Miracle-dz/UniFAR-FTUs huggingface dataset:
Nϵ-Carboxymethyl-Lysine Deteriorates Vascular Calcification in Diabetic Atherosclerosis Induced by Vascular Smooth Muscle Cell-Derived Foam Cells

Nϵ-carboxymethyl-lysine (CML), an advanced glycation end product, is involved in vascular calcification (VC) in diabetic atherosclerosis. This study aimed to investigate the effects of CML on VC in diabetic atherosclerosis induced by vascular smooth muscle cell (VSMC)–derived foam cells. Human studies, animal studies and cell studies were performed. The human study results from 100 patients revealed a poor blood glucose and lipid status and more severe coronary lesions and stenosis in patients with coronary artery disease and diabetes mellitus. Intraperitoneal injection of streptozotocin combined with a high-fat diet was used to build a diabetic atherosclerosis model in ApoE−/− mice. The animal study results indicated that CML accelerated VC progression in diabetic atherosclerosis by accelerating the accumulation of VSMC-derived foam cells in ApoE−/− mice. The cell study results illustrated that CML induced VSMC-derived foam cells apoptosis and aggravated foam cells calcification. Consistent with this finding, calcium content and the expression levels of alkaline phosphatase, bone morphogenetic protein 2 and runt-related transcription factor 2 were significantly elevated in A7r5 cells treated with oxidation-low-density lipoprotein and CML. Thus, we concluded that CML promoted VSMC-derived foam cells calcification to aggravate VC in diabetic atherosclerosis, providing evidence for the contribution of foam cells to diabetic VC.
Genetic architecture of a body color cline in Drosophila americana

Phenotypic variation within a species is often structured geographically in clines. In Drosophila americana, a longitudinal cline for body color exists within North America that appears to be due to local adaptation. The tan and ebony genes have been hypothesized to contribute to this cline, with alleles of both genes that lighten body color found in D. americana. These alleles are similar in sequence and function to the allele fixed in D. americana’s more lightly pigmented sister species, Drosophila novamexicana. To test this hypothesis, we examined the frequency and geographic distribution of D. novamexicana-like alleles of tan and ebony in D. americana. Among alleles from over 100 strains of D. americana isolated from 21 geographic locations, we failed to identify additional alleles of tan or ebony with as much sequence similarity to D. novamexicana as the alleles previously described. However, using genetic analysis of 51 D. americana strains derived from 20 geographic locations, we identified one new allele of ebony and one new allele of tan segregating in D. americana that are functionally equivalent to the D. novamexicana allele. An additional 5 alleles of tan also showed marginal evidence of functional similarity. Given the rarity of these alleles, however, we conclude that they are unlikely to be driving the pigmentation cline. Indeed, phenotypic distributions of the 51 backcross populations analyzed indicate a more complex genetic architecture, with diversity in the number and effects of loci altering pigmentation observed both within and among populations of D. americana. This genetic heterogeneity poses a challenge to association studies and genomic scans for clinal variation, but might be common in natural populations.
Evolutionary and functional lessons from human-specific amino acid substitution matrices

The characterization of human genetic variation in coding regions is fundamental to our understanding of protein function, structure, and evolution. Amino-acid (AA) substitution matrices such as BLOSUM (BLOcks SUbstitution Matrix) and PAM (Point Accepted Mutations) encapsulate the stochastic nature of such proteomic variation and are used in studying protein families and evolutionary processes. However, these matrices were constructed from protein sequences spanning long evolutionary distances and are not designed to reflect polymorphism within species. To accurately represent proteomic variation within the human population, we constructed a set of human-centric substitution matrices derived from genetic variations by analyzing the frequencies of >4.8M single nucleotide variants (SNVs). These human-specific matrices expose short-term evolutionary trends at both codon and AA resolution and therefore present an evolutionary perspective that differs from that implicated in the traditional matrices. Specifically, our matrices consider the directionality of variants, and uncover a set of AA pairs that exhibit a strong tendency to substitute in a specific direction. We further demonstrate that the substitution rates of nucleotides only partially determine AA substitution rates. Finally, we investigate AA substitutions in post-translational modification (PTM) and ion-binding sites. We confirm a strong propensity towards conservation of the identity of the AA that participates in such functions. The empirically-derived human-specific substitution matrices expose purifying selection over a range of residue-based protein properties. The new substitution matrices provide a robust baseline for the analysis of protein variations in health and disease. The underlying methodology is available as an open-access to the biomedical community.
The Mechanism Underlying the Protective Effects of Tannic Acid Against Isoproterenol-Induced Myocardial Fibrosis in Mice

