Miracle-dz/UniFAR-FTUs huggingface dataset:
Parallel genome-wide CRISPR analysis identifies a role for heterotypic ubiquitin chains in ER-associated degradation

The ubiquitin proteasome system (UPS) maintains the integrity of the proteome and controls the abundance of key regulators of cellular function by selective protein degradation, but how foldingdefective proteins in the secretory system are selected from the large and diverse constellation of membrane and secretory proteins and efficiently delivered to proteasomes in the cytosol is not well understood. To determine the basis of substrate selectivity in human cells, we developed a transcriptional shut off approach to conduct parallel, unbiased, genome-wide CRISPR analysis of structurally and topologically diverse ER-associated degradation (ERAD) clients. Highly quantitative screen metrics allowed precise dissection of entire pathways, enabling identification of unique substrate-specific combinations of recognition and ubiquitin conjugation modules. Our analysis identified cytosolic ubiquitin conjugating machinery that has not been previously linked to ERAD but collaborates with membrane-integrated ubiquitin ligases to conjugate branched or mixed ubiquitin chains to promote efficient and processive substrate degradation.
Australian Thripinae of the Anaphothrips genus-group (Thysanoptera), with three new genera and thirty-three new species

Relationships are considered among taxa of Thripinae lacking long setae on the pronotum, and these taxa are here discussed as the Anaphothrips genus-group. Seven genera from Australia are considered members of this group: Anaphothrips, Apterothrips, Aptinothrips, Caprithrips, Dodonaeathrips gen.n. , Ozanaphothrips gen. n. and Pandorathrips gen. n. Six new species are described in Ozanaphothrips, and one each in Dodonaeathrips and Pandorathrips. The worldwide genus Anaphothrips now comprises 79 species, of which 43 are here recorded from Australia, including 27 new species. In other parts of the world Anaphothrips species breed on grasses, but hostassociations of the Australian species are remarkably diverse, involving at least 20 plant families. Illustrated keys are provided for the identification of the Anaphothrips genus-group taxa from Australia. Variation is discussed in the form of the pore plates (=glandular areas or areae porosae) that occur on the sternites of males.
Energy partitioning at low temperatures in broiler breeders

The objective of the present study was to investigate how broiler breeder hens partition dietary metabolisable energy (ME) at low temperatures. Performance of caged broiler breeders fed equal quantities of essential nutrients (other than energy) was measured in six environmental chambers, with the temperature in each chamber being kept constant at 10°C, 12.5°C, 15°C (two chambers), 17.5°C or 20°C for two 6-week periods. Throughout these two trial periods, birds were fed 160 g/day of one of four diets containing 12.9, 11.9, 10.5 or 9.7 MJ apparent ME/kg, so that daily energy allocations ranged from 1552 to 2964 kJ/bird. Irrespective of the environmental temperature to which they were subjected, broiler breeders consumed virtually all of the feed allocated to them each day. Mean rate of lay and egg output in the final 3 weeks of each period of hens on the highest apparent ME feed was unaffected by the decrease in temperature from 19.5°C to 9.9°C, but equally depressed on the three lower energy levels. Both weight gain and egg weight increased marginally, but significantly, as the temperature decreased. As a function of body protein weight (BP, kg), egg output (EO, g/day) and growth (ΔW, g/day), the ME consumed (kJ/day) by broiler breeders over all treatments was partitioned as follows: 2423 (±30.3) BP + 7.04 (±0.41) EO + 13.5 (±1.10) ΔW. An ME intake of 1900 kJ/bird.day would appear to be adequate for broiler breeders over the range of temperatures used in the trial.
Environmentally driven fluctuations in condition factor of adult Gulf menhaden (Brevoortia patronus) in the northern Gulf of Mexico

