Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of ‘Omics’ Technologies

Rice, the main staple food for about half of the world’s population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial–rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.

Reduced sera neutralization to Omicron SARS-CoV-2 by both inactivated and protein subunit vaccines and the convalescents

Omicron variant continues to spread all over the world. There are lots of scientific questions remaining to be answered for such a devastating variant. There are a dozen of vaccines already in clinical use. The very urgent scientific question would be whether or not these vaccines can protect Omicron variant. Here, we tested the sera from both convalescents and vaccine recipients receiving either inactivated or protein subunits vaccines (CoronaVac from Sinovac, or BBIBP-CoV from Sinopharm, or ZF2001 from Zhifei longcom) for the binding antibody titers (ELISA) and neutralization antibodies titers (pseudovirus neutralization assay). We showed that Omicron do have severe immune escape in convalescents, with 15 of 16 were negative in neutralization. By contrast, in vaccinees who received three jabs of inactivated or protein subunit vaccine, the neutralizing activity was much better preserved. Especially in the ZF2001 group with an extended period of the second and third jab (4-6 months) remains 100% positive in Omicron neutralization, with only 3.1-folds reduction in neutralizing antibody (NAb) titer. In this case, we proposed that, the multi-boost strategy with an extended interval between the second and third jab for immune maturation would be beneficial for NAb against devastating variants such as Omicron.

Why ex post peer review encourages high-risk research while ex ante review discourages it

Peer review is an integral component of contemporary science. While peer review focuses attention on promising and interesting science, it also encourages scientists to pursue some questions at the expense of others. Here, we use ideas from forecasting assessment to examine how two modes of peer review—ex ante review of proposals for future work and ex post review of completed science—motivate scientists to favor some questions instead of others. Our main result is that ex ante and ex post peer review push investigators toward distinct sets of scientific questions. This tension arises because ex post review allows investigators to leverage their own scientific beliefs to generate results that others will find surprising, whereas ex ante review does not. Moreover, ex ante review will favor different research questions depending on whether reviewers rank proposals in anticipation of changes to their own personal beliefs or to the beliefs of their peers. The tension between ex ante and ex post review puts investigators in a bind because most researchers need to find projects that will survive both. By unpacking the tension between these two modes of review, we can understand how they shape the landscape of science and how changes to peer review might shift scientific activity in unforeseen directions.

Multiple Layers of Regulation on Leaf Senescence: New Advances and Perspectives

Leaf senescence is the last stage of leaf development and is an orderly biological process accompanied by degradation of macromolecules and nutrient recycling, which contributes to plant fitness. Forward genetic mutant screening and reverse genetic studies of senescence-associated genes (SAGs) have revealed that leaf senescence is a genetically regulated process, and the initiation and progression of leaf senescence are influenced by an array of internal and external factors. Recently, multi-omics techniques have revealed that leaf senescence is subjected to multiple layers of regulation, including chromatin, transcriptional and post-transcriptional, as well as translational and post-translational levels. Although impressive progress has been made in plant senescence research, especially the identification and functional analysis of a large number of SAGs in crop plants, we still have not unraveled the mystery of plant senescence, and there are some urgent scientific questions in this field, such as when plant senescence is initiated and how senescence signals are transmitted. This paper reviews recent advances in the multiple layers of regulation on leaf senescence, especially in post-transcriptional regulation such as alternative splicing.

From pre-processing to advanced dynamic modeling of pupil data

The pupil of the eye provides a rich source of information for cognitive scientists, as it can index a variety of bodily states (e.g., arousal, fatigue) and cognitive processes (e.g., attention, decision-making). As pupillometry becomes a more accessible and popular methodology, researchers have proposed a variety of techniques for analyzing pupil data. Here, we provide recommendations and offer an up-to-date account of how pupil data can be analyzed in hypothesis-testing experiments. We first introduce pupillometry, its neural underpinnings, and the relation between pupil measurements, visual features (e.g., luminance), and other oculomotor behaviors (e.g., blinks, saccades), to stress the importance of understanding what is being measured and what can be inferred from changes in pupillary activity. We discuss pre-processing steps and contend that the insights gained from pupillometry are constrained by the analysis techniques available. Then, in addition to the traditional approach of analyzing mean pupil size within some epoch of interest, we focus on time series-based analyses, which enable one to relate dynamic changes in pupil size over time with dynamic changes in a stimulus series, task of interest, behavioral outcome measures, or other participants' pupil traces. Analytic techniques considered include: correlation (auto-, and cross-, reverse-, and inter/intra-subject-), regression (including temporal response functions), classification, dynamic time warping, phase clustering, magnitude squared coherence, detrended fluctuation analysis, and recurrence quantification analysis. Assumptions of these techniques, and examples of the scientific questions each can address, are outlined, with references to key papers and software packages.

