Brain antibody sequence evaluation (BASE): an easy-to-use software for complete data analysis in single cell immunoglobulin cloning

Background: Repertoire analysis of patient-derived recombinant monoclonal antibodies is an important tool to study the role of B cells in autoimmune diseases of the human brain and beyond. Current protocols for generation of patient-derived recombinant monoclonal antibody libraries are time-consuming and contain repetitive steps, some of which can be assisted with the help of software automation. Results: We developed BASE, an easy-to-use software for complete data analysis in single cell immunoglobulin cloning. BASE consists of two modules: aBASE for immunological annotations and cloning primer lookup, and cBASE for plasmid sequence identity confirmation before expression. Comparing automated BASE analysis with manual analysis we confirmed the validity of BASE output: identity between manual and automated aBASE analysis was 100% for all outputs, except for immunoglobulin isotype determination. In this case, aBASE yielded correct results in 96% of cases, whereas 4% of cases required manual confirmation. cBASE automatically concluded expression recommendations in 89.8% of cases, 91.8% of which were identical to manually derived results and none of them were false-positive. Conclusions: BASE offers an easy-to-use software solution suitable for complete Ig sequence data analysis and tracking during recombinant mAb cloning from single cells. Plasmid sequence identity confirmation by cBASE offers functionality not provided by existing software solutions in the field and will help to reduce time-consuming steps of the monoclonal antibody generation workflow. BASE can be installed locally or accessed online at Code Ocean

Intensification options of small holders' cassava production in south-west Nigeria

Open Access Journal; Published online: 20 Aug 2020Cassava (Manihot esculenta Crantz) is a staple food crop in Nigeria, but root yields hardly exceed 10 t ha−1. Intensification of small holders’ cassava production is key to improved food security and income generation. We tested, in two demonstration trials and 20 on‐farm trials, different intensification options: cassava growth type (erect and branching), fertilizer application (with and without), and cassava − legume arrangement (0.5 by 2 m/1 by 1 m spacing of cassava) in demonstration trials. In on‐farm trials, farmers tested a subset of these treatments. The demonstration trials had median cassava yields of about 20 (Akindele village) and 15 (Osunwoyin village) t ha−1. Fertilizer application increased the yield of the erect cassava variety. Cassava intercropped with cowpea [Vigna unguiculata (L.) Walp.], reduced yield and the branching cassava variety produced lower yield than the erect variety. Median cowpea yields were about 1 and 1.5 t ha−1 pod yield. Median yields in the on‐farm trials were about 10 t ha−1. Intercropping with cowpea reduced cassava root yields (on average by 2.4 t ha−1), again, cowpea pod yields of 1−1.5 t ha−1 were attainable. In summary, this study confirmed that intensification measures need to be site and user or farmer specific

Effects of genotype, seed P concentration and seed priming on seedling vigor of rice

Seedling vigor is important to help ensure good crop establishment. In direct-seeded rice, this is particularly relevant when soil conditions are marginal. In Asia, about one third of the area of rainfed rice is situated on unfavorable soils, many of which are low in plant available P. In such environments, as farmers tend to have few resources, options to overcome poor crop establishment should be low cost and preferably seed-based. The P content of seed depends on genotype and can be augmented by soaking seeds in a P-containing solution prior to seeding (P-priming). In addition, the presence of the Pup1 quantitative trait locus can reportedly confer tolerance to low soil P availability. We tested combinations of seed priming (unprimed control, water priming, P-priming), and inherent seed P concentrations in contrasting rice genotypes (DJ123, Sadri Tor Misri), and two near isogenic sister lines of IR74 with (+Pup1) and without (−Pup1) the Pup1 QTL. Treatment effects on germination were studied in Petri dishes, while seedling growth and P accumulation were assessed using pots with P deficient soil. Germination was less than 75% in seeds with low seed P content. Seed priming with both water and P enhanced germination and seedling growth. In plants growing from high P seeds, water priming outperformed P-priming. In Sadri Tor Misri with low seed P, we observed a tendency for better performance in some parameters when P-primed. While the presence of the Pup1 QTL in IR74 increased shoot biomass and total root length, these effects could be further enhanced by water priming. Combining genetic and seed management approaches may contribute to improved rice establishment in P deficient soils but its effectiveness depends on genotype and seed attributes.By Anny Ruth Pame, Christine Kreye, David Johnson, Sigrid Heuer and Mathias Becke

Effects of expanding cassava planting and harvesting windows on root yield, starch content and revenue in southwestern Nigeria

