Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of EST-PCR markers for DNA fingerprinting and mapping in blueberry (vaccinium, section cyanococcus)

Expressed sequence tags (ESTs) produced from a cDNA library, derived from RNA from floral buds of cold acclimated plants, were used to develop EST-PCR markers for blueberry (Vaccinium spp). Thirty clones, picked at random from the cDNA library, were single-pass sequenced from the 5 and 3 ends. Thirty PCR primer pairs were designed from the ends of the best quality sequences that were generated and tested in amplification reactions with DNA from 19 blueberry genotypes, including two wild selections (the original parents of a mapping population), and 17 cultivars. Fifteen of the 30 primer pairs resulted in amplification of polymorphic fragments that were detectable directly after ethidium bromide staining of agarose gels. Several of the monomorphic amplification products were digested with the restriction enzyme AluI and approximately half resulted in polymorphic-sized fragments (cleaved amplified polymorphic sequences or CAPS markers). The polymorphic EST-PCR and CAPS markers developed in this study distinguished all the genotypes and many were polymorphic between the parent plants of the mapping population, indicating that these markers should have general utility for DNA fingerprinting and mapping in blueberry. Similarity values were calculated based on the molecular marker data, and a dendrogram was constructed based on the similarity matrix. Coefficients of coancestry were calculated for each pair of genotypes from complete pedigree information. A fair correlation between similarity coefficients calculated from marker data and coefficients of coancestry was found.
High Levels of IL-18 and IFN-γ in Chronically Inflamed Tissue in Chronic Granulomatous Disease

Background: Chronic granulomatous disease (CGD) is caused by a malfunctioning nicotinamide adenine dinucleotide phosphate (NADPH) oxidase complex in phagocytes, leading to impaired bacterial and fungal killing and hyperinflammation. Objective: To characterize macrophage subsets and cytokine/chemokine signaling loops involved in CGD tissue hyperinflammation. Methods: Cytokine/chemokine production and surface marker expression were analyzed in inflamed tissue of four CGD patients and compared to cytokine/chemokine released by CGD macrophages upon priming to different macrophage subpopulations. Furthermore, the re-priming capacity of CGD pro-inflammatory M1 to M2a anti-inflammatory macrophages was evaluated. Results: In human CGD inflammatory tissue, IL-18 and IFN-γ were detected in significant quantity. Immunofluorescence analysis identified macrophages as one source of IL-18 in inflamed tissue. In vitro, CGD macrophages could be primed and re-primed into all inflammatory/anti-inflammatory macrophage subpopulations. IL-18 was also released by M1 CGD and control macrophages. Conclusion: CGD pro-inflammatory M1 macrophages remain M1 primed in vivo. As CGD M1 macrophages can be re-primed to anti-inflammatory M2a phenotype in vitro, macrophages are kept in M1 state in vivo by a persistent pro-inflammatory environment. Our results suggest a paracrine signaling loop between M1 macrophage derived IL-18 and non-macrophage derived IFN-γ maintaining macrophage pro-inflammatory activity in CGD tissue.
Stress-Induced Microspore Embryogenesis Requires Endogenous Auxin Synthesis and Polar Transport in Barley

