Miracle-dz/UniFAR-FTUs huggingface dataset:
Age and growth of Alburnus mossulensis (Cyprinidae) in Bibi-Sayyedan River of Isfahan Province

Population structure and growth of Mossul bleak, Alburnus mossulensis, a native species of cyprinids in Bibi-Sayyedan River of Semirom, Isfahan, were investigated by monthly sampling during December 2010 to December 2011. For this purpose, 543 speciments (353 females, 159 males and 31 immature) were caught using seine net (5 mm mesh size) and a cast net. Age groups of males and females were 0 + to 5 + . The most frequent age group was 2 + in both sexes. The sex ratio was 1M:2.2F (p<0.01). Males outnumbered the females in younger age classes and females outnumbered the males in older age groups. The highest condition factor was observed in April for males and in March for females. The mean condition factor (CF) was not significantly different between the sexes among all fish during different months (p>0.05). The largest female was 16.80 cm in total length and 49.12 g in weight, while the largest male was 14.10 cm in total length and 28.19 g in body weight. The length-weight relationship was calculated as W = 0.0169L 3.0355 (r 2 =0.95) for males, W=0.0061L 3.1751 (r 2 =0.98) for females and W=0.0066L 3.139 (r 2 =0.99) for all fish (males, females and immature). Regression coefficient (b) based on Pauly test, was significantly different from 3 in females, but not in males (p<0.05), indicating an isometric growth pattern in males and a positive allometric growth pattern in females and all fish.
Cerebellar nuclei neurons dictate cortical growth through developmental scaling of presynaptic Purkinje cells

Efficient function of neural systems requires the production of specific cell types in the correct proportions. Here we report that reduction of the earliest born neurons of the cerebellum, excitatory cerebellar nuclei neurons (eCN), results in a subsequent reduction in growth of the cerebellar cortex due to an accompanying loss of their presynaptic target Purkinje cells. Conditional knockout of the homeobox genes En1 and En2 (En1/2) in the rhombic lip-derived eCN and granule cell precursors leads to embryonic loss of a subset of medial eCN and cell non-autonomous and location specific loss of Purkinje cells, with subsequent proportional scaling down of cortex growth. We propose that subsets of eCN dictate the survival of their specific Purkinje cell partners, and in turn sonic hedgehog secreted by Purkinje cells scales the expansion of granule cells and interneurons to produce functional local circuits and the proper folded morphology of the cerebellum.
The feasibility of using passive injectable transponders in field operations for individual identification of sheep in Italy

Abstract This trial evaluates the feasibility of using passive injectable transponders (PITs) in field operations by testing identification procedures on 185 one-year-old Biellese ewes reared under nomadic farming conditions. Commercial PITs of 3.85 ± 0.05 mm × 31.2 mm were used at two application sites, the armpit and the retro-auricular region. The two application sites were compared taking into account the ease of injection, animal reaction, injection duration, inflammatory response, PIT readability at up to 12 months post-injection and PIT recovery at the slaughterhouse. The injection site influenced the reaction of the animal and the ease and duration of the injection, but it did not affect the palpation and the reading findings during the rearing period. The injection site also influenced the PIT retrieval at the slaughterhouse depending on the operator who recovered the PIT. The readability values observed at the end of the observation period for both injection sites (83% in the retro-auricular region and 79% in the armpit region) were too low to be suitable for long-term animal identification. In addition, the failed retrieval of PITs at slaughter, determined the destruction of 40 (22%) carcases to avoid any risks in the food chain. These findings suggest that the limited use of PITs is indicated when other methods of electronic identification cannot be employed, while a wider application of the device tested in the present study is not recommended in farming practices.
Identification of methylation and hydroxymethylation haplotype blocks as distal regulatory elements aids in deconvolution of heterogeneous brain tissues

