Locus Length Research Articles

The length of the cut locus on convex surfaces

In this paper, we prove the conjecture stating that, on any closed convex surface, the cut locus of a finite set $M$ with more than two points has length at least half the diameter of the surface.

The length of the cut locus on convex surfaces

The length of the cut locus on convex surfaces

Differences in the center of pressure movement during standing with running shoes of different constructions: A cross-sectional study

PurposeThis study examined the differences in the center of pressure movement in a one-leg standing position with bare feet, thin-soled shoes, and thick-soled shoes. MethodsIn total, 21 male university students participated in this study. The task involved standing on one leg with the dominant foot for 30 s, and the center of pressure movement was measured using a grab coder (G-620; ANIMA, Tokyo, Japan). Three shoe-wearing states, including bare feet, thin-soled shoes, and thick-soled shoes, with the eyes closed and open in each condition. Statistical analysis was performed, with the significance level set as 5%. ResultsIn the multiple comparison results, the anteroposterior (AP) locus length, AP locus length per second, and maximum amplitude in the AP direction were significantly larger with thick-soled shoes than with bare feet in the closed eyes state. The locus length per unit area was significantly smaller with the thick-soled shoes than with the barefoot condition. Other items did not differ significantly between the shoe-wearing states. ConclusionThick-soled shoes caused a greater center of pressure movement in the AP direction in the static one-leg standing position than did the barefoot state. Our findings suggest that the condition with thick-soled shoes was more unstable in static environments.

Evaluation of 20 CODIS Core STR Loci For Touch DNA Analysis

The DNA profile is a combination of STR alleles loci as a result of template DNA amplification. The FBI has defined 20 core STR loci for human identification in forensic cases. The aim of this study was to evaluate the twenty CODIS core STR loci to be a reference in DNA touch examination. Nine donors with three shedder statuses, high, intermediate, and low, were holding the sample while tying two types of ropes, porous and non-porous. The touch sample is then sampled using two techniques on each rope: double swab and tape lift. DNA was extracted and quantified by real-time PCR technique to determine the concentration of DNA obtained from each treatment. Twenty-four STR loci of the DNA were amplified, and the fragments were analyzed by capillary electrophoresis. Two PCR cycles were chosen to determine the effect of adding cycles on the concentration of DNA that was not successfully amplified. The results of this study indicate that the quantity of touch DNA has a greater influence on the success rate of STR amplification. Each allele on 20 STR CODIS Loci failed to amplify from touch DNA concentration below 0.0625 ng/µl. It is shown that the longer the target allele at each locus, the easier it is for allelic drop-out to occur. However, the optimal STR locus length for DNA testing is under 200 nucleotides.

Current situation and genomic characterization of fowlpox virus in lower Egypt during 2022

A total of 45 samples of vaccinated and non-vaccinated layer chickens were collected from farms in the Egyptian governorates of Sharqia, Ismailia, Menofia, Gharbia, Kafr El Sheikh, Qalyubia, and Dakahlia in the year 2022. They exhibited nodular lesions on their combs, mouth corners, and eyelids, suggesting they were infected with pox disease, which was associated with a 3 to 5% mortality rate. The samples were grown on the chorioallantoic-membrane of embryonated chicken eggs to ensure their viability. In both vaccinated and non-vaccinated farms, 35 of 45 virus isolates were confirmed positive via polymerase chain reaction (PCR) of fpv167 (P4b), based on the amplicon length of the fpv167 gene locus. The 6 strains from various Egyptian governorates were chosen for sequencing and genetic characterization. Phylogenetic investigation of the fpv167 (P4b) gene of sequenced strains clustered within sub clade A1 showed 100% correlation between FWPVD, TKPV13401 and fowlpox-AN2, fowlpox-AN3, and fowlpox-AN6, but only a 98.6% correlation between fowlpox-AN1, fowlpox-AN4, and fowlpox-AN5. Comparing the fowlpox-AN1, fowlpox-AN4, and fowlpox-AN5 strains with commercial vaccine strains (HP1-444-(FP9), vaccine-VSVRI), they had 98.6% identity, while other strains had 100% identity. The results of this study's mutation research showed that fowlpox-AN1, fowlpox-AN4, and fowlpox-AN5 had acquired novel mutations; fowlpox-AN1 had R201G and T204A; fowlpox-AN4 and fowlpox-AN5 had L141F and H157P. Further research is required to determine the effectiveness of the current vaccine in order to develop a new vaccine.

