Miracle-dz/UniFAR-FTUs huggingface dataset:
Real-time DNA barcoding in a remote rainforest using nanopore sequencing

Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here we tested the feasibility for in situ molecular analyses of endemic fauna using a portable laboratory fitting within a single backpack, in one of the world’s most imperiled biodiversity hotspots: the Ecuadorian Chocó rainforest. We utilized portable equipment, including the MinION DNA sequencer (Oxford Nanopore Technologies) and miniPCR (miniPCR), to perform DNA extraction, PCR amplification and real-time DNA barcode sequencing of reptile specimens in the field. We demonstrate that nanopore sequencing can be implemented in a remote tropical forest to quickly and accurately identify species using DNA barcoding, as we generated consensus sequences for species resolution with an accuracy of >99% in less than 24 hours after collecting specimens. In addition, we generated sequence information at Universidad Tecnológica Indoamérica in Quito for the recently re-discovered Jambato toad Atelopus ignescens, which was thought to be extinct for 28 years, a rare species of blind snake Trilepida guayaquilensis, and two undescribed species of Dipsas snakes. In this study we establish how mobile laboratories and nanopore sequencing can help to accelerate species identification in remote areas (especially for species that are difficult to diagnose based on characters of external morphology), be applied to local research facilities in developing countries, and rapidly generate information for species that are rare, endangered and undescribed, which can potentially aid in conservation efforts.
Consumer preferences and water charging options in a large urban municipality: a case study

This paper uses limited dependent variable techniques to model the decision-making process in a dual-pricing household water system as employed in Brisbane, Australia. In this system, households could initially choose to remain on a standard rateable value principle of payment for water or move to a volumetric/user-pays system. Because of uncertainty associated with future household water demand, the option to remain on the existing system has value and is thereby incorporated into the appropriate decision-making model. A number of property/household characteristics are found to influence the choice of water charging system along with the value of the option. These include property size and rateable value, the number of household members, the type of garden vegetation, and the presence of various household appliances.
Molecular organization of the actin cortex in apical constriction and epithelial folding

Actin and myosin generate contractile forces to change tissue and cell shape. These shape changes are essential for many biological functions, ranging from muscle contraction to tissue morphogenesis in development. While the spatial organization and composition of the actin and myosin contractile force generating machine is well known in muscle, it is less understood in nonmuscle epithelia, which change shape during development and form functional barriers on an organism’s inner surfaces. Prevailing models for nonmuscle contractility suggest that the intrinsic ability of mixed polarity actin networks and uniformly distributed myosin to contract into asters drives nonmuscle contractility. Here, I provide insight into the mechanism of nonmuscle contraction by demonstrating that the apical actin cortex and associated proteins are spatially organized in epithelia. In addition, I demonstrate that this spatial organization forms a sarcomere-like actomyosin apparatus, which is essential for epithelial contractility. This updated model is likely to inform our understanding of a wide range of contractile forcegenerating systems, and may lead to advances in understanding of pathologies that involve defects in contractility, like cardiovascular disease and pulmonary fibrosis. Thesis Supervisor: Adam C. Martin Title: Associate Professor of Biology
Biocuration as an undergraduate training experience: Improving the annotation of the insect vector of Citrus greening disease

Shippy⍺,β,, Andrew Rosendale⍺,β,4, Chris Cordola, Tracey Bell, Hannah Mann, Gabe DeAvila, Daniel DeAvila, Zachary Moore, Kyle Buller, Kathryn Ciolkevich, Samantha Nandyal, Robert Mahoney, Joshua Van Voorhis, Megan Dunlevy, David Farrow, David Hunter, Taylar Morgan, Kayla Shore, Victoria Guzman, Allison Izsak, Danielle E Dixon, Liliana Cano , Andrew Cridge , Shannon Johnson , Brandi L Cantarel , Stephen Richardson, Adam English, Nan Leng, Xiaolong Cao, Haobo Jiang, Chris Childers⍺,, Mei-Ju Chen⍺,17, Mirella Flores⍺,Ƴ,, Wayne Hunter, Michelle Cilia,
Estimating sampling completeness of interactions in quantitative bipartite ecological networks: incorporating variation in species’ specialisation

