Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

Differences in tRNA expression have been implicated in a remarkable number of biological processes. There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of high-throughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in Arabidopsis thaliana, which exhibited many anciently conserved similarities with humans but also positions that appear to be “hot spots” for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.
Awareness of Breast Cancer and Breast Self Examination among women in Engugu Urban, Eastern Nigeria

Breast Cancer is the most predominant malignancy with the highest mortality rate in women. Regular periodic Breast Self-Examination (BSE) has been found to significantly reduce mobidity and mortality due to this disease. Out of a total of 476 women aged between 15 and 54 years in Enugu who were interviewed about their knowledge of breast cancer and practice of BSE, it was found that although 92% of the women knew of the disease, only 29% were aware that it commonly presents as a lump in the breast. 88% of all the women knew about BSE but only 62% out of these practice it. Out of those who practice Breast Self Examination, only 34% do it monthly or more often. The practice of BSE did not differ significantly among the various occupational groups (P> 0.05).
Disarticulation-Associated Femoral Head Separation in Clinically Normal Broilers: Histologic Documentation of Underlying and Predisposing Cartilage Abnormalities

SUMMARY. Routine and quantitative histologic studies on femoral head separation (FHS) associated with coxofemoral joint disarticulation at necropsy were conducted on 125 femoral heads collected from 21- to 50-day-old clinically normal broilers. The study compared groups demonstrating grossly detached femoral heads (DFHs) with those having attached femoral heads (AFHs). Marked microscopic lesions compatible with osteochondrosis (OCD) consistently occurred along the separation surface in the DFH population. The histologic changes consisted of cartilage degeneration and necrosis sometimes forming small clefts or microfractures. Hemorrhage and less frequent inflammatory cells were often present along the separation surfaces. Small foci of OCD in the femur occurred in the AFH group with lesser frequency and severity. The histologic changes were mainly found within the proximal proliferative zone of the physis near the epiphyseal junction. Histomorphometry disclosed significant quantitative reductions in chondrocyte density with increased pyknosis occurring adjacent to the separation site and to a lesser extent in deeper regions of the growth plate for the DFH compared with AFH. Measurements made along the separation surface of the percentage length occupied by osteochondrotic defects and actual separated cartilage disclosed significant differences between evaluation groups. However, determinations of vascular canal areas present within two or more regions of the growth plate revealed a slight and significant increased area for DFH compared with AFH. Severity scores for the occurrence of microthrombi within the growth plate showed no difference between the groups. The pathogenesis of FHS in broilers is related to defective cartilage production or degeneration resulting in increased fragility. This contrasts with the proposed pathogenesis of OCD in mammals, which involves ischemic necrosis due to underlying vascular defects. The results for the FHS-disarticulation model also differ from those reported for glucorticoid-induced femoral head necrosis in broilers. The FHS-associated lesions occurred without histologic evidence of bacterial chondritis or osteomyelitis.
Structural controllability predicts functional patterns and neuromodulatory benefits associated with working memory

The brain is an inherently dynamic system, and much work has focused on the ability to modify neural activity through both local perturbations and changes in the function of global network ensembles. Network controllability is a recent concept in network science that purports to predict the influence of individual cortical sites on global network states and state changes, thereby creating a unifying account of local influences on global brain dynamics. Here, we present an integrated set of multimodal brain–behavior relationships, acquired from functional magnetic resonance imaging during a transcranial magnetic stimulation intervention, that demonstrate how network controllability influences network function, as well as behavior. This work helps to outline a clear technique for integrating structural network topology and functional activity to predict the influence of a potential stimulation target on subsequent behaviors and prescribes next steps towards predicting neuromodulatory and behavioral responses after brain stimulation. Highlights - This study tested the strength of inferences given by network controllability using fMRI and rTMS - Controllability correlates with the modulation of a functional network associated with increasing working memory demand - Controllability is also correlated with the memory improvement from applied rTMS - These findings link network control theory with physiology and behavior. In brief Beynel et al. show that the benefits of functionally targeted brain stimulation on working memory performance can be predicted by network control properties at the stimulated site. Structural controllability and functional activity independently predict this cognitive benefit.
Repurposing the Streptococcus mutans CRISPR-Cas9 System to Understand Essential Gene Function

