Miracle-dz/UniFAR-FTUs huggingface dataset:
A command-like descending neuron that coordinately activates backward and inhibits forward locomotion

Command-like descending neurons can induce many behaviors, such as backward locomotion, escape, feeding, courtship, egg-laying, or grooming. In most animals it remains unknown how neural circuits switch between these antagonistic behaviors: via top-down activation/inhibition of antagonistic circuits or via reciprocal inhibition between antagonistic circuits. Here we use genetic screens, intersectional genetics, circuit reconstruction by electron microscopy, and functional optogenetics to identify a bilateral pair of larval “mooncrawler descending neurons” (MDNs) with command-like ability to coordinately induce backward locomotion and block forward locomotion; the former by activating a backward-specific premotor neuron, and the latter by disynaptic inhibition of a forward-specific premotor neuron. In contrast, direct reciprocal inhibition between forward and backward circuits was not observed. Thus, MDNs coordinate a transition between antagonistic larval locomotor behaviors. Interestingly, larval MDNs persist into adulthood, where they can trigger backward walking. Thus, MDNs induce backward locomotion in both limbless and limbed animals. Highlights MDN command-like descending neuron induces backward larval locomotion MDN neurons coordinately regulate antagonistic behaviors (forward/backward locomotion) MDN-motor circuit validated at structural (TEM) and functional (optogenetic) levels MDN neurons induce backward locomotion in both limbless larva and limbed adult
Functional decoupling of emotion coping network subserves automatic emotion regulation by implementation intention

Automatic emotion regulation (AER) aims at modifying emotional impact effortlessly. However, the effortless account and the neural mechanisms of AER are both undetermined. For this purpose, we collected functional neuroimages (fMRI) in thirty-one participants who attended to neutral and disgust pictures in three conditions: Watching, Goal Intention (GI) and Reappraisal by Implementation Intention (RII). RII decreased negative feelings and bilateral amygdala activity without eliciting cognitive efforts, evidenced by the reduced effort rating and less prefrontal engagement during RII compared to Watching and GI. These regulation effects should not be explained by emotional habituation, as Experiment 2 (n=40) observed no habituation to stimulus repetitions. Task-based network analysis showed similar functional connectivity (FC) of ventral anterior cingulate cortex to left insula and right precuneus during RII and GI conditions, both involving goal setup. Furthermore, RII relative to GI exhibited weaker FC in brain networks subserving effortful control (e.g. inferior-superior parietal FC), memory retrieval (e.g. inferior-middle temporal and lingual-putamen FCs), aversive anticipation and motor planning (e.g. Paracentral-superior temporal gyrus, putamen-operculum FCs). The FC strength of putamen to operculum/lingual, and paracentral to STG positively predicts regulatory difficulty. These results suggest that the setup of implementation intention automatizes emotion regulation, by reducing online mobilization of neural systems underlying the stream of emotion coping.
BayesENproteomics: Bayesian elastic nets for quantification of proteoforms in complex samples

Multivariate regression modelling provides a statistically powerful means of quantifying the effects of a given treatment while compensating for sources of variation and noise, such as variability between human donors and the behaviour of different peptides during mass spectrometry. However, methods to quantify endogenous post-translational modifications (PTMs) are typically reliant on summary statistical methods that fail to consider sources of variability such as changes in levels of the parent protein. Here, we compare three multivariate regression methods, including a novel Bayesian elastic net algorithm (BayesENproteomics) that enables assessment of relative protein abundances while also quantifying identified PTMs for each protein. We tested the ability of these methods to accurately quantify expression of proteins in a mixed-species benchmark experiment, and to quantify synthetic PTMs induced by stable isotope labelling. Finally, we extended our regression pipeline to calculate fold changes at the pathway level, providing a complement to commonly used enrichment analysis. Our results show that BayesENproteomics can quantify changes to protein levels across a broad dynamic range while also accurately quantifying PTM and pathway-level fold changes.
The role of abiotic and biotic environmental factors in shaping epiphyton on common reed in shallow, hydrologically transformed, temperate lakes