Background The analysis of ecological networks can be affected by sampling effort, potentially leading to bias. Ecological network structure is often summarised by descriptive metrics but these metrics can vary according to the proportion of the total interactions that have been observed. Therefore, to know the likely degree of bias, it is valuable to estimate the total number of interactions in a network, and so calculate the proportion of interactions that have been observed (sampling completeness of interactions). Existing approaches to estimate sampling completeness of interactions use the Chao family of asymptotic species richness estimators to predict the total number of interactions, but do not fully utilise information about the relative specialisation of species within the network. Results Here, we propose a modification of previously-used methods, that places equal weight on each interaction (whether or not it has been observed), rather than on each species. Our approach is therefore equivalent to weighting the interaction sampling completeness of each species in the network according to its relative specialisation. We demonstrate that, for the subset of species that are observed and when assuming that species richness estimators accurately project the number of unobserved interactions per observed species, our approach is mathematically more accurate. Our approach can be universally applied to any quantitative, bipartite network. We propose two methods to estimation using our approach, using abundance-based and incidence-based species richness estimators respectively, and give recommendations when each should be applied. We discuss the effect of unobserved species and the potential use of a threshold of minimum abundance for species inclusion. Finally, we consider these advances in the context of some of the main issues surrounding estimation of interaction sampling completeness in network ecology. Conclusions We recommend that future studies of bipartite networks utilise our approach and methods to estimate the sampling completeness of interactions, to assist with the quantitative and comparative analysis and interpretation of network properties.
The roles of MUSE1 and MUSE15 in plant innate immunity

ii Preface.iii Table of contents.iv List of figures.viii List of abbreviations.x Acknowledgements.xvii Dedication.xviii Chapter 1: Introduction.1 1.1 Plant immunity.1 1.1.1 Physical and chemical barriers.1 1.1.2 PAMP-triggered immunity (PTI). 2 1.1.3 effector-triggered immunity (ETI). 4 1.1.3.1 Pathogens use effectors to suppress host defense.4 1.1.3.2 Plant NLRs perceive effectors and trigger robust defense.5 1.1.3.3 Regulation of NLRs.7 1.1.3.4 Interplays among NLRs.9 1.2 Identifying novel defense components through forward genetic screens.10 1.2. 1 Autoimmune mutant snc1 harbors a gain-of-function mutation in a TNL.10 1.2. 2 The MOS genetic screen.11 1.2. 3 The MUSE genetic screen.11 1.2. 4 Regulation of NLR-mediated immunity by MUSE genes.12 1.3 Ubiquitination in NLR-mediated immunity.13 1.3.1 The ubiquitination pathway.13 1.3.2 Types of E3 ubiquitin ligases.15 1.3.3 E3 ubiquitin ligases play diverse roles in plants.16
Resveratrol effect on fructose-induced NASH: a mechanistic approach

Background: High-fructose beverages have been extensively used in recent years leading to the development of NAFLD and NASH. The present study evaluates the effect of resveratrol on fructose-induced metabolic abnormalities in rats. A number of genes known to be critically involved in lipid metabolism were investigated. Methods: Fructose-enriched diet (FED) was given to rats for 12 weeks. Resveratrol (RES) (70 mg/kg) was administered orally from the 9th week till the end of experimental period. Body weight, oral glucose tolerance test (OGTT), liver index, insulin resistance (HOMA), serum and liver triglycerides (TGs), oxidative stress (liver MDA, GSH and SOD), serum AST/ALT ratio and TNF-α were measured. Additionally, hepatic gene expression of suppressor of cytokine signaling -3 (SOCS-3), sterol regulatory element binding protein-1c (SREBP-1c), fatty acid synthase (FAS), malonyl CoA decarboxylase (MCD), transforming growth factor-β1 (TGF-β1) and adipose tissue gene expression of leptin and adiponectin was investigated. Results: Resveratrol treatment ameliorated the fructose-induced damaged liver, glucose tolerance impairment, insulin resistance, oxidative stress & dyslipidemia. There was an improvement in genes responsible for NASH development. Conclusions: Resveratrol improved the NASH-related fructose-induced disturbances due to its antioxidant and anti-inflammatory capacity beside its attenuating effects on hepatic genes expression and correcting the balance between adiponectin and leptin.
New Strains of Candidatus Liberibacter asiaticus in Citrus Plants in Bali

