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The diversity of beetle assemblages in different habitat types in Sabah, Malaysia

Chung AY, Eggleton P, Speight MR, Hammond PM, Chey VK

Bull. Entomol. Res., 2000 Dec;90(6):475-96.
PMID: 11107250

The diversity of beetle assemblages in different habitat types (primary forest, logged forest, acacia plantation and oil palm plantation) in Sabah, Malaysia was investigated using three different methods based on habitat levels (Winkler sampling, flight-interception-trapping and mist-blowing). The overall diversity was extremely high, with 1711 species recorded from only 8028 individuals and 81 families (115 family and subfamily groups). Different degrees of environmental changes had varying effects on the beetle species richness and abundance, with oil palm plantation assemblage being most severely affected, followed by acacia plantation and then logged forest. A few species became numerically dominant in the oil palm plantation. In terms of beetle species composition, the acacia fauna showed much similarity with the logged forest fauna, and the oil palm fauna was very different from the rest. The effects of environmental variables (number of plant species, sapling and tree densities, amount of leaf litter, ground cover, canopy cover, soil pH and compaction) on the beetle assemblage were also investigated. Leaf litter correlated with species richness, abundance and composition of subterranean beetles. Plant species richness, tree and sapling densities correlated with species richness, abundance and composition of understorey beetles while ground cover correlated only with the species richness and abundance of these beetles. Canopy cover correlated only with arboreal beetles. In trophic structure, predators represented more than 40% of the species and individuals. Environmental changes affected the trophic structure with proportionally more herbivores (abundance) but fewer predators (species richness and abundance) in the oil palm plantation. Biodiversity, conservation and practical aspects of pest management were also highlighted in this study.
Does logging and forest conversion to oil palm agriculture alter functional diversity in a biodiversity hotspot?

Edwards FA, Edwards DP, Larsen TH, Hsu WW, Benedick S, Chung A, et al.

Anim. Conserv., 2014 Apr;17(2):163-173.
PMID: 25821399

Forests in Southeast Asia are rapidly being logged and converted to oil palm. These changes in land-use are known to affect species diversity but consequences for the functional diversity of species assemblages are poorly understood. Environmental filtering of species with similar traits could lead to disproportionate reductions in trait diversity in degraded habitats. Here, we focus on dung beetles, which play a key role in ecosystem processes such as nutrient recycling and seed dispersal. We use morphological and behavioural traits to calculate a variety of functional diversity measures across a gradient of disturbance from primary forest through intensively logged forest to oil palm. Logging caused significant shifts in community composition but had very little effect on functional diversity, even after a repeated timber harvest. These data provide evidence for functional redundancy of dung beetles within primary forest and emphasize the high value of logged forests as refugia for biodiversity. In contrast, conversion of forest to oil palm greatly reduced taxonomic and functional diversity, with a marked decrease in the abundance of nocturnal foragers, a higher proportion of species with small body sizes and the complete loss of telecoprid species (dung-rollers), all indicating a decrease in the functional capacity of dung beetles within plantations. These changes also highlight the vulnerability of community functioning within logged forests in the event of further environmental degradation.
Fulltext Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation

Srinivasan S, Yeri A, Cheah PS, Chung A, Danielson K, De Hoff P, et al.

Cell, 2019 04 04;177(2):446-462.e16.
PMID: 30951671 DOI: 10.1016/j.cell.2019.03.024

Poor reproducibility within and across studies arising from lack of knowledge regarding the performance of extracellular RNA (exRNA) isolation methods has hindered progress in the exRNA field. A systematic comparison of 10 exRNA isolation methods across 5 biofluids revealed marked differences in the complexity and reproducibility of the resulting small RNA-seq profiles. The relative efficiency with which each method accessed different exRNA carrier subclasses was determined by estimating the proportions of extracellular vesicle (EV)-, ribonucleoprotein (RNP)-, and high-density lipoprotein (HDL)-specific miRNA signatures in each profile. An interactive web-based application (miRDaR) was developed to help investigators select the optimal exRNA isolation method for their studies. miRDar provides comparative statistics for all expressed miRNAs or a selected subset of miRNAs in the desired biofluid for each exRNA isolation method and returns a ranked list of exRNA isolation methods prioritized by complexity, expression level, and reproducibility. These results will improve reproducibility and stimulate further progress in exRNA biomarker development.
Did Descriptive and Prescriptive Norms About Gender Equality at Home Change During the COVID-19 Pandemic? A Cross-National Investigation

Saxler FM, Dorrough AR, Froehlich L, Block K, Croft A, Meeussen L, et al.

