Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of serosal cavity resident leukocytes in the orchestration of leukocyte recruitment following the induction of experimental inflammation

This study evaluated the role of resident peritoneal and pleural macrophages (M(|)) in neutrophil (PMN) recruitment in acute peritoneal and pleural inflammation. I also investigated the role of lymphocytes (Lp) in peritoneal inflammation by studying experimental peritonitis in mice deficient in various Lp populations. The conditional M(t> ablation mice used in these studies are transgenic for the human diphtheria toxin receptor (DTR) under the CDllb promoter (CDllb-DTR mice) and exhibit >97% depletion of resident serosal Mc() following intraperitoneal (IP) administration of diphtheria toxin (DT). I determined leukocyte numbers by flow cytometry in peritoneal or pleural lavage exudates at various time points after the initiation of inflammation with various agents following Mc() depletion (peritoneum: Brewer's thioglycollate [BTG], zymosan; pleural cavity: carrageenan and fixed staphylococci). I also induced BTG peritonitis in RAG-1 knockout (KO) mice (mature B and T Lp deficient), NUDE mice (T Lp deficient), pMT mice (B Lp deficient) and their respective controls. Mcj) ablation markedly inhibited peritoneal and pleural PMN recruitment at early time points compared to wild type (WT) controls. Administration of Mc|)-rich resident cells, unlike Mcj)-depleted resident cells, significantly restored PMN infiltration. Analysis of PMN C-X-C chemokines in lavage exudate showed that Mcj)-depleted mice had significantly reduced levels of peritoneal and pleural MIP-2 and KC at the lhr time point compared to control mice with more marked MIP-2 reduction compared to KC (>90% reduction vs 25-40%). Reduced levels of monocyte C-C chemokine and various cytokines were evident in the Mcj)-depleted
Grain yield, quality traits and grain yield stability of local oat cultivars

This study was conducted to define grain yield and quality traits of local oat cultivars and to assess the adaptability to and stability of cultivars in different environments of Central and West Black Sea Region of Turkey. Twenty-five oat genotypes were evaluated in a randomized block design with four replications in six different environments. Genotype, environment and genotype × environment interaction had highly significant effects on grain yield and quality traits. The oat genotypes exhibited significant variations in grain yield (2.15–5.81 t ha–1), test weight (40.8–46.7 kg), thousand–grain weight (21.8–34.2g), groat percentage (70.1–73.6 %), protein (12.0– 13.3%), ash (2.34–2.77%), starch (42.7-49.6 %), β-glucan (2.93-3.56%), ADF (13.6–16.4%), NDF (31.5–34.4 %) and fat (5.69–6.80). The genotypes G5, G7, G12, G15, and G17 were identified as the most stable cultivars for grain yield. These genotypes also had high values for desired quality traits. Therefore, these genotypes can be recommended for tested environments and similar environments. It was concluded that the genotypes with high values for desired quality traits could be used in further oat breeding programs to improve new cultivars with stable grain yield and high quality.
Does Removal of Invasive Garlic Mustard Affect Eastern Red-backed Salamanders?

Dayanandan, P., P.B. Kaufman and C.I. Franklin. 1983. Detection of silica in plants. American Journal of Botany 70:1079–1084. Duncan, C. 2014. Fall herbicide application timing improves crown vetch (Securigera varia) control. TechLine Invasive Plant News August 29. techlinenews.com/articles/2014/fall-herbicideapplication-timing-improves-crown-vetch-control. Hopwood, J.L. 2008. The contribution of roadside grassland restorations to native bee conservation. Biological Conservation 141:2632–2640. Klimešová, J. and F. de Bello. 2009. CLO-PLA: The database of clonal and bud bank traits of central European flora. Journal of Vegetation Science 20:511–516. Losure, D.A. , K.A. Moloney and B.J. Wilsey. 2009. Modes of crown vetch invasion and persistence. American Midland Naturalist 161:232–242. Molano-Flores, B. 2014. An invasive plant species decreases native plant reproductive success. Natural Areas Journal 34:465–469. Symstad, A.J. L. Temmen and E. Anderson. 2002. Mowing does not increase effectiveness of herbicide on crown vetch in tallgrass prairie (Illinois). Ecological Restoration 20:287–288. Tu, M. 2003. Element Stewardship Abstract for Coronilla varia L. The Nature Conservancy Wildland Invasive Species Team. Walck, J.L. , J.M. Baskin and C.C. Baskin. 1999. Effects of competition from introduced plants on establishment, survival, growth, and reproduction of the rare plant Solidago shortii (Asteraceae). Biological Conservation 88:213–219.
Changes in photosynthesis, growth, and sugar content of commercial sugarcane cultivars and Erianthus under flood conditions

