University of Puerto Rico at Río Piedras

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization. The human gut microbiome from a large cohort of more than 500 indivduals living on three continents with three distinct cultures is analysed, emphasizing the effect of host age, diet and environment on the composition and functional repertoire of fecal microbiota. The human gut microbiome is thought to be shaped by both host diet and genetics. Using a sample set of more than 500 individuals belonging to around 150 families from three different countries, Yatsunenko et al. analyse the impact of both factors on the composition and functional repertoire of the fecal microbiota.

The typical two-dimensional (2D) semiconductors MoS2, MoSe2, WS2, WSe2 and black phosphorus have garnered tremendous interest for their unique electronic, optical, and chemical properties. However, all 2D semiconductors reported thus far feature band gaps that are smaller than 2.0 eV, which has greatly restricted their applications, especially in optoelectronic devices with photoresponse in the blue and UV range. Novel 2D mono-elemental semiconductors, namely monolayered arsenene and antimonene, with wide band gaps and high stability were now developed based on first-principles calculations. Interestingly, although As and Sb are typically semimetals in the bulk, they are transformed into indirect semiconductors with band gaps of 2.49 and 2.28 eV when thinned to one atomic layer. Significantly, under small biaxial strain, these materials were transformed from indirect into direct band-gap semiconductors. Such dramatic changes in the electronic structure could pave the way for transistors with high on/off ratios, optoelectronic devices working under blue or UV light, and mechanical sensors based on new 2D crystals.

Defect-rich and ultrathin N doped carbon nanosheets exhibited low overpotentials and robust stability for simultaneous ORR, OER and HER.

Ice-repellent coatings can have significant impact on global energy savings and improving safety in many infrastructures, transportation, and cooling systems. Recent efforts for developing ice-phobic surfaces have been mostly devoted to utilizing lotus-leaf-inspired superhydrophobic surfaces, yet these surfaces fail in high-humidity conditions due to water condensation and frost formation and even lead to increased ice adhesion due to a large surface area. We report a radically different type of ice-repellent material based on slippery, liquid-infused porous surfaces (SLIPS), where a stable, ultrasmooth, low-hysteresis lubricant overlayer is maintained by infusing a water-immiscible liquid into a nanostructured surface chemically functionalized to have a high affinity to the infiltrated liquid and lock it in place. We develop a direct fabrication method of SLIPS on industrially relevant metals, particularly aluminum, one of the most widely used lightweight structural materials. We demonstrate that SLIPS-coated Al surfaces not only suppress ice/frost accretion by effectively removing condensed moisture but also exhibit at least an order of magnitude lower ice adhesion than state-of-the-art materials. On the basis of a theoretical analysis followed by extensive icing/deicing experiments, we discuss special advantages of SLIPS as ice-repellent surfaces: highly reduced sliding droplet sizes resulting from the extremely low contact angle hysteresis. We show that our surfaces remain essentially frost-free in which any conventional materials accumulate ice. These results indicate that SLIPS is a promising candidate for developing robust anti-icing materials for broad applications, such as refrigeration, aviation, roofs, wires, outdoor signs, railings, and wind turbines.

Sequencing of the genome of the butterfly Heliconius melpomene shows that closely related Heliconius species exchange protective colour-pattern genes promiscuously. Heliconius butterflies are an excellent system in which to study ecology, behaviour, mimicry and speciation. The genome of the postman butterfly Heliconius melpomene has now been sequenced. Using genomic resequencing of individuals from distinct lineages, the authors document heterogenous patterns of genomic diversity associated with adaptively divergent wing-colour patterns. As the second lepidopteran genome to be sequenced, Heliconius offers novel opportunities for comparative genomics within this economically significant insect order, which includes many pest species, as well as the only domesticated insect, the silkmoth Bombyx mori. The evolutionary importance of hybridization and introgression has long been debated1. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2,3,4,5. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation.

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Recent efforts in protein engineering have significantly increased the performance of GECIs. The state-of-the art single-wavelength GECI, GCaMP3, has been deployed in a number of model organisms and can reliably detect three or more action potentials in short bursts in several systems in vivo. Through protein structure determination, targeted mutagenesis, high-throughput screening, and a battery of in vitro assays, we have increased the dynamic range of GCaMP3 by severalfold, creating a family of "GCaMP5" sensors. We tested GCaMP5s in several systems: cultured neurons and astrocytes, mouse retina, and in vivo in Caenorhabditis chemosensory neurons, Drosophila larval neuromuscular junction and adult antennal lobe, zebrafish retina and tectum, and mouse visual cortex. Signal-to-noise ratio was improved by at least 2- to 3-fold. In the visual cortex, two GCaMP5 variants detected twice as many visual stimulus-responsive cells as GCaMP3. By combining in vivo imaging with electrophysiology we show that GCaMP5 fluorescence provides a more reliable measure of neuronal activity than its predecessor GCaMP3. GCaMP5 allows more sensitive detection of neural activity in vivo and may find widespread applications for cellular imaging in general.

