Associations between Johne's disease and fertility in UK dairy herds

The objective of this observational study was to quantify associations between Mycobacterium avium subspecies paratuberculosis (MAP) antibody status and a variety of fertility outcomes, in UK dairy cattle. Longitudinal milk recording, fertility and MAP antibody enzyme-linked immunosorbent assay (ELISA) milk test data were collated retrospectively from 121,762 lactations in 78 herds. Datasets were structured into appropriate units to suit outcomes and enable temporal association between current and future MAP status, and fertility measures. Current MAP status was categorised according to most recent status within 180 days, with time-related future MAP status assigned based on MAP antibody ELISA milk test data for each cow. Multilevel multivariable logistic regression models were used to evaluate associations between MAP status and 21-day pregnancy and submission rate and conception risk. Posterior predictions and cross-validation techniques were used to assess model fit and check model building assumptions. A negative association was found between risk of insemination (Odds Ratio [OR], 0.78; 95% Credible Interval [CI], 0.66-0.92) and conception occurring (OR, 0.65; CI, 0.5-0.84) and transition from negative to non-negative MAP test status in the next 30-90 days. A positive association was observed between risk of insemination (OR, 1.34; CI, 1.16-1.52) and conception occurring (OR, 1.26; CI, 1.11-1.43) and transition from negative to non-negative MAP test status in the next 90-180 days. Current positive MAP test status was negatively and positively associated with insemination (OR, 0.59; CI, 0.49-0.70) and conception risk (OR, 1.12; CI, 0.96-1.30), respectively. Herd managers will have had access to test results, declaring cows with past recent or multiple positive MAP antibody ELISA results not to be bred, negatively influencing insemination risk. Overall, these results demonstrate the temporal association between a positive MAP antibody ELISA result and dairy cow fertility outcomes, with particular variability prior to a positive MAP antibody ELISA result.

An engineered N-acyltransferase-LOV2 domain fusion protein enables light-inducible allosteric control of enzymatic activity

Transferases are ubiquitous across all known life. While much work has been done to understand and describe these essential enzymes, there have been minimal efforts to exert tight and reversible control over their activity for various biotechnological applications. Here, we apply a rational, computation-guided methodology to design and test a transferase-class enzyme allosterically regulated by light-oxygen-voltage 2 sensing domain. We utilize computational techniques to determine the intrinsic allosteric networks within N-acyltransferase (Orf11/∗Dbv8) and identify potential allosteric sites on the protein's surface. We insert light-oxygen-voltage 2 sensing domain at the predicted allosteric site, exerting reversible control over enzymatic activity. We demonstrate blue-light regulation of N-acyltransferase (Orf11/∗Dbv8) function. Our study for the first time demonstrates optogenetic regulation of a transferase-class enzyme as a proof-of-concept for controllable transferase design. This successful design opens the door for many future applications in metabolic engineering and cellular programming.

Beyond Content, Understanding What Makes Test Questions Most Challenging

When students answer test questions incorrectly, we often assume they don't understand the content; instead, they may struggle with certain cognitive skills or with how questions are asked. Our goal was to look beyond content to understand what makes assessment questions most challenging. On the basis of more than 76,000 answers to multiple-choice questions in a large, introductory biology course, we examined three question components—cognitive skills, procedural knowledge, and question forms—and their interactions. We found that the most challenging questions require the students to organize information and make meaning from it—skills that are essential in science. For example, some of the most challenging questions are presented as unstructured word problems and require interpretation; to answer correctly, the students must identify and extract the important information and construct their understanding from it. Our results highlight the importance of teaching students to organize and make meaning from the content we teach.

Molecular Mechanisms of Winter Survival

Winter provides many challenges for insects, including direct injury to tissues and energy drain due to low food availability. As a result, the geographic distribution of many species is tightly coupled to their ability to survive winter. In this review, we summarize molecular processes associated with winter survival, with a particular focus on coping with cold injury and energetic challenges. Anticipatory processes such as cold acclimation and diapause cause wholesale transcriptional reorganization that increases cold resistance and promotes cryoprotectant production and energy storage. Molecular responses to low temperature are also dynamic and include signaling events during and after a cold stressor to prevent and repair cold injury. In addition, we highlight mechanisms that are subject to selection as insects evolve to variable winter conditions. Based on current knowledge, despite common threads, molecular mechanisms of winter survival vary considerably across species, and taxonomic biases must be addressed to fully appreciate the mechanistic basis of winter survival across the insect phylogeny.

Postsecondary Faculty Attitudes and Beliefs about Writing-Based Pedagogies in the STEM Classroom

Writing is an important skill for communicating knowledge in science, technology, engineering, and mathematics (STEM) and an aid to developing students' communication skills, content knowledge, and disciplinary thinking. Despite the importance of writing, its incorporation into the undergraduate STEM curriculum is uneven. Research indicates that understanding faculty beliefs is important when trying to propagate evidence-based instructional practices, yet faculty beliefs about writing pedagogies are not yet broadly characterized for STEM teaching at the undergraduate level. Based on a nationwide cross-disciplinary survey at research-intensive institutions, this work aims to understand the extent to which writing is assigned in undergraduate STEM courses and the factors that influence faculty members' beliefs about, and reported use of, writing-based pedagogies. Faculty attitudes about the effectiveness of writing practices did not differ between faculty who assign and do not assign writing; rather, beliefs about the influence of social factors and contextually imposed instructional constraints informed their decisions to use or not use writing. Our findings indicate that strategies to increase the use of writing need to specifically target the factors that influence faculty decisions to assign or not assign writing. It is not faculty beliefs about effectiveness, but rather faculty beliefs about behavioral control and constraints at the departmental level that need to be targeted.