A recent genome-wide screen identified ∼300 essential or growth-supporting genes in the dental caries pathogen Streptococcus mutans. To be able to study these genes, we built a CRISPR interference tool around the Cas9 nuclease (Cas9Smu) encoded in the S. mutans UA159 genome. Using a xylose-inducible dead Cas9Smu with a constitutively active single-guide RNA (sgRNA), we observed titratable repression of GFP fluorescence that compared favorably to that of Streptococcus pyogenes dCas9 (Cas9Spy). We then investigated sgRNA specificity and proto-spacer adjacent motif (PAM) requirements. Interference by sgRNAs did not occur with double or triple base-pair mutations, or if single base-pair mutations were in the 3’ end of the sgRNA. Bioinformatic analysis of >450 S. mutans genomes allied with in vivo assays revealed a similar PAM recognition sequence as the Cas9Spy. Next, we created a comprehensive library of sgRNA plasmids that were directed at essential and growth-supporting genes. We discovered growth defects for 77% of the CRISPRi strains expressing sgRNAs. Phenotypes of CRISPRi strains, across several biological pathways, were assessed using fluorescence microscopy. A variety of cell structure anomalies were observed, including segregational instability of the chromosome, enlarged cells, and ovococci-to-rod shape transitions. CRISPRi was also employed to observe how silencing of cell wall glycopolysaccharide biosynthesis (rhamnose-glucose polysaccharide, RGP) affected both cell division and pathogenesis in a wax worm model. The CRISPRi tool and sgRNA library are valuable resources for characterizing essential genes in S. mutans, some of which could prove to be promising therapeutic targets.
A sex difference in the composition of the rodent postsynaptic density

SynGAP is a postsynaptic density (PSD) protein that binds to PDZ domains of the scaffold protein PSD-95. We previously reported that heterozygous deletion of synGAP in mice is correlated with increased steady-state levels of other key PSD proteins that bind PSD-95, although the level of PSD-95 remains constant (Walkup et al., 2016). For example, the ratio to PSD-95 of Transmembrane AMPA-Receptor-associated Proteins (TARPs), which mediate binding of AMPA-type glutamate receptors to PSD-95, was increased in young synGAP+/- mice. Here we show that a highly significant increase in TARP in the PSDs of young synGAP+/- rodents is present only in females and not in males. The data reveal a sex difference in the adaptation of the PSD scaffold to synGAP heterozygosity.
Size distribution and abundance of juvenile hilsa, Tenualosa ilisha in the major rivers of Bangladesh.

The study was conducted in the six major rivers (Padma, Meghna, Jamuna, Brahmaputra Surma and Andermanik) of Bangladesh to evaluate the abundance and distribution of juvenile hilsa, Tenualosa ilisha from February to April 2017. Fish samples are collected by using monofilament gill net. The total length and depth of the gill net was 100 m and 4.5 m respectively. The mesh size of first 25 m net was 2.5 cm; second 25 m was 3.5 cm; third 25 m was 4.5 cm and the last 25 m was 5.5 cm. Daytime sampling was done at all the sites on a monthly basis and the Catch per Unit Effort (CPUE), total length (cm) and weight (g) were recorded and analyzed. The result showed that the highest CPUE of juvenile T. ilisha was observed at Ramgati station which was 72 individuals/100 m gill net/30 minutes. The second and third highest CPUE was found in Nalchira (58 individuals/100 m net/30 min) and Charking (46 individuals/100m net/30 min), those stations are located in lower Meghna region. There was a significance variation (P<0.05) of CPUE among the 18 stations. It is clear that the high abundance of juvenile T. ilisha in the lower Meghna River while the low abundance in upper part of the rivers. The abundance of juvenile T. ilisha was the highest in March (19 individuals/100 m net/30 min) and the lowest was in April (14 individuals/100 m net/30 min), while there was no significant difference among the months. The study indicated that T. ilisha juvenile are distributed all over the months from lower to upper of the rivers. The average length of juvenile in February, March and April was 9.18±0.10 cm, 15.94±0.17 cm and 22.11±0.18 cm respectively. It was also observed that the average weight of juveniles in February was 9.88±0.25 g while it was 41.16±1.48 g in March and 100.94±1.29 g in April respectively. During the study period there no T. ilisha juveniles was found in the upper areas of Padma, Jamuna and Surma rivers. It may be concluded that major nursery grounds are between Chandpur and Hatya of Meghna River.
Distribution of Hermann’s tortoise across Serbia with implications for conservation

Hermann? s tortoise (Testudo hermanni) is among the conservation priorities in the European Union. Consequently, it is included in Annexes II and IV of the EU Habitats Directive, Annex II of the Bern Convention, and Annex II of the CITES Convention. Hermann? s tortoise conservation programs compile insights on the threats affecting population viability, along with factors shaping the species? distribution. Serbian populations of the eastern subspecies (Testudo hermanni boettgeri) seem numerous and therefore prosperous, but recent population viability analyses revealed that they are susceptible to rapid demographic changes and/or habitat destruction. This implies the need for effective population monitoring and protection, as well as mapping and preservation of suitable habitats. In this paper we summarized current knowledge about the geographic distribution of Hermann? s tortoise in Serbia and modeled its ecological niche. Our results corroborate and uphold the known species? distribution in Serbia. Most suitable habitats are situated in the lowland areas of eastern, central and southern Serbia, under semi-open habitats, such as pastures and shrubs, broadleaf forests, and all successional stages in between. The results provided in this paper should be considered in the selection and shaping of NATURA 2000 sites in Serbia. [Projects of the Serbian Ministry of Education, Science and Technological Development, Grant no. 173043 and Grant no. 173025]
Functional diversity in fish assemblages of the Tropical Eastern Pacific Ocean: A review of two decades of progress in the functional diversity approach

