DNA polymerase X of African swine fever virus: insertion fidelity on gapped DNA substrates and AP lyase activity support a role in base excision repair of viral DNA

DNA polymerase X (pol X) from African swine fever virus (ASFV) is the smallest naturally ocurring DNA-directed DNA polymerase (174 amino acid residues) described so far. Previous biochemical analysis has shown that ASFV pol X is a highly distributive, monomeric enzyme, lacking a proofreading 3'-5' exonuclease. Also, ASFV pol X binds intermediates of the single-nucleotide base excision repair (BER) process, and is able to efficiently repair single-nucleotide gapped DNA. In this work, we perform an extensive kinetic analysis of single correct and incorrect nucleotide insertions by ASFV pol X using different DNA substrates: (i) a primer/template DNA; (ii) a 1nt gapped DNA; (iii) a 5'-phosphorylated 1nt gapped DNA. The results obtained indicate that ASFV pol X exhibits a general preference for insertion of purine deoxynucleotides, especially dGTP opposite template C. Moreover, ASFV pol X shows higher catalytic efficiencies when filling in gapped substrates, which are increased when a phosphate group is present at the 5'-margin of the gap. Interestingly, ASFV pol X misinserts nucleotides with frequencies from 10(-4) to 10(-5), and the insertion fidelity varies depending on the substrate, being more faithful on a phosphorylated 1nt gapped substrate. We have analyzed the capacity of ASFV pol X to act on intermediates of BER repair. Although no lyase activity could be detected on preincised 5'-deoxyribose phosphate termini, ASFV pol X has lyase activity on unincised abasic sites. Altogether, the results support a role for ASFV pol X in reparative BER of damaged viral DNA during ASFV infection.     

Palynology: A useful tool in understanding palaeoclimatic changes through the Pliocene-Pleistocene from the deep offshore Niger Delta,Nigeria

Recent global ecological problems have necessitated more research into past environments so that accurate comparisons between past and present climatic conditions can be established and projections made for the future. In order to achieve this, palynological data from Well-C from the deep offshore (> 200 m) Niger Delta region were employed in an attempt to reconstruct the Late Pliocene-Pleistocene palaeoclimate. Four informal palynofloral assemblage zones (PAZ) I–IV are defined and correlated with four major cycles of alternating dry and wet climatic conditions. Within the major cycles, savanna and montane pollen assemblages became dominant in the late-Pliocene and mid-Pleistocene, while mangroves, brackishwater swamp, freshwater swamp and lowland rainforest prevailed during the early- and late-Pleistocene. The palaeoclimate of the late Pliocene and mid-Pleistocene was relatively colder and drier, with alternating relatively warmer and wetter conditions in the early and late Pleistocene, respectively. The pollen data from Well-C showed periods of climatic change during Late Pliocene-Pleistocene times, while the periods of climatic change revealed by pollen data from Lake Tilla, NE Nigeria, during Holocene times ranged from ∼2.0 to ∼3.8 Ka. Therefore, the cyclicity of climate change during Upper Pliocene-Pleistocene time is far greater than that of Holocene times. Our palaeo-climatic reconstruction conflicts with those that indicate predominantly dry climatic conditions in the Niger Delta region during the Pliocene-Pleistocene. The reconstructed palaeoclimate in this study can help to compare the past climatic conditions to that of the present and perhaps serve as a basis for studies of future climatic change.     

The genus Scaphidium Olivier in East China (Coleoptera,Staphylinidae, Scaphidiinae)

A review of 21 species of Scaphidium Olivier from East China is presented, including 6 new species: S. jinmingi sp. n. (Zhejiang, Anhui, Chongqing), S. crypticum sp. n. (Zhejiang, Fujian, Jiangxi, Guangxi), S. varifasciatum sp. n. (Zhejiang, An’hui), S. robustum sp. n. (Fujian, Guizhou, Chongqing, Guangxi, Yunnan), S. connexum sp. n. (Zhejiang, Fujian, Guangxi), and S. bayibini sp. n. (An’hui). New province records for S. comes Löbl, S. grande Gestro, S. sauteri Miwa & Mitono, S. formosanum Pic, S. carinense Achard, S. sinense Pic, S. delatouchei Achard, S. biwenxuani He, Tang & Li, S. klapperichi Pic, S. stigmatinotum Löbl, S. wuyongxiangi He, Tang & Li, and S. direptum Tang & Li as well as some biological notes are reported. Habitus and diagnostic characters of all species are photographed and a key to Scaphidium species of East China is provided.     

