Miracle-dz/UniFAR-FTUs huggingface dataset:
The polyphasic analysis of two native Raphidiopsis isolates supports the unification of the genera Raphidiopsis and Cylindrospermopsis (Nostocales, Cyanobacteria)

Abstract: Raphidiopsis and Cylindrospermopsis are planktic, freshwater bloom-forming cyanobacteria of great concern to human health due to the production of potent cyanotoxins. The presence (in Cylindrospermopsis) or absence (in Raphidiopsis) of heterocytes is the traditional character used to distinguish them. This has led to misidentifications and to questions about the validity of the genus Raphidiopsis. We studied two strains of R. mediterranea isolated from Argentinean shallow lakes using a polyphasic approach that included the morphological description of the natural populations and their ultrastructural, physiological and molecular characterisation. Heterocyte differentiation was not observed in the field or in cultures of R. mediterranea submitted to nitrogen deprivation. These results support the occurrence of stable native populations of R. mediterranea without heterocytes, which would not be a part of the Cylindrospermopsis complex life cycle. Based on 16S rRNA, 16S–23S ITS, and cpcBA-IGS sequences, these two genera are virtually identical. Thus, strains of Raphidiopsis and Cylindrospermopsis make up a monophyletic lineage in all phylogenetic reconstructions. Furthermore, the 16S–23S ITS secondary structure provided further evidence that these two genera cannot be separated. The intermixed position in the trees points to several losses of heterocytes during the evolution of these cyanobacteria. We conclude that these two genera should not be regarded as separate and distinct generic units and propose their unification under the name Raphidiopsis, respecting the principle of priority. Accordingly, we revisited and emended the description of Raphidiopsis.
Mapping Progression and Severity of a Southern Colorado Spruce Beetle Outbreak Using Calibrated Image Composites

An ongoing spruce beetle (Dendroctonus rufipennis Kirby.) epidemic in southern Colorado has resulted in the death of thousands of acres of forests primarily dominated by Engelmann spruce (Picea engelmannii Parry.). To evaluate the ecological and economic impacts of this massive mortality event, researchers and land managers need to efficiently track its progression, spread, and severity across large spatial extents. In this study, mortality severity (0–100% dead) was successfully mapped at the Landsat pixel scale (30 × 30 m) across a large (5000 km2), persistently cloud-covered study area using multi-sensor (Landsat 5 Thematic Mapper (TM), Landsat 7 Enhanced Thematic Mapper Plus (ETM+) and Landsat 8 Operational Land Imager (OLI)) harmonized tasseled cap image composites as spectral predictors of gray stage spruce beetle mortality. Our maps display the distribution and severity of this landscape-scale mortality event in 2011 (R2 = 0.48, root mean squared error (RMSE) = 7.7) and 2015 (R2 = 0.55, RMSE = 11.6). Potential applications of this study include efficient landscape-scale forest health monitoring, targeted forest and timber management, and assessment of ecological impacts of bark beetle outbreaks.
Factors triggering the ecotoxicity of metal-based nanoparticles towards aquatic invertebrates

Nanoparticles are produced and used in huge amounts increasing their probability to end up in surface waters. There, they are subject to environmentally driven modification processes. Consequently, aquatic life may be exposed to different nanoparticle agglomerate sizes, while after sedimentation benthic organisms are more likely to be affected. However, most ecotoxicity studies with nanoparticles exclusively investigated implications of their characteristics (e.g. size) on pelagic organisms, ignoring environmentally modified nanoparticles. Therefore, a systematic assessment of factors triggering the fate and toxicity of nanoparticles under environmentally relevant conditions is needed. The present thesis, therefore, investigates the implications of nanoparticle related factors (i.e., inherent material-properties and nanoparticle characteristics) as well as environmental conditions towards the pelagic living organism Daphnia magna and the benthic species Gammarus fossarum. In detail, inert titanium dioxide (nTiO2) and ion-releasing silver nanoparticles (nAg), both of varying particle characteristics (e.g. initial size), were tested for their toxicity under different environmental conditions (e.g. ultraviolet-light (UV-light)). The results indicate that the toxicity of nTiO2 and nAg is mainly determined by: their adsorption potential onto biota, and their fate in terms of reactive oxygen species or Ag+ ion release. Thus, inherent material-properties, nanoparticle characteristics and environmental conditions promoting or inhibiting these aspects revealed significant implications in the toxicity of nTiO2 and nAg towards daphnids. Furthermore, the presence of ambient UV-light, for example, adversely affected gammarids at 0.20 mg nTiO2/L, while under darkness no effects occurred even at 5.00 mg nTiO2/L. Hence, the currently associated risk of nanoparticles might be underestimated if disregarding their interaction with environmental parameters
Twelve new species of Cyrtodactylus Gray (Squamata: Gekkonidae) from isolated limestone habitats in east-central and southern Myanmar demonstrate high localized diversity and unprecedented microendemism

