Vegetation-edaphic correlation and importance value index in himalayan 'ecotone' temperate conifer forest using the multivariate technique.

Himalayan 'Ecotone' temperate conifer forest is the cradle of life for human survival and wildlife existence. In spite of the importance of these areas, they have not been studied in depth. This study aimed to quantify the floristic structure, important value index (IVI), topographic and edaphic variables between 2019 and 2020 utilizing circular quadrant method (10 m x 10 m). The upper-storey layer consisted of 17 tree species belongs to 12 families and 9 orders. Middle-storey shrubs comprised of 23 species representing 14 families and 12 orders. A total of 43 species of herbs, grasses, and ferns were identified from the ground-storey layer, representing 25 families and 21 orders. Upper-storey vegetation structure was dominated by Pinus roxburghii (22.45 %) and middle-storey by Dodonaea viscosa (7.69 %). However, the ground layer vegetation was diverse in species composition (43 species) and distribution. The floral vegetation structure was encompassing of three floral communities which were diverse in IVI, such as, in Piro-Aial (Group 2), Pinus roxburghii (54.46 x 15.94) had the highest IVI value, followed by Pinus wallichiana (45.21 x 14.85) in Piwa-Quin (Group 3) and Ailanthus altissima (22.84 x 19.25) in Aial-Qugal (Group 1). However, the IVI values for Aesculus indica, Celtis australis, and Quercus incana in Aial-Qugal (Group 1) were not determined due to low detection rate. Nevertheless, eleven of these species showed 0 IVI values in Piro-Aial (Group 2) and Piwa-Quin (Group 3). CCA ordination biplot illustrated the significant differences among floral communities and its distribution, which impacted by temperature, rainfall, soil pH, altitude, and topographic features. Ward's agglomerative clustering finding reflected 'Ecotone' temperate conifer forest is rich and diverse floristic structure.

First Report of Potato virus Y in Potato in West Java, Indonesia.

Potato (Solanum tuberosum) is an important vegetable crop in Indonesia. A small survey was conducted for virus diseases in November 2011 in Lembang, West Java, as part of assessing the sanitary status of potatoes produced in farmers' fields. Among the six potato fields surveyed, one field had nearly 20% of plants displaying stunted growth with leaves showing mild chlorotic spots and reduced size of lamina. Tubers harvested from symptomatic plants showed no necrosis symptoms. Symptomatic leaves from three representative potato plants were positive for Potato virus Y (PVY) when tested with PVY-specific immunostrips (Agdia Inc., Elkhart, IN). Leaf samples from virus-positive plants were imprinted on FTA Classic Cards (Whatman International Ltd., Maidstone, UK), air dried, and shipped to Washington State University for confirmatory diagnostic tests. Total nucleic acids were eluted from FTA cards (1) and subjected to reverse transcription (RT)-PCR using primers (PVY/Y4A and PVY/Y3S) specific to the coat protein (CP) of PVY (3). Nucleic acid extracts from samples infected with PVY ordinary strain (PVYO), tuber necrosis strain (PVYNTN), tobacco veinal necrosis strains (PVYEU-N and PVYNA-N), and a recombinant strain (PVYN:O) were included as standards to validate RT-PCR assays. The approximately 480-bp DNA fragment, representing a portion of the CP, amplified in RT-PCR was cloned into pCR2.1 (Invitrogen Corp., Carlsbad, CA). DNA isolated from four independent recombinant clones was sequenced from both orientations. Pairwise comparison of these sequences (GenBank Accession Nos. KF261310 to 13) showed 100% identity among themselves and 93 to 100% identity with corresponding sequences of reference strains of PVY available in GenBank (JQ743609 to 21). To our knowledge, this study represents the first confirmed report of PVY in potato in West Java, Indonesia. Studies are in progress to assess the prevalence of PVY in other potato-growing regions of Indonesia and document the presence of different strains of the virus (2). Since the majority of farmers in Indonesia plant seed selected from their previous potato crop, there is an increased risk of primary and secondary spread of PVY through the informal seed supply system, leading to its increased significance to potato production in Indonesia. Therefore, strengthening foundation seed potato and supply chain programs will promote the production of virus-free potatoes in Indonesia. References: (1) O. J. Alabi et al. Plant Dis. 96:107, 2012. (2) A. Karasev and S. M. Gray. Am. J. Potato Res. 90:7, 2013. (3) R. P. Singh et al. J. Virol. Methods 59:189, 1996.

