Miracle-dz/UniFAR-FTUs huggingface dataset:
Signals of range expansions and contractions of vascular plants in the high Alps: observations (1994–2004) at the GLORIA * master site Schrankogel, Tyrol, Austria

High mountain ecosystems are defined by low temperatures and are therefore considered to react sensitively to climate warming. Responding to observed changes in plant species richness on high peaks of the European Alps, an extensive setup of 1 m × 1 m permanent plots was established at the alpine‐nival ecotone (between 2900 and 3450 m) on Mount Schrankogel, a GLORIA master site in the central Tyrolean Alps, Austria, in 1994. Recording was repeated in a representative selection of 362 quadrats in 2004. Ten years after the first recording, we observed an average change in vascular plant species richness from 11.4 to 12.7 species per plot, an increase of 11.8% (or of at least 10.6% at a 95% confidence level). The increase in species richness involved 23 species (about 43% of all taxa found at the ecotone), comprising both alpine and nival species and was pronouncedly higher in plots with subnival/nival vegetation than in plots with alpine grassland vegetation. Only three species showed a decrease in plot occupancy: one was an annual species, one was rare, and one a common nival plant that decreased in one part of the area but increased in the uppermost part. Species cover changed in relation to altitudinal preferences of species, showing significant declines of all subnival to nival plants, whereas alpine pioneer species increased in cover. Recent climate warming in the Alps, which has been twice as high as the global average, is considered to be the primary driver of the observed differential changes in species cover. Our results indicate an ongoing range contraction of subnival to nival species at their rear (i.e. lower) edge and a concurrent expansion of alpine pioneer species at their leading edge. Although this was expected from predictive distribution models and different temperature‐related habitat preferences of alpine and nival species, we provide first evidence on – most likely – warming‐induced species declines in the high European Alps. The projected acceleration of climate warming raises concerns that this phenomenon could become the major threat to biodiversity in high mountains.
Co‐microencapsulation of human umbilical cord‐derived mesenchymal stem and pancreatic islet‐derived insulin producing cells in experimental type 1 diabetes

Post‐partum umbilical cord Wharton Jelly‐derived adult mesenchymal stem cells (hUCMS) hold anti‐inflammatory and immunosuppressive properties. Human pancreatic islet‐derived progenitor cells (hIDC) may de‐differentiate, and subsequently re‐differentiate into insulin producing cells. The two cell types share common molecules that facilitate their synergistic interaction and possibly crosstalk, likely useful for the cell therapy of type 1 diabetes (T1D).
Whole Exome Sequencing of Multi-Regional Biopsies from Metastatic Lesions to Evaluate Actionable Truncal Mutations Using a Single-Pass Percutaneous Technique

We investigate the feasibility of obtaining multiple spatially-separated biopsies from a single lesion to explore intratumor heterogeneity and identify actionable truncal mutations using whole exome sequencing (WES). A single-pass radiologically-guided percutaneous technique was used to obtain four spatially-separated biopsies from a single metastatic lesion. WES was performed to identify putative truncal variants (PTVs), defined as a non-synonymous somatic (NSS) variant present in all four spatially separated biopsies. Actionable truncal mutations—filtered using the FoundationOne panel—were defined as clinically relevant PTVs. Mutational landscapes of each biopsy and their association with patient outcomes were assessed. WES on 50 biopsied samples from 13 patients across six cancer types were analyzed. Actionable truncal mutations were identified in 9/13 patients; 31.1 ± 5.12 more unique NSS variants were detected with every additional multi- region tumor biopsy (MRTB) analyzed. The number of PTVs dropped by 16.1 ± 17.9 with every additional MRTB, with the decrease most pronounced (36.8 ± 19.7) when two MRTB were analyzed compared to one. MRTB most reliably predicted PTV compared to in silico analysis of allele frequencies and cancer cell fraction based on one biopsy sample. Three patients treated with actionable truncal mutation-directed therapy derived clinical benefit. Multi-regional sampling for genomics analysis is feasible and informative to help prioritize precision-therapy strategies.
Plant resistance to the Russian wheat aphid: effects on a nontarget aphid and the role of induction

