CONTRIBUTION OF THE HEART OF BORNEO (HoB) INITIATIVE TOWARDS BOTANICAL EXPLORATION IN SABAH, MALAYSIA

The Heart of   Borneo (HoB) declaration is a conservation agreement initiated by WWF and signed by three countries, i.e., Brunei       Darussalam, Indonesia and Malaysia in Bali, Indonesia on 12th February 2007 to protect more than 23 million hectares of forested region on Borneo Island. These forested areas could be well protected when conservation management plan is in place. One of the crucial activities to facilitate the planning and formulation of conservation plan is to conduct  scientific expeditions that include botanical exploration. The primary objective of the expedition is to identify the key conservation targets within the forest reserves. For the past five years, several expeditions have been conducted by the Sabah Forestry Department under the auspices of the HoB project to explore various forest reserves with conservation issues within the Heart of Borneo area. This paper will present the findings which include plant richness, endemism and plant conservation status in each forest reserves that has been explored. </p

Effects of logging on landscape-level tree diversity across an elevational gradient in Bornean tropical forests

Logging has caused a substantial loss of biodiversity and associated ecosystem services. Therefore, it is important to examine how logging affects biodiversity on a landscape scale to plan responsible management of a tropical forest. Although a number of plot-based studies have shown the effect of logging on local tree species richness (alpha diversity), the effect on species turnover along environmental gradients (beta diversity) remains largely unknown. In this study, we evaluated how logging disturbance affects alpha and beta diversity along an elevational gradient on the eastern slope of Mount Trus Madi in Borneo. We further investigated how pioneer and late-successional tree species differed in the habitat range to clarify the mechanism underlying the beta diversity pattern. We selected 90 plots, each with a radius of 20 m, with a range of disturbance intensity (five classes from highly degraded forests to pristine forests) in lower (285–600 m asl) and higher elevation areas (600–1105 m asl). The remaining above-ground biomass, which is an indicator of past disturbance intensity, strongly varied across the plots (5.4–570.6 and 3.1–771.6 Mg ha−1 in lower and higher elevation areas, respectively). Diameter at breast height (DBH) and species name were recorded for all trees with a DBH larger than 10 cm. We calculated the species number per 20 individual trees for each plot to represent alpha diversity. Beta diversity along the elevational gradient was calculated as the slope of the relationship between standardized compositional dissimilarity (beta deviation) and the elevational difference. Alpha diversity decreased in higher (17.3–12.3 species per 20 trees) and lower areas (16.8–11.3 species per 20 trees) with increasing logging intensity. Beta diversity along the elevational gradient also decreased to almost zero in highly disturbed areas. Pioneer tree species had a wider elevational range than late-successional species. These results suggest that the shift in dominant tree species after logging (from late-successional to pioneer species) was the main driver of the decline in beta diversity along the elevational gradient. We conclude that preserving and restoring beta diversity are important to sustain tropical production forests

Blood pressure intervention levels in preterm infants : pilot randomised trial

OBJECTIVE: To examine the feasibility of a trial allocating different blood pressure (BP) intervention levels for treatment in extremely preterm infants. DESIGN: Three-arm open randomised controlled trial performed between February 2013 and April 2015. SETTING: Single tertiary level neonatal intensive care unit. PATIENTS: Infants born <29 weeks' gestation were eligible to participate, if parents consented and they did not have a major congenital malformation. INTERVENTIONS: Infants were randomised to different levels of mean arterial BP at which they received cardiovascular support: active (<30 mm Hg), moderate (<gestational age mm Hg) or permissive (signs of poor perfusion or <19 mm Hg). Once this threshold was breached, all were managed using the same treatment guideline. BP profiles were downloaded continuously; cardiac output and carotid blood flow were measured at 1 day and 3 days, and amplitude integrated EEG was recorded during the first week. Cranial ultrasound scans were reviewed blind to study allocation. MAIN OUTCOME MEASURE: Inotrope usage and achieved BP. RESULTS: Of 134 cases screened, 60 were enrolled, with mean gestation 25.8 weeks (SD 1.5) and birth weight 817 g (SD 190). Invasively measured BP on the first day and inotrope usage were highest in the active and lowest in the permissive arms. There were no differences in haemodynamic or EEG variables or in clinical complications. Predefined cranial ultrasound findings did not differ significantly; no infants in the active arm had parenchymal brain lesions. CONCLUSION: The BP threshold used to trigger treatment affects the achieved BP and inotrope usage, and it was possible to explore these effects using this study design. TRIAL REGISTRATION NUMBER: ISRCTN83507686

Studies on Potheae (Araceae) of Borneo II: Pedicellarum M.Hotta subsumed into Pothos L., and recognition of three new species

