Low-Copy Nuclear Genes Reveal New Evidence of Incongruence in Relationships Within Malvaceae s. l.

Abstract— The family Malvaceae s. l. is a clade that comprises nine subfamilies. Phylogenetic relationships among them are not completely resolved and are inconsistent among studies, probably due to low phylogenetic informativeness of conventional molecular markers. In the present study, we provide new phylogenetic information for Malvaceae s. l. derived from newly-designed group-specific nuclear markers. By mining transcriptome data from the One Thousand Plants Project (1KP) and publicly available genome information from cotton, cacao, and Arabidopsis, we designed a set of molecular markers of potentially single- or low-copy nuclear genes for Malvaceae s. l. Phylogenetic potential of these new loci was compared to previously applied conventional markers (i.e. plastid trnK-matK region and rbcL gene and the nrDNA ITS region) using the phylogenetic informativeness method. The results show that, when the mined nuclear regions are used in combination, it is possible to resolve relationships at different taxonomic levels within the phylogeny. However, incongruence among nuclear loci is frequent in the group, explaining the prevalence of unresolved phylogenetic relationships.

In vivo pair correlation microscopy reveals dengue virus capsid protein nucleocytoplasmic bidirectional movement in mammalian infected cells

Flaviviruses are major human disease-causing pathogens, including dengue virus (DENV), Zika virus, yellow fever virus and others. DENV infects hundreds of millions of people per year around the world, causing a tremendous social and economic burden. DENV capsid (C) protein plays an essential role during genome encapsidation and viral particle formation. It has been previously shown that DENV C enters the nucleus in infected cells. However, whether DENV C protein exhibits nuclear export remains unclear. By spatially cross-correlating different regions of the cell, we investigated DENV C movement across the nuclear envelope during the infection cycle. We observed that transport takes place in both directions and with similar translocation times (in the ms time scale) suggesting a bidirectional movement of both C protein import and export.Furthermore, from the pair cross-correlation functions in cytoplasmic or nuclear regions we found two populations of C molecules in each compartment with fast and slow mobilities. While in the cytoplasm the correlation times were in the 2–6 and 40–110 ms range for the fast and slow mobility populations respectively, in the cell nucleus they were 1–10 and 25–140 ms range, respectively. The fast mobility of DENV C in cytoplasmic and nuclear regions agreed with the diffusion coefficients from Brownian motion previously reported from correlation analysis. These studies provide the first evidence of DENV C shuttling from and to the nucleus in infected cells, opening new venues for antiviral interventions.

Hard X-Ray Irradiation Potentially Drives Negative AGN Feedback by Altering Molecular Gas Properties

To investigate the role of active galactic nucleus (AGN) X-ray irradiation on the interstellar medium (ISM), we systematically analyzed Chandra and Atacama Large Millimeter/submillimeter Array CO (J = 2–1) data for 26 hard X-ray (>10 keV) selected AGNs at redshifts below 0.05. While Chandra unveils the distribution of X-ray-irradiated gas via Fe-Kα emission, the CO (J = 2–1) observations reveal that of cold molecular gas. At high resolutions ≲1″, we derive Fe-Kα and CO (J = 2–1) maps for the nuclear 2″ region and for the external annular region of 2″–4″, where 2″ is ∼100–600 pc for most of our AGNs. First, focusing on the external regions, we find the Fe-Kα emission for six AGNs above 2σ. Their large equivalent widths (≳1 keV) suggest a fluorescent process as their origin. Moreover, by comparing the 6–7 keV/3–6 keV ratio, as a proxy of Fe-Kα, and CO (J = 2–1) images for three AGNs with the highest significant Fe-Kα detections, we find a possible spatial separation. These suggest the presence of X-ray-irradiated ISM and the change in the ISM properties. Next, examining the nuclear regions, we find that (1) the 20–50 keV luminosity increases with the CO (J = 2–1) luminosity; (2) the ratio of CO (J = 2–1)/HCN (J = 1–0) luminosities increases with 20–50 keV luminosity, suggesting a decrease in the dense gas fraction with X-ray luminosity; and (3) the Fe-Kα-to-X-ray continuum luminosity ratio decreases with the molecular gas mass. This may be explained by a negative AGN feedback scenario: the mass accretion rate increases with gas mass, and simultaneously, the AGN evaporates a portion of the gas, which possibly affects star formation.