Enhanced Degradation of Juvenile Hormone Promotes Reproductive Diapause in the Predatory Ladybeetle Coccinella Septempunctata

Improved knowledge on the regulation of reproductive diapause in Coccinella septempunctata, an important predator of aphids, is crucial for improving shelf-life and mass production of the ladybeetles. In many insects, the absence of juvenile hormone (JH) is a central regulator of reproductive diapause. JH is principally degraded by JH esterase (JHE) and JH epoxide hydrolase (JHEH). Previous studies have shown that genes encoding these enzymes were upregulated in early diapause of C. septempunctata, but whether increased JH degradation contributes to the reduction of JH levels and facilitates reproductive diapause remains unknown. Here, we investigate the role of JH and JH degradation genes during reproductive diapause in C. septempunctata females. Applying methoprene, a JH analogue, to the diapause preparation females clearly elevated JH signaling and reversed diapause program, suggesting that a lower level of JH is critical for the induction of reproductive diapause in the ladybeetle. Full-length cDNA sequences of JHE and JHEH were cloned and characterized, and their deduced proteins contain all the conserved active domains and typical motifs as identified in other insects. The expressions of JHE and JHEH were both significantly increased in diapause preparation and remained at a high level for a period throughout diapause, and then decreased after the termination of diapause. Knocking down these JH degradation genes clearly increased the expression levels of JH-inducible genes Krüppel-homolog 1 (Kr-h1) and vitellogenin (Vg), indicating an elevated JH level. Simultaneously, silencing JH degradation genes distinctly reduced diapause-related features and promotes reproduction, indicated by accelerated ovary growth, yolk deposition, and suppressed lipid accumulation. These results indicate that the enhanced JH degradation plays a critical role in regulating reproductive diapause of C. septempunctata.

Teaching during a pandemic: Using high-impact writing assignments to balance rigor, engagement, flexibility, and workload

The COVID-19 pandemic has created new challenges for instructors who seek high-impact educational practices that can be facilitated online without creating excessive burdens with technology, grading, or enforcement of honor codes. These practices must also account for the possibility that some students may need to join courses asynchronously and have limited or unreliable connectivity. Of the American Association of Colleges and University's list of 11 high-impact educational practices, writing-intensive courses may be the easiest for science faculty to adopt during these difficult times. Not only can writing assignments promote conceptual learning, they can also deepen student engagement with the subject matter and with each other. Furthermore, writing assignments can be incredibly flexible in terms of how they are implemented online and can be designed to reduce the possibility of cheating and plagiarism. To accelerate the adoption of writing pedagogies, we summarize evidence-based characteristics of effective writing assignments and offer a sample writing assignment from an introductory ecology course. We then suggest five strategies to help instructors manage their workload. Although the details of the sample assignment may be particular to our course, this framework is general enough to be adapted to most science courses, including those taught in-person, those taught online, and those that must be able to switch quickly between the two.

Noncoding RNA Regulation of Dormant States in Evolutionarily Diverse Animals

Dormancy is evolutionarily widespread and can take many forms, including diapause, dauer formation, estivation, and hibernation. Each type of dormancy is characterized by distinct features; but accumulating evidence suggests that each is regulated by some common processes, often referred to as a common "toolkit" of regulatory mechanisms, that likely include noncoding RNAs that regulate gene expression. Noncoding RNAs, especially microRNAs, are well-known regulators of biological processes associated with numerous dormancy-related processes, including cell cycle progression, cell growth and proliferation, developmental timing, metabolism, and environmental stress tolerance. This review provides a summary of our current understanding of noncoding RNAs and their involvement in regulating dormancy.

Distinct microRNA and mRNA responses elicited by ecdysone, diapause hormone and a diapause hormone analog at diapause termination in pupae of the corn earworm, Helicoverpa zea

Ecdysone, diapause hormone and a diapause hormone analog are all capable of breaking pupal diapause and prompting initiation of adult development in the cotton earworm, Helicoverpa zea. In this study we asked whether these three chemically-distinct diapause terminators elicit the same effect on expression of a collection of microRNAs and transcripts encoding components of the ecdysone signaling pathway. Injection of all three endocrine agents resulted in downregulation of one miRNA, miR-277-3p, a miRNA previously linked to the insulin/FOXO signaling pathway, and all three agents promoted upregulation of spook, a member of the ecdysone biosynthesis pathway, and iswi, an ecdysone-responsive transcript. Other miRNA and mRNA responses varied depending on the agent used to terminate diapause, thus suggesting that different endocrine pathways and mechanisms can lead to the same final developmental response.

Student Learning Dispositions: Multidimensional Profiles Highlight Important Differences among Undergraduate STEM Honors Thesis Writers

Various personal dimensions of students-particularly motivation, self-efficacy beliefs, and epistemic beliefs-can change in response to teaching, affect student learning, and be conceptualized as learning dispositions. We propose that these learning dispositions serve as learning outcomes in their own right; that patterns of interrelationships among these specific learning dispositions are likely; and that differing constellations (or learning disposition profiles) may have meaningful implications for instructional practices. In this observational study, we examine changes in these learning dispositions in the context of six courses at four institutions designed to scaffold undergraduate thesis writing and promote students' scientific reasoning in writing in science, technology, engineering, and mathematics. We explore the utility of cluster analysis for generating meaningful learning disposition profiles and building a more sophisticated understanding of students as complex, multidimensional learners. For example, while students' self-efficacy beliefs about writing and science increased across capstone writing courses on average, there was considerable variability at the level of individual students. When responses on all of the personal dimensions were analyzed jointly using cluster analysis, several distinct and meaningful learning disposition profiles emerged. We explore these profiles in this work and discuss the implications of this framework for describing developmental trajectories of students' scientific identities.

Understanding the Complex Relationship between Critical Thinking and Science Reasoning among Undergraduate Thesis Writers

Developing critical-thinking and scientific reasoning skills are core learning objectives of science education, but little empirical evidence exists regarding the interrelationships between these constructs. Writing effectively fosters students' development of these constructs, and it offers a unique window into studying how they relate. In this study of undergraduate thesis writing in biology at two universities, we examine how scientific reasoning exhibited in writing (assessed using the Biology Thesis Assessment Protocol) relates to general and specific critical-thinking skills (assessed using the California Critical Thinking Skills Test), and we consider implications for instruction. We find that scientific reasoning in writing is strongly related to inference, while other aspects of science reasoning that emerge in writing (epistemological considerations, writing conventions, etc.) are not significantly related to critical-thinking skills. Science reasoning in writing is not merely a proxy for critical thinking. In linking features of students' writing to their critical-thinking skills, this study 1) provides a bridge to prior work suggesting that engagement in science writing enhances critical thinking and 2) serves as a foundational step for subsequently determining whether instruction focused explicitly on developing critical-thinking skills (particularly inference) can actually improve students' scientific reasoning in their writing.