Epiphytic algae are an important group of organisms involved in primary productivity, nutrient cycling, and energy transfer in littoral food webs. However, multifactorial studies conducted on epiphyton on the same substrate across a spectrum of environmental parameters are very limited. Here, we present first complex field study on the role of abiotic and biotic factors in shaping the species richness, diversity, abundance, and biomass composition of epiphyton on common reed in four shallow lakes with different trophic status, water and fish management, and the abundance and structure of potential algal grazers: littoral crustaceans and fish. The obtained results revealed that the algal taxa richness was the lowest in the hypertrophic lake and the highest in the meso-eutrophic lake. Epiphyton abundance (predominated by pennate diatoms) and biomass were found to be the highest in eutrophic water bodies. Biomass consisted primarily of diatoms, but we found the seasonal predominance of filamentous Chlorophyta (in the eutrophic lakes) and Chlorophyceae (in the meso-eutrophic lake). Redundancy analysis (RDA) showed that the frequency of water level fluctuations was the most significant variable in the composition of epiphyton. RDA also revealed the importance of grazing pressure of fish. Thus, in hydrologically transformed lakes, man-made factors may be of great relevance in the development of epiphytic algae.
Effect of different dose of NPK and vermicompost on growth and yield attributes of maize [Zea mays (L.)] Cv. MM 2255

The field experiment was carried out at soil science research farm of Sam Higginbottom institute of Agriculture, Technology and Sciences (deemed- to- be university) Allahabad, during Kharif season 2015-16. The design applied was 3x3 factorial randomized block design having three factors with three levels of NPK @ 0%, 50%, and 100 % ha-1, three levels of Vermicompost @ 0% &, 50% and 100% ha-1 respectively. The result obtained with treatment T8-[NPK@ 100% + Vermicompost@ 100%] that showed the highest yield regarding, gave the best results with respect to plant height 158.22 cm, number of leaves per plant 11.00, cob length 17.50 cm leaf length per plant 48.50 cm, and dry weight 163.46 g, it gave highest yield, 42.77 q ha-1, test weight 209.03 g. the maximum cost benefit ratio was recorded 1:2.55 and net profit. 44,624.96ha-1in treatment combinationT6-L2V0 [@ 100%NPK ha-1+0% Vermicompost ha-1] was found to be significant among other treatments in maize cultivation and soil quality improvement. It was also revealed that the application of NPK with Vermicompost were excellent source for fertilization than fertilizers.
The first UK survey and population estimate of breeding Snow Bunting Plectrophenax nivalis

ABSTRACT Capsule: The first national survey for Snow Bunting Plectrophenax nivalis in the UK was carried out in 2011 and estimated the breeding population at 60 territories (95% confidence intervals = 48–83). Aims: To estimate breeding population size for Snow Buntings in the UK by surveying all sites with a history of breeding season occupation. Methods: Surveys were carried out in June 2011 to detect males on territory at sites where Snow Bunting had been recorded during the breeding season since 1970. Each site was visited at least once during the survey period; suitable habitat was searched and vantage point watches were conducted in order to detect singing males. Repeated visits to a sample of sites allowed a correction factor to be calculated in order to account for birds undetected during surveys. Results: In 2011, the number of Snow Bunting breeding in the UK (including adjusting for imperfect detection) is a minimum of 60 territories (95% CI = 48–83) using confirmed and probable breeding records of males. A less conservative estimate of 99 territories (95% CI = 88–114) results from including all records of males in suitable habitat. The vast majority of the population was found in the Cairngorm region, with isolated records in the north and west Highlands. Conclusion: The results of the 2011 survey are consistent with well-informed estimates of the Snow Bunting population made previously. This work provides a baseline and repeatable fieldwork and analytical methods enabling future change in the population to be quantified more rigorously.
Fermentation and chemical composition of guinea grass silage added with wheat meal and Streptococcus bovis

