Miracle-dz/UniFAR-FTUs huggingface dataset:
Mass Spectrometry for the Sensitive Analysis of Intracellular Nucleotides and Analogues

Nowadays, mass spectrometry is very important and widely applied tool in nucleo‐ tide analysis. As a result of technological advances in sample preparation, separation and mass spectrometry detection, the developed methods allow sensitive and selective measurement of polar compounds occurring in low levels in various biological matri‐ ces. This enables more potential uses in clinical field. Direct methods require no special sample pre‐treatment before analysis in contrast to indirect methods, where fraction‐ ation, dephosphorylation and purification are needed. The use of ion‐pairing agent, ion exchange chromatography with pH gradient, porous graphitic carbon columns and HILIC in liquid chromatography represents the most common methods of nucleotide analysis. High separation efficiency is also achieved with the use of CE with MS detec‐ tion. Analysis of nucleotides was also described by the means of MALDI‐TOF, but poor reproducibility and lack of applications make a limitation for this approach. The chap‐ ter summarizes different techniques and approaches for determination of endogenous nucleotides and its analogues in various clinical applications.
The evolution of caste-specific morphology and colony structure in ants

An organism’s morphology is constrained by evolutionary history and the need of the organism to meet a variety of, and potentially competing, functions. The ant genus Pheidole is presently the most species-rich of the 324 described ant genera. Workers of Pheidole are almost always dimorphic, comprising a small minor subcaste and a major or soldier subcaste with a distinctively large head. This separation of workers into two distinct subcastes makes Pheidole an ideal genus to address questions on the evolution of morphology in relation to ecological specialization. Major workers can perform a variety of tasks, but they are usually specialized for defense and the retrieval and processing of food. Pheidole species vary in their diet but many species gather seeds and the majors are known to mill the seeds using the large jaws powered by mandible closer muscles that fill the head cavity. I examined the relationship between seedharvesting and head size, hypothesizing that seed harvesters have majors with larger heads compared to non-seed-harvesting species to accommodate more powerful mandibular muscles. By taking a phylogenetically controlled comparative approach, I found that majors of seedassociated Pheidole do not have larger heads (width and length) than do majors of non-seedharvesting species, but there is a positive relationship between seed-harvesting and minor head length. Additionally, there is a significant relationship of head width and length to seedharvesting when examining the difference in size of minors relative to majors within species. Seed-harvesting Pheidole species have smaller minors and larger majors than their non-seedharvesting congeners. This finding suggests that head size of major and minor subcastes can evolve for diet specialization, but they do so relative to the morphology of other worker castes.
The biophysicist’s guide to the bacterial flagellar motor

Graphical Abstract Abstract The bacterial flagellar motor (BFM) is a rotary electric nanomachine that drives swimming in a wide variety of bacterial species. There have been many milestones, both theoretical and experimental, that have furthered our understanding of this tiny motor since the first swimming flagellated bacteria was observed. In this article, we review some of these key events, and illustrate how theory and experiment intertwine and inform each other towards a deeper understanding of the BFM’s mechanism. Experimental results have inspired theoreticians to build and update models, while model predictions have served to guide experimental design. This cooperative and mutually beneficial communication is a prime example of the interdisciplinary and open nature of modern scientific research.
Anti-allergic and anti-atopic dermatitis effects of Gardenia Fructus extract