Changes in microRNA abundance may regulate diapause in the flesh fly, Sarcophaga bullata

Diapause, an alternative developmental pathway characterized by changes in developmental timing and metabolism, is coordinated by molecular mechanisms that are not completely understood. MicroRNA (miRNA) mediated gene silencing is emerging as a key component of animal development and may have a significant role in initiating, maintaining, and terminating insect diapause. In the present study, we test this possibility by using high-throughput sequencing and qRT-PCR to discover diapause-related shifts in miRNA abundance in the flesh fly, Sarcophaga bullata. We identified ten evolutionarily conserved miRNAs that were differentially expressed in diapausing pupae compared to their nondiapausing counterparts. miR-289-5p and miR-1-3p were overexpressed in diapausing pupae and may be responsible for silencing expression of candidate genes during diapause. miR-9c-5p, miR-13b-3p, miR-31a-5p, miR-92b-3p, miR-275-3p, miR-276a-3p, miR-277-3p, and miR-305-5p were underexpressed in diapausing pupae and may contribute to increased expression of heat shock proteins and other factors necessary for the enhanced environmental stress-response that is a feature of diapause. In S. bullata, a maternal effect blocks the programming of diapause in progeny of females that have experienced pupal diapause, and in this study we report that several miRNAs, including miR-263a-5p, miR-100-5p, miR-125-5p, and let-7-5p were significantly overexpressed in such nondiapausing flies and may prevent entry into diapause. Together these miRNAs appear to be integral to the molecular processes that mediate entry into diapause.

Changes in histone acetylation as potential mediators of pupal diapause in the flesh fly, Sarcophaga bullata

The growing appreciation that epigenetic processes are integral to the responses of many organisms to changes in the environment suggests a possible role for epigenetics in coordination of insect diapause. The results we present suggest that histone modification may be one type of epigenetic process that contributes to regulation of pupal diapause in the flesh fly, Sarcophaga bullata. Reduction in total histone H3 acetylation in diapausing pupae, shifts in mRNA expression profiles of genes encoding histone acetyltransferase (HAT) and histone deacetylase (HDAC) in pre-diapause, diapause and post-diapause flies compared to their nondiapause counterparts, and alterations in HDAC enzyme activity during and post-diapause lend support to the hypothesis that this specific type of histone modification is involved in regulating diapause programming, maintenance, and termination. Transcription of genes encoding HDAC1, HDAC3, HDAC6, and Sirtuin2 were all upregulated in photosensitive first instar larvae programmed to enter pupal diapause, suggesting that histone deacetylation may be linked to the early decision to enter diapause. A 50% reduction in transcription of hdac3 and a corresponding 30% reduction in HDAC activity during diapause suggest that removal of acetyl groups from histones primarily occurs prior to diapause entry and that further histone deacetylation is not necessary to maintain diapause. Transcription of the HDAC genes was quickly elevated when diapause was terminated, followed by an increase in enzyme activity after a short delay. A maternal effect operating in these flies prevents pupal diapause in progeny whose mothers experienced pupal diapause, even if the progeny are reared in strong diapause-inducing short-day conditions. Such nondiapausing pupae had HDAC transcription profiles nearly identical to the profiles seen in nondiapausing pupae generated under a long-day photoperiod. Together, these results provide consistent evidence for histone acetylation and deacetylation as regulators of this insect's developmental trajectory.

Concept Maps for Improved Science Reasoning and Writing: Complexity Isn't Everything

A pervasive notion in the literature is that complex concept maps reflect greater knowledge and/or more expert-like thinking than less complex concept maps. We show that concept maps used to structure scientific writing and clarify scientific reasoning do not adhere to this notion. In an undergraduate course for thesis writers, students use concept maps instead of traditional outlines to define the boundaries and scope of their research and to construct an argument for the significance of their research. Students generate maps at the beginning of the semester, revise after peer review, and revise once more at the end of the semester. Although some students revised their maps to make them more complex, a significant proportion of students simplified their maps. We found no correlation between increased complexity and improved scientific reasoning and writing skills, suggesting that sometimes students simplify their understanding as they develop more expert-like thinking. These results suggest that concept maps, when used as an intervention, can meet the varying needs of a diverse population of student writers.

Transcriptional evidence for small RNA regulation of pupal diapause in the flesh fly, Sarcophaga bullata

Understanding the molecular basis of diapause, a phenotypically plastic, alternative developmental pathway, is key to predicting the seasonal distribution of economically and medically important insect species. Small regulatory RNAs, including piwi-related RNAs, small-interfering RNAs, and miRNAs, represent one type of epigenetic process that can alter the phenotype of organisms independent of changes in genome sequence. We hypothesize that small RNAs regulate pupal diapause and a maternal block of diapause in the flesh fly Sarcophaga bullata. We assessed the relative abundance of eight genes related to small RNA biogenesis and function using qRT-PCR in pre-diapause and diapause stages compared to their non-diapause counterparts. Elevated mRNA expression of piwi and spindle-E, as well as argonaute2 and r2d2, in photosensitive 1st instar larvae reared in diapause-inducing conditions indicate involvement of the piwi-associated RNA and small-interfering RNA pathways, respectively, in programming the switch from direct development to a developmental pathway that includes diapause. Two genes, related to the microRNA pathway, argonaute1 and loquacious, are upregulated during pupal diapause, suggesting a role for this pathway in maintaining diapause. Substantial reduction in transcript abundance of small RNA-related genes in photosensitive 1st instar larvae from mothers with a diapause history compared to those from mothers with no diapause history also suggest a role for small RNA pathways in regulating a diapause maternal effect in S. bullata. Together, the results point to a role for small RNAs in regulating the developmental trajectory in this species.

RNA-Seq reveals early distinctions and late convergence of gene expression between diapause and quiescence in the Asian tiger mosquito, Aedes albopictus

Dormancy is a crucial adaptation allowing insects to withstand harsh environmental conditions. The pre-programmed developmental arrest of diapause is a form of dormancy that is distinct from quiescence, in which development arrests in immediate response to hardship. Much progress has been made in understanding the environmental and hormonal controls of diapause. However, studies identifying transcriptional changes unique to diapause, rather than quiescence, are lacking, making it difficult to disentangle the transcriptional profiles of diapause from dormancy in general. The Asian tiger mosquito, Aedes albopictus, presents an ideal model for such a study, as diapausing and quiescent eggs can be staged and collected for global gene expression profiling using a newly developed transcriptome. Here, we use RNA-Seq to contrast gene expression during diapause with quiescence to identify transcriptional changes specific to the diapause response. We identify global trends in gene expression that show gradual convergence of diapause gene expression upon gene expression during quiescence. Functionally, early diapause A. albopictus show strong expression differences of genes involved in metabolism, which diminish over time. Of these, only expression of lipid metabolism genes remained distinct in late diapause. We identify several genes putatively related to hormonal control of development that are persistently differentially expressed throughout diapause, suggesting these might be involved in the maintenance of diapause. Our results identify key biological differences between diapausing and quiescent pharate larvae, and suggest candidate pathways for studying metabolism and the hormonal control of development during diapause in other species.

