Miracle-dz/UniFAR-FTUs huggingface dataset:
Saturation mutagenesis genome engineering of infective ΦX174 bacteriophage via unamplified oligo pools and golden gate assembly

Here we present a novel protocol for the construction of saturation single-site—and massive multi-site—mutant libraries of a bacteriophage. We segmented the ΦX174 genome into 14 non-toxic and non-replicative fragments compatible with golden gate assembly. We next used nicking mutagenesis with oligonucleotides prepared from unamplified oligo pools with individual segments as templates to prepare near-comprehensive single-site mutagenesis libraries of genes encoding the F capsid protein (421 amino acids scanned) and G spike protein (172 amino acids scanned). Libraries possessed greater than 99% of all 11,860 programmed mutations. Golden Gate cloning was then used to assemble the complete ΦX174 mutant genome and generate libraries of infective viruses. This protocol will enable reverse genetics experiments for studying viral evolution and, with some modifications, can be applied for engineering of therapeutically relevant bacteriophages with larger genomes.
Impact of Funding Changes on Selected Education Service Centers Considerations for Programming and Staffing for Continued Effectiveness in Equlizaing Educational Opportunities

The purpose of this study was three-fold: 1. To determine the amount and direction of changes in sources of funding for the Regional Education Service Centers from 1979 to 1984. 2. To determine the percent of change in programming expenditures of the Regional Education Service Centers from 1979 to 1984. 3. To rate the changes in quality of programming as perceived by the superintendents of the local school districts receiving services from 1979 to 1984. A review of the literature and a brief history of the Regional Education Service Centers of Texas were followed by tabular and narrative descriptions of the findings. Deflated data, to account for inflation, were derived by applying Bureau of Labor statistics formulas to dollar amounts supplied by the Regional Education Service Centers. Each of the five Education Service Centers included in the study experienced a decrease in total funds, due chiefly to a cut in federal and state support. Although local contributions increased in four out of five of the Regions during the five-year period, the net result to the Centers was a decrease in funding ranging from 23.2 percent to 51.8 percent. The impact on programming was severe. Of the nine major services on which data was gathered—media services, data processing, counseling/guidance, special education, migrant education, bus driver training, staff development, drug education/crime prevention, and bilingual education— two had been eliminated in all of the Regions included in the study by 19 84, and some of the Regions had discontinued services in other areas as well. Surveys for rating the services of the Education Service Centers were sent to 126 current superintendents who held the same position in 1979. The results indicated that although fewer dollars had been expended and some services had been eliminated, the quality of programming had not diminished from 1979 to 1984.
Amylolytic activity and chemical composition of rehydrated ground maize ensiled with α-amylase or glucoamylase

Abstract A completely randomized experiment was designed to evaluate the effects of α-amylase (AMY) and glucoamylase (GLU) on total losses, fermentative profile, chemical composition and amylolytic activity of rehydrated maize. Eighty-four experimental silos of rehydrated maize [0.33 litres/kg ground maize, 4-mm theoretical particle size, and 625 g/kg dry matter (DM)] were assigned to the following treatments: (1) control (CON), no enzyme addition; (2) GLU added at 300 µl/kg of ground maize (as-fed); and (3) AMY added at 300 µl/kg of ground maize. Seven silos from each treatment were opened after 7, 14, 21 and 28 days. Differences among treatments were evaluated through orthogonal contrasts (CON v. enzymes, and AMY v. GLU). Time effects were decomposed using polynomial regression. Glucoamylase silage exhibited greater total losses than AMY. Enzymes increased acetate and lactic acid concentrations and decreased ethanol concentration. Regardless of treatment, gas, effluent and total fermentative losses linearly increased, whereas DM recovery linearly decreased with higher storage length. Glucoamylase silage had lower ammonia nitrogen and higher lactic acid concentrations than AMY. Enzyme treatments decreased silage neutral detergent fibre content and increased in vitro DM degradation. Glucoamylase silage exhibited a more moderate starch content and greater in vitro DM degradation than AMY. Storage time linearly decreased DM, starch and fibre content of rehydrated maize. In vitro degradation of DM linearly increased as the storage length increased. This study showed evidence that enzymes with amylolytic activity, particularly GLU, improve the fermentative profile and DM degradation of rehydrated maize silage.
The complete mitochondrial genome of Eastern Yellow Wagtail (Motacilla tschutschensis)

Abstract Motacilla tschutschensis is a species of small passerine bird belonging to the family Motacillidae. Complete mitochondrial genome of Eastern Yellow Wagtail (M. tschutschensis) has been sequenced in this study. The genome is 16,829 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop), and 22 tRNA genes. The phylogenetic tree was reconstructed using the Bayesian analysis method, indicating that M. tschutschensis was closely related to Motacillalugens and Motacillaalba.
Distinct Patterns of Genetic Connectivity Found for Two Frugivorous Bat Species in Mesoamerica