Abstract Several resistant lines of wheat, Triticum aestivum (L.) (Poaceae), have been developed to control populations of the Russian wheat aphid, Diuraphis noxia (Mordvilko) (Hemiptera: Aphididae). We examined the potential effects of D. noxia resistant lines on another aphid, the bird cherry-oat aphid (Rhopalosiphum padi (L.) (Hemiptera: Aphididae)), which commonly co-occurs with D. noxia. Because one type of resistance (mediated by the Dn1 gene) is purported to be induced rather than constitutive, we also determined the degree to which the suitability of resistant and susceptible plants is modified by previous infestation. Although resistant lines were derived from five different sources, we did not detect any differences in the population growth of R. padi on resistant and near-isogenic susceptible plants. The performance of D. noxia was reduced as expected on resistant plants but was unaffected by whether or not plants had been previously infested. In contrast, the performance of R. padi was reduced on plants that had been previously infested but was unaffected by whether plants were resistant or susceptible to D. noxia. Because neither species' performance was especially low on previously infested, resistant plants, there was no evidence that prior aphid feeding induces a higher level of resistance. Résumé Plusieurs lignées résistantes du blé tendre, Triticum aestivum (L.) (Poaceae), ont été développées pour lutter contre les populations du puceron russe du blé, Diuraphis noxia (Mordvilko) (Hemiptera: Aphididae). Nous avons étudié les effets potentiels des lignées résistantes à D. noxia sur un autre puceron commun, le puceron bicolore des céréales, Rhopalosiphum padi (L.) (Hemiptera: Aphididae). Puisqu'on croit que la résistance médiée par le gène Dn1 est induite plutôt que constitutive, nous avons aussi déterminé dans quelle mesure une infestation antérieure rend les plants résistants et vulnérables plus ou moins appropriés à l'insecte. Bien que les lignées résistantes proviennent de cinq sources distinctes, il n'y a pas de différence dans la croissance des populations de R. padi sur les plants résistants et les plants vulnérables quasi-isogéniques. Le succès de D. noxia est réduit, comme prévu, sur les plants résistants, mais il n'est pas modifié par une infestation antérieure de la plante. En revanche, le succès de R. padi est restreint sur les plants qui ont subi une infestation antérieure, mais il ne varie pas selon que les plants soient ou non résistants à D. noxia. Puisque la performance des deux espèces n'est pas particulièrement réduite sur des plants résistants qui ont subi une infestation antérieure, il n'y a pas d'indication que l'alimentation préalable par les pucerons entraîne une résistance accrue. [Traduit par la Rédaction]
Specific PCR based detection of Phytophthora medicaginis using the intergenic spacer region of the ribosomal DNA.

A technique based on the polymerase chain reaction (PCR) for the specific detection of Phytophthora medicaginis was developed using nucleotide sequence information of the ribosomal DNA (rDNA) regions. The complete IGS 2 region between the 5 S gene of one rDNA repeat and the small subunit of the adjacent repeat was sequenced for P. medicaginis and related species. The entire nucleotide sequence length of the IGS 2 of P. medicaginis was 3566 bp. A pair of oligonucleotide primers (PPED04 and PPED05), which allowed amplification of a specific fragment (364 bp) within the IGS 2 of P. medicaginis using the PCR, was designed. Specific amplification of this fragment from P. medicaginis was highly sensitive, detecting template DNA as low as 4 ng and in a host-pathogen DNA ratio of 1000000:1. Specific PCR amplification using PPED04 and PPED05 was successful in detecting P. medicaginis in lucerne stems infected under glasshouse conditions and field infected lucerne roots. The procedures developed in this work have application to improved identification and detection of a wide range of Phytophthora spp. in plants and soil.
Climate change causes rapid changes in the distribution and site abundance of birds in winter

