Mitochondrial Protein Synthesis Adapts to Influx of Nuclear-Encoded Protein.

Mitochondrial ribosomes translate membrane integral core subunits of the oxidative phosphorylation system encoded by mtDNA. These translation products associate with nuclear-encoded, imported proteins to form enzyme complexes that produce ATP. Here, we show that human mitochondrial ribosomes display translational plasticity to cope with the supply of imported nuclear-encoded subunits. Ribosomes expressing mitochondrial-encoded COX1 mRNA selectively engage with cytochrome c oxidase assembly factors in the inner membrane. Assembly defects of the cytochrome c oxidase arrest mitochondrial translation in a ribosome nascent chain complex with a partially membrane-inserted COX1 translation product. This complex represents a primed state of the translation product that can be retrieved for assembly. These findings establish a mammalian translational plasticity pathway in mitochondria that enables adaptation of mitochondrial protein synthesis to the influx of nuclear-encoded subunits.

Advancing Biological Understanding and Therapeutics Discovery with Small-Molecule Probes.

Small-molecule probes can illuminate biological processes and aid in the assessment of emerging therapeutic targets by perturbing biological systems in a manner distinct from other experimental approaches. Despite the tremendous promise of chemical tools for investigating biology and disease, small-molecule probes were unavailable for most targets and pathways as recently as a decade ago. In 2005, the NIH launched the decade-long Molecular Libraries Program with the intent of innovating in and broadening access to small-molecule science. This Perspective describes how novel small-molecule probes identified through the program are enabling the exploration of biological pathways and therapeutic hypotheses not otherwise testable. These experiences illustrate how small-molecule probes can help bridge the chasm between biological research and the development of medicines but also highlight the need to innovate the science of therapeutic discovery.

Engineering ethanologenicity into the extremely thermophilic bacterium Anaerocellum (f. Caldicellulosiriuptor) bescii.

The anaerobic bacterium Anaerocellum (f. Caldicellulosiruptor) bescii natively ferments the carbohydrate content of plant biomass (including microcrystalline cellulose) into predominantly acetate, H2, and CO2, and smaller amounts of lactate, alanine and valine. While this extreme thermophile (growth Topt 78 °C) is not natively ethanologenic, it has been previously metabolically engineered with this property, albeit initially yielding low solvent titers (∼15 mM). Herein we report significant progress on improving ethanologenicity in A. bescii, such that titers above 130 mM have now been achieved, while concomitantly improving selectivity by minimizing acetate formation. Metabolic engineering progress has benefited from improved molecular genetic tools and better understanding of A. bescii growth physiology. Heterologous expression of a mutated thermophilic alcohol dehydrogenase (AdhE) modified for co-factor requirement, coupled with bioreactor operation strategies related to pH control, have been key to enhanced ethanol generation and fermentation product specificity. Insights gained from metabolic modeling of A. bescii set the stage for its further improvement as a metabolic engineering platform.

Is There a Role for Environmental and Metabolic Factors Predisposing to Severe COVID-19?

The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) pandemic affects people around the world. However, there have been striking differences in the number of infected individuals and deaths in different countries. Particularly, within Central Europe in countries that are similar in ethnicity, age, and medical standards and have performed similar steps of containment, such differences in mortality rates remain inexplicable. We suggest to consider and explore environmental factors to explain these intriguing variations. Countries like Northern Italy, France, Spain, and UK have suffered from 5 times more deaths from the corona virus infection than neighboring countries like Germany, Switzerland, Austria, and Denmark related to the size of their respective populations. There is a striking correlation between the level of environmental pollutants including pesticides, dioxins, and air pollution such as NO2 known to affect immune function and healthy metabolism with the rate of mortality in COVID-19 pandemic in these European countries. There is also a correlation with the use of chlorination of drinking water in these regions. In addition to the improvement of environmental protective programs, there are possibilities to lower the blood levels of these pollutants by therapeutic apheresis. Furthermore, therapeutic apheresis might be an effective method to improve metabolic inflammation, altered vascular perfusion, and neurodegeneration observed as long-term complications of COVID-19 disease.