Background . One of the most relevant topics in ecology and evolution is understanding the relationship between biological and functional diversity at the ecosystem level; both important in the evolutionary processes and the structuring of complex communities. Goals. In this essay, the explanatory hypotheses focused on global patterns of the distribution of species are described along with selected hypotheses relating species richness/biodiversity to ecosystem function, and the differentiation of the terms guild and functional group are discussed. Methods. Both biodiversity and functional diversity are key in the evolutionary processes and the structuring of complex communities and thus examples of functional equivalence of convergent evolution derivatives are presented in terms of the form and ecological habits of fishes of the Tropical Eastern Pacific Ocean. Finally, the importance of redundancy in ecosystem functioning is examined as well as the impact of environmental disturbances on ecosystem function. Results . In general, systems with low species richness and redundancy within functional groups are more vulnerable to disturbances. However, despite the extensive effort to understand the relationship between species richness/biodiversity and ecosystem functioning, there is no consensus on the effect of species loss on the functioning of the ecosystem. Some hypothesize that each species is unique and plays a unique role in the ecosystem whereas alternate hypotheses indicate that species overlap in function supporting sustainability at the ecosystem level, such that the removal of one species function may be replaced by another. Conclusions . The most widely accepted concept is that a greater number of species increases the efficiency in the use of resources and also provides resilience against environmental changes or impacts through functional redundancy.
12-oxophytodienoic acid reductase 3 (OPR3) functions as NADPH-dependent α,β-ketoalkene reductase in detoxification and monodehydroascorbate reductase in redox homeostasis

Arabidopsis (Arabidopsis thaliana) 12-oxophytodienoic acid reductase isoform 3 (OPR3) is involved in the synthesis of jasmonic acid by reducing the α,β-unsaturated double bond of the cyclopentenone moiety in 12-oxo-phytodienoic acid. Recent research revealed that jasmonic acid synthesis is not strictly dependent on the peroxisomal OPR3. In addition, OPR3 is able to reduce trinitrotoluene suggesting that the old yellow enzyme homologue OPR3 has additional functions. Here we demonstrate that OPR3 catalyzes the reduction of a wide spectrum of electrophilic species that share a reactivity towards the major redox buffers glutathione (GSH) and ascorbate (ASC). Furthermore, we demonstrate that OPDA reacts with ascorbate to form an ASC-OPDA adduct, but in addition OPR3 has the ability to regenerate ASC from monodehydroascorbate (MDHA). The presented data characterize OPR3 as a bifunctional enzyme with NADPH-dependent α,β-ketoalkene double bond reductase and monodehydroascorbate reductase activities (MDHAR). opr3 mutants exhibited a slightly less reduced ASC pool in leaves in line with the MDHAR activity of OPR3 in vitro. These functions link redox homeostasis as mediated by ASC and GSH with OPR3 activity and metabolism of reactive electrophilic species (RES).
THE EFFECTS OF VIBRATION, PNF AND MIXTURE TRAINING ON FLEXIBILITY OF THE HAMSTRING MUSCLES

Introduction: The present study was conducted to investigate the effect of three stretching training methods (vibration, proprioceptive neuromuscular facilitation, combined) on the flexibility of hamstring muscles in non-athlete male students. Material and Methods: We selected 30 male non-athlete students through random goal-oriented sampling and randomized them to three equal groups of vibration, proprioceptive neuromuscular facilitation (PNF) and combined stretching. The flexibility of hamstring muscles was measured using passive straight leg raising. The three groups then underwent training for 4 weeks; subsequently, all participants were evaluated using active knee extension. Results: The results of statistical tests indicated that flexibility improved significantly in all groups after training (p=0.001). The vibration and PNF training groups were not significantly different in terms of hamstring flexibility (p>0.05); nevertheless, the combined group was significantly superior in flexibility compared to the other two groups (p=0.000). Conclusion: Although each of the PNF and vibration methods alone help improve flexibility, the findings of this study suggest that optimal flexibility is achieved with a combination of these two methods. Thus, we recommend the combined training method to athletes who require very high flexibility.
Tooth replacement in a specimen of Tyrannosaurus rex (Dinosauria, Theropoda) from the Hell Creek Formation (Maastrichtian), Montana

