Spatial and temporal variation of ecosystem properties at macroscales

Although spatial and temporal variation in ecological properties has been well‐studied, crucial knowledge gaps remain for studies conducted at macroscales and for ecosystem properties related to material and energy. We test four propositions of spatial and temporal variation in ecosystem properties within a macroscale (1000 km's) extent. We fit Bayesian hierarchical models to thousands of observations from over two decades to quantify four components of variation – spatial (local and regional) and temporal (local and coherent); and to model their drivers. We found strong support for three propositions: (1) spatial variation at local and regional scales are large and roughly equal, (2) annual temporal variation is mostly local rather than coherent, and, (3) spatial variation exceeds temporal variation. Our findings imply that predicting ecosystem responses to environmental changes at macroscales requires consideration of the dominant spatial signals at both local and regional scales that may overwhelm temporal signals.     

豚草入侵对中小型土壤动物群落结构特征的影响

豚草(Ambrosia artemisiifolia)是菊科豚草属的恶性杂草,在我国华南地区已成功入侵并造成严重危害。为了解豚草入侵对中小型土壤动物群落的影响效应,采用野外样地试验法研究了豚草入侵地中小型土壤动物的群落特征。全年4次采样共获得中小型土壤动物4174头,隶属于4门11纲26类,其中线虫类为优势类群,蜱螨目和弹尾目是常见类群。结果显示,豚草入侵改变了中小型土壤动物群落的结构特征,入侵地中小型土壤动物的总个体数以及线虫类、弹尾目动物的个体数显著增加,但中小型土壤动物类群数的变化不明显;在群落的物种多样性方面,豚草入侵显著提高了群落的密度-类群指数,物种丰富度、优势度指数亦有所上升,但差异不明显,而均匀度、Shannon-Wiener指数则趋于下降;在群落相似性方面,入侵区与其它处理区的差异较小。豚草入侵所引起的局部气候环境、凋落物、根系分泌物与土壤理化性质的变化可能是造成中小型土壤动物群落结构特征改变的主要原因。     

Degradation of phenol under meso- and thermophilic, anaerobic conditions

Based on the results of preliminary studies on phenol degradation under mesophilic conditions with a mixed methanogenic culture, we proposed a degradation pathway in which phenol is fermented to acetate: Part of the phenol is reductively transformed to benzoate while the rest is oxidised, forming acetate as end product. According to our calculations, this should result in three moles of phenol being converted to two moles of benzoate and three moles of acetate (3 phenol + 2 CO2 + 3 H2O --> 3 acetate + 2 benzoate): To assess the validity of our hypothesis concerning the metabolic pathway, we studied the transformation of phenol under mesophilic and thermophilic conditions in relation to the availability of hydrogen. Hence, methanogenic meso- and thermophilic cultures amended with phenol were run with or without an added over-pressure of hydrogen under methanogenic and non-methanogenic conditions. Bromoethanesulfonic acid (BES) was used to inhibit methanogenic activity. In the mesophilic treatments amended with only BES, about 70% of the carbon in the products found was benzoate. During the course of phenol transformation in these BES-amended cultures, the formation pattern of the degradation products changed: Initially nearly 90% of the carbon from phenol degradation was recovered as benzoate, whereas later in the incubation, in addition to benzoate formation, the aromatic nucleus degraded completely to acetate. Thus, the initial reduction of phenol to benzoate resulted in a lowering of H2 levels, giving rise to conditions allowing the degradation of phenol to acetate as the end product. Product formation in bottles amended with BES and phenol occurred in accordance with the hypothesised pathway; however, the overall results indicate that the degradation of phenol in this system is more complex. During phenol transformation under thermophilic conditions, no benzoate was observed and no phenol was transformed in the BES-amended cultures. This suggests that the sensitivity of phenol transformation to an elevated partial pressure of H2 is higher under thermophilic conditions than under mesophilic ones. The lack of benzoate formation could have been due to a high turnover of benzoate or to a difference in the phenol degradation pathway between the thermophilic and mesophilic cultures.     

Macromolecular crowding: qualitative and semiquantitative successes,quantitative challenges

The concept of excluded volume and the theory of effects of excluded volume on the equilibria and rates of macromolecular reactions in fluid media containing high total concentrations of macromolecules ('crowded' media) are summarized. Reports of experimental studies of crowding effects published during the last year are tabulated. Limitations of current excluded volume theory are discussed, and a determination is made of conditions under which this theory may and may not be validly applied. Recently suggested novel approaches to quantitative analysis of crowding phenomena, which may help to overcome some of the limitations of current theory, are summarized.     