Tannic acid (TA) belongs to a class of complex water-soluble polyphenolic derivatives that show anticarcinogenic, antiinflammatory, antioxidant, and scavenging activities. Here, we investigate the protective effects of TA against isoproterenol (ISO)-induced myocardial fibrosis (MF) in mice. Mice received TA and ISO dosing and were sacrificed 48 h later. The activities of creatine kinase (CK), creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH), and mitochondria enzymes were measured. Cardiac histopathology was done using H&E, Sirius red, and Masson’s Trichrome staining. Immunohistochemical staining was applied to indicate changes in B-cell lymphoma-2 (Bcl-2), Bcl-2-associated X protein (Bax), and basic fibroblast growth factor (bFGF) protein expressions in cardiac tissue. RT-PCR was used to measure the expression of atrial and brain natriuretic peptides (ANP and BNP, respectively), c-fos, and c-jun. Western blotting was used to measure the expression of nuclear factor-κB (NF-κB) p65, phosphorylated NF-κB p65), toll-like receptor 4 (TLR4), p38, phosphorylated p38, Bax, Bcl-2, and caspase-3. Compared to the ISO group, the TA group had reduced levels of TLR4, p38, p-p38, NF-κB (p65), p-NF-κB (p-p65), caspase-3, Bax, and Bcl-2, as well as CK, CK-MB, and LDH. These results indicate that TA protects against ISO-induced MF, possibly through its ability to suppress the TLR4-mediated NF-κB signaling pathway.
Coordinated crosstalk between microtubules and actin by a spectraplakin regulates lumen formation and branching

The establishment of branched structures by single cells involves complex cytoskeletal remodelling events. In Drosophila, epithelial tracheal system terminal cells (TCs) and dendritic arborisation neurons are models for these subcellular branching processes. During tracheal embryonic development, the generation of subcellular branches is characterized by extensive remodelling of the microtubule (MT) network and actin cytoskeleton, followed by vesicular transport and membrane dynamics. We have previously shown that centrosomes are key players in the initiation of subcellular lumen formation where they act as microtubule organizing centres (MTOCs). However, not much is known on the events that lead to the growth of these subcellular luminal branches or what makes them progress through a particular trajectory within the cytoplasm of the TC. Here, we have identified that the spectraplakin Short-stop (Shot) promotes the crosstalk between MTs and actin, which leads to the extension and guidance of the subcellular lumen within the TC cytoplasm. Shot is enriched in cells undergoing the initial steps of subcellular branching as a direct response to FGF signalling. An excess of Shot induces ectopic acentrosomal branching points in the embryonic and larval tracheal TC leading to cells with extra subcellular lumina. These data provide the first evidence for a role for spectraplakins in subcellular lumen formation and branching.
MFCNV: A New Method to Detect Copy Number Variations From Next-Generation Sequencing Data

