Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution and genetic basis of the plant-penetrating ovipositor, a key adaptation in herbivorous Drosophilidae

Herbivorous insects are extraordinarily diverse, yet are found in only one-third of insect orders. This skew may result from barriers to plant colonization, coupled with phylogenetic constraint on plant-colonizing adaptations. Physical barriers have been surmounted through the evolution of key morphological innovations, such as the plant-penetrating ovipositor. Despite their significance, the evolution and genetic basis of such innovations have not been well studied. Ovipositors densely lined with hard bristles have evolved repeatedly in herbivorous lineages within the Drosophilidae. Here, we focus on the evolution of this trait in Scaptomyza, an herbivorous radiation nested in a microbe-feeding clade, sister to Hawaiian Drosophila. Our phylogenetic approach revealed that ovipositor bristle number increased as herbivory evolved. We then dissected the genomic architecture of variation in ovipositor bristle number within S. flava through a genome wide association study. Top associated variants were enriched for transcriptional repressors, and the strongest associations included genes contributing to peripheral nervous system development. Genotyping individual flies replicated the association at a variant upstream of Gαi, a neural development gene, contributing to a gain of 0.58 bristles/major allele. These results suggest that regulatory variation involving conserved developmental genes contributes to a key morphological adaptation required for plant colonization.
Epigenetic Regulator miRNA Pattern Differences Among SARS-CoV, SARS-CoV-2, and SARS-CoV-2 World-Wide Isolates Delineated the Mystery Behind the Epic Pathogenicity and Distinct Clinical Characteristics of Pandemic COVID-19

Detailed molecular mechanism of SARS-CoV-2 pathogenesis is still elusive to address its deadlier nature and to design effective theraputics. Here, we present our study elucidating the interplay between the SARS-CoV and SARS-CoV-2 viruses’; and host’s miRNAs, an epigenetic regulator, as a mode of pathogenesis, and enlightened how the SARS-CoV and SARS-CoV-2 infections differ in terms of their miRNA mediated interactions with host and its implications in the disease complexity. We have utilized computational approaches to predict potential host and viral miRNAs, and their possible roles in different important functional pathways. We have identified several putative host antiviral miRNAs that can target the SARS viruses, and also SARS viruses’ encoded miRNAs targeting host genes. In silico predicted targets were also integrated with SARS infected human cells microarray and RNA-seq gene expression data. Comparison of the host miRNA binding profiles on 67 different SARS-CoV-2 genomes from 24 different countries with respective country’s normalized death count surprisingly uncovered some miRNA clusters which are associated with increased death rates. We have found that induced cellular miRNAs can be both a boon and a bane to the host immunity, as they have possible roles in neutralizing the viral threat, parallelly, they can also function as proviral factors. On the other hand, from over representation analysis, interestingly our study revealed that although both SARS-CoV and SARS-CoV-2 viral miRNAs could target broad immune signaling pathways; only some of the SARS-CoV-2 miRNAs are found to uniquely target some immune signaling pathways like-autophagy, IFN-I signaling etc, which might suggest their immune-escape mechanisms for prolonged latency inside some hosts without any symptoms of COVID-19. Further, SARS-CoV-2 can modulate several important cellular pathways which might lead to the increased anomalies in patients with comorbidities like-cardiovascular diseases, diabetes, breathing complications, etc. This might suggest that miRNAs can be a key epigenetic modulator behind the overcomplications amongst the COVID-19 patients. Our results support that miRNAs of host and SARS-CoV-2 can indeed play a role in the pathogenesis which can be further concluded with more experiments. These results will also be useful in designing RNA therapeutics to alleviate the complications from COVID-19.
Polycistronic gene expression in the model micro-organism Ustilago maydis