We evaluated the effects of a suite of environmental predictors on the relative condition (the relationship between individual weight and length) of adult Gulf Menhaden Brevoortia patronus sampled from the commercial fishery, from 1964 to 2011. A hierarchical linear model (HLM) was used to examine the association between relative condition and Mississippi River discharge. Generalized Additive Models (GAMs) were constructed to determine the impact on relative condition by El Niño Southern Oscillation (ENSO) and the spatially-variant influence of sea surface temperature (SST°C), chlorophyll a concentration (mg m) and wind vector components. The HLM revealed a positive correlation between Mississippi River discharge and relative condition that was consistent throughout the fishing season (April to October). Comparisons of spatially–variant and –invariant GAMs indicated that the effects of SST was consistent in the northern Gulf of Mexico (NGOM) and that the greatest relative condition was at temperatures associated with the Mississippi River plume front. The effect of wind vector components was spatially-variable, likely due to geographic differences in wind-related transport of productive plume waters across the NGOM. Relative condition was greatest during positive ENSO anomalies. Relative condition exhibited intra-annual variability with a small peak during April and May and increasing condition from August until November, likely caused by increased food availability and provisioning by individuals for spawning. We show that multiple bottom-up processes impact the individual dynamics of Gulf Menhaden in the NGOM and these results can be used to predict their impacts on the fisheries and ecology of the NGOM.
Tree standing dynamics after 30 years in a secondary forest of Bali, Indonesia

Siregar M, Undaharta NKE. 2018. Tree standing dynamics after 30 years in a secondary forest of Bali, Indonesia. Biodiversitas 19: 22-30. Tree standing dynamics in 0.5 ha plot after 30 years in Bukit Tapak secondary forests, Batukahu Nature Reserve, Province 0f Bali was studied by using plot method. The results showed that the tree species richness is same, 33 species, but there are six species disappear and be replaced by another species as a newcomer. Eight species persist as major species based on the importance value, namely: Homalanthus giganteus, Vernonia arborea, Dendrocnide stimulans, Meliosma angustifolia, Saurauia reinwardtiana, Trema orientalis, Macaranga triloba and Polyosma integrifolia. Tree density decreased 19.7%, but the total basal area increased 12.2% with an average basal area per tree were also increased by 39.7%. Shannon diversity index (H`) and Equitability index (E) was increased in 2016. Forests in the plot categorized as old secondary forest are still in the process of maturation toward the primary forest. Species predicted would disappear with a succession of increasingly advanced process is Trema orientalis, while the predicted to survive for much longer are Homalanthus giganteus, Acronichia trifoliolata, Meliosma angustifolia, Polyosma integrifolia, Saurauia reinwardtiana and Dendrocnide stimulans.
Isolation and characterization of bacteria flora from dumpsites in Benin City metropolis, southern Nigeria.

BACKGROUND : The waste dumps are indiscriminately placed at common sites in developing countries. It has been reported that over 5.2 million people, that includes 4 million children, die each year from waste related diseases. Waste is any substance, solution mixture or particle for which no direct use is envisaged but which is transported for reprocessing, dumping, elimination by incineration or other methods of disposal. Aim : The study is to isolate, identify and characterize bacteria from different dump sites in Benin City Metropolis, Edo State, Nigeria. Materials and Methods : Soil samples were collected from the various dumpsites and the adjacent control sites in a sterile universal container. The bacterial load count for the various dumpsites and the adjacent control sites was counted using mise and misra serial dilution method. Aerobic and facultative anaerobic bacteria were isolated from dump site samples using five different culture media. Phenotypic test was assayed using double disk method to check for Extended Spectrumβ-lactamase (ESBL) and metallo-β-lactamase enzyme among the Gram negative bacterial isolates. Results: The following bacteria in decreasing order of prevalence were isolated from the various dumpsites Bacillus spp (30.01%), Klebsiella spp (24.27%), Staphylococcus aureus (12.62%),Coagulate Negative S.aureus (CONS)(10.68%), Pseudomonas spp (6.79), E. coli (4.85%), Alcaligenes spp (4.85%) and Proteus spp (2.91%). Also the following bacteria in decreasing order of prevalence were isolated from the various adjacent control sites, Bacillus spp (66.67%), Klebsiella spp (9.52%), Coagulate Negative S.aureus (CONS) (7.14%) Pseudomonas spp (4.76%), Staphylococcus aureus (2.38%), and Proteus spp (2.38%). Antibiotic susceptibility tests on isolates were performed using standard disc diffusion method. Overall, Ciprofloxacin, Imipenem and Pefloxacin were the most effective agents on the isolates obtained from the various dumpsites. E. coli isolated from the various dumpsites 164 showed strong resistance to almost all antimicrobial agents employed. More so Proteus vulgaris isolated from Oregbeni market dumpsite showed resistance to almost all antimicrobial agent employed. Klebsiella aerogenes , Klebsiella oxytoca and Pseudomonas aeruginosa were observed to be positive to metallo- β-lactamase test. However, other bacterial isolates were observed to be negative for ESBL test. Nonethelessbacteria isolates could cause opportunistic infections which may cause more harm to immune-deficient individuals in the clinic, and in the residences. Conclusion : Waste managers and scavengers should endeavour to put on protective clothing, face mask and hand gloves while handling waste. Also proper sorting of waste material should be done prior to disposal in the general dumpsites. Key words :Waste, Dumpsites, ESBL, β-Lactamase, Coagulase Negative Staphylococcus (CONS).
Targeting the bacterial cell envelope by molecular coevolution and high throughput phenotyping

