramidase, although the domain name is annotated "SLT." At present, lytic transglycosylases and muramidases cannot be differentiated using amino acid sequence similarity. The peptidase M23 domain has hydrolytic activity, enabling it to digest the Gly-Gly bond. It is also known that LytM in Staphylococcus aureus has a peptidase M2...

No abstract

Effects of mixed cropping and barrier crops on the population density and parasitism of the diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), were evaluated in field plots of cabbage grown in Bali, Indonesia. The densities of P. xylostella at larval and pupal stages, as well as the overall density at larval plus pupal stages, were significantly lower in cabbage/coriander mixed cropping subplots than in cabbage monoculture subplots. Parasitism of P. xylostella by the larval parasitoid Diadegma semiclausum (Hellen) (Hymenoptera: Ichneumonidae) was not significantly different between the mixed and monocultural cropping systems. These results do not support the so-called enemies hypothesis, but suggest that disruption of the host searching behavior of female moths by neighboring non-host plants is the mechanism behind the associational resistance observed in the coriander mixed cropping system. The inclusion of a Napier grass barrier between mixed crop and monoculture subplots did not affect the influence of mixed cropping on larval and pupal densities. Therefore, Napier grass, which is used locally as a fence for preventing livestock invasion of fields, would not obstruct the pest-reducing effect of coriander/cabbage mixed cropping.

There is a high diversity of bees in the tropics, including honey bees and stingless bees, which are the main sources for honey and other ecosystem services. In Indonesia, beekeeping practices have been developed for centuries, and they have been part of many cultural practices in many traditional communities. The objective of this research was to study the beekeeping status and managed bee diversity in Indonesia and to investigate beekeepers’ perspectives on the factors and obstacles related to beekeeping. Direct interview and online interview were conducted to gain data on bees and beekeepers. In total, 272 beekeepers were interviewed across 25 provinces. Samplings of honey bees and stingless bees were also done during direct interviews for further identification and, when possible, pollen identification. All data and specimens were then sent to IPB Bogor for compilation and identification. We recorded 22 species of bees, including 3 species of honey bees and 19 species of stingless bees, that are reared by Indonesian beekeepers, with Apis cerana and Tetragonula laeviceps as the most common species. Our research also found that the majority of beekeepers fall into the category of the younger generation (30–39 years old) with educational background mostly from senior high school. Based on the beekeepers’ perspectives, there are several obstacles to beekeeping, especially the occurrence of death of bee foragers attributed to climate, food source, and pesticides. In conclusion, there is a need to develop a strategy for beekeeping and bee conservation in Indonesia, especially for adaptation and mitigation from environmental changes with a particular focus on climate and land-use change.

No abstract

The development of strawberry farming in Bali experiencing some obstacles that cause a decline in production, such as wilting disease. The disease was reported caused by the fungi base on morphological recognition.  There are two fungi were recognized caused the strawberry wilt disease in Bali, they are from genus Verticillium and Fusarium. More specific information about causal agent of wilt disease in strawberry especially in Bali is needed. The one accurate identification is done through the molecular approach by analyzing DNA that encode the ribosomal DNA (rDNA). The 18S rDNA, including the internal areas of transcribed spacers (ITS), ITS1 and ITS4 have been widely used in phylogenetic studies. The amplification results of this area produce bands in different sizes that can be used to identify fungal species. Based on that the identification of strawberry wilt disease using molecular analysis was conducted. The 542 bp of Internal Transcribed Spacer (ITS) DNA was successfully amplified using PCR with pairing primers ITS 1 (5-TCCGTAGGTGAACCTGCGG-3’), and ITS 4 (5’-TCCTCCGCTTATTGATATGC-3’). The sequences of three isolates were successfully obtained through sequencing. Homology levels were tested between sequences and showed that Candi Kuning sequence and Gobleg sequence had 95% similarity with sequence of Fusarium oxysporum NRRL 13307 (U34571) from America. While Pancasari sequence have 94% similarity with sequence of Fusarium oxysporum NRRL 13307 (U34571) from America. Candi Kuning, Gobleg, and Pancasari sequences had the same 86% with sequence of Fusarium oxysporum isolate C34-294 Brazil (KJ439088) and had 89% similarity with sequence Fusarium oxysporum f.sp. fragariae China (KT833080). Homology levels were tested between sequences and showed that Candi Kuning sequence and Gobleg sequence had 95% similarity with sequence of Fusarium oxysporum NRRL 13307 (U34571) from America. While Pancasari sequence have 94% similarity with sequence of Fusarium oxysporum NRRL 13307 (U34571) from America. Candi Kuning, Gobleg, and Pancasari sequences had the same 86% with sequence of Fusarium oxysporum isolate C34-294 Brazil (KJ439088) and had 89% similarity with sequence Fusarium oxysporum f.sp. fragariae China (KT833080). Based on phylogeny analysis of Pancasari, Gobleg and Candi Kuning isolates were obtained in one group with Fusarium oxysporum identified in America and Brazil, and also in one group with Fusarium oxysporum f. sp. fragariae that identified in China.

Until recently the use of synthetic pesticides to control pest and plant diseases proved effective, but on the other hand, the excessive use of synthetic pesticides cause many negative effects, such as the development of pest and disease resistance, second pest explosion, death of natural enemies and pesticide residues in food and environment. One alternative that can be done to solve this problem is the use of botanical pesticides. Botanical pesticides are compounds produced as a plant defence response to disturbances and stimulation. These compounds generally are of secondary metabolites that have many functions, such as growth hormones (Auxin, gibberellins and cytokinins), anti-fungal or anti-bacterial, antibiotics, and toxic to animals and insects. The advantage of botanical pesticides is that they have toxicity similar to synthetic pesticides, but the botanical pesticides can be used to support sustainable organic agriculture.  Experiments in the utilization of botanical pesticides to control plant pest have been carried out. One example application is the use of botanical insecticides from “Brotowali” leaf extract (Tinospora crispa) to control the diamond black caterpillars (Plutella xylostella)  on cabbage plants. In addition, the use of ‘basil’ oil (Ocimum tenuiflorum) has a real impact in population control of the fruit fly (Bactrocera dorsalis). In addition to pest control, botanical pesticides are also reported to effectively control plant diseases. Use of ‘galangal’ (Alpinia galanga) and papaya (Carica papaya) has a high ability to inhibit the growth of Ceratocystis sp. On PDA and fruits. The combination of ‘betel’ leaf extract (Piper betle) and ‘galangal’ (A galanga) can suppress the growth of banan wilt disease caused by Fusarium oxysporum and / or the Ralstonia solanacearum. The use of ‘galangal’ (A. Galanga) extract with a concentration of 5%, can also inhibit the growth of stem rot disease (F. oxisporum) on vanilla seedlings. In addition, the use of ‘betel’ ieaf P. Bettle in the field can suppress black rot disease on cocoa pods (cocoa black pd disease)