Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling the bioenergetics of protein-mediated membrane deformation

COMPUTATIONAL STUDY OF ENDOCYTOSIS: MODELING THE BIOENERGETICS OF PROTEIN-MEDIATED MEMBRANE DEFORMATION Neeraj J. Agrawal Ravi Radhakrishnan In eukaryotic cells, the internalization of extracellular cargo into the cytoplasm via the endocytosis machinery is an important regulatory process required for a large number of essential cellular functions, including nutrient uptake, cell-cell communication, and modulation of cell-membrane composition. Endocytosis is orchestrated by a variety of proteins implicated in membrane deformation, cargo recognition and vesicle scission. While the involvement and roles of these proteins in membrane deformation, cargo recognition, and vesicle scission have been identified, current conceptual understanding falls short of a mechanistic description of the cooperativity and the bioenergetics of the underlying vesicle nucleation event which we address here using theoretical models based on an elastic continuum representation for the membrane and coarse-grained representations for the proteins. We describe the energetics of deformations of membranes by solving the Helfrich Hamiltonian by two different formalisms: Monge formalism and surface of evolution formalism. The Monge approach is limited to small deformations of the membrane and thermal effects are included while the surface of evolution approach is versatile in describing membrane geometries in both small and large deformation limits but is limited to axis-symmetric profiles of membrane. To explicitly calculate the role of entropy change due to membrane bud formation, we employ thermodynamic integration method in conjugation with thermodynamic cycle. In our model, curvature inducing proteins and protein assembly like epsin and clathrin coat affect the membrane Hamiltonian by changing the preferred mean curvature of the membrane. This integrated multiscale approach results in a unified description of membrane behavior at the mesoscale, under the influence of curvature-inducing proteins at the nanoscale. Using this toolkit of the methods, we demonstrate the role of the endocytic protein assembly in driving membrane vesiculation and further quantify the energetics of the underlying process.
Evolution and expression of the superoxide dismutase of the archaebacterium halobacterium cutirubrum

Archaebacteria are a diverse group of bacteria that share a number of fundamental biochemical characteristics that distinguish them from other bacteria (eubacteria) and eucaryotes. They are believed to be an independent lineage that diverged from other organisms more than 3.5x10$ years ago. To study the evolution of oxygen tolerance in the archaebacteria, the superoxide dismutase (SOD) and SOD-encoding gene of the extremely halophilic archaebacterium Halobacterium cutirubrum were investigated. Purification of the SOD activity of this organism resulted in a single Mn-containing enzyme with subunits of Mr 25000 that probably associate as tetramers. It has maximal activity in 2 M KC1, reflecting adaptation to the high salt concentrations within halobacterial cells. Assays of activity in the presence of SOD inhibitors (cyanide, azide, and hydrogen peroxide) gave a unique pattern of responses. The sequence of 51 of 56 amino acid residues at the amino-terminus was determined and found to be homologous to the amino-terrnini of SODs of eubacteria. The gene, designated sod, that encodes the halobacterial Mn SOD was cloned by using as a probe a mixture of 20mer oligonucleotides corresponding to codons for amino acid residues 27-33. The sod gene and 5' and 3' untranslated regions were located on a Sau3AI genomic DNA fragment of 1127 nucleotides. The deduced amino acid sequence is 200 residues long and has 39 to 42% identity with Mn-containing SODs of eubacteria and mitochondria. This homology may be due to either lateral transfer of the gene between eubacteria and archaebacteria or to high amino acid sequence conservation in the enzyme during the divergent evolution of eubacteria and archaebacteria. Transcription of the gene
Validation and association of candidate markers for adult migration timing and fitness in Chinook Salmon