Abstract Sugarcane (Saccharum spp.) is an economical crop in the tropical and subtropical countries. However, because of global climate change, flooding has become problematic, particularly during the rainy season, in Thailand. We investigated the effects of floods on three commercial sugarcane cultivars, namely NiF8, U-thong 6 (UT6), and U-thong 9 (UT9), as well as Erianthus spp. Growth was assessed using a pot experiment in a glasshouse with two treatments: (1) control and (2) 60 d of flooding followed by 30 d of normal conditions. In comparison with control, during prolonged flooding, Erianthus showed greatly decreased CO2 assimilation, whereas NiF8, UT6, and UT9 showed slightly declined CO2 assimilation. Growth in plants subjected to 60 d of flooding was less influenced by floods while sucrose content was not affected except in UT6. During flooding, some roots died, resulting in plants compensating adventitious roots to offset the negative effects of root death and to assist them in maintaining their growth, which appeared from the submerged nodes, with different characteristics for each cultivar. However, 30 d after draining, roots remained damaged, while adventitious roots died, resulting in lesser growth as compared with the control, but it did not significantly affect sucrose content and sugar yield. This study suggests that sugarcane plants need to produce the adventitious roots to compensate their roots’ death during flooding and require time to recover their root system after flooding for obtaining the optimum yield and quality at harvest.
Genetic Diversity and Population Structure of Plum Accessions from a Romanian Germplasm Collection Assessed by Simple Sequence Repeat (SSR) Markers

In Romania, Prunus genetic resources are held in collections located mainly in research and development institutes or in fruit growing stations. A possible disadvantage of the utilization of these resources for genetic studies and also for breeding programmes is the lack of reliable data for correct identification and characterization of accessions. In this study, 27 plum accessions from Râmnicu-Vâlcea Fruit Research Station, Romania, were assessed using nine SSR markers generating a total of 134 distinct alleles, with an average of 14.89 alleles per locus. Differentiation between the Romanian plum cultivars and international reference cultivars was low, but significant, for all the nine loci ( Fst = 0.012; P < 0.0001). Plum accessions were grouped in two clades, both including old and newly developed Romanian cultivars and also international reference cultivars, according to an UPGMA dendrogram. Bayesian analysis of genetic structure revealed significant admixture among examined accessions while principal coordinate analysis performed on the molecular data illustrated a substantial dispersion of old and newly developed Romanian plum accessions in the three-dimensional PCoA scatter plot. These results could make them attractive for future breeding programs and long-term conservation strategies based on identified genetic dissimilarities.
KARAKTERISASI SIFAT FISIK DAN KIMIA TEPUNG KACANG MERAH (Phaseolus vulgaris L.) DENGAN BEBERAPA PERLAKUAN PENDAHULUAN

