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The infrared (IR) analysis of dried samples of DNA and DNA-polypeptide complexes is still scarce. Here we have studied the FT-IR profiles of these components to further the understanding of the FT-IR signatures of chromatin and cell nuclei. Calf thymus and salmon testis DNA, and complexes of histone H1, protamine, poly-L-lysine and poly-L-arginine (histone-mimic macromolecules) with DNA were analyzed in an IR microspectroscope equipped with an attenuated total reflection diamond objective and Grams software. Conditions including polypeptides bound to the DNA, DNA base composition, and single-stranded form were found to differently affect the vibrational characteristics of the chemical groups (especially, PO(2)(-)) in the nucleic acid. The antisymmetric stretching (ν(as)) of the DNA PO(2)(-) was greater than the symmetric stretching (ν(s)) of these groups and increased in the polypeptide-DNA complexes. A shift of the ν(as) of the DNA PO(2)(-) to a lower frequency and an increased intensity of this vibration were induced especially by lysine-rich histones. Lysine richness additionally contributed to an increase in the vibrational stretching of the amide I group. Even in simple molecules such as inorganic phosphates, the vibrational characteristics of the phosphate anions were differently affected by different cations. As a result of the optimization of the DNA conformation by binding to arginine-rich polypeptides, enhancements of the vibrational characteristics in the FT-IR fingerprint could be detected. Although different profiles were obtained for the DNA with different base compositions, this situation was no longer verified in the polypeptide-DNA complexes and most likely in isolated chromatin or cell nuclei. However, the ν(as) PO(2)(-)/ν(s) PO(2)(-) ratio could discriminate DNA with different base compositions and DNA in a single-stranded form. FT-IR spectral profiles are a valuable tool for establishing the vibrational characteristics of individualized chromatin components, such as DNA and DNA-polypeptide complexes in dried samples.

Feedstock particle sizing can impact the economics of cellulosic ethanol commercialization through its effects on conversion yield and energy cost. Past studies demonstrated that particle size influences biomass enzyme digestibility to a limited extent. Physical size reduction was able to increase conversion rates to maximum of ≈50%, whereas chemical modification achieved conversions of >70% regardless of biomass particle size. This suggests that (1) mechanical pretreatment by itself is insufficient to attain economically feasible biomass conversion, and, therefore, (2) necessary particle sizing needs to be determined in the context of thermochemical pretreatment employed for lignocellulose conversion. Studies of thermochemical pretreatments that have taken into account particle size as a factor have exhibited a wide range of maximal sizes (i.e., particle sizes below which no increase in pretreatment effectiveness, measured in terms of the enzymatic conversion resulting from the pretreatment, were observed) from <0.15 to 50 mm. Maximal sizes as defined above were dependent on the pretreatment employed, with maximal size range decreasing as follows: steam explosion > liquid hot water > dilute acid and base pretreatments. Maximal sizes also appeared dependent on feedstock, with herbaceous or grassy biomass exhibiting lower maximal size range (<3 mm) than woody biomass (>3 mm). Such trends, considered alongside the intensive energy requirement of size reduction processes, warrant a more systematic study of particle size effects across different pretreatment technologies and feedstock, as a requisite for optimizing the feedstock supply system.

Geometry in the simplex has been developed in the last 15 years mainly based on the contributions due to J. Aitchison. The main goal was to develop analytical tools for the statistical analysis of compositional data. Our present aim is to get a further insight into some aspects of this geometry in order to clarify the way for more complex statistical approaches. This is done by way of orthonormal bases, which allow for a straightforward handling of geometric elements in the simplex. The transformation into real coordinates preserves all metric properties and is thus called isometric logratio transformation (ilr). An important result is the decomposition of the simplex, as a vector space, into orthogonal subspaces associated with nonoverlapping subcompositions. This gives the key to join compositions with different parts into a single composition by using a balancing element. The relationship between ilr transformations and the centered-logratio (clr) and additive-logratio (alr) transformations is also studied. Exponential growth or decay of mass is used to illustrate compositional linear processes, parallelism and orthogonality in the simplex.[PUBLICATION ABSTRACT]