Eukaryotic microorganisms transcribe monocistronic mRNAs to encode proteins. For synthetic biological approaches like metabolic engineering, precise co-expression of several proteins in space and time is advantageous. A straightforward approach is the application of viral 2A peptides to design synthetic polycistronic mRNAs in eukaryotes. Here, we establish such a system in the well-studied model microorganism Ustilago maydis. Using two fluorescence reporter proteins, we compared the activity of five viral 2A peptides. Their activity was evaluated in vivo using fluorescence microscopy and validated using fluorescence resonance energy transfer (FRET). Activity ranged from 20 to 100% and the best performing 2A peptide was P2A from porcine teschovirus-1. As proof of principle, we followed regulated gene expression efficiently over time and synthesised a tri-cistronic mRNA encoding biosynthetic enzymes to produce mannosylerythritol lipids (MELs). In essence, we evaluated 2A peptides in vivo and demonstrated the applicability of 2A peptide technology for U. maydis in basic and applied science.
Three-dimensional reconstructions of the internal structures of haustoria in parasitic Orobanchaceae

Parasitic plants infect other plants by forming haustoria, specialized multicellular organs consisting of several cell types each of which has unique morphological features and physiological roles associated with parasitism. Understanding the spatial organization of cell types is, therefore, of great importance in elucidating the functions of haustoria. Here, we report a three-dimensional (3-D) reconstruction of haustoria from two Orobanchaceae species, the obligate parasite Striga hermonthica infecting rice and the facultative parasite Phtheirospermum japonicum infecting Arabidopsis. Our images reveal the spatial arrangements of multiple cell types inside haustoria and their interaction with host roots. The 3-D internal structures of haustoria highlight differences between the two parasites, particularly at the xylem connection site with the host. Our study provides structural insights into how organs interact between hosts and parasitic plants. One-sentence summary Three-dimensional image reconstruction was used to visualize the spatial organization of cell types in the haustoria of parasitic plants with special reference to their interaction with host roots.
Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis

Significance Rhizobia are soil-dwelling bacteria that form symbioses with legumes and provide biologically useable nitrogen as ammonium for the host plant. High-throughput DNA sequencing has led to a rapid expansion in publication of complete genomes for numerous rhizobia, but analysis of gene function increasingly lags gene discovery. Mariner-based transposon insertion sequencing has allowed us to characterize the fitness contribution of bacterial genes and determine those functionally important in a Rhizobium–legume symbiosis at multiple stages of development. By analyzing successive lifestyle stages of a model Rhizobium–legume symbiosis using mariner-based transposon insertion sequencing (INSeq), we have defined the genes required for rhizosphere growth, root colonization, bacterial infection, N2-fixing bacteroids, and release from legume (pea) nodules. While only 27 genes are annotated as nif and fix in Rhizobium leguminosarum, we show 603 genetic regions (593 genes, 5 transfer RNAs, and 5 RNA features) are required for the competitive ability to nodulate pea and fix N2. Of these, 146 are common to rhizosphere growth through to bacteroids. This large number of genes, defined as rhizosphere-progressive, highlights how critical successful competition in the rhizosphere is to subsequent infection and nodulation. As expected, there is also a large group (211) specific for nodule bacteria and bacteroid function. Nodule infection and bacteroid formation require genes for motility, cell envelope restructuring, nodulation signaling, N2 fixation, and metabolic adaptation. Metabolic adaptation includes urea, erythritol and aldehyde metabolism, glycogen synthesis, dicarboxylate metabolism, and glutamine synthesis (GlnII). There are 17 separate lifestyle adaptations specific to rhizosphere growth and 23 to root colonization, distinct from infection and nodule formation. These results dramatically highlight the importance of competition at multiple stages of a Rhizobium–legume symbiosis.
Insect pollinators of anise plants (Pimpinella anisum L.) and the important role of honey bees (apis mellifera L.) on their yield productivity

The present investigation aimed to identify the insect pollinators and the efficiency of honeybees in pollination of anise plant during flowering periods of 2008 and 2009 seasons at Assiut Governorate, Egypt. Obtained results indicated that the total insect counts attained 11 species, belonging to four orders; Hemiptera (one species), Coleoptera (two species), Diptera (five species) and Hymenoptera (three species). Honeybees were the most abundant of hymenopterous insects during anise flowering and the daily peak activities were detected between 12.00 noon and 2.00 p.m. for the two seasons. Regarding the effect of prevailing air temperature and relative humidity percentage (RH%) on the occurrence of insect pollinators, it is clear that the effects of the two factors were moderate in the two seasons. Also, the results showed a significant effect of open pollination on the seed yield/feddan (1024.12 kg) followed by honeybees pollination (781.55 kg), while insect exclusion recorded the lowest value (300.24 kg).
The Role of Negative Affectivity in Concurrent Relations Between Caregiver Psychological Distress and Social‐Emotional Difficulties in Infants With Early Signs of Autism