1Herpetology Laboratory, Department of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, CA 92515, USA 2Department of Biology, Brigham Young University, 150 East Bulldog Boulevard, Provo, UT 84602, USA 3Myanmar Environment Sustainable Conservation, Yangon, Myanmar 4School of Biological Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Penang, Malaysia 5Fauna and Flora International, No(35), 3rd Floor, Shan Gone Condo, Myay Ni Gone Market Street, Sanchaung Township, Yangon, Myanmar
Brucellosis in Mirpur, Azad Kashmir Pakistan: a livestock threat for neighboring zones

Brucellosis is a most common livestock and public health issue in terms of abortions, repeat breeding, reduced milk production, birth of weak calves and treatment cost. It is widespread in 86 countries of the world, particularly in developing countries, and imparts a wide range of socio-economic impacts especially where dairy products and livestock breeding are major sources of income (3, 4). In addition, the significance of this disease cannot be neglected as an occupational risk for farmers, shepherds, butchers, laboratory workers and veterinarians. As brucellosis causes dangerous consequences, like the prevention of trading animals and animal products, and also inhibits public and economic development of breeders in pastoral regions. Therefore the prevalence of this disease should be known for proper control and eradication programs, especially in border areas that can infect other countries by accidental or illegal movement of animals. In addition, purchasing diseased animals from an affected area may be risky. Keeping in view the above mentioned context the present study was designed to determine the presence of brucellosis in the animals (small and large ruminants) and humans of Mirpur, Pakistan. As Mirpur shares its borders with India the information obtained from this study could be beneficial for both countries. Therefore the main objective of this study was to determine the prevalence of brucellosis in household animals of Mirpur, Azad Kashmir, due to its geographic importance.
Functions of the transcription factor Lyl-1 in the development of the macrophage lineage

Microglia are tissue macrophages (MΦ) of the central nervous system that control tissue homeostasis. Different fate mapping models have shown that microglia originates from the yolk sac (YS). Macrophages production in the YS occurs in two independent waves. In the first, primitive MΦ originate from restricted progenitors, while in the second, definitive MΦ are produced by erythro-myeloid progenitors. Because primitive and definitive MΦ progenitors share the same phenotype and differentiation pathway, their specific features and contribution to further developmental steps are still poorly understood. We here show that the expression of thee transcription factor Lyl-1 discriminates primitive and definitive MΦ populations. YS-derived Lyl-1+ primitive MΦ contribute to embryonic microglia. Moreover, Lyl-1 disruption results in an increased production of primitive MΦ progenitors in the early YS. It also leads to the reduction of the microglia pool at two specific development stages. Lyl-1 is specifically expressed in microglia, but not other brain cells and its inactivation leads to behavioral changes typical for social anxiety disorders. Thus, we identify Lyl-1 as a marker for YS primitive MΦ that will give rise to the entire microglia. We show that Lyl-1 controls microglia expansion and differentiation and is involved in the regulation of neurodevelopmental processes.
Effects of sleeve gastrectomy in leptin deficient (ob/ob) mice and diet induced obese mice

