Miracle-dz/UniFAR-FTUs huggingface dataset:
Sociodemographic, Clinical and Functional Profile of Nonagenarians from Two Areas of Sardinia Characterized by Distinct Longevity Levels.

Introduction: Among the world's longest-lived communities the so-called Longevity Blue Zone (LBZ) of Sardinia, Italy, has attracted a lot of interest. In the present study, health profile and functional characteristics of LBZ oldest-old were compared with an age-matched sample from Northern Sardinia (NSS) with a lower longevity level. Methods: Cognitive status, symptomatic depression, disability, and nutritional status were assessed by standardized instruments. In addition, the proportion of escapers (illness-free medical history), delayers (illness only after age 80), and survivors (at least one disease before age 80) was calculated. Results: Three hundred individuals, 150 from the LBZ (age range 89-101, 89 women), and 150 from NSS (age range 89-101, 101 women) were enrolled. The proportion of married individuals in the LBZ cohort was significantly greater compared with the NSS (55% vs. 32%, p = 0.0001). The educational level among nonagenarians in the LBZ was almost half compared with NSS (p < 0.0001). Unskilled workers, shepherds, and peasants prevailed in the LBZ (79% vs. 21%, p < 0.0001). Institutionalized subjects were 1% in the LBZ and 14% in the NSS (p < 0.0001). Disability, comorbidity, and daily physical activity were more represented in LBZ. There was a significantly higher percentage of delayers (37% vs. 18%, p < 0.0002), and a reduction in the number of survivors (30% vs. 44%, p = 0.012) in the LBZ compared with the NSS group. The proportion of escapers was similar in both groups (33% vs. 38%, n.s.). Conclusion: These findings suggest that in the LBZ there are factors enabling frail individuals to live longer despite a greater burden of comorbidity.
At the crossroads of botanical collections and molecular genetics laboratory: testing methods to obtain amplifiable DNA from moss herbarium material

Background. Museum collections, including herbarium specimens, are considered an invaluable source of DNA. They constitute a source of a precious commodity, particularly when it is difficult to obtain living material of rare species, or extant populations occurred only in hard to access geographical territories. It is apparent that herbaria should be directly linked with molecular genetics laboratories making them a quick, open-source for molecular projects. However, herbarium DNA is inherently characterised by high degradation and chemical modifications such as the presence of various secondary compounds. A wide range of DNA molecular techniques dedicated to the preserved plant material has been published so far. However, contrasting with a general interest in the application of molecular analyses in moss biology, no comprehensive assessment of DNA isolation and amplification methods from moss herbarium material, is available. Methods. To assess the feasibility of using DNA from moss herbarium specimens, we have tested and compared the silica column-based method and three variants of CTAB-based DNA extraction protocol. We used herbarium collections of twenty-five moss species collected between 1979 and 2013 and specifically focused on austral polar regions to assess the potential of herbarium as a source of biological material from geographical regions of difficult and restricted access. Results. Here, we present an optimized CTAB-based approach which effectively suppresses inhibitors in the herbarium DNA as was measured by amplification success. In this report, DNA purity and the length of the target genetic region are the fundamental agents which drive the successful PCR reaction. Conversely, the specimen age seems to be less relevant. Moreover, the size distribution of the DNA fragments extracted using Qiagen protocol is shown to be comparable to our original CTAB-based approach. Our modified CTAB-based method provides a high-purity genomic DNA allowing efficient downstream amplification. It is not outcompeted by the column-based method and appears as a method of choice in molecular studies of moss herbarium material.
Distribution model and habitat characteristics of Morimus asper funereus Mulsant, 1863 (Coleoptera: Cerambycidae) in Bulgaria 