Sturnira parvidens and Sturnira hondurensis are two frugivorous bat species distributed throughout the Mesoamerican region. Sturnira parvidens inhabits tropical lowland forests and S. hondurensis montane cloud forests. Their populations are respectively separated by the intervening highlands or lowlands. We used mitochondrial DNA control region sequences to compare genetic structure among the populations of these two species in the region of the Gulf of Mexico. We also measured genetic connectivity among their populations and assessed the distribution model for each species. We found high genetic diversity in both species: the FST comparisons values were low to high in S. hondurensis and low in S. parvidens. For S. hondurensis, we found isolation by landscape resistance (IBR) where the highland habitat heterogeneity may have restricted gene flow among the populations of the Sierra Madre Oriental, Sierra de Los Tuxtlas, Chiapas and Guatemala. For S. parvidens, the isolation is explained by geographic distance rather than by landscape heterogeneity.
DNA demethylation is a driver for chick retina regeneration

Background A promising avenue toward human retina regeneration lies in identifying the factors that promote cellular reprogramming to retinal neurons in organisms able to undergo retina regeneration. The embryonic chick can regenerate a complete neural retina, after retinectomy, via retinal pigment epithelium (RPE) reprogramming in the presence of FGF2. Cellular reprogramming resets the epigenetic landscape to drive shifts in transcriptional programs and cell identity. Here, we systematically analyzed the reprogramming competent chick RPE prior to injury, and during different stages of reprogramming. We examined the dynamic changes in the levels and distribution of histone marks and DNA modifications, as well as conducted a comprehensive analysis of the DNA methylome during this process. Results In addition to changes in the expression of genes associated with epigenetic modifications during RPE reprogramming, we observed dynamic changes in histone marks and intermediates of the process of DNA demethylation. At early times after injury, H3K27me3 and 5mC repression marks decreased while 5caC and the H3K4me3 activation mark increased, suggesting genome-wide changes in the bivalent chromatin, impaired DNA methylation, and active DNA demethylation in the chromatin reconfiguration of reprogramming RPE. Comprehensive analysis of the methylome by whole-genome bisulfite sequencing (WGBS) confirmed extensive rearrangements of DNA methylation patterns including differentially methylated regions (DMRs) found at promoters of genes associated with chromatin organization and fibroblast growth factor production. In contrast, genes associated with early RPE reprogramming are hypomethylated in the intact RPE and remain hypomethylated during the process. During the generation of a neuroepithelium (NE) at later stages of reprogramming, decreased levels of H3K27me3, 5mC, and 5hmC coincide with elevated levels of H3K27Ac and 5caC, indicating an active demethylation process and genome-wide changes in the active regulatory landscape. Finally, we identify Tet methylcytosine dioxygenase 3 (TET3) as an important factor for DNA demethylation and retina regeneration in the embryonic chick, capable of reprogramming RPE in the absence of exogenous FGF2. Conclusion Our results demonstrated that injury signals early in RPE reprogramming trigger genome-wide dynamic changes in chromatin, including bivalent chromatin and DNA methylation. In the presence of FGF2 these dynamic modifications are further sustained in the commitment to form a new retina. We identify DNA demethylation as a key process driving the process of RPE reprogramming and identified TET3 as a factor able to reprogram RPE in absence of FGF2. Our findings reveal active DNA demethylation as an important process that may be applied to remove the epigenetic barriers in order to regenerate retina in mammals.
Polyjet 3D printing of tissue-mimicking materials: how well can 3D printed synthetic myocardium replicate mechanical properties of organic myocardium?

Anatomical 3-D printing has potential for many uses in education, research and development, implant training, and procedure planning. Conventionally, the material properties of 3D printed anatomical models have often been similar only in form and not in mechanical response compared to biological tissue. The new Digital Anatomy material from Stratasys utilizes composite printed materials to more closely mimic the mechanical properties of tissue. Work was done to evaluate Digital Anatomy myocardium under axial loading for comparison with porcine myocardium regarding puncture, compliance, suturing, and cutting performance. In general, the Digital Anatomy myocardium showed promising comparisons to porcine myocardium. For compliance testing, the Digital Anatomy was either within the same range as the porcine myocardium or stiffer. Specifically, for use conditions involving higher stress concentrations or smaller displacements, Digital Anatomy was stiffer. Digital Anatomy did not perform as strongly as porcine myocardium when evaluating suture and cutting properties. The suture tore through the printed material more easily and had higher friction forces both during needle insertion and cutting. Despite these differences, the new Digital Anatomy myocardium material was much closer to the compliance of real tissue than other 3D printed materials. Furthermore, unlike biological tissue, Digital Anatomy provided repeatability of results. For tests such as cyclic compression, the material showed less than two percent variation in results between trials and between parts, resulting in lower variability than tissue. Despite some limitations, the myocardium Digital Anatomy material can be used to configure structures with similar mechanical properties to porcine myocardium in a repeatable manner, making this a valuable research tool.
Genetic diversity and structure of the binturong Arctictis binturong (Carnivora: Viverridae) – status of the elusive Palawan binturong and implications for conservation

