How to be an effective ally.

Inclusivity in biomedical research provides many positive attributes, including increased productivity, higher creativity, and improved wellness for all. While marginalized individuals work tirelessly to achieve equity and inclusion, this task should not be left solely to those most affected by exclusionary tactics. These individuals and the organizations with whom they are affiliated would benefit from the support of an ally. An ally is defined as a person or organization that actively supports the rights of a marginalized group without being a member of it. Allies have a unique opportunity to play a pivotal role in promoting fairness, equity, and inclusion, and thus serve as positive change agents within an organizational setting. We summarize here the importance of being an effective and dynamic ally and offer guidance on how to achieve that goal.

Establishing the short course in transferable skills training program.

While PhD programs prepare graduate students to perform biomedical research, a defined systematic training program for transferable skills is generally lacking. When provided, this training is often informal, unstructured, or inconsistent. Therefore, there is a need to provide critical skills in marketing, relationship building, project management, and budgeting to prepare trainees to navigate into a productive, engaging, and rewarding biomedical research career. To address this gap in training, the School of Graduate Studies at Meharry Medical College has developed the SHort Course In transFerable skills Training (SHIFT) Program, a 1-year professional development program accessible to graduate students in the United States who are enrolled in graduate biomedical research related programs. The SHIFT Program has been launched to equip trainees with skills essential for success in all biomedical science careers. PhD students will be taught the primary constituents of career management through the use of four training modules. In Module I, students complete self-assessments and are assigned to a small peer-mentoring team with mentors. Module II consists of a 5-day workshop that encompasses instruction on the transferable skills identified as essential for career success. Module III entails monthly interactive discussions over a 6-month period involving case study review and mentor-guided discussions to further reinforce skills learned. In Module IV, students compile the information learned from Modules I-III to develop an Individual Development Plan that incorporates 3-5 specific, measurable, attainable, relevant, and time-based career goals. Collectively, the SHIFT Program will allow participants to train, practice, and refresh skills, empowering them to navigate career transitions and obtain success in the career of their choice.

Reduction of large vessel traffic improves water quality and alters fish habitat-use throughout a large river.

Rivers are increasingly used as superhighways for the continental-scale transportation of freight goods, but the ecological impact of large vessel traffic on river ecosystems is difficult to study. Recently, the temporary maintenance closure of lock and dam systems on the Illinois Waterway (USA) brought commercial vessel traffic to a halt along the river's length, offering a rare opportunity to study the response of the ecosystem before, during, and after an extended pause of this persistent anthropogenic disturbance. We observed improvements in main- and side-channel water quality and a redistribution of fish habitat-use during a months-long, near-complete reduction of large vessel traffic. Over 3600 water quality and 1300 fish community samples indicate that large vessel traffic reduction coincided with a 33 % reduction in turbidity as well as increased use of sampling strata near vessel navigation corridors by sound-sensitive and rheophilic fishes. Gizzard shad (Dorosoma cepedianum), the most abundant species in the system, also expanded their use of these 'impact' areas. Though inland waterway transport is an economically- and climate-friendly alternative to trucking and rail for the shipment of freight, our data suggest that intense vessel traffic may have profound physical and biological impacts across a large river. Monitoring and mitigation of ecological impacts of the ongoing expansion of inland waterway transport around the world will be critical to balancing large rivers as both useful navigation corridors and functional ecosystems.

Structural modeling of ion channels using AlphaFold2, RoseTTAFold2, and ESMFold.

Ion channels play key roles in human physiology and are important targets in drug discovery. The atomic-scale structures of ion channels provide invaluable insights into a fundamental understanding of the molecular mechanisms of channel gating and modulation. Recent breakthroughs in deep learning-based computational methods, such as AlphaFold, RoseTTAFold, and ESMFold have transformed research in protein structure prediction and design. We review the application of AlphaFold, RoseTTAFold, and ESMFold to structural modeling of ion channels using representative voltage-gated ion channels, including human voltage-gated sodium (NaV) channel - NaV1.8, human voltage-gated calcium (CaV) channel - CaV1.1, and human voltage-gated potassium (KV) channel - KV1.3. We compared AlphaFold, RoseTTAFold, and ESMFold structural models of NaV1.8, CaV1.1, and KV1.3 with corresponding cryo-EM structures to assess details of their similarities and differences. Our findings shed light on the strengths and limitations of the current state-of-the-art deep learning-based computational methods for modeling ion channel structures, offering valuable insights to guide their future applications for ion channel research.

Energetic landscape of polycystin channel gating.