Screening Indels from the whole genome to identify the candidates and their association with economic traits in several goat breeds

In the present study, the re-sequencing of our previous whole-genome sequencing (WGS) for selected individuals of Dazu-black goat (DBG) and Inner-Mongolia Cashmere goat (IMCG) breeds was used to detect and compare the differentiation in Indels depending on the reference genome of goat. Then, three selected candidate Indels rs668795676, rs657996810, and rs669452874 of the three genes SUFU, SYCP2Land GLIPR1L1, respectively, have been chosen, based on the results of prior GWAS across the genome, and examined for their association with body weight and dimensions (body height, body length, heart girth, chest width, cannon circumference, and chest depth) by kompetitive allele specific PCR assay for 342 goats from the three studied goat breeds (DBG, n = 203; ♂99, ♀104), IMCG (n = 65; 15♂, 50♀), and Hechuan white goat (HWG, n = 74; 34♂, 40♀) breeds. The analysis of 192.747Gb WGS revealed an average 334,151 Indels in the whole genome of DBG and IMCG breeds. Chromosome 1 had a maximum number of mutations (Indels) of 58,497 and 55,527 for IMCG and DBG, respectively, while chromosome 25 had the least number of mutations of 15,680 and 16,103 for IMCG and DBG, respectively. The majority of Indels were either Ins or Del of short fragments of 1-5bp, which covered 79.06 and 71.78% of the total number of Indels mutations in IMCG and DBG, respectively. Comparing the differences of Indels between the studied goat breeds revealed 100 and 110 unique Indels for IMCG and DBG, respectively. The Indels loci in the intron region were unique for both studied goat breeds which were related to 30 and 38 candidate genes in IMCG and DBG, respectively, including SUFU, SYCP2L, and GLIPR1L1 genes. Concerning rs669452874 locus, body height and body length of Del/Del genotype in DBG were significantly higher (P < 0.05) than that of Ins/Del genotype, while body height and body length of Del/Del genotype in IMCG were significantly higher (P < 0.01) than those of Ins/Ins genotype, whereas body height and body length and heart girth of Del/Del genotype in HWG were significantly higher (P < 0.01) than those of the Ins/Del and Ins/Ins genotypes. Thus, Del/Del genotype of rs669452874 locus can be used as a candidate molecular marker related to the body dimensions in the studied goat breeds.

Wearing high-heeled shoes on a side slope makes standing balance unstable

IntroductionMany women wearing high-heeled footwear are at high risk of falls. Past studies have examined the balance on level ground or balance during walking. We measured the standing balance on the ground and side slopes for 18 healthy women. MethodBody sway was evaluated based on the center of pressure (COP) while participants stood on level ground on a side slope. The total locus length as well as rectangular and outer peripheral areas were then measured using a Zebris system. Measurements were compared under bare feet, normal shoe, and high-heeled shoe conditions. ResultsOn level ground, there were no significant differences among the three conditions. On the side slope, the total locus length (TLL), rectangular area (RA) and outer peripheral areas (OPA) were significantly greater for the high-heeled shoes than for the bare feet and normal shoes. Standing on the side slope caused larger body sway than on the level ground, along with a higher risk of falling. DiscussionIn TLL, OPA, and RA, the COP moved outside substantially when participants stood on a slope in high heels than in shoes. High heels were highly unstable for standing on a slope since the ankle joint of one leg is in plantar flexion, the foot is pronated, and the other side is plantarflexed at the ankle with pronation of the foot. ConclusionHigh-heeled shoes significantly alter a person's balance when standing on a side slope, suggesting a high risk of falling.