Correlating chemical sensitivity and basal gene expression reveals mechanism of action.

Changes in cellular gene expression in response to small-molecule or genetic perturbations have yielded signatures that can connect unknown mechanisms of action (MoA) to ones previously established. We hypothesized that differential basal gene expression could be correlated with patterns of small-molecule sensitivity across many cell lines to illuminate the actions of compounds whose MoA are unknown. To test this idea, we correlated the sensitivity patterns of 481 compounds with ∼19,000 basal transcript levels across 823 different human cancer cell lines and identified selective outlier transcripts. This process yielded many novel mechanistic insights, including the identification of activation mechanisms, cellular transporters and direct protein targets. We found that ML239, originally identified in a phenotypic screen for selective cytotoxicity in breast cancer stem-like cells, most likely acts through activation of fatty acid desaturase 2 (FADS2). These data and analytical tools are available to the research community through the Cancer Therapeutics Response Portal.

Maternal health in India: A survey of birth attendant competency through completeness of prescribed care during perinatal visits, in 12 randomly chosen districts of Uttar Pradesh, India.

We assessed the completeness of care provided during perinatal visits at public institutions in Uttar Pradesh (UP), India. Self-reported data from 53 interviews with birth attendants throughout 12 districts in UP showed that 52% of the items from a procedural checklist were covered during visits. Routine visits were found to be incomplete, provider training related to pharmaceuticals and counseling were suggested to be low, and the monitoring of vitals to be infrequent and inconsistent. We suggest further grassroots research be conducted in developing nations so that strategic and precise reform can be made to lower global maternal mortality.

Differences between Platelets Derived from Neonatal Cord Blood and Adult Peripheral Blood Assessed by Mass Spectrometry.

It has been proposed that differences may exist between umbilical cord blood (CB) platelets and adult peripheral blood (APB) platelets, including altered protein levels of the main platelet integrins. We have now compared the protein expression profiles of CB and APB platelets employing a label-free comparative proteomics approach. Aggregation studies showed that CB platelets effectively aggregate in the presence of thromboxane A2 analogue, collagen, and peptide agonists of the proteinase-activated receptors 1 and 4. In agreement with previous studies, higher concentrations of the agonists were required to initiate aggregation in the CB platelets. Mass spectrometry analysis revealed no significant difference in the expression levels of critical platelet receptors like glycoprotein (GP)Ib, GPV, GPIX, and integrin αIIbß3. This was confirmed using flow cytometry-based approaches. Gene ontology enrichment analysis revealed that elevated proteins in CB platelets were in particular enriched in proteins contributing to mitochondrial energy metabolism processes. The reduced proteins were enriched in proteins involved in, among others, platelet degranulation and activation. In conclusion, this study reveals that the CB and APB platelets are distinct. In particular, changes were observed for proteins that belong to metabolic and energy generation processes and not for the critical adhesive platelet integrins and glycoproteins.

Using Pose Estimation and 3D Rendered Models to Study Leg-Mediated Self-righting by Lanternflies.

