Degradation of Root Community Traits as Indicator for Transformation of Tropical Lowland Rain Forests into Oil Palm and Rubber Plantations

Conversion of tropical forests into intensely managed plantations is a threat to ecosystem functions. On Sumatra, Indonesia, oil palm (Elaeis guineensis) plantations are rapidly expanding, displacing rain forests and extensively used rubber (Hevea brasiliensis) agro-forests. Here, we tested the influence of land use systems on root traits including chemical traits (carbon, nitrogen, mineral nutrients, potentially toxic elements [aluminium, iron] and performance traits (root mass, vitality, mycorrhizal colonization). Traits were measured as root community-weighed traits (RCWTs) in lowland rain forests, in rubber agro-forests mixed with rain forest trees, in rubber and oil palm plantations in two landscapes (Bukit Duabelas and Harapan, Sumatra). We hypothesized that RCWTs vary with land use system indicating increasing transformation intensity and loss of ecosystem functions. The main factors found to be related to increasing transformation intensity were declining root vitality and root sulfur, nitrogen, carbon, manganese concentrations and increasing root aluminium and iron concentrations as well as increasing spore densities of arbuscular mycorrhizas. Mycorrhizal abundance was high for arbuscular and low for ectomycorrhizas and unrelated to changes in RCWTs. The decline in RCWTs showed significant correlations with soil nitrogen, soil pH and litter carbon. Thus, our study uncovered a relationship between deteriorating root community traits and loss of ecosystem functionality and showed that increasing transformation intensity resulted in decreasing root nutrition and health. Based on these results we suggest that land management that improves root vitality may enhance the ecological functions of intense tropical production systems.     

Spatial Distribution and Temporal Patterns of Cassin’s Auklet Foraging and Their Euphausiid Prey in a Variable Ocean Environment

Krill (Euphausiids) play a vital ecosystem role in many of the world’s most productive marine regions, providing an important trophic linkage. We introduce a robust modeling approach to link Cassin’s auklet (Ptychoramphus aleuticus) abundance and distribution to large-scale and local oceanic and atmospheric conditions and relate these patterns to similarly modeled distributions of an important prey resource, krill. We carried out at-sea strip transect bird surveys and hydroacoustic assessments of euphausiids (2004–2013). Data informed separate, spatially-explicit predictive models of Cassin’s auklet abundance (zero-inflated negative binomial regression) and krill biomass (two-part model) based on these surveys. We established the type of prey responsible for acoustic backscatter by conducting net tows of the upper 50 m during surveys. We determined the types of prey fed to Cassin’s auklet chicks by collecting diet samples from provisioning adults. Using time-depth-recorders, we found Cassin’s auklets utilized consistent areas in the upper water column, less than 30 m, where krill could be found (99.5% of dives were less than 30 m). Birds primarily preyed upon two species of euphausiids, Euphausia pacifica and Thysanoessa spinifera, which were available in the upper water column. Cassin’s auklet abundance was best predicted by both large scale and localized oceanic processes (upwelling) while krill biomass was best predicted by local factors (temperature, salinity, and fluorescence) and both large scale and localized oceanic processes (upwelling). Models predicted varying krill and bird distribution by month and year. Our work informs the use of Cassin’s auklet as a valuable indicator or krill abundance and distribution and strengthens our understanding of the link between Cassin’s auklet and its primary prey. We expect future increases in frequency and magnitude of anomalous ocean conditions will result in decreased availability of krill leading to declines in the Farallon Islands population of Cassin’s auklets.     

Direct discrimination of different plant populations and study on temperature effects by Fourier transform infrared spectroscopy

Fourier transform infrared spectroscopy was used to characterise highland and lowland populations of Polygonum minus Huds. grown in different controlled environments. A thermal perturbation technique of two-dimensional correlation infrared spectroscopy (2D-IR) correlation spectra was applied to establish differences between the populations. The absorption peaks at 3,480 cm^?1 (hydroxyl group), 2,927 cm^?1 (methyl group), 1,623 cm^?1 (carbonyl group), and 1,068 cm^?1 (C–O group) were particularly powerful in separating the populations. These peaks, which indicate the presence of carbohydrate, terpenes, amide and flavonoids were more intense for the highland populations than lowland populations, and increased in environments with a higher temperature. Wavenumbers (1,634, 669 cm^?1) and (1,634, 1,555 cm^?1) in the 2D-IR correlation spectra provided fingerprint signals to differentiate plants grown at different temperatures. This study demonstrates that IR fingerprinting, which combines mid-IR spectra and 2D-IR correlation spectra, can directly discriminate different populations of P. minus and the effects of temperature.     