Morimus asper funereus is a protected longhorn beetle species of community interest and conservation importance. It is included in Annex II of the Habitats Directive (as M. funereus) and protected under the Bulgarian Biodiversity Act. Although this saproxylic beetle is widespread in old-growth forests or well-structured woodlands in Central and Southeast Europe, its populations are currently threatened by forest practices, such as the removal of wood (branches and logs) (Hardersen et al. 2017). The species is with limited dispersal ability (due to lack of wings) and is very likely to possess very isolated and localized populations. In addition, M. asper funereus is of considerable interest from a taxonomic point of view with unclear taxonomic status for as much as Morimus asper is a morphologically highly variable species. At present, at least three species/subspecies of the genus Morimus are known from the territory of Bulgaria - Morimus asper, M. orientalis and M. vercundus bulgaricus (Danilevsky et al. 2016). Although, it is considered M. asper to be met almost everywhere in Bulgaria, its distribution is still not sufficiently known. We started a systematic and more intensive study on the species distribution in 2012 with the mapping of NATURA 2000 sites. Until the present study 54 localities from the literature had been known, after 562 new records have been added. The available information is organised in a database incorporated into the platform “SmartBirds Pro” - https://smartbirds.org (Popgeorgiev et al. 2015), part of which gives the possibility for registration of protected beetle species. In addition, the platform provides free access to all data (type, location, coordinates, date, observer). Here we present all available data for the species records, and its potential distribution and habitat preference for the territory of Bulgaria via deductive model, using the possibilities of GIS and MAXENT (Fourcade et al. 2014).
Comparative genomics unravels mechanisms of genetic adaptation for the catabolism of the phenylurea herbicide linuron in Variovorax

Biodegradation of the phenylurea herbicide linuron appears a specialization within a specific clade of the Variovorax genus. The linuron catabolic ability is likely acquired by horizontal gene transfer but the mechanisms involved are not known. The full genome sequences of six linuron degrading Variovorax strains isolated from geographically distant locations were analyzed to acquire insight in the mechanisms of genetic adaptation towards linuron metabolism in Variovorax. Whole genome sequence analysis confirmed the phylogenetic position of the linuron degraders in a separate clade within Variovorax and indicated their unlikely origin from a common ancestral linuron degrader. The linuron degraders differentiated from non-degraders by the presence of multiple plasmids of 20 to 839 kb, including plasmids of unknown plasmid groups. The linuron catabolic gene clusters showed (i) high conservation and synteny and (ii) strain-dependent distribution among the different plasmids. All were bordered by IS1071 elements forming composite transposon structures appointing IS1071 as key for catabolic gene recruitment. Most of the strain carried at least one broad host range plasmid that might have been a second instrument for catabolic gene acquisition. We conclude that clade 1Variovorax strains, despite their different geographical origin, made use of a limited genetic repertoire to acquire linuron biodegradation. Importance The genus Variovorax and especially a clade of strains that phylogenetically separates from the majority of Variovorax species, appears to be a specialist in the biodegradation of the phenyl urea herbicide linuron. Horizontal gene transfer (HGT) likely played an essential role in the genetic adaptation of those strain to acquire the linuron catabolic genotype. However, we do not know the genetic repertoire involved in this adaptation both regarding catabolic gene functions as well as gene functions that promote HGT neither do we know how this varies between the different strains. These questions are addressed in this paper by analyzing the full genome sequences of six linuron degrading Variovorax strains. This knowledge is important for understanding the mechanisms that steer world-wide genetic adaptation in a particular species and this for a particular phenotypic trait as linuron biodegradation.
Inhibition of CD83 Alleviates Systemic Inflammation in Herpes Simplex Virus Type 1-Induced Behçet's Disease Model Mouse