Stress-induced microspore embryogenesis is a model in vitro system of cell reprogramming, totipotency acquisition, and embryo development. After induction, responsive microspores abandon their developmental program to follow an embryogenic pathway, leading to in vitro embryo formation. This process is widely used to produce doubled-haploid lines, essential players to create new materials in modern breeding programs, particularly in cereals, although its efficiency is still low in many crop species, because the regulating mechanisms are still elusive. Stress signaling and endogenous hormones, mainly auxin, have been proposed as determinant factors of microspore embryogenesis induction in some eudicot species; however, much less information is available in monocot plants. In this study, we have analyzed the dynamics and possible role of endogenous auxin during stress-induced microspore embryogenesis in the monocot Hordeum vulgare, barley. The results showed auxin accumulation in early proembryo cells, from embryogenesis initiation and a further increase with embryo development and differentiation, correlating with the induction and expression pattern of the auxin biosynthesis gene HvTAR2-like. Pharmacological treatments with kynurenine, inhibitor of auxin biosynthesis, and α-(p-chlorophenoxy)-isobutyric acid (PCIB), auxin antagonist, impaired embryogenesis initiation and development, indicating that de novo auxin synthesis and its activity were required for the process. Efflux carrier gene HvPIN1-like was also induced with embryogenesis initiation and progression; auxin transport inhibition by N-1-naphthylphthalamic acid significantly reduced embryo development at early and advanced stages. The results indicate activation of auxin biosynthesis with microspore embryogenesis initiation and progression, in parallel with the activation of polar auxin transport, and reveal a central role of auxin in the process in a monocot species. The findings give new insights into the complex regulation of stress-induced microspore embryogenesis, particularly in monocot plants for which information is still scarce, and suggest that manipulation of endogenous auxin content could be a target to improve in vitro embryo production.
KSHV encoded viral processivity factor, ORF59, regulates multiple pathways for viral replication

Kaposi’s Sarcoma-Associated Herpesvirus (KSHV), or human herpesvirus 8 (HHV-8), is a tumorigenic herpesvirus tightly linked with various human malignancies including Kaposi’s Sarcoma, Primary Effusion Lymphomas (PELs), and Multicentric Castleman’s Disease (1). Immunocompetent individuals infected with KSHV are asymptomatic, but the immunocompromised individuals are at risk for developing cancers (2). ORF59, a DNA processivity factor of the viral DNA polymerase, is essential for lytic reactivation and is highly expressed during de novo primary infection. To better understand the role of ORF59, we performed an ORF59-immunoprecipitation from KSHV infected cells and identified ORF59 interacting proteins through protein sequencing and LC/MS spectrometry analysis. From a large number of ORF59 interacting proteins, we selected few candidates for further study, which includes host proteins Nucleolin and MCM4, in addition to viral protein, ORF57. Our characterization of the interaction between KSHV ORF59 and these associating factors yielded exciting new insights on host-virus interactions that we believe to be valuable for understanding KSHV pathogenesis. Nucleolin (NCL), involved in ribosome assembly, pre-mRNA metabolism, cytoplasmic RNA stability, and nucleo-cytoplasmic transport as well as ORF57, an mRNA transcript accumulation (MTA) viral early protein involved in posttranscriptional regulation, splicing of viral RNA transcripts, RNA stability, and transcriptional activation, bound specifically to ORF59. ORF59 also associated with minichromosome maintenance proteins (MCMs), a complex of DNA replication licensing factor required for cellular
Texture Modification Technologies and Their Opportunities for the Production of Dysphagia Foods: A Review.

Dysphagia or swallowing difficulty is a common morbidity experienced by those who have suffered a stroke or those undergone such treatments as head and neck surgeries. Dysphagic patients require special foods that are easier to swallow. Various technologies, including high-pressure processing, high-hydrodynamic pressure processing, pulsed electric field treatment, plasma processing, ultrasound-assisted processing, and irradiation have been applied to modify food texture to make it more suitable for such patients. This review surveys the applications of these technologies for food texture modification of products made of meat, rice, starch, and carbohydrates, as well as fruits and vegetables. The review also attempts to categorize, via the use of such key characteristics as hardness and viscosity, texture-modified foods into various dysphagia diet levels. Current and future trends of dysphagia food production, including the use of three-dimensional food printing to reduce the design and fabrication time, to enhance the sensory characteristics, as well as to create visually attractive foods, are also mentioned.
Shade tolerance within the context of the successional process in tropical rain forests