ABSTRACT Atopic dermatitis (AD) is a common allergic, inflammatory skin disease. Here, we focused on the anti-allergic and anti-inflammatory effects of Gardenia jasminoides Ellis fructus extracts (GFE) in DNCB treated NC/Nga mice. In an in vivo study, GFE treatment significantly decreased immunoglobulin E (IgE) levels and cytokines expression in spleen and serum of treatment groups mice, compared with the negative controls (administered 0.2% DNCB only). Mice treated with GFE had fewer inflammatory cell infiltrates in the dermis and hypodermis compared to the negative controls. In addition, we also studied β-Hexosaminidase release assay and possible anti-inflammatory mechanism of GFE in RBL-2H3 cells. GFE suppressed the expression of COX-2 and TNF-α, the translocation of NF-κβ, and the phosphorylation of Syk, p38, JNK, and Erk1/2 in stimulated RBL-2H3 cells. These results strongly suggest that GFE inhibits the allergic response by reducing mast cell activation and may have therapeutic potential as an anti-atopic dermatitis agent. GRAPHICAL ABSTRACT
Complete mitochondrial genome of Simao pine caterpillar moth, Dendrolimus kikuchii (Lepidoptera: Lasiocampidae) and the related phylogenetic analysis

Abstract Dendrolimus kikuchii, the Simao pine caterpillar moth is an economically important forest pest causing great damage to coniferous trees in south China. The whole mitogenome for the moth was sequenced using next-generation sequencing technology. The moth has a total length of 15,422 bp in mitogenome size. The nucleotide composition is biased toward adenine and thymine, accounting for 79.2%: A = 40.7%, T = 38.5%, G = 8.1%, and C = 12.7%. The phylogeny showed that D. kikuchii was closely grouped with D. punctatus, D. tabulaeformis, Euthrix laeta, and Trabala vishnou guttata to form the monophyletic clad for the Lasiocampidae family of Bombycoidea superfamily with strong nodal support.
Free-moving artificial eggs containing temperature loggers reveal remarkable within-clutch variance in incubation temperature

Incubation is a crucial aspect of avian parental care and measuring incubation temperature in the wild can improve our understanding of life history tradeoffs and inform conservation efforts. However, there are challenges associated with measuring the temperature of eggs in natural nests. Most studies to date have measured incubation temperature by using a single, stationary logger in each nest. However, real eggs are rotated and moved throughout the nest by the parent during the incubation period, and thus, a stationary logger may not accurately represent the temperature experienced by individual eggs within the entire clutch. We recorded incubation temperature in nests by using multiple, mobile artificial egg temperature loggers. We installed six mobile loggers and one stationary logger in wood duck Aix sponsa nests to compare the two logger types in the field. We found that at a given ambient temperature, mobile loggers recorded lower average and more variable temperatures than stationary loggers. Further, temperatures recorded by stationary loggers showed no relationship with clutch size, while mobile loggers captured temperatures that were lower and more variable as clutch size increased. Also, the multiple mobile loggers revealed that eggs within a nest experienced a substantial range of temperatures throughout the incubation period. We discuss potential limitations of this method, but believe that it is a promising way to collect biologically‐relevant incubation temperature data and provides an opportunity to advance our understanding of incubation temperature as a parental effect.
Distinguishing discrete polymorphism from continuous variation in throat colour of tree lizards, Urosaurus ornatus

Within population colour variation in animals is ubiquitous and can range from discrete polymorphism to continuous variation. Distinguishing discrete polymorphism from continuous variation can be challenging, and this hinders our ability to test hypotheses about colour variation. We tested whether throat colour variation in the ornate tree lizard [ Urosaurus ornatus (U. ornatus) ; Baird & Girard, 1852) is discrete or continuous using photographs of 617 individuals from seven study sites in the Chiricahua Mountains of Arizona, USA. Using principal component analyses on ten colour variables derived from photographs, we found throat colour to be highly repeatable for both males and females. Cluster analyses suggested that there are different groups of individuals based on their throat colours in males and in females, but distinguishing between the groups was difficult due to significant overlap in colour. Therefore, it appears that there is a significant amount of continuous variation in both male and female tree lizard throat colours. We suggest quantifying trait variation before assuming a colour trait is discrete. By using numerical descriptors of colour, more information is retained than by using discrete groups. Quantifying individual variation in colour is important for linking colour with other traits such as reproductive strategy, immune function, and size and for testing hypotheses about the evolution and maintenance of colour polymorphism.
Influence of organic sources of nutrients on vanilla (Vanilla planifolia) as an intercrop in coconut garden