Transcriptome sequencing as a platform to elucidate molecular components of the diapause response in the Asian tiger mosquito, Aedes albopictus

Diapause has long been recognized as a crucial ecological adaptation to spatio-temporal environmental variation. More recently, rapid evolution of the diapause response has been implicated in response to contemporary global warming and during the range expansion of invasive species. Although the molecular regulation of diapause remains largely unresolved, rapidly emerging next-generation sequencing (NGS) technologies provide exciting opportunities to address this longstanding question. Herein, a new assembly from life-history stages relevant to diapause in the Asian tiger mosquito, Aedes albopictus (Skuse) is presented, along with unique methods for the analysis of NGS data and transcriptome assembly. A digital normalization procedure that significantly reduces computational resources required for transcriptome assembly is evaluated. Additionally, a method for protein reference-based and genomic reference-based merged assembly of 454 and Illumina reads is described. Finally, a gene ontology analysis is presented, which creates a platform to identify physiological processes associated with diapause. Taken together, these methods provide valuable tools for analyzing the transcriptional underpinnings of many complex phenotypes, including diapause, and provide a basis for determining the molecular regulation of diapause in Ae. albopictus.

Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus

Seasonal environments present fundamental physiological challenges to a wide range of insects. Many temperate insects surmount the exigencies of winter by undergoing photoperiodic diapause, in which photoperiod provides a token cue that initiates an alternative developmental programme leading to dormancy. Pre-diapause is a crucial preparatory phase of this process, preceding developmental arrest. However, the regulatory and physiological mechanisms of diapause preparation are largely unknown. Using high-throughput gene expression profiling in the Asian tiger mosquito, Aedes albopictus, we reveal major shifts in endocrine signalling, cell proliferation, metabolism, energy production and cellular structure across pre-diapause development. While some hallmarks of diapause, such as insulin signalling and stress response, were not important at the transcriptional level, two genes, Pepck and PCNA, appear to show diapause-induced transcriptional changes across insect taxa. These processes demonstrate physiological commonalities between Ae. albopictus pre-diapause and diapause strategies across insects, and support the idea of a genetic 'toolkit' for diapause. Observations of gene expression trends from a comparative developmental perspective suggest that individual physiological processes are delayed against a background of a fixed morphological ontogeny. Our results demonstrate how deep sequencing can provide new insights into elusive molecular bases of complex ecological adaptations.

Transcript profiling reveals mechanisms for lipid conservation during diapause in the mosquito, Aedes albopictus

The Asian tiger mosquito, Aedes albopictus, is a medically important invasive species whose geographic distribution has expanded dramatically during the past 20 years, and one of the key elements of its success is its capacity to survive long distance transport as a diapausing pharate first instar larva, encased within the chorion of the egg. We report that pharate larvae entering diapause are larger and contain 30% more lipid than their nondiapausing counterparts. To improve our understanding of the molecular regulation of lipid metabolism during diapause, we assessed the relative mRNA abundance of 21 genes using qRT-PCR. Elevated expression of lipid storage droplet protein 2 during embryonic development likely contributes to the higher amounts of lipid we noted in diapausing individuals. The conservation of lipids during diapause is reflected in downregulation of genes involved in lipid catabolism, including lipase 2, lipase 3, lipase 4, acyl-CoA dehydrogenase 4, and isovaleryl-CoA dehydrogenase. Two genes involved in fatty acid synthesis and modification, Δ(9)-desaturase, and fatty acyl-CoA elongase, were both upregulated in diapausing pharate larvae, suggesting roles for their gene products in generating unsaturated fatty acids to enhance membrane fluidity at low temperatures and generating precursors to the surface hydrocarbons needed to resist desiccation, respectively. Together, the results point to substantial distinctions in lipid metabolism within the embryo as a consequence of the diapause program, and these differences occur both before the actual onset of diapause as well as during the diapause state.

Writing-to-learn in undergraduate science education: a community-based, conceptually driven approach

Despite substantial evidence that writing can be an effective tool to promote student learning and engagement, writing-to-learn (WTL) practices are still not widely implemented in science, technology, engineering, and mathematics (STEM) disciplines, particularly at research universities. Two major deterrents to progress are the lack of a community of science faculty committed to undertaking and applying the necessary pedagogical research, and the absence of a conceptual framework to systematically guide study designs and integrate findings. To address these issues, we undertook an initiative, supported by the National Science Foundation and sponsored by the Reinvention Center, to build a community of WTL/STEM educators who would undertake a heuristic review of the literature and formulate a conceptual framework. In addition to generating a searchable database of empirically validated and promising WTL practices, our work lays the foundation for multi-university empirical studies of the effectiveness of WTL practices in advancing student learning and engagement.

A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation

Background

Many temperate insects survive the harsh conditions of winter by undergoing photoperiodic diapause, a pre-programmed developmental arrest initiated by short day lengths. Despite the well-established ecological significance of photoperiodic diapause, the molecular basis of this crucial adaptation remains largely unresolved. The Asian tiger mosquito, Aedes albopictus (Skuse), represents an outstanding emerging model to investigate the molecular basis of photoperiodic diapause in a well-defined ecological and evolutionary context. Ae. albopictus is a medically significant vector and is currently considered the most invasive mosquito in the world. Traits related to diapause appear to be important factors contributing to the rapid spread of this mosquito. To generate novel sequence information for this species, as well as to discover transcripts involved in diapause preparation, we sequenced the transcriptome of Ae. albopictus oocytes destined to become diapausing or non-diapausing pharate larvae.

Results

454 GS-FLX transcriptome sequencing yielded >1.1 million quality-filtered reads, which we assembled into 69,474 contigs (N50 = 1,009 bp). Our contig filtering approach, where we took advantage of strong sequence similarity to the fully sequenced genome of Aedes aegypti, as well as other reference organisms, resulted in 11,561 high-quality, conservative ESTs. Differential expression estimates based on normalized read counts revealed 57 genes with higher expression, and 257 with lower expression under diapause-inducing conditions. Analysis of expression by qPCR for 47 of these genes indicated a high correlation of expression levels between 454 sequence data and qPCR, but congruence of statistically significant differential expression was low. Seven genes identified as differentially expressed based on qPCR have putative functions that are consistent with the insect diapause syndrome; three genes have unknown function and represent novel candidates for the transcriptional basis of diapause.

