Miracle-dz/UniFAR-FTUs huggingface dataset:
Evidence of rapid adaptive trait change to local salinity in the sperm of an invasive fish

Invasive species may quickly colonize novel environments, which could be attributed to both phenotypic plasticity and an ability to locally adapt. Reproductive traits are expected to be under strong selection when the new environment limits reproductive success of the invading species. This may be especially important for external fertilizers, which release sperm and eggs into the new environment. Despite adult tolerance to high salinity, the invasive fish Neogobius melanostomus (round goby) is absent from fully marine regions of the Baltic Sea, raising the possibility that its distribution is limited by tolerance during earlier life stages. Here, we investigate the hypothesis that the spread of N. melanostomus is limited by sperm function in novel salinities. We sampled sperm from two invasion fronts with higher and lower salinities in the Baltic Sea and tested them across a range of salinity levels. We found that sperm velocity and percentage of motile sperm declined in salinity levels higher and lower than those currently experienced by the Baltic Sea populations, with different performance curves for the two fronts. Sperm velocity also peaked closer to the home salinity conditions in each respective invasion front, with older localities showing an increased fit to local conditions. By calculating how the sperm velocity has changed over generations, we show this phenotypic shift to be in the range of other fish species under strong selection, indicating ongoing local adaptation or epigenetic acclimation to their novel environment. These results show that while immigrant reproductive dysfunction appears to at least partly limit the distribution of invasive N. melanostomus in the Baltic Sea, local adaptation to novel environments could enable future spread beyond their current boundaries.
RAD-Behavior (Recombining Atomized, Discretized, Behavior): A new framework for the quantitative analysis of behavioral execution

The ability to precisely describe and numerically evaluate organismal phenotypes is a prerequisite for addressing most questions in evolutionary biology and ecology. The quantification and comparison of behavior, loosely defined as an external response to stimuli, is particularly challenging because the myriad axes of variation that exist make comparisons, both within and among species, difficult. Such evaluations often boil down to comparisons of time-budgets (e.g. relative investment in courtship displays) or probabilities (e.g. likelihood of engaging in a class of behaviors in a particular context) – which we refer to as behavioral strategies. A focus on variation in behavioral strategies underlies most research in evolutionary and ecological studies of behavior. Equally important, however, is perhaps the question of ‘how’ animals are actually performing the complex motor sequences that comprise behaviors (i.e. behavioral execution). What are the patterns of movement, the relative transition rates, and kinematics underlying the behaviors exhibited in particular contexts? Understanding how behavioral execution differs among individuals, populations, and species has the potential to provide new insights into the factors shaping variation in behavior and the processes shaping behavioral evolution at different scales. Here, we propose a broad framework for comparing behavioral execution (RAD-behavior: recombining atomized, discretized behavior) that leverages string-matching/bioinformatic tools to understand phenotypic variation in behavioral execution and which holds the potential to yield novel insights about the evolutionary ecology of behavior at multiple scales.
Couples and the Silicon Chip: Applying Information Technology to Couple Relationship Services

Information technology (IT) is developing at a phenomenal rate and has the potential to play an important role in dissemination and enhancement of couple services. IT applications have the capacity to substantially increase availability of couple services and can be adapted to facilitate both two-way (professional and client) or multiple (group) communication. We review existing applications of IT in the couple relationship services literature and propose a number of ways in which IT could be used to enhance the quality and accessibility of couple services. Drawing our experience in developing IT applications, we discuss the challenges in designing such applications and suggest a number of issues that should be considered in order to maximize the potential of this new development in couple services.
Role of benthic habitat structure and riverine connectivity in controlling the spatial distribution and ecology of estuarine fish

Estuaries are among the most productive ecosystems per unit area, but this productivity is unevenly distributed across a complex mosaic of habitats. Identifying the qualities of different habitats that influence the composition and productivity of biotic communities is fundamental to understanding the dynamics of these ecosystems. We combined field surveys, hydrological modelling and stable isotope analysis to understand the roles of habitat, hydrological connectivity, salinity and temperature in determining assemblage composition, species abundance and trophic ecology of an estuarine fish community. Hydrodynamics, vegetation matrices of macroalgae and seagrass and the presence of epiphytes on vegetation explained spatial patterns in taxonomic biodiversity, multivariate assemblage structure and the occurrence of juvenile black bream Acanthopagrus butcheri, a species that possesses ecological traits common to many demersal estuarine fish species. Juvenile bream abundance was related to vegetation composition (particularly epiphyte presence), supporting the hypothesis that juvenile habitats that provided resources or conditions that ex tended beyond just structure conferred more ecological advantages. This was further evidenced by stable isotope-based estimates of basal resource contributions of epiphytes. Our findings suggest that hydrodynamic connectivity with riverine water masses acts as a coarse determinant for estuarine fish communities at large spatial scales. At smaller scales, habitat-level associations influence local abundances and the identity and importance of specific trophic resources. Coupling hydro dynamic modelling with natural biomarkers provides a powerful approach for assessing the spatial context of habitat use that can help resource managers prioritize monitoring and habitat preservation efforts for coastal fish communities in a changing global environment.
HOPS recognizes each SNARE, assembling ternary trans-complexes for sudden fusion upon engagement with the 4th SNARE