A begomovirus associated with Ageratum yellow vein disease in Indonesia: evidence for natural recombination between tomato leaf curl Java virus and Ageratum yellow vein virus-[Java].

A begomovirus (2747 nucleotides) and a satellite DNA beta component (1360 nucleotides) have been isolated from Ageratum conyzoides L. plants with yellow vein symptoms growing in Java, Indonesia. The begomovirus is most closely related to Tomato leaf curl Java virus (ToLCJV) (91 and 98% in the total nucleotide and coat protein amino acid sequences, respectively), although the products of ORFs C1 and C4 are more closely related to those of Ageratum yellow vein virus-[Java] (91 and 95% identity, respectively). For this reason, the begomovirus it is considered to be a strain of ToLCJV and is referred to as ToLCJV-Ageratum. The virus probably derives from a recombination event in which nucleotides 2389-2692 of ToLCJV have been replaced with the corresponding region of the AYVV-[Java] genome, which includes the 5' part of the intergenic region and the C1 and C4 ORFs. Infection of A. conyzoides with ToLCJV-Ageratum alone produced no symptoms, but co-infection with DNAbeta induced yellow vein symptoms. Symptoms induced in Nicotiana benthamiana by ToLCJV-Ageratum, ToLCJV and AYVV-[Java] are consistent with the exchange of pathogenicity determinant ORF C4 during recombination.

Molecular Characterization of Pepper yellow leaf curl Indonesia virus in Leaf Curl and Yellowing Diseased Tomato and Pepper in Indonesia.

Yellowing and leaf curl symptoms were observed in tomato and pepper fields near Bogor, Java, Indonesia in 2000. Samples were collected from one diseased tomato (Lycopersicum esculentum) and three diseased chili pepper (Capsicum annuum) plants. Viral DNA was extracted (2) and tested for the presence of geminiviral DNA-A, DNA-B, and associated satellite DNA using polymerase chain reaction (PCR) with previously described primers (1,3,4). The begomovirus DNA-A general primer pair PAL1v1978/PAR1c715 amplified the predicted 1.4-kb DNA fragment from the tomato and two of the chili samples. DNA-B and satellite DNA were not detected using PCR with DNA-B general primer pairs (DNABLC1/DNABLV2 and DNABLC2/DNABLV2) and satellite detection primer pair (Beta01/Beta02). The amplicons from the tomato and from one of the chili samples were cloned and sequenced. On the basis of the 1.4-kb DNA sequences, specific primers were designed to complete the DNA-A sequences. Following sequence assembly, the full-length DNA-A nucleotide sequences were determined as 2,744 nt (GenBank Accession No. DQ083765) for the tomato- and 2,743 nt (GenBank Accession No. DQ083764) for the chili-infecting begomoviruses. Sequence comparisons and analyses were conducted using the DNAMAN sequence analysis software (Lynnon Corporation, Quebec, Canada). The DNA-A of both begomoviruses contained six open reading frames, including two in the virus sense and four in the complementary sense, and the geminivirus conserved nanosequence-TAATATTAC in the loop of the hairpin structure of the intergenic region. Because of their high nucleotide sequence identities of 99%, the tomato- and chili-infecting begomovirus are considered the same virus. When compared by using BLAST with available gem-iniviral sequences in the GenBank database, the DNA-A sequences of the tomato and the chili isolates showed highest nucleotide sequence identity (95%) with the partially sequenced Pepper yellow leaf curl Indonesia virus (GenBank Accession No. AB189849) in the 1,842 nt to 660 nt region and in the 1,841 nt to 659 nt region, respectively. Comparisons with full-length DNA-A sequences of begomoviruses available in the GenBank database indicated high sequence identities of 76 and 77% for the tomato and chili isolates, respectively, with an eggplant isolate of Tomato yellow leaf curl Kanchanaburi virus (GenBank Accession No. AF511530) from Thailand. According to our knowledge, this is the first report of full-length DNA-A sequence of the Pepper yellow leaf curl Indonesia virus and its natural occurrence in tomato and pepper in the Bogor area of Indonesia. References: (1) R. W. Briddon et al. Virology 312:106, 2003. (2) R. L. Gilbertson et al. J. Gen. Virol. 72:2843, 1991. (3) S. K. Green et al. Plant Dis. 85:1286, 2001. (4) M. R. Rojas et al. Plant Dis. 77:340, 1993.