Pedicellarum is subsumed into Pothos as Pothos paiei. Four species, three taxonomically novel (Pothos degenerans, ecclesiae and P. fractiflexus) and one pre-existing (Pothos oliganthus) are discussed. The reproductive structures are reinterpreted and floral terminology used in this paper is in line with paving the way to interpreting the ‘inflorescence’ of Pothos, and indeed of all other aroids, as a unique array of structures that are neither flowers nor inflorescences as defined by current prevailing orthodoxy, but something of both

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae)

We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. Although codon partitioning did not result in any substantial topological differences, the inclusion of flanking noncoding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of data sets increased convergence between analysis methods but did not reduce gene-tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. Although the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of data sets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution. [Artocarpus; Moraceae; noncoding sequences; phylogenomics; target enrichment.

The glyceraldehyde-3-phosphate dehydrogenase gene of Moniliophthoraperniciosa, the causal agent of witches' broom disease of Theobroma cacao

This report describes the cloning, sequence and expression analysis of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene of Moniliophthora perniciosa, the most important pathogen of cocoa in Brazil. Southern blot analysis revealed the presence of a single copy of the GAPDH gene in the M. perniciosa genome (MpGAPDH). The complete MpGAPDH coding sequence contained 1,461 bp with eight introns that were conserved in the GAPDH genes of other basidiomycete species. The cis-elements in the promoter region of the MpGAPDH gene were similar to those of other basidiomycetes. Likewise, the MpGAPDH gene encoded a putative 339 amino acid protein that shared significant sequence similarity with other GAPDH proteins in fungi, plants, and metazoans. Phylogenetic analyses clustered the MPGAPDH protein with other homobasidiomycete fungi of the family Tricholomataceae. Expression analysis of the MpGAPDH gene by real-time PCR showed that this gene was more expressed (~1.3X) in the saprotrophic stage of this hemibiotrophic plant pathogen than in the biotrophic stage when grown in cacao extracts

Incorporating connectivity into conservation planning for the optimal representation of multiple species and ecosystem services

Funding was provided by the Rainforest Trust foundation. Support was also provided by the Sabah Forest Department, Forest Research Centre, the South East Asia Rainforest Research Partnership, the U.N. Development Programme, the Universiti Malaysia Sabah (FRGS0414-STWN-1/2015), PACOS Trust, BC Initiative, the Natural Environment Research Council UK (grant NE/R009597/1), and the Universities of Aberdeen, Montana, and York. We are grateful to the numerous researchers that collected the data used in our analyses, as well as the local communities and government staff who manage forested areas across Sabah.Peer reviewedPostprin

The Genomic and Immune Landscapes of Lethal Metastatic Breast Cancer.

The detailed molecular characterization of lethal cancers is a prerequisite to understanding resistance to therapy and escape from cancer immunoediting. We performed extensive multi-platform profiling of multi-regional metastases in autopsies from 10 patients with therapy-resistant breast cancer. The integrated genomic and immune landscapes show that metastases propagate and evolve as communities of clones, reveal their predicted neo-antigen landscapes, and show that they can accumulate HLA loss of heterozygosity (LOH). The data further identify variable tumor microenvironments and reveal, through analyses of T cell receptor repertoires, that adaptive immune responses appear to co-evolve with the metastatic genomes. These findings reveal in fine detail the landscapes of lethal metastatic breast cancer.CRUK

Conservation assessment and spatial distribution of endemic orchids in Sabah, Borneo

Orchids are among the most threatened plants due to habitat loss and illegal harvesting for horticultural demands. Sabah is a centre of orchid diversity, with approximately 1300 species of which 250 orchid taxa are endemic to Sabah. In this study, we conducted an IUCN Red List assessment on 136 endemic species and used Maximum Entropy (MaxEnt) to develop species distribution models for 47 species. The species distribution models were developed using presence-only data and six environmental predictors. The accuracy of the models were assessed using the area under the curve (AUC) and models with an AUC of higher than 0.8 stacked together to produce a species richness heatmap. We found that 83% of the researched species were threatened, of which 14 species were assessed to be Critically Endangered, eight species as Endangered and 93 species as Vulnerable. The heatmap shows that all of the species occurred within the Totally Protected Area (TPA) network in western Sabah. The heatmap highlighted the mid-altitude areas adjacent to the Kinabalu and Crocker Range parks and Ulu Sipitang regions as areas with a high species richness that were outside the TPA network. These areas are also important for the conservation of the majority of the species assessed as Critically Endangered and Endangered. Urgent conservation actions are needed to protect these species from extinction. The results from this work will be used as part of an intensive conservation action plan for threatened endemic orchids of Sabah and used to identify important plant areas currently not within the existing TPA networ