Detecting coherent signals of climate change is best achieved by conducting expansive, long‐term studies. Here, using counts of waders (Charadrii) collected from ca. 3500 sites over 30 years and covering a major portion of western Europe, we present the largest‐scale study to show that faunal abundance is influenced by climate in winter. We demonstrate that the ‘weighted centroids’ of populations of seven species of wader occurring in internationally important numbers have undergone substantial shifts of up to 115 km, generally in a northeasterly direction. To our knowledge, this shift is greater than that recorded in any other study, but closer to what would be expected as a result of the spatial distribution of ecological zones. We establish that year‐to‐year changes in site abundance have been positively correlated with concurrent changes in temperature, but that this relationship is most marked towards the colder extremities of the birds' range, suggesting that shifts have occurred as a result of range expansion and that responses to climate change are temperature dependent. Many attempts to model the future impacts of climate change on the distribution of organisms, assume uniform responses or shifts throughout a species' range or with temperature, but our results suggest that this may not be a valid approach. We propose that, with warming temperatures, hitherto unsuitable sites in northeastern Europe will host increasingly important wader numbers, but that this may not be matched by declines elsewhere within the study area. The need to establish that such changes are occurring is accentuated by the statutory importance of this taxon in the designation of protected areas.
Divergent biotic and abiotic filtering of root endosphere and rhizosphere soil fungal communities along ecological gradients.

Plant roots assemble two distinct microbial compartments: the rhizosphere (microbes in soil surrounding roots) and the endosphere (microbes within roots). Our knowledge of fungal community assembly in these compartments is limited, especially in wetlands. We tested the hypothesis that biotic factors would have direct effects on rhizosphere and endosphere assembly, while abiotic factors would have direct and indirect effects. Using a field study, we examined the influences of salinity, water level and biotic factors on baldcypress (Taxodium distichum) fungal communities. We found that endosphere fungi were correlated with host density and canopy cover as opposed to rhizosphere, suggesting that hosts can impose selective filters on fungi colonizing into their roots. Meanwhile, local abiotic conditions strongly influenced both rhizosphere and endosphere diversity in opposite patterns: e.g. highest endosphere diversity (hump-shaped) while lowest rhizosphere diversity (U-shaped) at intermediate salinity levels. These results indicate that the assembly and structure for the root endosphere and rhizosphere within a host can be shaped by different processes. Our results also highlight the importance of assessing how environmental changes affect plant and plant-associated fungal communities in wetland ecosystems where saltwater intrusion and sea level rise are major threats to both plant and fungal communities.
A Sustainable Approach for the Green Synthesis of Silver Nanoparticles from Solibacillus isronensis sp. and Their Application in Biofilm Inhibition

The use of bacteria as nanofactories for the green synthesis of nanoparticles is considered a sustainable approach, owing to the stability, biocompatibility, high yields and facile synthesis of nanoparticles. The green synthesis provides the coating or capping of biomolecules on nanoparticles surface, which confer their biological activity. In this study, we report green synthesis of silver nanoparticles (AgNPs) by an environmental isolate; named as AgNPs1, which showed 100% 16S rRNA sequence similarity with Solibacillus isronensis. UV/visible analysis (UV/Vis), transmission electron microscopy (TEM), atomic force microscopy (AFM), dynamic light scattering (DLS), and Fourier-transform infrared spectroscopy (FTIR) were used to characterize the synthesized nanoparticles. The stable nature of nanoparticles was studied by thermogravimetric analysis (TGA) and inductively coupled plasma mass spectrometry (ICP-MS). Further, these nanoparticles were tested for biofilm inhibition against Escherichia coli and Pseudomonas aeruginosa. The AgNPs showed minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of 3.12 µg/mL and 6.25 µg/mL for E. coli, and 1.56 µg/mL and 3.12 µg/mL for P. aeruginosa, respectively.
Innate Immune Response against Hepatitis C Virus: Targets for Vaccine Adjuvants

