Miracle-dz/UniFAR-FTUs huggingface dataset:
The Slide Hammer Seeder: A Novel Tool for Planting Small Seeds

Many important herbs [e.g., mint (Mentha sp.), thyme (Thymus sp.)], underused and nutritious vegetables [e.g., purslane (Portulaca oleracea), amaranth (Amaranthus tricolor)], and important biological control plants [e.g., sweet alyssum (Lobularia maritima)] have small seeds (≤ 1.5-mm long) that are difficult to plant with raw (i.e., nonpelleted) seed using existing seeders. A novel tool known as the slide hammer (SH) seeder was developed for the precise seeding of raw seeds of small-seeded plants. The SH seeder is a jab-type planter made primarily from electrical conduit tubing and other materials that are inexpensive and readily available in a hardware store or on the Internet. The interchangeable seed hopper is made from a plastic snap cap vial that has one or more holes of varying diameter depending on the desired seeding rate and seed size. Seed forms a “bridge” above the hole in the vial until they are dislodged from the force of the SH that discharges seeds to fall to the soil. Detailed plans are provided for how to make and use the SH seeder. The fabrication time is 2 to 4 hours with a material cost of ≈$32. I determined the seed vial hole specifications for the precise seeding of a variety of small-seeded plants, including chives (Allium schoenoprasum), chinese chives (Allium tuberosum), basil (Ocimum basilicum), grain amaranth (Amaranthus sp.), sweet alyssum, purslane, creeping thyme (Thymus serpyllum), and spearmint (Mentha spicata) that ranged in size from ≈200 to 11,000 seeds per gram. The diameter of the hole that was suitable for discharging the seed from the vial was always larger than the average seed length, and the ratio of hole diameter to seed length ranged from 1.07 to 1.62. Seeding rate uniformity evaluations were conducted for these species using vials with one vs. two holes and showed that the seeding rate was higher by an average of 58% to 173% from a vial with two holes compared with one hole. For most plant species evaluated, the SH seeder was able to dispense as few as one to three seeds consistently. Seed discharge increased somewhat with increasing SH weight for all species evaluated. The SH seeder can be useful for interplanting sweet alyssum as an insectary plant for aphid (Aphidoidea) control between existing plants of organic lettuce (Lactuca sativa), and for intercropping cultivars of purslane as a novel vegetable in between transplanted organic broccoli (Brassica oleracea Italica group) plants. This novel seeding tool has many potential uses for direct, hand seeding in vegetable and herb production systems and in weed research trials. The seeder could be automated and made with a variety of alternative materials.
Immunobiology of an alphavirus infection in mice

This thesis describes some aspects of the immunobiology of the alphavirus Semliki Forest Virus (SFV) infection in the mouse. Both innate and adaptive immune responses are explored. Chapter 2 describes experiments comparing the immune response to two strains of SFV, virulent and avirulent. Differences between these strains were identified in virus replication in spleen and brain, and their ability to induce IFN-a. In chapter 3, lethality of vSFV was compared in B6 wild type mice and mice defective in exocytosis and or Fas-mediated pathways of cytolytic activity. Defective mice show more resistance than wild type B6 mice to the lethal vSFV infection. Absence of Tcmediated cytolytic activity did not affect the outcome of vSFV infection, whereas NK cell-depletion delayed the mean time to death. This indicates a possible NK cell involvement in immunopathology. In chapter 4, B6 wild type mice and vSFV-resistant mice (perfxgzmAB'/_, gld, Fas';', FasxgzmAB'7', and perf^xgld) were tested for changes in tissue virus titres. Reduced SFV replication was detected in perf! 'xgld mice compared to all other mouse strains. In naive perf^xgld mice, expanded population of activated macrophage and elevated expression levels of mRNA of IFN-y and TNF-a were detected. These factors may be responsible for the observed reduced virus titres. In chapter 5, the cell surface expressions of activation markers CD69, CD86 and CD25 on lymphocytes were investigated following vSFV and aSFV infections. A generalised and systemic elevation of CD69 and CD86, but not CD25, expression was detected at day 1 postinfection and returned to baseline by day 5 postinfection. This is also a feature of infections with other viruses, such as Adenovirus and Flavivirus. Using interferon receptor knockout mice, it could be concluded that this activation marker expression was mainly due to the action of IFN-I.
Structural insights into unique features of the human mitochondrial ribosome recycling

