Miracle-dz/UniFAR-FTUs huggingface dataset:
Hybrid Testing in Pigeonpea Using DNA Fingerprinting by SSR-Markers

Pigeonpea (Cajanus cajan (L.) of Fabaceae family belongs to genus Cajanus usually grown in semi-arid tropics of Asia and Oceania, Africa and America. This crop has been a best source for improving food and soil quality amongst farmers. However, its seed have been always questioned for purity. This problem is managed by using polymorphic SSR markers. In present study, a DNA fingerprints generated by seven SSR markers and hybrid testing is performed on Pigeonpea test samples along with parental lines. The seed samples of pigeonpea were germinated in laboratory and three week old leaves samples were used for DNA isolation by CTAB method. A total of 9 alleles were observed in three test samples using three primers out of seven primers. The screening of the allelic data associated with the three cultivated varieties, revealed markers (CcM0246) displayed unique allelic profiles for one variety. Yet, the genetic fingerprinting data is not well resolved to potentially distinguished two bands of hybrid that are merely of 4–8 bp to confirm hybrid testing of seed. Hybrid testing of may be confirmed including more SSR primers prepared from genomic DNA of pigeonpea.
Rapid Functional Optoacoustic Imaging of Brain Activity in Murine and Zebrafish Models

Longitudinal functional imaging studies of neurological diseases are key in identifying the disease progression and possible therapeutic interventions. Optoacoustic imaging is an emerging method that promises high tissue penetration and non-invasive imaging of optical contrast in whole volumes. This thesis demonstrates the advantages of optoacoustic imaging and works to apply the method for neuroimaging applications.
Isolation and identification of indigenous entomopathogenic nematode (EPN) isolate from Egyptian fauna

Abstract Soil samples from different Egyptian Governorates as Giza, Behera, Alexandria, Sohag, Qulupeia, El-Sadat City, Sharkia, Bani-Swif, North Sinai (El-Arish) and South Sinai (Ras-Seder), Tanta, Fayoum and Suez have been surveyed for isolation of new entomopathogenic nematode isolates. One isolate coded as IB was isolated from Sharkia (Belbies). Based on morphometric characters, the isolate was found to belong to Heterorhabditidae and identified as Heterorhabditis indica. The isolate individuals were reproduced by in vivo method using sixth larval instars of Galleria mellonella. The survival of native isolate H. indica was better at low temperature (15 °C) compared to room temperature (27 °C). The bioassay results showed reduction in stored IJs activity against G. mellonella compared with fresh IJs where the median lethal concentration LC50 which recorded to be 46.87 for fresh IJs/ml then increased to 571.38 and to 1181.87 IJs/ml after storage for 2 and 4 weeks, respectively.
Microbial Dysbiosis and polyamine metabolism as predictive markers for early detection during progression of pancreatic adenocarcinoma in spontaneous mouse model

The lack of tools for early detection of pancreatic ductal adenocarcinoma (PDAC) is directly correlated to the abysmal survival rate in patients. In addition to several potential detection tools under active investigation, we present the gut microbiome and its metabolic complement as one of the earliest detection tools that could be useful in patients at high-risk for PDAC. A combination of 16s pyrosequencing and whole-genome sequencing of gut microbiota in a spontaneous genetically engineered PDAC murine model (KRASG12DTP53R172HPdxCre or KPC) showed a progressive Proteobacterial and Firmicutes dominance in gut microbiota in early stages of PDAC development. Upon in silico reconstruction of active metabolic pathways within the altered microbial flora, polyamine and nucleotide biosynthetic pathways were found to be significantly elevated. These metabolic products are known to be actively assimilated by the host and eventually utilized by rapidly dividing cells for proliferation validating their importance in the context of tumorigenesis. In KPC mice, as well as PDAC patients, we show significantly elevated serum polyamine concentration. Therefore, at the early stages of tumorigenesis, the gut microbial composition changes in a way to promote inflammation and release metabolites that foster host tumorigenesis, thereby fulfilling the ‘vicious cycle hypothesis’ of the role of the microbiome in health and disease states. Our results provide a potential, precise, non-invasive tool for early detection of PDAC, which will result in improved outcomes.
Simulations and Electrostatic Analysis Suggest an Active Role for DNA Conformational Changes During Genome Packaging by Bacteriophages