Copy number variation (CNV) is a very important phenomenon in tumor genomes and plays a significant role in tumor genesis. Accurate detection of CNVs has become a routine and necessary procedure for a deep investigation of tumor cells and diagnosis of tumor patients. Next-generation sequencing (NGS) technique has provided a wealth of data for the detection of CNVs at base-pair resolution. However, such task is usually influenced by a number of factors, including GC-content bias, sequencing errors, and correlations among adjacent positions within CNVs. Although many existing methods have dealt with some of these artifacts by designing their own strategies, there is still a lack of comprehensive consideration of all the factors. In this paper, we propose a new method, MFCNV, for an accurate detection of CNVs from NGS data. Compared with existing methods, the characteristics of the proposed method include the following: (1) it makes a full consideration of the intrinsic correlations among adjacent positions in the genome to be analyzed, (2) it calculates read depth, GC-content bias, base quality, and correlation value for each genome bin and combines them as multiple features for the evaluation of genome bins, and (3) it addresses the joint effect among the factors via training a neural network algorithm for the prediction of CNVs. We test the performance of the MFCNV method by using simulation and real sequencing data and make comparisons with several peer methods. The results demonstrate that our method is superior to other methods in terms of sensitivity, precision, and F1-score and can detect many CNVs that other methods have not discovered. MFCNV is expected to be a complementary tool in the analysis of mutations in tumor genomes and can be extended to be applied to the analysis of single-cell sequencing data.
Upregulation of Human Endogenous Retroviruses in Bronchoalveolar Lavage Fluid of COVID-19 Patients

SARS-CoV-2 emerged in late 2019 in China, causing a global pandemic. Severe COVID-19 is characterized by intensive inflammatory responses, and older age is an important risk factor for unfavorable outcomes. ABSTRACT Severe COVID-19 pneumonia has been associated with the development of intense inflammatory responses during the course of infections with SARS-CoV-2. Given that human endogenous retroviruses (HERVs) are known to be activated during and participate in inflammatory processes, we examined whether HERV dysregulation signatures are present in COVID-19 patients. By comparing transcriptomes of bronchoalveolar lavage fluid (BALF) of COVID-19 patients and healthy controls, and peripheral blood monocytes (PBMCs) from patients and controls, we have shown that HERVs are intensely dysregulated in BALF of COVID-19 patients compared to those in BALF of healthy control patients but not in PBMCs. In particular, upregulation in the expression of specific HERV families was detected in BALF samples of COVID-19 patients, with HERV-FRD being the most highly upregulated family among the families analyzed. In addition, we compared the expression of HERVs in human bronchial epithelial cells (HBECs) without and after senescence induction in an oncogene-induced senescence model in order to quantitatively measure changes in the expression of HERVs in bronchial cells during the process of cellular senescence. This apparent difference of HERV dysregulation between PBMCs and BALF warrants further studies in the involvement of HERVs in inflammatory pathogenetic mechanisms as well as exploration of HERVs as potential biomarkers for disease progression. Furthermore, the increase in the expression of HERVs in senescent HBECs in comparison to that in noninduced HBECs provides a potential link for increased COVID-19 severity and mortality in aged populations. IMPORTANCE SARS-CoV-2 emerged in late 2019 in China, causing a global pandemic. Severe COVID-19 is characterized by intensive inflammatory responses, and older age is an important risk factor for unfavorable outcomes. HERVs are remnants of ancient infections whose expression is upregulated in multiple conditions, including cancer and inflammation, and their expression is increased with increasing age. The significance of this work is that we were able to recognize dysregulated expression of endogenous retroviral elements in BALF samples but not in PBMCs of COVID-19 patients. At the same time, we were able to identify upregulated expression of multiple HERV families in senescence-induced HBECs in comparison to that in noninduced HBECs, a fact that could possibly explain the differences in disease severity among age groups. These results indicate that HERV expression might play a pathophysiological role in local inflammatory pathways in lungs afflicted by SARS-CoV-2 and their expression could be a potential therapeutic target.
Reconsidering Species Extinctions in National Parks: Reply to Berger