To avoid predation by visual predators, caterpillars can be cryptic to decrease detectability or aposematic to warn predators of potential unpalatability. However, for some species, it is not clear if conspicuous patches are selected to avoid predation. For example, Pandora sphinx (Eumorpha pandorus, Lepidoptera: Sphingidae) caterpillars are assumed to be palatable and have both cryptic (green, brown) and conspicuous (orange, red) color morphs. Five lateral, off‐white to yellow patches on either side may serve as a warning for predators or to draw attention away from the caterpillar's form to function as distractive marks. We conducted a field study in three temperate fragmented forests in Massachusetts to investigate the potential utility of E. pandorus coloration and conspicuous patches. Using four plasticine caterpillar prey model treatments, green and red with and without lateral conspicuous patches, we tested the effects of color, patch patterning, and seasonality on attack rates by a variety of taxa. We found that 43% of the prey models (n = 964) had bite marks by an array of predators including arthropods (67.5%), birds (18.2%), rodents (11.5%), and large mammals (2.8%). Arthropods as dominant predators align with conclusions from previous studies of prey models placed near ground level. Attack rates peaked for arthropods in late August and early September but were more constant across trials for vertebrates. Arthropods, a heterogeneous group, as indicated by the variety of bite marks, showed significantly higher attack rates on green colored prey models and a tendency of higher attack on solid (non‐patch patterned) prey models. Vertebrates, more visually oriented predators, had significantly higher attack rates on red colored prey models and patch patterned prey models. Thus, our results did not suggest that conspicuous patch patterning reduced predation and therefore, we did not find support for the distractive mark hypothesis or warning hypothesis. Further, our study shows clear contrasting interpretations by different predators regarding visual defensive strategies. We used the artificial prey technique to test the distractive marks hypothesis and warning hypothesis using the Pandora sphinx caterpillar as a model. Arthropod predators showed significantly higher attack rates on green colored prey models than red but only a tendency of higher attack on solid (non‐patch patterned) prey models, whereas vertebrates, more visually oriented predators, had significantly higher attack rates on red colored and patch patterned prey models. Thus, our results did not suggest that conspicuous patch patterning reduced predation and therefore, we did not find support for the distractive mark hypothesis or warning hypothesis.

Transcription factors and their associated DNA binding sites are key regulatory elements of cellular differentiation, development, and environmental response. New tools that predict transcriptional regulation of biological processes are valuable to researchers studying both model and emerging-model plant systems. SeqEnrich predicts transcription factor networks from co-expressed Arabidopsis or Brassica napus gene sets. The networks produced by SeqEnrich are supported by existing literature and predicted transcription factor-DNA interactions that can be functionally validated at the laboratory bench. The program functions with gene sets of varying sizes and derived from diverse tissues and environmental treatments. SeqEnrich presents as a powerful predictive framework for the analysis of Arabidopsis and Brassica napus co-expression data, and is designed so that researchers at all levels can easily access and interpret predicted transcriptional circuits. The program outperformed its ancestral program ChipEnrich, and produced detailed transcription factor networks from Arabidopsis and Brassica napus gene expression data. The SeqEnrich program is ideal for generating new hypotheses and distilling biological information from large-scale expression data.

Objectives: Low birth weight (LBW) has been associated with common adult-onset chronic diseases, including obesity, cardiovascular disease, type II diabetes and some cancers. The etiology of LBW is multi-factorial. However, recent evidence suggests exposure to antibiotics may also increase the risk of LBW. The mechanisms underlying this association are unknown, although epigenetic mechanisms are hypothesized. In this study, we evaluated the association between maternal antibiotic use and LBW and examined the potential role of altered DNA methylation that controls growth regulatory imprinted genes in these associations. Methods: Between 2009–2011, 397 pregnant women were enrolled and followed until delivery. Prenatal antibiotic use was ascertained through maternal self-report. Imprinted genes methylation levels were measured at differentially methylated regions (DMRs) using bisulfite pyrosequencing. Generalized linear models were used to examine associations among antibiotic use, birth weight and DMR methylation fractions. Results: After adjusting for infant gender, race/ethnicity, maternal body mass index, delivery route, gestational weight gain, gestational age at delivery, folic acid intake, physical activity, maternal smoking and parity, antibiotic use during pregnancy was associated with 138 g lower birth weight compared with non-antibiotic use ( β -coefficient=−132.99, s.e.=50.70, P =0.008). These associations were strongest in newborns of women who reported antibiotic use other than penicillins ( β -coefficient=−135.57, s.e.=57.38, P =0.02). Methylation at five DMRs, IGF2 ( P =0.05), H19 ( P =0.15), PLAGL1 ( P =0.01), MEG3 ( P =0.006) and PEG3 ( P =0.08), was associated with maternal antibiotic use; among these, only methylation at the PLAGL1 DMR was also associated with birth weight. Conclusion: We report an inverse association between in utero exposure to antibiotics and lower infant birth weight and provide the first empirical evidence supporting imprinted gene plasticity in these associations.