Background/ Aims: Vertical sleeve gastrectomy improves weight loss and metabolic complications in obese humans. The aim of the present study was to show the outcome of sleeve gastrectomy in obese and super obese mice. Methods: In an animal study, male wild type (WT) C57BL/6 diet-induced obese (DIO) mice were used to mimic obesity, and ob/ob mice were used for leptin deficiency-induced super obesity. To investigate whether sleeve gastrectomy works in leptin-deficient mice, the two groups were compared in weight course for 7 weeks after sleeve gastrectomy. Results: In WT mice, vertical sleeve gastrectomy induced weight loss over the initial study period followed by weight regain over the presurgery level. In leptindeficient ob/ob mice body weight was as well clearly reduced during the first weeks with an increase thereafter to the presurgery level. Conclusion: Those data demonstrate that ob/ob mice and DIO mice responded differently to sleeve gastrectomy. In leptin deficient super obesity restrictive sleeve gastrectomy promotes an effective weight loss procedure. Sleeve gastrectomy leads to leptin-independent changes with favourable weight course. hyperphagia, hypometabolism and obesity. The impact of leptin-feedback in loss and controlling of weight after sleeve gastrectomy is not known. The present study was conducted to explore mechanisms of weight reduction including the impact of leptin-deficiency in obesity and super obesity following restrictive sleeve gastrectomy. Materials and methods Animals All experiments were approved by the Institutional Animal Care and Use Committee of the University Hospital Tübingen. The institutional guidelines for the care and use of laboratory animals were followed throughout the study. The mice were housed in the small animal facility of the University hospital of Tübingen under a light dark cycle of 12 to 12 hours. In the study design wild type male C65Bl/6 mice (n=19) were used in diet induced obesity (DIO) group. DIO mice were generated by feeding with a high-fat diet (D12451; 60% calories from fat, 20% proteins, 20% carbohydrates, vitamins and minerals. Research Diets, Inc., New Brunswick, NJ) and a fructose sweetened beverage (3%) and given free access to water for 12 weeks. After surgery DIO mice were continously fed with high-fat diet. Correspondence to: Robert Bachmann, University Hospital Tübingen, General, Visceral and Transplantation Surgery, Hoppe-Seylerstrasse 3, 72076 Tübingen, Germany, E-mail: robert.bachmann@med.uni-tuebingen.de
Evaluation the Suitability of Saliva for DNA Profiling Analysis in Comparative with Blood Samples.

Collection, preservation and analysis of body fluids are important aspect of forensic science. Isolated DNA from saliva has become an attractive alternative to the use of blood-derived DNA in performance characteristics. The objectives of this study were to determine the suitability of saliva for DNA profiling analysis and compare blood and saliva as biological source in the performance characteristics. Saliva and buccal swab (as the reference source of genomic DNA) samples were collected from 7 healthy volunteers. The saliva samples were taken with different volumes (100, 200, 300, 400) μl of whole saliva. On the other hand, blood and saliva samples were collected from 25 healthy volunteers in a comparative study. Extraction of DNA was done by Phenol Chloroform method. The results showed difference in the mean DNA concentration which was quantified by using Real-Time PCR from various volumes of saliva samples (100, 200, 300, 400) μl recording (1.23, 2.21, 3.40, 8.24) ng / μl respectively. The mean allele’s percentage of 15 STR loci that appeared in profile of different volumes mentioned above were (73.3, 83.7, 89.5, 99.04)% respectively. The mean DNA concentration and the purity from saliva and blood samples were measured by using nonadrop spectrophotometer recording (10.736, 51.164) ng/ μl (1.64, 1.72) respectively. It is concluded that, saliva samples can be taken at different volumes in the field of criminal research instead of the traditional a way of taking blood samples.
Exploring saiga horn consumption in Singapore

Abstract The Critically Endangered saiga antelope Saiga tatarica faces an uncertain future, with populations dwindling from epidemics in its range countries, and ongoing demand for its horns in the traditional Chinese medicine trade. Singapore is a major hub for the global trade in saiga horn and an important consumer country, with saiga horn products widely available in the domestic market. Despite this, little is known about the consumers that drive domestic demand. Before interventions are carried out, it is important to understand who the consumers are, and their motivations. We conducted an investigation into consumption prevalence and consumer demographics, knowledge and motivations. We surveyed 230 Chinese Singaporeans, through a combination of face-to-face interviews and self-administered questionnaires. Recent consumption incidence (in the previous 12 months) was relatively high, at 13%. Younger respondents (18–35 years) had the highest prevalence of recent consumption (25%), often as a result of influence from an older family member or friend. Bottled saiga horn cooling water was the most popular product among recent users (50%), followed by horn shavings (31%) and tablets (13%). Awareness of conservation issues and regulations was uniformly low. Awareness raising may have an effect in reducing consumer demand in Singapore. However, given the exploratory nature of this study, it is best used to guide and inform future research underlying behavioural change interventions in a relatively understudied but important consumer group, Chinese Singaporeans.
Complete mitochondrial genome sequence of Cicindela anchoralis Chevrolat, 1845 (Coleoptera: Carabidae)