Conclusions

Our transcriptome database provides a rich resource for the comparative genomics and functional genetics of Ae. albopictus, an invasive and medically important mosquito. Additionally, the identification of differentially expressed transcripts related to diapause enriches the limited knowledge base for the molecular basis of insect diapause, in particular for the preparatory stage. Finally, our analysis illustrates a useful approach that draws from a closely related reference genome to generate high-confidence ESTs in a non-model organism.

Metabolic restructuring during energy-limited states: insights from Artemia franciscana embryos and other animals

Many life history stages of animals that experience environmental insults enter developmental arrested states that are characterized by reduced cellular proliferation, with or without a concurrent reduction in overall metabolism. In the case of the most profound metabolic arrest reported in invertebrates, i.e., anaerobic quiescence in Artemia franciscana embryos, acidification of the intracellular milieu is a major factor governing catabolic and anabolic downregulation. Release of ions from intracellular compartments is the source for approximately 50% of the proton equivalents needed for the 1.5 unit acidification that is observed. Recovery from the metabolic arrest requires re-sequestration of the protons with a vacuolar-type ATPase (V-ATPase). The remarkable facet of this mechanism is the ability of embryonic cells to survive the dissipation of intracellular ion gradients. Across many diapause-like states, the metabolic reduction and subsequent matching of energy demand is accomplished by shifting energy metabolism from oxidative phosphorylation to aerobic glycolysis. Molecular pathways that are activated to induce these resilient hypometabolic states include stimulation of the AMP-activated protein kinase (AMPK) and insulin signaling via suite of daf (dauer formation) genes for diapause-like states in nematodes and insects. Contributing factors for other metabolically depressed states involve hypoxia-inducible factor-1 and downregulation of the pyruvate dehydrogenase complex. Metabolic similarities between natural states of stasis and some cancer phenotypes are noteworthy. Reduction of flux through oxidative phosphorylation helps prevent cell death in certain cancer types, similar to the way it increases viability of dauer stages in Caenorhabditis elegans. Mechanisms that underlie natural stasis are being used to pre-condition mammalian cells prior to cell biostabilization and storage.

Want to improve undergraduate thesis writing? Engage students and their faculty readers in scientific peer review

One of the best opportunities that undergraduates have to learn to write like a scientist is to write a thesis after participating in faculty-mentored undergraduate research. But developing writing skills doesn't happen automatically, and there are significant challenges associated with offering writing courses and with individualized mentoring. We present a hybrid model in which students have the structural support of a course plus the personalized benefits of working one-on-one with faculty. To optimize these one-on-one interactions, the course uses BioTAP, the Biology Thesis Assessment Protocol, to structure engagement in scientific peer review. By assessing theses written by students who took this course and comparable students who did not, we found that our approach not only improved student writing but also helped faculty members across the department--not only those teaching the course--to work more effectively and efficiently with student writers. Students who enrolled in this course were more likely to earn highest honors than students who only worked one-on-one with faculty. Further, students in the course scored significantly better on all higher-order writing and critical-thinking skills assessed.

Empirical correlation between hydrophobic free energy and aqueous cavity surface area

The unitary free energy of transfer of a hydrocarbon molecule from a hydrocarbon solvent to an aqueous medium is a measure of the hydrophobic interaction in the aqueous medium. We have reexamined available data on this phenomenon and have confirmed that the free energy for saturated hydrocarbons is proportional to the surface area of the cavity created by the solute in the aqueous solution, with the same proportionality constant for linear, branched, and cyclic hydrocarbon molecules. The numerical value of the proportionality constant is uncertain because absolute and self-consistent area measurements are not available. We estimate that it falls between 20 and 25 cal/mole per A(2) at 25 degrees (for areas measured at the distance of closest approach of water molecules), which is significantly less than the figure of 33 cal/mole per A(2) that has been assigned to the same parameter by Hermann [J. Phys. Chem. 76, 2754-2759 (1972)]. A small discrepancy exists when similar data for homologous series of alkyl derivatives are compared with results based on hydrocarbons themselves, and possible reasons for it are discussed.

Decoupling development and energy flow during embryonic diapause in the cricket, Allonemobius socius

Respiration rate increases 6.3-fold during 15 days of post-oviposition development in embryos of the Southern ground cricket, Allonemobius socius. This ontogenetic increase in metabolism of non-diapause insects is blocked during diapause, such that metabolic rate is only 36% of the rate measured for 15 days developing embryos. Surprisingly, however, there is not an acute metabolic depression during diapause entry at the point when developmental ceases (4-5 days post-oviposition), as measured by blockage of morphological change and DNA proliferation. The results indicate a decoupling of developmental arrest from metabolism. Both non-diapause and diapause embryos have unusually high [AMP]:[ATP] ratios and low [ATP]:[ADP] ratios during early embryogenesis, which suggests embryos may have experienced hypoxia as a result of an insect chorion that limits water loss but may restrict oxygen diffusion. The similar adenylate profiles for these two developmental states indicate the atypical energy status is not a specific feature of diapause. In addition embryos at day 3 have high levels of lactate that decrease as development proceeds up to day 7. Calorimetric-respirometric (CR) ratios of -353 (day 3) to -333 (day 7) kJ mol(-1) O2 are consistent with embryos that are aerobically recovering from hypoxia, but are inconsistent with an ongoing anaerobic contribution to metabolism. Superfusing 3-day embryos with O2 enriched air (40% O2) forces these metabolic indicators toward a more aerobic poise, but only partially. Taken together these biochemical data indicate the metabolic poise of A. socius is only partly explained by hypoxia in early development, and that the atypical set points are also intrinsic features of this ontogenetic period in the life cycle.

Embryonic diapause highlighted by differential expression of mRNAs for ecdysteroidogenesis, transcription and lipid sparing in the cricket Allonemobius socius

Embryos of the ground cricket, Allonemobius socius, enter diapause 4-5 days post-oviposition and overwinter in this dormant state that is characterized by developmental arrest. Suppressive subtractive hybridization and quantitative real-time PCR reveal eight candidate genes in pre-diapause embryos that show promise as regulators of diapause entry, when compared with embryos not destined for diapause. Identifications are based both on the magnitude/consistency of differential mRNA abundances and the predicted functions of their products when placed in context of the physiological and biochemical events of diapause characterized in our companion paper. The proteins CYP450, AKR and RACK1 (associated with ecdysteroid synthesis and signaling) are consistently upregulated in pre-diapause, followed by major downregulation later in diapause. The pattern suggests that elevated ecdysone may facilitate onset of diapause in A. socius. Upregulation seen for the transcription factors Reptin and TFDp2 may serve to depress transcription and cell cycle progression. Cathpesin B-like protease, ACLY and MSP are three downregulated genes associated with yolk mobilization and/or metabolism that we predict may promote lipid sparing. Finally, embryos that have been in diapause for 10 days show a substantially different pattern of mRNA expression compared with either pre-diapause or embryos not destined for diapause, with the majority of mRNAs examined being downregulated. These transcript levels in later diapause suggest that a number of upregulated genes in pre-diapause are transiently expressed and are less essential as diapause progresses.