Behçet's disease (BD) is an autoinflammatory disease that can lead to life- and sight-threating complications. Dendritic cells (DCs) are the most potent antigen-presenting cells that can regulate multiple inflammatory pathways. The objective of this study was to investigate the association of the DC stimulatory molecule CD83 with BD. Frequencies of costimulatory molecules expressing DCs in peripheral blood leukocytes (PBL) were measured by flow cytometry (FACS). The severity of symptoms in HSV-1-induced BD symptomatic mice was also assessed. Frequencies of CD83-positive cells were significantly increased in mice exhibiting BD symptoms, compared to those in asymptomatic mice. Abatacept, a CD80/86 blocker, significantly decreased the frequencies of CD83-positive cells in a time- and dose-dependent manner. BD symptomatic mice treated with Abatacept showed gradual reduction in the severity score of symptoms. Intraperitoneal injection of CD83 siRNA significantly reduced the frequencies of CD83-positive cells in PBL and peritoneal macrophages. After CD83 siRNA injection, BD symptoms of mice were improved and disease severity was decreased. Discontinuation of CD83 siRNA deteriorated symptoms while readministration of CD83 siRNA again improved BD symptoms of mice. These results clearly indicate the involvement of CD83-expressing cells in the inflammatory symptoms of BD. Therefore, CD83 might be useful as a therapeutic target for BD.
Experience-dependent reorganization drives the development of a binocularly unified representation of orientation in ferret visual cortex

Across sensory areas, neural microcircuits consolidate diverse streams of sensory information into unified, representations of the external world, but the developmental process underlying alignment of sensory representations remains poorly understood. Using two-photon and widefield epifluorescence calcium imaging in developing ferret visual cortex, we find an early developmental period in which monocular stimulation reveals two divergent representations of orientation at the network and cellular-scales. During the period of monocular network misalignment, binocular stimulation drives a third orientation representation, distinct from the constituent monocular representations. Alignment towards a single, binocularly unified representation requires binocular visual experience shortly after eye-opening. Chronic imaging demonstrates that the monocular and binocular orientation representations functionally reorganize towards a single representation resembling the early binocular representation through concerted shifts in preferred orientation across the cellular-scale and network-scale representations. Thus, we propose that an experience-dependent learning process drives the emergence of a unified binocular representation of orientation.
Muscle Synergies in Response to Biofeedback-Driven Gait Adaptations in Children With Cerebral Palsy

Background Children with cerebral palsy (CP) often show impaired selective motor control (SMC) that induces limitations in motor function. Children with CP can improve aspects of pathological gait in an immediate response to visual biofeedback. It is not known, however, how these gait adaptations are achieved at the neural level, nor do we know the extent of SMC plasticity in CP. Aim Investigate the underlying SMC and changes that may occur when gait is adapted with biofeedback. Methods Twenty-three ambulatory children with CP and related (hereditary) forms of spastic paresis (Aged: 10.4 ± 3.1, 6–16 years, M: 16/F: 9) were challenged with real-time biofeedback to improve step length, knee extension, and ankle power while walking on an instrumented treadmill in a virtual reality environment. The electromyograms of eight superficial muscles of the leg were analyzed and synergies were further decomposed using non-negative matrix factorization (NNMF) using 1 to 5 synergies, to quantify SMC. Total variance accounted for (tVAF) was used as a measure of synergy complexity. An imposed four synergy solution was investigated further to compare similarity in weightings and timing patterns of matched paired synergies between baseline and biofeedback trials. Results Despite changes in walking pattern, changes in synergies were limited. The number of synergies required to explain at least 90% of muscle activation increased significantly, however, the change in measures of tVAF1 from baseline (0.75 ± 0.08) were less than ±2% between trials. In addition, within-subject similarity of synergies to baseline walking was high (>0.8) across all biofeedback trials. Conclusion These results suggest that while gait may be adapted in an immediate response, SMC as quantified by synergy analysis is perhaps more rigidly impaired in CP. Subtle changes in synergies were identified; however, it is questionable if these are clinically meaningful at the level of an individual. Adaptations may be limited in the short term, and further investigation is essential to establish if long term training using biofeedback leads to adapted SMC.
Essential oils from Bolivia. xiv. Lamiaceae: Clinopodium axillare