The ability to upright quickly and efficiently when overturned on the ground (terrestrial self-righting) is crucial for living organisms and robots. Previous studies have mapped the diverse behaviors used by various animals to self-right on different substrates, and proposed physical models to explain how body morphology can favor specific self-righting methods. However, to our knowledge, no studies have quantified and modeled all of an animal's limb motions during these complicated behaviors. Here, we studied terrestrial self-righting by immature invasive spotted lanternflies (Lycorma delicatula), an insect species that must frequently recover from being overturned after jumping and falling in its native habitat. These nymphs self-righted successfully in 92-100% of trials on three substrates with different friction and roughness, with no significant difference in the time or number of attempts required. They accomplished this using three stereotypic sequences of movements. To understand these motions, we combined 3D poses tracked on multi-view high-speed video with articulated 3D models created using photogrammetry and Blender rendering software. The results were used to calculate the mechanical properties (e.g., potential and kinetic energy, angular speed, stability margin, torque, force, etc.) of these insects during righting trials. We used an inverted physical pendulum model (a "template") to estimate the kinetic energy available in comparison to the increase in potential energy required to flip over. While these insects began righting using primarily quasistatic motions, they also used dynamic leg motions to achieve final tip-over. However, this template did not describe important features of the insect's center of mass trajectory and rotational dynamics, necessitating the use of an "anchor" model comprising the 3D rendered body model and six articulated two-segment legs to model the body's internal degrees of freedom and capture the role of the legs' contribution to inertial reorientation. This anchor elucidated the sequence of highly coordinated leg movements these insects used for propulsion, adhesion, and inertial reorientation during righting, and how they frequently pivot about a body contact point on the ground to flip upright. In the most frequently used method, diagonal rotation, these motions allowed nymphs to spin their bodies to upright with lower force with a greater stability margin compared to the other less frequently used methods. We provide a concise overview of necessary background on 3D orientation and rotational dynamics, and the resources required to apply these low-cost modeling methods to other problems in biomechanics.

Phenotype-driven assessment of the ancestral trajectory of sulfur biooxidation in the thermoacidophilic archaea Sulfolobaceae.

Certain members of the family Sulfolobaceae represent the only archaea known to oxidize elemental sulfur, and their evolutionary history provides a framework to understand the development of chemolithotrophic growth by sulfur oxidation. Here, we evaluate the sulfur oxidation phenotype of Sulfolobaceae species and leverage comparative genomic and transcriptomic analysis to identify the key genes linked to sulfur oxidation. Metabolic engineering of the obligate heterotroph Sulfolobus acidocaldarius revealed that the known cytoplasmic components of sulfur oxidation alone are not sufficient to drive prolific sulfur oxidation. Imaging analysis showed that Sulfolobaceae species maintain proximity to the sulfur surface but do not necessarily contact the substrate directly. This indicates that a soluble form of sulfur must be transported to initiate cytoplasmic sulfur oxidation. Conservation patterns and transcriptomic response implicate an extracellular tetrathionate hydrolase and putative thiosulfate transporter in a newly proposed mechanism of sulfur acquisition in the Sulfolobaceae.IMPORTANCESulfur is one of the most abundant elements on earth (2.9% by mass), so it makes sense that the earliest biology found a way to use sulfur to create and sustain life. However, beyond evolutionary significance, sulfur and the molecules it comprises have important technological significance, not only in chemicals such as sulfuric acid and in pyritic ores containing critical metals but also as a waste product from oil and gas production. The thermoacidophilic Sulfolobaceae are unique among the archaea as sulfur oxidizers. The trajectory for how sulfur biooxidation arose and evolved can be traced using experimental and bioinformatic analyses of the available genomic data set. Such analysis can also inform the process by which extracellular sulfur is acquired and transported by thermoacidophilic archaea, a phenomenon that is critical to these microorganisms but has yet to be elucidated.

Beyond low lignin: Identifying the primary barrier to plant biomass conversion by fermentative bacteria.

Renewable alternatives for nonelectrifiable fossil-derived chemicals are needed and plant matter, the most abundant biomass on Earth, provide an ideal feedstock. However, the heterogeneous polymeric composition of lignocellulose makes conversion difficult. Lignin presents a formidable barrier to fermentation of nonpretreated biomass. Extensive chemical and enzymatic treatments can liberate fermentable carbohydrates from plant biomass, but microbial routes offer many advantages, including concomitant conversion to industrial chemicals. Here, testing of lignin content of nonpretreated biomass using the cellulolytic thermophilic bacterium, Anaerocellum bescii, revealed that the primary microbial degradation barrier relates to methoxy substitutions in lignin. This contrasts with optimal lignin composition for chemical pretreatment that favors high S/G ratio and low H lignin. Genetically modified poplar trees with diverse lignin compositions confirm these findings. In addition, poplar trees with low methoxy content achieve industrially relevant levels of microbial solubilization without any pretreatments and with no impact on tree fitness in greenhouse.