Effects of rituximab on resistant SLE disease including lung involvement

We present a retrospective review of 11 patients with refractory systemic lupus erythematosus (SLE) treated with rituximab after failing corticosteroids and at least one other immunosuppressive drug. We measured clinical response using the Classic British Isles Lupus Assessment Group (BILAG) index, serum complement and reduction in maintenance prednisolone dose. B cells were measured using flow cytometry, and lung function testing was used to assess severe pulmonary disease (three patients). The median patient age was 42 years (range, 25–64) with median disease duration 6 years (range, 2–12). In all, 10 of 11 patients responded initially, with median global BILAG reduction of 7.5 at 6 months ( P = 0.007), with loss of all A and B scores by 7 months. Rituximab treatment was associated with normalisation of complement (C3 P = 0.008, C4 P = 0.018) and reduction in steroid requirement, median reduction 15 mg/day ( P = 0.036). In 9 of 10 patients who responded, all other immunosuppressants were stopped. There was no significant difference in anti-dsDNA antibody titres in these responders, but they were negative or had low titres at baseline. B-cell depletion continued for median 4 months (range, 2–9), and disease flare occurred at a median 6.6 months (range, 1.5–23) and was preceded by B-cell recovery in all but two patients. Rituximab was beneficial in refractory SLE including severe neurological and cardiorespiratory disease by inducing disease remission, allowing withdrawal of other agents and reduction in steroid requirement. Rituximab appeared to stabilise and possibly improve progressive lung disease.

Acupuncture for irritable bowel syndrome an exploratory randomised controlled trial

BACKGROUND

The evidence on the effectiveness of acupuncture for irritable bowel syndrome (IBS) is inconclusive. However, many patients with IBS are self referring for acupuncture, therefore it is of interest to know whether acupuncture is effective or not. The aim of this study was to establish variability in the primary outcome measure to enable a sample size to be calculated for a full scale trial, and to explore feasibility and design criteria.

METHODS

A pragmatic randomised controlled trial compared 10 sessions of acupuncture plus usual GP care with usual GP care alone. Thirty patients were recruited from four GP databases in Birmingham, UK, and randomised one-to-two to acupuncture or usual care alone. The primary outcome was the IBS Symptom Severity Score (SSS) at three months (maximum score 500). Analysis was by intention-to-treat, and multiple imputation was used for missing data.

RESULTS

From the databases, 189 patients with IBS were identified, of whom 30 were eligible and consented to randomisation. At three months, a statistically and clinically significant difference between groups of 138 points (SD 90) in favour of acupuncture was observed on the IBS SSS (95% CI: 66 to 210; P=0.001) using multiple imputation. For a full scale trial, we estimate that a sample size of 108 patients per arm is required, based on a minimum clinically significant change of 50 points, drawn from a primary care population of 140 000.

CONCLUSIONS

We established the feasibility of a full scale trial, successfully recruiting patients and calculating the sample size required. The results of our pilot analysis suggest that more definitive research into acupuncture for IBS is merited. A pragmatic trial design will not be able to distinguish between acupuncture specific effects and placebo effects; however, it is the design of choice to determine cost effectiveness.

Gender differences among medical students in attitudes to learning about complementary and alternative medicine

OBJECTIVES

To explore gender differences in attitudes to CAM among Year 1, 2 and 3 medical students.

DESIGN

Survey; seven-item self-administered questionnaire.

SETTING

Plenary lectures at the start of semester 2 of the academic year at the University of Birmingham Medical School.

RESULTS

35.6% of 662 students were male and 64.4% female. Females were more likely than males to feel CAM has an important role in healthcare (p < 0.001). This difference increased through the medical course (p < 0.05). Females gave a more positive rating than males to the use of five therapies in healthcare (p < 001). Females were more positive than males about learning the theory (p < 0.001) and practice (p < 0.001) of CAM and a greater amount of CAM curriculum time (p < 0.001).

CONCLUSIONS

If CAM teaching is optional females may be more likely to choose it. An unexpected consequence of more women than men entering medical school may be a positive impact on the development of integrated medicine.

Differences in Isolated Mitochondria Are Insufficient to Account for Respiratory Depression during Diapause inArtemia franciscanaEmbryos

In response to cues signifying the approach of winter, adult Artemia franciscana produce encysted embryos that enter diapause. We show that respiration rates of diapause embryos collected from the field (Great Salt Lake, Utah) are reduced up to 92% compared with postdiapause embryos when measured under conditions of normoxia and full hydration. However, mitochondria isolated from diapause embryos exhibit rates of state 3 and state 4 respiration on pyruvate that are equivalent to those from postdiapause embryos with active metabolism; a reduction in these rates (15%-27%) is measured with succinate for two of three collection years. Respiratory control ratios for diapause mitochondria are comparable to or higher than those from postdiapause embryos. The P : O flux ratios are statistically identical. Our calculations suggest that respiration of intact, postdiapause embryos is operating close to the state 3 oxygen fluxes measured for isolated mitochondria. Cytochrome c oxidase (COX) activity is 53% lower in diapause mitochondria during one collection year; the minimal impact of this COX reduction on mitochondrial respiration appears to be due to the 31% excess COX capacity in A. franciscana mitochondria. Transmission electron micrographs of embryos reveal mitochondria that are well differentiated and structurally similar in both states. As inferred from the similar amounts of mitochondrial protein extractable, tissue contents of mitochondria in diapause and postdiapause embryos are equivalent. Thus, metabolic depression during diapause cannot be fully explained by altered properties of isolated mitochondria. Rather, mechanisms for active inhibition or substrate limitation of mitochondrial metabolism in vivo may be operative.

