Integrative analyses of Nervilia (Orchidaceae) section Linervia reveal further undescribed cryptic diversity in Thailand

The delimitation of cryptic species is necessary to accurately classify and appropriately conserve biodiversity. Integrative analyses can be incisive in detecting and circumscribing cryptic diversity, especially in species complexes whose members are delineated by minor or overlapping morphological variation. We adopt an integrative approach to assess species relationships and resolve species boundaries in the taxonomically difficult Nervilia adolphi/punctata species alliance of N. sect. Linervia, an Old World complex of reduced, one-flowered terrestrial orchids that is both species-rich and poorly known in tropical and warm temperate Asia. We sampled 12 of the 27 known species of the alliance in Asia, including all four species reported from Thailand and a further 20 plants collected in that country that could not be satisfactorily identified using morphology alone. Phylogenetic analyses using one nuclear (ITS) and two plastid (matK and trnL-F) markers confirmed both N. sect. Linervia and the alliance itself as monophyletic, and corroborated 11 of the 12 sampled species; N. punctata proved polyphyletic, with the Thai samples referred to this Indonesian species falling sister to the Himalayan N. mackinnonii. The 20 unidentified Thai samples formed three distinct, strongly supported clades. STACEY, a Bayesian coalescence approach to species delimitation, resolved the same three clusters, but provided evidence suggesting that one comprised two distinct sub-clades. Building on this genetic evidence, we identify subtle morphological differences and invoke a diagnosable species concept to circumscribe three previously unrecognized cryptic species from Thailand. This objective approach to species delimitation validates ostensibly minor morphological differences as a basis for differentiating species within the alliance, paving the way for a global analysis of species boundaries throughout the genus as a whole.     

Effects of methylation-sensitive enzymes on the enrichment of genic SNPs and the degree of genome complexity reduction in a two-enzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm (<Emphasis Type="Italic">Elaeis guineensis</Emphasis>)

Advances in next generation sequencing have facilitated a large-scale single nucleotide polymorphism (SNP) discovery in many crop species. Genotyping-by-sequencing (GBS) approach couples next generation sequencing with genome complexity reduction techniques to simultaneously identify and genotype SNPs. Choice of enzymes used in GBS library preparation depends on several factors including the number of markers required, the desired level of multiplexing, and whether the enrichment of genic SNP is preferred. We evaluated various combinations of methylation-sensitive (AatII, PstI, MspI) and methylation-insensitive (SphI, MseI) enzymes for their effectiveness in genome complexity reduction and enrichment of genic SNPs. We discovered that the use of two methylation-sensitive enzymes effectively reduced genome complexity and did not require a size selection step. On the contrary, the genome coverage of libraries constructed with methylation-insensitive enzymes was quite high, and the additional size selection step may be required to increase the overall read depth. We also demonstrated the effectiveness of methylation-sensitive enzymes in enriching for SNPs located in genic regions. When two methylation-insensitive enzymes were used, only 16% of SNPs identified were located in genes and 18% in the vicinity (± 5 kb) of the genic regions, while most SNPs resided in the intergenic regions. In contrast, a remarkable degree of enrichment was observed when two methylation-sensitive enzymes were employed. Almost two thirds of the SNPs were located either inside (32–36%) or in the vicinity (28–31%) of the genic regions. These results provide useful information to help researchers choose appropriate GBS enzymes in oil palm and other crop species.     