Lead chelates of meso- and racemic-dimercaptosuccinic acid

Lead chelates of racemic- and meso-dimercaptosuccinic acid (DMSA) were synthesized and isolated from aqueous solutions and characterized by potentiometric measurements and infrared spectroscopy. Two types of lead chelates of racemic DMSA were isolated: one in which racemic-DMSA is coordinated to Pb+2 via one oxygen and one sulfur atom and the other in which the Pb2+ is coordinated via two sulfur atoms. The latter form of the chelate is converted into the former upon dissolution in dimethylsulfoxide. Only one type of Pb2+ chelate of the meso form of the ligand was formed. In this case, meso-DMSA is coordinated to Pb+2 via one oxygen and one sulfur atom. Meso- and racemic-DMSA have very different solubilities in aqueous solutions. Meso-DMSA is slightly soluble in water, whereas racemic-DMSA is very soluble in water even in the presence of strong acids. The solubilities of the chelates were found to be pH dependent. When the uncoordinated sulfhydryl and carboxylic acid groups dissociate, the chelates dissolve and remain in aqueous solution. The infrared spectra of meso- and racemic-DMSA show distinct features that can be used to detect the presence of either diastereoisomer.     

Computational approaches to disease-gene prediction: rationale, classification and successes

The identification of genes involved in human hereditary diseases often requires the time-consuming and expensive examination of a great number of possible candidate genes, since genome-wide techniques such as linkage analysis and association studies frequently select many hundreds of 'positional' candidates. Even considering the positive impact of next-generation sequencing technologies, the prioritization of candidate genes may be an important step for disease-gene identification. In this paper we develop a basic classification scheme for computational approaches to disease-gene prediction and apply it to exhaustively review bioinformatics tools that have been developed for this purpose, focusing on conceptual aspects rather than technical detail and performance. Finally, we discuss some past successes obtained by computational approaches to illustrate their beneficial contribution to medical research.     

保护生物学、保护生态学与生物多样性科学

正在查阅生物多样性方面的文献时,经常会遇到3个学科,即保护生物学、保护生态学和生物多样性科学。三者的关系如何?各自具有怎样的特点和发展过程?为了更好地理解3个学科的产生背景和特点,需要回顾一下始于19世纪中叶的保护运动     

The story of science: successes,failures, luck,privilege, and bias

I am incredibly honored to receive the 2021 WICB Junior Award for Excellence in Research in WICB’s golden jubilee year. In this essay, I traverse my scientific journey starting with my PhD, highlighting the highs and the lows and how these intersect with luck, privilege, and bias.