The production of ammonia (NH3) from molecular dinitrogen (N2) under mild conditions is one of the most attractive and challenging processes in chemistry. Here by means of density functional theory (DFT) computations, we systematically investigated the potential of single transition metal atoms (Sc to Zn, Mo, Ru, Rh, Pd, and Ag) supported on the experimentally available defective boron nitride (TM–BN) monolayer with a boron monovacancy as a N2 fixation electrocatalyst. Our computations revealed that the single Mo atom supported by a defective BN nanosheet exhibits the highest catalytic activity for N2 fixation at room temperature through an enzymatic mechanism with a quite low overpotential of 0.19 V. The high spin-polarization, selective stabilization of N2H* species, or destabilizing NH2* species are responsible for the high activity of the Mo-embedded BN nanosheet for N2 fixation. This finding opens a new avenue of NH3 production by single-atom electrocatalysts under ambient conditions.

Abstract The (14 s 11 p 5 d ) primitive basis set of Dunning for the third‐row main group atoms Ga‐Kr has been contracted [6 s 4 p 1 d ]. The core functions have been relatively highly contracted while those which represent the valence region have been left uncontracted to maintain flexibility. Calculations with the [6 s 4 p 1 d ] contraction are reported for a variety of molecules involving third‐row atoms. This basis set is found to satisfactorily reproduce experimental properties such as geometric configurations, dipole moments, and vibrational frequencies for a range of molecules. Comparisons are made with the performance of the uncontracted basis set. Polarization functions for the contracted basis set are reported and performance of the basis set with and without polarization functions is examined. A relaxation of the [6 s 4 p 1 d ] contraction to [9 s 6 p 2 d ] for higher level evergy calculations is also presented.

All in-text\treferences\tunderlined\tin\tblue\tare\tlinked\tto\tpublications\ton\tResearchGate, letting you\taccess\tand\tread\tthem\timmediately.

Developing efficient catalysts for nitrogen fixation is becoming increasingly important but is still challenging due to the lack of robust design criteria for tackling the activity and selectivity problems, especially for electrochemical nitrogen reduction reaction (NRR). Herein, by means of large-scale density functional theory (DFT) computations, we reported a descriptor-based design principle to explore the large composition space of two-dimensional (2D) biatom catalysts (BACs), namely, metal dimers supported on 2D expanded phthalocyanine (M2-Pc or MM′-Pc), toward the NRR at the acid conditions. We sampled both homonuclear (M2-Pc) and heteronuclear (MM′-Pc) BACs and constructed the activity map of BACs by using N2H* adsorption energy as the activity descriptor, which reduces the number of promising catalyst candidates from over 900 to less than 100. This strategy allowed us to readily identify 3 homonuclear and 28 heteronuclear BACs, which could break the metal-based activity benchmark toward the efficient NRR. Particularly, using the free energy difference of H* and N2H* as a selectivity descriptor, we screened out five systems, including Ti2-Pc, V2-Pc, TiV-Pc, VCr-Pc, and VTa-Pc, which exhibit a strong capability of suppressing the competitive hydrogen evolution reaction (HER) with favorable limiting potential of −0.75, −0.39, −0.74, −0.85, and −0.47 V, respectively. This work not only broadens the possibility of discovering more efficient BACs toward N2 fixation but also provides a feasible strategy for rational design of NRR electrocatalysts and helps pave the way to fast screening and design of efficient BACs for the NRR and other electrochemical reactions.