Performance of vanilla, as influenced by organic source of nutrition when grown as intercrop in coconut garden, was studied in sandy loam soil at ICAR-CPCRI, Kasaragod, Kerala for seven years. Field experiments were carried out with different sources of organic manures, recommended NPK fertilizer and no fertilizer treatments. Application of cow dung slurry (6 tonnes ha -1 ) resulted in vigorous growth of vine (vine length of 5.5 m) and higher number of beans per vine (208) and a significantly higher mean fresh yield of bean (1.87 kg vine -1 ). Application of vermicompost (5 kg plant -1 ) + biofertilizers ( Bacillus and Azospirillum ) and vermiwash were on par and recorded mean fresh yield of 1.47 kg vine -1 and 1.30 kg vine -1 , respectively. Control treatment without fertilizer application recorded significantly lower fresh bean yield (0.55 kg vine -1 ) due to lower number of beans per vine (72 nos.). In the rhizosphere of vanilla, no significant difference for either bacterial or actinomycetes population was noticed among the treatments. The fungal population differed significantly among the treatments and the highest population level was found with application of biogas slurry (62.1x10 3 cfu g -1 soil), which was on par with application of cow dung slurry (59x10 3 cfu g -1 soil). Among the function specific microbial communities, the highest population of P-solubilisers (98x10 3 cfu g -1 soil) was recorded in the biogas slurry treatment, and it was the lowest in control and vermiwash application treatments. The average coconut yield realized during experimental period(2004-05 to 2009-10) was 136 nuts per palm, recording 53 per cent increase in yield compared to pre-experimental yield (89 nuts per palm).
The advertisement call of Physalaemus ephippifer (Anura: Leiuperidae) from Brazilian Amazonia

Physalaemus is recognized as an important system for the study of mechanisms and evolution of animal communication, especially because of studies involving the P. pustulosus species group. Physalaemus ephippifer is considered, together with P. fischeri (enesefae) and an undescribed species, to be the most similar species to the P. pustulosus group in external morphology, osteology, and characteristics of the call. Because of this, P. ephippifer has been included as an outgroup in studies to interpret patterns of signal-receiver evolution in the genus. Whereas details of the advertisement call structure of P. fischeri have been described (Tárano 2001), information (e.g., detailed graphic representation and range of variation) on P. ephippifer calls remains unavailable. We recorded calls of 18 P. ephippifer in the riverine Maracá Island, Roraima State, Brazil (3°15’–3°35’N; 61°22’– 61°54’W). Individuals from this locality were previously identified as P. ephippifer by Nascimento et al. (2005). We used a Marantz PMD-660 digital recorder and a Sennheiser K6/ME66 directional microphone, and analyzed three calls per male with the software Raven 1.2 (Blackman window, DFT 4080). Call traits were based on Ryan and Rand (1999), with five additional traits (number of pulses: pulses added after the whine component of the call; call rate: mean number of calls per minute; intercall interval: silence interval between two consecutive calls; initial frequency: first harmonic frequency at the call beginning; and peak frequency: frequency of higher intensity of the first harmonic) (Fig. 1). Mean air temperature was 24.95 C ± 0.59 (23.7–25.7) and mean male SUL was 29.5 mm ± 0.88 (27.8–30.8). Voucher specimens (26502–26512) were deposited at INPA-H, Manaus, Brazil.
Cooperation of Pax2 and Pax5 in midbrain and cerebellum development