Old specimens for old branches: Assessing effects of sample age in resolving a rapid Neotropical radiation of squirrels

Ultraconserved Elements (UCEs) have been useful to resolve challenging phylogenies of non-model clades, unpuzzling long-conflicted relationships in key branches of the Tree of Life at both deep and shallow levels. UCEs are often reliably recovered from historical samples, unlocking a vast number of preserved natural history specimens for analysis. However, the extent to which sample age and preservation method impact UCE recovery as well as downstream inferences remains unclear. Furthermore, there is an ongoing debate on how to curate, filter, and properly analyze UCE data when locus recovery is uneven across sample age and quality. In the present study we address these questions with an empirical dataset composed of over 3800 UCE loci from 219 historical and modern samples of Sciuridae, a globally distributed and ecologically important family of rodents. We provide a genome-scale phylogeny of two squirrel subfamilies (Sciurillinae and Sciurinae: Sciurini) and investigate their placement within Sciuridae. For historical specimens, recovery of UCE loci and mean length per locus were inversely related to sample age; deeper sequencing improved the number of UCE loci recovered but not locus length. Most of our phylogenetic inferences—performed on six datasets with alternative data-filtering strategies, and using three distinct optimality criteria—resulted in distinct topologies. Datasets containing more loci (40% and 50% taxa representativeness matrices) yielded more concordant topologies and higher support values than strictly filtered datasets (60% matrices) particularly with IQ-Tree and SVDquartets, while filtering based on information content provided better topological resolution for inferences with the coalescent gene-tree based approach in ASTRAL-III. We resolved deep relationships in Sciuridae (including among the five currently recognized subfamilies) and relationships among the deepest branches of Sciurini, but conflicting relationships remain at both genus- and species-levels for the rapid Neotropical tree squirrel radiation. Our results suggest that phylogenomic consensus can be difficult and heavily influenced by the age of available samples and the filtering steps used to optimize dataset properties.

Scalp acupuncture combined with suspension training for balance dysfunction in patients with stroke: a randomized controlled trial

To explore the effect of scalp acupuncture combined with suspension training on balance ability and motor function in stroke patients with balance dysfunction. A total of 105 stroke patients with balance dysfunction were randomly divided into a combined group (35 cases, 2 cases dropped off), a scalp acupuncture group (35 cases, 3 cases dropped off) and a suspension training group (35 cases, 2 cases dropped off). The scalp acupuncture group was treated with scalp acupuncture at bilateral suboccipital lateral line, parietal midline, upper 1/5 line of anterior oblique line of parietal and temporal and line 1 of the parietal lateral line on the opposite side of hemiplegia. The suspension training group was treated with suspension training. The combined group was treated with suspension training at the same time of scalp acupuncture. All the treatment was given once a day, 30 min each time, 5 days a week, for a total of 6 weeks. The Berg balance scale (BBS) score, balance tester and Fugl-Meyer assessment (FMA) score were used to evaluate the motor function and balance ability before treatment, 3 and 6 weeks into treatment. The clinical efficacy was evaluated in the 3 groups. The scores of BBS and FMA in each group at 3 and 6 weeks into treatment were higher than those before treatment (P<0.05); the scores of BBS and FMA in the combined group were higher than those in the scalp acupuncture group and the suspension training group (P<0.05). At 3 and 6 weeks into treatment, the length and area of centroid locus of balance tester in each group were lower than those before treatment (P<0.05); the length and area of centroid locus of balance tester in the combined group were lower than those in the scalp acupuncture group and the suspension training group (P<0.05). The total effective rate of the combined group was 97.0% (32/33), which was higher than 87.5% (28/32) in the scalp acupuncture group and 90.9% (30/33) in the suspension training group (P<0.05). Scalp acupuncture combined with suspension training could improve the balance ability and motor function in stroke patients with balance dysfunction, and the curative effect is better than simple scalp acupuncture and simple suspension training.