5-Hydroxymethylcytosine (5hmC) is an oxidation product of 5-methylcytosine (5mC), and adjacent CpG sites in the mammalian genome can be co-methylated and co-hydroxymethylated due to the processivity of DNMT and TET enzymes. We applied TAB-seq and oxBS-seq to selectively detect 5hmC and 5mC, respectively, at base resolution in the mouse cortex, olfactory bulb and cerebellum tissues. We found that majority of the called 5hmC CpG sites frequently had 5mC modification simultaneously and enriched in gene body regions of neuron development related genes in brain tissues. These results supported a prominent role of oxidizing 5mC to 5hmC as new epigenetic mark. Strikingly, by a systematic search of regions that show highly coordinated methylation and hydroxymethylation (MHBs and hMHBs), we found that MHBs significantly overlapped with hMHBs in gene body regions which further supported that oxidized 5mC to 5hmC co-ordinately in a subset of cells within heterogeneous brain tissues. Consistently, using a metric called methylation haplotype load, we defined a subset of 1,361 tissue-specific MHBs and 3,818 shared MHBs which were predominantly regulatory elements, and aids in deconvolution of heterogeneous brain tissues. Our results provide new insights into the role of co-ordinately oxidized 5mC to 5hmC as distal regulatory elements may involve in regulating tissue identity.
Postmortem Metabolic, Physicochemical, and Lipid Composition Changes in Litopenaeus vannamei in Response to Harvest Procedures

ABSTRACT Ante-mortem stress is recognized as one of the factors that could reduce shelf life in fish, although this topic has been scarcely addressed in crustaceans, particularly in cultivated penaeid shrimp where common harvest practices involves stressful conditions such as chasing, emersion, and confinement. This study analyzes indices of freshness in shrimp in response to such practices before storage in ice for six days. During ice storage, several indicators follow the typical postmortem pattern, although most of them (hypoxanthine, change in pH, and color) did not reach critical levels at day 6. Adenosine-5’-triphosphate (ATP) and degradation products (adenosine monophosphate, AMP, and inosine monophosphate, IMP), as well as several indicators of freshness (pH, expressible water, hardness, color, and the overall fatty acid composition) were not significantly affected by harvest. Other variables such as lower springiness, higher hypoxanthine, lipid hydroperoxides, and 20:4n-6/20:5n-3 ratio were observed in shrimp subjected to common harvest practices. However, under the current conditions of harvesting, these effects were marginal and probably do not substantially affect meat quality for human consumption, but care should be taken at higher environmental temperatures (e.g. harvest in summer) and for a duration of ice-storage over 6 days.
Delayed Foliar Symptoms Caused by Verticillium dahliae as an Alternative Resistance Trait in Iceberg Lettuce

Verticillium wilt caused by Verticillium dahliae Kleb. is an economically damaging disease of iceberg lettuce on the Central Coast of California. Foliar wilting symptoms that manifest near or at peak market maturity (MM) lead to collapse of the head, making it unmarketable. Complete resistance to race 1 of the pathogen is known, but adequate levels of resistance are not available against race 2. Additional mechanisms or traits that reduce foliar symptoms (FS) are needed to lessen economic losses from this disease. Since the disease affects leaves, the harvested product, identiﬁcation of iceberg cultivars that delay the onset of FS past peak MM could reduce yield loss from the disease. The goal of this research was to identify iceberg lettuce germplasm with delayed onset of FS. Diverse iceberg cultivars were evaluated in replicated ﬁeld experiments for MM, FS severity, and adaptation. A few winter-adapted cultivars showed fewer FS past MM and seem to be promising candidates for breeding. These cultivars are not adapted to the California Central Coast where the disease currently predominates. Further studies will determine the usefulness of this trait for breeding improved cultivars for use in V. dahliae –infested ﬁelds. Developing
First Report of a New, Unnamed Lesion Nematode Pratylenchus sp. Infecting Soybean in North Dakota