Reconnecting the Hand and Arm to the Brain: Efficacy of Neural Interfaces for Sensorimotor Restoration After Tetraplegia.

BACKGROUND AND OBJECTIVES: Paralysis after spinal cord injury involves damage to pathways that connect neurons in the brain to peripheral nerves in the limbs. Re-establishing this communication using neural interfaces has the potential to bridge the gap and restore upper extremity function to people with high tetraplegia. We report a novel approach for restoring upper extremity function using selective peripheral nerve stimulation controlled by intracortical microelectrode recordings from sensorimotor networks, along with restoration of tactile sensation of the hand using intracortical microstimulation. METHODS: A 27-year-old right-handed man with AIS-B (motor-complete, sensory-incomplete) C3-C4 tetraplegia was enrolled into the clinical trial. Six 64-channel intracortical microelectrode arrays were implanted into left hemisphere regions involved in upper extremity function, including primary motor and sensory cortices, inferior frontal gyrus, and anterior intraparietal area. Nine 16-channel extraneural peripheral nerve electrodes were implanted to allow targeted stimulation of right median, ulnar (2), radial, axillary, musculocutaneous, suprascapular, lateral pectoral, and long thoracic nerves, to produce selective muscle contractions on demand. Proof-of-concept studies were performed to demonstrate feasibility of using a brain-machine interface to read from and write to the brain for restoring motor and sensory functions of the participant's own arm and hand. RESULTS: Multiunit neural activity that correlated with intended motor action was successfully recorded from intracortical arrays. Microstimulation of electrodes in somatosensory cortex produced repeatable sensory percepts of individual fingers for restoration of touch sensation. Selective electrical activation of peripheral nerves produced antigravity muscle contractions, resulting in functional movements that the participant was able to command under brain control to perform virtual and actual arm and hand movements. The system was well tolerated with no operative complications. CONCLUSION: The combination of implanted cortical electrodes and nerve cuff electrodes has the potential to create bidirectional restoration of motor and sensory functions of the arm and hand after neurological injury.

Sizing up spotted lanternfly nymphs for instar determination and growth allometry.

A major ongoing research effort seeks to understand the behavior, ecology and control of the spotted lanternfly (SLF) (Lycorma delicatula), a highly invasive pest in the U.S. and South Korea. These insects undergo four nymphal stages (instars) before reaching adulthood, and appear to shift host plant preferences, feeding, dispersal and survival patterns, anti-predator behaviors, and response to traps and chemical controls with each stage. However, categorizing SLF life stage is challenging for the first three instars, which have the same coloration and shape. Here we present a dataset of body mass and length for SLF nymphs throughout two growing seasons and compare our results with previously-published ranges of instar body lengths. An analysis using two clustering methods revealed that 1st-3rd instar body mass and length fell into distinct clusters consistently between years, supporting using these metrics to stage nymphs during a single growing season. The length ranges for 2nd-4th instars agreed between years in our study, but differed from those reported by earlier studies for diverse locations, indicating that it is important to obtain these metrics relevant to a study's region for most accurate staging. We also used these data to explore the scaling of SLF instar bodies during growth. SLF nymph body mass scaled with body length varied between isometry (constant shape) and growing somewhat faster than predicted by isometry in the two years studied. Using previously published data, we also found that SLF nymph adhesive footpad area varies in direct proportion to weight, suggesting that footpad adhesion is independent of nymphal stage, while their tarsal claws display positive allometry and hence disproportionately increasing grasp (mechanical adhesion). By contrast, mouthpart dimensions are weakly correlated with body length, consistent with predictions that these features should reflect preferred host plant characteristics rather than body size. We recommend future studies use the body mass vs length growth curve as a fitness benchmark to study how SLF instar development depends on factors such as hatch date, host plant, temperature, and geographic location, to further understanding of life history patterns that help prevent further spread of this invasive insect.

Reconnecting the Hand and Arm to the Brain: Efficacy of Neural Interfaces for Sensorimotor Restoration after Tetraplegia.