Members of the polycystin family (PKD2 and PKD2L1) of transient receptor potential (TRP) channels conduct Ca2+ and depolarizing monovalent cations. Variants in PKD2 cause autosomal dominant polycystic kidney disease (ADPKD) in humans, whereas loss of PKD2L1 expression causes seizure susceptibility in mice. Understanding structural and functional regulation of these channels will provide the basis for interpreting their molecular dysregulation in disease states. However, the complete structures of polycystins are unresolved, as are the conformational changes regulating their conductive states. To provide a holistic understanding of the polycystin gating cycle, we use computational prediction tools to model missing PKD2L1 structural motifs and evaluate more than 150 mutations in an unbiased mutagenic functional screen of the entire pore module. Our results provide an energetic landscape of the polycystin pore, which enumerates gating sensitive sites and interactions required for opening, inactivation, and subsequent desensitization. These findings identify the external pore helices and specific cross-domain interactions as critical structural regulators controlling the polycystin ion channel conductive and nonconductive states.

New records of Spotted Bass, Micropterus punctulatus, within the Mississippi River Basin, Illinois.

Spotted Bass Micropterus punctulatus, like many sport fishes, have experienced range expansion through intentional introductions (i.e., legal stocking and illegal transfers) and migration across the United States. In Illinois, USA, native populations of Spotted Bass occur along the eastern and southern border of the state. We report new records of Spotted Bass in their non-native range of the Illinois Waterway and the Illinois portion of the Upper Mississippi River in addition to collections in their native range in the Illinois sections of the Ohio and Wabash rivers to better understand their current distribution. Continuous, collaborative efforts to track the distribution and expansion of non-native fishes are important for maintaining and establishing native and non-native fisheries management objectives and education, as non-native fishes can influence native species population distribution and dynamics.

The COVID Season: U.S. Collegiate Esports Programs' Material Challenges and Opportunities During the 2020-21 Pandemic.

During the COVID-19 pandemic, universities were among the first institutions to shift to an online model. As they did so, nascent collegiate esports program lost access to campus spaces and in-person connections, potentially destabilizing this rising industry. Conversely, universities also worked to provide students remote access to resources, and many components of esports already occur online. Therefore, collegiate esports may have adjusted to distancing measures, potentially strengthening their footholds on US campuses. This paper draws on in-depth interviews with collegiate esports players, student employees, program directors, and administrators to address different programs' reactions to the pandemic, specifically the challenges and opportunities they faced. Overall, interviews reveal how COVID-19 shifted the understandings of and practices around gaming and esports, highlighted the intermittent relationship of online and offline spheres, and presented various possibilities and challenges for different stakeholders during the global pandemic.

Single amino acid residue mediates reciprocal specificity in two mosquito odorant receptors.

The southern house mosquito, Culex quinquefasciatus, utilizes two odorant receptors, CquiOR10 and CquiOR2, narrowly tuned to oviposition attractants and well conserved among mosquito species. They detect skatole and indole, respectively, with reciprocal specificity. We swapped the transmembrane (TM) domains of CquiOR10 and CquiOR2 and identified TM2 as a specificity determinant. With additional mutations, we showed that CquiOR10A73L behaved like CquiOR2. Conversely, CquiOR2L74A recapitulated CquiOR10 specificity. Next, we generated structural models of CquiOR10 and CquiOR10A73L using RoseTTAFold and AlphaFold and docked skatole and indole using RosettaLigand. These modeling studies suggested space-filling constraints around A73. Consistent with this hypothesis, CquiOR10 mutants with a bulkier residue (Ile, Val) were insensitive to skatole and indole, whereas CquiOR10A73G retained the specificity to skatole and showed a more robust response than the wildtype receptor CquiOR10. On the other hand, Leu to Gly mutation of the indole receptor CquiOR2 reverted the specificity to skatole. Lastly, CquiOR10A73L, CquiOR2, and CquiOR2L74I were insensitive to 3-ethylindole, whereas CquiOR2L74A and CquiOR2L74G gained activity. Additionally, CquiOR10A73G gave more robust responses to 3-ethylindole than CquiOR10. Thus, we suggest the specificity of these receptors is mediated by a single amino acid substitution, leading to finely tuned volumetric space to accommodate specific oviposition attractants.

A mobile robotic chemist.