Genome-Wide Comparative Analysis of 20 Miniature Inverted-Repeat Transposable Element Families in Brassica rapa and B. oleracea

Miniature inverted-repeat transposable elements (MITEs) are ubiquitous, non-autonomous class II transposable elements. Here, we conducted genome-wide comparative analysis of 20 MITE families in B. rapa, B. oleracea, and Arabidopsis thaliana. A total of 5894 and 6026 MITE members belonging to the 20 families were found in the whole genome pseudo-chromosome sequences of B. rapa and B. oleracea, respectively. Meanwhile, only four of the 20 families, comprising 573 members, were identified in the Arabidopsis genome, indicating that most of the families were activated in the Brassica genus after divergence from Arabidopsis. Copy numbers varied from 4 to 1459 for each MITE family, and there was up to 6-fold variation between B. rapa and B. oleracea. In particular, analysis of intact members showed that whereas eleven families were present in similar copy numbers in B. rapa and B. oleracea, nine families showed copy number variation ranging from 2- to 16-fold. Four of those families (BraSto-3, BraTo-3, 4, 5) were more abundant in B. rapa, and the other five (BraSto-1, BraSto-4, BraTo-1, 7 and BraHAT-1) were more abundant in B. oleracea. Overall, 54% and 51% of the MITEs resided in or within 2 kb of a gene in the B. rapa and B. oleracea genomes, respectively. Notably, 92 MITEs were found within the CDS of annotated genes, suggesting that MITEs might play roles in diversification of genes in the recently triplicated Brassica genome. MITE insertion polymorphism (MIP) analysis of 289 MITE members showed that 52% and 23% were polymorphic at the inter- and intra-species levels, respectively, indicating that there has been recent MITE activity in the Brassica genome. These recently activated MITE families with abundant MIP will provide useful resources for molecular breeding and identification of novel functional genes arising from MITE insertion.     

Lack of Clinical Manifestations in Asymptomatic Dengue Infection Is Attributed to Broad Down-Regulation and Selective Up-Regulation of Host Defence Response Genes

Objectives

Dengue represents one of the most serious life-threatening vector-borne infectious diseases that afflicts approximately 50 million people across the globe annually. Whilst symptomatic infections are frequently reported, asymptomatic dengue remains largely unnoticed. Therefore, we sought to investigate the immune correlates conferring protection to individuals that remain clinically asymptomatic.

Methods

We determined the levels of neutralizing antibodies (nAbs) and gene expression profiles of host immune factors in individuals with asymptomatic infections, and whose cognate household members showed symptoms consistent to clinical dengue infection.

Results

We observed broad down-regulation of host defense response (innate, adaptive and matrix metalloprotease) genes in asymptomatic individuals as against symptomatic patients, with selective up-regulation of distinct genes that have been associated with protection. Selected down-regulated genes include: TNF α (TNF), IL8, C1S, factor B (CFB), IL2, IL3, IL4, IL5, IL8, IL9, IL10 and IL13, CD80, CD28, and IL18, MMP8, MMP10, MMP12, MMP15, MMP16, and MMP24. Selected up-regulated genes include: RANTES (CCL5), MIP-1α (CCL3L1/CCL3L3), MIP-1β (CCL4L1), TGFβ (TGFB), and TIMP1.

Conclusion

Our findings highlight the potential association of certain host genes conferring protection against clinical dengue. These data are valuable to better explore the mysteries behind the hitherto poorly understood immunopathogenesis of subclinical dengue infection.     

Phage display antibodies for diagnostic applications

With major developments in molecular biology, numerous display technologies have been successfully introduced for recombinant antibody production. Even so, phage display still remains the gold standard for recombinant antibody production. Its success is mainly attributed to the robust nature of phage particles allowing for automation and adaptation to modifications. The generation of monospecific binders provides a vital tool for diagnostics at a lower cost and higher efficiency. The flexibility to modify recombinant antibodies allows great applicability to various platforms for use. This review presents phage display technology, application and modifications of recombinant antibodies for diagnostics.     

Endometrial gene expression profiling of recurrent implantation failure after in vitro fertilization

Molecular Biology Reports - Recurrent implantation failure (RIF) is diagnosed when good-quality embryos repeatedly fail to implant after transfer in several in vitro fertilization (IVF) treatment...     

The investigation of glutamate transporter 1 (GLT-1) degradation pathway in glioblastoma cells

Molecular Biology Reports - Glioblastoma multiform is a primary brain tumor derived from glial cells. The aim of this study is to investigate how glutamate metabolism is regulated by glutamate...     

Enhancing food waste biodegradation rate in a food waste biodigester with the synergistic action of hydrolase-producing Bacillus paralicheniformis GRA2 and Bacillus velezensis TAP5 co-culture inoculation

Food waste (FW) minimization at the source by using food waste biodigester (FWBs) has a vast potential to lower down the impact of increasing organic fraction in municipal solid waste generation. To this end, this research sought to check the performance of locally isolated hydrolase-producing bacteria (HPB) to improve food waste biodegradation rate. Two under-explored HPB identified as Bacillus paralicheniformis GRA2 and Bacillus velezensis TAP5 were able to produce maximum amylase, cellulase, protease and lipase activities, and demonstrated a significant hydrolase synergy in co-culture fermentation. In vitro biodegradation analysis of both autoclaved and non-autoclaved FW revealed that the HPB inoculation was effective to degrade total solids (>62%), protein (>19%), total fat (>51), total sugar (>86%), reducing sugar (>38%) and starch (>50%) after 8-day incubation. All co-culture treatments were recorded superior to the respective monocultures and the uninoculated control. The results of FW biodegradation using batch-biodigester trial indicated that the 1500 mL and 1000 mL inoculum size of HPB inoculant reached a plateau on the 4th day, with gross biodegradation percentage (GBP) of >85% as compared to control (66.4%). The 1000 mL inoculum was sufficient to achieve the maximum GBP (>90%) of FW after an 8-day biodigestion in a FWB.