Candidatus Liberibacter asiaticus is the most widely known bacteria causing citrus greening (Huanglongbing) from three species of Candidatus Liberibacter. This study was conducted to ascertain the phylogenetic relationship between Can. Liberibacter asiaticus Indian isolates which have a higher diversity in 16S rDNA with Asian isolates in general. An citrus leaves samples with CVPD disease symptoms were collected from several locations in Bali. Detection of Can. L. asiaticus in the sample was performed by PCR using a 16S rDNA-specific primer F: 0I1 and R: 0I2c. Based on the DNA amplification results, six samples taken from Citrus nobilis reacted positively, and each one taken from C. amblycarpa, C. aurantium and C. grandis were also reacted positively. DNA of nine positive samples were purified and sequenced. The sequencing results showed a close relationship between C. nobilis samples with C. aurantium at a distance of 0.000, but the relationship is relatively far away with the other seven samples and with strains of Poona India, L. africanum strains of Nelspruit South Africa and nine isolates Can. L. asiaticus accessed from GenBank NCBI is with a distance of 0.600-0.603. Two samples (JBC1311 and JBC1351) are different from Indian Poona strain in Purine base positions with Pyrimidine, and Pyrimidine base positions with Purines in the 16S rDNA sequence. Based on these results, one sample each taken from Citrus nobilis JBC1311) and C. aurantium (JBC1351) are considered as new strains and different from other strains occurred in Bali, and also different from the strains of Poona (India) and the strain of Nelpruit (South Africa), while 7 (seven) other samples are the same strains. Keywords : Citrus greening ,CVPD, Candidatus Liberibacter asiaticus, 16S rDNA
Spatial Distribution Modelling of Kobresia pygmaea (Cyperaceae) on the Qinghai-Tibetan Plateau

Abstract: Kobresia pygmaea Willd. dominates the alpine meadow ecosystem on the Qinghai-Tibet Plateau. Knowledge of this species' distribution and ecological environment could provide valuable insights into the alpine ecosystem and key species living there, support species and ecosystem conservation in alpine regions, and build on species origin and evolutionary research. To avoid modelling uncertainty encountered in a single approach, four species distribution model algorithms (Surface Range Envelope (SRE), Generalized Linear Model (GLM), Generalized Boosted Regression (GBM) and Maximum Entropy (MAXENT)), were used to simulate the distribution of K. pygmaea based on occurrence samples that were verified using DNA sequencing techniques. Species distribution modelling revealed a vast distribution region of K. pygmaea in the northern Tibetan Highlands and alpine meadows in the southern and eastern declivity of the plateau. A high evaluation performance was found for the GLM, GBM and MAXENT models. Different potential range size patterns for the four models were found between 374340–482605 km2 (average = 421591 km2). Precipitation during growing seasons was found to be the dominant factor accounting for the distribution, consistent with patterns of heat and water patterns conditions of alpine ecosystems on the plateau. Species distribution models provide a simple and reliable approach to simulating the spatial patterns of species inhabiting the Qinghai-Tibet Plateau.
Taxonomy of the bivalve Ptychomya in the Lower Cretaceous of the Neuquén basin (west‐central Argentina)

In the Lower Cretaceous Agrio Formation, Neuquén Basin (west‐central Argentina), the highly variable genus Ptychomya Agassiz has challenged traditional taxonomists for over a century. Here we apply a previously outlined quantitative protocol in order to settle the taxonomy of the genus based on specimens recorded from the base to the top of the Agrio Formation. The shell outline and ribbing pattern, two prominent external features of the valves, were quantified using geometric morphometric measurements of closed and open outlines, respectively. Morphological groupings were identified using model‐based clustering, and the presence of significant morphological gaps between them was statistically tested. Our results show that the variation historically attributed to a single species, namely Ptychomya koeneni Behrendsen, corresponds to intra‐ and interspecific variability of at least four species, one of which was previously unknown (Ptychomya esbelta sp. nov.) whereas another was regarded as a subspecies of P. koeneni, namely Ptychomya windhauseni Weaver. We were also able to confirm the specific rank of Ptychomya coihuicoensis Weaver and the presence of P. koeneni in the upper Hauterivian of the Agrio Formation. This study represents a significant improvement over the previous state of knowledge of the genus Ptychomya in the Andes of Argentina, enhancing its biostratigraphical usefulness and palaeobiogeographical significance, and may serve as a model for the study of other poorly known bivalve faunas from other Andean basins of South America.
Diversity of Maize Kernels from a Breeding Program for Protein Quality III: Ionome Profiling