Midbrain and cerebellum development de- pendsonanorganizingcenterthatislocatedatthemidbrain- hindbrainjunctionofthevertebrateembryo.Expressionofthe two closely related transcription factors Pax2 and Pax5 over- laps spatially and temporally in this region of the developing central nervous system. To study a possible interaction of these transcription factors in midbrain and cerebellum pat- terning,wehavegeneratedPax5,Krddoublemutantmice.The transgene-induced Krd mutation corresponds to an '7- centimorgan chromosome 19 deletion that eliminates the entirePax2locus.TheheterozygousKrdmutationdeletingone Pax2 allele had no effect on midbrain and cerebellum devel- opment. Moreover, only minor developmental defects were previously observed at the midline of the inferior colliculus and anterior cerebellum in mice that were homozygous for a targeted Pax5 mutation. Similar morphological alterations were observed in 80% of all compound heterozygous Pax5 (1y2) Krd(1y2) mice. However, in the remaining 20% of compound heterozygotes, the inferior colliculi were missing, and the vermis of the cerebellum was severely disrupted due tothefailureofthecerebellarprimordiatofuseatthemidline. Inactivation of the second Pax5 allele in Pax5 (2y2) Krd (1y2) mice resulted in complete loss of the posterior mid- brain and cerebellum, as the tissue originating from the midbrain-hindbrain boundary region was deleted in the embryo as early as day 9.5. On the basis of these data, we proposethatthecooperationofPax2andPax5isessentialfor normal functioning of the organizing center at the midbrain- hindbrain junction. Early patterning of the central nervous system (CNS) results in subdivision of the neural tube along the anterior-posterior axis into the forebrain, midbrain, hindbrain, and spinal cord. Different strategies are subsequently used for the regional specialization of these CNS domains. Segmentation plays a prominent role in the compartmentalization and differentia- tion of the hindbrain (for review, see ref. 1). In contrast, the development of the midbrain and cerebellum depends on an organizing center that is located at the midbrain-hindbrain junction known as the isthmus (for review, see ref. 2). Isthmic tissue grafts were shown to induce an ectopic midbrain or cerebellum when transplanted into the chicken forebrain or hindbrain, respectively (for review, see ref. 3). Two secreted signaling molecules, Wnt1 and Fgf8, are specifically expressed in the organizing center at the isthmus and have thus been implicatedinpatterningofthemidbrainregion(4,5). TheFgf8
Recoding and multidimensional analyses of vegetation data: a comparison

Two simulated coenoclines and a real data set were differently recoded with respect to the Braun-Blanquet coding (including presence/absence) and analysed through the most common multidimensional scaling methods. This way, we aim at contributing to the debate concerning the nature of the Braun-Blanquet coding and the consequent multidimensional scaling methods to be used. Procrustes, Pearson, and Spearman correlation matrices were computed to compare the resulting sets of coordinates and synthesized through their Principal Component Analyses (PCA). In general, both Procrustes and Pearson correlations showed high coherence of the obtained results, whereas Spearman correlation values were much lower. This proves that the main sources of variation are similarly identified by most of used methods/transformations, whereas less agreement results on the continuous variations along the detected gradients. The conclusion is that Correspondence Analysis on presence/absence data seems the most appropriate method to use. Indeed, presence/absence data are not affected by species cover estimation error and Simple Correspondence Analysis performs really well with this coding. As alternative, Multiple Correlation Analysis provides interesting information on the species distribution while showing a pattern of releves very similar to that issued by PCA.
Prevalence and antibiotic resistance of Salmonella spp. in meat products, meat preparations and minced meat

This study aimed to determine Salmonella spp. prevalence in meat products, meat preparations and minced meat. Over a period of three years, a total of 300 samples were taken (100 RTE meat products, 100 meat preparations and 100 minced meat) and examined for the presence of Salmonella spp. Sampling was carried out at the warehouses of the food manufacturers. Salmonella spp. were not detected in RTE meat products, while 7% of semi-finished meat products (fresh sausages, grill meat formed and unformed) contained Salmonella, as did 18% of minced meats (minced pork II category, minced beef II category, mixed minced meat). The 25 Salmonella isolates obtained were examined for antibiotic resistance by the disk diffusion test, according to the NCCLS and CLSI guidelines. Isolates showed resistance to ampicillin and nalidixic acid (80%), tetracycline (72%), cefotaxime/clavulanic acid (48%), but not to gentamicin (8%) or trimethoprim/sulfamethoxazole (0%).
EFEKTIFITAS PENGGUNAAN PENDEKATAN PEMBELAJARAN BERBASIS MASALAH (PROBLEM BASED LEARNING) DALAM PEMBELAJARAN MATAKULIAH METODOLOGI PENELITIAN BAHASA ARAB