Motors that move DNA, or that move along DNA, play essential roles in DNA replication, transcription, recombination, and chromosome segregation. The mechanisms by which these DNA translocases operate remain largely unknown. Some double-stranded DNA (dsDNA) viruses use an ATP-dependent motor to drive DNA into preformed capsids. These include several human pathogens, as well as dsDNA bacteriophages – viruses that infect bacteria. We previously proposed that DNA is not a passive substrate of bacteriophage packaging motors but is, instead, an active component of the machinery. Computational studies on dsDNA in the channel of viral portal proteins reported here reveal DNA conformational changes consistent with that hypothesis. dsDNA becomes longer (“stretched”) in regions of high negative electrostatic potential, and shorter (“scrunched”) in regions of high positive potential. These results suggest a mechanism that couples the energy released by ATP hydrolysis to DNA translocation: The chemical cycle of ATP binding, hydrolysis and product release drives a cycle of protein conformational changes. This produces changes in the electrostatic potential in the channel through the portal, and these drive cyclic changes in the length of dsDNA. The DNA motions are captured by a coordinated protein-DNA grip-and-release cycle to produce DNA translocation. In short, the ATPase, portal and dsDNA work synergistically to promote genome packaging.
Durian rind soda-anthraquinone pulp and paper: effects of elemental chlorine-free bleaching and beating

A study was conducted to investigate the preliminary characteristics of soda-anthraquinone (soda-AQ) durian rind waste pulp and paper with the effects of elemental chlorine-free (ECF) bleaching and beating revolutions. Pulping was carried out using rotary digester with 0.1% antraquinone, 20% active alkali (NaOH), cooking time of 120 min and temperature of 170 °C. ECF bleaching with chlorine dioxide – alkali extraction – chlorine dioxide – alkali extraction – peroxide sequence and beating in the range of 0 to 1000 revolutions were applied to the unbeaten and unbleached pulp. ECF bleached pulp produced soda-AQ durian rind paper with greater tensile index, burst index, tear index, number of folds, brightness and scattering coefficients, but with slightly lower opacity compared with paper made from unbleached pulp. The results also showed that beating revolutions improved the overall physical and mechanical characteristics of durian rind soda-AQ pulp. Bleaching and beating enhanced the durian rind soda-AQ pulp fiber-to-fiber bonding and strength. Durian rind has potential characteristics as promising new material for papermaking.
Patterns of base composition within and between animal mitochondrial genomes

Nucleotide composition of a DNA molecule is a product of base substitution. Variation in nucleotide composition indicates a change in the pattern of substitution at either the level of the underlying mutational spectrum or the constraints imposed by natural selection. This work explores patterns of nucleotide usage within and between animal mitochondrial genomes and the evolutionary mechanisms that have shaped these patterns. Fourfold degenerate sites are expected to reflect the underlying mutational spectrum. Three simple measures of compositional bias, taking into account the strand-specific nature of nucleotide distribution in mtDNA, reveal considerable variation among fourfold degenerate sites of metazoan mitochondrial genomes. Log-linear analysis of intramolecular compositional patterns of mammalian mtDNA demonstrates that fourfold degenerate sites from even a single strand of the genome are not homogeneous. Rather, base composition varies among codon families and around the circular genome. A companion analysis of two additional taxonomic groups, molluscs and insects, also reveals compositional variation among codon families and between strands. The observed intramolecular variation cannot be explained solely by a simple strandspecific mutational pressure, but requires either a contextual bias to the mutational process or translational level natural selection as well. First and second codon position base composition and amino acid frequencies regressed on fourfold degenerate site composition show how mutational biases at the DNA level translate to amino acid biases in mitochondrial proteins.
Variation in Tree Community Composition and Carbon Stock under Natural and Human Disturbances in Andean Forests, Peru