ABSTRACT A well-preserved skull of Tyrannosaurus rex from the Late Cretaceous (Maastrichtian) Hell Creek Formation of Montana is used to document its tooth replacement with the help of high-resolution medical CT scanning. A pattern of retaining only one single replacement tooth before replacing the functional tooth is reconstructed for most alveoli of the jaws, with exception of the second alveolus of the left maxilla, and the fourth alveolus of the right dentary, where another, second replacement tooth can be seen. The youngest replacement teeth have only a thin layer of enamel around the tooth crown, the larger replacement teeth have thicker enamel, fortified at the apex as in the functional teeth. The Zahnreihen approach allows to reconstruct a z-spacing of 2 in the upper jaws, whereas the right dentary displays a z-spacing of 1 in the rostral and distal third of the tooth row and a z-spacing of 2 in its medial part. In MB.R. 91216, teeth of the upper jaws and the medial part of the dentary were probably replaced in a regular alternating pattern between odd and even teeth, whereas the mesial and distal teeth of the dentary were replaced simultaneously.
Document Title: Police Intervention and the Repeat of Domestic Assault

We use the National Crime Victimization Survey to examine whether domestic violence is less likely to be repeated if it is reported to the police and if the offender is arrested. Our longitudinal analyses suggest that reporting has a fairly strong deterrent effect, whereas the effect of arrest is small and statistically insignificant. We find no support for the hypothesis that offenders retaliate when victims (rather than third parties) call the police or when victims sign complaints. We also find no evidence that the effects of reporting or arrest depend on the seriousness of the offense, a history of violence by the offender or sociodemographic characteristics. Our results suggest that the best policies for deterrence will be those that encourage victims and third parties to report violence by intimate partners to the police.
Quantitative Proteomic and Genetic Analyses of the Schizophrenia Susceptibility Factor Dysbindin Identify Novel Roles of the BLOC-1 Complex

The Biogenesis of Lysosome-Related Organelles Complex 1 (BLOC-1) is a protein complex containing the schizophrenia susceptibility factor dysbindin, which is encoded by the gene DTNBP1. However, mechanisms engaged by dysbindin defining schizophrenia susceptibility pathways have not been quantitatively elucidated. Here, we discovered prevalent and novel cellular roles of the BLOC-1 complex in neuronal cells by performing large-scale Stable Isotopic Labeling of Cells in Culture quantitative proteomics (SILAC) combined with genetic analyses in dysbindin-null mice (Mus musculus) and the genome of schizophrenia patients. We identified 24 proteins that associate with the BLOC-1 complex many of which were altered in content/ distribution in cells or tissues deficient in BLOC-1. New findings include BLOC-1 interactions with the COG complex, a Golgi apparatus tether, and antioxidant enzymes peroxiredoxins 1-2. Importantly, loci encoding eight of the 24 proteins are affected by genomic copy number variation in schizophrenia patients. Thus, our quantitative proteomic studies expand the functional repertoire of the BLOC-1 complex and provide insight into putative molecular pathways of schizophrenia susceptibility.
Effects of acute heat stress on skeletal muscle gene expression associated with energy metabolism in rats

Study objectives were to determine the effects of acute heat stress (HS) on the expression of genes associated with energy metabolism in type I and II skeletal muscles. Male Sprague Dawley rats (n = 12; 9 mo) were randomly assigned to either thermal neutral (TN; 21.1°C) or HS conditions (39.4°C) for 6 h. Rats were anesthetized and the soleus (type I; oxidative) and tibialis anterior (TA; type II; glycolytic) muscles were collected. Total RNA was isolated and cDNA generated for real‐time PCR analysis (iQ5 Real‐Time PCR detection system). Exposure to HS tended to increase soleus and decrease TA AMP‐activated protein kinase (AMPK) mRNA abundance. Hyperthermia increased and tended to increase PPAR‐γ Co‐activator ‐1α (PGC‐1α) gene expression in soleus and TA, respectively. Pyruvate dehydrogenase kinase 4 (PDK4) mRNA abundance was increased by HS in the soleus but was unaltered in the TA. Lactate dehydrogenase‐α (LDHα) gene expression tended to increase in TA during HS but LDHα mRNA abundance did not differ in soleus between treatments. In conclusion, exposure to HS induced the differential expression of several energy metabolism genes based on muscle type (soleus versus TA). Moreover, changes in gene expression are consistent with impaired cellular energy status, perhaps due to mitochondrial dysfunction, in oxidative compared to glycolytic muscle fibers during hyperthermia.