Disassembling the Nature of Capsid: Biochemical, Genetic, and Imaging Approaches to Assess HIV-1 Capsid Functions

The human immunodeficiency virus type 1 (HIV-1) capsid and its disassembly, or capsid uncoating, has remained an active area of study over the past several decades. Our understanding of the HIV-1 capsid as solely a protective shell has since shifted with discoveries linking it to other complex replication events. The interplay of the HIV-1 capsid with reverse transcription, nuclear import, and integration has led to an expansion of knowledge of capsid functionality. Coincident with advances in microscopy, cell, and biochemistry assays, several models of capsid disassembly have been proposed, in which it occurs in either the cytoplasmic, nuclear envelope, or nuclear regions of the cell. Here, we discuss how the understanding of the HIV-1 capsid has evolved and the key methods that made these discoveries possible.

Accurate Segmentation of Nuclear Regions with Multi-Organ Histopathology Images Using Artificial Intelligence for Cancer Diagnosis in Personalized Medicine

Accurate nuclear segmentation in histopathology images plays a key role in digital pathology. It is considered a prerequisite for the determination of cell phenotype, nuclear morphometrics, cell classification, and the grading and prognosis of cancer. However, it is a very challenging task because of the different types of nuclei, large intraclass variations, and diverse cell morphologies. Consequently, the manual inspection of such images under high-resolution microscopes is tedious and time-consuming. Alternatively, artificial intelligence (AI)-based automated techniques, which are fast and robust, and require less human effort, can be used. Recently, several AI-based nuclear segmentation techniques have been proposed. They have shown a significant performance improvement for this task, but there is room for further improvement. Thus, we propose an AI-based nuclear segmentation technique in which we adopt a new nuclear segmentation network empowered by residual skip connections to address this issue. Experiments were performed on two publicly available datasets: (1) The Cancer Genome Atlas (TCGA), and (2) Triple-Negative Breast Cancer (TNBC). The results show that our proposed technique achieves an aggregated Jaccard index (AJI) of 0.6794, Dice coefficient of 0.8084, and F1-measure of 0.8547 on TCGA dataset, and an AJI of 0.7332, Dice coefficient of 0.8441, precision of 0.8352, recall of 0.8306, and F1-measure of 0.8329 on the TNBC dataset. These values are higher than those of the state-of-the-art methods.

Single-stranded nucleic acid sensing and coacervation by linker histone H1

The linker histone H1 is the most abundant group of eukaryotic chromatin-binding proteins. The mechanism underlying the diverse physiological functions of H1 remains unclear. Here we used single-molecule fluorescence and force microscopy to observe the behavior of H1 on DNA under different tensions. Unexpectedly, we found that H1 coalesces around nascent ssDNA. Molecular dynamics simulations revealed that multivalent and transient interactions between H1 and ssDNA mediate their phase separation. We further showed that longer and unpaired nucleic acids result in more viscous, gel-like H1 droplets. Finally, we imaged H1 puncta in cells under normal and stressed conditions and observed that RPA and H1 occupy separate nuclear regions. Overall, our results provide a new perspective to understanding the role of H1 in genome organization and maintenance.

Accuracy of ARFI elastography in the differentiation of cataract stages in dogs

ABSTRACT: Objective was to evaluate the accuracy of elastography in the differentiation between normal and cataract lenses One hundred forty-five eyes of 98 dogs were divided into groups according to cataract stage. Forty-twoeyes were submitted to phacoemulsification. Biometric parameters, echogenicity and echotexture patterns of the anterior, posterior and vitreous chambers, lens and retina-choroid-sclera complexes were evaluated by ocular ultrasound in modes A and B. Deformability, and color (blue color = indicated less rigid structures, color red = more rigid structures) of the lenses were evaluated by the elastogram. The shear wave velocity (SWV; m/s) was calculated in three regions of the lens, both in the cortex and in the nucleus. The SWV of nucleus was statistically different between the normal lenses and with cataracts, and between the stages of cataract (P<0.001). Healthy lenses and incipient cataracts had a more rigid nucleus. Mature cataracts presented lowest nuclear rigidity (P<0.001). On cortical region the SWV was significantly higher (P<0.01) in intumescent and incipient cataracts. SWV less than 2.67m/s indicates cataract with a sensitivity of 72% and specificity of 94%. Values lower than 2.23m/s suggest mature cataract, with sensitivity of 71% and specificity of 76%. SWV greater than 2.66 m/s are associated with normal lenses or incipient cataract, presenting sensitivity of 94% and specificity of 84%. Qualitative method allowed differentiation between healthy and affected lenses and the classification of evolutionary stages. There was a correlation between the degree of stiffness of lens in cortical and nuclear regions (p=00165, r=0.37) and between the balanced saline solution quantitative and surgical time (P<0.01, r=0.73). Degree of stiffness of lens did not correlate with parameters of phacoemulsification. Elastographic proved feasible for evaluating the lens of dogs, characterizing the types of cataracts, and demonstrating increased stiffness of the diseased lenses.