How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae)

Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coalescent-based species tree inference. The modified RADseq protocol presented here targets ca. 5,000 loci of 300-600nt length, sequenced with the latest short-read-sequencing (SRS) technology, has the potential to overcome this drawback. To illustrate the advantages of this approach we use the study group Aichryson Webb & Berthelott (Crassulaceae), a plant genus that diversified on the Canary Islands. The data analysis approach used here aims at a careful quality control of the long loci dataset. It involves an informed selection of thresholds for accurate clustering, a thorough exploration of locus properties, such as locus length, coverage and variability, to identify potential biased data and a comparative phylogenetic inference of filtered datasets, accompanied by an evaluation of resulting BS support, gene and site concordance factor values, to improve overall resolution of the resulting phylogenetic trees. The final dataset contains variable loci with an average length of 373nt and facilitates species tree estimation using a coalescent-based summary approach. Additional improvements brought by the approach are critically discussed.

Genome analysis of an OXA-48-producing carbapenem- and colistin-resistant Klebsiella pneumoniae sequence type 11 clone isolated from an inpatient

BackgroundColistin is one of the last-resort therapeutic antibiotics used to control carbapenem-resistant Klebsiella pneumoniae. However, the emergence of colistin-resistant strains with high mortality and morbidity has become a new challenge. Therefore, it is crucial to characterize the genotypic features of carbapenem- and colistin-resistant K. pneumoniae (CCKP) isolates to implement public health intervention strategies. MethodsIn this study, we analyzed the whole genome of an OXA-48-producing CCKP strain for molecular characterization of antimicrobial resistance (AMR) as well as comparative genome and plasmid analysis. ResultsThe whole-genome analysis showed that IRAN-43 genome possessed 140 contigs with 5,585,691 bp length, GC content of 56.9% and N50 score of 200,728. Multi-locus sequence typing (MLST) analysis showed that this K. pneumoniae strain belonged to sequence type (ST) 11. Single amino acid substitutions associated with colistin resistance were found in PhoP (D150G), PmrB (R256G) and RamA (I25T). In addition, two plasmids harboring qnrS1, tetR, tetB (plasmid-1) and blaOXA-48 (plasmid-2) were discovered. No plasmid-mediated colistin resistance (mcr) genes were detected. Integrative conjugative element of K. pneumoniae (ICEKp)4 variant was detected as well as cps locus length of 22,156 bp encoding 17 open reading frames (ORFs) which belonged to K. pneumoniae capsular locus (KL)15-1. ConclusionCCKP has been increasingly reporting from Iran. High frequency of antibiotic resistance genes among ST11 suggests that stricter control measures are needed to prevent the spread of this clone in hospital settings.

Physical effects of motion sickness for comfortable VR viewing

AbstractIn accordance with developments in the image technology over recent years, it has become easier to watch 3D video clips. As the viewing of 3D video has become more commonplace, symptoms such as visually induced motion sickness (VIMS) and eye fatigue have been reported. Although various theories regarding the underlying causes of the VIMS have been proposed, these causes have yet to be fully investigated. In a previous study, the background of an image was shown to influence the equilibrium function of a subject viewing a 3D video clip. In this study, the authors investigated the influence of image elements such as the size of the visual field especially in the backgrounds of the projected image and velocity of the visual target speed on the body of a subject viewing a 3D video clips by measuring their body sway, the electrocardiogram signals, and the cerebral blood flow using functional near‐infrared spectroscopy (fNIRS). Our results has indicated that the value of the total locus length is significantly higher while viewing a video clip whose visual fields of backgrounds is not narrowed than that with narrower backgrounds. This suggests that stability in the system to control their posture can be enhanced by reducing the amount of visual information.