Deforestation and forest degradation in Andean forests is influenced by natural and social environments including a wide elevation range and anthropogenic disturbance. Tree community composition is receiving attention as a key indicator of forest degradation. However, difference in factors affecting community composition at different elevation zones remains unclear. We aimed at elucidating factors (natural and human disturbances, and forest characteristics) that influence the variations in community composition in Andean forests. We conducted a ground-based survey setting 45 plots across a wide elevation range (ca. 600 to 3500 m a.s.l.) in Cusco region, Peru. Above ground biomass (AGB) decreased with increasing elevation. The generalized linear models for multivariate abundance data suggested that a factor affecting community composition was natural disturbance (erosion) at low elevation (<1000 m), while human disturbance (infrastructure such as sheds and trails) at high elevation (≥2400 m). Within each of the different elevation zones, the AGB affected community composition only at mid elevation (1000–2400 m), whereas mean tree height showed a consistent effect on community composition across the three elevations. Our results suggest that the effects of human disturbance on community composition were more prominent at higher elevation. The results also suggest that mean tree height may have a potential to be a key measure for evaluating variations in community composition in Andean forests.
Spatial and Temporal Variation in Thermal Melanism in the Aposematic Common Wasp (Vespula vulgaris) in Northern Europe

Climate affects the survival and distribution of animals in various ways. Insects respond to the changing environment with shift in geographical range or with modification of phenotypic characteristics. Conspicuous melanin-based warning colouration may be a traded off against thermal melanism, as darker individuals often have a thermoregulatory advantage in cold climates. Our study focused on climate-related phenotypic adaptations in the common wasp, Vespula vulgaris, which is an important predator and plant pollinator. Wasp workers were collected from three regions in Finland (Oulu, Turku and Kuopio) using beer traps. The analyses of the individual body size, melanisation and fluctuating asymmetry (FA) of wasps from different climatic conditions revealed that thermoregulation may constrain aposematism in colder environments. Wasps from higher latitudes were darker and bigger, however this tendency was not linear and there might be some location-specific differences between coastal and continental zones. The overall FA decreased with an increase of melanisation area. Variation in temperature and rainy days in different years affected abundance and body size to some degree but long-term studies are needed to validate the association between climate and morphology of the common wasp.
Estudo funcional do gene gluc31 que codifica uma β-1,3-glucanase da família GH16 de Trichoderma harzianum

O genero Trichoderma inclui especies que possuem habilidade de antagonizar patogenos de plantas em um processo complexo que vao desde antibiose, competicao por nutrientes, micoparasitismo, inducao de mecanismos de defesa em plantas ou ainda uma combinacao desses. Especies de Trichoderma sao conhecidas por sua capacidade de produzir enzimas liticas tais como exoglucanases, endoglucanases, quitinases e proteases que desempenham papeis importantes na degradacao da parede de fitopatogenos. Nos processos de desenvolvimento e diferenciacao de Trichoderma, as β-glucanases contribuem de forma significativa no processo morfogeneticomorfolitico uma vez que a β-glucanas e o componente principal da sua parede. Nesse trabalho, realizou-se o estudo do papel funcional do gene gluc31 que codifica uma endo β-1,3-glucanase da familia GH16 de Trichoderma harzianum ALL42, atraves da delecao deste gene. Observamos que a ausencia do gene gluc31 nao afetou a capacidade de micoparasitismo, in vitro, da especie mutante de T. harzianum ALL42, entretanto, o envolvimento deste gene na sintese e remodelamento da parede celular foi demonstrado. Na ausencia do gene gluc31, uma maior quantidade de polimero de quitina na parede celular das hifas da linhagem mutante Δgluc31 foi observado. A ausencia do gene gluc31 em T. harzianum demonstrou ainda um efeito sobre a expressao dos outros genes pertencentes a familia 16 de glicosil hidrolases em ensaios de RT-qPCR, devido a redundância de funcao entre as glucanases.
Glutathione, the redox sensitive transcription factors AP-1 and NF-κB, and early one adenoviral protein in human lung in smoking related lung disease