Background: Paralysis after spinal cord injury involves damage to pathways that connect neurons in the brain to peripheral nerves in the limbs. Re-establishing this communication using neural interfaces has the potential to bridge the gap and restore upper extremity function to people with high tetraplegia. Objective: We report a novel approach for restoring upper extremity function using selective peripheral nerve stimulation controlled by intracortical microelectrode recordings from sensorimotor networks, along with restoration of tactile sensation of the hand using intracortical microstimulation. Methods: A right-handed man with motor-complete C3-C4 tetraplegia was enrolled into the clinical trial. Six 64-channel intracortical microelectrode arrays were implanted into left hemisphere regions involved in upper extremity function, including primary motor and sensory cortices, inferior frontal gyrus, and anterior intraparietal area. Nine 16-channel extraneural peripheral nerve electrodes were implanted to allow targeted stimulation of right median, ulnar (2), radial, axillary, musculocutaneous, suprascapular, lateral pectoral, and long thoracic nerves, to produce selective muscle contractions on demand. Proof-of-concept studies were performed to demonstrate feasibility of a bidirectional brain-machine interface to restore function of the participant's own arm and hand. Results: Multi-unit neural activity that correlated with intended motor action was successfully recorded from intracortical arrays. Microstimulation of electrodes in somatosensory cortex produced repeatable sensory percepts of individual fingers for restoration of touch sensation. Selective electrical activation of peripheral nerves produced antigravity muscle contractions. The system was well tolerated with no operative complications. Conclusion: The combination of implanted cortical electrodes and nerve cuff electrodes has the potential to allow restoration of motor and sensory functions of the arm and hand after neurological injury.

The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits.

Associations between human genetic variation and clinical phenotypes have become a foundation of biomedical research. Most repositories of these data seek to be disease-agnostic and therefore lack disease-focused views. The Type 2 Diabetes Knowledge Portal (T2DKP) is a public resource of genetic datasets and genomic annotations dedicated to type 2 diabetes (T2D) and related traits. Here, we seek to make the T2DKP more accessible to prospective users and more useful to existing users. First, we evaluate the T2DKP's comprehensiveness by comparing its datasets with those of other repositories. Second, we describe how researchers unfamiliar with human genetic data can begin using and correctly interpreting them via the T2DKP. Third, we describe how existing users can extend their current workflows to use the full suite of tools offered by the T2DKP. We finally discuss the lessons offered by the T2DKP toward the goal of democratizing access to complex disease genetic results.

Mapping protein interactions in the active TOM-TIM23 supercomplex.

Nuclear-encoded mitochondrial proteins destined for the matrix have to be transported across two membranes. The TOM and TIM23 complexes facilitate the transport of precursor proteins with N-terminal targeting signals into the matrix. During transport, precursors are recognized by the TIM23 complex in the inner membrane for handover from the TOM complex. However, we have little knowledge on the organization of the TOM-TIM23 transition zone and on how precursor transfer between the translocases occurs. Here, we have designed a precursor protein that is stalled during matrix transport in a TOM-TIM23-spanning manner and enables purification of the translocation intermediate. Combining chemical cross-linking with mass spectrometric analyses and structural modeling allows us to map the molecular environment of the intermembrane space interface of TOM and TIM23 as well as the import motor interactions with amino acid resolution. Our analyses provide a framework for understanding presequence handover and translocation during matrix protein transport.

A Call to Action. A Critical Review of Mental Health Related Anti-stigma Campaigns.