Microbial species exhibit a wide repertoire of phenotypic responses to their surroundings, be it stresses posed by their environment, or signals from their bacterial community. Despite advances in computer vision, reporting such phenotypic responses is often done in a qualitative manner. In the course of my work I developed a user-friendly software tool to address the lack of a standardized, quantitative method to measure microbial phenotypes macroscopically. This freely available software, called Iris, can quantify a wide range of microbial phenotypes at the colony level and in a high-throughput fashion. Iris is already used by several research groups, and I present some of its diverse applications and potential for hypothesis generation. One such application is the quantification of the impact of each gene on the cell envelope permeability in E. coli. The Gram-negative bacterial cell envelope forms a barrier against antimicrobial drugs, drastically limiting the list of treatments effective against these organisms. To expand our knowledge on how this multi-layered is built and perturbed, we developed a rapid screening method to detect mutants with envelope defects. By screening a systematic gene deletion mutant collection in E. coli across 4 conditions, we identified a number of mutants with defects in envelope assembly. Among those were genes known to be involved in envelope biogenesis, as well as 102 genes of unknown function. In the course of my work I built upon and improved this screening approach, to acquire quantitative membrane permeability measurements that can be used for high- throughput chemical genomics approaches. Gram-negative bacterial envelope is both a permeability barrier, and a structural barrier. The structural component mainly consists of the rigid peptidoglycan (PG) sacculus, which gives the cells the ability to withstand both turgor pressure and environmental insults. Although biosynthesis of PG is central to bacteria and a target of β-lactam antibiotics, its regulation remains largely elusive. Recently, a number of regulators of PG biosynthesis have been identified, and shown to have coevolved with domains in PG synthases. With the aim of uncovering potential regulatory connections, I developed a computational approach to explore the coevolution of domains in proteins involved in cell wall biosynthesis and remodeling with other proteins in the cell. The method correctly identified existing regulatory interactions, and is readily applied to species across the bacterial kingdom.
Urbanization as a driver of taxonomic, functional, and phylogenetic diversity losses in bird communities

Urbanization is one of the most important threats to biodiversity worldwide, as it drives declines in species diversity, functional diversity, and phylogenetic diversity and increases functional redundancy among species. We estimated taxonomic, functional, and phylogenetic diversities, as well as the abundance of several functional groups, in bird communities from a town in east-central Argentina in 1985–1986 and 30 years after (2015–2016). In 1985–1986, we found that taxonomic diversity (abundance, species richness, and alpha diversity), functional richness, and basal phylogenetic diversity were negatively related to building cover, whereas terminal phylogenetic diversity showed a positive relationship with building cover. Moreover, the abundance of specialized functional groups (ground, aerial, and foliage insectivores; nectarivores/insectivores; ground/canopy and ground granivores) decreased with increased building cover, whereas the reverse pattern for the abundance of generalists (medium-sized/large and small omnivores) was found. In 2015–2016, by contrast, taxonomic, functional, and phylogenetic diversities were not related to building cover. Our results not only support the hypothesis that urbanization affects the potential number of ecosystem functions, but also that this relationship may change through time. Given the accelerated rate of urbanization worldwide, an integrative approach between different facets of biodiversity is promoted to gain insight into the response of bird communities in urban environments.
Polar marine diatoms likely take up a small fraction of dissolved dimethylsulfoniopropionate relative to bacteria in oligotrophic environments