ABSTRACT The objective of this study was to evaluate the effects of wheat meal alone or combined with Streptococcus bovis on the fermentation and chemical composition of guinea grass silage. A completely randomised design was used in the following treatments: deionised water, untreated; fresh forage plus 100 g kg−1 of wheat meal; S. bovis JB1 plus 100 g kg−1 of wheat meal; and S. bovis HC5 plus 100 g kg−1 of wheat meal, with six replications. There were a higher number of enterobacteria, moulds and yeast populations in the untreated silage (P < .05) compared to treated silages. The association of S. bovis with wheat meal resulted in lower pH and concentration of NH3-N (P < .05) than silages untreated and treated only with wheat meal. The use of both S. bovis JB1 and HC5 combined with 100 g kg−1 wheat meal can also be a good alternative to farmers for improving the silage quality of guinea grass silage.
Mineralogy, magnetic susceptibility and geochemistry of Fe-rich Oxisols developed from several parent materials

Fe-rich Oxisols on mafic rocks in Brazil generally have high magnetic susceptibility with high contents of some trace elements. These are taxonomically similar soils; however, differences in magnetic and geochemical properties may affect agricultural or environmental usability and subsequent management. This study investigated the pedogenesis of Fe-rich Oxisols from various parent materials and evaluated the lithogenetic influence on magnetic susceptibility and trace elements contents. Soil samples were collected from Bw horizons in 13 Rhodic Oxisols and a Typic Oxisol developed from several parent materials in Minas Gerais State, Brazil. Soils were analyzed by X-ray diffractometry (XRD) and magnetometry. Soil chemical analyses consisted of sulfuric and total (tri-acid) digestions and selective Fe oxides dissolutions and statistical correlations were determined. Fe-rich Oxisols presented a typical mineralogical composition of highly weathered soils with structural stability. The results confirm the difficulty to identify accurately magnetic minerals in different grain sizes using XRD. However, coarse fractions still exert dominant influence on the magnetic properties of the Fe-rich Rhodic Oxisols. In addition, coarse fractions probably contribute to the enrichment of superparamagnetic particles for the clay fraction. Although highly weathered, Fe-rich Oxisols may have their geochemical attributes still controlled by the parent material, where trace elements seem to be correlated with the magnetic minerals in the coarse fractions. Thus, the natural replacement of some trace elements from soil-solution equilibrium reactions during plant development could be more effective in soils with higher magnetic particles concentrations in the coarse fractions.
Performance of hydrogel on seed germination and growth of young coffee seedlings in nursery

An investigation was carried out to study the performance of hydrogel on seed germination and growth of young coffee seedlings in nursery at Central Coffee Research Institute, coffee Research Station, Balehonnur, Karnataka, during the year 2017-18. Results revealed that, nursery bed without gel achieved higher percent of seed germination (90 %) and was taken less number of days (35) to 50 % germination. Among the growth parameters, control recorded significantly maximum plant height (40 cm), number of leaves per plant (14), stem girth (0.51cm), total nodes per plant (7) and shoot dry matter partitioning (11gm) and the parameters like tap root length, root volume and root dry matter partitioning (29 cm, 9 cc/gm and 3 gm, respectively) was significantly higher in treatment T2 (1 gm gel per polybag. Hence, ash treatment (control) is the best and effective method to improve the germination and growth of young coffee seedlings.
Interactions between abiotic gradients determine functional and phylogenetic diversity patterns in Mediterranean‐type climate mountains in the Andes

1Departamento de Biología, Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnológicas, Universidad Rey Juan Carlos, Móstoles, Spain 2Department of Biology, University of Maryland, College Park, MD, USA 3Departmento de Botánica, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile 4Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile
Burkholderia fungorum strain Rifle: growth on and interaction with uranium

ii ACKNOWLEDGMENTS v TABLE OF CONTENTS vii LIST OF TABLES xi LIST OF FIGURES xii CHAPTER I – Introduction 1 Biotic Reduction of Uranium 3 Other Mechanisms of Toxicity Resistance 6 Enzymatic Basis for Uranium Interactions 8 Objectives 11 CHAPTER II – Spatial Distribution of an Uranium13 Respiring Betaproteobacterium at the Rifle, Co Field Research Site Abstract 13 Introduction 14 Methods 16 Field site 16 Isolation of a bacterium capable of growth on uranium 17 Testing of aerobic growth and identification of the isolate 17 Verification of growth on uranium as an electron acceptor 18 Measurement of uranium by mass spectroscopy 19
A New Fossil Species of Boa Linnaeus, 1758 (Squamata, Boidae), from the Pleistocene of Marie-Galante Island (French West Indies)