Recent studies have begun to elucidate the genetic basis for phenotypic traits in salmonid species, but many questions remain before these candidate genes can be directly incorporated into conservation management. In Chinook Salmon (Oncorhynchus tshawytscha), a region of major effect for migration timing has been discovered that harbors two adjacent candidate genes (greb1L, rock1), but there has been limited work to examine the association between these genes and migratory phenotypes at the individual, compared to the population, level. To provide a more thorough test of individual phenotypic association within lineages of Chinook Salmon, 33 candidate markers were developed across a 220 Kb region on chromosome 28 previously associated with migration timing. Candidate and neutral markers were genotyped in individuals from representative collections that exhibit phenotypic variation in timing of arrival to spawning grounds from each of three lineages of Chinook Salmon. Association tests confirmed the majority of markers on chromosome 28 were significantly associated with arrival timing and the strongest association was consistently observed for markers within the rock1 gene and the intergenic region between greb1L and rock1. Candidate markers alone explained a wide range of phenotypic variation for Lower Columbia and Interior ocean‐type lineages (29% and 78%, respectively), but less for the Interior stream‐type lineage (5%). Individuals that were heterozygous at markers within or upstream of rock1 had phenotypes that suggested a pattern of dominant inheritance for early arrival across populations. Finally, previously published fitness estimates from the Interior stream‐type lineage enabled tests of association with arrival timing and two candidate markers, which revealed that fish with homozygous mature genotypes had slightly higher fitness than fish with premature genotypes, while heterozygous fish were intermediate. Overall, these results provide additional information for individual‐level genetic variation associated with arrival timing that may assist with conservation management of this species.
Group I intron mediated trans-splicing of highly conserved dengue virus sequences & a mutational analysis of the piggyBac transposase

by James H. Keith The piggyBac mobile element is quickly gaining popularity as a tool for the transgenesis of many eukaryotic organisms. By studying the transposase (TPase) which catalyzes the movement of piggyBac, modification of this vector system may be possible in order to make it a more effective transgenesis tool. In a previous publication (Sarkar et al., 2003) proposed the presence of the widespread ‘DDE/DDD’ motif for piggyBac at amino acid positions D268, D346, and D447. A PSORTII analysis of the TPase amino acid sequence predicts several nuclear localization signals (NLS) near the C-terminus, just upstream of a putative zinc finger (ZnF). This study utilizes directed mutagenesis and plasmid-based mobility assays to assess the importance of conserved aspartate residues as the catalytic core of the piggyBac TPase. Individual point-mutations have been functionally analyzed with respect to charge and physical size in all three proposed residues of the ‘DDD’ motif, as well as another nearby, highly conserved aspartate at D450. Results indicate that all four aspartates are necessary, to one degree or
Characterization of Anaphylatoxin Receptor Expression and C3a/C5a Functions in Anaphylatoxin Receptor Reporter Mice

The anaphylatoxins (AT) C3a and C5a are effector molecules of C3 and C5 exerting multiple biologic functions through binding and activation of their cognate G protein−coupled receptors. C3a interacts with the C3a receptor (C3aR), whereas C5a and its primary degradation product C5a‐desArg engage C5aR1 and C5aR2. In the past, analysis of AT expression has been hampered by cross reaction of antibodies designed to recognize the different AT receptors. Furthermore, assessment of effects mediated by cell‐specific activation has been difficult. Here, floxed AT receptor reporter mice are described as tools to monitor AT receptor expression in cells and tissues and to study the functions of C3a and C5a by cell‐specific deletion of their cognate AT receptors. © 2020 The Authors.
Sex modification in pointed gourd (Trichosanthes dioica Roxb.)

Application of silver nitrate (AgNO3) at different concentrations (50-2,000 mg/litre) showed toxic effect on treated vines. Toxicity increased at higher concentrations. The treated vines died at the concentration of 1,200-2,000 mg/litre. Of the treatments, only 800 and 1000 mg/litre of AgNO3 produced hermaphrodite flowers. Several morphological changes occurred in hermaphrodite flowers. Among them, tri-furcated stigma fused together and made a single structure and 3 anthers developed. The newly-developed rudimentary anther was not able to produce pollen grains. The flowers treated with 100–1000 mg/litre of AgNO3 induced parthenocarpic fruits. In all aspects, pathenocarpic fruits showed lower performance compared to normal open-pollinated fruits.
An Introduction to the Aquatic Insects of North America