First Report of a New, Unnamed Lesion Nematode Pratylenchus sp. Infecting Soybean in North Dakota | Plant Disease http://apsjournals.apsnet. org/doi/10.1094/PDIS-12-16-1749-PDN[7/13/2017 11:02:02 AM] 17.7 to 25.6), c’ (2.3, 2.2 to 2.4), spicule (17.5, 15.0 to 20.0), and gubernaculum (5.8, 4.5 to 7.5). DNA was extracted from single nematodes (n = 12) collected from soil and roots. D2-D3 of 28S rRNA (Subbotin et al. 2008) and ITS of rDNA (Yan and Smiley 2010) were amplified and sequenced. The ITS rDNA (KY200666, 981 bp) shared 95% sequence identity with P. alleni and low identity (≤87%) with other Pratylenchus spp. The D2-D3 (KY200665, 766 bp) had the highest identity of 96% with P. scribneri and 95% identity with P. hexincisus. No sequence of P. gibbicaudatus or P. flakkensis is available in GenBank. This species is very close to P. alleni but differs in having a slightly longer stylet, variations in tail shape, truncate to bluntly or broadly rounded tail with an annulated to occasionally smooth tail terminus, 4 to 6 lines in lateral field and 2 to 3 head annules. It is closely related to P. hexincisus, P. gibbicaudatus, and P. flakkensis but differs from them by one or more other characters: shape of head, number of head annules, tail shape, and V%. To our knowledge, this North Dakota Pratylenchus sp. population represents a new species of lesion nematode able to parasitize soybean.
Using SCAR molecular marker to detect resistance genes to Fusarium oxysporum f. sp. ciceris in chickpea cultivars and lines

The occurrence of fusarium wilt disease is reported from 32 countries around the world. It is estimated that this disease results in 10-90% crop yield loss annually. It is difficult to control this disease because of the ability of the pathogen to survive in soil for several years, even without the host. The most effective method for controlling fusarium wilt is the cultivation of resistant chickpea cultivars. In this experiment, SCAR molecular marker was used to detect chickpea genotypes resistant to the disease. The DNA of 42 chickpea genotypes was extracted by CTAB method. After that, polymerase chain reaction was conducted by CS-27 and OPM-20 molecular markers. Results showed that 41 genotypes out of the 42 tested genotypes were sensitive to all five races of the pathogen. The only resistant genotype was Flip 06-152c which was resistant to the five races. Finally, the pathogenesis test confirms all results obtained in the genetic studies.
Mass spectrometry approaches in proteomic and metabolomic studies

With the development of the systems biology concept proteomic and metabolomic studies have become even more attractive. The advancement in separation methods of proteins and metabolites, and particularly the pro- gress that has been made in the field of mass spectrometry significantly facilitated high-throughput analyses and substantially increased both quality and quantity of the data. In this short review we discuss some aspects of the analytical strategies used in proteome and metabolome research in which mass spectrometry plays a crucial role.
Two SecA/SecY Systems with Distinct Roles in the Ecological Adaptations of Bacteria

Bacteria interact with their environment through the secretion of a specific set of proteins (known as secretome) through various secretion systems. Molecular modifications of these secretion systems may lead to the emergence of new bacterial-environment interactions, although this remains unexplored. In this study we investigate the possible link between molecular and functional changes in secretion proteins and the ecological diversity of bacteria. We studied functional modifications in secretion proteins by identifying events of functional evolutionary divergence—that is, changes at the molecular level that have driven changes of protein’s function. We present data supporting that these functional diversifications occurred in essential secretion proteins in bacteria. In particular, functional divergence of the two most important secretion proteins SecA and SecY in pathogenic bacteria suggests that molecular changes at these proteins are responsible for their adaptations to the host. Functional divergence has mainly occurred at protein domains involved in ATP hydrolysis in SecA and membrane pore formation in SecY. This divergence is stronger in pathogenic bacteria for protein copies resulting from the duplication of SecA/SecY, known as SecA2/SecY2. In concert with these results, we find that the secretome of bacteria with the strongest functional divergence is enriched for proteins specialized in the interaction with specific environments. We unravel evolutionary signatures that link mutations at secretion proteins to the ecological diversification of bacteria.
Arbuscular mycorrhizal fungi and phosphate fertilization on star fruit tree seedlings