Recent evidence suggests the link between caregiver psychological distress and offspring social‐emotional difficulties may be accounted for by offspring temperament characteristics. However, existing studies have only focused on neurotypical children; thus, the current study sought to provide an initial examination of this process among children with varying levels of early autism features. Participants included 103 infants aged 9–16 months (M = 12.39, SD = 1.97; 68% male) and their primary caregiver (96% mothers) referred to a larger study by community healthcare professionals. We utilized caregiver‐reported measures of psychological distress (Depression Anxiety Stress Scales), infant temperament (Infant Behavior Questionnaire‐Revised) and internalizing and externalizing symptoms (Infant‐Toddler Social and Emotional Assessment) and administered the Autism Observation Schedule for Infants (AOSI) at an assessment visit to quantify autism features. Infant negative affectivity was found to mediate positive concurrent relations between caregiver psychological distress and infant internalizing and externalizing symptoms, irrespective of the infants' AOSI score. While preliminary and cross‐sectional, these results replicate and extend previous findings suggesting that the pathway from caregiver psychological distress to negative affectivity to social‐emotional difficulties might also be apparent among infants with varying levels of autism features. More rigorous tests of causal effects await future longitudinal investigation.
Developmental trajectories of illicit drug use, prescription drug misuse and cannabis practices among young adult cannabis users in Los Angeles.

INTRODUCTION AND AIMS Young adults have the highest rates of drug use and contribute significantly to the growing population of medical cannabis patients (MCP). This study examined relationships between longitudinal patterns of illicit/prescription drug use/misuse and cannabis practices among young adult cannabis users. DESIGN AND METHODS In 2014-2015, 210 young adult MCP and 156 nonpatient users were recruited in Los Angeles and surveyed annually over four waves. The analytical sample was limited to completers of all four waves (n = 301). Distinct developmental trajectories of illicit drug use and prescription drug misuse were identified. Fixed effects regression analysis evaluated changes in cannabis practices by trajectory groups. RESULTS Results supported two-trajectory solutions (high/low) for illicit drug use and prescription drug misuse. Decreases in use within all four trajectories occurred by wave 4. Low illicit drug use trajectory members were more likely to self-report medical cannabis use. Membership in both types of high-use trajectories was associated with use of concentrates and edibles. The prevalence of MCP, edibles use and cannabis days decreased significantly by wave 4. DISCUSSION AND CONCLUSIONS While alternative cannabis forms use was associated with membership in high drug use trajectories, self-reported medical cannabis use (not MCP) was negatively associated with high illicit drug use trajectory membership. Reductions in the prevalence of MCP, cannabis days, edibles use and other drug use by wave 4 alongside stable levels of self-reported medical cannabis use might reflect the changing legal status of cannabis in California, maturing out phenomenon and safer patterns of cannabis use.
Hybridization between Fish Species in Nature