The major factor in the development of chronic obstructive airways disease (COPD) is cigarette smoking, although not all smokers develop chronic obstructive pulmonary disease. Inflammation and destruction has been shown in the lungs of smokers with chronic obstructive pulmonary disease. Oxidative stress, both from cigarette smoke and oxidants generated endogenously by cellular processes, contribute to the inflammation that occurs in the lungs in chronic obstructive pulmonary disease. It remains unclear why certain individuals appear susceptible to the effects of cigarette smoke and go on to develop inflammation and airflow limitation. The glutathione redox system is an important antioxidant protective system within the lungs, and this system may play a critical role in the development of inflammation. An alteration in the transcription of pro-inflammatory cytokines and mediators is also likely to contribute to the inflammation within the lung. Nuclear factor kappa-B (NF-kB) and activator protein-1 (AP-1) are both redox sensitive transcription factors, and are involved in the regulation of the gene transcription of many pro-inflammatory mediators. Activator protein-1 and nuclear factor kappa-B have a close relationship with y-glutamylcysteine synthetase (y-GCS) (glutamate cysteine ligase, GCL), the rate limiting enzyme in the synthesis of glutathione, with the y-glutamylcysteine synthetase gene containing various elements including an Activator protein-1 binding site. Susceptibility to the effects of cigarette smoke is likely to explain why certain individuals develop chronic obstructive pulmonary disease, and this susceptibility may arise from an earlier viral infection such as adenoviral infection that lies dormant, but which in the face of an oxidant stimulus such as cigarette smoke augments the inflammatory process. The in vivo studies herein have examined glutathione and y-glutamylcysteine synthetase, gene transcription, oxidant/antioxidant imbalance, the redox sensitive transcription factors nuclear factor kappa-B and activator protein-1, and have
Evolution of Environmentally-Enforced, Repeat Protein Topology in the Outer Membrane

Outer membrane beta barrels (OMBBs) are the proteins on the surface of Gram negative bacteria. These proteins have diverse functions but only a single topology, the beta barrel. It has been suggested that this common fold is a repeat protein with the repeating unit of a beta hairpin. By grouping structurally solved OMBBs by sequence, a detailed evolutionary story unfolds. A strand-number based pathway manifests with progression from a primordial 8-stranded barrel to 16-stranded and then to 18-stranded barrels. The transitions from 16- to 18-stranded barrels show mechanisms of strand number variation without domain duplication, such as a loop to hairpin transition. This indicates that repeat protein topology can be perpetuated without genetic duplication likely because the topology is being enforced by the membrane environment. Moreover, we find the evolutionary trace is particularly prominent in the C-terminal half of OMBBs which may be relevant to understanding OMBB folding pathways.
The Identification Of Cortical Pyramidal Neurons Using A Rpp Based Algorithm

Appropriately classifying neuronal subgroups is critical to numerous downstream procedures in several disciplines of biomedical research. The cortical pyramidal neuron characterization technology has achieved rapid development in recent years. However, capturing true neuronal features for accurate pyramidal neuron characterization and segmentation has remained elusive. In the current study, a novel global preserving estimate algorithm is used to capture the non-linearity in the features of cortical pyramidal neuron after Factor Algorithm. Our results provide evidence for the effective integration of the original linear and nonlinear neuronal features and achieves better characterization performance on multiple cortical pyramidal neuron databases through array matching.
Deletion of the Creatine Transporter in dopaminergic neurons leads to hyperactivity in mice