Significance The human mitochondrial ribosome (mitoribosome) recycling factor (RRFmt) is known to play essential roles in mitochondrial physiology, including protein synthesis, and it has been implicated in human genetic diseases. The RRFmt is among the few protein molecules that carry their N-terminal signal peptide sequence into the mitochondrial matrix that is required for RRFmt’s interaction with the mitoribosome. In this study, we present a cryo-electron microscopic structure of the human mitoribosome in complex with the RRFmt. The structure reveals hitherto unknown features of RRFmt and its interactions with the functionally important regions of the ribosomal RNA that constitute the peptidyl-transferase center and that are linked to the GTPase-associated center of the mitoribosome, shedding light on the mechanism of ribosome recycling in mitochondria. Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with bacteria, the composition and structure of the human mitoribosome and its translational factors are significantly different from those of their bacterial counterparts. The mammalian mitoribosome recycling factor (RRFmt) carries a mito-specific N terminus extension (NTE), which is necessary for the function of RRFmt. Here we present a 3.9-Å resolution cryo-electron microscopic (cryo-EM) structure of the human 55S mitoribosome-RRFmt complex, which reveals α-helix and loop structures for the NTE that makes multiple mito-specific interactions with functionally critical regions of the mitoribosome. These include ribosomal RNA segments that constitute the peptidyl transferase center (PTC) and those that connect PTC with the GTPase-associated center and with mitoribosomal proteins L16 and L27. Our structure reveals the presence of a tRNA in the pe/E position and a rotation of the small mitoribosomal subunit on RRFmt binding. In addition, we observe an interaction between the pe/E tRNA and a mito-specific protein, mL64. These findings help understand the unique features of mitoribosome recycling.
Fine‐scale genetic diversity and landscape‐scale genetic structuring in three foundational bulrush species: implications for wetland revegetation

The appropriate sourcing of seeds for restoration is critical for establishing foundational plant species that support ecosystem functions and services. Genetic analyses of such species can yield insights into patterns of genetic diversity and structuring to inform seed collections. Here we document, for three foundational bulrush species, distinct genetic patterns to guide restoration of wetlands along the iconic Great Salt Lake, the largest lake in western North America. Specifically, Schoenoplectus acutus and Schoenoplectus americanus had moderate levels of site‐scale genet richness and relatively low genet richness levels within 1‐m2 plots. These patterns contrast with Bolboschoenus maritimus, which had higher levels of site‐ and plot‐level genet richness, and has therefore likely experienced more recent seedling establishment. At the landscape scale, we found some evidence for genetic isolation of individuals at more remote sites (namely Fish Springs National Wildlife Refuge in the West Desert of Utah), but all species are relatively well dispersed over hundreds of kilometers, a pattern most likely to occur via avian dispersal. In our mechanistic dispersal assessment, we found abundant bulrush seeds present in waterfowl gizzards and those seeds germinated readily despite (or because of) partial digestion. Migratory waterfowl likely facilitate the broad dispersal of all species and may aid in bulrush establishment by breaking seed dormancy. These findings suggest that seeds for restoration should be collected within and among seed source sites to ensure a diverse restoration seed lot that does not disrupt gene flow patterns.
System-wide Identification of Enzyme Substrates by Thermal Analysis (SIESTA)