ABSTRACT Several studies have reported the occurrence of fossil remains of a now extinct Boa snake from the upper Pleistocene of Marie-Galante Island, French West Indies. However, these remains have never been fully investigated and no complete description of this possible new species has been published. In this paper, we try to bridge this gap by providing a detailed morphological study of the Boa remains discovered in the three major fossil deposits of Marie-Galante Island. Our study reveals the specific morphological aspects of this fossil snake and allows us to identify it as a new species, Boa blanchardensis. We also reconstructed its body size, carried out a paleohistological investigation, and suggest that this snake may have been a dwarf species. We then discuss the possible explanation for the extinction of this snake on Marie-Galante Island and possibly also on other Guadeloupe islands.
Nucleolar stress triggers the irreversible cell cycle slow down leading to cell death during replicative aging in Saccharomyces cerevisiae

Asymmetric division in Saccharomyces cerevisiae generates an aging mother cell and a rejuvenated daughter cell. The accumulation of Extrachromosomal rDNA Circles (ERCs) and their specific retention in mothers have been hypothesized to be responsible for replicative aging. However, it remains unclear by which molecular mechanisms ERCs would trigger the cell cycle slow-down occurring during replicative aging and leading to cell death. In this study, we show that ERCs accumulation is initiated within the 5 divisions preceding the onset of cell cycle decline. The generation of ERCs is also concomitant with a nucleolar stress characterized by an up-regulation of RNA polymerase I activity and an accumulation of pre-rRNAs in the nucleolus which do not lead neither to a higher production of ribosomes, nor to an increased growth rate. We further demonstrate that this nucleolar stress observed in old mothers is not inherited by daughters, which recover basal RNA polymerase I activity and normal cell cycle durations following an asymmetrical nuclear division. In the long-lived mutant fob1Δ, we identified a sub-population, with a further extended longevity, which does not present neither a nucleolar stress nor a cell cycle slow down prior to cell death. Altogether, these findings support a causal role for the nucleolar stress in entering cellular senescence.
Stiffness Sensing and Cell Motility: Durotaxis and Contact Guidance

Mechanical properties of the substrate plays a vital role in cell motility. Cells are shown to migrate up stiffness gradient (durotaxis) and along aligned fibers in the substrate (contact guidance). Here we present a simple mechanical model for cell migration, by placing a cell on lattice models for biopolymer gels and hydrogels. In our model cells attach to the substrate via focal adhesions (FAs). As the cells contract, forces are generated at the FAs, determining their maturation and detachment. At the same time, the cell also allowed to move and rotate to maintain force and torque balance. Our model, in which the cells only take the information of forces at the FAs, without a prior knowledge of the substrate stiffness or geometry, is able to reproduce both durotaxis and contact guidance.
The effect of acetaminophen (analgesic) and diphenhydramine (antihistamine) on nociception response of Caenorhabditis elegans, heart rate of Eisenia fetida, and mortality of both E. fetida and C. elegans

Pharmaceutical pollution continues to increase each year but its adverse effects on the environment are still largely unknown. Pharmaceuticals can enter the terrestrial ecosystem when animal manure and sewage sludge are applied to land as a fertilizer or when irrigated with contaminated water. To understand the extent to which common drugs impact the ecosystem, two commonly polluting pharmaceuticals, acetaminophen and diphenhydramine, which have been found in many cities such as Chicago, Dallas, and most notably The Great Lakes, were studied. Various concentrations were tested on E. fetida and C. elegans. Indicators such as heart rate were observed for E. fetida, nociception response for C. elegans, and mortality for both. It was hypothesized that when acetaminophen and diphenhydramine were introduced, all indicators would be negatively affected. Thirty trials were conducted for each test. The results indicated the pharmaceuticals had a significant impact on heart rate, nociception response, and mortality of both E. fetida and C. elegans respectively: (F(6,48)=262.33, p<0.001), (F(6,27)=169.67, p<0.001), (F(8,48)=2.98, p=0.0086), (F(6,27)=169.67, p<0.001). With heart rates increasing by 171% for E. fetida in some cases and nociception response decreasing by over 46% for C. elegans, it was concluded that both populations were negatively affected by acetaminophen and diphenhydramine. Based on experimentation, even small concentrations of pharmaceuticals in the environment can have detrimental effects to certain organisms, severely impacting the ecosystem.
Different SUMO Paralogs Determine the Fate of WT and Mutant CFTRs: Biogenesis vs. Degradation