Older adults and special populations (living with disability and/or chronic illness that may limit mobility and/or physical endurance) can benefit from practicing a more physically active lifestyle, typically by increasing ambulatory activity. Step counting devices (accelerometers and pedometers) offer an opportunity to monitor daily ambulatory activity; however, an appropriate translation of public health guidelines in terms of steps/day is unknown. Therefore this review was conducted to translate public health recommendations in terms of steps/day. Normative data indicates that 1) healthy older adults average 2,000-9,000 steps/day, and 2) special populations average 1,200-8,800 steps/day. Pedometer-based interventions in older adults and special populations elicit a weighted increase of approximately 775 steps/day (or an effect size of 0.26) and 2,215 steps/day (or an effect size of 0.67), respectively. There is no evidence to inform a moderate intensity cadence (i.e., steps/minute) in older adults at this time. However, using the adult cadence of 100 steps/minute to demark the lower end of an absolutely-defined moderate intensity (i.e., 3 METs), and multiplying this by 30 minutes produces a reasonable heuristic (i.e., guiding) value of 3,000 steps. However, this cadence may be unattainable in some frail/diseased populations. Regardless, to truly translate public health guidelines, these steps should be taken over and above activities performed in the course of daily living, be of at least moderate intensity accumulated in minimally 10 minute bouts, and add up to at least 150 minutes over the week. Considering a daily background of 5,000 steps/day (which may actually be too high for some older adults and/or special populations), a computed translation approximates 8,000 steps on days that include a target of achieving 30 minutes of moderate-to-vigorous physical activity (MVPA), and approximately 7,100 steps/day if averaged over a week. Measured directly and including these background activities, the evidence suggests that 30 minutes of daily MVPA accumulated in addition to habitual daily activities in healthy older adults is equivalent to taking approximately 7,000-10,000 steps/day. Those living with disability and/or chronic illness (that limits mobility and or/physical endurance) display lower levels of background daily activity, and this will affect whole-day estimates of recommended physical activity.

Abstract The criteria of restoration success should be clearly established to evaluate restoration projects. Recently, the Society of Ecological Restoration International (SER) has produced a Primer that includes ecosystem attributes that should be considered when evaluating restoration success. To determine how restoration success has been evaluated in restoration projects, we reviewed articles published in Restoration Ecology (Vols. 1[1]–11[4]). Specifically, we addressed the following questions: (1) what measures of ecosystem attributes are assessed and (2) how are these measures used to determine restoration success. No study has measured all the SER Primer attributes, but most studies did include at least one measure in each of three general categories of the ecosystem attributes: diversity, vegetation structure, and ecological processes. Most of the reviewed studies are using multiple measures to evaluate restoration success, but we would encourage future projects to include: (1) at least two variables within each of the three ecosystem attributes that clearly related to ecosystem functioning and (2) at least two reference sites to capture the variation that exist in ecosystems.

Endophytes are microorganisms that live within plant tissues without causing symptoms of disease. They are important components of plant microbiomes. Endophytes interact with, and overlap in function with, other core microbial groups that colonize plant tissues, e.g., mycorrhizal fungi, pathogens, epiphytes, and saprotrophs. Some fungal endophytes affect plant growth and plant responses to pathogens, herbivores, and environmental change; others produce useful or interesting secondary metabolites. Here, we focus on new techniques and approaches that can provide an integrative understanding of the role of fungal endophytes in the plant microbiome. Clavicipitaceous endophytes of grasses are not considered because they have unique properties distinct from other endophytes. Hidden from view and often overlooked, endophytes are emerging as their diversity, importance for plant growth and survival, and interactions with other organisms are revealed.

BACKGROUND: Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results. RESULTS: The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified. CONCLUSIONS: This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.

Most studies of the human microbiome have focused on westernized people with life-style practices that decrease microbial survival and transmission, or on traditional societies that are currently in transition to westernization. We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics. AR genes are likely poised for mobilization and enrichment upon exposure to pharmacological levels of antibiotics. Our findings emphasize the need for extensive characterization of the function of the microbiome and resistome in remote nonwesternized populations before globalization of modern practices affects potentially beneficial bacteria harbored in the human body.

Phosphorene, an emerging two-dimensional material, has received considerable attention due to its layer-controlled direct bandgap, high carrier mobility, negative Poisson's ratio and unique in-plane anisotropy. As cousins of phosphorene, 2D group-VA arsenene, antimonene and bismuthene have also garnered tremendous interest due to their intriguing structures and fascinating electronic properties. 2D group-VA family members are opening up brand-new opportunities for their multifunctional applications encompassing electronics, optoelectronics, topological spintronics, thermoelectrics, sensors, Li- or Na-batteries. In this review, we extensively explore the latest theoretical and experimental progress made in the fundamental properties, fabrications and applications of 2D group-VA materials, and offer perspectives and challenges for the future of this emerging field.