The binturong or bearcat is a forest mesocarnivore ranging from Nepal to Indonesia and the Philippines. Several subspecies of binturongs are recognized but a revision is needed. The binturong from Palawan was described as a species and is now considered a subspecies, but its status has never been checked using molecular approaches. Owing to its restricted range and the pressure on its habitat, the Palawan binturong may be endangered. It is, therefore, of crucial importance to clarify its taxonomic status, particularly for the management of captive populations. We sequenced one nuclear and two mitochondrial markers for binturongs from locations across the species range and from zoos. Our results provide an assessment of the genetic polymorphism and structure within the binturong, resulting in two groups, corresponding to the Indochinese and the Sundaic regions. Within the latter were found the Palawan binturongs on one side, and an individual from Sulu archipelago (a locality not reported before) on the other side. The Palawan binturongs form a monophyletic group, genetically close to Bornean binturongs, which suggests that they may have dispersed from Borneo, and represents a lineage worth preserving, but which is not a separate species nor a separate subspecies.
Localization of β-Catenin and Islet in the Pelvic Fin Field in Zebrafish

In zebrafish, pelvic fin buds appear at 3 weeks post fertilization (wpf) during the larval to juvenile transition (metamorphosis), but their fate is already determined during embryogenesis. Thus, presumptive pelvic fin cells appear to memorize their positional information for three weeks, but no factors expressed in the pelvic fin field from the embryonic to the metamorphic stages have been identified. In mice, Islet1 is proposed to promote nuclear accumulation of β-catenin in the hindlimb field, which leads to the initiation of hindlimb bud outgrowth through activation of the Wnt/βcatenin pathway. Here, we examined the distribution of β-catenin and islet proteins in the pelvic fin field of zebrafish from the embryonic to the metamorphic stages. We found that transcripts of islet2a, but not islet1, are detected in the posterior lateral plate mesoderm, including the presumptive pelvic fin field, at the embryonic stage as well as in the pelvic fin bud at the metamorphic stage. Immunolocalization revealed that β-catenin and islet proteins, which are synthesized during the embryonic stage, remain in the cytoplasm of the presumptive pelvic fin cells during the larval stage, and are then translocated into the nuclei of the pelvic fin bud at the metamorphic stage. We propose that cytoplasmic localization of these proteins in the presumptive pelvic fin cells that remained during the larval stage may underlie the mechanism by which pelvic fin cells memorize their positional information from the embryonic stage to the metamorphic stage.
Effect of Tuna Based Formulated Diet on Growth and Play Behaviour of Domestic Cats

Feline diet plays a vital role in growth and behaviour of cats. The amount of Taurine (an essential amino acid) in the diet is a limiting factor for growth and the high cost of commercial feline feeds is a problem especially in developing countries. The objectives of the study were to formulate a cat diet using locally available cheaper ingredients and to evaluate its effect on growth rates, skin/coat conditions, activity levels based on play behaviour (social play and object play) of cats and sensory attributes for cat faeces. The key ingredient of the formulated diet was tuna as it enriched with the Taurine requirement of feline. Eight weaned domestic kittens were tested as two groups fed with two diet types; formulated and commercial, independently. Sensory attributes of faecal samples, skin and coat, periodic weights, social and individual behaviours were monitored. The growth rate of the kittens of two diet groups showed that there was no significant difference (p>0.05). The sensory test showed that the faeces from commercial diet group had stronger odours (p 0.05). All social play behaviour types for two diet groups were significantly different (p<0.05) and, the felines from the formulated diet group showed higher frequency in play behaviour. Formulated diet group had significantly (p<0.05) higher activity rates for arching and stalking. Commercial diet fed group cried more often compared to the formulated diet group. Thus, the formulated diet comprises a balanced nutritional profile that meets the normal growth rates of felines and satisfying activity levels for the cats.
Effect of Plant Growth Hormones and Liquid Fertilizer on Rooting and Tuberization of Yam (Dioscorea rotundata Poir.) Vine Cuttings

