Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic diversity of reintroduced American martens in Michigan's Lower Peninsula

Reintroductions are an important conservation and management technique used to restore extirpated populations. Negative genetic consequences (e.g., diversity loss, bottlenecks, inbreeding) are often an unintentional result of reintroductions, due to a small number of founders or suboptimal habitat at release sites. American martens (Martes americana) were extirpated from Michigan's Lower Peninsula in 1911 due to habitat loss and unregulated trapping. Martens were reintroduced into 2 areas of the Lower Peninsula in 1985–1986. The Lower Peninsula reintroduction was characterized by a relatively small number of founders (85 individuals) released into 2 geographically disparate, fragmented sites. We genotyped martens sampled at the 2 release sites approximately 20–25 years since reintroduction, using 11 microsatellite loci. We detected low average allelic richness (3.92 alleles per locus), moderate levels of inbreeding (mean FIS = 0.106), and multiple loci with significant heterozygote deficiencies. Effective population size estimates were small, ranging between 6 and 27 individuals depending on the estimator and the sample group. We also detected significant population structuring between the release sites (FST = 0.093 using the most recent sample). With small population size and limited to no gene flow, we predict the 2 Lower Peninsula marten populations will continue to diverge and potentially further lose genetic diversity. This study highlights the importance of long-term genetic monitoring of reintroduced populations.
Comparing phylogenetics and linear morphometrics to solve the generic assignment of Parabolinella? triarthroides Harrington (Trilobita, Olenidae)

Abstract. The use of different methodological approaches together with an exhaustive qualitative study has helped to recognize important morphological traits to distinguish species in a systematic and phylogenetic framework. Parabolinella triarthroides Harrington, 1938 was described based on two cranidia from the Quebrada de Coquena, Purmamarca, Jujuy province. The generic assignment of P. triarthroides has been questioned by a phylogenetic analysis, which resolves this species as the sister group of Bienvillia Clark, 1924. To explore the generic assignment of this species, a revision of the type material, plus a morphometric analysis including specimens of Parabolinella Brøgger, 1882 and Bienvillia were performed. In addition, the original matrix used in the published phylogeny was reviewed and enlarged, including more species of Bienvillia. Continuous characters were coded in different ways in order to compare how they could affect the ordering of specimens and their phylogenetic relationships. Finally, both methodologies were compared, especially in regard to the behavior of the quantitative characters included in the analyses. From the combined analyses, it is shown that similarities between the cranidium of P. triarthroides and all other Parabolinella species are true homologies instead of a by-product of evolutionary convergence. Therefore, P. triarthroides should be considered a member of this genus. Finally, this study demonstrates that the best strategy for solving systematic problems in groups where the morphological variation is the only source of information (i.e., fossil taxa without living representatives) is the implementation of an integrative approach, combining different methodological techniques and a good description of specimens.
Spatial sampling in human visual cortex is modulated by both spatial and feature-based attention

Spatial attention changes the sampling of visual space. Behavioral studies suggest that feature-based attention modulates this resampling to optimize the attended feature’s sampling. We investigate this hypothesis by estimating spatial sampling in visual cortex while independently varying both feature-based and spatial attention. Our results show that spatial and feature-based attention interacted: resampling of visual space depended on both the attended location and feature (color vs. temporal frequency). This interaction occurred similarly throughout visual cortex, regardless of an area’s overall feature preference. However, the interaction did depend on spatial sampling properties of voxels that prefer the attended feature. These findings are parsimoniously explained by variations in the precision of an attentional gain field. Our results demonstrate that the deployment of spatial attention is tailored to the spatial sampling properties of units that are sensitive to the attended feature.
Transfer of ice algae carbon to ice-associated amphipods in the high-Arctic pack ice environment