The success of star fruit cultivation deployment begins with the use of good quality seedlings Thus the inoculation of mycorrhizal fungi in culture seedling can be an alternative, since it was found success in both growth as nutritional aspect fruit species. In this sense, the aim of this study was to evaluate the effects of arbuscular mycorrhizal fungi (AMFs) on growth and mineral composition of star fruit seedlings, cultivated under different doses of phosphorus (P). The experiment was conducted in a greenhouse and the experimental design used was randomized blocks in a 3 x 4 factorial scheme, with three microbiological treatments (without inoculation, Rhizofagus clarum, Glomus etunicatum) and four doses of P (0, 50, 100 and 200 mg kg-1 soil) with four replications. Plants were harvested four months after sowing for biometric and nutritional analysis. In the soil without phosphate fertilization, R. clarum, provided increments of 49% in height, 99% in dry matter production and 86, 129 and 108% in the contents of N, K, and Ca, respectively, in relation to the control. Regardless of phosphate fertilization, the content of P, Mg, and S in the dry matter weight was 19.2, 17.6 and 23.6% higher in the treatment inoculated with R. clarum, in relation to the control. Mycorrhizal dependence of star fruit tree varied according to fungus species and the P dose used, being greater when the fungus R. clarum was used in absence of P.
Assessing tACS-induced phosphene perception using closed-loop Bayesian optimization

Transcranial alternating current stimulation (tACS) can evoke illusory flash-like visual percepts known as phosphenes. The perception of phosphenes represents a major experimental challenge when studying tACS-induced effects on cognitive performance. Besides growing concerns that retinal phosphenes themselves could potentially have neuromodulatory effects, the perception of phosphenes may also modify the alertness of participants. Past research has shown that stimulation intensity, frequency and electrode montage affect phosphene perception. However, to date, the effect of an additional tACS parameter on phosphene perception has been completely overlooked: the relative phase difference between stimulation electrodes. This is a crucial and timely topic given the confounding nature of phosphene perception and the increasing number of studies reporting changes in cognitive function following tACS phase manipulations. However, studying phosphene perception for different frequencies and phases simultaneously is not tractable using standard approaches, as the physiologically plausible range of parameters results in a combinatorial explosion of experimental conditions, yielding impracticable experiment durations. To overcome this limitation, here we applied a Bayesian optimization approach to efficiently sample an exhaustive tACS parameter space. Moreover, unlike conventional methodology, which involves subjects judging the perceived phosphene intensity on a rating scale, our study leveraged the strength of human perception by having the optimization driven based on a subject’s relative judgement. Applying Bayesian optimization for two different montages, we found that phosphene perception was affected by differences in the relative phase between cortical electrodes. The results were replicated in a second study involving new participants and validated using computational modelling. In summary, our results have important implications for the experimental design and conclusions drawn from future tACS studies investigating the effects of phase on cognition.
Invasion of the Hawaiian Islands by a parasite infecting imperiled stream fishes

Points of origin and pathways of spread are often poorly understood for introduced parasites that drive disease emergence in imperiled native species. Co-introduction of parasites with non-native hosts is of particular concern in remote areas like the Hawaiian Islands, where the introduced nematode Camallanus cotti has become the most prevalent parasite of at-risk native stream fishes. In this study, we evaluated the prevailing hypothesis that C. cotti entered the Hawaiian Islands with poeciliid fishes from the Americas, and spread by translocation of poeciliid hosts across the archipelago for mosquito control. We also considered the alternative hypothesis of multiple independent co-introductions with host fishes originating from Asia. We inferred conduits of introduction and spread of C. cotti across the archipelago from geographic patterns of mtDNA sequence variation and allelic variation across 11 newly developed microsatellite markers. The distribution of haplotypes suggests that C. cotti spread across the archipelago following an initial introduction on O`ahu. Approximate Bayesian Computation modeling and allelic variation also indicate that O`ahu is the most likely location of introduction, from which C. cotti dispersed to Maui followed by spread to the other islands in the archipelago. Evidence of significant genetic structure across islands indicates that contemporary dispersal is limited. Our findings parallel historical records of non-native poeciliid introductions and suggest that remediating invasion hotspots could reduce the risk of infection in native stream fishes, which illustrates how inferences on parasite co-introductions can improve conservation efforts by guiding responses to emerging infectious disease in species of concern.
Cytotoxic T Cells Class I- Dependent Lymphocyte Killing by NLRC5 Deficiency Selectively Impairs MHC