We conducted an observational study to assess the etiology, clinical features and outcomes of bloodstream infection (BSI) in 172 hematopoietic SCT (HCST) recipients. One hundred episodes of BSI in the pre-engraftment period (early onset) were compared with 89 episodes in the post-engraftment phase (late onset). More patients with late-onset BSI received an allogeneic HSCT, had GVHD and had received corticosteroids, whereas patients with early-onset BSI were more likely to have neutropenia, severe mucositis and a central venous catheter (CVC) in place. CVC was the most frequent site of infection, followed by an endogenous source. Pneumonia and gastrointestinal infection were particularly frequent in late-onset BSI, whereas mucositis was more frequent in the early-onset group. Gram-positive organisms predominated over Gram negatives. Streptococcus pneumoniae was more frequent in patients with late-onset BSI. Patients with late-onset BSI presented worse outcomes regarding septic shock, intensive care unit admission and early and overall case-fatality rates. Early-onset BSI was mainly related to the presence of neutropenia, mucositis and CVC, whereas late-onset BSI mainly affected severely immunosuppressed allogeneic HSCT recipients with GVHD and corticosteroids. Late-onset BSI caused high case-fatality rates. BSI due to S. pneumoniae was especially frequent late after transplantation. The development of better vaccination strategies is needed.

Cytology-based screening for invasive cervical cancer (ICC) lacks sensitivity and specificity to discriminate between cervical intraepithelial neoplasia (CIN) likely to persist or progress from cases likely to resolve. Genome-wide approaches have been used to identify DNA methylation marks associated with CIN persistence or progression. However, associations between DNA methylation marks and CIN or ICC remain weak and inconsistent. Between 2008-2009, we conducted a hospital-based, case-control study among 213 Tanzania women with CIN 1/2/3 or ICC. We collected questionnaire data, biopsies, peripheral blood, cervical scrapes, Human papillomavirus (HPV) and HIV-1 infection status. We assessed PEG3 methylation status by bisulfite pyrosequencing. Multinomial logistic regression was used to estimate odds ratios (OR) and confidence intervals (CI 95%) for associations between PEG3 methylation status and CIN or ICC. After adjusting for age, gravidity, hormonal contraceptive use and HPV infection, a 5% increase in PEG3 DNA methylation was associated with increased risk for ICC (OR = 1.6; 95% CI 1.2-2.1). HPV infection was associated with a higher risk of CIN1-3 (OR = 15.7; 95% CI 5.7-48.6) and ICC (OR = 29.5, 95% CI 6.3-38.4). Infection with high risk HPV was correlated with mean PEG3 differentially methylated regions (DMRs) methylation (r = 0.34 p<0.0001), while the correlation with low risk HPV infection was weaker (r = 0.16 p = 0.047). Although small sample size limits inference, these data support that PEG3 methylation status has potential as a molecular target for inclusion in CIN screening to improve prediction of progression. Impact statement: We present the first evidence that aberrant methylation of the PEG3 DMR is an important co-factor in the development of Invasive cervical carcinoma (ICC), especially among women infected with high risk HPV. Our results show that a five percent increase in DNA methylation of PEG3 is associated with a 1.6-fold increase ICC risk. Suggesting PEG3 methylation status may be useful as a molecular marker for CIN screening to improve prediction of cases likely to progress.