The chemical composition of the essential oil obtained from two subspecies of Clinopodium axillare growing wild in the High Valley Region of Bolivia, Province of Cochabamba, was determined by a combination of GC and GC/MS measurements. It is dominated by oxygenated monoterpenes. Piperitenone oxide (20-30 %), piperitone epoxide (15-19 %), piperitenone (13 %), pulegone (3-5 %) and piperitone (4-5 %) as well as limonene (8-12 %) and -pinene (1-5 %) are the major constituents. These results, in conjunction with a recent description of the genus Clinopodium, provide a better understanding of the classification of this plant.
Akkermansia muciniphila-Derived Extracellular Vesicles as a Mucosal Delivery Vector for Amelioration of Obesity in Mice

Recent evidence suggests that probiotics can restore the mucosal barrier integrity, ameliorate inflammation, and promote homeostasis required for metabolism in obesity by affecting the gut microbiota composition. In this study, we investigated the effect of Akkermansia muciniphila and its extracellular vesicles (EVs) on obesity-related genes in microarray datasets and evaluated the cell line and C57BL/6 mice by conducting RT-PCR and ELISA assays. A. muciniphila-derived EVs caused a more significant loss in body and fat weight of high-fat diet (HFD)-fed mice, compared with the bacterium itself. Moreover, treatment with A. muciniphila and EVs had significant effects on lipid metabolism and expression of inflammatory markers in adipose tissues. Both treatments improved the intestinal barrier integrity, inflammation, energy balance, and blood parameters (i.e., lipid profile and glucose level). Our findings showed that A. muciniphila-derived EVs contain various biomolecules, which can have a positive impact on obesity by affecting the involved genes. Also, our results showed that A. muciniphila and its EVs had a significant relationship with intestinal homeostasis, which highlights their positive role in obesity treatment. In conclusion, A. muciniphila-derived EVs can be used as new therapeutic strategies to ameliorate HFD-induced obesity by affecting various mechanisms.
Complete plastome sequence of Rumex japonicus (Polygonaceae) in Dok-do Island, Korea

Abstract We reported the complete chloroplast genome sequence of Rumex japonicus in Dok-do Island, Korea. The genome size was 159,223 bp in total length with one large single-copy (LSC; 84,962 bp), one small single-copy (SSC; 12,999 bp), and 2 inverted repeat (IR) regions (IRa and IRb, each with 30,631 bp). The overall GC content was 37.5% and the genome contained 131 genes, including 83 protein-coding, 38 transfer RNA and 8 ribosomal RNA genes. Phylogenetic analysis supported monophyly of subgenus Rumex and determined the phylogenetic position of R. japonicus as sister to the clade containing R. crispus and R. nepalensis.
Examining the Functions of Master Regulators in Maintaining Pluripotency and Inducing Reprogramming

Author(s): Lo, Hung-Hao | Advisor(s): Smale, Stephen T | Abstract: Pluripotency factors Oct4, Sox2, and Nanog orchestrate an elaborate hierarchy of gene regulation governing embryonic stem cell (ESC) identity. The capability of differentiating into cell from any of the three germ layers offers a potential solution and path toward the discovery of novel therapies for devastating diseases. The differentiation of ESCs requires three fundamentally distinct transitions in the transcriptional state: 1) the activation of silent genes in ESCs that are transcribed in differentiated states, 2) the silencing of ESC-transcribed genes that are entirely inactive in the differentiated cells, 3) the modulation of transcription for genes that are expressed in both populations. Deciphering the mechanisms regulating the transitions of these transcriptional states will illuminate how the pluripotent state is established and maintained by the regulation of pluripotency factors. Because Oct4 and Sox2 are the core regulators of the transcriptional regulatory network for pluripotency, we focused our studies on mechanisms regulated by Oct4 and Sox2 in ESCs. Oct4 and Sox2 bind to thousands of enhancer composite sites at pluripotency genes and differentiation-promoting genes. These Oct4/Sox2 target genes exhibit distinct transitions of transcriptional states for the establishment of pluripotency. As distinct mechanisms are likely to regulate different transcriptional states, a critical step toward a mechanistic understanding of pluripotency is to delineate the genes with well-defined transcription characteristic. Because most studies have relied on low stringency criteria to define differential expression to infer regulatory mechanisms, they did not rigorously evaluate the selective functions of Oct4/Sox2 composite binding critical for establishing pluripotency. To scrutinize how Oct4 and Sox2 account for possible differences in the regulatory mechanisms necessary for distinct transcriptional states, we refined the gene classification and interrogated the role of Oct4/Sox2 binding at enhancer composite motifs at distinct gene classes. By combining RNA-seq, ChIP-seq, and ATAC-seq with functional validation employed by CRISPR/Cas9 mutagenesis, we discovered that Oct4/Sox2 function differently across gene groups with various transcriptional states. In addition to a role in transcriptional activation at ESC-specific and Dynamic genes, my data suggest that Oct4/Sox2 motifs at silent genes may mediate the transcriptional repression in ESCs. In Chapter 3, we also employed a gene-centric approach to quantitatively compare transcription factor co-binding, histone modifications, chromatin accessibility, enhancer properties, and the genomic context of transcriptional regulation by Oct4 and Sox2 in ESCs. Together, we extended our understanding of the critical role played by Oct4 and Sox2 in the establishment of pluripotency.
Enhancement of drought tolerance on guinea grass by dry alginate macrobeads as inoculant of Bacillus strains