Abstract The tiger beetle, Cicindela anchoralis Chevrolat, 1845 (Coleoptera: Carabidae), has been listed as an Endangered insect in South Korea. We sequenced the complete mitochondrial genome (mitogenome) of this organism (16,388 bp). The genome includes a typical set of genes (13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes) and 1 non-coding region with an arrangement identical to that observed in most insect genomes. Twelve PCGs had the typical ATN start codon, whereas ND1 had the atypical TTG codon. The AT-rich region is 1629-bp long, composed of 80.0% A + T nucleotides, and has no long repeat sequences. Phylogenetic analyses with concatenated sequences of the 13 PCGs and 2 rRNA genes, using the Bayesian inference (BI) method, placed C. anchoralis as a sister to the within-subfamilial species Habrodera capensis, with the highest nodal support presented by both BI and maximum likelihood (ML) methods. Three subfamilies represented by more than one species (Cicindelinae, Harpalinae, and Carabinae) were all determined by both BI and ML analyses to form strong monophyletic groups.
Cross-platform meta-analysis reveals common matrisome variation associated with tumor genotypes and immunophenotypes in human cancers

Background Recent sequencing efforts unveil genomic landscapes of the tumor microenvironment. Yet, little is known about the extent to which matrisome pattern is conserved in progressive tumors across diverse cancer types, and thus its clinical impact remains largely unexplored. Findings Using a newly generated, unified data resource, we conducted cross-platform assessment of a measure of altered extra-cellular matrix (ECM) composition and remodeling associated with tumor progression, termed as the matrisome index (TMI). Parallel analyses with TCGA in over 30,000 patient-derived biopsies revealed that TMI is closely associated with mutational load, tumor histopathology, and predictive of patient outcomes. We found an enrichment of specific tumor-infiltrating immune cell populations, signatures predictive of immunotherapy resistance, and several immune checkpoints in tumors with high TMI, suggesting potential role of ECM interaction with immunophenotyes and tumor immune escape mechanisms. Both epithelial cancer cells and carcinoma-associated fibroblasts are potential cellular contributors of such deregulated matrisome. Conclusions Despite wide spectrum of genetic heterogeneity and dynamic nature, matrisome abnormalities are integral to disease progression. Our resource of a curated compendium of 8,386 genome-wide profiles, molecular and clinical associations, and matrisome-tumor genotype-immunophenotype relationships identify potentially actionable immune targets that may guide personalized immunotherapy.
Genetic divergence studies in clusterbean [Cyamopsis Tetragoloba (L.) Taub.] genotypes for seed yield and gum content under rain-fed conditions

The genetic diversity among 33 cluster bean genotypes was evaluated under rain fed conditions during kharif 2012. The genetic material exhibited wide range of genetic diversity for all the twelve characters investigated. All the genotypes were grouped into seven different clusters. Cluster I was the largest comprising 11 genotypes followed by cluster II consisting of 8 genotypes, cluster V (5), cluster VI (4), cluster IV (2), cluster VII (2), cluster III (1). The clustering pattern indicated that there was lot of diversity among the genotypes and there was no relationship and independent. The intra cluster distance was highest at cluster VI followed by cluster I and II over others. The between the genetic and geographical diversity of the genotypes, but the distribution of the genotypes was random higher magnitude of inter-cluster distance were observed between cluster IV and VI (7.644) followed by cluster IV and cluster III and IV (5.861) and cluster II and V (5.834) indicating wider genetic diversity between the genotypes in V (7.582); cluster II and IV (6.802); cluster IV and VII (6.682); cluster I and IV (6.569); cluster II and VII (6.052); likely to produce more transgressive segregants. It is suggested that genotypes belonging to the clusters I, IV and VII these clusters. The uses of genotypes in hybridization from these clusters having most of the desirable characters are having diversified growth habit may be crossed with genotypes belonging to cluster II as they may be expected to produce good segregants with high yield potential.
Life table parameters and development of Neoseiulus longispinosus (Acari: Phytoseiidae) reared on citrus red mite, Panonychus citri(Acari: Tetranychidae) at different temperatures