Densities of single and multiple macro- and micronutrients were estimated in the mature kernels of 1348 accessions in 13 maize genotypes. The germplasm belonged to stiff stalk (SS) and non-stiff stalk (NS) heterotic groups (HGs) with one (S1) to four (S4) years of inbreeding (IB), or open pollination (OP), and with opaque or translucent endosperm (OE and TE, respectively). Indices were calculated for macronutrients (M-Index), micronutrients (m-Index) and an index based on Fe and Zn densities (FeZn-Index). The objectives were to (1) build predictive models and quantify multivariate relationships between single and multiple nutrients with physical and biochemical constituents of the maize kernel; (2) quantify the effects of IB stages and endosperm textures, in relation to carbon and nitrogen allocation, on nutrients and their indices; and (3) develop and test the utility of hierarchical multi-way classification of nutrients with kernel color space coordinates. Differences among genotypes and among IB stages accounted for the largest amount of variation in most nutrients and in all indices, while genotypic response to IB within HGs explained 52.4, 55.9, and 76.0% of variation in the M-Index, m-Index, and FeZn-Index, respectively. Differences in C and N allocation among HGs explained more variation in all indices than respective differences in allocation among endosperm (E) textures, while variation decreased with sequential inbreeding compared to OP germplasm. Specific color space coordinates indicated either large macronutrient densities and M-Index, or large micronutrient densities, m-Index, and FeZn-Index. These results demonstrated the importance of genotypes and the C:N ratio in nutrient allocation, as well as bivariate and multiple interrelationships.
Common inhibitors of membrane H+‐transport also inhibit carbonic anhydrase

Selective pharmacological inhibitors of membrane H+‐equivalent transport are useful tools for studying pHi regulation. The enzyme carbonic anhydrase (CA) facilitates rapid CO2/HCO3− interconversion, and may also facilitate membrane H+‐transport. CA inhibition is commonly achieved with sulphonamides or their derivatives. More recently, some non‐sulphonamides have been reported to inhibit the enzyme. We have investigated effects of dimethylamiloride (DMA), cariporide (selective Na+/H+ exchange inhibitors), and DIDS (a stilbene HCO3−‐transport inhibitor) on purified CA II activity, and on total CA activity in rat cardiac ventricular homogenates. CA activity (CO2 hydration rate) was assayed by following the time‐course of pH change after addition of CO2‐saturated water to a HEPES‐buffered solution (pH 8.0, 2°C), containing either CA II, or cardiac CA‐homogenate. DMA had no effect, but cariporide and DIDS were inhibitory. For CA II, the IC50 values for cariporide and DIDS were 12. 4μM and 42μM, respectively. For cardiac CA homogenate, they were 60μM and 316μM. Thus two commonly used H+‐transport inhibitors also inhibit CA. Some inhibition of H+‐transport by these drugs may therefore be secondary to inhibition of CA.
A polymerisation-associated conformational switch in FtsZ that enables treadmilling

Bacterial cell division in many organisms involves a constricting cytokinetic ring that is orchestrated by the tubulin-like protein FtsZ. FtsZ forms dynamic filaments close to the membrane at the site of division that have recently been shown to treadmill around the division ring, guiding septal wall synthesis. Here, using X-ray crystallography of Staphylococcus aureus SaFtsZ we reveal how an FtsZ can adopt two functionally distinct conformations, open and closed. The open form is found in SaFtsZ filaments formed in crystals and also in soluble filaments of E. coli FtsZ as deduced by cryoEM. The closed form is found within several crystal forms of two non-polymerising SaFtsZ mutants and corresponds to many previous FtsZ structures from other organisms. We argue that FtsZ undergoes a polymerisation-associated conformational switch. We show that such a switch provides explanations for both how treadmilling may occur within a single-stranded filament, and why filament assembly is cooperative.
Behaviour of the Little Raven Corvus mellori on Phillip Island, Victoria