One year in Antarctica: mucosal immunity at three Australian stations

The effect of a year's isolation in Antarctica on the human mucosal immune system was assessed during the winter of 1992 at three Australian Antarctic stations: Casey, Davis and Mawson. Saliva samples were collected from each expeditioner prior to their departure from Australia and during each month in Antarctica. The concentrations of salivary immunoglobulins IgA and IgG were significantly different between the three stations, but there were no differences for salivary IgM and albumin. The mean concentrations of IgA were higher at Mawson (P < 0.008), and the mean concentrations of IgG were lower at Davis (P < 0.001) compared with the other stations. Ranges of values observed at the stations over the 12-13 months were similar. The variability of values within individuals showed station differences for salivary IgM and IgG only. The study revealed significant changes in salivary immunoglobulin values over the period in Antarctica, with similar patterns at the three Australian stations. The salivary IgA and IgM levels were lower in the first 4 months in Antarctica (January-April) and increased to maximum values in July-August, before returning to mean levels when isolation was broken in October-November. The patterns of salivary IgA and IgM suggest that stressors due to isolation may play a role in alterations of mucosal immunity in expeditioners in Antarctica.

Second malignant neoplasms after treatment for Hodgkin's disease in childhood or adolescence

PURPOSE

To determine the frequency of and risk factors for second malignant neoplasms (SMNs) after treatment for Hodgkin's disease diagnosed in children and adolescents.

PATIENTS AND METHODS

One hundred eighty-two consecutive, previously untreated patients with Hodgkin's disease who were younger than 20 years of age at diagnosis and who were referred to Roswell Park Cancer Institute (Buffalo, NY) for treatment between January 1, 1960, and December 31, 1989, were studied. Sex-specific standardized incidence ratios (SIRs) were calculated. Kaplan-Meier survival estimates and Cox regression analyses were performed to determine the relationship of several demographic and treatment variables to SMN incidence.

RESULTS

Twenty-eight patients developed an SMN at a mean of 14.93 +/- 8.09 years (range, 2.65 to 29.88 years) after diagnosis of Hodgkin's disease. The cumulative percentage of patients who developed an SMN was 26.27 +/- 6.75% at 30 years after diagnosis. The SIR was 9.39 (95% confidence interval [CI], 4.05 to 18.49) for male patients and 10.16 (95% CI, 5.56 to 17.05) for female patients. The most frequent SMNs were thyroid cancer, breast cancer, nonmelanoma skin cancer, non-Hodgkin's lymphoma, and acute leukemia. Multivariate analysis of sex, treatment with any alkylating agent, treatment with doxorubicin, splenectomy, and relapse (as a time-dependent covariate) with time to SMN onset gave nonsignificant results.

CONCLUSION

Successfully treated children and adolescents with Hodgkin's disease have a substantial risk for the occurrence of subsequent neoplasms. The most frequent SMNs (skin, thyroid, and breast) are readily detected by physical examination and available screening procedures.

Resolution of a left ureteral stone using electrohydraulic lithotripsy in a thoroughbred colt

A 3-year-old Thoroughbred colt was presented for evaluation of azotemia and anorexia. Physical examination revealed a ureterolith in the left ureter, approximately 10 cm from the bladder, which was thought to obstruct urine flow by approximately 90% when viewed cystoscopically. Ultrasonographic examination of both kidneys revealed indistinct corticomedullary junctions, and the right kidney was more hyperechoic. A percutaneous biopsy of the right kidney revealed chronic interstitial nephritis with marked interstitial medullary fibrosis. Medical therapy consisting of IV fluids, sodium chloride PO, and ammonium chloride PO was initiated. Ureteroscopic electrohydraulic lithotripsy via a perineal urethrostomy was used to successfully remove the stone. Klebsiella oxytoca, which responded to oral enrofloxacin therapy, was cultured from the urine after surgery. Azotemia resolved and the horse resumed training.

Effects of doxazosin on atherosclerosis in cholesterol-fed rabbits

Doxazosin was administered to rabbits fed diets enriched in cholesterol and peanut oil for 7.5 or 12 weeks, in 2 separate experiments. Doxazosin suppressed the accumulation of cholesterol and formation of atherosclerotic plaques in the aortas of treated rabbits and prevented a diet-induced increase in aortic collagen and wall mass. Doxazosin was more effective in the thoracic and abdominal segments of the aorta than in the aortic arch. Pharmacokinetic analysis indicated that treated rabbits were exposed to concentrations of doxazosin, integrated over 24 h, which were consistent with the therapeutic range of doxazosin measured in patients treated for hypertension. Doxazosin did not alter serum levels of cholesterol or triglycerides, nor were there any consistent effects on glucose, free fatty acid or ketone levels. Hypotheses of the mechanism of action of doxazosin are discussed, including the possible involvement of alpha 1-adrenergic receptors in recruitment of smooth muscle cells by subintimal macrophages and nonadrenergic mechanisms of inhibition of lipid infiltration.

Cytogenetic abnormalities in renal oncocytic neoplasms

We have performed cytogenetic studies on five renal oncocytic neoplasms (three grade 2 tumors and two grade 1 tumors) identified histologically by light microscopy. One grade 1 tumor failed to produce mitotic cells. The other four tumors exhibited both normal and abnormal cell lines. Numerical abnormalities were found in both the single grade 1 and two of the grade 2 tumors whereas structural abnormalities were limited to grade 2 tumors. Aneuploidy of chromosome 12 was observed in both grade 1 and 2 tumors. Grade 2 tumors showed more extensive numerical change than the grade 1 tumors. Abnormalities of chromosome 3 characteristic of renal cell carcinoma were not found in any tumor in this series. A combination of C-banding and HaeIII endonuclease banding was used to identify an ambiguous marker. In our four cases and in the cases previously reported, loss of a sex chromosome, abnormalities of chromosomes 1 and 22, and trisomy 12 are findings most often observed in renal oncocytoma.

Differences between the manganese- and the iron-containing superoxide dismutases of Escherichia coli detected through sedimentation equilibrium, hydrodynamic, and spectroscopic studies

The genome of Escherichia coli codes for two superoxide dismutases that may contain either iron (FeSOD) or manganese (MnSOD) at the active site. The crystal structures of MnSODs from two bacterial sources (but not E. coli) have been completed, and structural comparisons with the crystal structure of the FeSOD from either E. coli or Pseudomonas ovalis have been made. Despite the low degree (less than 50%) of sequence homology between the E. coli enzymes, the two proteins are suggested to be structurally homologous. Nonetheless, these enzymes exhibit absolute metal cofactor specificity in conferring enzymatic activity to the inactive apoenzyme. This observation is surprising considering the identity of the active site ligands and the similarities in their geometry and surrounding environment. Using analytical ultracentrifugation, we have determined that the solution properties of these two proteins are different. Thus dialysis of FeSOD but not of MnSOD against phosphate buffer in the presence or absence of EDTA caused dissociation of the homodimer. This dissociation appeared to be related to the loss of iron from native FeSOD. Thus, apoFeSOD but not apoMnSOD existed predominantly as a monomer at protein concentrations below 150 micrograms/mL. ApoMnSOD showed no evidence for dissociation under these conditions. Fluorescence data suggest that the tryptophan environments for the two enzymes are also different. The results of these physical measurements lead us to propose that subtle differences, perhaps at the subunit contact faces, exist in the structures of these crystallographically similar proteins.