Vacuole fusion requires SNAREs, Sec17/18, a Rab, and HOPS. We find that co-incubation of HOPS, proteoliposomes bearing the Rab and R-SNARE, and proteoliposomes with the Rab and any two Q-SNAREs yields a trans complex which includes these 3 SNAREs. The missing Q-SNARE then triggers a burst of fusion, indicating that each HOPS, R-, and QxQy-SNARE trans-complex is an activated intermediate for functional Qz-SNARE incorporation. HOPS can assemble activated fusion intermediates because it recognizes each of the four SNAREs, binding them independently. HOPS-dependent fusion is saturable for each Q-SNARE, indicating saturable functional sites on HOPS. Though a nonspecific tether allows fusion with pre-assembled Q-SNAREs, only HOPS catalyzes fusion when the Q-SNAREs are not pre-assembled by ushering each Q-SNARE into a functional complex. In contrast, there is little spontaneous functional assembly of the 3 Q-SNAREs. HOPS thus recognizes each of the 4 SNAREs to assemble a versatile set of activated fusion intermediates.
Expression of Heat Shock Protein 70 Is Insufficient To Extend Drosophila melanogaster Longevity

It has been known for over 20 years that Drosophila melanogaster flies with twelve additional copies of the hsp70 gene encoding the 70 kD heat shock protein lives longer after a non-lethal heat treatment. Since the heat treatment also induces the expression of additional heat shock proteins, the biological effect can be due either to HSP70 acting alone or in combination. This study used the UAS/GAL4 system to determine whether hsp70 is sufficient to affect the longevity and the resistance to thermal, oxidative or desiccation stresses of the whole organism. We observed that HSP70 expression in the nervous system or muscles has no effect on longevity or stress resistance but ubiquitous expression reduces the life span of males. We also observed that the down-regulation of hsp70 using RNAi did not affect longevity.
Functional characterization of fatty acyl desaturase Fads2 and Elovl5 elongase in the Boddart’s goggle-eyed goby, Boleophthalmus boddarti (Gobiidae) suggest an incapacity for long-chain polyunsaturated fatty acid biosynthesis

Long-chain polyunsaturated fatty acid biosynthesis, a process to convert C18 polyunsaturated fatty acids to eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) or arachidonic acid (ARA) requires the concerted activities of two enzymes, the fatty acyl desaturase (Fads) and elongase (Elovl). This study highlights the cloning, functional characterisation and tissue expression pattern of a Fads and Elovl from the Boddart’s goggle-eyed goby (Boleophthalmus boddarti), a mudskipper species widely distributed in the Indo-Pacific region. Phylogenetic analysis revealed that the cloned Fads and Elovl are clustered with other teleost Fads2 and Elovl5 orthologs, respectively. Interrogation of the genome of several mudskipper species, namely B. pectinirostris, Periophthalmus schlosseri and P. magnuspinnatus revealed a single Fads2 for each respective species while two elongases, Elovl5 and Elovl4 were detected. Using a heterologous yeast assay, the B. boddarti Fads2 was shown to possess low desaturation activity on C18 PUFA. In addition, there was no desaturation of C20 and C22 substrates. In comparison, the Elovl5 showed a wide range of substrate specificity, with capacity to elongate C18, C20 and C22 PUFA substrates. We identified an amino acid residue in the B. boddarti Elovl5 that affect the capacity to bind C22 PUFA substrate. Both genes are highly expressed in brain tissue. Among all tissues, DHA is highly concentrated in neuron-rich tissues while EPA is highly deposited in gills. Taken together, the results showed that due to disability of desaturation steps, B. boddarti is unable to biosynthesis LC-PUFA, relying on dietary intake to acquire these nutrients.
Probing of mortality rate by staying alive: The growth‐reproduction trade‐off in a spatially heterogeneous environment