Trypanosome alternative oxidase, a potential therapeutic target for sleeping sickness, is conserved among Trypanosoma brucei subspecies

Trypanosoma brucei rhodesiense and T. b. gambiense are known causes of human African trypanosomiasis (HAT), or “sleeping sickness,” which is deadly if untreated. We previously reported that a specific inhibitor of trypanosome alternative oxidase (TAO), ascofuranone, quickly kills African trypanosomes in vitro and cures mice infected with another subspecies, non-human infective T. b. brucei, in in vivo trials. As an essential factor for trypanosome survival, TAO is a promising drug target due to the absence of alternative oxidases in the mammalian host. This study found TAO expression in HAT-causing trypanosomes; its amino acid sequence was identical to that in non-human infective T. b. brucei. The biochemical understanding of the TAO including its 3 dimensional structure and inhibitory compounds against TAO could therefore be applied to all three T. brucei subspecies in search of a cure for HAT. Our in vitro study using T. b. rhodesiense confirmed the effectiveness of ascofuranone (IC₅₀ value: 1 nM) to eliminate trypanosomes in human infective strain cultures.     

Drought tolerance processes in soybeans

Fifteen soybean cultivars were evaluated in two water supply conditions, inducing or not a drought stress. Main canopy traits were measured several times during the reproductive period and, at maturity date, the yield components were estimated. Using principal components analysis, the main physiological functions involved in soybean drought tolerance are described: leaf cells enlargement and assimilates transport. These processes could be a good basis on which to define new selection criteria for soybean drought tolerance.     

Isolation and Characterization of a Free Gibberellin and Glucosyl Esters of Gibberellins in Mature Seeds of Phaseolus vulgaris

Treatment of N⁶,N⁶,5′-O-tribenzoyl-2′,3′-O-isopropylidenetubercidin (VI) with aqueous acetic acid afforded N⁶,5′-O-dibenzoyltubercidin (V), which was mesylated to yield the dimesylate X. On treatment of X with sodium iodide and zinc dust, the 2′,3′-unsaturated derivatives of tubercidin XI and XIII were obtained.

N⁶,5′-O-Dibenzoyltubercidin 2′,3′-thionocarbonate (XIV), prepared from V by treatment with Corey-Winter reagent, was converted to the 1-methyl-2′,3′-unsaturated derivative XV in refluxing trimethyl phosphite.     

Paddyfield Warbler,Acrocephalus agricola,at Van Gölü, eastern Turkey

Abstract

A Paddyfield Warbler was mist-netted at Van in eastern Anatolia on 8.5 1987. This is the second record for Turkey.     

DNA methylome profiling identifies novel methylated genes in African American patients with colorectal neoplasia

The identification of genes that are differentially methylated in colorectal cancer (CRC) has potential value for both diagnostic and therapeutic interventions specifically in high-risk populations such as African Americans (AAs). However, DNA methylation patterns in CRC, especially in AAs, have not been systematically explored and remain poorly understood. Here, we performed DNA methylome profiling to identify the methylation status of CpG islands within candidate genes involved in critical pathways important in the initiation and development of CRC. We used reduced representation bisulfite sequencing (RRBS) in colorectal cancer and adenoma tissues that were compared with DNA methylome from a healthy AA subject’s colon tissue and peripheral blood DNA. The identified methylation markers were validated in fresh frozen CRC tissues and corresponding normal tissues from AA patients diagnosed with CRC at Howard University Hospital. We identified and validated the methylation status of 355 CpG sites located within 16 gene promoter regions associated with CpG islands. Fifty CpG sites located within CpG islands—in genes ATXN7L1 (2), BMP3 (7), EID3 (15), GAS7 (1), GPR75 (24), and TNFAIP2 (1)—were significantly hypermethylated in tumor vs. normal tissues (P < 0.05). The methylation status of BMP3, EID3, GAS7, and GPR75 was confirmed in an independent, validation cohort. Ingenuity pathway analysis mapped three of these markers (GAS7, BMP3 and GPR) in the insulin and TGF-β1 network—the two key pathways in CRC. In addition to hypermethylated genes, our analysis also revealed that LINE-1 repeat elements were progressively hypomethylated in the normal-adenoma-cancer sequence. We conclude that DNA methylome profiling based on RRBS is an effective method for screening aberrantly methylated genes in CRC. While previous studies focused on the limited identification of hypermethylated genes, ours is the first study to systematically and comprehensively identify novel hypermethylated genes, as well as hypomethylated LINE-1 sequences, which may serve as potential biomarkers for CRC in African Americans. Our discovered biomarkers were intimately linked to the insulin/TGF-B1 pathway, further strengthening the association of diabetic disorders with colon oncogenic transformation.     

