DirtyGenes: testing for significant changes in gene or bacterial population compositions from a small number of samples

High throughput genomics technologies are applied widely to microbiomes in humans, animals, soil and water, to detect changes in bacterial communities or the genes they carry, between different environments or treatments. We describe a method to test the statistical significance of differences in bacterial population or gene composition, applicable to metagenomic or quantitative polymerase chain reaction data. Our method goes beyond previous published work in being universally most powerful, thus better able to detect statistically significant differences, and through being more reliable for smaller sample sizes. It can also be used for experimental design, to estimate how many samples to use in future experiments, again with the advantage of being universally most powerful. We present three example analyses in the area of antimicrobial resistance. The first is to published data on bacterial communities and antimicrobial resistance genes (ARGs) in the environment; we show that there are significant changes in both ARG and community composition. The second is to new data on seasonality in bacterial communities and ARGs in hooves from four sheep. While the observed differences are not significant, we show that a minimum group size of eight sheep would provide sufficient power to observe significance of similar changes in further experiments. The third is to published data on bacterial communities surrounding rice crops. This is a much larger data set and is used to verify the new method. Our method has broad uses for statistical testing and experimental design in research on changing microbiomes, including studies on antimicrobial resistance

Relação entre a lesão condral e o pico de torque após reconstrução do ligamento cruzado anterior do joelho: estudo de casos Relationship between chondral lesion and peak torque following anterior cruciate ligament reconstruction of the knee: case study

CONTEXTUALIZAÇÃO: A associação entre lesão do ligamento cruzado anterior (LCA) e desenvolvimento de osteoartrite (OA) secundária tem sido objeto de vários estudos. A lesão ligamentar predispõe a lesões da cartilagem articular, influenciando, assim, o controle motor e o pico de torque. OBJETIVO: Avaliar a influência do grau de lesão condral no pico de torque da musculatura anterior e posterior da coxa após lesão e reconstrução do LCA. MÉTODO: Seis sujeitos do sexo masculino com lesão total e unilateral do LCA foram avaliados pré-cirurgia (24 horas antes da cirurgia) e pós-cirurgia em dois momentos distintos, 4,66 ± 1,03 e 15,83 ± 2,63 meses, respectivamente. As avaliações isocinéticas foram realizadas no modo concêntrico de flexão e extensão do joelho, nas velocidades de 60º/s e 180º/s, em que foram a analisadas as variáveis PT dos isquiotibiais (PTI), PT do quadríceps (PTQ) e a relação entre eles (I/Q). A escala histológica de Mankin modificada foi utilizada para avaliar o grau macroscópico de lesão condral. O teste estatístico ANOVA (p< 0,05) comparou os resultados nos três períodos estudados e o post-hoc teste de Newman Keuls foi utilizado como pós-teste. Posteriormente, foi aplicado o teste de Correlação de Spearman para avaliar a influência do grau de lesão condral com o PT da musculatura da coxa. RESULTADOS: Os resultados mostraram diferenças estatisticamente significativas na relação entre I/Q na velocidade de 60º/s (p= 0,01). O grau de lesão condral variou de 1 a 5, entretanto não houve correlação com os achados isocinéticos. CONCLUSÃO: Identificamos que ocorreu desequilíbrio na relação agonista/antagonista, no que se refere ao torque, entre os grupos musculares do joelho após reconstrução do LCA, entretanto o grau da lesão condral secundária não influenciou o ganho progressivo desse mesmo grupo muscular dentro do período estudado.<br>CONTEXT: The association between anterior cruciate ligament (ACL) injury and the development of secondary osteoarthritis has been the subject of several studies. Ligament injury predisposes joint cartilage lesions, thus influencing motor control and peak torque. OBJECTIVE: To evaluate the influence of the degree of chondral lesion on peak torque of the anterior and posterior musculature of the thigh following ACL injury and reconstruction. METHOD: Six male subjects with total unilateral ACL injury were evaluated 24 hours before surgery and at two times after surgery (4.66 ± 1.03 and 15.83 ± 2.63 months, respectively). Isokinetic evaluations of knee flexion and extension were made in concentric mode, at velocities of 60º/s and 180º/s, and the variables of hamstring peak torque (HPT) and quadriceps peak torque (QPT) and hamstring/quadriceps ratio (H/Q) were analyzed. The modified Mankin histological scale was used to evaluate the macroscopic degree of chondral injury. The ANOVA statistical test (p< 0.05) was used to compare the results between the three times studied, with the Newman-Keuls post-hoc test. Spearman's correlation test was then applied to evaluate the influence of the degree of chondral injury on the peak torque of the thigh musculature. RESULTS: There were statistically significant differences in the H/Q ratio at the velocity of 60º/s (p= 0.01). The degree of chondral injury degree ranged from 1 to 5, although there was no correlation with the isokinetic findings. CONCLUSION: There was an imbalance in agonist/antagonist relationship, with regard to torque, between muscle groups of the knee following ACL reconstruction. However, the degree of secondary chondral lesion did not influence the progressive gains in this muscle groups over the study period