ABSTRAK Tujuan penelitian ini adalah mempelajari pengaruh kombinasi perlakuan terhadap sifat kimia, fisik, dan fungsional pada tepung kacang merah. Penelitian ini menggunakan rancangan acak lengkap dengan taraf faktor tanpa perlakuan pendahuluan dengan kulit (F1), perendaman 24 jam dengan kulit (F2), perebusan 90 menit dengan kulit (F3), tanpa perlakuan pendahuluan tanpa kulit (F4), perendaman 24 jam tanpa kulit (F5), dan perebusan 90 menit tanpa kulit (F6). Hasil penelitian menunjukkan bahwa kombinasi perlakuan dapat mempengaruhi sifat kimia, fisik, dan fungsional pada tepung kacang merah secara signifikan (p<0,05). Dilihat dari sifat kimia, perendaman 24 jam dan perebusan 90 menit baik dengan kulit maupun tanpa kulit meningkatkan kadar air, namun dapat menurunkan kadar abu, protein, lemak, dan asam fitat dibandingkan dengan tepung tanpa perlakuan pendahuluan, sedangkan pengupasan kulit dengan berbagai perlakuan pendahuluan meningkatkan kadar asam fitat, namun menurunkan kadar air dan lemak pada tepung kacang merah. Dilihat dari sifat fisik, tepung kacang merah pada perendaman 24 jam dan perebusan 90 menit baik dengan kulit maupun tanpa kulit meningkatkan densitas kamba, densitas padat, dan kelarutan, namun menurunkan kecerahan, derajat putih, dan waktu basah, sedangkan pengupasan meningkatkan kecerahan, derajat putih, dan waktu basah, namun menurunkan densitas kamba dan padat dengan berbagai perlakuan pendahuluan. Perebusan 90 menit tanpa kulit menurunkan serat pangan tidak larut, serat pangan larut, dan total serat pangan tepung kacang merah. Kata kunci : pengupasan, perebusan, perendaman, sifat fisik, sifat kimia, tepung kacang merah
Living and lost mammals of Rio de Janeiro's largest biological reserve: an updated species list of Tinguá

The Tinguá Biological Reserve (TBR) is the largest protected area of this category in Rio de Janeiro state. Here, for the first time, we present the historical composition of terrestrial mammals’ assemblage of TBR region. An inventory was conducted using transect surveys, nonstandard transects, survey of museum specimens and informal reports. Considering all the data, eighty-five species were recorded, placing TBR as the second one in the number of mammals recorded in “Serra do Mar” ecoregion of Atlantic Forest and in the Rio de Janeiro state. Among the species with historical records are the jaguar (Panthera onca) and the golden-lion-tamarin (Leontopithecus rosalia) while the current presence of the maned wolf (Chrysocyon brachyurus) was recorded for the first time. Priority studies should focus on Chiroptera, Rodentia and Didelphimorphia orders, especially in the most remote areas of the reserve, and long-term surveys of endangered species. Besides hunting, fragmentation of its interior by roads, pipelines and transmission lines and exotic species, TBR is also threatened by the urban growth around it and the pressure to reduce its area and its protection category, demanding greater attention by the high levels of governance of protected areas in Brazil.
Water motion as a transformation mechanism of algal communities structure in Lake Baikal

The diversity of algal communities of phytoplankton and meio-and macrophytes was investigated in Lake Baikal. Fragments of Spirogyra thallomes were recorded in the phytoplankton community of Southern Baikal, which had never been recorded before in its composition. It was also established that the structure of benthic algal communities changed in comparison with that in 2000 due to intense development of filamentous algae, particularly Spirogyra. Its lowest biomass was recorded in the surf zone and wave breaking, whereas the highest biomass was registered in the area of weakened effect of waves on the bottom. The cover percent of the bottom with filamentous algae in different areas of the coastal zone varied from 0 to 100%. Hydraulic characteristics of Spirogyra were the same as those of planktonic diatoms. The circulation currents and wave effect on the bottom favoured transfer and distribution of Spirogyra from the location of its intense development into the coastal area of Lake Baikal.
Regulação pós-transcricional da enzima glutaminase por HuR e sua relação com os altos níveis glutaminolíticos tumorais = Post-transcriptional regulation of glutaminase enzyme by HuR and its relationship with high glutaminolytic levels in tumors