Molecular Characterization of Mitochondrial Genome From Trichostrongylus Species (Nematoda: Trichostrongylidae) in Northern Iran

Background: The members of Trichostrongylus spp. are gastrointestinal nematodes of ruminants with worldwide distribution. The nematodes are considered as major health challenges especially in endemic regions of Iran. Several species of the parasite are reported from humans and animals in the country. Frequently, molecular analyses for identification of different species focus on nuclear regions and there is lack of information regarding the mitochondrial genes of Trichostrongylus spp. Therefore, the aim of the present study was to identify Trichostrongylus species by molecular analysis of mitochondrial gene in Guilan province, northern Iran.Methods: The nematodes were collected from the abomasum contents of sheep, goats and cattle. Morphological survey was performed for initial screening. Total DNA was extracted, and the partial region of cytochrome c oxidase subunit I (Cox1) gene was amplified and sequenced. Genetic diversity was calculated and phylogenetic analysis of the nucleotide sequence data was conducted.Results: Three species of Trichostrongylus including T. colubriformis, T. vitrines and T. axei were identified by morphological characterizations. The genetic divergence within the species in the present study was observed for T. axei (0-2.5%), T. colubriformis (0.77%) and T. vitrinus (0%). The mean inter-species difference between the Trichostrongylus species obtained in this study was 14.4- 15.4%.Conclusions: The Cox1 sequences of members of the Trichostrongylus spp. are highly variable and this could be used as a valuable measure for achieving a proper assessment of biodiversity. Sequence data generation from additional species of Trichostrongylus will be needed to reconstruct the phylogenetic relationships of this genus of nematodes.

MUSE view of Arp220: Kpc-scale multi-phase outflow and evidence for positive feedback

Context. Arp220 is the nearest and prototypical ultra-luminous infrared galaxy; it shows evidence of pc-scale molecular outflows in its nuclear regions and strongly perturbed ionised gas kinematics on kpc scales. It is therefore an ideal system for investigating outflow mechanisms and feedback phenomena in detail. Aims. We investigate the feedback effects on the Arp220 interstellar medium (ISM), deriving a detailed picture of the atomic gas in terms of physical and kinematic properties, with a spatial resolution that had never before been obtained (0.56″, i.e. ∼210 pc). Methods. We use optical integral-field spectroscopic observations from VLT/MUSE-AO to obtain spatially resolved stellar and gas kinematics, for both ionised ([N II]λ6583) and neutral (Na IDλλ5891, 96) components; we also derive dust attenuation, electron density, ionisation conditions, and hydrogen column density maps to characterise the ISM properties. Results. Arp220 kinematics reveal the presence of a disturbed kpc-scale disc in the innermost nuclear regions as well as highly perturbed multi-phase (neutral and ionised) gas along the minor axis of the disc, which we interpret as a galactic-scale outflow emerging from the Arp220 eastern nucleus. This outflow involves velocities up to ∼1000 km s−1 at galactocentric distances of ≈5 kpc; it has a mass rate of ∼50 M⊙ yr−1 and kinetic and momentum power of ∼1043 erg s−1 and ∼1035 dyne, respectively. The inferred energetics do not allow us to distinguish the origin of the outflows, namely whether they are active galactic nucleus- or starburst-driven. We also present evidence for enhanced star formation at the edges of – and within – the outflow, with a star-formation rate SFR ∼ 5 M⊙ yr−1 (i.e. ∼2% of the total SFR). Conclusions. Our findings suggest the presence of powerful winds in Arp220: They might be capable of heating or removing large amounts of gas from the host (“negative feedback”) but could also be responsible for triggering star formation (“positive feedback”).