Dimethylsulfoniopropionate (DMSP) constitutes a major compound in the global sulfur cycle. A few studies over the last decade have revealed that not only bacteria but also eukaryotic phytoplankton may take up DMSP from the dissolved pool, although the mechanisms and quantitative importance of this undefined DMSP uptake pathway, particularly by polar phytoplankton, remain poorly known. To fill this gap, we undertook short-term 35S-DMSP uptake kinetic experiments in axenic laboratory batch cultures of 3 polar marine diatoms (Thalassiosira gravida, Chaetoceros neogracilis, and Chaetoceros gelidus). DMSP uptake by C. neogracilis and C. gelidus was below the detection limit, but significant DMSP uptake by T. gravida was ob served. These differences might be explained by the presence of a putative OpuD/DddT-like DMSP transporter in various Thalassiosira spp. , which is absent in the transcriptomes of Chaetoceros spp. Based on conservative extrapolation of DMSP uptake kinetics measured in T. gravida cultures to the complex consortium of diatoms found in oligotrophic Arctic environments, the fraction of dissolved DMSP taken up by polar diatoms is probably small compared to that taken up by bacteria and (perhaps) other eukaryotic algae.
Coevolution of structural variation and optimization in sound systems of human language

Evolution of sound systems of human language is an optimization process to improve communicative effectiveness: The intrinsic structures of sound systems are constantly organized with respect to constraints in speech production and perception. However, there lack sufficient quantitative descriptions of this process, large-scale investigations on universal tendencies in sound systems, and explicit evidence on whether demographic and/or geographic factors can influence linguistic typology of sound systems. Here, we proposed two composite parameters, namely structural variation and optimization, to capture linguistic typology of sound systems, vowel systems in particular. Synchronic comparisons based on a large-scale vowel corpus of world languages revealed a universal negative correlation between the two parameters. Phylogenetic comparative analyses identified a correlated evolution of the two, but with distinct evolutionary modes: a gradual evolution of the structural variation and a punctuated equilibrium of the optimization. Mixed-effect models also reported significant effects of speaker population size and longitude on shaping vowel systems of world languages. All these findings elaborate the intrinsic evolutionary mechanism of sound systems, clarify the extrinsic, non-linguistic effects on shaping human sound systems, and quantitatively describe and interpret the evolution and typology of sound systems.
Effects of Haloxyfop on Corn (Zea mays) and Soybean (Glycine max) Cell Suspension Cultures

To investigate the mode of action of a grass-specific herbicide, haloxyfop {2-[4-[[3-chloro-5-(trifluoromethyl)-2-pyridinyl] oxy] phenoxy] propanoic acid} was added to corn and soybean cell suspension cultures containing metabolic intermediates such as sucrose [14C-U], sodium acetate [14C-1,2], or L-leucine [14C-U]. Death of the corn suspension cells occurred within 3 days after haloxyfop was added at a concentration of 1.0 μM to supplemented Murashige and Skoog's medium. At 0.1 μM haloxyfop, 14C-sucrose uptake and 14C loss due to respiration of the corn cells declined without a significant reduction in cell fresh weight, cell viability, cellular ATP level, free sugar content, cell wall materials, or level of glycolytic intermediates. The proportions of sucrose, glucose, and fructose in the free sugar fraction were not affected. However, the 14C-labeled free amino acid level was increased. During a 24-h incubation period, incorporation of leucine [14C] as a precursor revealed that haloxyfop did not inhibit protein synthesis. Incorporation of acetate [14C-1,2] showed that total lipid synthesis was inhibited by 42% at 0.1 μM haloxyfop (sublethal). Similar responses were observed in the soybean suspension cells; however, the calculated 50% lethal concentration (LC50) was 47 times higher than for corn cells. The results of this study suggest that the site of action of haloxyfop is located where metabolic intermediates enter the Kreb's cycle and lipid synthesis. Glycolysis is not inhibited.
Game theory of vaccination and depopulation for managing avian influenza on poultry farms