Open Access Article; Published online: 28 Jul 2022Cassava (Manihot esculenta Crantz) is an important staple crop in Nigeria. It provides approximately 80 % of the caloric intake in Nigeria. High starch content and fresh root yields are important for the commercialization of cassava. Cassava is a perennial crop, and it can be produced all year round. However, cassava fresh root yield and starch content are strongly influenced by environmental conditions such as rainfall. Therefore, it is important to identify planting and harvest periods to attain maximum yields and starch content and to increase profitability. The present study aimed at (i) comparing changes in fresh root yields and starch contents of cassava planted and harvested at different times around the year (ii) identifying the cassava harvest phase attaining maximum fresh root yields and starch content (iii) assessing how price fluctuations and root yields affect the revenue and income generation across the year. This study was carried from 2017 to 2019 in southwestern Nigeria. Existing cassava fields planted at different months were visited and the planting dates were recorded. Harvesting for each planting month was done at 9, 11 and 13 months after planting (MAP). Fresh root yield and starch content varied across planting months. For all crop ages, the highest fresh root yields were recorded when planted in September and December. The highest root starch content was observed in 9- and 13-months old cassava when planted in March and November, respectively. Cassava fresh root yield and starch content varied across Julian day of harvest with lowest yields obtained between Julian day 60–120 (March and April) which coincides with the beginning of rainfall. Highest fresh root yields and starch content were attained between Julian day 180–330. Revenue showed seasonal variation and was dependent Julian day of harvest. Gross revenue was lowest between Julian day 60 and 120 (March and April) and highest from Julian day 180 (July). Lowest incomes or profits were recorded when cassava was harvested between Julian day 60 and 120 (March and April). About 9.1 % of farmers had negative revenues or lost income when they harvested at 9 MAP hence losing between 150 and 200 USD ha−1 compared with 2.8 % of farmers that lost income when harvesting was done at 11 and 13 MAP losing between 100 and 150 USD ha−1. Thus, farmers’ income generation critically depends on cassava planting and harvest dates. Choosing the right time to plant and harvest cassava is one of the most important decisions farmers can make to maximize profit

Using geospatial tools to optimize cassava agronomy trials in Nigeria and Tanzania

Cassava (Manihot esculenta) is an important staple crop for over half a billion people in Africa yet current yield at farmers’ field is only 20% of the potential yield. The African Cassava Agronomy Initiative (ACAI) project is initiated to mitigate the yield gap through developing site-specific recommendations based on a demand-driven approach. The project responds to specific agronomy-related needs of partners already engaged in cassava dissemination and value chain activities in Nigeria and Tanzania. ACAI is developing site-specific recommendation, where processing geospatial information related to climate, soil and remote sensing data is crucial. We are using spatial multivariate analysis to delineate our partners’ operational area into homogeneous clusters to ensure the representativeness of trial sites and optimize the number of trial sites for maximum operational efficiency

Human cerebrospinal fluid monoclonal LGI1 autoantibodies increase neuronal excitability

OBJECTIVE: Leucine-rich glioma-inactivated 1 (LGI1) encephalitis is the second most common antibody-mediatedencephalopathy, but insight into the intrathecal B-cell autoimmune response, including clonal relationships, isotype dis-tribution, frequency, and pathogenic effects of single LGI1 antibodies, has remained limited. METHODS: We cloned, expressed, and tested antibodies from 90 antibody-secreting cells (ASCs) and B cells from thecerebrospinalfluid (CSF) of several patients with LGI1 encephalitis. RESULTS: Eighty-four percent of the ASCs and 21% of the memory B cells encoded LGI1-reactive antibodies, whereasreactivities to other brain epitopes were rare. All LGI1 antibodies were of IgG1, IgG2, or IgG4 isotype and had under-gone affinity maturation. Seven of the overall 26 LGI1 antibodies efficiently blocked the interaction of LGI1 with itsreceptor ADAM22 in vitro, and their mean LGI1 signal on mouse brain sections was weak compared to the remaining,non–ADAM22-competing antibodies. Nevertheless, both types of LGI1 antibodies increased the intrinsic cellular excit-ability and glutamatergic synaptic transmission of hippocampal CA3 neurons in slice cultures. Interpretation: Our data show that the patients’intrathecal B-cell autoimmune response is dominated by LGI1 anti-bodies and that LGI1 antibodies alone are sufficient to promote neuronal excitability, a basis of seizure generation.Fundamental differences in target specificity and antibody hypermutations compared to the CSF autoantibody reper-toire in N-methyl-D-aspartate receptor encephalitis underline the clinical concept that autoimmune encephalitides arevery distinct entities

Cassava-maize intercropping systems in southern Nigeria: radiation use efficiency, soil moisture dynamics, and yields of component crops