Despite the immense importance of enzyme-substrate reactions, there is a lack of generic and unbiased tools for identifying the molecular components participating in these reactions on a cellular level. Here we developed a universal method called System-wide Identification of Enzyme Substrates by Thermal Analysis (SIESTA). The approach assumes that enzymatic post-translational modification of substrate proteins changes their thermal stability, and applies the concept of specificity to reveal potential substrates. For selenoprotein thioredoxin reductase 1, SIESTA confirmed several known protein substrates and suggested novel candidates. For poly-(ADP-ribose) polymerase-10, SIESTA revealed a number of putative substrates, which were confirmed by targeted mass spectrometry and functional assays. Wider application of SIESTA can enhance our understanding of the role of enzymes in homeostasis and disease, and facilitate drug discovery. One sentence summary Monitoring protein stability can reveal changes due to specific enzymatic post-translational modifications at the proteome level.
Hematological and biochemical reference intervals for adult Croatian Posavac horse

The aim of the study was to establish breed-specific hematological and biochemical reference intervals (RI) for Croatian Posavac horses. Strict criteria were established for inclusion of reference subjects, blood specimen collection and handling. Blood samples from 125 healthy, adult Croatian Posavac horses of both sexes (94 mares and 31 stallions) were used to determine RIs. Statistical analysis was performed according to the 2012 ASVCP guidelines for nonparametric RIs. RIs for hematological parameters from this study were quite compatible with RIs for warmblood horses for 11 out of the 20 measured parameters. The reported biochemical RIs in our study agree well with RIs for a mixed population of Croatian coldblood breeds, except for LDH, GGT and ALP. The RI for total protein and albumin differ substantially from the published RIs, and from a clinical viewpoint further investigation is warranted. The RIs established in this study provide a useful baseline for the clinical assessment of hematological and biochemical data of Croatian Posavac horses.
Better people analytics

“We have charts and graphs to back us up. So f*** off. ” New hires in Google’s people analytics department began receiving a laptop sticker with that slogan a few years ago, when the group probably felt it needed to defend its work. Back then people analytics—using statistical insights from employee data to make talent management decisions—was still a provocative idea with plenty of skeptics who feared it might lead companies to reduce individuals to numbers. HR collected data on workers, but the notion that it could be actively mined to understand and manage them was novel—and suspect.
Understanding Quality Work in Mathematics: Supporting Teachers in Leading Professional Development

Teacher leaders are often responsible for providing professional development to improve teacher effectiveness and student learning. Leading professional development for teachers can be highly effective when the focus is on student learning in on-going and relevant contexts. This article describes a school-based, teacher-led collaborative process conceptualized and facilitated by two teacher leaders using a modified protocol for examining students work in mathematics. The focus of the professional development aligned with a school-wide initiative of increasing the quality of students’ mathematical work across a kindergarten through eighth-grade school. This paper shares the structure of the professional development, the nature of the protocol, and how it was implemented followed by a discussion for teacher leaders who are interested in facilitating a similar type of collaborative professional development experience within their own schools. Findings suggest that the use of a well-developed protocol helped focus teachers’ attention to specific attributes expected in quality work and served as a reference point for considering how important structures of learning such as whole-class discourse could be evident in individual students’ quality work.
Atomic force microscopy in cell biology