African Studies Keyword: Malaria

From nearly any perspective and metric, the effects of malaria on the African continent have been persistent and deep. By focusing on the malady of malaria and the last century of biomedical interventions, Graboyes and Alidina raise critical historical, ethical, and scientific questions related to truth telling, African autonomy, and the obligations of foreign researchers. They provide a condensed history of malaria activities on the continent over the past 120 years, highlighting the overall history of failures to eliminate or control the disease. A case study of the risks of rebound malaria illustrates the practical and moral problems that abound when historical knowledge is ignored. In light of current calls for renewed global eradication efforts, Graboyes and Alidina provide evidence for why historical knowledge must be better integrated into global health epistemic realms.

CLARITY: comparing heterogeneous data using dissimilarity

Integrating datasets from different disciplines is hard because the data are often qualitatively different in meaning, scale and reliability. When two datasets describe the same entities, many scientific questions can be phrased around whether the (dis)similarities between entities are conserved across such different data. Our method, CLARITY, quantifies consistency across datasets, identifies where inconsistencies arise and aids in their interpretation. We illustrate this using three diverse comparisons: gene methylation versus expression, evolution of language sounds versus word use, and country-level economic metrics versus cultural beliefs. The non-parametric approach is robust to noise and differences in scaling, and makes only weak assumptions about how the data were generated. It operates by decomposing similarities into two components: a ‘structural’ component analogous to a clustering, and an underlying ‘relationship’ between those structures. This allows a ‘structural comparison’ between two similarity matrices using their predictability from ‘structure’. Significance is assessed with the help of re-sampling appropriate for each dataset. The software, CLARITY, is available as an R package from github.com/danjlawson/CLARITY .

The Wake Forest IASDR: A Resource for Studying the Effects of Caloric Restriction on Health Outcomes in Older Adults

Over the past 25+ years, a focus of the Wake Forest Claude D. Pepper Older Americans Independence Center (OAIC) has been to study the consequences of and treatments for geriatric obesity. The Wake Forest OAIC has provided support for 18 clinical trials of caloric restriction (CR), with and without various exercise regimens, in 2,545 adults (71% women, 21% African American) with a mean±SD age of 67.5±5.9 years and BMI ≥27 kg/m2. A priority of the Wake Forest OAIC is to collate and store common data (e.g., demographics, physical performance, cognitive function), biospecimens (blood, muscle, adipose), and images (DXA, CT) from these trials in the Integrated Aging Studies Databank and Repository (IASDR; https://www.peppercenter.org/public/dspIASDR.cfm). This IASDR serves as a resource for the scientific community to foster new scientific questions and analyses. This symposium will provide an overview of CR trials and participants included in the IASDR and how the IASDR supports secondary analyses of CR by highlighting several secondary analyses using data and/or samples from the IASDR. Justice and colleagues examined the effect of CR on a geroscience-guided biomarker index using blood samples from the biorepository. Weaver and colleagues examined the effect of different exercise regimens on CT-derived muscle and bone measures during CR. Miller and colleagues pooled data from 11 trials to determine if CR-induced appendicular lean mass loss is associated with changes in physical performance. Finally, Hsieh and colleagues pooled data from eight trials to examine whether the effect of CR on gait speed differed by baseline BMI and inflammation.

Zooming in on the cell biology of disease

Today’s cell biology could be considered a fusion of disciplines that blends advanced genetics, molecular biology, biochemistry, and engineering to answer fundamental as well as medically relevant scientific questions. Accordingly, our understanding of diseases is greatly aided by an existing vast knowledge base of fundamental cell biology. Gunter Blobel captured this concept when he said, “the tremendous acquisition of basic knowledge will allow a much more rational treatment of cancer, viral infection, degenerative disease and mental disease.” In other words, without cell biology can we truly understand, prevent, or effectively treat a disease?

Simultaneous Infrared Spectroscopy, Raman Spectroscopy and Luminescence Sensing: A Multi-Spectroscopic Analyti-cal Platform

Scientific questions in fields such as catalysis, monitoring of biological processes or environmental chemistry demand for analytical technologies combining orthogonal spectroscopies. Combined spectroscopic concepts facilitate in-situ on-line monitoring of dynamic processes providing for a better understanding of the involved reaction pathways. In the present study, a low-liquid-volume multi-spectroscopic platform was developed based on infrared attenuated total reflection (IR-ATR) spectroscopy combined with Raman spectroscopy and lumines-cence sensing. For demonstrating the measurement capabilities, exemplary analyte systems including water / heavy water and aqueous solutions of ammonium sulfate were analyzed as proof-of-principle studies. It was successfully demonstrated that three optical techniques may be integrated into a single analytical platform with-out interference providing synchronized and complementary datasets by probing the same minute sample vol-ume. In addition, the developed assembly provides a gas-tight lid sealing the headspace above the probed liq-uid for monitoring the concentration of molecular oxygen also in the gas phase via luminescence quenching. Hence, the entire assembly may be operated at inert conditions, as required for example during the analysis of photocatalytic processes.