V. AnanthanarayananMy pursuit for a PhD started with a hiccup—I had applied to several places in the United States, but barely got any offers due to the economic upheaval that happened that year (2008). I had to forgo any dreams of a PhD in the United States and remained in Bangalore, India to complete a project I had started with William (Bill) Thies at Microsoft Research India on a programming language for expressing biology protocols. Applying to U.S. schools was an expensive task, one which I was unwilling to put my family through again. So, a year later, when I recommenced my search for a PhD position, I set my sights on Europe. I had heard about the PhD program at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG ) at Dresden from a friend who had just joined the institute for her PhD. Fortunately, I received an interview call from MPI-CBG. At the end of a crucial interview week at Dresden, I “matched” with Iva Tolic´’s (now Institut Ruđer Boškovic´, Croatia) lab for my PhD. At the start of my PhD, I knew next to nothing about the cytoskeleton, motor proteins, or microscopy, but I found Iva and my lab members to be some of the warmest and most welcoming people. I made friends for life and graduated with a PhD in Biophysics, with a thesis focused on understanding the regulation of the motor protein cytoplasmic dynein. I was lucky to have been able to get a position at MPI-CBG and join Iva’s lab—of the other three places in Europe I had applied to for a PhD, only one other institute invited me for an interview, which also proved to be unsuccessful.On completing my PhD in 2014, I didn’t quite know what I wanted to do. Due to personal reasons, I had to return to India and was open to options in both industry and academia. But with my training in motor protein and cytoskeleton research, I had some ideas for exploring scientific questions related to dynein activation. However, most labs I approached for a postdoctoral position were not open to a project that was outside the realm of their research focus. Nonetheless, Iva, Nenad Pavin (University of Zagreb), and Jonathon (Joe) Howard (Yale University), who were members of my thesis advisory committee, gave me the courage to continue in academia. In my naïveté, I went ahead and applied for the INSPIRE Faculty Fellowship, which is targeted at fresh PhDs and junior postdoctoral fellows to establish their own independent group at an Indian institute. To my surprise, I ended up getting the fellowship. The next issue was finding a host institute that was preferably in Bangalore, where my partner was based. I applied at a few different places, but only after I attended IndiaBioscience’s Young Investigator Meeting in 2014 did I get the chance to meet representatives of potential host institutes, including the Indian Institute of Science (IISc). After a couple of research seminars at IISc, my application was assessed and I was offered the position of INSPIRE Faculty Fellow at the newly formed Centre for BioSystems Science and Engineering, IISc.While I did not have any additional start-up funding, I was given the infrastructure and the independence to pursue my research program. It was slow and frustrating at the start, not unlike most starting labs. I always wondered if it might have been easier if I had had a regular postdoctoral stint. During this time, I also started recognizing how hard it was to be a woman in Indian academia. As a woman principal investigator, one’s authority, expertise, and ability are constantly called into question. Justifying your presence in academia on a daily basis is an exhausting task. I had a great mentor in Sandhya Visweswariah (IISc) who helped me navigate the system. I also had an extremely supportive partner, who kept me going through some of the worst times. Eventually, my lab and I landed on our feet (more about this in “My INSPIRE’d Journey”). Our research has been recognized with grants and awards, but one of the most rewarding parts of the job is seeing other lab members discovering the joy of science (I wrote about my approach to mentorship recently [https://www.nature.com/articles/s41580-020-0256-6]).Three years into the faculty fellowship, I was able to transition to an Assistant Professor position in the same institute. However, this did not change my experience as a young woman in Indian science, and the implicit and explicit biases continued. In 2020, I accepted a fantastic opportunity to further my lab’s science as an EMBL Australia Group Leader at the Single Molecule Science Node at UNSW Sydney and made the move during a pandemic. My lab’s research focus is in understanding how stochastic and rare events pertaining to cytoskeleton and motor proteins give rise to complexity in intracellular organization. With this theme as the essence of our research, we ask specific questions about motor protein regulation to effect differential cellular trafficking, mitochondria-microtubule interactions, and their role in mitochondrial dynamics, and we aim to determine barcodes of global organelle positioning in health and disease.I have the privilege of being able-bodied, born in an upper middle-class family to college-educated parents who were extremely supportive of my choices. I have also inordinately benefitted from the fact that I was born to an Indian ‘upper caste’ family. I therefore had an undue head start in life. These were circumstances beyond my control and yet played a huge role in how my story turned out. I was embarrassingly ignorant of the rampant misogyny in academia until I had to contend with explicit and implicit gender-based biases myself when I started my independent research group in India. Women make up ∼40% of science PhDs awarded in India but represent only ∼13% of Indian academia (biaswatchindia.com), highlighting the stark gender biases at play in creating a leaky pipeline. While I tried my best to voice my discontent and affect changes to create an equitable environment within my department and institute, it was slow work. In 2020, when the pandemic hit and all conferences and meetings went virtual, conference posters advertised on social media made it immediately apparent just how much women were underrepresented in Indian STEM conferences. So, I teamed up with Shruti Muralidhar (now a scientist at Deep Genomics, Canada) to found BiasWatchIndia, an initiative to document women representation and combat gender-biased panels in Indian STEM conferences.BiasWatchIndia has been in existence for a little over a year now—we have achieved several milestones, but there’s still so much to do. “Manels” (conferences that feature only men) are still as rampant as they were when we first started—40% of all Indian STEM conferences are manels. And while we have just about started to tackle the underrepresentation of women in Indian STEM, we are conscious of the intersectionality of bias with gender, caste, ableism, and socioeconomic background and aim to understand how best we can advocate for all minorities.People who are in power in academia and who oppose equity, diversity, and inclusion initiatives and instead preach merit and equality as the gold standard need to introspect, because when options and opportunities are offered without consideration to the millennia of oppression based on gender, race, and background, it is not promoting equality but upholding values that will continue to oppress underrepresented groups. Still, I am optimistic and hope to see real changes that will result in equity in academia in my lifetime.     

湿生中小型土壤动物生物量测定方法

对于体型较小的湿生中小型土壤动物,目前还没有较好的方法可以直接测定其生物量。模型估算法作为一种间接测定法,由于测定费时没有得到广泛应用。因而,目前发表的大部分文献中均缺少湿生中小型土壤动物生物量这一指标。本文采用重铬酸钾容量法和氯仿熏蒸浸提法测定了湿生中小型土壤动物的有机碳含量,同时与模型估算法的测定结果进行了比较。结果表明,重铬酸钾容量法快速,操作简便,适合于大批量样品采集情况下湿生中小型土壤动物生物量的测定。     

Mutant onco-proteins as drug targets: successes, failures, and future prospects

Mutant onco-proteins play a direct, causal role in cancer and are therefore considered attractive drug targets. Clinical experience has supported this view, with some exceptions. However, clinical benefit has often been restricted by rapid emergence of drug-resistant clones through several distinct mechanisms. This problem can, in principle, be addressed through cocktails containing several drugs. However, the number of tumors whose survival is dependent on a single, druggable mutant onco-protein is currently unknown. The majority of tumors may be driven either by single drivers that are un-druggable, or by combinations of drivers. In both cases, new approaches will be necessary. Development of systemic RNA interference may be a solution to these problems.     

