Functional compensation in a savanna scavenger community.

Functional redundancy, the potential for the functional role of one species to be fulfilled by another, is a key determinant of ecosystem viability. Scavenging transfers huge amount of energy through ecosystems and is, therefore, crucial for ecosystem viability and healthy ecosystem functioning. Despite this, relatively few studies have examined functional redundancy in scavenger communities. Moreover, the results of these studies are mixed and confined to a very limited range of habitat types and taxonomic groups. This study attempts to address this knowledge gap by conducting a field experiment in an undisturbed natural environment assessing functional roles and redundancy in vertebrate and invertebrate scavenging communities in a South African savanna. We used a large-scale field experiment to suppress ants in four 1 ha plots in a South African savanna and paired each with a control plot. We distributed three types of small food bait: carbohydrate, protein and seed, across the plots and excluded vertebrates from half the baits using cages. Using this combination of ant suppression and vertebrate exclusion, allowed us explore the contribution of non-ant invertebrates, ants and vertebrates in scavenging and also to determine whether either ants or vertebrates were able to compensate for the loss of one another. In this study, we found the invertebrate community carried out a larger proportion of overall scavenging services than vertebrates. Moreover, although scavenging was reduced when either invertebrates or vertebrates were absent, the presence of invertebrates better mitigated the functional loss of vertebrates than did the presence of vertebrates against the functional loss of invertebrates. There is a commonly held assumption that the functional role of vertebrate scavengers exceeds that of invertebrate scavengers; our results suggest that this is not true for small scavenging resources. Our study highlights the importance of invertebrates for securing healthy ecosystem functioning both now and into the future. We also build upon many previous studies which show that ants can have particularly large effects on ecosystem functioning. Importantly, our study suggests that scavenging in some ecosystems may be partly resilient to changes in the scavenging community, due to the potential for functional compensation by vertebrates and ants.

Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division.

Stem cells divide and differentiate to form all of the specialized cell types in a multicellular organism. In the Arabidopsis root, stem cells are maintained in an undifferentiated state by a less mitotically active population of cells called the quiescent center (QC). Determining how the QC regulates the surrounding stem cell initials, or what makes the QC fundamentally different from the actively dividing initials, is important for understanding how stem cell divisions are maintained. Here we gained insight into the differences between the QC and the cortex endodermis initials (CEI) by studying the mobile transcription factor SHORTROOT (SHR) and its binding partner SCARECROW (SCR). We constructed an ordinary differential equation model of SHR and SCR in the QC and CEI which incorporated the stoichiometry of the SHR-SCR complex as well as upstream transcriptional regulation of SHR and SCR. Our model prediction, coupled with experimental validation, showed that high levels of the SHR-SCR complex are associated with more CEI division but less QC division. Furthermore, our model prediction allowed us to propose the putative upstream SHR regulators SEUSS and WUSCHEL-RELATED HOMEOBOX 5 and to experimentally validate their roles in QC and CEI division. In addition, our model established the timing of QC and CEI division and suggests that SHR repression of QC division depends on formation of the SHR homodimer. Thus, our results support that SHR-SCR protein complex stoichiometry and regulation of SHR transcription modulate the division timing of two different specialized cell types in the root stem cell niche.

tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks.

Predicting gene regulatory networks (GRNs) from expression profiles is a common approach for identifying important biological regulators. Despite the increased use of inference methods, existing computational approaches often do not integrate RNA-sequencing data analysis, are not automated or are restricted to users with bioinformatics backgrounds. To address these limitations, we developed tuxnet, a user-friendly platform that can process raw RNA-sequencing data from any organism with an existing reference genome using a modified tuxedo pipeline (hisat 2 + cufflinks package) and infer GRNs from these processed data. tuxnet is implemented as a graphical user interface and can mine gene regulations, either by applying a dynamic Bayesian network (DBN) inference algorithm, genist, or a regression tree-based pipeline, rtp-star. We obtained time-course expression data of a PERIANTHIA (PAN) inducible line and inferred a GRN using genist to illustrate the use of tuxnet while gaining insight into the regulations downstream of the Arabidopsis root stem cell regulator PAN. Using rtp-star, we inferred the network of ATHB13, a downstream gene of PAN, for which we obtained wild-type and mutant expression profiles. Additionally, we generated two networks using temporal data from developmental leaf data and spatial data from root cell-type data to highlight the use of tuxnet to form new testable hypotheses from previously explored data. Our case studies feature the versatility of tuxnet when using different types of gene expression data to infer networks and its accessibility as a pipeline for non-bioinformaticians to analyze transcriptome data, predict causal regulations, assess network topology and identify key regulators.