Creatine (Cr) is required for proper neuronal function, as evidenced by the intellectual disability and epileptic phenotype seen in patients with cerebral Cr deficiency syndromes (CCDS). In addition, attention-deficit hyperactivity disorder (ADHD) is a frequent co-morbidity of Cr transporter (Crt) deficiency, the leading cause of CCDS. While the effects of the loss of Cr in the whole brain is clear, it is unknown if Cr is required for the proper function of all neurons. Of particular interest are dopaminergic neurons, as many CCDS patients have ADHD and Cr has been implicated in dopamine-associated neurodegenerative disorders, such as Parkinson’s and Huntington’s diseases. The purpose of this study was to examine the effect of a loss of the Slc6a8 (Cr transporter; Crt) gene in cells expressing the dopamine transporter (Slc6a3; DAT) on activity levels and motor function as the animals age. DAT-specific Crt-knockout (DAT-Crt) mice were tested along with control (Crt-FLOX) mice monthly from 3 to 12 months of age in locomotor activity, the challenging beam test, and spontaneous activity. DAT-Crt mice were hyperactive compared with controls and this finding persisted throughout the lifetime of the mice. No changes were observed in errors to cross a narrow bridge in the challenging beam test. In a measurement of spontaneous activity, DAT-Crt mice showed increased rearing and hind limb steps, suggesting the hyperactivity carried over to this task. Taken together, these data suggest that the lack of Cr in dopaminergic neurons causes hyperactivity while sparing motor function. Abbreviations Cr Creatine CK Creatine Kinase P-Cr Phosphocreatine PD Parkinson’s Disease MPTP 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine 6-OHDA 6-hydroxydopamine Crt Creatine Transporter Crt-/y ubiquitous creatine transporter knockout mouse DAT-Crt-/y dopamine-specific creatine transporter knockout mouse ADHD: Attention-deficit hyperactivity disorder
Acceleration or deceleration of litter decomposition by herbivory depends on nutrient availability through intraspecific differences in induced plant resistance traits

Herbivores often induce changes in plant defensive chemistry or nutrient content that may respectively inhibit or promote microbial decomposition of senesced litter. Often the directional impact of herbivores on decomposition is considered to be a property of a species or ecosystem. While rarely explored, plasticity in the induction of defensive strategies across environmental gradients may also result in divergent impacts of herbivores on decomposition (deceleration vs. acceleration). Here, we examined how soil nutrient conditions determine legacy effects of herbivory, using nine goldenrod genotypes grown across four levels of nutrient supply and with or without grasshopper herbivory. In this species, herbivory induces defensive traits in genotypes grown in high nutrient conditions but induces tolerance (compensatory growth) in low nutrient conditions. We combined senesced litter from each treatment with a common soil inoculum in microcosms and measured soil respiration and litter mass loss over 100 days as estimates of decomposition. Plant genotype, nutrient environment, and herbivory each altered decomposition. The legacy effect of herbivory overwhelmed the positive effect of high soil nutrient supply on decomposition. This significant herbivory × nutrient environment interaction meant that herbivore‐induced plants grown in high nutrient environments produced litter that was more resistant to microbial breakdown than litter from the same genotype not exposed to herbivores. But the opposite occurred at low nutrient levels where litter from herbivore‐induced plants was most readily decomposed. Furthermore, we mechanistically tie treatment‐induced changes in leaf traits to decomposition rates. Lastly, we demonstrate a significant correlation between herbivore growth rates on living tissue and decomposition efficiency by the microbial community of senesced tissue, suggesting that herbivores and microbes perceive the “quality” of the induced substrate similarly. Synthesis. Herbivore‐induced changes in leaf palatability and trait expression due to defense induction or compensatory growth can cascade through to either inhibit or promote the decomposability of leaf litter within a single species. Here, the key determinant of which occurs is the soil fertility environment of the goldenrod clone. These findings offer mechanistic understanding of how spatial heterogeneity in ecosystem process rates may be generated by spatial variation in herbivory and nutrient availability.
Global species delimitation and phylogeography of the circumtropical ‘sexy shrimp’ Thor amboinensis reveals a cryptic species complex and secondary contact in the Indo‐West Pacific

The “sexy shrimp” Thor amboinensis is currently considered a single circumtropical species. However, the tropical oceans are partitioned by hard and soft barriers to dispersal, providing ample opportunity for allopatric speciation. Herein, we test the null hypothesis that T. amboinensis is a single global species, reconstruct its global biogeographical history, and comment on population‐level patterns throughout the Tropical Western Atlantic.