The effects of continuous administration of murine interleukin-1 alpha in the rat

Recombinant murine IL-1 alpha was administered continuously to rats by means of osmotic pumps implanted intraperitoneally. Continuous infusion of rIL-1 alpha in a range between 0.12 and 12.0 micrograms/day for four days was found to produce concentration-dependent weight loss. Behavioral parameters were continuously monitored and recorded at the 3.0 micrograms/day concentration in electronically-monitored activity cages during Days 2 through 5 of rIL-1 alpha administration. Parameters were separated into those affected during the dark phase (active period) or the light phase (resting period). Eating activity was found to be significantly reduced during each dark period through day 5, when compared with either untreated or PBS vehicle-infused animals. During the fourth and fifth days of infusion, however, eating behavior in animals infused with rIL-1 alpha began to increase toward control level in the latter, but not the earlier, half of the dark period. In contrast, drinking behavior was found to be significantly elevated only during the light periods. Continuous infusion of rIL-1 alpha also produced significant reductions in both horizontal locomotor activity (crossovers) and vertical locomotor activity (rears). However, in contrast to the trend toward a return of normal eating behavior, locomotor activity remained decreased through the fifth day of rIL-1 alpha infusion. These results suggest changes that could be produced by IL-1 in chronic inflammatory disease and infection.

Sarcoplasmic reticulum calcium pump: a model for Ca2+ binding and Ca2+-coupled phosphorylation

The conventional alternating access model for Ca2+ transport by the sarcoplasmic reticulum Ca2+ pump is modified, partly on the basis of the proposed MacLennan-Green domain structure for the Ca2+-pump protein. The present model divides the uptake state (E1) of the protein into three substates, differing in the condition of the Ca2+-binding domain. The domain is an open cavity in the first substate and can bind only a single Ca2+ ion. A fast "jaw-closing" (or "hinge-bending") step then partially closes the cavity to generate the second substate that has a second Ca2+-binding site. Occupation of this site is followed by another jaw-closing step that closes the binding cavity and occludes the bound ions. The subsequent translocation step (to form E2) remains unchanged from previous models. The modified model predicts a constant transport stoichiometry of two Ca2+ per pump reaction cycle. It suggests a plausible mechanism for coupling between Ca2+ binding and ATP utilization: the model predicts (in agreement with experiment) that Ca2+ binding should be a mandatory requirement for phosphorylation of the pump protein, though ATP binding per se does not require Ca2+. The model is consistent with high cooperativity in equilibrium binding of Ca2+, both in the absence and presence of ATP.

Circular dichroism of the two major conformational states of mammalian (Na+ + K+)-ATPase

No alteration in the circular dichroic spectrum of fully active, membrane-bound (Na+ + K+)-ATPase is observed when the protein is cycled between the two major conformational states, E1 and E2. This finding is in agreement with the infrared study by Chetverin and Brazhnikov (J. Biol. Chem. 260 (1985) 7817) and demonstrates that any difference in secondary structure between the two conformers must be less than 2%.

Prophylaxis of Rift Valley fever with antiviral drugs, immune serum, an interferon inducer, and a macrophage activator

Rift Valley fever virus (RVFV), a member of the family Bunyaviridae, extended its range from sub-Saharan Africa into Egypt in 1977. Its clinical spectrum is recognized to include severe manifestations such as hemorrhagic fever and encephalitis. For these reasons, as well as the limited knowledge of specific therapy for Bunyaviridae infections, we investigated several prophylactic regimens for RVF in a mouse model. Rimantadine, thiosemicarbazone, and inosiplex were ineffective. Pretreatment with glucan was of some use, but the most encouraging results were obtained with the antiviral drug ribavirin, passive antibody, or an interferon inducer polyriboinosinic-polyribocytidylic acid complexed with poly-L-lysine and carboxymethylcellulose (poly[ICLC]). Ribavirin and poly(ICLC) were also shown to be efficacious in preventing disease in hamsters. Ribavirin (loading dose of 50 mg/kg followed by 10 mg/kg at 8-h intervals for 9 days) suppressed viremia in RVF-infected rhesus monkeys. Ribavirin also reduced virus yield in infected cell cultures; sensitivity varied markedly with cell type but not with virus strain. Immune mouse ascitic fluid, with a plaque reduction neutralization titer of 1:1024, was effective in a dose of 4 ml/kg, a volume approximately equivalent to administration of a unit of convalescent plasma to a human. Poly(ICLC) may well have functioned through interferon induction, since RVFV was shown to be sensitive to interferon in cell culture, and since another macrophage activator (glucan) was only marginally effective. These studies suggest that ribavirin, poly(ICLC), and convalescent plasma may have a role in prevention or therapy of human RVF.

Variable stoichiometry in active ion transport: theoretical analysis of physiological consequences

Active ion transport systems with fixed stoichiometry are subject to a thermodynamic limit on the ion concentration gradients that they can generate and maintain, and their net rates of transport must inevitably decrease as this limit is approached. The capability to vary stoichiometry might thus be physiologically advantageous: a shift to lower stoichiometry (fewer ions pumped per reaction cycle) at increasing thermodynamic load could increase the limit on the supportable concentration gradient and could accelerate the rate of transport under high-load conditions. Here we present a theoretical and numerical analysis of this possibility, using the sarcoplasmic reticulum ATP-driven Ca pump as the example. It is easy to introduce alternate pathways into the reaction cycle for this system to shift the stoichiometry (Ca2+/ATP) from the normal value of 2:1 to 1:1, but it cannot be done without simultaneous generation of a pathway for uncoupled leak of Ca2+ across the membrane. This counteracts the advantageous effect of the change in transport stoichiometry and a physiologically useful rate acceleration cannot be obtained. This result is likely to be generally applicable to most active transport systems.