TCA cycle anaplerosis by glutamine, an important energetic and biosynthetic source for rapidly dividing cells, is impaired by glutaminase inhibition. Glutaminase inhibition by CB-839 is currently under clinical trials for treating multiple solid and haematological tumors. HuR (Human antigen R) is a protein encoded by the ELAVL1 gene. HuR contains three RNA-binding domains and binds cis-acting AU-rich elements, affecting mRNA stability and splicing. Previous findings have linked HuR to GLS mRNA stabilization in renal acidosis, and its ortholog, HuD, to GLS splicing in neuronal cells. We then hypothesized that HuR was an important glutaminase regulator in cancer. We first inquired a TCGA pan-cancer cohort and found that patients with higher ELAVL1 expression had increased risk of tumor recidive (Cox HR of 1.82 for breast cancer). Moreover, by using publicly available RNA-Seq, RIP-Seq and PAR-CLIP-Seq data we showed that HuR binds to GLS intron 14 and controls GLS splicing, leading to kidney type glutaminase (KGA) choice over glutaminase C (GAC). Using breast and prostate cancer and HEK293 (with a CRISPR/Cas9 knock in) cell lines we further confirmed that HuR increases KGA by affecting splicing and mRNA stability. Lentiviral ELAVL1 silencing impaired breast cancer cell’s proliferation, migration, invasion and increased glutamine addiction in vitro. Treating silenced ELAVL1 breast cancer cells with CB839 further impaired proliferation and invasion. We proposed HuR as a prognostic factor in breast cancer, with special impact on glutamine metabolism through splicing regulation. In this thesis, we also present seven published articles on which I participated as a co-author, being four as co-first author.
Determinants of Adaptation and their Interactions in Experimental Populations of Saccharomyces cerevisiae

The goal of my M.Sc. thesis research was to investigate the link between divergent adaptation and reproductive isolation in speciation, the process by which one species becomes two over time. Previous studies followed the evolution of 12 replicate experimental populations of the yeast Saccharomyces cerevisiae in either of two non-optimal environments, high-salt or low-glucose, over 500 generations. In this research, I re-sequenced the whole genomes of six diploid strains of these populations, three from high salt and three from low glucose. Among the replicates, there was remarkable degree of parallelism in the underlying determinants of adaptation including multiple mutations in PMA1, encoding the main proton exporter, in highsalt and in several genes in the ras signalling pathway in both environments. A variety of positive and negative epistatic interactions were found among mutations from within and among populations, emphasizing the importance of epistasis in adaptation and potentially in speciation.
Simple Sequence Repeat (SSR) Marker Assay-Based Genetic Diversity among Dolichos Bean (Lablab purpureus L. Sweet) Advanced Breeding Lines Differing for Productivity per se Traits

Dolichos bean is one of the ancient crops widely distributed in Indian subcontinent, Africa, and Southeast Asia (Smartt, 1985), where it has been used as a grain legume and vegetable for more than 3500 years (Fuller, 2003). Despite its wide distribution in the tropics and range of adaptability and diversity, it remains as an important, but underutilized crop in many of these regions (Engle and Altoveros, 2000), as evidenced from limited area planted to this crop and efforts towards its genetic improvement (Ramesh and Byregowda, 2016). However, it’s utility as a vegetable and pulse (Ramesh and Byregowda, Increased and continued use of the diverse genotypes is a prerequisite for developing and diversifying the genetic base of crop cultivars. DNA markers which are crop-stage nonspecific environmental neutral, easily assayable and amenable for automation are being used to assess the diversity of germplasm accessions and/or breeding lines. DNA markers also provide information on the population structure, allelic richness, and parameters that specify diversity among the genotypes to help breeders to choose those most appropriate for use in cultivar development. Hence SSR markers were used to assess diversity at marker loci among 16 phenotypically diverse dolichos bean genotypes. In the present study, 52 of 55 SSR-based markers were polymorphic, resulting in 94.55% polymorphism. Amplification of genomic DNA segments complementary to 55 SSR primers resulted in 133 scorable alleles with an average of 2.5 alleles per SSR loci. SSR markers exhibited differential ability to discriminate 16 genotypes as indicated by the estimates of effective multiplex ratio which ranged from 1.89 to 4.73 and marker index ranged from 0.69 to 3.40. The average gene diversity in the present study is more than that reported in dolichos bean. The estimates of Shanon’s diversity index complemented those of average gene diversity. These results indicate that these SSR markers are highly informative and could be used to assess genetic diversity among the genotypes. The genotypes, HA 10-8, FPB 15 and RIL 162 share different alleles, FPB 8 and RIL 21 share similar alleles. Hence, the genotypes, HA 10-8, FPB 15 and RIL 162 could be used in crossing programme to derive genotypes with combination of desired traits. K e y w o r d s
Assessment of human impact on the genetic diversity of tropical forest taxa