Preface, Bhanu P. Jena & Heinrich Horber. Local Probe Techniques, J.K. Heinrich Horber. AFM in the Study of Membrane Fusion and Exocytosis, Bhanu P. Jena, Sang-Joon Cho. AFM Imaging of Cells and Membranes, Christian Le Grimellec, Eric Lesniewska, Pierre Milhiet, Marie-Cecile Giocondi. Measuring the Elastic Properties of Living Cells by AFM, Manfred Radmacher. Cell Adhesion Measured by Force Spectroscopy on Living Cells, Martin Benoit. Molecular Recognition Studies Using AFM, Peter Hinterdorfer. The Biophysics of Sensory Cells of the Inner Ear examined by AFM and Patch Clamp, Matthias G. Langer, Assen Koitschev. Biotechnological Applications of Atomic Force Microscopy, Mike Horton, Guillaume Charras, Petri Lehenkari. Cellular Membranes Studied by Photonic Force Microscopy, Arnd Pralle, Ernst-Ludwig Florin. Methods for Biological Probe Microscopy in Aqueous Fluids, Helen G. Hansma, Johannes H. Kindt, John C. Sitko, Emin Oroudjev, Mario B. Viani, Nathan Becker, Lia I. Pietrasanta. Supported Lipid Bilayers as Effective Substrates for Atomic Force Microscopy, Zhifeng Shao, Daniel M. Czajkowsky. Cryo Atomic Force Microscopy, Zhifeng Shao, Sitong Sheng. Conformations, Flexibility and Interactions Observed on Individual Membrane Proteins by Atomic Force Microscopy, Daniel J. Muller, Andreas Engel. Single Molecule Force Measurements, Vincent T. Moy, Aileen Chen. Forced Unfolding of Single Proteins, Pierre-Francois Lenne, S.M. Altmann. Developments in Dynamic Force Microscopy and Spectroscopy, Mervyn Miles, A.D.L. Humphris. SFM Studies on the Structure and Dynamics of Single DNA Molecules, Bruno Samori, Giampaolo Zuccheri.
Biochemical techniques in the heart

Preparation of Cardiac Sarcoplasmic Reticulum, J.J. Leddy and B.S. Tauna The Isolation of Myocardial Sarcolemma, G.F. Tibbits Measurement of Na+-Ca2+ Exchange, G.F. Tibbits Measurement of Sodium/Potassium ATPase in Myocardium, V. Elimban, A. Lukas, and N.S. Dhalla Molecular Assessment of Cardiac Sodium Pump Activity, V. Elimban, K. Kato, and N.S. Dhalla Methods for Measuring Sodium-Hydrogen Exchange in the Heart, H. Massaeli and G.N. Pierce Preparation of Cardiomyocytes, B. Rodrigues and D.L. Severson
Moisture transport through asymmetric porous membranes with finger-like holes for indoor humidity control: A lattice Boltzmann simulation approach

Asymmetric porous membranes with finger-like holes are one sort of promising membrane materials for indoor humidity control. Moisture transport in these materials is the key factor influencing humidity control performance. To overcome the difficulties in modelling meso-scale mass transfer in these materials, a lattice Boltzmann simulation (LBM) methodology has been proposed to model the pore-scale gas flow and mass transfer in the asymmetric membranes with finger-like holes. A typical membrane is classified into three sub-layers: a porous support layer, a layer with finger holes, and a denser skin layer. Simulated annealing technique was used in our study to reconstruct the calculating domain. Then fluid flow and mass transfer in the membrane were predicted with LBM, and permeability and effective diffusivity were evaluated. The existence of finger holes in the matrix could dramatically enhance the overall mass transfer in the membranes. Besides, the inhomogeneity in membrane structures would make the macro-scale lumped parameter prediction of membrane performance questionable. Our findings show differences in comparison to previous macro-scale multi-layer analysis. The dominant resistance is in the skin layer. There should be a change in emphasis for membrane optimization with a focus on the skin layer rather than the porous layer.
Mechanisms of Plastic Rescue in Novel Environments