Using a knowledge-attitudes-behavior practice (KABP) paradigm, professionals have focused on educating the public in biomedical explanations of mental illness. Especially in high-income countries, it is now common for education-based campaigns to also include some form of social contact and to be tailored to key groups. However, and despite over 20 years of high-profile national campaigns (e.g., Time to Change in England; Beyond Blue in Australia), examinations suggest that the public continue to Other those with experiences of mental ill-health. Furthermore, evaluations of anti-stigma programs are found to have weak- to no significant long-term effects, and serious concerns have been raised over their possible unintended consequences. Accordingly, this article critically re-engages with the literature. We evidence that there have been systematic issues in problem conceptualization. Namely, the KABP paradigm does not respond to the multiple forms of knowledge embodied in every life, often outside conscious awareness. Furthermore, we highlight how a singular focus on addressing the public's perceived deficits in professionalized forms of knowledge has sustained public practices which divide between "us" and "them." In addition, we show that practitioners have not fully appreciated the social processes which Other individuals with experiences of mental illness, nor how these processes motivate the public to maintain distance from those perceived to embody this devalued form of social identity. Lastly, we suggest methodological tools which would allow public health professionals to fully explore these identity-related social processes. Whilst some readers may be frustrated by the lack of clear solutions provided in this paper, given the serious unintended consequences of anti-stigma campaigns, we caution against making simplified statements on how to correct public health campaigns. Instead, this review should be seen as a call to action. We hope that by fully exploring these processes, we can develop new interventions rooted in the ways the public make sense of mental health and illness.

Sidechain Diversification of Grandifloracin Allows Identification of Analogues with Enhanced Anti-Austerity Activity against Human PANC-1 Pancreatic Cancer Cells.

The natural product (+)-grandifloracin is a potent "anti-austerity" agent, able to suppress the ability of various pancreatic cancer cell lines to tolerate conditions of nutrient deprivation. Such anti-austerity agents represent a promising approach to cancer chemotherapy. Here we report the synthesis and biological evaluation of racemic analogues of grandifloracin bearing diverse sidechains, of which two show enhanced potency in comparison with the natural product. Additionally, several unexpected by-products containing modifications of the grandifloracin core were isolated, identified and similarly evaluated for biological activity.

The Global Invasion of the Suckermouth Armored Catfish Genus Pterygoplichthys (Siluriformes: Loricariidae): Annotated List of Species, Distributional Summary, and Assessment of Impacts.

Alexander Benjamin Orfinger and Daniel Douglas Goodding (2018) The suckermouth armored catfish genus Pterygoplichthys (Siluriformes: Loricariidae) includes popular aquarium fishes and constitutes one of the most successful freshwater invasive taxa, having achieved global distribution. To date, however, no comprehensive distributional record nor impact assessment exist for the spread of the genus, precluding informed management strategies. To provide these tools, our study aims to (1) provide an annotated checklist of species for this taxonomically confusing genus, (2) survey all available literature on the spread of the genus and summarize and map its invasive distribution, and (3) assess the overall socioeconomic and environmental impact of the genus on a global scale using the Generic Impact Scoring System (GISS). First, we provide an updated annotated species list. We then summarize seventy-one unique invasion records along with twenty-one instances of demonstrated impacts. Species of the genus Pterygoplichthys have now invaded five continents and twenty-one countries, and show an extended range in their native South America. Impact analysis yielded a GISS score of 18 to 19, indicating low to moderate levels of socioeconomic and environmental threats. However, to bolster the confidence in this analysis in future iterations, more research should aim to move beyond just "first records" and instead empirically evaluate species' effects on native ecosystems.

Motor recruitment to the TIM23 channel's lateral gate restricts polypeptide release into the inner membrane.

The presequence translocase of the mitochondrial inner membrane (TIM23 complex) facilitates anterograde precursor transport into the matrix and lateral release of precursors with stop-transfer signal into the membrane (sorting). Sorting requires precursor exit from the translocation channel into the lipid phase through the lateral gate of the TIM23 complex. How the two transport modes are regulated and balanced against each other is unknown. Here we show that the import motor J-protein Pam18, which is essential for matrix import, controls lateral protein release into the lipid bilayer. Constitutively translocase-associated Pam18 obstructs lateral precursor transport. Concomitantly, Mgr2, implicated in precursor quality control, is displaced from the translocase. We conclude that during motor-dependent matrix protein transport, the transmembrane segment of Pam18 closes the lateral gate to promote anterograde polypeptide movement. This finding explains why a motor-free form of the translocase facilitates the lateral movement of precursors with a stop-transfer signal.