Despite successful treatments, hepatitis C virus (HCV) infections continue to be a significant world health problem. High treatment costs, the high number of undiagnosed individuals, and the difficulty to access to treatment, particularly in marginalized susceptible populations, make it improbable to achieve the global control of the virus in the absence of an effective preventive vaccine. Current vaccine development is mostly focused on weakly immunogenic subunits, such as surface glycoproteins or non-structural proteins, in the case of HCV. Adjuvants are critical components of vaccine formulations that increase immunogenic performance. As we learn more information about how adjuvants work, it is becoming clear that proper stimulation of innate immunity is crucial to achieving a successful immunization. Several hepatic cell types participate in the early innate immune response and the subsequent inflammation and activation of the adaptive response, principally hepatocytes, and antigen-presenting cells (Kupffer cells, and dendritic cells). Innate pattern recognition receptors on these cells, mainly toll-like receptors, are targets for new promising adjuvants. Moreover, complex adjuvants that stimulate different components of the innate immunity are showing encouraging results and are being incorporated in current vaccines. Recent studies on HCV-vaccine adjuvants have shown that the induction of a strong T- and B-cell immune response might be enhanced by choosing the right adjuvant.
The lateral plate mesoderm

ABSTRACT The lateral plate mesoderm (LPM) forms the progenitor cells that constitute the heart and cardiovascular system, blood, kidneys, smooth muscle lineage and limb skeleton in the developing vertebrate embryo. Despite this central role in development and evolution, the LPM remains challenging to study and to delineate, owing to its lineage complexity and lack of a concise genetic definition. Here, we outline the processes that govern LPM specification, organization, its cell fates and the inferred evolutionary trajectories of LPM-derived tissues. Finally, we discuss the development of seemingly disparate organ systems that share a common LPM origin. Summary: The lateral plate mesoderm is the origin of several major cell types and organ systems in the vertebrate body plan. How this mesoderm territory emerges and partitions into its downstream fates provides clues about vertebrate development and evolution.
Current management strategies in Osgood Schlatter: A cross‐sectional mixed‐method study

Osgood Schlatter disease (OSD) is the most common knee condition in adolescent athletes aged 9‐16. Without evidence to guide clinical practice, it is unclear how OSD is managed. The aim of this study was to investigate how international healthcare professionals (general practitioners, physiotherapists, rheumatologists, sports and exercise medicine doctors, and orthopedic surgeons) diagnose and manage OSD.
Wolbachia (Rickettsiales: Alphaproteobacteria) Infection in the Leafhopper Vector of Sugarcane White Leaf Disease

Abstract Wolbachia is a maternally inherited bacterium ubiquitous in insects that has attracted interest as a prospective insect pest-control agent. Here, we detected and characterized Wolbachia in the leafhoppers Matsumuratettix hiroglyphicus (Matsumura) (Cicadellidae: Hemiptera) and Yamatotettix flavovittatus Matsumura (Cicadellidae: Hemiptera), insect vectors of the phytoplasma that cause white leaf disease in sugarcane. The 16S rRNA and wsp gene markers revealed that Wolbachia was not present in the M. hiroglyphicus but naturally occurs in Y. flavovittatus. Additionally, the infection rates in adult leafhoppers ranged from 0 to 100% depending on geographic location. Moreover, Wolbachia was detected in the eggs and first- to fifth-instar nymphs of Y. flavovittatus. A phylogenic tree of Wolbachia indicated that it resided in the monophyletic supergroup B clade and clustered in the Ori subgroup. Furthermore, fluorescence in situ hybridization revealed that Wolbachia localized to the egg apices, randomly distributed in the egg cytoplasm, and was concentrated in the nymph and adult bacteriomes, as well as occasional detection in the thorax and abdomen. To the best of our knowledge, the present study is the first to demonstrate the prevalence of Wolbachia in the leafhopper Y. flavovittatus. The obtained results would provide useful information for the future development of Wolbachia as a biological control agent for the leafhopper vectors.
Bean Beetles, Callosobruchus maculatus, a Model System for Inquiry-Based Undergraduate Laboratories