Biodiversity in Southeast Asia has been decreasing as a result of human activities. The findings of the Millennium Ecosystem Assessment, reported in 2005, demonstrated that environmental change, such as deforestation, has resulted in recent major loss of biodiversity at the species level and increased rates of extinction; however, it is unknown whether a similar deficit has occurred at the level of genetic diversity within species. This study aims to understand how the past has shaped the current pattern of genetic diversity, the impact of recent forest loss on genetic diversity and how this information can be used to develop effective conservation strategy.To achieve this aim, microsatellites were developed by sequencing genomic libraries and from comparisons of database sequences. The utility of these markers for population genetics studies has been tested and confirmed for the three main study taxa and across a broad range of other squirrel species. These microsatellites and mitochondrial sequence data (cytochrome b gene) were utilized to determine the genetic diversity and population structure of three squirrel taxa with varying degrees of forest dependency on Thailand’s tropical forests. The most forest dependent taxon is Phayre’s flying squirrel (Hylopetes phayrei). The second taxon is the moderately forest-dependent tree squirrel, the Grey-bellied squirrel (Callosciurus caniceps). The third, and least forest dependent taxon, is the Indochinese ground squirrel, Menetes berdmorei.Our data revealed far more biodiversity in these taxa than previously recognized; there were three genetically distinct lineages in H. phayrei and M. berdmorei and two lineages in C. caniceps. This demonstrates that biodiversity in this region has been underestimated. In the two most forest dependent taxa lineage divergence dated to the Pleistocene indicating that this biodiversity was generated by isolation in allopatric forest refugia during the cool, dry periods of the Pleistocene. In H. phayrei, the most forest-dependent taxon, at least two of the lineages were distinct species occurring sympatrically in Thailand on the border with Myanmar. This taxon supported the biogeographical hypothesis developed in forest dependent mosquitoes of allopatric isolation in northwest and northeastern Pleistocene refugia. Callosciurus caniceps had evidence of a southern refugium in peninsular Thailand or Malaysia. The lower levels of structuring in the least forest dependent taxon M. berdmorei suggest a limited impact of Pleistocene environmental change. All three taxa had eastern lineages which may have been due to Pleistocene forest fragmentation in some of the species. These eastern populations typically had lower levels of microsatellite and mtDNA genetic diversity. This is likely due to the recent loss of genetic diversity as in recent decades these forests have been highly fragmented and reduced in size due to human activity. Our finding that the northern Thai-Myanmar border region is a suture zone in highly dependent forest species and has…
Soil microbial communities changed with a continuously monocropped processing tomato system

ABSTRACT To reveal the regulatory mechanisms underlying the productivity of long-term continuous cropping of processing tomato, a multi-year study was carried out to understand the effects of long-term continuous cropping on the community structures of the root zone microbes. Soil samples collected from continuous cropping of processing tomato after 3, 5 and 7 years were used for this study. Results showed that soil microbial biomass C (SMBC), N (SMBN) and microbial quotient (qMB) significantly decreased with longer cropping. After seven years of continuous cropping, the SMBC and SMBN contents, and qMB respectively significantly decreased by 52.3%, 78.8% and 48.2% (p < 0.01). In contrast, soil microbial biomass P (SMBP) increased during the first three years of continuous cropping, peaking to up to 1.6 times higher than that of the control, which also declined in the succeeding years. Continuous cropping significantly increased the PLFA of fungi, whereas the opposite trend was observed for bacteria, total PLFAs biomass, and the ratios of bacteria and fungi. The PLFA of actinomycetes have no change throughout. This suggests that fungi were better adapted to nutrient poor conditions than bacteria. Microbial diversity indices reached the highest after three years of continuous cropping, with the lowest observed after seven years. This indicated that microbial community diversity and uniformity decreased with increasing number of planting years. Furthermore, our results revealed that the microbial community structure in processing tomato soils changed with extended cropping, resulting to a decline in soil microbial biomass, which may be both a cause and a reflection of the poor soil quality.