Abstract Development time, survival, reproduction, and sex ratio were determined for the predatory mite Neoseiulus longispinosus (Evans) at six constant temperatures (20, 25, 27.5, 30, 32.5 and 35 °C) reared on citrus red spider mite Panonychus citri (McGregor). No predatory mite reached adulthood at 35°C. All female and male immature stages of N. longispinosus developed significantly faster as the temperature increased from 20 to 30°C, but development slowed down as the temperature exceeded 30 °C. The mean total developmental time of females was longest at 20 °C (9.73 days), followed by 25°C (5.67 days), 27.5°C (4.46 days), and 32.5 °C (4.55 days) and was shortest at 30°C (3.69 days). The oviposition rate and lifetime fecundity were highest at 27.5 °C (2.80 eggs/female/day and 43.76 eggs/female, respectively) and lowest at 20 °C (0.78 eggs/female/day and 21.64 eggs/female, respectively). However, temperature had no influence on the sex ratio of offspring with the proportion of females ranging from 0.62 to 0.65. The intrinsic rate of increase (r) of N. longispinosus averaged 0.323, 0.303, 0.267, 0.189 and 0.107 females female-1 day-1 at 30, 27.5, 32.5, 25, and 20°C, respectively. These values suggested that the most optimal temperatures for the population growth of N. longispinosus were between 27.5 and 30°C.
Sex-specific timing of autumn migration in birds: the role of sexual size dimorphism, migration distance and differences in breeding investment

Multiple studies have investigated differential migration of sexes during spring migration, while such differences during autumn migration are poorly studied.We tested several functional hypotheses explaining differences in autumnmigration dates between sex and age classes and whether these patterns vary between short- and long-distance migrants (SDMs andLDMs, respectively). We used data of ringed birds from the Hanko and Lågskär Bird Observatory, Finland, North Europe. Altogether data for c. 200,000 ringed birds including 14 passerine species were used. Protogyny,with femalesmigrating earlier than males, was common among young birds, and this difference was clearer in LDMs than inSDMs.However, in adults protogyny was not found, whereas protandy,malesmigrating earlier than females,was found in two species. Furthermore, species-specific sexual size dimorphism, SSD, was significantly connected with the time differences in migration between the sexes in SDMs, but not in LDMs. These results suggest thatmultiple factors are likely affecting differential timing of autumnmigration in birds. It can be beneficial for males, especially young birds, to spend additional time at the breeding grounds to prospect for future nesting sites. The connection between SSD and autumn migration dates in SDM could be linked with the pattern where larger sized individuals can winter closer to the breeding grounds. In addition, later migration dates of adult females compared to adultmales could suggest that larger reproductive investment by adult females on breeding may delay their autumn migration.
Keragaman Genetik Kultivar Padi Beras Hitam Lokal Berdasarkan Penanda Mikrosatelit

Indonesia has diverse accessions of local black rice, which are important sources of germplasm. However, some of the local black rice cultivars have different names, leading a need to be identified to determine their genetic diversity using molecular marker. This study aimed to identify genetic diversity of eleven cultivars of local black rice, collection of the Assessment Institute for Agricultural Technology, Yogyakarta and compared them with two white rice varieties using four microsatellite markers. Detection of microsatellite alleles polymorphism was carried out by visualization of PCR amplicons by electrophoresis on agarose gel. To estimate their genetic diversity, phylogenetic tree and principal coordinate analysis were performed using binary data of SSR alleles. The results revealed that total markers enabled to differentiate black rice cultivars as reflected by high value of polymorphic information content (PIC) mean (0.695). This value was consistent with the high genetic diversity of black rice (genetic diversity index, h = 0.283) in comparison with white rice cultivars (h = 0.020). The phylogenetic and main coordinate analyses suggested that black rice cultivars genetically differed from white rice. The local black rice cultivars were preferentially grouped based on their genetic those were distributed in three coordinates and did not represent their local geographic origin. Genetic diversity analysis in this study will be useful as an initial basis for proper identification and selection for appropriate parents to assist breeding program of black rice in Indonesia.