Nucleotide-binding oligomerization domain-like receptors (NLRs) are intracellular proteins involved in innate-driven inﬂammatory responses. The function of the family member NLR caspase recruitment domain containing protein 5 (NLRC5) remains a matter of debate, particularly with respect to NF- k B activation, type I IFN, and MHC I expression. To address the role of NLRC5, we generated Nlrc5 -deﬁcient mice ( Nlrc5 D / D ). In this article we show that these animals exhibit slightly decreased CD8 + T cell percentages, a phenotype compatible with deregulated MHC I expression. Of interest, NLRC5 ablation only mildly affected MHC I expression on APCs and, accordingly, Nlrc5 D / D macrophages efﬁciently primed CD8 + T cells. In contrast, NLRC5 deﬁciency dramatically impaired basal expression of MHC I in T, NKT, and NK lymphocytes. NLRC5 was sufﬁcient to induce MHC I expression in a human lymphoid cell line, requiring both caspase recruitment and LRR domains. Moreover, endogenous NLRC5 localized to the nucleus and occupied the proximal promoter region of H-2 genes. Consistent with downregulated MHC I expression, the elimination of Nlrc5 D / D lymphocytes by cytotoxic T cells was markedly reduced and, in addition, we observed low NLRC5 expression in several murine and human lymphoid-derived tumor cell lines. Hence, loss of NLRC5 expression represents an advantage for evading CD8 + T cell-mediated elimination by downmodulation of MHC I levels—a mechanism that may be exploited by transformed cells. Our data show that NLRC5 acts as a key transcriptional regulator of MHC I in lymphocytes and support an essential role for NLRs in directing not only innate but also adaptive immune responses. Journal of Immunology , 2012, 188: 000–000. cDNA). pCR3 (Invitrogen)
Effects of Dietary Supplementation of Fermented Rice Bran (FRB) or Fermented Broken Rice (FBR) on Laying Performance, Egg Quality, Blood Parameter, and Cholesterol in Egg Yolk of Hy-Line Brown Laying Hens

This experiment was aimed at investigating the effects of dietary supplementation with fermented rice bran (FRB) or fermented broken rice (FBR) on egg-laying performance, egg quality, blood parameters, and cholesterol level in egg yolk of Hy-Line Brown egg-laying hens. Altogether, 144 Hy-Line Brown egg-laying hens (32-week-old) were randomly allocated to one of 4 dietary treatment groups, with 4 replicates per treatment. Of them, 3 treatments diets were prepared by supplementing the basal diet with 0.1% probiotics (PRO), 1% fermented rice bran (FRB), or 1% fermented broken rice (FBR) at the expense of corn. Hen-day egg production was higher (P<0.05) in PRO and FRB treatment groups than in the basal treatment groups. However, feed intake, egg weight, egg mass, and feed conversion ratio did not differ among the treatment groups. Additionally, supplementation with FRB or FBR did not affect eggshell strength, eggshell thickness, egg yolk color, and Haugh unit during the feeding trial. There was no significant difference in leukocyte count. Total cholesterol level was lower (P<0.05) in the FRB treatment group than in the basal treatment groups. Asparate aminotransferase, alanine transferase, glucose, and albumin levels were unaffected by dietary supplementation with FRB or FBR. Egg yolk cholesterol level was lower (P<0.05) in the FRB and FBR treatment groups than in the basal treatment groups. In conclusion, dietary supplementation with FRB or FBR improved egg-laying performance, and reduced the levels of total serum cholesterol and cholesterol in egg yolk of Hy-Line Brown egg-laying hens. (
Evaluating the Survival of Translocated Adult and Captive-reared, Juvenile Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis)

Abstract Recent amphibian declines have been addressed with a variety of conservation tools, including translocations. It is important to evaluate the success of ongoing amphibian conservation programs. In Indiana, USA, because of the documented decline of the Eastern Hellbender (Cryptobranchus a. alleganiensis) population, translocations of wild-captured and captive-reared individuals have been implemented as a management strategy. Our study was developed to estimate the annual survivorship of translocated versus resident Eastern Hellbenders and to compare the efficacy of translocating wild adults and captive-reared juveniles. Adult residents, and translocated adult and juvenile subjects, were implanted with radio transmitters in a staggered entry design and tracked for up to 2 yr. A Cox proportional hazards model indicated that captive-reared, juvenile hellbenders had lower annual survival rates than did either resident or translocated adults. The relatively high survival rates of all groups indicated the potential utility of both types of translocations as a tool to increase local densities, although there might be room for improvement of the survival rates for captive-reared juveniles through either increased rearing periods or environmental conditioning prior to release.