Estimation of the associations between GH and DGAT1 genes and growth traits by using decision tree in Awassi sheep

GH and DGAT1 are candidate genes associated with growth traits in sheep breeds. This study aims to determine the association between growth traits and GH and DGAT1 gene polymorphism using three statistical methods in Awassi sheep. The polymorphism was detected by the PCR-RFLP method. Three genotypes (AA, AB and BB) were observed for GH gene locus with allele and genotype frequency 0.70(A) and 0.30(B); 0.60(AA), 0.20(AB) and 0.20(BB). Three genotypes (CC, CT and TT) were found for DGAT1 gene locus with allele and genotype frequency 0.58(C) and 0.42(T); 0.47(CC), 0.23(CT) and 0.30(TT). The genes were in agreement with Hardy–Weinberg equilibrium (p > 0.05). CHAID, CRT and GLM were used to identify the association between growth traits and gene polymorphism. The results showed an association between GH locus and body weight and tail length. Also, found an association between DGAT1 locus and tail length. The three methods showed similar results in determining the association between genes and growth traits. Thus, the CHAID and CRT methods can evaluate the association between genes and growth traits.

Physical Effects of Motion Sickness for Comfortable VR Viewing

In accordance with developments in the image technology over recent years, it has become easier to watch 3D video clips. As the viewing of 3D video has become more commonplace, symptoms such as visually induced motion sickness (VIMS) and eye fatigue have been reported. Although various theories regarding the underlying causes of the VIMS have been proposed, these causes have yet to be fully investigated. In a previous study, the background of an image was shown to influence the equilibrium function of a subject viewing a 3D video clip. In this study, the authors investigated the influence of image elements such as the size of the visual field especially in the backgrounds of the projected image and velocity of the visual target speed on the body of a subject viewing a 3D video clips by measuring their body sway, the electrocardiogram signals, and the cerebral blood flow using functional near-infrared spectroscopy (fNIRS). Our results has indicated that the value of the total locus length is significantly higher while viewing a video clip whose visual fields of backgrounds is not narrowed than that with narrower backgrounds. This suggests that stability in the system to control their posture can be enhanced by reducing the amount of visual information.

Autosomal, sex-linked and mitochondrial loci resolve evolutionary relationships among wrens in the genus Campylorhynchus

Although there is general consensus that sampling of multiple genetic loci is critical in accurate reconstruction of species trees, the exact numbers and the best types of molecular markers remain an open question. In particular, the phylogenetic utility of sex-linked loci is underexplored. Here, we sample all species and 70% of the named diversity of the New World wren genus Campylorhynchus using sequences from 23 loci, to evaluate the effects of linkage on efficiency in recovering a well-supported tree for the group. At a tree-wide level, we found that most loci supported fewer than half the possible clades and that sex-linked loci produced similar resolution to slower-coalescing autosomal markers, controlling for locus length. By contrast, we did find evidence that linkage affected the efficiency of recovery of individual relationships; as few as two sex-linked loci were necessary to resolve a selection of clades with long to medium subtending branches, whereas 4–6 autosomal loci were necessary to achieve comparable results. These results support an expanded role for sampling of the avian Z chromosome in phylogenetic studies, including target enrichment approaches. Our concatenated and species tree analyses represent significant improvements in our understanding of diversification in Campylorhynchus, and suggest a relatively complex scenario for its radiation across the Miocene/Pliocene boundary, with multiple invasions of South America.