IntroductionAnxiety is one of the most common Mental Health diagnosis in underage population. We decided to study if there was any variable that would lead us to a specific diagnosis, using the MASC questionnaire (Multidimensional Anxiety Scale for Children).Objectives1. Describe the prevalence of the different anxiety disorders and the differences in its prevalence according to sex. 2. Examine possible differences and associtions between MASC questionnaire scores and a specific anxiety diagnosis.MethodsThis is a descriptive, observational, retrospective, quantitative study with data from patients between June 2016 and 2023. Inclusion criteria: 3-18 year-old-spanish-speakers who met criteria for a ICD-11 disorder. Exclusion criteria: absence of legal representatives, intellectual disability. Variables: sex, ICD-11 diagnosis, MASC’s subscales (Physical Symptoms, Harm Avoidance, Social Anxiety and Separation Anxiety) and CGI. Statistical analyzes were performed with STATA-15 program, using as independent variables MASC questionnaire and dependent one Anxiety Diagnosis.ResultsThe sample contains 1024 patients. Figure 1 shows the distribution of Anxiety Disorders: Unspecified Anxiety Disorder (47%), Separation Anxiety Disorder (23%), Simple Phobias (9%) and Social Anxiety Disorder (7%). Figure 2 represents the distribution by sex, with the differences being statistically significant (p<0.05) for all anxiety disorders, meaning that girls have higher prevalence of all anxiety disorders. Figure 3 shows how age correlates significantly and directly with all the subscales, meaning the older the patients are the higher the scores. We also found that boys have lower scores and a lower percentage of alteration in all subscales. CGI scale also correlates positively with all the subscales, specially with Physical Symptoms. All these data have been adjusted.Image:Image 2:Image 3:ConclusionsAnxiety disorders are the most common form of Mental Disorder in young people (lobal prevalence of 6.5%, Rapee et al.2023). Prevalence for specific Anxiety Disorders in underage population are less reliable, because of the unequal age of samples (Rapee et al.2023). Separation Anxiety disorder is the most prevalent among children (La Maison et al., 2018), while Social Anxiety disorder is among adolescents (Lawrence et al.2015). We did not categorized our sample, being Separation Anxiety disorder the most frequent followed by Social Anxiety. We observed a correlation between some subscales and a specific diagnosis: the risk of presenting a Social Anxiety disorder is multiplied by 1.08 for each point of increase in that subscale and the risk of presenting a Separation Anxiety disorder is multiplied by 1.05 for each increase of 1 point in Separation Anxiety subscale. However, the diagnosis of Simple Phobia decreases with the increase in scores in all subscales, maybe due to the fact that there are not many items that specifically evaluate fears.Disclosure of InterestNone Declared

IntroductionAnxiety is one of the most common Mental Health diagnosis in underage population. We decided to study if there was any variable that would lead us to a specific treatment indication using the MASC (Multidimensional Anxiety Scale for Children).ObjectivesPrevalence of psychiatric disorders and comorbidities in an underage population.Possible association between MASC questionnaire scores and the indication for pharmacological and/or psychological treatment.MethodsThis is a descriptive, observational, retrospective, quantitative study with data from patients between June 2016 and 2023. Inclusion criteria: 3-18 year-old-spanish-speakers who met criteria for a ICD-11 disorder. Exclusion criteria: absence of legal representatives, intellectual disability. Variables: Age, sex, psychiatric family history, ICD-11 diagnosis, treatment indication and MASC’s subscales (physical symptoms, harm avoidance, social anxiety and separation anxiety). Statistical analyzes were performed with STATA-15 program, using as independent variables MASC questionnaire, and dependent ones the indication treatment and diagnosis.ResultsThe sample contains 1024 patients, with a mean age of 12 (SD 4.028). Table 1 shows that the most frequent diagnosis is ADHD, with combined presentation with a prevalence of 22.27%, followed by Anxiety Disorders, without differentiating by subtypes (17.93%). It also shows that Defiant and Oppositional Disorder is the most prevalent comorbidity (9.66%) followed by Anxiety Disorder not specified (4.99%). Table 2 stands that there are significantly higher scores in all MASC subscales in those patients who do have prior psychiatry family history. We founf in Table 3 statistically significant differences were found between the score on the Physical Symptoms subscale based on whether the patient was undergoing previous treatment, both pharmacological (8.45 vs. 7.59) and psychological treatment (9.01 vs. 7.95) compared to those who were not (pharmacological 7.36 vs. 7.06), psychological (7.21 vs. 6.92). All these data have been adjusted.Image:Image 2:Image 3:ConclusionsAnxiety disorders are the most common form of Mental Disorder in young people, with a global prevalence of 6.5% (Rapee et al.2023). However, in our sample the most common one is ADHD as our center is specialized in it. We found that the most prevalent one was Oppositional Defiant Disorder, as it is the most frequent comorbidity of ADHD (Vallejo-Valdivielso et al,2019; Faraone et al,2021). The increase of one point in the Physical Anxiety subscale increases the probability of indicating pharmacological treatment, which could be explained because of how functional limitation these symptoms cause. The increase in all the subscales of the MASC implies an increase in the probability of an indication for psychological treatment as it is the gold-standard treatment for anxiety in children.Disclosure of InterestNone Declared