Sympagic (ice-associated) amphipods channel carbon into the marine ecosystem. With Arctic sea ice extent in decline, it is becoming increasingly important to quantify this transfer of sympagic energy. Recently, a method for quantifying sympagic particulate organic carbon (iPOC) in filtered water samples was proposed based on the abundances of the Arctic sea ice biomarker IP25. Here, we tested the hypothesis that adoption of this method could also provide quantitative estimates of iPOC transfer within Arctic amphipods. We analysed five amphipod species collected north of Svalbard and compared findings to some previous studies. Estimates showed that Onisimus glacialis and Apherusa glacialis contained the most iPOC, relative to dry mass (23.5 ± 4.5 and 9.8 ± 1.9 mg C g, respectively), while Gammarus wilkitzkii had the highest grazing impact on the available ice algae (0.48 mg C m, for an estimated 24 h), equating to 73% of algal standing stock. Our findings are also broadly consistent with those obtained by applying the H-Print biomarker approach to the same samples. The ability to obtain realistic quantitative estimates of iPOC transfer into sympagic and pelagic fauna will likely have important implications for modelling energy flow in Arctic food webs during future climate scenarios.
ANATOMICAL STUDY OF THE TRACHEAL CAST AND LUNG IN LOCAL BREED CATS Felis Cactus Domesticus.L.

Cast technique includes ten cats (5 male, 5 female) used the polymerizing resin (cold acrylic) to study the bronchial tree and blood vessels. the examination of bronchial tree of the cats (felis catus) Lung is done by using cold resin in order to prepare cast specimens. The diameter of right principal bronchi of cats mean (7.34 mm± 0.36) and diameter of left principal bronchi means (6.07mm 0.36). The right principal bronchi large than left principal. The air flow in right Lung faster than the left. This result is supported by the researcher . These results are obtained from the cast model showing that the pulmonary trunk divides into right and left pulmonary arteries after arising from the right ventricle of heart. The right pulmonary artery the diameter about (4.18 mm) and diameter of left pulmonary artery about (3.40 mm) that the right pulmonary larger than the left pulmonary artery
PCR validation of predicted virulence factors in a collection of Xanthomonas campestris (pv. musacearum and vascolurum) strains

Bacterial plant pathogens belonging to the Xanthomonas genus are adapted to their host plants and are not known to colonize other environments. Xanthomonas colonize host parts such as leaves, stems and roots before entering vascular tissues and engaging in an invasive pathogenic phase. These bacterial strains have evolved strategies to adapt to life in this environment. The host-pathogen interactions of Xanthomonas vasicola (Xv) need to be well understood to properly map the target genes in the host and pathogen so as to understand the mechanism of resistance. Genotypic characterization, based on the analysis of restriction fragment length polymorphism of virulence factor fragment products was performed on members of the X. vasicola pv. musacearum (Xcm) and X. vasicola pv. vasculorum (Xvv) from varying geographical locations. The study showed that Xcm and Xvv are different from each other based on amplification of virulence factors within fragments of their DNA. Bacterial strains of similar species can have unique Type four pili (Tfp) and Tfp pilus assembly protein PilF a fimbrial biogenesis protein was amplified in all Xanthomonas strains except NCPPB1131 only. Type III effector protein RipT was confirmed to be present in all strains of Xcm and Xvv but not NCPPB1131 and NCPPB1132. All the Xcm and Xvv strains under test yielded bands of type III effector HopAF1 except Xvv206, NCPPB1131 and NCPPB1132. YopJ type III secretion system effector protein hybridizes in DNA of all Xcm strains tested but not in NCPPB1131 or NCPPB1132. This study confirmed the predicted presence or absence of virulence factors especially effectors across bacterial strains and within strains of the same species and other clusters conserved in gram negative bacteria. Key words: Banana, effectors, pathogen-host, Xanthomonas wilt, Xanthomonas campestris, Xanthomonas vasicola.
Down regulation of APETALA3 homolog resulted in defect of floral structure critical to explosive pollen release in Cornus canadensis