An Introduction to Aquatic Bird RehabilitationAquatic Mesocosm Studies in Ecological Risk AssessmentAquatic Monocotyledons of North AmericaAquatic PhotosynthesisTrophic Interactions Within Aquatic EcosystemsHandbook of Methods in Aquatic Microbial EcologyAquatic EntomologyWestern Wetland FloraHandbook of Inland Aquatic Ecosystem ManagementField Guide to Freshwater Invertebrates of North AmericaAquatic EntomologyEcological Assessment of Selenium in the Aquatic EnvironmentA Guide to Common Freshwater Invertebrates of North AmericaAquatic PlantsAn Introduction to Aquatic ToxicologyWater ChemistryAquatic Dicotyledons of North AmericaHandbook of Scaling Methods in Aquatic EcologyMethods in Stream EcologyFundamentals Of Aquatic ToxicologyFreshwater Algae of North AmericaTrace Metals in Aquatic SystemsChemotherapy and Aquatic TherapeuticsEcology and Classification of North American Freshwater InvertebratesPond Aquaculture Water Quality ManagementTexas Aquatic ScienceWater Resource Systems Planning and ManagementAquatic EcotoxicologyFreshwater MicrobiologyAn Introduction to the Aquatic Insects of North AmericaForest HydrologyFreshwater Macroinvertebrates of Northeastern North AmericaAn Introduction to the Aquatic Insects of North AmericaParticulate Plastics in Terrestrial and Aquatic EnvironmentsEcological Strategies of Aquatic InsectsFundamentals of Aquatic EcologyAquatic Ecosystems in a Changing ClimateAquatic Chemistry Concepts, Second EditionAn Introduction to the Aquatic Insects of North AmericaWater Technology
Biochemical Correlates of Calling Activity in Neotropical Frogs

Variation in behavioral performance among animals often is closely matched to the functional capacity of muscles that support the activity. In frogs, a general correlation exists between calling activity and characteristics of the trunk muscles that support call production. I determined hourly calling rates and call durations from males of six tropical hylid species and two leptodactylid species. Samples of trunk- and leg-muscle tissue were collected and assayed for activity levels of the catabolic enzymes citrate synthase (CS) and β-hydroxyacyl-CoA dehydrogenase (HOAD), which generally are correlated with tissue capacities for aerobic metabolism and fatty acid oxidation, respectively. Enzyme activity levels in the more aerobic trunk muscles were several times greater than in the more anaerobic leg muscle and were significantly correlated with average calling rates. Overall, species with higher calling rates had trunk muscles with higher enzyme activity levels. This study demonstrates a significant relationship among related species between characteristics of a natural activity, calling, and the biochemistry and physiology of the muscles involved in call production.
Stoichiometrically coupled carbon and nitrogen cycling in the MIcrobial-MIneral Carbon Stabilization model version 1.0 (MIMICS-CN v1.0)

Abstract. Explicit consideration of microbial physiology in soil biogeochemical models that represent coupled carbon–nitrogen dynamics presents opportunities to deepen understanding of ecosystem responses to environmental change. The MIcrobial-MIneral Carbon Stabilization (MIMICS) model explicitly represents microbial physiology and physicochemical stabilization of soil carbon (C) on regional and global scales. Here we present a new version of MIMICS with coupled C and nitrogen (N) cycling through litter, microbial, and soil organic matter (SOM) pools. The model was parameterized and validated against C and N data from the Long-Term Inter-site Decomposition Experiment Team (LIDET; six litter types, 10 years of observations, and 13 sites across North America). The model simulates C and N losses from litterbags in the LIDET study with reasonable accuracy (C: R2=0.63 ; N: R2=0.29 ), which is comparable with simulations from the DAYCENT model that implicitly represents microbial activity (C: R2=0.67 ; N: R2=0.30 ). Subsequently, we evaluated equilibrium values of stocks (total soil C and N, microbial biomass C and N, inorganic N) and microbial process rates (soil heterotrophic respiration, N mineralization) simulated by MIMICS-CN across the 13 simulated LIDET sites against published observations from other continent-wide datasets. We found that MIMICS-CN produces equilibrium values in line with measured values, showing that the model generates plausible estimates of ecosystem soil biogeochemical dynamics across continental-scale gradients. MIMICS-CN provides a platform for coupling C and N projections in a microbially explicit model, but experiments still need to identify the physiological and stoichiometric characteristics of soil microbes, especially under environmental change scenarios.
Impacts of computerization and digitization: some health issues

Computerization and digitization are effects and the engines of development at the same time. Computers surround both work activities and beyond. There are several benefits available, including the faster, easier, and cheaper way of managing our tasks. However, there are undesirable health impacts to consider, but these are less pronounced. Exploring these impacts and preventing the occurrence is essential for improving the efficiency of computerization. The study focuses on the effects of computer work by analyzing its exhausting characteristics and the tiredness or pain in different body parts. The research method uses a survey of full-time and parttime higher education students. The sample consists of 200 randomly selected responses collected between 2018 and 2019. It allows analyzing the differences of perceptions between respondents with and without job experience. Beyond descriptive statistics, ANOVA and correlation analysis was conducted for exploring the relations. Data analysis was supported by IBM SPSS version 25. The results show that the perceived undesirable health impacts are timeless and ageless. Eye-related problems, as well as back and shoulder, are considered the most critical by the respondents. The main implication of the study is that more attention must be paid to the field, appearing in regulations and developing training programs for computer users. The results presented in this paper aim to highlight the importance of the prevention of harmful symptoms of computer work, which are not in the mainstream right now.
Response

We thank Drs. Jun Zhang, Jianhong Wang, Ke Li, Weijun Tang, and Daoying Geng for their comments on our article, ‘‘Correlation of iron in the hippocampus with MMSE in patients with Alzheimer’s disease’’ (1). The major problem that they identified concerns the illustrations. Figures 1 and 2 were actually fusions of the corrected-phase imaging and the T1weighted imaging results. The corrected-phase map is only useful in measuring iron content and does not offer a sufficient signal intensity-to-noise ratio (SNR). Therefore, we combined the phase map with information from the T1-weighted structural MRI to make more accurate locations of the ROIs. In our article, we described these methods in the third paragraph of the Subjects and Methods section: ‘‘The T1-weighted fast spoiled gradient recalled echo (fGRE) images using the same field of view (FOV) and coverage range were used to assist in anatomic identification. ’’ Perhaps we did not provide a clear description in the figure captions. Regarding the artifacts, we believe that like many other novel techniques, time is needed to improve and adjust the sequences. Fortunately, some recent improvements have been made. Haacke and colleagues (2) suggested adjusting to a kernel-sized filter to determine the phase of SWI, which could be used to remove artifacts due to air/tissue interface especially in the frontal brain regions. Du et al (3) reported that, with a multi-echo acquisition, the SWI data acquired at a shorter TE can have a substantially higher SNR than that acquired at a longer TE. Ishimori et al (4) used a short-TE phase mask to reduce the phase-aliasing artifacts. In conclusion, we believe that the phase value measurement is valid for quantitative iron analysis and could be widely used in the future.
Predicting survivors: animal temperament and translocation

Translocation is an important conservation management tool. However, not all individuals are equally suited to translocation, and temperament traits (e.g., boldness, reactivity, exploration, sociability, and aggression) are likely to influence survival in a new environment. A few empirical studies have examined the consequences of personality differences on captive-bred translocated animals, but this has not been done for wild-caught animals. We compared behavioral responses to trapping, processing, holding, and release for 56 wild common brushtail possums (Trichosurus vulpecula). Twenty individuals were captured twice, once to attach radio-tracking collars, the second time (2 weeks later) for the translocation. Consistency of behavioral responses was compared between capture events and radio-tracking allowed estimates of pretranslocation home range, rest site selection, and foraging behavior. Survivors (n = 10 survivors, 5 months later) were individuals showing the most fear or emotional reactivity during holding (less likely to have slept, eaten, defecated, or nested) and those that had the smallest home ranges and selected the safest den sites in their original habitat. Conversely, the greatest increase in body mass was recorded for individuals that had demonstrated "unsafe" behavior in their original habitat. To our knowledge, this is the first time this type of behavioral screening during handling and holding prior to release as part of a translocation has been undertaken. These methods have broad applicability for screening potential translocation candidates and are easily translated to a range of threatened and vulnerable animal species.
Deficiency of IL-6 versus IL-6 Receptor Differences in Wound Healing in Mice with