Shade tolerance (the capacity to survive and grow over long periods under shade) is a key component of plant fitness and the foundation of current theories of forest succession in tropical rain forests. It serves as a paradigm to understand the optimal allocation of limited resources under dynamic light regimes. I analyze how tropical rain forest succession influences the expression of ecophysiological mechanisms leading to shade tolerance, and identify future areas that will increase our understanding of the ecological and evolutionary consequences of this phenomenon. Shade tolerance is a multivariate, continuous functional trait reflecting the growth-mortality trade-off of investing resources under limited light vs. exploiting high light conditions. I propose the life cycle successional trajectory model of Gómez-Pompa & Vázquez-Yanes as an integrative tool to understand tropical rain forest succession. This model shows how species distribute along the successional environmental gradient based on their degree of shade tolerance and represents a more integrative paradigm to understand the interface between different aspects of species diversity (ontogenetic variation and functional diversity) throughout succession. It proposes that different trait combinations determining shade tolerance are expressed at different stages of the life cycle, which affects how and when plants enter the successional trajectory. Models explaining the expression of shade tolerance (resource availability, carbon gain, CSR, resource competition) are based on whole-plant economics and are not mutually exclusive. The analysis of shade tolerance is biased towards tree seedlings in the understory of mature forests. Other life stages (juvenile and adult trees), life forms, and microhabitats throughout the forest profile are almost always excluded from these analyses. More integrative explanations based on the distribution of functional traits among species, ontogenetic stages, and the nature of the environmental gradient are being developed based on long-term data and chronosequence comparisons. In summary, shade-tolerance is a complex phenomenon, is determined by multiple characters that change ontogenetically over space and time and entails considerable plasticity. Current methods do not account for this plasticity. Understanding the nature of shade tolerance and its functional basis is critical to comprehending plant performance and improving the management, restoration and conservation of tropical rain forests given the combined threats of global warming and habitat loss
Primary investigation of the diversity and distribution characteristics of Trichoderma spp. in the specific soil of volcanoic forest park and volcano platform

Trichoderma spp. are used in biological plant protection as biofungicides as well as in bioremediation. Trichodrma spp. are also utilized as bio-fertilizer to improve and amend soil. To obtain more optimized germplasm resources of Trichodrma spp. , the diversity and distribution of Trichoderma species were investigated and explored in the Volcanic Forest Park and volcanic platform in Heilongjiang Province, China. Twenty-eight soil samples near the root, including the rhizosphere of different plants were collected. The Trichoderma strains were screened by dilution plate method. Species were identified through morphological characteristics, analyses of Internal Transcribed Spacer (ITS) sequences and genetic relationships based on phylogenetic tree. As a result, a total of 201 Trichoderma strains were isolated from the two sampling spots and they were identified to be members of 13 known species of Trichoderma, including T. harzianum, T. hamatum, T. atroviride, T. citrinoviride, T. virens, T. koningii, T. koningiopsis, T. viride, T. tomentosum, T. petersenii, H. stellate, T. saturnisporum and T. asperellum. Among all the identified species, T. harzianum was the dominant species, accounting for 43.28% of the total, followed by T. viride, which accounted for 14.93%. 12 species were obtained from the soil of the Volcanic Forest Park, while 8 species were acquired from the volcanic platform, which showed the difference of species diversity of Trichoderma between the two spots. In addition, there were differences in Trichoderma species and stains according to the differences of plants at each sampling spot. In short, our results would illustrate the elementary diversity and distribution characteristics of Trichoderma spp. in the two specific types of soil and provide novel germplasm resources for improved mixed Trichoderma bio-fertilizer.
A unified picture of neuronal avalanches arises from the understanding of sampling effects

To date, it is still impossible to sample the entire mammalian brain with single-neuron precision. This forces one to either use spikes (focusing on few neurons) or to use coarse-sampled activity (averaging over many neurons, e.g. LFP). Naturally, the sampling technique impacts inference about collective properties. Here, we emulate both sampling techniques on a spiking model to quantify how they alter observed correlations and signatures of criticality. We discover a general effect: when the inter-electrode distance is small, electrodes sample overlapping regions in space, which increases the correlation between the signals. For coarse-sampled activity, this can produce power-law distributions even for non-critical systems. In contrast, spikes enable one to distinguish the underlying dynamics. This explains why coarse measures and spikes have produced contradicting results in the past — that are now all consistent with a slightly subcritical regime.
Human mitochondrial DNA is extensively methylated in a non-CpG context