In mature buds of the dwarf dogwood lineage (DW) of Cornus, petals and filaments form an “x”‐like box containing mechanical energy from the filaments to allow explosive pollen dispersal. As a start to understand the molecular mechanisms responsible for the origin of this unique structure in Cornus, we cloned and characterized the sequences of APETALA3 (AP3) homologs from Cornus canadensis of the DW lineage and five other Cornus species, given the function of AP3 on petal and stamen development in Arabidopsis, and tested the function of CorcanAP3 using a stable Agrobacterium‐mediated transformation system. The cloned CorAP3s (AP3‐like genes in Cornus) were confirmed to belong to the euAP3 lineage. qRT‐PCR analysis indicated strong increase of CorcanAP3 expression in floral buds of wildtype C. canadensis. A hairpin construct of CorcanAP3 was successfully introduced into wild type plants of C. canadensis, resulting in significant reduction of CorcanAP3 expression and abnormal floral development. The abnormal floral buds lost the “x” form and opened immaturely due to delay or retard of petal and stamen elongation and the push of style elongation. The results suggested CorcanAP3 may function to regulate the coordinated rate of development of petals and stamens in C. canadensis, necessary for the x‐structure formation, although the exact molecular mechanism remains unclear. Comparison among six Cornus species indicated a greater ratio of stamen to petal and style growth in C. canadensis, suggesting an evolutionary change of CorAP3 expression pattern in the DW lineage, leading to the greater growth of filaments to form the “x”‐box.
Epigenomic studies of twins for cancer and cancer risk factors

A complex interaction of environmental factors, stochastic events, and genetic susceptibility can lead to cancer development. The aim of this thesis is to investigate the DNA methylome for cancer, cancer risk, and prediction potential. Studies were performed in peripheral blood to explore systemic changes associated with cancer, and in skin for an in-depth view of total body naevus count, the strongest risk factor for melanoma. Peripheral blood DNA methylomes of 41 cancer-discordant female monozygotic (MZ) twin-pairs were assessed for changes associated with any cancers. The epigenome-wide association study (EWAS) identified one genome-wide significant and several suggestive differential methylated positions (DMPs), three of these showed predictive biomarker potential (near SASH1, COL11A2, and LINC00340 ). Early breast cancer specific DNA methylation changes were identified in peripheral blood obtained prior to diagnosis. The DNA methylomes were assessed by two genome-wide DNA methylation techniques in a total of 28 breast cancer discordant MZ twin-pairs. Three novel significant breast-cancer differential methylated regions (DMRs) were identified (in MECOM, PCGF3, and near ELN ) that were suggestive of predictive biomarker potential. Skin DNA methylomes were investigated in association with the number of naevi across the body in 322 female individuals. Three genome-wide significant DMPs were identified in novel genes METRNL, C15orf48, and ARRDC1. Suggestive results included CTC1 and RAF, which are known genes involved in naevi
DIVERSITY OF IRANIAN STRAINS OF PSEUDOMONAS SYRINGAE pv. SYRINGAE AND PSEUDOMONAS SYRINGAE pv. LACHRYMANS

Strains of Pseudomonas syringae pv. syringae (Pss), Pseudomonas syringae pv. lachrymans (Psl) and Pseudomonas tolaasii (P. tolaasii) were analyzed for genetic diversity. For molecular identification of the strains, three primer pairs were used. Molecular analysis was done with random amplified polymorphic DNA (RAPD) and Insertion Sequence (IS50) primers. IS50-PCR and RAPD-PCR analysis divided 51 strains into eight sub clusters that were grouped in three clusters. Cluster I comprised all Pss with four sub clusters from stone fruits, pome fruit and cereal hosts, cluster II contained Psl strains from cucumber with two sub clusters and cluster III contained three strains of P. tolaasii with two sub clusters from mushroom. These results indicated that a combination of IS50-PCR and RAPD-PCR fingerprinting can be used as a high resolution genomic fingerprinting methods for differentiates species of Pseudomonas and pathovars of P. syringae strains.
Robust and Bright Genetically Encoded Fluorescent Markers for Highlighting Structures and Compartments in Mammalian Cells

To increase our understanding of cells, there is a need for specific markers to identify biomolecules, cellular structures and compartments. One type of markers comprises genetically encoded fluorescent probes that are linked with protein domains, peptides and/or signal sequences. These markers are encoded on a plasmid and they allow straightforward, convenient labeling of cultured mammalian cells by introducing the plasmid into the cells. Ideally, the fluorescent marker combines favorable spectroscopic properties (brightness, photostability) with specific labeling of the structure or compartment of interest. Here, we report on our ongoing efforts to generate robust and bright genetically encoded fluorescent markers for highlighting structures and compartments in living cells.
Functional significance of spectrotemporal response functions obtained using magnetoencephalography