Role of Kazachstania humilis and Saccharomyces cerevisiae in the strain-specific assertiveness of Fructilactobacillus sanfranciscensis strains in rye sourdough

Sourdough is a common ingredient for baked goods as it improves their texture, shelf life and flavor. One of the dominant key species in type I sourdoughs is Fructilactobacillus sanfranciscensis (formerly Lactobacillus sanfranciscensis), which occurs with a multitude of different strains. Noticeably, this species often shares its habitat with the yeasts Saccharomyces cerevisiae or Kazachstania humilis. It is still unclear, which relationship exists between these organisms and whether it is characterized by coexistence, interaction, or mutualism. In this study, competitiveness of different F. sanfranciscensis strains in rye sourdough was examined and its dependence of co-existing yeasts was explored. In particular, it was investigated whether competitiveness of F. sanfranciscensis strains depends on the presence/absence of S. cerevisiae or K. humilis when co-inoculated in the sourdough. Competitiveness of strains was monitored in rye sourdough using the CRISPR locus length polymorphism (CLLP)—PCR for strain differentiation. It was found that F. sanfranciscensis TMW 1.1150, TMW 1.1221 and TMW 1.1597 were dominant regardless of the presence/absence of both yeast species. Dominance of F. sanfranciscensis TMW 1.392, TMW 1.907 and TMW 1.2137 was significantly and diversely influenced by the presence of S. cerevisiae or K. humilis. F. sanfranciscensis TMW 1.2138 and TMW 1.726 were not able to compete against the other F. sanfranciscensis strains. It was possible to sort the eight strains into three different groups: 1. Strain competitiveness was independent of the presence/absence of yeasts; 2. Strain competitiveness was dependent on yeast species and 3. Strains were not competitive in the presence of strains belonging to group 1 or 2. Interestingly, in fermentations that were not inoculated with any yeast a spontaneous occurrence of S. cerevisiae or K. humilis was observed depending on the synergistic competitiveness of the respective F. sanfranciscensis used. Thus, the level of competitiveness was strain specific and, in some strains, dependent on the presence/absence of specific yeast species.

Surgical Outcomes of Postural Instability in Patients With Cervical Myelopathy.

This is a retrospective study. The objective of this study was to investigate the surgical outcomes of postural instability and its predictors in patients with cervical myelopathy (CM). Although several studies have shown impaired postural stability in CM patients, there remains a paucity of literature examining its surgical outcome. Postural stability was assessed using a stabilometer preoperatively, at the early phase (3-6 months postoperatively), and 1-year postoperatively, employing 2 stabilometric parameters: sway area [SwA (cm): the amount of sway of gravity center assessed by the outer peripheral area of the stabilogram] and sway density [SwD (/cm): the indicator of proprioceptive reflexes calculated by the locus length of the stabilogram per SwA]. Twenty-seven healthy age-matched, sex-matched, and body mass index-matched subjects were recruited as controls. To investigate the predictors of postoperative postural instability, univariate, and multivariate analyses were performed, including demographic data, preoperative neurological symptom severity, radiographic findings, and preoperative stabilometric parameters as independent variables. Altogether, 54 CM patients were included in the present study. SwA was 7.89±0.84, 4.78±0.68, and 4.85±0.49, and SwD was 14.63±0.85, 20.41±1.23, and 19.36±1.40 preoperatively, at the early phase, and 1-year postoperatively, respectively, and significant improvement was found in both parameters postoperatively. However, at all timepoints, these parameters were significantly worse in CM patients than in the healthy subjects (SwA: 2.68±0.24, SwD: 24.91±1.83). Multivariate analyses showed that worse preoperative stabilometric parameters were significantly related to worse postoperative stabilometric parameters. Surgery significantly improved postural stability in CM patients; however, it did not reach the level observed in healthy controls, even postoperatively. A predictor of greater residual postoperative postural instability was a greater level of preoperative postural instability. In CM patients, to achieve better surgical outcome of postural stability, surgical intervention is recommended before the symptoms related to bodily imbalance deteriorate. Level III.

Poly-Enrich: count-based methods for gene set enrichment testing with genomic regions.