Open Access Article; Published online: 30 Apr 2022Efficient utilization of incident solar radiation and rainwater conservation in rain-fed smallholder cropping systems require the development and adoption of cropping systems with high resource use efficiency. Due to the popularity of cassava-maize intercropping and the food security and economic importance of both crops in Nigeria, we investigated options to improve interception of photosynthetically active radiation (IPAR), radiation use efficiency (RUE), soil moisture retention, and yields of cassava and maize in cassava-maize intercropping systems in 8 on-farm researcher-managed multi-location trials between 2017 and 2019 in different agro-ecologies of southern Nigeria. Treatments were a combination of (1) maize planting density (low density at 20,000 maize plants ha-1 versus high density at 40,000 maize plants ha-1, intercropped with 12,500 cassava plants ha-1); (2) fertilizer application and management targeting either the maize crop (90 kg N, 20 kg P and 37 kg K ha-1) or the cassava crop (75 kg N, 20 kg P and 90 kg K ha-1), compared with control without fertilizer application. Cassava and maize development parameters were highest in the maize fertilizer regime, resulting in the highest IPAR at high maize density. The combined intercrop biomass yield was highest at high maize density in the maize fertilizer regime. Without fertilizer application, RUE was highest at low maize density. However, the application of the maize fertilizer regime at high maize density resulted in the highest RUE, soil moisture content, and maize grain yield. Cassava storage root yield was higher in the cassava fertilizer regime than in the maize fertilizer regime. We conclude that improved IPAR, RUE, soil moisture retention, and grain yield on nutrient-limited soils of southern Nigeria, or in similar environments, can be achieved by intercropping 40,000 maize plants ha-1 with 12,500 cassava plants ha-1 and managing the system with the maize fertilizer regime. However, for higher cassava storage root yield, the system should be managed with the cassava fertilizer regime

Developing recommendations for increased productivity in cassava-maize intercropping systems in southern Nigeria

Open Access Article; Published online: 31 Aug 2021Cassava-maize intercropping is a common practice among smallholder farmers in Southern Nigeria. It provides food security and early access to income from the maize component. However, yields of both crops are commonly low in farmers’ fields. Multi-locational trials were conducted in Southern Nigeria in 2016 and 2017 to investigate options to increase productivity and profitability through increased cassava and maize plant densities and fertilizer application. Trials with 4 and 6 treatments in 2016 and 2017, respectively were established on 126 farmers’ fields over two seasons with a set of different designs, including combinations of two levels of crop density and three levels of fertilizer rates. The maize crop was tested at low density (LM) with 20,000 plants ha−1 versus high density (HM) with 40,000 plants ha−1. For cassava, low density (LC) had had 10,000 plants ha−1 versus the high density (HC) with 12,500 plants ha−1.; The fertilizer application followed a regime favouring either the maize crop (FM: 90 kg N, 20 kg P and 37 kg K ha−1) or the cassava crop (FC: 75 kg N, 20 kg P and 90 kg K ha−1), next to control without fertilizer application (F0). Higher maize density (HM) increased marketable maize cob yield by 14 % (3700 cobs ha−1) in the first cycle and by 8% (2100 cobs ha−1) in the second cycle, relative to the LM treatment. Across both cropping cycles, fertilizer application increased cob yield by 15 % (5000 cobs ha−1) and 19 % (6700 cobs ha−1) in the FC and FM regime, respectively. Cassava storage root yield increased by 16 % (4 Mg ha−1) due to increased cassava plant density, and by 14 % (4 Mg ha−1) due to fertilizer application (i.e., with both fertilizer regimes) but only in the first cropping cycle. In the second cycle, increased maize plant density (HM) reduced cassava storage root yield by 7% (1.5 Mg ha−1) relative to the LM treatment. However, the negative effect of high maize density on storage root yield was counteracted by fertilizer application. Fresh storage root yield increased by 8% (2 Mg ha−1) in both fertilizer regimes compared to the control without fertilizer application. Responses to fertilizer by cassava and maize varied between fields. Positive responses tended to decline with increasing yields in the control treatment. The average value-to-cost ratio (VCR) of fertilizer use for the FM regime was 3.6 and higher than for the FC regime (VCR = 1.6), resulting from higher maize yields when FM than when FC was applied. Revenue generated by maize constituted 84–91% of the total revenue of the cropping system. The highest profits were achieved with the FM regime when both cassava and maize were grown at high density. However, fertilizer application was not always advisable as 34 % of farmers did not realize a profit. For higher yields and profitability, fertilizer recommendations should be targeted to responsive fields based on soil fertility knowledge

Combination of (M)DSC and surface analysis to study the phase behaviour and drug distribution of ternary solid dispersions

Purpose: Miscibility of the different compounds that make up a solid dispersion based formulation play a crucial role in the drug release profile and physical stability of the solid dispersion as it defines the phase behaviour of the dispersion. The standard technique to obtain information on phase behaviour of a sample is (modulated) differential scanning calorimetry ((M)DSC). However, for ternary mixtures (M)DSC alone is not sufficient to characterize their phase behaviour and to gain insight into the distribution of the active pharmaceutical ingredient (API) in a two-phased polymeric matrix. Methods: MDSC was combined with complementary surface analysis techniques, specifically time-of-flight secondary ion mass spectrometry (ToF-SIMS) and atomic force microscopy (AFM). Three spray-dried model formulations with varying API/PLGA/PVP ratios were analyzed. Results: The distribution of the API in the ternary solid dispersions depended on formulation parameters. The extent of API surface coverage and therefore the distribution of the API over both polymeric phases differed significantly for the three formulations. Conclusions: Combining (M)DSC and surface analysis rendered additional insights in the composition of mixed phases in complex systems, like ternary solid dispersions