The spectrotemporal response function (STRF) model of neural encoding quantitatively associates dynamic auditory neural (output) responses to a spectrogram-like representation of a dynamic (input) stimulus. STRFs were experimentally obtained via whole-head human cortical responses to dynamic auditory stimuli using magnetoencephalography (MEG). The stimuli employed consisted of unpredictable pure tones presented at a range of rates. The predictive power of the estimated STRFs was found to be comparable to those obtained from the cortical single and multiunit activity literature. The STRFs were also qualitatively consistent with those obtained from electrophysiological studies in animal models; in particular their local-field-potential-generated spectral distributions and multiunit-activity-generated temporal distributions. Comparison of these MEG STRFs with others obtained using natural speech and music stimuli reveal a general structure consistent with common baseline auditory processing, including evidence for a transition in low-level neural representations of natural speech by 100 ms, when an appropriately chosen stimulus representation was used. It is also demonstrated that MEG-based STRFs contain information similar to that obtained using classic auditory evoked potential based approaches, but with extended applications to long-duration, non-repeated stimuli. Author summary The spectrotemporal response function (STRF) model of linking dynamic acoustic stimuli to dynamic neural responses is applied to whole-head non-invasive magnetoencephalography (MEG) recordings of the human auditory cortex. MEG STRFs were consistent predictors of neural activity, quantitatively and qualitatively, by comparison to those obtained from animal models using local field potential or multiunit activity as neural responses. Comparison of STRFs using stimuli as diverse as tone clouds, natural speech, and music revealed a common structure consistent with shared baseline auditory processing, when an appropriately chosen stimulus representation was used.
Winter climate affects torpor patterns and roost choice in New Zealand lesser short‐tailed bats

Variation in winter conditions differentially impacts thermoregulation of endotherms, with some species using torpor as an energy-saving strategy during periods of negative energy balance. We evaluated how differences in energy balance due to winter ambient temperatures (Ta), would lead to differing torpor expression and roost choice between populations. Here, we monitored Ta and skin temperatures (Tsk) of New Zealand lesser short-tailed bats (Mystacina tuberculata) using temperature telemetry from an inland population from Pureora, North Island and another from Hauturu/Little Barrier Island (Hauturu), an offshore island. Relative to Pureora, all recorded Ta variables were higher in Hauturu. Hauturu bats used short torpor (<24 h) more frequently (51% of observational days) than their Pureora conspecifics (33%). Furthermore, minimum Tsk of Hauturu bats correlated positively with mean Ta and Hauturu bats were more likely to arouse on nights with warmer sunset Ta. No correlation was found for Pureora bats. Torpor bout duration did not differ between sites. On Hauturu, bats preferred thermally unstable roosts and preferentially roosted inside dead punga/silver fern-trees (Cyathea dealbata). As punga thermal characteristics did not differ from Ta, Hauturu bats may take advantage of warm Ta to reduce rewarming costs. We did not observe differences in any thermoregulatory variables between sexes in Hauturu. Differences in winter Ta may differentially impact populations across a latitudinal gradient. Although bat populations in warmer climates are under less thermoregulatory stress, site and climate specific adaptations appear to be employed that affect roost choice and torpor patterns.
The synthesis of polyhydroxy sterone 2β,3α,5-trihydroxy-5α-androst-6-one and its neuroprotection

Neuroactive steroids exhibit better neuroprotective properties in vitro and in vivo, and will be a potential neuroprotective effect. In this study, polyhydroxy sterone 2β,3α,5-trihydroxy-5α- androst-6-one (YC-10) was designed and synthesized from androst-5-en-3-ol by 6 steps reactions. Its absolute structure was characterized by X-SRD and its structure was characterized by NMR, IR, and MS. Its neuroprotective action was determined by MTT assay with two models of neurotoxicity. The maximum protective effect was at a concentration of 40μM for neurotoxicity induced by glutamate, and showing better cell viability in a dose-dependent manner; Moreover it cloud significantly protect the cerebellar granule neurons against neuronal death mediated by low K + , its effective protective concentration was 50μM.
Coding Complete Genome for the Mogiana Tick Virus, a Jingmenvirus Isolated from Ticks in Brazil