Effects of Malaria Parasite Density on Blood Cell Parameters

Changes in blood cell parameters are already a well-known feature of malarial infections. To add to this information, the objective of this study was to investigate the varying effects that different levels of parasite density have on blood cell parameters. Patients diagnosed with malaria at Phobphra Hospital, Tak Province, Thailand between January 1^st 2009 and January 1^st 2012 were recruited as subjects for data collection. Blood cell parameters of 2,024 malaria-infected patients were evaluated and statistically analyzed. Neutrophil and platelet counts were significantly higher, however, RBC count was significantly lower in patients with P. falciparum infection compared to those with P. vivax infection (p<0.0001). Leukocyte counts were also significantly higher in patients with high parasitemia compared to those with low and moderate parasitemia. In terms of differential leukocyte count, neutrophil count was significantly higher in patients with high parasitemia compared to those with low and moderate parasitemia (p<0.0001). On the other hand, both lymphocyte and monocyte counts were significantly lower in patients with high parasitemia (p<0.0001). RBC count and Hb concentration, as well as platelet count were also significantly reduced (p<0.05) and (p<0.0001), respectively. To summarize, patients infected with different malaria parasites exhibited important distinctive hematological parameters, with neutrophil and eosinophil counts being the two hematological parameters most affected. In addition, patients infected with different malarial densities also exhibited important changes in leukocyte count, platelet count and hemoglobin concentration during the infection. These findings offer the opportunity to recognize and diagnose malaria related anemia, help support the treatment thereof, as well as relieve symptoms of severe malaria in endemic regions.     

Direction-specific recruitment of rotator cuff muscles during bench press and row

Recent studies indicate that rotator cuff (RC) muscles are recruited in a reciprocal, direction-specific pattern during shoulder flexion and extension exercises. The main purpose of this study was to determine if similar reciprocal RC recruitment occurs during bench press (flexion-like) and row (extension-like) exercises. In addition, shoulder muscle activity was comprehensively compared between bench press and flexion; row and extension; and bench press and row exercises. Electromyographic (EMG) activity was recorded from 9 shoulder muscles sites in 15 normal volunteers. All exercises were performed at 20, 50 and 70% of subjects’ maximal load. EMG data were normalized to standard maximal voluntary contractions. Infraspinatus activity was significantly higher than subscapularis during bench press, with the converse pattern during the row exercise. Significant differences in activity levels were found in pectoralis major, deltoid and trapezius between the bench press and flexion exercises and in lower trapezius between the row and extension exercises. During bench press and row exercises, the recruitment pattern in each active muscle did not vary with load. During bench press and row exercises, RC muscles contract in a reciprocal direction-specific manner in their role as shoulder joint dynamic stabilizers to counterbalance antero-posterior translation forces.     

SSR markers in transcripts of genes linked to post-transcriptional and transcriptional regulatory functions during vegetative and reproductive development of Elaeis guineensis

Background  

The oil palm (Elaeis guineensis Jacq.) is a perennial monocotyledonous tropical crop species that is now the world's number one source of edible vegetable oil, and the richest dietary source of provitamin A. While new elite genotypes from traditional breeding programs provide steady yield increases, the long selection cycle (10-12 years) and the large areas required to cultivate oil palm make genetic improvement slow and labor intensive. Molecular breeding programs have the potential to make significant impacts on the rate of genetic improvement but the limited molecular resources, in particular the lack of molecular markers for agronomic traits of interest, restrict the application of molecular breeding schemes for oil palm.     

Vitex glabrata R.Br.悬浮培养细胞的生长条件优化及20-羟基蜕皮激素的生产

研究了培养基、植物生长调节素以及接种量对Vitex glabrata R.Br.悬浮培养细胞的生长情况以及对20-羟基蜕皮激素形成的作用。当细胞在添加有2.0mg/L BAP (6-苯甲酸嘌呤)和1.0mg/L 2,4-D的Gamborg's B5培养基中培养时细胞生长和20-羟基蜕皮激素的形成达到了最高水平。当接种量为20％PCV（积压细胞体积）时观察到了20-羟基蜕皮激素的最高产量,大约是1.1mg/(L·d)。实验数据也表明当接种量增加到20％PCV时,产量提高了7倍。     

Enhanced boron transport into the ear of wheat as a mechanism for boron efficiency