Respiratory symptoms, lung function, and nasal cellularity in Indonesian wood workers: a dose-response analysis.

OBJECTIVES: It was hypothesised that inflammation plays a dominant part in the respiratory effects of exposure to wood dust. The purpose of this study was to relate the nasal inflammatory responses of workers exposed to meranti wood dust to (a) levels of exposure, (b) respiratory symptoms and (c) respiratory function. METHODS: A cross sectional study was carried out in 1997 in a woodworking plant that used mainly meranti, among 982 workers exposed to different concentrations of wood dust. Personal sampling (n=243) of inhalable dust measurements indicated mean exposure in specific jobs, and enabled classification of 930 workers in three exposure classes (<2, 2-5, and >5 mg/m(3)) based on job title. Questionnaires were used to screen respiratory symptoms in the entire population. Lung function was measured with two different techniques, conventional flow-volume curves and the forced oscillation technique. Nasal lavage was done to assess inflammation in the upper respiratory tract. RESULTS: A negative trend between years of employment and most flow-volume variables was found in men, but not in women workers. Current exposure, however, was not related to spirometric outcomes, respiratory symptoms, or nasal cellularity. Some impedance variables were related to current exposure but also with better function at higher exposure. CONCLUSIONS: Exposure to meranti wood dust did not cause an inflammation in the upper respiratory tract nor an increase of respiratory symptoms or decrease of lung function. These data do not corroborate the hypothesis that inflammation plays a part in airway obstruction induced by wood dust.

Carboxyl-terminal region conserved among phosphoinositide-kinase-related kinases is indispensable for mTOR function in vivo and in vitro.

BACKGROUND: The mammalian target of rapamycin (mTOR) belongs to the family of phosphoinositide (PI)-kinase-related kinases that includes the ataxia-telangiectasia gene product (ATM). mTOR plays a critical role in controlling translational effectors such as p70 S6 kinase alpha (p70 alpha) and eukaryotic initiation factor 4E binding protein 1 (4EBP1). RESULTS: We show that the C-terminal region of mTOR, which is highly conserved among the PI-kinase-related kinases, plays a critical role in the mTOR protein kinase activity. Deletion of the C-terminal residues did not adversely affect the expression of mTOR, but caused a nearly complete loss of the mTOR protein kinase activity toward both 4EBP1 and p70 alpha in vitro. These deletions also abolished the ability of a rapamycin-resistant mTOR mutant to rescue the activity of p70 alpha from inhibition induced by rapamycin in vivo. Furthermore, replacement of Trp2545, a conserved residue in the C-terminal region throughout the PI-kinase-related kinase family, abolished the function of the mTOR kinase, both in vivo and in vitro. However, substitution of 32 C-terminal residues of mTOR with those of ATM did not restore the mTOR function. CONCLUSIONS: These findings define an indispensable role for the noncatalytic C-terminal region of mTOR and indicate that, although this highly conserved region may be important throughout the PI-kinase-related kinase family, it is not functionally interchangeable within the family.

Structural requirement of leucine for activation of p70 S6 kinase.

The addition of leucine induced activation of p70S6k in amino acid-depleted H4IIE cells. Whereas the activation of p70S6k by leucine was transient, the complete amino acid stimulated p70S6k more persistently. The effect of leucine on p70S6k was sensitive to rapamycin, but less sensitive to wortmannin. Using various amino acids and derivatives of leucine, we found that the chirality, the structure of the four branched hydrocarbons, and the primary amine are required for the ability of leucine to stimulate p70S6k, indicating that the structural requirement of leucine to induce p70S6k activation is very strict and precise. In addition, some leucine derivatives exhibited the ability to stimulate p70S6k and the other derivatives acted as inhibitors against the leucine-induced activation of p70S6k.