Abstract : Mogiana tick virus (MGTV) is a segmented Jingmenvirus isolated in 2011 from cattle ticks in Brazil. Here, we present a coding complete genome for MGTV isolate MGTV/V4/11, including all four segments. MGTV is evolutionarily related to the Jingmen tick virus isolates SY84 and RC27.The Jingmenviruses are a group of segmented, and likely multicomponent, viruses that are evolutionarily related to the unsegmented viruses of the genus Flavivirus (1). Although the Jingmenvirus group has only recently been recognized, with the first virus descriptions published in 2014 (2, 5), known viruses in this group are diverse, globally distributed and capable of infecting a wide range of animal hosts (1, 2, 46). Here, we report the coding complete genome (i.e. only missing portions of terminal untranslated regions) (7) of MGTV/V4/11 isolated from cattle ticks (Rhipicephalus microplus) collected from Holstein bulls in Ribeiro Preto, state of So Paulo, Brazil (2). MGTV was one of the earliest Jingmenviruses to be reported, and at the time of publication, the segmented nature of the genome was not understood. Therefore, only the two genome segments with detectable sequence homology to flaviviruses were originally reported (2). We revisited the dataset of (Maruyama et al. 2014) and assembled coding complete sequences for all four genome segments.
Study the antioxidant and In vitro Anti-inflammatory activity by membrane stabilization method of Amaranthus gangeticus leaf extract

Since the ancient time nature provides several herbal phyto-chemicals for the beneficial of human. Amaranthus gangeticus of the family amaranthaceae, is such a leafy edible vegetable widely used in eastern zone of India. In the current study, qualitative screening of antioxidant property and membrane stabilization property was checked in aqueous and alcoholic extract of Amaranthus gangeticus. Three different concentration 50, 75, 100 microgram/ml ethanolic and aqueous extract was taken for membrane stabilization method using 50 microgram/ml sodium diclofenec as a reference drug and only aqueous extract of the same concentration was used in total antioxdidant determination method using ascorbic acid as reference. The study revealed that Amaranthus gangeticus have several significant membrane stabilization and antioxidant property. Presence of delicate chemical balance of the whole plant, or mixtures of plants, not one particular active ingredient, may help to scavenge the reactive oxygen, potent membrane destabilizing agent in human. So, in future it could be possible to develop a new phyto derived drug for membrane destabilization related disease in human.
Study of Rigor Mortis and Factors Affecting its Development for Determination of Postmortem Interval

Rigor mortis, a physico-chemical change that occurs within muscles after death, is one of the significant component in determination of post-mortem interval in warm countries like India, though its development is affected by various factors. This prospective study was carried out to evaluate and interpret variations in development of rigor mortis with respect to cause of death and media from which the body was brought and to determine time and sequence of its development in various muscle groups and joints. It was observed that commencement and full development of rigor mortis is earlier in deaths due to infectious conditions, regional injuries, head injury and deaths due to poisoning as compared to that of deaths due to hanging. Rigor commenced late and developed fully late in water media as compared to air media. It appeared first in the eyelid, then in the face, followed by neck, upper limbs, trunk, lower limbs and lastly the fingers and toes. It disappeared in the same order as it appeared.
Molecular and phylogenetic identification of unique isolates of hammerhead viroid-like RNA from ‘Pacific Gala’ apple (Malus domestica) in Canada

Abstract Ten isolates of apple hammerhead viroid-like RNA (AHVd RNA) were detected by next-generation sequencing (NGS) and/or by RT-PCR analysis of apple (Malus domestica) ‘Pacific Gala’ (PG) from Canada. All consisted of 433 nucleotides in size, and their circular structure and sequence were supported by reverse transcription amplification with two separate pairs of abutted primers, cloning and sequencing. Two regions were defined for the computer-predicted secondary structure of AHVd RNA-PG isolates – a hammerhead region (HHR) and a loop-rich region (LRR). The HHR contained the core and flanking nucleotides typical of natural hammerhead ribozymes. The secondary structure associated with the LRR was distinct from that predicted for the corresponding region of AHVd RNA isolates previously described in ‘Fuji’ apple in China. However, both structures share conserved stem-loops in the LRR, identified as S1, S2, S3 and S4.