THE Jordan school of ichthyology, in which I was nurtured, held steadfastly to the view that the lines between fish species are almost never crossed. This mistaken idea was perhaps in part a holdover of the pre-Darwinian concept of the immutability of species, but was, more pointedly, a reaction against the tendency of some European ichthyologists to explain as hybrids specimens that proved difficult to identify. This view that there is little or no natural hybridization between fish species may be further attributed to the circumstance that systematic ichthyology in America from about 1890 to 1920 was still essentially in the exploratory and species-naming stage, and dealt chiefly with marine fishes, which, as I shall point out, hybridize much less often than do freshwater fishes. Early in my ichthyological career I encountered evidence that fish species do cross in nature, at times in considerable frequency. The analysis of such hybridization has ever since engaged my attention, in so far as other activities would allow. This report lays particular emphasis on the researches that I have conducted during the past thirty-five years, largely with the collaboration of my wife and of several students and colleagues, to all of whom I pay tribute. They might all appear as co-authors of this report. The studies continue. During the first ten years of my intensive studies of the freshwater fishes of North America, from 1919 to 1929, I gathered strong circumstantial indications that the species lines are rather often crossed in nature, and during the following fifteen years, from 1929 to 1944, I was able, with the constant aid of Mrs. Hubbs, to confirm these indications, not only by the accumulation of much more circumstantial evidence, in part subjected to critical statistical analysis, but also by breeding experiments in the aquarium of the Division of Fishes of the then new Museum of Zoology at the University of Michigan.
A multifunctional small RNA binding protein for sensing and signaling cell envelope precursor availability in bacteria

Synthesis of glucosamine-6-phosphate (GlcN6P) by the enzyme GlmS initiates bacterial cell envelope biosynthesis. To ensure ongoing synthesis, GlcN6P homeostasis is required. Escherichia coli achieves this through a post-transcriptional control mechanism comprising the RNA-binding protein RapZ and small RNAs (sRNAs) GlmY and GlmZ. GlmZ stimulates glmS translation by base-pairing. When GlcN6P is abundant, GlmZ is cleaved and inactivated by endoribonuclease RNase E. Cleavage depends on RapZ, which binds GlmZ and recruits RNase E. Decreasing GlcN6P concentrations provoke up-regulation of the decoy sRNA GlmY which sequesters RapZ, thereby suppressing GlmZ decay. In our current study we identify RapZ as the GlcN6P sensor. GlcN6P-free RapZ interacts with and stimulates phosphorylation of the two-component system (TCS) QseE/QseF triggering glmY expression. Thereby generated GlmY sequesters RapZ into stable complexes, allowing for glmS expression. Sequestration by GlmY also disables RapZ to stimulate QseE/QseF, providing a negative feed-back loop limiting the response. When GlcN6P is replenished, GlmY is released from RapZ and rapidly degraded. Our work has revealed a complex regulatory scenario, in which an RNA binding protein senses a metabolite and communicates with two sRNAs, a TCS and ribonuclease RNase E to achieve metabolite homeostasis.
The interaction between cereal type and lactose level on piglet performance and diet digestibility post weaning

Both barley and wheat contain anti-nutritive factors such as glucans and xylans respectively. However, β-glucans have been shown to promote lactic acid bacteria in the large intestine and this would be very beneficial in the absence of in-diet antimicrobial growth promoter. A 2 × 2 factorial was used to investigate the interaction between cereal type (wheat v . barley) and lactose inclusion (170 v . 275 g/kg) on piglet performance post weaning. Two hundred and sixteen weaned piglets (24 days of age, 6·0 kg weight) were blocked on the basis of weight and were assigned to one of four dietary treatments. The treatments were as follows (T1) 170 g/kg lactose and wheat, (T2) 275 g/kg lactose and wheat, (T3) 170 g/kg lactose, wheat and 200 g/kg barley and (T4) 275 g/kg lactose, wheat and 200 g/kg barley. The diets were formulated to have identical concentrations of digestible energy (16 MJ/kg) and total lysine (16 g/kg). The pigs were offered the diets ad libitum for 33 days post weaning. There was a significant interaction ( P P P P P P
Clinical Presentation and Surgical Treatment of Retrosternal Goiter: A Case Series Study