Pers Soc Psychol Bull, 2024 Jan 29.
PMID: 38284645 DOI: 10.1177/01461672231219719

Using data from 15 countries, this article investigates whether descriptive and prescriptive gender norms concerning housework and child care (domestic work) changed after the onset of the COVID-19 pandemic. Results of a total of 8,343 participants (M = 19.95, SD = 1.68) from two comparable student samples suggest that descriptive norms about unpaid domestic work have been affected by the pandemic, with individuals seeing mothers' relative to fathers' share of housework and child care as even larger. Moderation analyses revealed that the effect of the pandemic on descriptive norms about child care decreased with countries' increasing levels of gender equality; countries with stronger gender inequality showed a larger difference between pre- and post-pandemic. This study documents a shift in descriptive norms and discusses implications for gender equality-emphasizing the importance of addressing the additional challenges that mothers face during health-related crises.
Fulltext A multimodal atlas of hepatocellular carcinoma reveals convergent evolutionary paths and 'bad apple' effect on clinical trajectory

Chen J, Kaya NA, Zhang Y, Kendarsari RI, Sekar K, Lee Chong S, et al.

J Hepatol, 2024 May 21.
PMID: 38782118 DOI: 10.1016/j.jhep.2024.05.017

BACKGROUND & AIMS: Hepatocellular carcinoma (HCC) is a highly fatal cancer characterized by high intra-tumor heterogeneity (ITH). A panoramic understanding of its tumor evolution, in relation to its clinical trajectory, may provide novel prognostic and treatment strategies.
METHODS: Through the Asia-Pacific Hepatocellular Carcinoma trials group (NCT03267641), we recruited one of the largest prospective cohorts of patients with HCC, with over 600 whole genome and transcriptome samples from 123 treatment-naïve patients.
RESULTS: Using a multi-region sampling approach, we revealed seven convergent genetic evolutionary paths governed by the early driver mutations, late copy number variations and viral integrations, which stratify patient clinical trajectories after surgical resection. Furthermore, such evolutionary paths shaped the molecular profiles, leading to distinct transcriptomic subtypes. Most significantly, although we found the coexistence of multiple transcriptomic subtypes within certain tumors, patient prognosis was best predicted by the most aggressive cell fraction of the tumor, rather than by overall degree of transcriptomic ITH level - a phenomenon we termed the 'bad apple' effect. Finally, we found that characteristics throughout early and late tumor evolution provide significant and complementary prognostic power in predicting patient survival.
CONCLUSIONS: Taken together, our study generated a comprehensive landscape of evolutionary history for HCC and provides a rich multi-omics resource for understanding tumor heterogeneity and clinical trajectories.
IMPACT AND IMPLICATIONS: This prospective study, utilizing comprehensive multi-sector, multi-omics sequencing and clinical data from surgically resected hepatocellular carcinoma (HCC), reveals critical insights into the role of tumor evolution and intra-tumor heterogeneity (ITH) in determining the prognosis of HCC. These findings are invaluable for oncology researchers and clinicians, as they underscore the influence of distinct evolutionary paths and the 'bad apple' effect, where the most aggressive tumor fraction dictates disease progression. These insights not only enhance prognostic accuracy post-surgical resection but also pave the way for personalized treatment strategies tailored to specific tumor evolutionary and transcriptomic profiles. The coexistence of multiple subtypes within the same tumor prompts a re-appraisal of the utilities of depending on single samples to represent the entire tumor and suggests the need for clinical molecular imaging. This research thus marks a significant step forward in the clinical understanding and management of HCC, underscoring the importance of integrating tumor evolutionary dynamics and multi-omics biomarkers into therapeutic decision-making.
CLINICAL TRIAL NUMBER: NCT03267641 (Observational cohort).
Thresholds for adding degraded tropical forest to the conservation estate

Ewers RM, Orme CDL, Pearse WD, Zulkifli N, Yvon-Durocher G, Yusah KM, et al.

Nature, 2024 Jul;631(8022):808-813.
PMID: 39020163 DOI: 10.1038/s41586-024-07657-w

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (<29% biomass removal) retain high conservation value and a largely intact functional composition, and are therefore likely to recover their pre-logging values if allowed to undergo natural regeneration. Second, the most extreme impacts occur in heavily degraded forests with more than two-thirds (>68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked.