Miracle-dz/UniFAR-FTUs huggingface dataset:
Age-Dependent Search Behavior in the Colorado Checkered Whiptail (Aspidoscelis neotesselatus)

Abstract. We compared movement and space use patterns of foraging adult and juvenile Colorado checkered whiptails (Aspidoscelis neotesselatus) in pinyon pine–juniper woodland. Through focal observations, we characterized (1) movement paths as a series of step lengths and turn angles at 30-s intervals, and (2) habitat use reflected by the proportion of time spent in different vegetation types and in the open. Adults and juveniles differed in both movement and habitat use. Adults spent more time in the open and in association with mountain mahogany (Cercocarpus montanus), while juveniles were more frequently found in association with dead wood, grass, and juniper (Juniperus monosperma). Adults also moved greater distances than juveniles and made use of larger areas. Movement patterns differed between age classes, with adults having longer step lengths. Adults and juveniles also engaged in different step length–turn angle sequences. For both classes, movement characteristics differed with habitat type.
Pig pigmentation: testing Gloger's rule

Comparative studies indicate that several mammalian clades obey Gloger's rule in that they exhibit darker coloration in humid warm climates, although the mechanisms responsible for this association still are poorly understood. We surveyed external appearances of a single species, the feral pig (Sus scrofa), shot at 48 hunting lodges across North America and matched these to potential abiotic drivers, namely: relative humidity, temperature, precipitation, and ultraviolet (UV) radiation, and to biotic factors of habitat shade and predation pressure. We found that darker animals occupy locations of greater precipitation and warmer temperatures, as expected from Gloger's rule. The recent range expansion of S. scrofa implies selection for pelage coloration has occurred very rapidly. Separating pelage coloration into eumelanin- and phaeomelanin-based pigmentation, we found more pronounced eumelanin-based pelage in areas of higher rainfall and temperatures and UV radiation, whereas pelage phaeomelanin is related to cool dry climates with lower UV radiation. This implies that humidity or UV protection but not crypsis are the mechanisms underlying Gloger's rule in this species and the factors driving eumelanin and phaeomelanin expression in mammalian pelage are different, reinforcing new interpretations of this venerable rule.
Examining the Effects of Heterospecific Abundance on Dispersal in Forest Small Mammals

The effects of conspecific densities on dispersal have been well documented. However, while positive and negative density-dependent dispersal based on conspecific densities often are shown to be the result of intraspecific competition or facilitation, respectively, the effects of heterospecific densities on dispersal have been examined far less frequently. This gap in knowledge warrants investigation given the potential for the analogous processes of interspecific competition and heterospecific attraction to influence dispersal patterns and behavior. Here we use a long-term live-trapping study of deer mouse (Peromyscus maniculatus), eastern chipmunk (Tamias striatus), red-backed vole (Myodes gapperi), and jumping mice (Napaeozapus insignis and Zapus hudsonius) to examine the effects of variation in conspecific and heterospecific abundances on dispersal frequency. In terms of conspecific abundance, jumping mice were more likely to disperse from areas with fewer conspecifics, while red-backed voles and chipmunks did not respond to variation in conspecific abundances in their dispersal frequencies. While there were no statistically significant effects of variation in heterospecific abundances on dispersal frequency, some effect sizes for heterospecific abundance effects on dispersal met or exceeded those of conspecific abundances. Conspecific abundances clearly can affect dispersal by some species in this system, but the effects of heterospecific abundances on dispersal frequency are less clear. Based on effect sizes, it appears that there may be potential for heterospecific effects on dispersal by some species in the community, although the strength and causes of these relationships remain unclear.
Parasitic manipulation or by-product of infection: an experimental approach using trematode-infected snails

Abstract Natural selection should favour parasite genotypes that manipulate hosts in ways that enhance parasite fitness. However, it is also possible that the effects of infection are not adaptive. Here we experimentally examined the phenotypic effects of infection in a snail–trematode system. These trematodes (Atriophallophorus winterbourni) produce larval cysts within the snail's shell (Potamopyrgus antipodarum); hence the internal shell volume determines the total number of parasite cysts produced. Infected snails in the field tend to be larger than uninfected snails, suggesting the hypothesis that parasites manipulate host growth so as to increase the space available for trematode reproduction. To test the hypothesis, we exposed juvenile snails to trematode eggs. Snails were then left to grow for about one year in 800-l outdoor mesocosms. We found that uninfected males were smaller than uninfected females (sexual dimorphism). We also found that infection did not affect the shell dimensions of males. However, infected females were smaller than uninfected females. Hence, infection stunts the growth of females, and (contrary to the hypothesis) it results in a smaller internal volume for larval cysts. Finally, infected females resembled males in size and shape, suggesting the possibility that parasitic castration prevents the normal development of females. These results thus indicate that the parasite is not manipulating the growth of infected hosts so as to increase the number of larval cysts, although alternative adaptive explanations are possible.
Isolation and Identification of taxonomically diverse bacterial endophytes from citrus in Punjab Pakistan

Citrus is an economically important fruit crop grown in all provinces of Pakistan, while Punjab accounting for 95 percent of total production due to its favorable climate for citrus production. Commercially grown varieties in Pakistan include sweet oranges, grapefruits, Mandarine, Lime, and lemon. The goal of this research was to see how diverse the cultivable bacterial populations are found in citrus cultivars. Out of 90 isolated cultures, 37 endophytic bacterial species and 15 different genera of bacteria were characterized based on morphological, biochemical, and molecular methods from citrus leaves. All the isolated bacteria were subjected to PCR amplification through 16S rDNA followed by sequencing. RDP base classification revealed that class Bacilli has the largest percentage of isolates, whereas class Alpha, Beta, and Gamma Proteobacteria have the lowest percentage among all genotypes used. According to the findings, the phylum Firmicutes contains a common genus (Brevibacterium, 1%; Enterococcus, 6%; Staphylococcus, 7% and Bacillus, 60%). Alpha (Rhizobium) beta (Burkholderia cepacia; Comamonas terigena) gamma Proteobacteria (Enterobacter hermachei (1%), Klebsiella pneumoniae (1%), Proteus mirabilis (8%), Pseudomonas aeruginosa (5%), Psychrobacter pulmonis and Yersinia molalretti (1%) respectively. These results revealed that cultivars of the plants might contribute to the structure and endophytic bacterial communities associated with citrus. Endophytes extracted from leaf samples of different citrus cultivars in Pakistan are reported for the first time. The idea of employing endophytes bacteria to produce enzymes stimulate plant growth, and its purpose as a biological control agent will be investigated in the future.
GWAS and functional studies implicate a role for altered DNA repair in the evolution of drug resistance in Mycobacterium tuberculosis

The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis (GWAS) using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, for the first time, we identified a strong association between the mutations in the DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis (Msm) and Mtb. Results show that variant mutations abrogated the function of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. Notably, in an in vivo Guinea pig infection model, the MutY variant outcompeted the wild-type strain. Collectively, we show that novel variant mutations in the DNA repair genes abrogate their function and contribute to better survival under antibiotic/host stress conditions.
The AMA1-RON complex drives Plasmodium sporozoite invasion in the mosquito and mammalian hosts

Plasmodium sporozoites that are transmitted by blood-feeding female Anopheles mosquitoes invade hepatocytes for an initial round of intracellular replication, leading to the release of merozoites that invade and multiply within red blood cells. Sporozoites and merozoites share a number of proteins that are expressed by both stages, including the Apical Membrane Antigen 1 (AMA1) and the Rhoptry Neck Proteins (RONs). Although AMA1 and RONs are essential for merozoite invasion of erythrocytes during asexual blood stage replication of the parasite, their function in sporozoites is still unclear. Here we show that AMA1 interacts with RONs in mature sporozoites. By using DiCre-mediated conditional gene deletion in P. berghei, we demonstrate that loss of AMA1, RON2 or RON4 in sporozoites impairs colonization of the mosquito salivary glands and invasion of mammalian hepatocytes, without affecting transcellular parasite migration. Our data establish that AMA1 and RONs facilitate host cell invasion across Plasmodium invasive stages, and suggest that sporozoites use the AMA1-RON complex to safely enter the mosquito salivary glands without causing cell damage, to ensure successful parasite transmission. These results open up the possibility of targeting the AMA1-RON complex for transmission-blocking antimalarial strategies.
hPSC-Derived Enteric Ganglioids Model Human ENS Development and Function

The enteric nervous system (ENS) plays a central role in gut physiology and mediating the crosstalk between the gastrointestinal (GI) tract and other organs. The human ENS has remained elusive, highlighting the need for an in vitro modeling and mapping blueprint. Here we map out the developmental and functional features of the human ENS, by establishing robust and scalable 2D ENS cultures and 3D enteric ganglioids from human pluripotent stem cells (hPSCs). These models recapitulate the remarkable neuronal and glial diversity found in primary tissue and enable comprehensive molecular analyses that uncover functional and developmental relationships within these lineages. As a salient example of the power of this system, we performed in-depth characterization of enteric nitrergic neurons (NO neurons) which are implicated in a wide range of GI motility disorders. We conducted an unbiased screen and identified drug candidates that modulate the activity of NO neurons and demonstrated their potential in promoting motility in mouse colonic tissue ex vivo. We established a high-throughput strategy to define the developmental programs involved in NO neuron specification and discovered that PDGFR inhibition boosts the induction of NO neurons in enteric ganglioids. Transplantation of these ganglioids in the colon of NO neuron-deficient mice results in extensive tissue engraftment, providing a xenograft model for the study of human ENS in vivo and the development of cell-based therapies for neurodegenerative GI disorders. These studies provide a framework for deciphering fundamental features of the human ENS and designing effective strategies to treat enteric neuropathies.
Host kinase CSNK2 is a target for inhibition of pathogenic β-coronaviruses including SARS-CoV-2

Inhibition of the protein kinase CSNK2 with any of 30 specific and selective inhibitors representing different chemotypes, blocked replication of pathogenic human and murine β-coronaviruses. The potency of in-cell CSNK2A target engagement across the set of inhibitors correlated with antiviral activity and genetic knockdown confirmed the essential role of the CSNK2 holoenzyme in β-coronavirus replication. Spike protein uptake was blocked by CSNK2A inhibition, indicating that antiviral activity was due in part to a suppression of viral entry. CSNK2A inhibition may be a viable target for development of new broad spectrum anti-β-coronavirus drugs. GRAPHICAL ABSTRACT
Rotavirus RNA chaperone mediates global transcriptome-wide increase in RNA backbone flexibility

Due to genome segmentation, rotaviruses must co-package a set of eleven distinct genomic RNAs. The packaging is mediated by the RNA chaperone NSP2. While the activities of RNA chaperones are well studied with short RNAs, little is known about their global effect on the entire viral transcriptome. Here we used Selective 2′-hydroxyl Acylation Analyzed by Primer Extension and Mutational Profiling (SHAPE-MaP) to systematically examine the secondary structure of the rotavirus transcriptome alone and in the presence of NSP2. Surprisingly, SHAPE-MaP data reveal that despite the well-characterized helix-unwinding activity of NSP2 in vitro, its incubation with rotavirus transcripts does not induce a significant change in the SHAPE reactivities. However, a quantitative analysis of the per nucleotide mutation rate, from which SHAPE reactivities are derived, reveals a global five-fold rate increase in the presence of molar excess of NSP2. Further analysis of the mutation rate in the context of structural classification reveals a larger effect on stems rather than loop elements. Together, these data provide the first experimentally derived secondary structure model of the rotavirus transcriptome and reveal that NSP2 exerts a larger effect on stems, while acting by globally increasing RNA backbone flexibility in a protein concentration-dependent manner.
Multivalent Interactions Drive the Toxoplasma AC9:AC10:ERK7 Complex To Concentrate ERK7 in the Apical Cap

The phylum Apicomplexa consists of obligate, intracellular parasites, including the causative agents of toxoplasmosis, malaria, and cryptosporidiosis. Hallmarks of these parasites are the IMC and the apical complex, both of which are unique structures that are conserved throughout the phylum and required for parasite survival. ABSTRACT The Toxoplasma inner membrane complex (IMC) is a specialized organelle that is crucial for the parasite to establish an intracellular lifestyle and ultimately cause disease. The IMC is composed of both membrane and cytoskeletal components, further delineated into the apical cap, body, and basal subcompartments. The apical cap cytoskeleton was recently demonstrated to govern the stability of the apical complex, which controls parasite motility, invasion, and egress. While this role was determined by individually assessing the apical cap proteins AC9, AC10, and the mitogen-activated protein kinase ERK7, how the three proteins collaborate to stabilize the apical complex is unknown. In this study, we use a combination of deletion analyses and yeast two-hybrid experiments to establish that these proteins form an essential complex in the apical cap. We show that AC10 is a foundational component of the AC9:AC10:ERK7 complex and demonstrate that the interactions among them are critical to maintaining the apical complex. Importantly, we identify multiple independent regions of pairwise interaction between each of the three proteins, suggesting that the AC9:AC10:ERK7 complex is organized by multivalent interactions. Together, these data support a model in which multiple interacting domains enable the oligomerization of the AC9:AC10:ERK7 complex and its assembly into the cytoskeletal IMC, which serves as a structural scaffold that concentrates ERK7 kinase activity in the apical cap. IMPORTANCE The phylum Apicomplexa consists of obligate, intracellular parasites, including the causative agents of toxoplasmosis, malaria, and cryptosporidiosis. Hallmarks of these parasites are the IMC and the apical complex, both of which are unique structures that are conserved throughout the phylum and required for parasite survival. The apical cap portion of the IMC has previously been shown to stabilize the apical complex. Here, we expand on those studies to determine the precise protein-protein interactions of the apical cap complex that confer this essential function. We describe the multivalent nature of these interactions and show that the resulting protein oligomers likely tether ERK7 in the apical cap. This study represents the first description of the architecture of the apical cap at a molecular level, expanding our understanding of the unique cell biology that drives Toxoplasma infections.
Influence of sequencing depth on bacterial classification and abundance in bacterial communities