The evolutionary impact of population size, mutation rate and virulence on pathogen niche width.

Understanding the evolution of pathogen niche width is important for predicting disease spread and the probability that pathogens can emerge in novel hosts. Findings from previous theoretical studies often suggest that pathogens will evolve to be specialists in specific host environments. However, several of these studies make unrealistic assumptions regarding demographic stochasticity and the ability of pathogens to select their hosts. Here, an individual-based model was used to predict how population size, virulence and pathogen mutation rate affects the evolution niche specialism in pathogens. Pathogen specialism evolved regardless of virulence or populations size; thus, the findings of this study are somewhat consistent with those of previous work. However, because specialist pathogens had only a weak selective advantage over generalist pathogens, high mutation rates caused random trait variation to accumulate, preventing the evolution of specialism. Mutation rate varies greatly across different species and strains of pathogen. By showing that high mutation rates may prevent pathogen specialism evolving, this study highlights an intrinsic pathogen trait that may influence the evolution of pathogen niche width.

Acoustofluidic device for acoustic capture of Bacillus anthracis spore analogues at low concentration.

A portable device for the rapid concentration of Bacillus subtilis var niger spores, also known as Bacillus globigii (BG), using a thin-reflector acoustofluidic configuration is described. BG spores form an important laboratory analog for the Bacillus anthracis spores, a serious health and bioterrorism risk. Existing systems for spore detection have limitations on detection time and detection that will benefit from the combination with this technology. Thin-reflector acoustofluidic devices can be cheaply and robustly manufactured and provide a more reliable acoustic force than previously explored quarter-wave resonator systems. The system uses the acoustic forces to drive spores carried in sample flows of 30 ml/h toward an antibody functionalized surface, which captures and immobilizes them. In this implementation, spores were fluorescently labeled and imaged. Detection at concentrations of 100 CFU/ml were demonstrated in an assay time of 10 min with 60% capture. We envisage future systems to incorporate more advanced detection of the concentrated spores, leading to rapid, sensitive detection in the presence of significant noise.

Mate-finding Allee effects can be exacerbated or relieved by sexual cannibalism.

Allee effects occur when individual or population survival decreases due to populations being small or sparse. A key mechanism underlying Allee effects is difficulty in finding mates at low densities. Species may be particularly vulnerable to mate-finding Allee effects if females rely on an abundance of males to reproduce successfully. In sexually cannibalistic species, females may consume males before or after copulation, potentially reducing the supply of males to the point where a mate-finding Allee effect occurs. In this study, we investigate the extent to which sexual cannibalism can modulate mate-finding Allee effects, and the conditions under which sexual cannibalism is likely to be particularly detrimental to population viability. We created an individual-based model that tracked specific females throughout the breeding season and used extinction risk and per capita growth rate to measure the strength of the Allee effects. We varied both founder population size and mate encounter rate independently of each other to expose the mechanism driving the Allee effects. We also analysed how cannibalism-derived female fecundity benefits affected extinction risk. We found that sexual cannibalism could lead to high extinction risk, particularly when cannibalism occurred before copulation, founder population size was small and mate encounter rates were low. However, post-copulatory cannibalism reduced extinction risk, if cannibalism increased female fecundity enough. We found that there were strong threshold effects, in which small changes in encounter rate could strongly alter population extinction risk. We find that sexual cannibalism is likely to negatively impact population survival as population size and mate encounter rate decrease. This may be exacerbated if male quality declines and female hunger increases in declining populations. As many top invertebrate predators, such as spiders and mantises, are sexually cannibalistic, this may have ecosystem-wide impacts. We also suggest that other reproductive behaviours, such as rejecting all but high-quality mates or requiring multiple mates to ensure fertility, are also likely to cause mate-finding Allee effects when habitat quality degrades.

Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells.

Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is essential for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. To accomplish this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference. We leveraged the topology of our networks to infer potential major regulators. Specifically, through mathematical modeling and experimental validation, we identified PERIANTHIA (PAN) as an important molecular regulator of quiescent center function. The results presented in this work show that our combination of molecular biology, computational biology, and mathematical modeling is an efficient approach to identify candidate factors that function in the stem cells.

An Overview of Drug Substance Manufacturing Processes.