Abstract : The aim of this research is to describe the effectiveness of using Problem Based Learning (PBL) approach in Arabic Language Research Method Class. It uses a quasi-experimental (pre- experimental design). The result shows that generally using PBL is effective in both aspects of the learning process and the learning outcomes. The specific findings in this research is that the using PBL is not effective for students in the lower class category both from the aspect of competence, learning attitude, willingness to learn, learn discipline, and activeness in class Permalink/DOI: dx.doi. org/10.17977/um015v45i22017p197
Characterization of Root and Shoot Traits in Wheat Cultivars with Putative Differences in Root System Size

Root system size is a key trait for improving water and nitrogen uptake efficiency in wheat (Triticum aestivum L.). This study aimed (i) to characterize the root system and shoot traits of five wheat cultivars with apparent differences in root system size; (ii) to evaluate whether the apparent differences in root system size observed at early vegetative stages in a previous semi-hydroponic phenotyping experiment are reflected at later phenological stages in plants grown in soil using large rhizoboxes. The five wheat cultivars were grown in a glasshouse in rhizoboxes filled to 1.0 m with field soil. Phenology and shoot traits were measured and root growth and proliferation were mapped to quantify root length density (RLD), root length per plant, root biomass and specific root length (SRL). Wheat cultivars with large root systems had greater root length, more root biomass and thicker roots, particularly in the top 40 cm, than those with small root systems. Cultivars that reached anthesis later had larger root system sizes than those that reached anthesis earlier. Later anthesis allowed more time for root growth and proliferation. Cultivars with large root systems had 25% more leaf area and biomass than those with small root systems, which presumably reflects high canopy photosynthesis to supply the demand for carbon assimilates to roots. Wheat cultivars with contrasting root system sizes at the onset of tillering (Z2.1) in a semi-hydroponic phenotyping system maintained their size ranking at booting (Z4.5) when grown in soil. Phenology, particularly time to anthesis, was associated with root system size.
Effect of Innate Immune Collectin Surfactant Protein D and Adaptive Immune Protein IgM on Enhancing Clearance of Late Apoptotic Cells by Alveolar Macrophages

The innate immune protein surfactant protein (SP-) D is a carbohydrate binding protein that was originally isolated from mucosal lung tissues. Recently, studies show that SP-D binds to antibodies, including immunoglobulin M (IgM), which interacts with late apoptotic cells. Here we focus on the interaction between SP-D and IgM as they pertain to late apoptotic cell clearance. We hypothesized that the three-way interaction between IgM, SP-D and late apoptotic cells is functionally applicable to clearing late apoptotic cells from the lungs, thereby reducing lung inflammation. We show that SP-D binds to IgM and that IgM binds to the late apoptotic subclass of dying cells. We demonstrate that IgM and SP-D can both bind to late apoptotic cells in mutually distinct regions while also displaying some regional overlap. We show evidence that during LPS-induced lung inflammation both IgM and SP-D levels are elevated and this corresponds to an augmentation of apoptotic cell clearance. We illustrate that the protein interaction of IgM and SP-D is functionally relevant to apoptotic cell clearance in the lungs by showing that late apoptotic cells coated in IgM and/or SP-D are cleared more efficiently than control cells, by alveolar macrophages in vivo. Our ex vivo studies further show that these cells internalize apoptotic cells by engulfing very small particles released from the dying cells.