Genotypic variation in boron (B) efficiency in wheat (Triticum aestivum L.) is expressed as large differences in grain set and pollen fertility under low soil B, but the mechanisms responsible for such differences are unknown. This paper aims to determine whether differences in B transport and retranslocation can explain cultivar differences in B efficiency between B-efficient (Fang 60) and B-inefficient (SW41) wheat cultivars. Plants were grown with adequate ¹¹B (10 μM), until the premeiotic interphase stage in anther development, then transferred into ¹⁰B at 0.1 or 10 μM. After five days, ending at the young microspore stage, plants were returned to adequate ¹¹B. Plants were harvested at 0, 1 and 5 days after transferring into ¹⁰B, and at anthesis when fresh pollen was examined for viability. After 5 days in 0.1 μM B, pollen viability in SW41 was depressed by 47%, but pollen of Fang 60 was not affected. When B supply was low, the proportion of plant B partitioned into the ear of Fang 60 was almost twice as high as that in SW 41, enabling Fang 60 to maintain B concentration in the ear at 6.8 mg kg^?1 dry weight (DW), whereas it dropped to 3.8 mg kg^?1 DW in SW 41. Boron accumulation in the ear, when external supply was restricted, did not come from the ¹¹B previously taken up by the plant. The greater ¹⁰B accumulation in ears of Fang 60 compared to SW 41, with limited external B supply, indicated that B efficiency was associated with xylem transport of B. The greater increase of ¹⁰B:¹¹B ratio in the ear of Fang 60 compared to SW 41, over the 5 days of B interruption further indicated that greater B efficiency was associated with a stronger capability for long distance transport of B from the rooting medium into the ear via the xylem rather with than retranslocation of B from vegetative parts.     

Evaluation of antioxidant capacities of green microalgae

Three strains of green microalgae, Chlorococcum sp.C53, Chlorella sp. E53, and Chlorella sp.ED53 were studied for their antioxidant activities. Crude extracts of these microalgae in hot water and in ethanol were examined for their total phenolic contents and for their antioxidant capacities. In order to determine their phenolic contents, the Folin–Ciocalteu method was used. As for the determination of their antioxidant capacities, four different assays were used: (1) total antioxidant capacity determination; (2) DPPH radical scavenging assay; (3) ferrous ion chelating ability assay; and (4) inhibition of lipid peroxidation (using thiobarbituric acid reactive substance). For all the strains we have studied, their ethanolic extract showed more antioxidant activities than their hot water extract. Categorically, the ethanolic extract of Chlorella sp.E53 exhibited both the highest total phenolic content of 35.5?±?0.14 mg gallic acid equivalent (GAE) g^?1 dry weight and the highest DPPH radical scavenging of 68.18?±?0.38 % at 1.4 mg mL^?1 (IC₅₀ 0.81 mg mL^?1), whereas Chlorella sp.ED53 showed both the highest ferrous ion chelation activity of 42.78?±?1.48 % at 1 mg mL^?1 (IC₅₀ 1.23 mg mL^?1) and the highest inhibition of lipid peroxidation of 87.96?±?0.59 % at 4 mg mL^?1. This high level of inhibition is comparable to 94.42?±?1.39 % of butylated hydroxytoluene, a commercial synthetic antioxidant, at the same concentration.     

The Chloroplast Genome Sequence of Mungbean (Vigna radiata) Determined by High-throughput Pyrosequencing: Structural Organization and Phylogenetic Relationships

Mungbean is an economically important crop which is grown principally for its protein-rich dry seeds. However, genomic research of mungbean has lagged behind other species in the Fabaceae family. Here, we reported the complete chloroplast (cp) genome sequence of mungbean obtained by the 454 pyrosequencing technology. The mungbean cp genome is 151 271 bp in length which includes a pair of inverted repeats (IRs) of 26 474 bp separated by a small single-copy region of 17 427 bp and a large single-copy region of 80 896 bp. The genome contains 108 unique genes and 19 of these genes are duplicated in the IR. Of these, 75 are predicted protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. Relative to other plant cp genomes, we observed two distinct rearrangements: a 50-kb inversion between accD/rps16 and rbcL/trnK-UUU, and a 78-kb rearrangement between trnH/rpl14 and rps19/rps8. We detected sequence length polymorphism in the cp homopolymeric regions at the intra- and inter-specific levels in the Vigna species. Phylogenetic analysis demonstrated a close relationship between Vigna and Phaseolus in the phaseolinae subtribe and provided a strong support for a monophyletic group of the eurosid I.