Microbial diversity is the most abundant form of life. Next Generation Sequencing technologies provide the capacity to study complex bacterial communities, in which the depth and the bioinformatic tools can influence the results. In this work we explored two different protocols for bacterial classification and abundance evaluation, using 10 bacterial genomes in a simulated sample at different sequencing. Protocol A consisted of metagenome assembly with Megahit and Ray Meta and taxonomic classification with Kraken2 and Centrifuge. In protocol B only taxonomic classification. In both protocols, rarefaction, relative abundance and beta diversity were analyzed. In the protocol A, Megahit had a mean contig length of 1,128 and Ray Meta de 8,893 nucleotides. The number of species correctly classified in all depth assays were 6 out of 10 for protocol A, and 9 out of 10 using protocol B. The rarefaction analysis showed an overestimation of the number of species in almost all assays regardless of the protocol, and the beta diversity analysis results indicated significant differences in all comparisons. Protocol A was more efficient for diversity analysis, while protocol B estimated a more precise relative abundance. Our results do not allow us to suggest an optimal sequencing depth at specie level.
Follicular Helper T-Cell-Based Classification of Endometrial Cancer Promotes Precise Checkpoint Immunotherapy and Provides Prognostic Stratification

Despite the fact that management of EC is moving towards four TCGA-based molecular classifications, a pronounced variation in immune response among these molecular subtypes limits its clinical use. We aimed to investigate the determinant biomarker of ICI response in endometrial cancer (EC). We characterized transcriptome signatures associated with tumor immune microenvironment in EC. Two immune infiltration signatures were identified from the TCGA database (n = 520). The high- and low-infiltration clusters were compared for differences in patient clinical characteristics, genomic features, and immune cell transcription signatures for ICI prediction. A Lasso Cox regression model was applied to construct a prognostic gene signature. Time-dependent receiver operating characteristic curve, Kaplan–Meier curve, nomogram, and decision curve analyses were used to assess the prediction capacity. The efficacy of potential biomarker was validated by the Karolinska endometrial cancer cohort (n = 260). Immune signature profiling suggested that T follicular helper–like cells (Tfh) may be an important and favorable factor for EC; high Tfh infiltration showed potential for clinical use in the anti-PD-1 treatment. A Tfh Infiltration Risk Model (TIRM) established using eight genes was validated, and it outperformed the Immune Infiltration Risk Model. The TIRM had a stable prognostic value in combination with clinical risk factors and could be considered as a valuable tool in a clinical prediction model. We identified CRABP1 as an individual poor prognostic factor in EC. The Tfh-based classification distinguishes immune characteristics and predicts ICI efficacy. A nomogram based on Tfh-related risk score accurately predicted the prognosis of patients with EC, demonstrating superior performance to TCGA-based classification.
Online Gain Adaptation of Whole-Body Control for Legged Robots with Unknown Disturbances

This paper proposes an online gain adaptation approach to enhance the robustness of whole-body control (WBC) framework for legged robots under unknown external force disturbances. Without properly accounting for external forces, the closed-loop control system incorporating WBC may become unstable, and therefore the desired task goals may not be achievable. To study the effects of external disturbances, we analyze the behavior of our current WBC framework via the use of both full-body and centroidal dynamics. In turn, we propose a way to adapt feedback gains for stabilizing the controlled system automatically. Based on model approximations and stability theory, we propose three conditions to ensure that the adjusted gains are suitable for stabilizing a robot under WBC. The proposed approach has four contributions. We make it possible to estimate the unknown disturbances without force/torque sensors. We then compute adaptive gains based on theoretic stability analysis incorporating the unknown forces at the joint actuation level. We demonstrate that the proposed method reduces task tracking errors under the effect of external forces on the robot. In addition, the proposed method is easy-to-use without further modifications of the controllers and task specifications. The resulting gain adaptation process is able to run in real-time. Finally, we verify the effectiveness of our method both in simulations and experiments using the bipedal robot Draco2 and the humanoid robot Valkyrie.