Adaptive phenotypic plasticity provides a mechanism of developmental rescue in novel and rapidly changing environments. Understanding the underlying mechanism of plasticity is important for predicting both the likelihood that a developmental response is adaptive and associated life-history trade-offs that could influence patterns of subsequent evolutionary rescue. Although evolved developmental switches may move organisms toward a new adaptive peak in a novel environment, such mechanisms often result in maladaptive responses. The induction of generalized physiological mechanisms in new environments is relatively more likely to result in adaptive responses to factors such as novel toxins, heat stress, or pathogens. Developmental selection forms of plasticity, which rely on within-individual selective processes, such as shaping of tissue architecture, trial-and-error learning, or acquired immunity, are particularly likely to result in adaptive plasticity in a novel environment. However, both the induction of plastic responses and the ability to be plastic through developmental selection come with significant costs, resulting in delays in reproduction, increased individual investment, and reduced fecundity. Thus, we might expect complex interactions between plastic responses that allow survival in novel environments and subsequent evolutionary responses at the population level.
Nuclear export in somatic cyst cells controls cyst cell-germline coordination and germline differentiation in the Drosophila testis

Nucleocytoplasmic communication is crucial for proper cell function and coordination of intrinsic cues with signaling responses emanating from the neighboring cells and the local tissue microenvironment. In the Drosophila male germline system, germ cells proliferate and progressively differentiate enclosed in supportive somatic cyst cells, forming a small cyst, the functional unit of differentiation. Here we show that the peripheral nucleoporins Nup62, Nup214 and Nup88, and the exportin Emb are critically required in cyst cells to maintain cyst cell survival and germline encapsulation in order to protect cyst cell-germline communication and promote germ cell differentiation. Knockdown of nup62, emb, nup214 or nup88 in cyst cells leads to cell-autonomous defects in mRNA export, and cell non-autonomous overproliferation of early germ cells in the absence of cyst cell-derived differentiation signals. Suppression of apoptosis can reverse cyst cell elimination and partially restored those defects. Interestingly, overexpression of the Drosophila Profilin gene chickadee can rescue cyst cell survival and restore germline encapsulation and differentiation, by counteracting Ntf-2 mediated export, suggesting that the function of Profilin in cyst cells is linked to nuclear export.
The Cloacal Microbiome Changes with the Breeding Season in a Wild Bird

Abstract The symbiotic microbial communities, or “microbiomes,” that reside on animals are dynamic, and can be affected by the behavior and physiology of the host. These communities provide many critical beneficial functions for their hosts, but they can also include potential pathogens. In birds, bacteria residing in the cloaca form a complex community, including both gut and sexually-transmitted bacteria. Transmission of cloacal bacteria among individuals is likely during the breeding season, when there is direct cloacal contact between individuals. In addition, the major energetic investment in reproduction can draw resources away from immune responses that might otherwise prevent the successful establishment of microbes. We assessed dynamic variation in the cloacal microbiome of free-living rufous-collared sparrows (Zonotrichia capensis) through sequential breeding and non-breeding seasons. We found that the cloacal bacterial communities differed between the sexes when they were in breeding condition. Further, in males, but not in females, the bacterial community became more diverse with the onset of reproduction, and then decreased in diversity as males transitioned to non-breeding condition. Individuals sampled across sequential breeding seasons did not accumulate more bacterial taxa over seasons, but bacterial community composition did change. Our results suggest that the cloacal microbiome in birds is dynamic and, especially in males, responsive to breeding condition.
Regulation and dynamics of force transmission at individual cell-matrix adhesion bonds

Fluorescent molecular tension sensors reveal the dynamics of force transmission at cellular adhesion complexes. Integrin-based adhesion complexes link the cytoskeleton to the extracellular matrix (ECM) and are central to the construction of multicellular animal tissues. How biological function emerges from the tens to thousands of proteins present within a single adhesion complex remains unclear. We used fluorescent molecular tension sensors to visualize force transmission by individual integrins in living cells. These measurements revealed an underlying functional modularity in which integrin class controlled adhesion size and ECM ligand specificity, while the number and type of connections between integrins and F-actin determined the force per individual integrin. In addition, we found that most integrins existed in a state of near-mechanical equilibrium, a result not predicted by existing models of cytoskeletal force transduction. A revised model that includes reversible cross-links within the F-actin network can account for this result and suggests one means by which cellular mechanical homeostasis can arise at the molecular level.