Impact of neonatal vitamin A supplementation on infant morbidity and mortality.

OBJECTIVE: To determine whether vitamin A supplementation at birth could reduce infant morbidity and mortality. STUDY DESIGN: We conducted a placebo-controlled trial among 2067 Indonesian neonates who received either 52 micromol (50,000 IU) orally administered vitamin A or placebo on the first day of life. Infants were followed up at 1 year to determine the impact of this intervention on infant mortality. A subgroup (n = 470) was also examined at 4 and 6 months of age to examine the impact on morbidity. RESULTS: Vital status was confirmed in 89% of infants in both groups at 1 year. There were 19 deaths in the control group and 7 in the vitamin A group (relative risk = 0.36; 95% confidence interval = 0.16, 0.87). The impact was stronger among boys, infants of normal compared with low birth weight, and those of greater ponderal index. Among infants examined at 4 months of age, the 1-week period prevalence of common morbidities was similar for vitamin A and control infants. However, during this same 4-month period, 73% and 51% more control infants were brought for medical treatment for cough (p = 0.008) and fever (p = 0.063), respectively. CONCLUSIONS: Neonatal vitamin A supplementation may reduce the infant mortality rate and the prevalence of severe respiratory infection among young infants.

Safety of one 52-mumol (50,000 IU) oral dose of vitamin A administered to neonates.

A placebo-controlled trial was carried out among 2067 Indonesian neonates to assess the safety of administering one oral 52-mumol (50,000 IU) dose of vitamin A. Infants were assessed for potential acute side-effects before and throughout 48 hours after the dose. The first 965 infants were examined by cranial ultrasound before and at 24 hours after dosing to rule out intracranial haemorrhage and determine the resistive index (RI) of the anterior cerebral artery using duplex Doppler. Groups were comparable at the baseline. A bulging fontanelle occurred in the control and vitamin A groups, respectively, among 2.7% and 4.6% of the infants at 24 hours, and 2.4% and 4.5% of the infants at 48 hours. The groups did not differ in any other sign or symptom assessed. No infant developed intracranial haemorrhage. Mean RI values were normal and not different between groups at baseline or at 24 hours. Mean RI fell during the 24 hours, as normally occurs; the mean decrease was nearly identical in the two groups. A bulging fontanelle was not associated with increased rates of any sign or symptom or with an increase in RI. The 52-mumol dose of oral vitamin A may cause a small increase in intracranial volume in a small proportion of infants, but no increase in intracranial pressure. Acute side-effects following this intervention were rare and mild.

Pseudorecombination between infectious cloned DNA components of tomato mottle and bean dwarf mosaic geminiviruses.

A newly described whitefly-transmitted geminivirus infecting tomato plants in Florida induces yellow mottling symptoms on leaves, and stunted and distorted growth. The DNA-A and DNA-B components were cloned from extracts of field-infected tomato tissue; excised monomers or uncut tandem dimers of these clones were infectious when co-inoculated on to Nicotiana benthamiana by rub-inoculation. Tomato plants inoculated directly with the DNA-A and DNA-B dimers, or indirectly by sap or graft transmission from N. benthamiana plants previously infected with the dimers, developed symptoms similar to those observed in field-infected plants. This tomato geminivirus is different from previously characterized geminiviruses, and has been named tomato mottle geminivirus (ToMoV). DNA sequence comparisons revealed that ToMoV is closely related to bean dwarf mosaic geminivirus (BDMV) and abutilon mosaic geminivirus. Infectious pseudorecombinants were made by exchanging the cloned infectious DNA components of ToMoV and BDMV and inoculating N. benthamiana plants. The presence of the inoculated DNA components in systemically infected plants was confirmed by characterization of DNA-A and DNA-B fragments amplified by the polymerase chain reaction. This is the first report of pseudorecombination between two distinct geminiviruses. The implications of this finding in geminivirus evolution are discussed.