Highly pathogenic avian influenza is endemic in domestic poultry populations in East and South Asia and is a major threat to human health, animal health, and the poultry production industry. The behavioral response of farmers to the disease and its epidemiological effects are still poorly understood. We considered a symmetric game in a region with widespread smallholder poultry production, where the players are broiler poultry farmers and between-farm disease transmission is both environmental (local) and mediated by the trade of infected birds. Three types of farmer behaviors were modelled: vaccination, depopulation, and cessation of poultry farming. We found that the transmission level of avian influenza through trade networks had strong qualitative effects on the system’s epidemiological-economic equilibria. In the case of low trade-based transmission, when the monetary cost of infection is sufficiently high, depopulation behavior persists and maintains a disease-free equilibrium. In the case of high trade-based transmission, depopulation behavior has perverse epidemiological effects - as it accelerates the spread of disease via poultry traders - but has a high enough payoff to farmers that it persists at the system’s game theoretic equilibrium. In this situation, state interventions should focus on making effective vaccination technologies available at a low price rather than penalizing infected farms. Our results emphasize the need in endemic countries to further investigate the commercial circuits through which birds from infected farms are traded.
Comparative effects of two indole-producing trichoderma strains and two exogenous phytohormones on the growth of zea mays l., with or without tryptophan

This research evaluated the growth responses of maize plants due to the inoculation of two indole-producing Trichoderma strains in comparison to the application of two exogenous phytohormones. Either T. tomentosum (EMMFRS1C2) or T. harzianum (MichV6S3C2) were inoculated as conidia or as fungal filtrates obtained from Luria-Bertani, liquid medium, with or without the addition of L-Tryptophan (1 g L-1). In addition, two concentrations (5 and 10 mg L-1) of indole acetic acid (IAA) and indole butyric acid (IBA) from which 2 mL were applied per plant. Twelve treatments and six replicates distributed in a completely randomized design. Plants were maintained for 50 days in microcosms (perlite and vermiculite, 2:1 v/v), under greenhouse conditions (38oC±5) and watered every 48 h. The best plant growth responses (height, root length, leaf area, and root, stem and total dry weight were achieved by inoculating conidia of either T. tomentosum (EMMFRS1C2) or T. harzianum (MichV6S3C2) in combination with tryptophan (1 g L-1) when compared to control plants; but T. harzianum (MichV6S3C2) only resulted in beneficial effects in root length. Moreover, the application of fungal filtrates had similar plant growth responses than the application of either IAA or IBA at 5 mg L-1.
Effect of an 1800 MHz electromagnetic field emitted during embryogenesis on the blood picture of one-day-old domestic hen chicks ( Gallus gallus domesticus )

Exposure to artificial electromagnetic fields emitted mainly by mobile telephony has been steadily increasing with the development of modern technology. Haematological indices are among the most common indicators of the body’s physiological status. The aim of the study was to determine the effect of an 1800 MHz electromagnetic field emission on the blood picture of one-day-old domestic hen chicks. During the experiment, chick embryos were exposed to artificial electromagnetic fields throughout incubation for 13 ´ 2 min/day, 4 ´ 10 min/day and 1 ´ 40 min/day. After hatching, blood was collected from 10 one-day-old chicks from each group to determine: red blood cell count, haemoglobin concentration, haematocrit, mean corpuscular volume, mean corpuscular haemoglobin, mean corpuscular haemoglobin concentration, white blood cell count, and leukocyte differential count. In addition, the heterophil/lymphocyte ratio was calculated. The present study is probably the first to show an increase in the red blood cell count, haemoglobin concentration, haematocrit, white blood cell count, segmented heterophils and the heterophil/lymphocyte ratio, and a decrease in lymphocyte percentage of embryos exposed to an 1800 MHz electromagnetic field. The observed changes may be indicative of the stress-inducing effect of EMF on living organisms.