Technologies such as batteries, biomaterials and heterogeneous catalysts have functions that are defined by mixtures of molecular and mesoscale components. As yet, this multi-length-scale complexity cannot be fully captured by atomistic simulations, and the design of such materials from first principles is still rare1-5. Likewise, experimental complexity scales exponentially with the number of variables, restricting most searches to narrow areas of materials space. Robots can assist in experimental searches6-14 but their widespread adoption in materials research is challenging because of the diversity of sample types, operations, instruments and measurements required. Here we use a mobile robot to search for improved photocatalysts for hydrogen production from water15. The robot operated autonomously over eight days, performing 688 experiments within a ten-variable experimental space, driven by a batched Bayesian search algorithm16-18. This autonomous search identified photocatalyst mixtures that were six times more active than the initial formulations, selecting beneficial components and deselecting negative ones. Our strategy uses a dexterous19,20 free-roaming robot21-24, automating the researcher rather than the instruments. This modular approach could be deployed in conventional laboratories for a range of research problems beyond photocatalysis.

Phakomatous Choristoma of the Orbit With Involvement of the Inferior Oblique Muscle.

The authors report a case of phakomatous choristoma presenting as an orbital tumor with involvement of the inferior oblique muscle. This is the only known case of this rare tumor directly invading and incorporating the inferior oblique. This tumor should be included in the differential of eyelid tumors and orbital tumors in infants. Finally, the authors review the histopathological and embryological characteristics of this lenticular tumor.

Microtubule seams are not mechanically weak defects.

Microtubule rigidity is important for many cellular functions to support extended structures and rearrange materials within the cell. The arrangement of the tubulin dimers within the microtubule can be altered to affect the protofilament number and the lattice type. Prior electron microscopy measurements have shown that when polymerized in the presence of a high concentration of NaCl, microtubules were more likely to be ten protofilaments with altered intertubulin lattice types. Specifically, such high-salt microtubules have a higher percentage of seam defects. Such seams have long been speculated to be a mechanically weak location in the microtubule lattice, yet no experimental evidence supported this claim. We directly measured the persistence length of freely fluctuating filaments made either with high salt or without. We found that the microtubules made with high salt were more flexible, by a factor of 2, compared to those polymerized the same way without salt present. The reduced persistence length of the high-salt microtubules can be accounted for entirely by a smaller cross-sectional radius of these microtubules, implying that the mixed lattice interactions have little effect on the bending rigidity. Our results suggest that the microtubule seam is not weaker than the typical lattice structure as previously speculated from structural studies.

Hemorrhagic Stroke in a Young Healthy Male Following Use of Pre-Workout Supplement Animal Rage XL.

So-called "pre-workout" supplements are substances marketed as natural dietary supplements with claims of helping athletes achieve more focused and intense workouts. The use of such products remains popular among American youth as a whole, but is especially high among active duty service members. Supplements are minimally regulated by the Food and Drug Administration (FDA), and unlike pharmaceuticals, supplements are often brought to market without any testing to show neither efficacy nor safety. Several case reports have documented serious adverse events and raise the question of whether supplement use was a causative factor. Reported events occurring after use of pre-workout supplements include, among others, ischemic stroke, hemorrhagic stroke, myocardial infarction, hepatitis, and death. Here, we present the case of a healthy 25-year-old active duty male who experienced a bilateral cerebellar hemorrhagic stroke occurring shortly after taking a supplement named Animal Rage XL. Hemorrhagic stroke occurring in a healthy 25-year-old male with no risk factors is exceedingly rare. This is the first known case of stroke temporally associated with this particular supplement, which is currently available for purchase at military exchanges. Additionally, several of the active ingredients in this supplement have been shown to cause hypertension, tachycardia, and vasospasm. All of these effects could increase the likelihood and severity of a hemorrhagic stroke. The investigated ingredients in this abstract include ß-phenethylamine, creatine-monophosphate, and caffeine.

Mercury BLASTP: Accelerating Protein Sequence Alignment.

Large-scale protein sequence comparison is an important but compute-intensive task in molecular biology. BLASTP is the most popular tool for comparative analysis of protein sequences. In recent years, an exponential increase in the size of protein sequence databases has required either exponentially more running time or a cluster of machines to keep pace. To address this problem, we have designed and built a high-performance FPGA-accelerated version of BLASTP, Mercury BLASTP. In this paper, we describe the architecture of the portions of the application that are accelerated in the FPGA, and we also describe the integration of these FPGA-accelerated portions with the existing BLASTP software. We have implemented Mercury BLASTP on a commodity workstation with two Xilinx Virtex-II 6000 FPGAs. We show that the new design runs 11-15 times faster than software BLASTP on a modern CPU while delivering close to 99% identical results.