Gene set enrichment (GSE) testing enhances the biological interpretation of ChIP-seq data and other large sets of genomic regions. Our group has previously introduced two GSE methods for genomic regions: ChIP-Enrich for narrow regions and Broad-Enrich for broad regions. Here, we introduce Poly-Enrich, which has wider applicability, additional capabilities and models the number of peaks assigned to a gene using a generalized additive model with a negative binomial family to determine gene set enrichment, while adjusting for gene locus length. As opposed to ChIP-Enrich, Poly-Enrich works well even when nearly all genes have a peak, illustrated by using Poly-Enrich to characterize pathways and types of genic regions enriched with different families of repetitive elements. By comparing Poly-Enrich and ChIP-Enrich results with ENCODE ChIP-seq data, we found that the optimal test depends more on the pathway being regulated than on properties of the transcription factors. Using known transcription factor functions, we discovered clusters of related biological processes consistently better modeled with Poly-Enrich. This suggests that the regulation of certain processes may be modified by multiple binding events, better modeled by a count-based method. Our new hybrid method automatically uses the optimal method for each gene set, with correct FDR-adjustment.

Monitoring of Lactobacillus sanfranciscensis strains during wheat and rye sourdough fermentations by CRISPR locus length polymorphism PCR

Lactobacillus (L.) sanfranciscensis is a competitive key species in sourdough fermentations. However, the principles involved in establishing the commonly observed phenomenon of strain dominance are unresolved. This has been studied little because the methods for fast and reliable differentiation of strains and their monitoring during fermentation are tedious and cannot be done with large numbers of isolates. In this contribution, we present a strain-specific, PCR-based typing method that uses length heterogeneities of the clustered regularly interspaced short palindromic repeats (CRISPR) loci as they occur in the genomes of different strains. In silico analysis of 21 genomes revealed 14 different CRISPR genotypes. We then designed a primer set to simultaneously detect different strains in a multiplex PCR assay designated CRISPR locus length polymorphism PCR (CLLP-PCR). The usefulness of this method was evaluated in lab-scale sourdough fermentations conducted with rye and wheat flours. First, the flour was mixed with water to a dough yield of 200. Then each dough was inoculated with four different L. sanfranciscensis strains (TMW 1.1150, TMW 1.392, TMW 1.2142, and TMW 1.2138) at levels of 109 cfu/g each. Sourdoughs were propagated at 28 °C for 5 days by back slopping 5% to the flour mass every 24 h. Samples were collected each day; DNA was isolated, and the presence of strains was detected qualitatively in the sourdoughs with PCR.L. sanfranciscensis TMW 1.392 became dominant as early as 2 days into the fermentation and remained the only detectable strain for the rest of the sampling period. CLLP-PCR proved to be useful in investigating the assertiveness of different strains of L. sanfranciscensis in sourdoughs. Therefore, CLLP-PCR may be used as a tool to investigate assertiveness of microorganisms in food fermentations at the strain level.

Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation

Accounting for historical demographic features, such as the strength and timing of gene flow and divergence times between closely related lineages, is vital for many inferences in evolutionary biology. Approximate Bayesian computation (ABC) is one method commonly used to estimate demographic parameters. However, the DNA sequences used as input for this method, often microsatellites or RADseq loci, usually represent a small fraction of the genome. Whole genome sequencing (WGS) data, on the other hand, have been used less often with ABC, and questions remain about the potential benefit of, and how to best implement, this type of data; we used pseudo-observed data sets to explore such questions. Specifically, we addressed the potential improvements in parameter estimation accuracy that could be associated with WGS data in multiple contexts; namely, we quantified the effects of (a) more data, (b) haplotype-based summary statistics, and (c) locus length. Compared with a hypothetical RADseq data set with 2.5Mbp of data, using a 1Gbp data set consisting of 100Kbp sequences led to substantial gains in the accuracy of parameter estimates, which was mostly due to haplotype statistics and increased data. We also quantified the effects of including (a) locus-specific recombination rates, and (b) background selection information in ABC analyses. Importantly, assuming uniform recombination or ignoring background selection had a negative effect on accuracy in many cases. Software and results from this method validation study should be useful for future demographic history analyses.