Abstract Mitochondrial dysfunction plays critical roles in cancer development and related therapeutic response; however, exact molecular mechanisms remain unclear. Recently, alongside the discovery of mitochondrial-specific DNA methyltransferases, global and site-specific methylation of the mitochondrial genome has been described. Investigation of any functional consequences however remains unclear and debated due to insufficient evidence of the quantitative degree and frequency of mitochondrial DNA (mtDNA) methylation. This study uses WGBS to provide the first quantitative report of mtDNA methylation at single base pair resolution. The data show that mitochondrial genomes are extensively methylated predominantly at non-CpG sites. Importantly, these methylation patterns display notable differences between normal and cancer cells. Furthermore, knockdown of DNA methyltransferase enzymes resulted in a marked global reduction of mtDNA methylation levels, indicating these enzymes may be associated with the establishment and/or maintenance of mtDNA methylation. DNMT3B knockdown cells displayed a comparatively pronounced global reduction in mtDNA methylation with concomitant increases in gene expression, suggesting a potential functional link between methylation and gene expression. Together these results demonstrate reproducible, non-random methylation patterns of mtDNA and challenge the notion that mtDNA is lowly methylated. This study discusses key differences in methodology that suggest future investigations must allow for techniques that assess both CpG and non-CpG methylation.
De novo assembly of a Tibetan genome and identification of novel structural variants associated with high-altitude adaptation

Structural variants (SVs) may play important roles in human adaption to extreme environments such as high altitude but have been under-investigated. Here, combining long-read sequencing with multiple scaffolding techniques, we assembled a high-quality Tibetan genome (ZF1), with a contig N50 length of 24.57 mega-base pairs (Mb) and a scaffold N50 length of 58.80 Mb. The ZF1 assembly filled 80 remaining N-gaps (0.25 Mb in total length) in the reference human genome (GRCh38). Markedly, we detected 17,900 SVs, among which the ZF1-specific SVs are enriched in GTPase activity that is required for activation of the hypoxic pathway. Further population analysis uncovered a 163-bp intronic deletion in the MKL1 gene showing large divergence between highland Tibetans and lowland Han Chinese. This deletion is significantly associated with lower systolic pulmonary arterial pressure, one of the key adaptive physiological traits in Tibetans. Moreover, with the use of the high quality de novo assembly, we observed a much higher rate of genome-wide archaic hominid (Altai Neanderthal and Denisovan) shared non-reference sequences in ZF1 (1.32%-1.53%) compared to other East Asian genomes (0.70%-0.98%), reflecting a unique genomic composition of Tibetans. One such archaic-hominid shared sequence, a 662-bp intronic insertion in the SCUBE2 gene, is enriched and associated with better lung function (the FEV1/FVC ratio) in Tibetans. Collectively, we generated the first high-resolution Tibetan reference genome, and the identified SVs may serve as valuable resources for future evolutionary and medical studies.
Feeding leucaena to dairy cows in intensive silvopastoral systems in Colombia and Mexico

Keynote paper presented at the International Leucaena Conference, 1‒3 November 2018, Brisbane, Queensland, Australia.The demand for milk and dairy products globally is expected to grow in future decades, leading to an increase in the global dairy cattle population. Therefore it is important to identify production options that both improve efficiency and help reduce negative effects on the environment. Intensive silvopastoral systems have been proposed as a sustainable strategy in the tropics to increase the availability and quality of forage throughout the year for milk production from cattle. This paper reports the effects of silvopastoral systems that include leucaena at the farm level on milk production and on the environment in both Colombia and Mexico. Evaluation of different milk production systems has shown that the leucaena-based systems increased milk production both per cow and per hectare, increased the production of milk solids, improved the fatty acid profile in the milk and resulted in environmental benefits when compared with conventional systems.
Genetic description of Manania handi and Manania gwilliami

Staurozoa is an intriguing lineage of cnidarians bearing both polypoid and medusoid characters in the adult body plan. Miranda et al. (2016) provided a massive descriptive effort of specimen collection, sequencing, and character evolution. We also recently described the neuromusculature of two staurozoan species: Manania handi and Haliclystus “sanjuanensis. ” We found that our M. handi samples genetically matched Manania gwilliami samples used in Miranda et al. (2016). Taking advantage of newly-deposited M. gwilliami sequence data, we confirm the identity of our M. handi samples, and provide additional sequence data for M. handi and H. sanjuanensis for future staurozoan identification efforts.
Blood Gene Markers and Natural Selection: A Study in Four Primitive Tribal Groups of North-Coastal Andhra Pradesh, India