We concur with Joel Berger’s (2003) gut feeling that the intuitive answer towhether a species should be allowed to become extinct in a national park is no. Berger also acknowledges there isprobably no unanimous answer for all species in all parks but then presents a case supporting the negative,anticipated reply. Although there is probably no net benefit to conservation from extinction of a nativespecies within a national park, we view this problem from a different perspective, demonstrated by a case fromCentral Europe. The question of whether a species should be allowed to become extinct in a national park can only be addressed for those species that are not confined to one or a small number of parks or species for which substantial proportions of their population do not occur within the park in question. There can be little doubt that it is entirely unacceptable to let an endemic species go extinct in a park that is in fact its sole refuge. The question should focus on native species only because the extermination of introduced species is sometimes essential, an issue beyond the problem we discuss here (Atkinson 2001). Berger states that pronghorn (Antilocapra americana) in Grand Teton National Park comprise only a small fraction of the state’s population of this species, and he argues his case with scientific and educational values of the phenomenon of overland migration. Given that most species are less charismatic than large, open-country mammals and may therefore contribute little to overall park setting and public experience, their local extinction would probably go unnoticed among nonprofessional visitors. If their general populations were unaffected by the local extinction within a park and if the functional integrity of the park’s ecosystem would not suffer from the absence of this species, would it then be acceptable to let this species go extinct? Being aware that in most cases we may not be
Myeloid Cell-Derived Arginase in Cancer Immune Response

Amino acid metabolism is a critical regulator of the immune response, and its modulating becomes a promising approach in various forms of immunotherapy. Insufficient concentrations of essential amino acids restrict T-cells activation and proliferation. However, only arginases, that degrade L-arginine, as well as enzymes that hydrolyze L-tryptophan are substantially increased in cancer. Two arginase isoforms, ARG1 and ARG2, have been found to be present in tumors and their increased activity usually correlates with more advanced disease and worse clinical prognosis. Nearly all types of myeloid cells were reported to produce arginases and the increased numbers of various populations of myeloid-derived suppressor cells and macrophages correlate with inferior clinical outcomes of cancer patients. Here, we describe the role of arginases produced by myeloid cells in regulating various populations of immune cells, discuss molecular mechanisms of immunoregulatory processes involving L-arginine metabolism and outline therapeutic approaches to mitigate the negative effects of arginases on antitumor immune response. Development of potent arginase inhibitors, with improved pharmacokinetic properties, may lead to the elaboration of novel therapeutic strategies based on targeting immunoregulatory pathways controlled by L-arginine degradation.
Pathogenesis in Aspergillus ear rot of maize: light microscopy of fungal spread from wounds.

We describe the histology of fungal development in maize ears wound inoculated with Aspergillus flavus. Plants were inoculated 21 days after style emergence; wounded grains and adjacent spikelets (with their rachis segments) were harvested at intervals up to 28 days later. Tissues were processed for plastic embedding and 1.5-μm thick sections were examined by bright field microscopy. The fungus spread from the wound sometime after 14 days postinoculation, and at 28 days postinoculation it could be found in small amounts throughout all rachis tissues except the pith and lignified fibers (.)
The effect of nutrition in mid pregnancy and ewe liveweight change on birth weight and management for lamb survival in highly fecund ewes

The effect of moderate undernutrition in mid pregnancy on lamb birth weight and survival of single- and multiple-bearing ewes is reported. A total of 1220 ewes of 3 crossbred types with different fecundity, Booroola Merino x Dorset (BD), Trangie Fertility Merino x Dorset (TD) and Border Leicester x Merino (BLM), were examined over 2 years. The treatments were low (L) and high (H) nutrition at pasture for 4 weeks from about day 75 of pregnancy. Ewe liveweight of the L group at the end of the treatments was 5 kg lower in 1984 and 8 kg lower in 1985 (P TD > BD. Maximum survival was achieved at birth weights of 4-5 kg from BD and TD ewes and 5-6 kg from BLM ewes. The L treatment reduced (P<0.01) ewe greasy fleece weight by 0.15 kg but did not affect staple strength. Plasma glucose concentration at the end of treatment was lower (P<0.01) for L ewes, but there was no difference between L and H ewes in late pregnancy. Glucose declined with increasing fetal number. Plasma B-hydroxybutyrate concentration was lower for the H group than for L, and also for BLM than TD and BD ewes (P<0.01).
Genome-wide mapping of histone modifications in two species of Leptosphaeria maculans showing contrasting genomic organization and host specialization