To develop a comprehensive understanding of pharmaceutical drug substance manufacturing (DSM) processes, we conducted a data mining study to examine 50 new drug applications (NDAs) approved in 2010-2016. We analyzed the prevalence of several frequently deployed in-process control (IPC) techniques and postreaction workup procedures, as well as the operational conditions specified for reactions and workups. Our findings show that crystallization and high-performance liquid chromatography (HPLC) were the most commonly used workup steps and in-process controls, respectively, in drug substance manufacturing. On average, each NDA implemented 12.6 in-process controls and 11.3 workups. Operation time for reactions and workup procedures varied from a few minutes to multiple days, though 61% of these were between 1 and 10 h.

Attachment Versus Differentiation: The Contemporary Couple Therapy Debate.

This paper reviews the current debate between differentiation and attachment in treating couples through exploring the tenets of crucible therapy (Schnarch, 1991) and emotionally focused couple therapy (Johnson, 2004). We provide a review of the two theories-as well as the two "pure form" example models-and explore the debate in light of the integrative movement in couple and family therapy (Lebow, 2014). We also examine points of convergence of the two theories and models, and provide clinicians and researchers with an enhanced understanding of their divergent positions. Both differentiation and attachment are developmental theories that highlight the human experience of balancing individuality and connection in adulthood. The two models converge in terms of metaconcepts that pervade their respective theories and approach. Both models capitalize on the depth and importance of the therapeutic relationship, and provide rich case conceptualization and processes of therapy. However, they substantially differ in terms of how they view the fundamental aspects of adult development, have vastly divergent approaches to how a therapist intervenes in the room, and different ideas of how a healthy couple should function. In light of the deep polarization of the two models, points of integration-particularly between the broader theories of attachment and differentiation-are offered for therapists to consider.

Engineered oligosaccharyltransferases with greatly relaxed acceptor-site specificity.

The Campylobacter jejuni protein glycosylation locus (pgl) encodes machinery for asparagine-linked (N-linked) glycosylation and serves as the archetype for bacterial N-linked glycosylation. This machinery has been functionally transferred into Escherichia coli, enabling convenient mechanistic dissection of the N-linked glycosylation process in this genetically tractable host. Here we sought to identify sequence determinants in the oligosaccharyltransferase PglB that restrict its specificity to only those glycan acceptor sites containing a negatively charged residue at the -2 position relative to asparagine. This involved creation of a genetic assay, glycosylation of secreted N-linked acceptor proteins (glycoSNAP), that facilitates high-throughput screening of glycophenotypes in E. coli. Using this assay, we isolated several C. jejuni PglB variants that could glycosylate an array of noncanonical acceptor sequences, including one in a eukaryotic N-glycoprotein. These results underscore the utility of glycoSNAP for shedding light on poorly understood aspects of N-linked glycosylation and for engineering designer N-linked glycosylation biocatalysts.

Systematic analysis of intracellular mechanisms of propanol production in the engineered Thermobifida fusca B6 strain.

Thermobifida fusca is a moderately thermophilic actinobacterium naturally capable of utilizing lignocellulosic biomass. The B6 strain of T. fusca was previously engineered to produce 1-propanol directly on lignocellulosic biomass by expressing a bifunctional butyraldehyde/alcohol dehydrogenase (adhE2). To characterize the intracellular mechanisms related to the accumulation of 1-propanol, the engineered B6 and wild-type (WT) strains were systematically compared by analysis of the transcriptome and intracellular metabolome during exponential growth on glucose, cellobiose, and Avicel. Of the 18 known cellulases in T. fusca, 10 cellulase genes were transcriptionally expressed on all three substrates along with three hemicellulases. Transcriptomic analysis of cellodextrin and cellulose transport revealed that Tfu_0936 (multiple sugar transport system permease) was the key enzyme regulating the uptake of sugars in T. fusca. For both WT and B6 strains, it was found that growth in oxygen-limited conditions resulted in a blocked tricarboxylic acid (TCA) cycle caused by repressed expression of Tfu_1925 (aconitate hydratase). Further, the transcriptome suggested a pathway for synthesizing succinyl-CoA: oxaloacetate to malate (by malate dehydrogenase), malate to fumarate (by fumarate hydratase), and fumarate to succinate (by succinate dehydrogenase/fumarate reductase) which was ultimately converted to succinyl-CoA by succinyl-CoA synthetase. Both the transcriptome and the intracellular metabolome confirmed that 1-propanol was produced through succinyl-CoA, L-methylmalonyl-CoA, D-methylmalonyl-CoA, and propionyl-CoA in the B6 strain.