Effects of stretching on morphological and biochemical aspects of the extracellular matrix of the rat calcaneal tendon

Several studies have demonstrated the relationship between exercise and the extracellular matrix of muscle tendons, and have described alterations in their structural and biochemical properties when subjected to strenuous exercise. However, little is known about what happens to tendons when they are subjected to stretching. We evaluated the changes in the composition and structure of rat calcaneal tendons subjected to a stretching program. The animals had their muscles stretched for 30 s with 30 s of rest, with 10 repetitions, three and five times a week for 21 days. For morphological analysis, the sections were stained with hematoxylin-eosin and toluidine blue. For biochemical analysis, the tendons were treated with 4 M guanidine hydrochloride and analyzed in SDS-PAGE. The contents of total proteins and glycosaminoglycans were also measured. In the sections stained with toluidine blue, we could observe an increase of rounded cells, especially in the enthesis region. In the region next to the enthesis was a metachromatic region, which was more intensely stained in the stretched groups. In the tension regions, the cells appeared more aligned. Cellularity increased in both regions. The SDS-PAGE analysis showed a larger amount of collagen in the stretched groups and a polydispersed component of 65 kDa in all the groups. The amounts of proteins and glycosaminoglycans were also larger in the stretched tendons. The agarose-gel electrophoresis confirmed the presence of dermatan sulfate in the tension and compression regions, and of chondroitin sulfate only in the latter. Our results showed that the stretching stimulus changed the cellularity and the amount of the extracellular matrix compounds, confirming that tendons are dynamic structures with a capacity to detect alterations in their load.34219710

Cephalopods in neuroscience: regulations, research and the 3Rs

Cephalopods have been utilised in neurosci- ence research for more than 100 years particularly because of their phenotypic plasticity, complex and centralised nervous system, tractability for studies of learning and cellular mechanisms of memory (e.g. long-term potentia- tion) and anatomical features facilitating physiological studies (e.g. squid giant axon and synapse). On 1 January 2013, research using any of the about 700 extant species of ‘‘live cephalopods’’ became regulated within the European Union by Directive 2010/63/EU on the ‘‘Protection of Animals used for Scientific Purposes’’, giving cephalopods the same EU legal protection as previously afforded only to vertebrates. The Directive has a number of implications, particularly for neuroscience research. These include: (1) projects will need justification, authorisation from local competent authorities, and be subject to review including a harm-benefit assessment and adherence to the 3Rs princi- ples (Replacement, Refinement and Reduction). (2) To support project evaluation and compliance with the new EU law, guidelines specific to cephalopods will need to be developed, covering capture, transport, handling, housing, care, maintenance, health monitoring, humane anaesthesia, analgesia and euthanasia. (3) Objective criteria need to be developed to identify signs of pain, suffering, distress and lasting harm particularly in the context of their induction by an experimental procedure. Despite diversity of views existing on some of these topics, this paper reviews the above topics and describes the approaches being taken by the cephalopod research community (represented by the authorship) to produce ‘‘guidelines’’ and the potential contribution of neuroscience research to cephalopod welfare