Background: The retrosternal goiter (RSG) is a slow-growing mass often benign in nature; thyroidectomy remains the preferred standard curative treatment. This study aimed to explore the local experience of RSG with respect to the clinical presentation, classifications, management, and outcomes. Method: A retrospective chart review was conducted to include all cases diagnosed with RSG and underwent thyroidectomy between January 1998 and December 2013. Results: A total of 1210 patients underwent thyroidectomy; of which 30 (2.5%) patients were diagnosed to have RSG. The commonly reported symptoms were dyspnea (40%), pain and discomfort (30%), dysphagia (26.7%), and hoarseness (20%). Thirteen patients (43.3%) were completely asymptomatic. The fine-needle aspiration cytology was performed in 22 (73.3%) patients, of whom the majority was benign (77.3%). The grading classification showed that grade 1 is the most frequent (73.3%). Total bilateral thyroidectomy was the most prevailing procedure in 57% cases followed by partial thyroidectomy. All patients underwent retrosternal thyroidectomy through a cervical incision except for one case. Postoperative histopathology showed frequent benign multinodular goiter (83.3%), followed by papillary thyroid cancer (10%) and thyroiditis (6.7%). The most common complication after thyroidectomy was tracheomalacia (13.4%), transient hypocalcemia (10%), and hypoparathyroidism (6.7%). There was no intraoperative or perioperative mortality. Conclusion: RSG is a rare entity often presented with pressure symptoms, mostly involving anterior mediastinum and had a challenging surgical procedure. A large multicenter study is needed to include more cases in order to have a consensus on the definition and classification system for such important clinical goiter presentation.
A holistic approach to iron chelation therapy in transfusion‐dependent thalassemia patients with serum ferritin below 500 μg/L

Transfusion-dependent thalassemia (TDT) patients require chronic iron chelation therapy (ICT) 1 to balance the rate of accumulation due to blood transfusion and minimize the amount of non-transferrin bound iron (NTBI) which is toxic for lipids, proteins, and DNA through reactive oxygen species 2 . ICT requires careful dose adjustments to avoid over-chelation 1 . Currently, ICT is initiated after 10-20 units (about 100 mL/kg) of packed red blood cells or when there is evidence of chronic iron overload or serum ferritin (SF) is >1000 µg/L 3 . Few studies have evaluated the management of ICT in TDT in the presence of low SF levels. Deferasirox (DFX) is currently the first-line oral iron chelator worldwide, and its label suggests considering interruption when SF constantly falls below 500 µg/L, while no specific indication is available for Deferoxamine and Deferiprone. However, this cut-off has been arbitrarily defined. Renal and hepatic adverse events (AEs) and increases in serum creatinine (SCr) and alanine aminotransferase (ALT) have been reported This study aims to determine the safety of iron chelation therapy in TDT patients with a mean value of SF <500 µg/L for a sustained period. We collected data for TDT patients with mean SF <500 µg/L for at least 24 months between January 2007 and December 2018. Linear (or quadratic when adequate) regression models were fitted; standard errors (SE) were corrected by taking into account clustering of outcomes within subjects. Statistical analyses were performed with Stata 16 (StataCorp. 2019). The study was approved by the Ethics Committee of our institution. results show that the continuation of DFX treatment in the presence of SF values <500 µg/L is safe and not associated with an increased risk of renal and hepatic AEs. Previous studies showed that renal and liver AEs mainly appear for high doses of DFX irrespective of ferritin levels 6 and are usually reversible after treatment interruption. To our best knowledge, no studies have evaluated the safety of DFX treatment or other chelators when ferritin is constantly <500 µg/L.
Polyploidy and Speciation in Pteris (Pteridaceae)

The highest frequency of polyploidy among plants is considered to occur in the Pteridophytes. In this study, we focused on polyploidy displayed by a specific fern taxon, the genus Pteris L. (Pteridaceae), comprising over 250 species. Cytological data from 106 Pteris species were reviewed. The base number of chromosomes in Pteris is 29. Polyploids are frequently found in Pteris, including triploids, tetraploids, pentaploids, hexaploids, and octoploids. In addition, an aneuploid species, P. deltodon Bak. , has been recorded. Furthermore, the relationship between polyploidy and reproductive biology is reviewed. Among these 106 Pteris species, 60% exhibit polyploidy: 22% show intraspecific polyploidy and 38% result from polyploid speciation. Apogamous species are common in Pteris. Diploids are the most frequent among Pteris species, and they can be sexual or apogamous. Triploids are apogamous; tetraploids are sexual or apogamous. Most Pteris species have one to two ploidy levels. The diverse ploidy levels suggest that these species have a complex evolutionary history and their taxonomic problems require further clarification.