In plant-associated fungi, the role of the epigenome is increasingly recognized as an important regulator of genome structure and of the expression of genes involved in interaction(s) with the host plant. Two closely-related phytopathogenic species, Leptosphaeria maculans ‘brassicae’ (Lmb) and L. maculans ‘lepidii’ (Lml) exhibit a large conservation of genome synteny but contrasting genome structure. Lmb has undergone massive invasion of its genome by transposable elements amounting to one third of its genome and clustered in large TE-rich regions on chromosomal arms, while Lml genome has only a small amount of repeats (3% of the genome). Previous studies showed that the TE-rich regions of Lmb harbour a few species-specific effector genes, expressed during plant infection. The distinct genome structures shown by Lmb and Lml thus provides an excellent model for comparing the organization of pathogenicity/effector genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation during axenic culture, targeting either histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyse the influence of chromatin organisation on gene expression. In both species, we found that facultative heterochromatin landscapes associated with H3K27me3-domains are enriched with genes lacking functional annotation, including numerous candidate effector and species-specific genes. Notably, orthologous genes located in H3K27me3-domains in both species are enriched with genes encoding putative proteinaceous and metabolic effectors. These genes are mostly silenced in axenic growth conditions and are likely to be involved in interaction with the host. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3-domains associated with TE-rich regions that contain numerous species-specific effector-encoding genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection, and the selective advantage to the fungus to host effector genes in H3K9me3- or H3K27me3-domains.
Oxytocin signals via Gi and Gq to drive persistent CA2 pyramidal cell firing and strengthen CA3-CA1 neurotransmission

The oxytocin receptor (OXTR) is concentrated in specific brain regions, exemplified by hippocampal subregion CA2, that support social information processing. Oxytocinergic modulation of CA2 directly affects social behavior, yet how oxytocin regulates activity in CA2 remains incompletely understood. We found that OXTR stimulation acts via closure of M-current potassium channels in all OXT-sensitive CA2 neurons. M-current inhibition was persistent in CA2 pyramidal cells, whose prolonged burst firing required functional coupling of the OXTR to both Gαq and Gαi proteins. Other neuromodulators acted via distinct patterns of G-protein signaling to induce CA2 pyramidal neuron burst firing, underscoring its likely importance. CA2 burst firing impacted hippocampal subregion CA1 where stratum oriens-resident CA1 interneurons were targeted more strongly than CA1 pyramidal cells. Oxytocinergic modulation of interneurons, via CA2 pyramidal cell input and directly, triggered a long-lasting enhancement of CA3-CA1 transmission. Thus, transient activation of oxytocinergic inputs may initiate long-lasting recording of social information.
Flanker Task-Elicited Event-Related Potential Sources Reflect Human Recombinant Erythropoietin Differential Effects on Parkinson's Patients

We used EEG source analysis to identify which cortical areas were involved in the automatic and controlled processes of inhibitory control on a flanker task and compared the potential efficacy of recombinant-human erythropoietin (rHuEPO) on the performance of Parkinson’ s Disease patients. The samples were 18 medicated PD patients (nine of them received rHuEPO in addition to their usual anti-PD medication through random allocation and the other nine patients were on their regular anti-PD medication only) and 9 age and education-matched healthy controls (HCs) who completed the flanker task with simultaneous EEG recordings. N1 and N2 event-related potential (ERP) components were identified and a low-resolution tomography (LORETA) inverse solution was employed to localize the neural generators. Reaction times and errors were increased for the incongruent flankers for PD patients compared to controls. EEG source analysis identified an effect of rHuEPO on the lingual gyri for the early N1 component. N2-related sources in middle cingulate and precuneus were associated with the inhibition of automatic responses evoked by incongruent stimuli differentiated PD and HCs. From our results rHuEPO, seems to mediate an effect on N1 sources in lingual gyri but not on behavioural performance. N2-related sources in middle cingulate and precuneus evoked by incongruent stimuli differentiated PD and HCs.