Drought is responsible for almost 70% of total crop damage in tropical and subtropical countries. In the Colombian Caribbean, drought has caused low availability of Guinea grass (Megathyrsus maximus) in forage amount and quality, generating increase in production costs in livestock systems. In this study, we aimed at designing and evaluating dry macro-polymeric inoculants of Bacillus strains and used them successfully to mitigate drought effect on Guinea grass (M. maximus). We chose Bacillus sp XT13 and Bacillus megaterium XT14 strains, previously selected for their capacity to mitigate drought stress on Guinea grass. For the inoculant formulation process, a concentration of 3.2% alginate was used for both microorganisms, selecting the polymer-bacterium ratio of 70:30 for XT13 and 80:20 for XT14. The results of the experiments in greenhouse showed that drought had a negative effect on Guinea grass growth, but the PGPB application with or without macro-polymeric dry matrix improved plant growth significantly. We also observed that co-inoculation of the strains generated a greater beneficial effect than individual inoculation. Interestingly, co-inoculation of XT13 and XT14 under the dry macro-polymeric formulation increased biomass production of the aerial part (7.32%), root biomass, (25.3%), nutritional quality parameters, such as digestibility (3.32%), protein (20.3%); proline accumulation increased (21.06%) and both neutral digestible fiber (2.43%) and APX antioxidant activity (24.2%) decreased with respect to co-inoculation of both bacteria without formulation. These findings have shown that dry macrobeads immobilization has a significantly positive influence on the capacity of XT13 and XT14 bacterial strains to induce drought stress tolerance in Guinea grass.
Characterization of Saccharomyces cerevisiae Strains from Palm Wine for Baking Leaven Production in Republic of Congo

This study was carried out to select the autochthon yeast strains from the palm wine. The work aims to wildly isolate, characterize and identify Saccharomyces cerevisiae in order to locally and safely produce a bio-leaven and to assess their ability to ferment wheat flour dough used for the bread making and other products. Palm wine samples have been bought in the village around Brazzaville. Samples have been collected in sterile glass bottles then stored under refrigeration condition at 4°C until they were processed. Yeasts were enumerated and isolated on Dichloran Rose Bengal Chloramphenicol agar medium at 37°C. Molecular identification was carried out by a PCR-based method using species-specific primer pairs to Saccharomyces genus without sequencing stage. The results showed that palm wine contains about 3.3106 CFUmL-1. Fifty-one isolates were obtained with a percentage of 13% corresponding to Saccharomyces cerevisiae. This identity was confirmed by the molecular characterization. Five yeast strains showed high ability to ferment wheat flour dough analogous of the control. The better growth of isolates was between 28 and 37°C. However, the near neutral pH gives the higher growth. High concentration of NaCl and glucose in medium has a strong negative impact on the growth of isolates.