An engineered eukaryotic protein glycosylation pathway in Escherichia coli.

We performed bottom-up engineering of a synthetic pathway in Escherichia coli for the production of eukaryotic trimannosyl chitobiose glycans and the transfer of these glycans to specific asparagine residues in target proteins. The glycan biosynthesis was enabled by four eukaryotic glycosyltransferases, including the yeast uridine diphosphate-N-acetylglucosamine transferases Alg13 and Alg14 and the mannosyltransferases Alg1 and Alg2. By including the bacterial oligosaccharyltransferase PglB from Campylobacter jejuni, we successfully transferred glycans to eukaryotic proteins.

Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants.

BACKGROUND: Asymmetric cell divisions are formative divisions that generate daughter cells of distinct identity. These divisions are coordinated by either extrinsic ('niche-controlled') or intrinsic regulatory mechanisms and are fundamentally important in plant development. SCOPE: This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants. It further highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms. For example, the regulation of embryonic asymmetric divisions is described, including the first divisions of the zygote, formative vascular divisions and divisions that give rise to the root stem cell niche. Asymmetric divisions of the root cortex endodermis initial, pericycle cells that give rise to the lateral root primordium, procambium, cambium and stomatal cells are also discussed. Finally, a perspective is provided regarding the role of other hormones or regulatory molecules in asymmetric divisions, the presence of segregated determinants and the usefulness of modelling approaches in understanding network dynamics within these very special cells. CONCLUSIONS: Asymmetric cell divisions define plant development. High-throughput genomic and modelling approaches can elucidate their regulation, which in turn could enable the engineering of plant traits such as stomatal density, lateral root development and wood formation.

Sex ratio distorting microbes exacerbate arthropod extinction risk in variable environments.

Maternally-inherited sex ratio distorting microbes (SRDMs) are common among arthropod species. Typically, these microbes cause female-biased sex ratios in host broods, either by; killing male offspring, feminising male offspring, or inducing parthenogenesis. As a result, infected populations can experience drastic ecological and evolutionary change. The mechanism by which SRDMs operate is likely to alter their impact on host evolutionary ecology; despite this, the current literature is heavily biased towards a single mechanism of sex ratio distortion, male-killing. Furthermore, amidst the growing concerns surrounding the loss of arthropod diversity, research into the impact of SRDMs on the viability of arthropod populations is generally lacking. In this study, using a theoretical approach, we model the epidemiology of an understudied mechanism of microbially-induced sex ratio distortion-feminisation-to ask an understudied question-how do SRDMs impact extinction risk in a changing environment? We constructed an individual-based model and measured host population extinction risk under various environmental and epidemiological scenarios. We also used our model to identify the precise mechanism modulating extinction. We find that the presence of feminisers increases host population extinction risk, an effect that is exacerbated in highly variable environments. We also identified transmission rate as the dominant epidemiological trait responsible for driving extinction. Finally, our model shows that sex ratio skew is the mechanism driving extinction. We highlight feminisers and, more broadly, SRDMs as important determinants of the resilience of arthropod populations to environmental change.

A network of regulatory innovations to improve FDA quality assessments of human drug applications.

A network of regulatory innovations brings a holistic approach to improving the submission, assessment, and lifecycle management of pharmaceutical quality information in the U.S. This dedicated effort in the FDA's Center for Drug Evaluation and Research (CDER) aims to enhance the quality assessment of submissions for new drugs, generic drugs, and biological products including biosimilars. These regulatory innovations include developing or contributing: (i) the Knowledge-Aided Assessment and Structured Application (KASA), (ii) a new common technical document for quality (ICH M4Q(R2)), (iii) structured data on Pharmaceutical Quality/Chemistry, Manufacturing and Controls (PQ/CMC), (iv) Integrated Quality Assessment (IQA), (v) the Quality Surveillance Dashboard (QSD), and (vi) the Established Conditions tool from the ICH Q12 guideline. The innovations collectively drive CDER toward a more coordinated, effective, and efficient quality assessment. Improvements are made possible by structured regulatory submissions, a systems approach to quality risk management, and data-driven decisions based on science, risk, and effective knowledge management. The intended result is better availability of quality medicines for U.S. patients.

Glycans-by-design: engineering bacteria for the biosynthesis of complex glycans and glycoconjugates.