The recently initiated Arecibo Legacy Fast ALFA (ALFALFA) survey aims to map 7000 square degrees of the high galactic latitude sky visible from Arecibo, providing a HI line spectral database covering the redshift range between -1600 km/s and 18,000 km/s with 5 km/s resolution. Exploiting Arecibo's large collecting area and small beam size, ALFALFA is specifically designed to probe the faint end of the HI mass function in the local universe and will provide a census of HI in the surveyed sky area to faint flux limits, making it especially useful in synergy with wide area surveys conducted at other wavelengths. ALFALFA will also provide the basis for studies of the dynamics of galaxies within the Local and nearby superclusters, will allow measurement of the HI diameter function, and enable a first wide-area blind search for local HI tidal features, HI absorbers at z < 0.06 and OH megamasers in the redshift range 0.16 < z < 0.25. Although completion of the survey will require some five years, public access to the ALFALFA data and data products will be provided in a timely manner, thus allowing its application for studies beyond those targeted by the ALFALFA collaboration. ALFALFA adopts a two-pass, minimum intrusion, drift scan observing technique which samples the same region of sky at two separate epochs to aid in the discrimination of cosmic signals from noise and terrestrial interference. Survey simulations, which take into account large scale structure in the mass distribution and incorporate experience with the ALFA system gained from tests conducted during its commissioning phase, suggest that ALFALFA will detect on the order of 20,000 extragalactic HI line sources out to z=0.06, including several hundred with HI masses of less than 10^{7.5} msun.

Abstract The mean spherical approximation for the primitive model of electrolytic solutions is solved for the most general case of an arbitrary charge and size. It is found that the excess thermodynamic properties are scaled to the charge and the size by means of a rational expression involving a single parameter. This parameter is found by solving an algebraic equation. The explicit form of this equation is obtained for the cases of a binary mixture and in the limit of low concentrations.

Optoelectronic applications require materials both responsive to objective photons and able to transfer carriers, so new two-dimensional (2D) semiconductors with appropriate band gaps and high mobilities are highly desired. A broad range of band gaps and high mobilities of a 2D semiconductor family, composed of monolayer of Group 15 elements (phosphorene, arsenene, antimonene, bismuthene) is presented. The calculated binding energies and phonon band dispersions of 2D Group 15 allotropes exhibit thermodynamic stability. The energy band gaps of 2D semiconducting Group 15 monolayers cover a wide range from 0.36 to 2.62 eV, which are crucial for broadband photoresponse. Significantly, phosphorene, arsenene, and bismuthene possess carrier mobilities as high as several thousand cm(2) V(-1) s(-1) . Combining such broad band gaps and superior carrier mobilities, 2D Group 15 monolayers are promising candidates for nanoelectronics and optoelectronics.

Genetically encoded calcium indicators (GECIs) are powerful tools for systems neuroscience. Here we describe red, single-wavelength GECIs, "RCaMPs," engineered from circular permutation of the thermostable red fluorescent protein mRuby. High-resolution crystal structures of mRuby, the red sensor RCaMP, and the recently published red GECI R-GECO1 give insight into the chromophore environments of the Ca(2+)-bound state of the sensors and the engineered protein domain interfaces of the different indicators. We characterized the biophysical properties and performance of RCaMP sensors in vitro and in vivo in Caenorhabditis elegans, Drosophila larvae, and larval zebrafish. Further, we demonstrate 2-color calcium imaging both within the same cell (registering mitochondrial and somatic [Ca(2+)]) and between two populations of cells: neurons and astrocytes. Finally, we perform integrated optogenetics experiments, wherein neural activation via channelrhodopsin-2 (ChR2) or a red-shifted variant, and activity imaging via RCaMP or GCaMP, are conducted simultaneously, with the ChR2/RCaMP pair providing independently addressable spectral channels. Using this paradigm, we measure calcium responses of naturalistic and ChR2-evoked muscle contractions in vivo in crawling C. elegans. We systematically compare the RCaMP sensors to R-GECO1, in terms of action potential-evoked fluorescence increases in neurons, photobleaching, and photoswitching. R-GECO1 displays higher Ca(2+) affinity and larger dynamic range than RCaMP, but exhibits significant photoactivation with blue and green light, suggesting that integrated channelrhodopsin-based optogenetics using R-GECO1 may be subject to artifact. Finally, we create and test blue, cyan, and yellow variants engineered from GCaMP by rational design. This engineered set of chromatic variants facilitates new experiments in functional imaging and optogenetics.