Blood samples of four Primitive Tribal Groups (PTGs) viz., the Porja (155), tlze Klwnd (149) from 2 Mandals of Visakhapatnam District, tile Gadaba (169) from 2 Mandals of Vizianagararm District, and the Savara (163) from 2 Mmzdals of Srikakulam District of Andlzra Pradesh were analyzed for ABO and Rlz (D) blood group systems, Sickle-Cell Haemoglobin. All the PTGs are characterized to show high frequency of A blood group except the Gadaba wllo show it for B and AB blood groups, a deviation from the trend perceived for Andhra Tribal Populations. Thus, this locus tends to reveal the advantage ofheterozygotes as well surviving than homozygotes arising out of ABO incompatibility, or coupling with disease or orthogonal trend in frequency distribution. The frequency of d allele in R/z( D) system in these populations do not vary much for tlte range observed for Indian Population in general and tlte Tribal Populations of Andltra Pradesh, in particular. However, the Sickle-Cell haemoglobin display gre. ;;ter frequency of heterozygotes i.e., Sickle-Cell Trait compared to other neighbouring tribal groups of Andlzra Pradesh. The incidence of Sickle-Cell Trait among the Jour PTGs coincides with the prevalence of malaria at district level and support Allison's Sickle-Cell-Malarial hypothesis in the context of differential natural selection.
Life in linear habitats: the movement ecology of an endangered mammal in a peri‐urban landscape

Animal movement can be significantly altered in human‐dominated landscapes such as urban and peri‐urban areas, where habitat is often fragmented and/or linear. Knowledge regarding how wildlife respond to anthropogenic change is vital for informing conservation efforts in such landscapes, including the design of nature reserves and wildlife corridors. To better understand how threatened species persist and behave within human‐dominated landscapes, we examined the home range and space use of the nationally endangered southern brown bandicoot Isoodon obesulus obesulus in peri‐urban Melbourne, Australia’s second‐largest city. Specifically, we examined whether: (1) bandicoots were confined to linear strips of remnant vegetation or also made use of the broader highly modified landscape matrix; (2) the configuration of the linear vegetated strips affected home range shape; and (3) home range area differed between bandicoots living in linear strips and those in larger remnant habitat patches. We found that: (1) 71% of adult males and 33% of adult females used the matrix, but non‐dispersing juveniles were entirely confined to the linear strips; males also travelled greater distances into the matrix (away from the vegetated strips) than females; (2) bandicoots had longer home ranges in narrower strips and males had longer home ranges than females; and (3) home range area for both sexes was smaller in linear strips than has been recorded in other studies in larger remnant habitats. Our study highlights the importance of retaining narrow, fragmented and modified vegetation to accommodate threatened biodiversity within human‐dominated landscapes, but suggests the surrounding matrix may also offer important resources for adaptable species, such as bandicoots. Supporting off‐reserve conservation of biodiversity in novel ecosystems is increasingly pertinent in our rapidly urbanizing world.
Estudo do Comportamento Reprodutivo do Gato-palheiro, Leopardus colocola (Molina, 1782) (Carnivora: Felidae) em Ambiente Cativo

Muitas espécies são difíceis de serem estudadas em ambiente natural devido aos hábitos reservados que impedem estudos ecológicos mais aprofundados, como por exemplo, investigações sobre a ecologia e comportamento reprodutivo. Este estudo objetivou avaliar os comportamentos reprodutivos do gato-palheiro (Leopardus colocola) mantido em zoológico, de forma a contribuir com informações sobre a espécie. Como resultados foram registrados e avaliados 598 comportamentos divididos entre individuais, sociais e reprodutivos. O ambiente cativo propiciou a oportunidade de gerar informações comportamentais sobre a espécie com foco no manejo e nos programas de reprodução ex situ.