There is an urgent need for new tools that enable better understanding of the structure, recognition, metabolism, and biosynthesis of glycans as well as the production of biologically important glycans and glycoconjugates. With the discovery of glycoprotein synthesis in bacteria and functional transfer of glycosylation pathways between species, Escherichia coli cells have become a tractable host for both understanding glycosylation and the underlying glycan code of living cells as well as for expressing glycoprotein therapeutics and vaccines. Here, we review recent efforts to harness natural biological pathways and engineer synthetic designer pathways in bacteria for making complex glycans and conjugating these to lipids and proteins. The result of these efforts has been a veritable transformation of bacteria into living factories for scalable, bottom-up production of complex glycoconjugates by design.

Evolutionary engineering for industrial microbiology.

Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

Product Quality Research for Developing and Assessing Regulatory Submissions for Generic Cyclosporine Ophthalmic Emulsions.

Approval of the first generic 0.05% cyclosporine ophthalmic emulsion (COE) in the U.S. represents a milestone achievement of the science and research program in the U.S. Food and Drug Administration's Center for Drug Evaluation and Research (CDER). COE is a locally acting complex drug product indicated to increase tear production in patients whose production is presumed to be suppressed due to ocular inflammation associated with keratoconjunctivitis sicca. The path to approval required overcoming numerous scientific challenges to determining therapeutic equivalence to the reference listed drug. Researchers in CDER's Office of Pharmaceutical Quality and Office of Generic Drugs developed a quality by design approach to understand the effects of process and formulation variables on the product's critical quality attributes, including globule size distribution (GSD), turbidity, viscosity, zeta potential, surface tension, and osmolality. CDER researchers explored multiple techniques to perform physicochemical characterization and analyze the GSD including laser diffraction, nanoparticle tracking analysis, cryogenic transmission electron microscopy, dynamic light scattering, asymmetric field flow fractionation, and two-dimensional diffusion ordered spectroscopy nuclear magnetic resonance. Biphasic models to study drug transfer kinetics demonstrated that COEs with qualitative and quantitative sameness and comparable GSDs, analyzed using earth mover's distance, can be therapeutic equivalents. This body of research facilitated the review and approval of the first U.S. generic COE. In addition, the methods and fundamental understanding developed from this research may support the development and assessment of other complex generics. The approval of a generic COE should improve the availability of this complex drug product to U.S. patients.

Lessons from CDER's Quality Management Maturity Pilot Programs.

Between October 2020 and March 2022, FDA's Center for Drug Evaluation and Research (CDER) completed two pilot programs to assess the quality management maturity (QMM) of drug manufacturing establishments. Mature quality systems promote proactive detection of vulnerabilities, prevent problems before they occur, and foster a culture that rewards process and system improvements. A CDER QMM program may help to advance supply chain resiliency and robustness and mitigate drug shortages. One pilot program evaluated seven establishments located within the U.S. that produce finished dosage form products marketed in the U.S. A second pilot program evaluated eight establishments located outside the U.S. that produce active pharmaceutical ingredients used in drug products marketed in the U.S. The execution of these pilot programs afforded FDA the opportunity to learn important lessons about the establishment QMM assessment process, scoring approach, assessor behaviors, and perceptions of the assessment questions, reports, and ratings. Many of the participating establishments reported that the QMM pilot assessments helped to identify their strengths, weaknesses, and new areas for improvement which they had not previously identified through internal audits or CGMP inspections. There has been a great deal of interest in the outcomes of CDER's QMM pilot programs and this paper describes, for the first time, the lessons CDER learned and will continue to heed in the development of a QMM program.

AgScP2S6 van der Waals Layered Crystal: A Material with a Unique Combination of Extreme Nonlinear Optical Properties.

Research in two-dimensional layered materials (2DLMs) has exploded over the past several years for a variety of applications in photonics and optoelectronics. The 2D nature of these materials allows for a very local electronic probe of material as well as flexible integration with other functional components. Herein, using the femtosecond Z-scan technique, we report a giant two photon absorption (TPA) process and its saturation in the van der Waals gapped silver scandium thiophosphate (AgScP2S6) crystal. We have found a TPA coefficient of the order of 104 cm/GW which is orders of magnitude larger compared to many existing semiconductors and nonlinear crystals. Furthermore, we found a TPA cross-section of 103 GM and characterized the optical limiting (OL) response (0.2 mJ/cm2) and the multipulse laser damage threshold (1.09 ± 0.19 J/cm2). The combination of giant TPA, extremely low OL, and very high damage threshold suggests that this material could be extremely useful in applications like optical limiters or switches.