Time-budgets of Little Raven s Corvus m e llori were studied o n Phillip I s l a nd , Vict o ri a, in mi d autumn (April) 2002 , by scoring behaviour duri n g observ a ti o n s o n focal indi v idu a l s (n = 1 99), instantan e ous scans of R a ven gro up s (n = 189) , and ave rag e count s of birds a t eac h o f t hr ee s i tes. Ravens occurred mostly in groups; p ea k numbers o c curr e d in th e ea rl y m o rnin gs and evenings, w ith midd a y lows. C ommunal roosting occurr e d in e arly mornin g, midd ay a nd e v e n i n g, and foraging in mid morning and mid afternoon. Much of their time was spent roostin g . F oca l birds a l so spe n t much time foraging, whereas birds in groups di v ided most of th e ir r e m a inin g time between foraging and flying. Ravens spen t most of their fora g ing time f e edin g on in se ct s (72 % ) , followed by berries (17 % ), seabird carrion (16 % ) and hum a n food sc r a p s (br ea d , 3 % ) . Some intr a - and interspecific aggr ess ive interact i ons a r e de s cribed .
The Growth Efficiency and Carcass Characteristics of Dorper Sheep Treated by Corn Inclusion as Energy into Palm Kernel Cake Based-Diet

This study investigated the effect of energy as partial replacement of a diet based on palm kernel cake (PKC) on the growth performance, nutrient intake, digestibility, carcass quality, and economic cost of Dorper sheep. Twenty-seven Dorper rams (initial body weight 15 ± 0.59 kg) were kept in individual pens and divided randomly into dietary groups consisting of T1: basal diet + 0% corn (control), T2: basal diet + 5% corn, and T3: basal diet + 10% corn. Feed intake was recorded on a daily basis. On day 110, 4 lambs from each group were randomly chosen and transferred into metabolism crates to determine nutrient digestibility and completely randomized design was used. The results showed that high feed intake was in T3 while, the DM, CP, NDF, and ADF digestibility were decreased significantly with the increasing level of corn as an energy source. The carcass cuts were not affected by the dietary treatments. Significant differences were noted in the non-carcass parts (heart, lungs and trachea, defattted kidneys, liver, spleen, and kidney fat) with T3 having the highest value. The feeding cost was slightly increased when PKC was replaced by corn. In conclusion, inclusion of 10% corn as a source of energy in 65.3% PKC as fattening diets had effects on growth BW, ADG, and organs performance on Dorper lambs.
Loss of mCHH islands in maize chromomethylase and DDM1-type nucleosome remodeler mutants

Plants make use of three types of DNA methylation, each characterized by distinct DNA methyltransferases. One type, RNA-directed DNA methylation (RdDM), is guided by siRNAs to the edges of transposons that are close to genes, areas called mCHH islands in maize. Another type, chromomethylation, is guided by histone H3 lysine 9 methylation to heterochromatin across the genome. We examined DNA methylation and small RNA expression in plant tissues that were mutant for both copies of the genes encoding chromomethylases as well as mutants for both copies of the genes encoding DDM1-type nucleosome remodelers, which facilitate chromomethylation. Both sets of double mutants were nonviable but produced embryos and endosperm. RdDM was severely compromised in the double mutant embryos, both in terms of DNA methylation and siRNAs. Loss of 24nt siRNA from mCHH islands was coupled with a gain of 21, 22, and 24nt siRNAs in heterochromatin. These results reveal a requirement for both chromomethylation and DDM1-type nucleosome remodeling for RdDM in mCHH islands, which we hypothesize is due to dilution of RdDM components across the genome when heterochromatin is compromised.
Integrating over uncertainty in spatial scale of response within multispecies occupancy models yields more accurate assessments of community composition

Species abundance and community composition are affected not only by the local environment, but also by broader landscape and regional context. Yet determining the spatial scale at which landscapes affect species remains a persistent challenge that hinders ecologists’ abilities to understand how environmental gradients influence species presence and shape entire communities, especially in the face of data deficient species and imperfect species detection. Here we present a Bayesian framework that allows uncertainty surrounding the ‘true’ spatial scale of species’ responses (i.e., changes in presence/absence) to be integrated directly into a community hierarchical model. This scale selecting multi-species occupancy model (ssMSOM) estimates the scale of response, and shows high accuracy and correct type I error rates across a broad range of simulation conditions. In contrast, ensembles of single species GLMs frequently fail to detect the correct spatial scale of response, and are often falsely confident in favoring the incorrect spatial scale, especially as species’ detection probabilities deviate from perfect. Integrating spatial scale selection directly into hierarchical community models provides a means of formally testing hypotheses regarding spatial scales of response, and more accurately determining the environmental drivers that shape communities.