Vine cutting is an effective solution to solve the problem of seed availability in yam cultivation. This study was conducted to improve the recovery and rooting rate of vine cuttings of Dioscorea rotundata. Two-node cuttings from five (5)-month-old hybrid plants were grown in liquid media consisting of phytohormones (AIA3 and GA3) and liquid fertilizer (NPK 8-8-8) at different concentrations. Observations were made weekly from the 21st day after transplanting and focused on the survival rate of the cuttings, the number of roots emitted and the number of minitubers initiated. The results obtained showed a significant effect of the different growing media on the survival rate, rooting and production of minitubers. The best survival rates were obtained for cuttings grown in NPK (8-8-8) at 0.25% (100%) and AIA3 at 25 ppm (93.3%). The highest averages root number was recorded with growing media containing 0.25% NPK 8-8-8 (20.3) and 25 ppm AIA3 (17.7). Growing media with 0.25% NPK (8-8-8) and 25 ppm AIA3 provided the highest average numbers of minitubers initiated, respectively 5 and 4.6. Growing medium containing 0.25% NPK 8-8-8 has been identified as the one that allows better roots emission and minitubers production by yam vines cuttings.
Antifungal Activity of Euclea divinorum Root and Study of its Ethnobotany and Phytopharmacology

The ethnobotanical survey of Euclea divinorum Hiern (Ebenaceae) was conducted on Soqotra Island, Yemen. The root bark is used to treat mouth, dental, dermal and blood diseases in the traditional medicine of the island. The study is the first report about the effect of the plant root barks against six human pathogenic fungi. The non-polar dichloromethane extract of Euclea divinorum root bark showed stronger antifungal activities compared to polar direct and sequential methanolic extracts. These extracts showed significant broad antifungal activity against Absidia corymbifera, Aspergillus fumigatus, Candida krusei, Microsporum gypseum, Mucor sp. and Trichophyton mentagrophytes compared to the standard antibiotic drug nystatin. Thin-layer chromatography (TLC) revealed the presence of the naphthoquinones in the extracts. The results showed an extraction process to separate most antifungal naphthoquinones from the root bark by using non-polar solvent dichloromethane, while flavonoids remained in the polar methanolic extracts; therefore, the polar sequential and direct methanolic extracts recorded higher antioxidant activity than the non-polar extracts with less toxicity. The biological and chemical results identified the presence of antifungal and antioxidant constituents in the root bark and confirm its traditional use in Soqotra Island as crude powder to treat dental and dermal diseases and to clean teeth. Moreover, our results are compared with literature review on ethnobotany and phytopharmacology of the E. divinorum to present a medicinal monograph about the plant.
An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells

Tracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Particularly in the context of stem cell biology, analysis of single cell lineages in their native state has elucidated novel fates and highlighted heterogeneity of function. Coupling of such ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CARLIN (for CRISPR Array Repair LINeage tracing) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo. This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures based on in vivo stem cell function without a need for markers or cell sorting.
The complete mitochondrial genome of Glycera chirori Izuka (Annelida: Polychaeta): an evidence of conservativeness between gene arrangement and phylogenesis in Glycera

Abstract The complete mitochondrial genome of Glycera chirori Izuka (Annelida: Polychaeta) was presented, which is a circular molecule of 15,930 bp nucleotides. It encodes 37 genes, including 13 PCGs, 22 tRNAs, and two rRNAs. The length of non-coding regions is 1428 bp, and the longest one (1346 bp) is speculated as the control region, which is located between trnA and trnL2 and is longer than most species in Glycera. The complete mitogenome of G. chirori Izuka consists of 31.2% A, 23.6% C, 12.9% G, and 32.2% T, which has T vs. A skew (−0.02) and C vs. G skew (−0.29), respectively. Phylogenetic analysis indicates the classification status of G. chirori Izuka and the relationship with other species in Glycera, which is closer with Glycera unicornis and Glycera fallax (bootstrap = 100). By comparisons, the gene arrangement of G. chirori Izuka and other seven species in Glycera are identical and they also cluster together in phylogenetic tree with higher support rate, which indicates the conservativeness between gene arrangement and phylogenetic analysis in Glycera. In conclusion, the complete mitochondrial genome of G. chirori Izuka can provide supportive data for further molecular and evolutionary analysis of Glycera.
The complete chloroplast genome of Vitis amurensis Rupr., an economic plant to China

Abstract The chloroplast (cp) genome sequence of Vitis amurensis has been characterized from Illumina pair-end sequencing. The complete cp genome was 161,014 bp in length, containing a large single-copy region (LSC) of 89,239 bp and a small single-copy region (SSC) of 19,067 bp, which were separated by a pair of 26,354 bp inverted repeat regions (IRs). The genome contained 133 genes, including 88 protein coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 37.4%, while the corresponding values of the LSC, SSC, and IR regions are 35.3%, 31.7%, and 43.0%, respectively. Further, phylogenetic analysis suggested that the V. amurensis was sister to Vitis coignetiae.