IL-6 modulates immune responses and is essential for timely wound healing. As the functions mediated by IL-6 require binding to its speciﬁc receptor, IL-6R a , it was expected that mice lacking IL-6R a would have the same phenotype as IL-6–deﬁcient mice. However, although IL-6R a –deﬁcient mice share many of the inﬂammatory deﬁcits seen in IL-6–deﬁcient mice, they do not display the delay in wound healing. Surprisingly, mice with a combined deﬁcit of IL-6 and IL-6R a , or IL-6–deﬁcient mice treated with an IL-6R a –blocking Ab, showed improved wound healing relative to mice with IL-6 deﬁciency, indicating that the absence of the receptor contributed to the restoration of timely wound healing, rather than promiscuity of IL-6 with an alternate receptor. Wounds in mice lacking IL-6 showed delays in macrophage inﬁltration, ﬁbrin clearance, and wound contraction that were not seen in mice lacking IL-6R a alone and were greatly reduced in mice with a combined deﬁcit of IL-6 and IL-6R a . MAPK activation-loop phosphorylation was elevated in wounds of IL-6R a –deﬁcient mice, and treatment of wounds in these mice with the MEK inhibitor U0126 resulted in a delay in wound healing suggesting that aberrant ERK activation may contribute to improved healing. These ﬁndings underscore a deeper complexity for IL-6R a function in inﬂammation than has been recognized previously. The Journal of Immunology , 2010, 184: 000–000.
Interleukin‐12

Interleukin‐12 (IL‐12) is a newly characterized cytokine that has a unique heterodimeric structure. It was initially cloned from B lymphoblastoid cell lines, but the majority of IL‐12 is produced by macrophages/monocytes following appropriate stimulation. IL‐12 can (1) enhance the cytolytic activity of a number of effector cells including T cells, natural killer (NK) cells, lymphokine activated killer (LAK) cells, and macrophages, (2) increase proliferation of activated NK and T cells, (3) induce production of cytokines, such as interferon gamma, (4) stimulate the induction of ThI cells, (5) upregulate a number of cell surface molecules, (6) inhibit IgE secretion, and (7) act as a synergistic factor for hematopoietic stem cells. Based on these potent immunomodulatory activities, IL‐12 has been evaluated in several disease models for parasitic infections and malignancies. Marked activity of IL‐12 against both Lcishmania and Toxoplasma has been reported. Likewise, antimetastatic and antitumor activity, including tumor regression, has been observed against a number of murine malignancies treated with IL‐12 using doses that result in little toxicity. The results suggest that IL‐12 may be a useful cytokine for the treatment of a number of diseases. J. Leukoc. Biol. 55: 280–288; 1994.
GEOENGINEERING WITH SEA SPRAY: AEROSOL DIRECT AND INDIRECT EFFECTS

In recent years, altering the climate system deliberately has been a target of extensive research. One of these geoengineering ideas is to seed lowlevel marine clouds with sea spray aerosol in order to increase cloud droplet concentration (CDNC) (Latham, 1990). Increased CDNC would lead to higher cloud albedo (first indirect effect, Twomey 1997), which in turn would affect Earth’s radiative balance and cool the climate. Previous model studies have shown that that increased CDNC would indeed have a major effect on Earth’s radiative balance (Latham et al., 2008; Jones et al., 2008; Rasch et al., 2009). In these studies a fixed CDNC in the modified regions was assumed. Explicit calculation of aerosol microphysics and cloud activation with a chemical transport model shows that suffcient and homogeneous increase in CDNC is hard to achieve with previously suggested sea spray fluxes (Korhonen et al., 2010).
THE TITLE OF YOUR PAPER GOES HERE

This study numerically investigates the interaction between multiple thin vortex rings and an inclined solid surface at Reynolds numbers of 585 and 1170. The flow mechanics can be considered partially representative of a helicopter rotor in ground effect. Although a significant simplification to the helicopter downwash, vortex ring interactional dynamics provide insight into the fundamental flow features that underlie the complex flow field.