In many annual plants, mollusks, crustaceans and ectothermic vertebrates, growth accompanies reproduction. The growth curves of these organisms often exhibit a complex shape, with episodic cessations or accelerations of growth occurring long after maturation. The mixed allocation to growth and reproduction has poorly understood adaptive consequences, and the life‐history theory does not explain if complex growth in short‐lived organisms can be adaptive. We model the trade‐off between growth and reproduction in a short‐lived organism evolving in a metapopulation. Individuals occupy risky or safe sites throughout their lives, but are uncertain regarding the risk of death. Modelled organisms are allowed to grow and produce offspring at specified time points (moults), although we also consider scenarios that approximate continuous growth and reproduction. Certain combinations of risky to safe sites select for strategies with mixed allocation to growth and reproduction that bet‐hedge offspring production in safe and risky sites. Our model shows that spatially heterogeneous environments select for mixed allocation only if safe sites do not become the prevailing source of recruits, for example, when risky sites are frequent. In certain conditions, growth curves are multi‐phasic, with allocation to growth that stops, remains constant or accelerates during adult life. The resulting complex growth curves are more likely to evolve in short‐lived organisms that moult several times per adult life. Our work shows that spatial heterogeneity can select for growth that accompanies reproduction and provides insights into the adaptive significance of complex growth curves. Short‐lived crustaceans are particularly predisposed to exhibit complex growth patterns as an adaptive response to spatially heterogeneous environments. Our results suggest that standard statistical growth models assuming adult growth rate to only decelerate over life are not well suited to approximate growth curves of short‐lived crustaceans. A free Plain Language Summary can be found within the Supporting Information of this article.
The hunger games: sensing host arginine is essential for Leishmania parasite virulence

Arginine homeostasis in lysosomes is critical for growth and metabolism of mammalian cells. They employ a specific sensor (SLC38A9) that monitors intra-lysosome arginine sufficiency and subsequently up-regulates cellular mTORC1 activity. Lysosomes of macrophages (phagolysosomes) are the niche where the parasitic protozoan Leishmania resides and causes important human disease. Several years ago, we discovered that upon arginine starvation, cultured Leishmania parasites promptly activate a MAPK2-mediated Arginine Deprivation Response (ADR) pathway, resulting in up-regulation of the Leishmania arginine transporter (AAP3), as well as a small group of other transporters. Significantly, ADR is also activated during macrophage infection, implying that the intracellular parasite actively depletes arginine within the host phagolysosome, likely to prevent mTORC1 activation and enhance intracellular development. We hypothesize that ADR-mediated up-regulation of AAP3 activity is necessary to withstand the resultant arginine starvation. Both copies of the AAP3 genes are located (in tandem) on a tetrasomic chromosome (chr31), but only one (AAP3.2) is responsive to arginine deprivation. CRISPR/Cas9-mediated disruption of the AAP3 locus yielded mutants that retain a basal level of arginine transport (mediated by AAP3.1), but lack a functional copy of AAP3.2 and are therefore not responsive to arginine starvation. While these mutants grow normally in culture as promastigotes, they were impaired in their ability to develop inside THP1 macrophages grown under physiological concentrations of arginine (0.1 mM). However, flooding the macrophage growth medium with arginine (1.5 mM) restored parasite infectivity and intracellular growth to that of wild type. The results indicate that inside the host macrophage, Leishmania must overcome the arginine “Hunger Games” by up-regulating transport of arginine via the ADR. Furthermore, the AAP3.2 mutants were ~70-80% less virulent in Balb/C mice, showing, for the first time, that the ability to monitor and respond to changes in host metabolite levels is essential for pathogenesis.
Intergenerational fluctuations in colour morph frequencies may maintain elytral polymorphisms in the ladybird beetle Cheilomenes sexmaculata (Coleoptera: Coccinellidae)

Phenotypic polymorphisms are found in a wide array of taxa, and unravelling the mechanisms that maintain them is of great interest to evolutionary and ecological biologists. Temporal environmental heterogeneity may play a role in the maintenance of polymorphisms but is poorly understood. In the present study, we analysed trends in intergenerational elytral colour morph frequencies in relation to changes in fitness and life history traits (i.e. body size, mortality, fecundity, hatching rate and mate preference) in the ladybird beetle Cheilomenes sexmaculata (Coleoptera: Coccinellidae). A long-term field survey spanning nine years showed that the frequency of dark morphs increases over winter and then decreases in spring. Dark morphs may have an advantage in winter due to their higher tolerance of low temperatures compared with light morphs. Light-morph females were heavier in winter than dark-morph females. They also mated more frequently and had higher hatching rates, potentially causing an increase in light morphs in spring. These results suggest that fluctuations in morph frequencies resulting from the conflicting directions of selection pressures between overwintering and spring generations may help to maintain genetic polymorphism.
Lingual tonsilin primer lenfomas: Bir olgu sunumu

Extranodal non-Hodgkin lymphomas of the head and neck are rare. Most of the oral cavity lymphomas originate from Waldeyer ring and present as a mass in the oropharynx or nasopharynx. Tongue base is the most common location. 57year-old male patient presented to our clinic with a painless swelling in the neck which had grown for two months. He had dysphagia. Physical examination revealed an eryhtematous mass resulted tonsil hypertrophy and asymmetry in the tongue base. In the neck there was a palpable jugulodigastric lymphadenopathy. Computed tomography of the patient revealed a mass from tongue base to vallecula and multiple lymphadenopathies in the cervical chain. The patient was diagnosed as lymphoma. As a result since lingual tonsil lymphomas are rare tumors therefore they should be thought in the differential diagnosis of oral cavity masses.
Isolation and initial propagation of guinea pig adenovirus (GPAdV) in Cavia porcellus cell lines