SaudiVeg ecoinformatics: Aims,current status and perspectives

During the last decade many electronic databases of vegetation plots were established in many countries around the world. These databases contain valuable phytosociological information assisting both governmental and NGO (Non-governmental organizations) agencies to formulate strategies and on-ground plans to manage and protect nature resources. This paper provides an account on aims, current status and perspectives of building of a vegetation database for the Central Region (Najd) of Saudi Arabia – the founding element of the Saudi Vegetation Database (SVD). The data stored by the database are sample plots (vegetation relevés) collected according to the field techniques of the Braun-Blanquet approach (lists of taxa accompanied by semi-quantitative cover assessment), and are accompanied by general vegetation characteristics such as vegetation layering and cover, information on life-form of the recorded species, geographical coordinates, altitude, soil typology, topography and many more. More than 2900 vegetation-plot records (relevés) have so far been collected in the Najd region; of these more than 2000 have already been stored using the Turboveg database platform. These field records cover many habitats such as depressions, wadis (dry river beds), agricultural lands, sand dunes, sabkhas, and ruderal habitats. The ecological information collected in the database is currently the largest set of vegetation data collated into a database in the Middle East. These data are of great importance for biodiversity studies in Saudi Arabia, since the region is recording a loss of biodiversity at a fast rate due to environmental problems such as global warming and land-use changes. We envisage that this database would catalyze further data collection on vegetation of the entire Arabian Peninsula, and shall serve as one of the most important datasets for classification and mapping of the vegetation of the Kingdom of Saudi Arabia.     

Experiments with trap crops against African bollowrm, Heliothis armigera, in Ethiopia

In a 1 ha haricot bean (HB) (Phaseolus vulgaris L.) field strip-cropped with 2 rows of maize (MZ) (Zea mays L.) on either side and then at 25 m intervals, the number of African bollworm (ABW) (Heliothis armigera (Hubner) (Lepidoptera: Noctuidae)) eggs + larvae on MZ was higher than that on HB by a factor of nearly 18. In a replicated experiment where five trap crops were compared with HB, as a check, all of them contained significantly greater numbers of ABW eggs + larvae than the check. Among the crops tested, lupin (LP) (Lupinus termis Forsk.) and pigeon pea (Cajanus cajan (L.) Millsp.) followed by hyacinth bean (Dolichos lalab L.) contained the highest ABW egg + larval population while sunflower (Helianthus annuus L.) contained the lowest; MZ was intermediate. On the other hand, HB plots bordered with MZ suffered significantly lower percent pod damage by ABW than did the check. Although grain yield differences among treatments were not significant, MZ-bordered plots gave nearly 22% higher yield than the check during the heavy ABW infestation in 1982. These differences were less obvious during the 1983 season because of low ABW infestation. In hot pepper (Capsicum spp.) strip-cropped with lupin, egg + larval counts on the latter were greater by a factor of nearly four in 1981 and 18 in 1982. It is concluded that trap-cropping has a great potential in the integrated management of ABW.

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Résumé En 1981, dans un champ de haricot (Phaseolus vulgaris), des cultures pièges de maïs (Zea mays) ont été semées en rangs doubles tous les 25 m et de chaque côté du champ, soit un total de 5 rangs doubles. Le nombre d'H. armigera (oeufs + chenilles) a été près de 18 fois plus élevé sur maïs que sur haricot.En 1982 et 1983, l'attractivité de 5 cultures pièges: Dolichos lablab, Lupinus termis, Z. mays, Cajanus cajan et Helianthus annuus, a été comparée à celle du haricot. Toutes ces plantes portaient un nombre d'oeufs et de chenilles supérieur au témoin (P. vulgaris). L'ordre décroissant des contaminations était: L. termis, C. cajan, D. lablab, Z. mays et H. annuus. Les rangs de P. vulgaris bordés par des rangs de Z. mays étaient moins contaminés que les témoins. Bien que les différences de rendements en graines suivant les expériences n'aient pas été significatives, les parcelles bordées de maïs ont fourni une récolte supérieure de 22%, pendant l'année 1982, où la contamination par H. armigera a été forte. En 1983, où l'infestation a été faible, les différences étaient moins claires.En 1981 et 1982, 5 rangs de L. tremis à 25 m d'intervalle ont été utilisés comme pièges pour protéger le piment fort (Capsicum spp.). Les décomptes d'oeufs et de chenilles ont été respectivement près de 4 et 18 fois plus élevés.La conclusion est que les cultures pièges ont un grand avenir dans la lutte intégrée contre H. armigera.