A pathway for CFTR degradation is initiated by Hsp27 which cooperates with Ubc9 and binds to the common F508del mutant to modify it with SUMO-2/3. These SUMO paralogs form poly-chains, which are recognized by the ubiquitin ligase, RNF4, for proteosomal degradation. Here, protein array analysis identified the SUMO E3, PIAS4, which increased WT and F508del CFTR biogenesis in CFBE airway cells. PIAS4 increased immature CFTR three-fold and doubled expression of mature CFTR, detected by biochemical and functional assays. In cycloheximide chase assays, PIAS4 slowed immature F508del degradation 3-fold and stabilized mature WT CFTR at the PM. PIAS4 knockdown reduced WT and F508del CFTR expression by 40-50%, suggesting a physiological role in CFTR biogenesis. PIAS4 modified F508del CFTR with SUMO-1 in vivo and reduced its conjugation to SUMO-2/3. These SUMO paralog specific effects of PIAS4 were reproduced in vitro using purified F508del NBD1 and SUMOylation reaction components. PIAS4 reduced endogenous ubiquitin conjugation to F508del CFTR by ~50%, and blocked the impact of RNF4 on mutant CFTR disposal. These findings indicate that different SUMO paralogs determine the fates of WT and mutant CFTRs, and they suggest that a paralog switch during biogenesis can direct these proteins to different outcomes: biogenesis vs. degradation.
Aging in Macaws

Macaws are noted for being hardy and long-lived. Estimates of their natural life span are often quoted as 60 years or longer. In actuality, little documented evidence of the life span or aging process of macaws exists in the literature. This review of health records on a group of known age macaws provides some insight into the aging process and longevity of macaws in captivity and may assist in understanding population dynamics in wild macaw populations. Parrot Jungle and Gardens in Miami, Florida, was founded in 1936 as a tourist attraction featuring parrots in a jungle hammock setting. Free-flying parrots, especially macaws, were the leading attraction. These birds were kept for ornamental and entertainment purposes, and breeding was a secondary consideration. Nonetheless if birds chose to breed they were allowed to do so and a breeding facility was provided. Many of the birds that hatched at Parrot Jungle in the early years have remained at the park for their entire lives, making a study of their aging possible. In order to document some of the clinical aspects of aging in macaws, 57 birds known or estimated to be in excess of 25 years old were examined yearly for three years. Of these, 26 were captive-bred and ranged in ages from 25 to 52 years old. Thirty-one (31) were wild caught birds which had been in residence at Parrot Jungle and Gardens for 20 years or longer. The oldest bird at Parrot Jungle, a Military Macaw, was recently euthanized due to frequent and severe seizure activity. This bird was one of the original birds imported in 1936 for the opening of the park and was, therefore, at least 57 years old. This bird, however, had been blind and had a chronic neurologic disorder for many years. The onset of these disabilities was not recorded. Histopathologic examination of the brain revealed mesencephalic tectal neuronal atrophy affecting neurons of all strata, neuronal lipofucscinosis of the cerebellar nucleus, medulla oblongata and some mesenchephalic nuclei, focal calcinosis of the ventral region of the medulla oblongata, and aortic and pulmonary arteriosclerosis. Neuronal lipofuscinosis is a common finding in aged birds and mammals. The first macaw hatched at Parrot Jungle is still in the collection and is now 52 years old. His sibling died at age 49. Seven captive-bred birds in the collection are known to be between 41 and 48 years old. All of these birds have cataracts that have reduced or obscured vision. Most also show degenerative diseases associated with advanced age, including joint stiffness (suggestive of arthritic changes), loss of skin tone and elasticity, muscle wasting, and degenerative neurological disease.