Bean beetles, Callosobruchus maculatus (Coleoptera: Bruchidae), are tropical and subtropical agricultural pest insects. This species is among the most tractable and robust laboratory animal systems but it is not widely used outside of research laboratories. C. maculatus is extremely easy to manipulate, maintain and has a very rapid life cycle. Extensive past and present research on C. maculatus (more than 150 journal articles in the past 10 years) provides opportunities for connections between undergraduate laboratory studies and research in ecology, evolutionary biology and animal behavior. We present general information on bean beetles that is necessary for using this species in laboratory courses. This information can be found at www.beanbeetles. org. In addition, we introduce an experiment that evaluates oviposition substrate choice. The experiment can be readily implemented as an inquiry-based study in introductory or advanced undergraduate laboratory courses. In this experiment, we will test the hypothesis that female bean beetles discriminate between seeds of the species from which they emerged (natal seeds) and seeds of another species that also are a suitable oviposition substrate.
Multimeric and monomeric photosystem II supercomplexes represent structural adaptations to low- and high-light conditions

An intriguing molecular architecture called the “semi-crystalline photosystem II (PSII) array” has been observed in the thylakoid membranes in vascular plants. It is an array of PSII–light-harvesting complex II (LHCII) supercomplexes that only appears in low light, but its functional role has not been clarified. Here, we identified PSII–LHCII supercomplexes in their monomeric and multimeric forms in low light–acclimated spinach leaves and prepared them using sucrose-density gradient ultracentrifugation in the presence of amphipol A8-35. When the leaves were acclimated to high light, only the monomeric forms were present, suggesting that the multimeric forms represent a structural adaptation to low light and that disaggregation of the PSII–LHCII supercomplex represents an adaptation to high light. Single-particle EM revealed that the multimeric PSII–LHCII supercomplexes are composed of two (“megacomplex”) or three (“arraycomplex”) units of PSII–LHCII supercomplexes, which likely constitute a fraction of the semi-crystalline PSII array. Further characterization with fluorescence analysis revealed that multimeric forms have a higher light-harvesting capability but a lower thermal dissipation capability than the monomeric form. These findings suggest that the configurational conversion of PSII–LHCII supercomplexes may serve as a structural basis for acclimation of plants to environmental light.
Development of Nerve Cells in Hydrozoan Planulae: I. Differentiation of Ganglionic Cells

The cytomorphosis of ganglionic cells in hy- drozoan planulae of Halocordyle disticha is described at the fine-structural level. Ganglionic cells arise from un- differentiated interstitial cells (I-cells). I-cells originate at 8 hours postfertilization as a central core of cells in the endoderm. Such I-cells possess a centrally located nu cleus with one to several tiny nucleoli, a few segments of rough endoplasmic reticulum, a few mitochondria, elec tron-dense granules, and free ribosomes. Interstitial cells destined to form ganglionic cells migrate as single cells through the mesoglea to the base of the ectoderm where they can divide and subsequently differentiate. Early stages of neural differentiation are characterized by the enlargement of the I-cell nucleoli, the loss of electron- dense granules, and the appearance of a Golgi complex, numerous mitochondria, and microtubules. Next, neu- rites grow out from both sides of the ganglionic cell body and join neuntes from adjacent ganglionic cells to form an extensive neural plexus just apical to the mesoglea in the planula. Neurites are rich in mitochondria and mi crotubules and extend in both a longitudinal and trans verse direction with respect to the planular anterior-pos terior axis. Some neurites extend down from the neural plexus and abut the mesoglea. The last phase of gangli onic cell development occurs when electron-dense drop lets appear within the region of the Golgi and eventually in the neurites. Neurites contain both electron-dense droplets and dense cored vesicles located in clusters at specific intervals along their length. Such droplets and vesicles are often found in close association with the mesoglea in neurites which contact the mesoglea. Two morphological types of ganglionic cells are identifiable at the fine-structural level: a light ganglionic cell and a dark