Background: The lack of adequate in vitro systems to isolate and propagate guinea pig adenovirus (GPAdV), a prevalent cause of respiratory illness of varaible severity in laboratory guinea pig colonies worldwide, has precluded its formal characterization to allow for the development of comprehensive diagnostic assays, and for the execution of complex pathogenesis and basic virology studies. Methods: Two strains of GPAdV were isolated in guinea pig ( Cavia porcellus) cell cultures from frozen archival infected animal tissue originated from colony outbreaks of pneumonia in Australia and the Czech Republic in 1996. Results: Commercially available guinea pig cell lines from colorectal carcinoma (GPC-16), fetal fibroblast (104-C1) and lung fibroblast (JH4 C1), and the tracheal epithelial cell line GPTEC-T developed in this study were able to support viral infection and early propagation. Sufficient viral DNA was recovered from cell cultures to PCR-amplify and obtain sequence data for the complete hexon gene and partial DNA polymerase and penton base genes. Phylogenetic analysis for the three regions of the genome provided strong evidence confirming GPAdV as a unique species in the genus Mastadenovirus. Conclusions: This study demonstrated the feasibility of propagating GPAdV in cultures of immortalized lines of GP cells of a variety of types, thus establishing a critical foundation for the development of a robust culture platform for virus stock production and titration. The generation and analysis of whole GPAdV genome sequences will provide additional data for a comprehensive description of the genetic organization of the viral genome and for a better assessment of genetic diversity between the two isolated strains.
Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters

Next-generation sequencing based base-by-base distance measures have become an integral complement to epidemiological investigation of infectious disease outbreaks. This study introduces PANPASCO, a computational pan-genome mapping based, pairwise distance method that is highly sensitive to differences between cases, even when located in regions of lineage specific reference genomes. We show that our approach is superior to previously published methods in several datasets and across different Mycobacterium tuberculosis lineages, as its characteristics allow the comparison of a high number of diverse samples in one analysis - a scenario that becomes more and more likely with the increased usage of whole-genome sequencing in transmission surveillance. Author summary Tuberculosis still is a threat to global health. It is essential to detect and interrupt transmissions to stop the spread of this infectious disease. With the rising use of next-generation sequencing methods, its application in the surveillance of Mycobacterium tuberculosis has become increasingly important in the last years. The main goal of molecular surveillance is the identification of patient-patient transmission and cluster detection. The mutation rate of M. tuberculosis is very low and stable. Therefore, many existing methods for comparative analysis of isolates provide inadequate results since their resolution is too limited. There is a need for a method that takes every detectable difference into account. We developed PANPASCO, a novel approach for comparing pairs of isolates using all genomic information available for each pair. We combine improved SNP-distance calculation with the use of a pan-genome incorporating more than 100 M. tuberculosis reference genomes for read mapping prior to variant detection. We thereby enable the collective analysis and comparison of similar and diverse isolates associated with different M. tuberculosis strains.
EVALUATION AND IDENTIFICATION OF TOBACCO BREEDING LINES FOR WATER STRESS TOLERANCE

industrial crop grown in the states of Andhra Pradesh, Gujarat, Tamil Nadu, Karnataka, West Bengal, Bihar and Uttar Pradesh. The tobacco crop is relatively drought stress tolerant plant but the loss of quality leaf yield in response to water-deficit stress is witnessed in many areas. For selection of drought tolerant genotype the lines need to be screened under artificial condition to ensure that all the genotypes undergo drought stress. In this study artificial water stress has been created for screening the genotypes under in vitro and in vivo condition and the genotypes were selected based on morphological and physiological characteristics. The minimum germination per cent with 1% PEG was found to be 10% and maximum was 90%. Twenty five genotypes showed 90 % germination under stress whereas the susceptible check showed only 10 % germination. In greenhouse, water stress was induced at 35 days after transplantation in pots and the soil moisture (SM) and relative water content (RWC) were recorded three times at weekly intervals. RWC of tolerant lines varied from 40-50 per cent when the soil moisture was below 20%. The height of the genotypes varied from 80 to 100 cm, whereas the height of the susceptible check was 34 cm. A total of 12 genotypes were selected based on the RWC which showed a balanced RWC during three intermittent water stress and the recorded higher photosynthetic rate between 12-18 mmol CO2 m -2s1,stomatal conductance 0.2-0.8 H2O m -2 s-1, transpiration rate 69 H2O m -2 s-1 and Ci/Ca ratio 0.60. 797.