Biotechnology and bioremediation: successes and limitations

With advances in biotechnology, bioremediation has become one of the most rapidly developing fields of environmental restoration, utilizing microorganisms to reduce the concentration and toxicity of various chemical pollutants, such as petroleum hydrocarbons, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, phthalate esters, nitroaromatic compounds, industrial solvents, pesticides and metals. A number of bioremediation strategies have been developed to treat contaminated wastes and sites. Selecting the most appropriate strategy to treat a specific site can be guided by considering three basic principles: the amenability of the pollutant to biological transformation to less toxic products (biochemistry), the accessibility of the contaminant to microorganisms (bioavailability) and the opportunity for optimization of biological activity (bioactivity). Recent advances in the molecular genetics of biodegradation and studies on enzyme-tailoring and DNA-shuffling are discussed in this paper.     

Change in facial shape in micro-, macro- and normocephalics

In view of the dubious scientific validity of traditional cephalometric analyses, the more accurate technique of biorthogonal analysis was used in this study. Developed from D'Arcy Thompson's transformation grids, this technique showed similar craniofacial shape changes in micro-, macro- and normocephalics between the ages of 12 and 16 years, implying the contrasts in facial form between these 3 samples predominantly reflect size rather than shape differences.     

Cultivation and Conservation in Ngorongoro Conservation Area, Tanzania

Ngorongoro Conservation Area (NCA), Tanzania, contains renowned wildlife, an expanding human population, and cultivation by Maasai agro-pastoralists and non-Maasai agriculturalists. We used integrated assessments to explore some effects of cultivation on livestock, resident wildlife, and people. Using a Landsat image from 2000, we mapped 3,967 ha [9,803 acres (ac)] of cultivation within NCA, or 39.7 km² of the 8,283 km² conservation area. Using integrative ecosystem (Savanna) and household (PHEWS) models, we assessed effects of: up to 50,000 ac (20,234 ha) of cultivation; cultivation concentrated into two blocks totaling 10,000 ac (4,047 ha) and 20,000 ac (8,094 ha) that may be more palatable to tourists; and human population growth. Simulations with from 10,000 to 50,000 ac in cultivation showed no large changes in ungulate populations relative to there being no cultivation. When cultivation was altered to be in two blocks, some wildlife populations changed (≤15%) and ungulate biomass remained the same. When cultivation was increased linearly with human population, poor households needed 25% of their diets to come from relief as populations tripled, because livestock could not increase significantly. Our results indicate that having <1% of NCA in cultivation, in its current distribution, is not overly detrimental to wildlife or livestock populations, and is important to Maasai well-being.     

Cloning, expression and characterization of meso-2,3-butanediol dehydrogenase from Klebsiella pneumoniae

The budC gene encoding the meso-2,3-BDH from Klebsiella pneumoniae XJ-Li was expressed in E. coli BL21 (DE3) pLys. Hypothetical amino acid sequence alignments revealed that the enzyme belongs to the short chain dehydrogenase/reductase family. After purification and refolding, the recombinant enzyme had activities of 218 U/mg for reduction of acetoin and 66 U/mg for oxidation of meso-2,3-butanediol. Highest activities were at pH 8.0 and 9.0 respectively. These are higher than other meso-2,3-butanediol dehydrogenases from K. pneumoniae. The low K (m) value (0.65 mM) for acetoin indicated that the enzyme can easily reduce acetoin to meso-2,3-butanediol. There were no significant activities towards 2R,3R-2,3-butanediol, 1,4-butanediol and 2S,3S-2,3-butanediol, suggesting that the enzyme has a high stereospecificity for the meso-dihydric alcohol.     

Conservation of the horseshoe crab at Kinmen, Taiwan: strategies and practices

In order to conserve the horseshoe crab, Tachypleus tridentatus, a famous living fossil in Kinmen and Taiwan, several investigations related to its basic biology were conducted, and public education/participation programs were implemented. Biological investigations included artificially inducing spawning in the laboratory and field, rearing of juveniles, monitoring of habitat characteristics, and establishing a protected area. The grain size of the sediment of the spawning ground was 0.4–1.8mm in diameter and that of the juvenile nursing ground was 0.11–0.19mm. The most suitable water temperature for incubating eggs and rearing juveniles ranged from 28 to 31°C. A total of 800ha of the coastal zone on Kinmen was designated a protected area for the horseshoe crab, based on the Fishery Law, in December 1999. Fishing is prohibited for the 5-year period from 2000 to 2004. Public education programs were conducted to help local people learn about the basic biology of the horseshoe crab, to become aware of its importance and the necessity for conservation, and to empower them to actively participate in the conservation of this species. In addition, a horseshoe crab conservation program has also been incorporated as an element of the local ecotourism industry. Biotechnology business opportunities that may be created as a result of viable horseshoe crab populations will also be promoted.